WO2020050905A1 - Compositions and methods for controlling plant pests - Google Patents

Compositions and methods for controlling plant pests Download PDF

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WO2020050905A1
WO2020050905A1 PCT/US2019/039258 US2019039258W WO2020050905A1 WO 2020050905 A1 WO2020050905 A1 WO 2020050905A1 US 2019039258 W US2019039258 W US 2019039258W WO 2020050905 A1 WO2020050905 A1 WO 2020050905A1
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protein
plant
cell
seq
cry
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PCT/US2019/039258
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French (fr)
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Wenqian MEI
Katherine SEGUIN
Matthew BRAMLETT
Ming Sun
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Sygenta Participations Ag
Syngenta Biotechnology China Co.
Huazhong Agricultural University
Syngenta Crop Protection Llc
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Publication of WO2020050905A1 publication Critical patent/WO2020050905A1/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
    • C12N15/8271—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance
    • C12N15/8279—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for biotic stress resistance, pathogen resistance, disease resistance
    • C12N15/8286—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for biotic stress resistance, pathogen resistance, disease resistance for insect resistance
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/32—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Bacillus (G)
    • C07K14/325—Bacillus thuringiensis crystal peptides, i.e. delta-endotoxins
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A40/00—Adaptation technologies in agriculture, forestry, livestock or agroalimentary production
    • Y02A40/10—Adaptation technologies in agriculture, forestry, livestock or agroalimentary production in agriculture
    • Y02A40/146—Genetically Modified [GMO] plants, e.g. transgenic plants

Definitions

  • sequence listing is submitted electronically as an ASCII formatted sequence listing with a file named "81292-CN-REG-ORG- P_SeqList_ST25.txt", created on August 27, 2018, and having a size of 247 kilobytes and is filed concurrently with the specification.
  • sequence listing contained in this ASCII formatted document is part of the specification and is herein incorporated by reference in its entirety.
  • This invention relates to pesticidal proteins and the nucleic acid molecules that
  • Bacillus thuringiensis ( Bt ) is a gram-positive spore forming soil bacterium
  • compositions comprising Bacillus thuringiensis strains or their insecticidal proteins can be used as environmentally- acceptable insecticides to control agricultural insect pests or insect vectors of a variety of human or animal diseases.
  • Crystal (Cry) proteins from Bacillus thuringiensis have potent insecticidal activity against predominantly lepidopteran, dipteran, and coleopteran pest insects. These proteins also have shown activity against pests in the Orders Hymenoptera, Homoptera, Phthiraptera, Mallophaga, and Acari pest orders, as well as other invertebrate orders such as
  • Nemathelminthes, Platyhelminthes, and Sarcomastigorphora (Feitelson, J. 1993. The Bacillus Thuringiensis family tree. In Advanced Engineered Pesticides. Marcel Dekker, Inc., New York, N.Y.). These proteins were originally classified as Cryl to Cry VI based primarily on their insecticidal activity. The major classes were Lepidoptera- specific (I), Lepidoptera- and Dip tera- specific (II), Coleoptera- specific (III), Dip tera- specific (IV), and nematode- specific (V) and (VI).
  • the proteins were further classified into subfamilies; more highly related proteins within each family were assigned divisional letters such as CrylA, Cry IB, CrylC, etc. Even more closely related proteins within each division were given names such as CrylC(a), CrylC(b), etc.
  • the terms“Cry toxin” and“delta-endotoxin” have been used interchangeably with the term“Cry protein.” Current nomenclature for Cry proteins and genes is based upon amino acid sequence homology rather than insect target specificity (Crickmore el al. (1998) Microbiol. Mol. Biol. Rev. 62:807-813).
  • each toxin is assigned a unique name incorporating a primary rank (an Arabic number), a secondary rank (an uppercase letter), a tertiary rank (a lowercase letter), and a quaternary rank (another Arabic number).
  • a primary rank an Arabic number
  • secondary rank an uppercase letter
  • tertiary rank a lowercase letter
  • quaternary rank another Arabic number.
  • Roman numerals have been exchanged for Arabic numerals in the primary rank. For example,“CrylA(a)” under the older nomenclature is now“CrylAa” under the current nomenclature. According to Bennett et al. (2010, Bioeng.
  • the Cry toxins can still be separated into six major classes according to their insect host specificities and include: Group 1— lepidopteran e.g., Cryl, Cry9 and Cryl5); group 2— lepidopteran and dipteran (e.g., Cry2); group 3— coleopteran (Cry3, Cry7 and Cry8); group 4— dipteran (Cry4, CrylO, Cryl l, Cryl6, Cryl7, Cry 19 and Cry 20); group 5— lepidopteran and coleopteran (Cryll); and group 6— nematodes (Cry6).
  • the Cryll, Cry2, Cry3, CrylO and Cryl l toxins (73-82 kDa) are unique because they appear to be natural truncations of the larger Cryl and Cry4 proteins (130-140 kDa).
  • Cry proteins are globular protein molecules which accumulate as protoxins in
  • the crystals After ingestion by a pest, the crystals are typically solubilized to release protoxins, which can range in size, for example, from 130-140 kDa for many of the lepidopteran- active Cry proteins, such as Cryl and Cry9, and 60-80 kDa for the coleopteran- active Cry3 proteins and the lepidopteran/dipteran-active Cry2 proteins.
  • protoxins can range in size, for example, from 130-140 kDa for many of the lepidopteran- active Cry proteins, such as Cryl and Cry9, and 60-80 kDa for the coleopteran- active Cry3 proteins and the lepidopteran/dipteran-active Cry2 proteins.
  • the released protoxins After the crystals are solubilized by a susceptible insect the released protoxins are processed by proteases in the insect gut, for example trypsin and chymotrypsin, to produce a protease- resistant core Cry protein toxin.
  • Cry protoxins that are 130-140 kDa are typically activated through the proteolytic removal of an N-terminal peptide of 25-30 amino acids and approximately half of the remaining protein from the C-terminus resulting in an approximately 60-70 kDa mature Cry toxin.
  • the protoxins that are 60-80 kDa e.g. Cry2 and Cry3, are also processed but not to the same extent as the larger protoxins.
  • the smaller protoxins typically have equal or more amino acids removed from the N-terminus than the larger protoxins but less amino acids removed from the C-terminus.
  • proteolytic activation of Cry2 family members typically involves the removal of approximately 40-50 N-terminal amino acids. Many of the Cry proteins are quite toxic to specific target insects, but many have narrow spectrums of activity.
  • Cry proteins generally have five conserved sequence domains, and three conserved structural domains (see, for example, de Maagd et al. (2001) Trends Genetics 17:193-199).
  • the first conserved structural domain, called Domain I typically consists of seven alpha helices and is involved in membrane insertion and pore formation.
  • Domain II typically consists of three beta- sheets arranged in a Greek key configuration, and domain III typically consists of two antiparallel beta-sheets in‘jelly-roll’ formation (de Maagd et ah, 2001, supra). Domains II and III are involved in receptor recognition and binding, and are therefore considered determinants of toxin specificity.
  • plant pests including insect and nematode pests, causing substantial reductions in crop yield and quality.
  • plant pests are a major factor in the loss of the world's important agricultural crops. About 15-20 percent of harvestable grain in China is lost every year to insect pests and diseases. In addition, about $8 billion are lost every year in the United States alone due to infestations of invertebrate pests including insects. Insect pests are also a burden to vegetable and fruit growers, to producers of ornamental flowers, and to home gardeners.
  • Insect pests are mainly controlled by intensive applications of chemical pesticides, which are active through inhibition of insect growth, prevention of insect feeding or reproduction, or cause death.
  • Biological pest control agents such as Bacillus thuringiensis strains expressing pesticidal toxins such as Cry proteins, have also been applied to crop plants with satisfactory results, offering an alternative or compliment to chemical pesticides.
  • the genes coding for some of these Cry proteins have been isolated and their expression in heterologous hosts such as transgenic plants have been shown to provide another tool for the control of economically important insect pests.
  • the invention provides compositions and methods for conferring pesticidal activity to bacteria, plants, plant cells, tissues and seeds.
  • chimeric genes comprising novel polynucleotides that encode Cry proteins derived from assembled polynucleotides and sequences substantially identical thereto, whose expression results in proteins with toxicity to economically important insect pests, particularly insect pests that infest plants, are provided.
  • the invention is further drawn to novel Cry proteins resulting from the expression of the polynucleotides, and to compositions and formulations containing the Cry proteins, which are toxic to insects by inhibiting the ability of insect pests to survive, grow and reproduce, or of limiting insect-related damage or loss to crop plants.
  • Cry proteins of the invention include Cry proteins derived from assembled polynucleotides and mutant or variant Cry proteins that have one or more amino acid substitutions, additions or deletions.
  • mutant Cry proteins include without limitation those that are mutated to have a broader spectrum of activity or higher specific activity than native Cry protein counterparts, those mutated to introduce an epitope to generate antibodies that differentially recognize the mutated protein from a native protein or those mutated to modulate expression in a transgenic organism.
  • the novel Cry proteins of the invention are highly toxic to insect pests.
  • the Cry proteins of the invention may be used to control one or more economically important insect pests such as Asian com borer ⁇ Ostrinia furnacalis), black cutworm ( Agrotis ipsilon ), cotton bollworm ( Helicoverpa armigera ), yellow peach borer ( Conogethes punctiferalis), Oriental armyworm ( Mythimna sepatate), European com borer ( Ostrinia nubilalis ), fall armyworm (Spodoptera frugiperda), corn earworm ( Helicoverpa zea), sugarcane borer ( Diatraea saccharalis ), velvetbean caterpillar ( Anticarsia gemmatalis ), soybean looper ( Chrysodeixis includes), southwest corn borer ( Diatraea grandio ella), western bean cutworm ( Richia albicosta), tobacco budworm ( Heliothis virescens), striped stem borer ( Chile suppressalis), pink stem borer ( Sesamia cal
  • the invention is further drawn to expression cassettes and recombinant vectors
  • the invention also provides transformed bacteria, plants, plant cells, tissues, and seeds comprising a chimeric gene, or an expression cassette or a recombinant vector which are useful in expressing a Cry protein of the invention in the transformed bacteria, plants, plant cells, tissues and seeds.
  • the invention is also drawn to isolated Bacillus thuringiensis ( Bt ) strains that produce Cry proteins of the invention.
  • the invention is also drawn to methods of using the polynucleotides of the
  • nucleotide or amino acid sequences may be assembled, native or codon optimized sequences that have been designed for expression in an organism such as a plant or bacteria, or in making hybrid Cry toxins with enhanced pesticidal activity.
  • the invention is further drawn to methods of making Cry proteins and to methods of using the polynucleotide sequences and Cry proteins, for example in microorganisms to control insects or in transgenic plants to confer protection from insect damage.
  • Another aspect of the invention includes insecticidal compositions and formulations comprising the Cry proteins or Bacillus thuringiensis strains of the invention, and methods of using the compositions or formulations to control insect populations, for example by applying the compositions or formulations to insect-infested areas, or to prophylactically treat insect-susceptible areas or plants to confer protection against the insect pests.
  • compositions or formulations of the invention may, in addition to the Cry protein or Bt strain of the invention, comprises other pesticidal agents such as chemical pesticides in order to augment or enhance the insect-controlling capability of the composition or formulation.
  • compositions and methods of the invention are useful for controlling insect pests that attack plants, particularly crop plants.
  • compositions of the invention are also useful for generating altered or improved Cry proteins that have pesticidal activity, or for detecting the presence of a Cry protein or nucleic acids in commercial products or transgenic organisms.
  • SEQ ID NO:l represents a nucleotide sequence encoding a BT264 protein.
  • SEQ ID NO:2 represents a nucleotide sequence encoding a BT288 protein.
  • SEQ ID NO:3 represents a nucleotide sequence encoding a BT302 protein.
  • SEQ ID NO:4 represents a nucleotide sequence encoding a BT454 protein.
  • SEQ ID NO:5 represents a nucleotide sequence encoding a BT485 protein.
  • SEQ ID NO:6 represents a codon optimized sequence encoding a BT264 protein.
  • SEQ ID NO:7 represents a codon optimized sequence encoding a BT288 protein.
  • SEQ ID NO:8 represents a codon optimized sequence encoding a BT302 protein.
  • SEQ ID NO:9 represents a codon optimized sequence encoding a BT454 protein.
  • SEQ ID NO: 10 represents a codon optimized sequence encoding a BT485 protein.
  • SEQ ID NO: 11 represents a nucleotide sequence encoding a mutant BT264 protein.
  • SEQ ID NO: 12 represents a nucleotide sequence encoding a mutant BT288 protein.
  • SEQ ID NO: 13 represents a nucleotide sequence encoding a mutant BT302 protein.
  • SEQ ID NO: 14 represents a nucleotide sequence encoding a mutant BT454 protein.
  • SEQ ID NO: 15 represents a nucleotide sequence encoding a mutant BT485 protein.
  • SEQ ID NO: 16 represents an amino acid sequence of a BT264 protein.
  • SEQ ID NO: 17 represents an amino acid sequence of a BT288 protein.
  • SEQ ID NO: 18 represents an amino acid sequence of a BT302 protein.
  • SEQ ID NO: 19 represents an amino acid sequence of a BT454 protein.
  • SEQ ID NO:20 represents an amino acid sequence of a BT485 protein.
  • SEQ ID NO:2l represents an amino acid sequence of a mutant BT264 protein.
  • SEQ ID NO:22 represents an amino acid sequence of a mutant BT288 protein.
  • SEQ ID NO:23 represents an amino acid sequence of a mutant BT302 protein.
  • SEQ ID NO:24 represents an amino acid sequence of a mutant BT454 protein
  • SEQ ID NO:25 represents an amino acid sequence of a mutant BT485 protein.
  • SEQ ID NO:26 represents an N-terminus of SEQ ID NO: 17.
  • SEQ ID NO:27 represents a C-terminus of SEQ ID NO: 17.
  • SEQ ID NO:28 represents an N-terminus of SEQ ID NO: 18.
  • SEQ ID NO:29 represents a C-terminus of SEQ ID NO: 18.
  • SEQ ID NO:30 represents an N-terminus of SEQ ID NO:20.
  • SEQ ID NO:3l represents a C-terminus of SEQ ID NO:20.
  • SEQ ID NO:32 is an amino acid sequence of a Cry54Aa protein.
  • SEQ ID NO:33 is an amino acid sequence of a Cry4Aa protein.
  • SEQ ID NO:34 is an amino acid sequence of a Cry39Aa protein.
  • SEQ ID NO:35 is an amino acid sequence of a Cryl9Ca protein.
  • SEQ ID NO:36 is an amino acid sequence of a Cry50Ba protein.
  • SEQ ID NO:37 is an amino acid sequence of a Cry4Ba protein.
  • the term “about” is used herein to mean approximately, roughly, around, or in the region of. When the term “about” is used in conjunction with a numerical range, it modifies that range by extending the boundaries above and below the numerical values set forth. In general, the term “about” is used herein to modify a numerical value above and below the stated value by a variance of 20 percent, preferably 10 percent up or down (higher or lower). With regard to a temperature the term“about” means ⁇ 1 °C, preferably ⁇ 0.5°C. Where the term“about” is used in the context of this invention (e.g., in combinations with temperature or molecular weight values) the exact value (i.e., without“about”) is preferred.
  • the term "amplified” means the construction of multiple copies of a nucleic acid molecule or multiple copies complementary to the nucleic acid molecule using at least one of the nucleic acid molecules as a template.
  • Amplification systems include the polymerase chain reaction (PCR) system, ligase chain reaction (LCR) system, nucleic acid sequence based amplification (NASBA, Cangene, Mississauga, Ontario), Q-Beta Replicase systems, transcription-based amplification system (TAS), and strand displacement amplification (SDA). See, e.g., Diagnostic Molecular Microbiology: Principles and
  • sequence is a synthetic polynucleotide made by aligning overlapping sequences of polynucleotides or portions of sequenced polynucleotides, i.e. k-mers (all the possible subsequences of length k from a read obtained through DNA sequencing), that are determined from genomic DNA using DNA sequencing technology.
  • Assembled sequences typically contain base-calling errors, which can be incorrectly determined bases, insertions and/or deletions compared to the native DNA sequence comprised in the genome from which the genomic DNA is obtained. Therefore, for example, an“assembled polynucleotide” may encode a protein and according to the invention both the polynucleotide and the protein are not products of nature, but exist only by human activity.
  • chimeric construct or“chimeric gene” or“chimeric polynucleotide” or “chimeric nucleic acid” (or similar terms) as used herein refers to a construct or molecule comprising two or more polynucleotides of different origin assembled into a single nucleic acid molecule.
  • chimeric construct refers to any construct or molecule that contains, without limitation, (1) polynucleotides (e.g., DNA) , including regulatory and coding polynucleotides that are not found together in nature (i.e., at least one of the polynucleotides in the construct is heterologous with respect to at least one of its other polynucleotides), or (2) polynucleotides encoding parts of proteins not naturally adjoined, or (3) parts of promoters that are not naturally adjoined.
  • polynucleotides e.g., DNA
  • regulatory and coding polynucleotides that are not found together in nature (i.e., at least one of the polynucleotides in the construct is heterologous with respect to at least one of its other polynucleotides)
  • polynucleotides e.g., DNA
  • regulatory and coding polynucleotides that are not found together in nature (i.e., at
  • a chimeric construct, chimeric gene, chimeric polynucleotide or chimeric nucleic acid may comprise regulatory polynucleotides and coding polynucleotides that are derived from different sources, or comprise regulatory polynucleotides and coding polynucleotides derived from the same source, but arranged in a manner different from that found in nature.
  • the chimeric construct, chimeric gene, chimeric polynucleotide or chimeric nucleic acid comprises an expression cassette comprising a polynucleotide of the invention under the control of regulatory polynucleotides, particularly under the control of regulatory polynucleotides functional in plants or bacteria.
  • a "coding sequence” is a nucleic acid sequence that is transcribed into RNA such as mRNA, rRNA, tRNA, snRNA, sense RNA or antisense RNA. Preferably the RNA is then translated in an organism to produce a protein.
  • a“codon optimized” sequence means a nucleotide sequence wherein the codons are chosen to reflect the particular codon bias that a host cell or organism may have. This is typically done in such a way so as to preserve the amino acid sequence of the polypeptide encoded by the nucleotide sequence to be optimized.
  • the DNA sequence of the recombinant DNA construct includes sequence that has been codon optimized for the cell (e.g., an animal, plant, or fungal cell) in which the construct is to be expressed.
  • a construct to be expressed in a plant cell can have all or parts of its sequence (e.g., the first gene suppression element or the gene expression element) codon optimized for expression in a plant. See, for example, U.S. Pat. No. 6,121,014, incorporated herein by reference.
  • control insects means to inhibit, through a toxic effect, the ability of insect pests to survive, grow, feed, or reproduce, or to limit insect-related damage or loss in crop plants or to protect the yield potential of a crop when grown in the presence of insect pests.
  • To "control” insects may or may not mean killing the insects, although it preferably means killing the insects.
  • transitional phrase“consisting essentially of’ means that the scope of a claim is to be interpreted to encompass the specified materials or steps recited in the claim” and those that do not materially alter the basic and novel characteristic(s)” of the claimed invention.
  • the term“consisting essentially of’ when used in a claim of this invention is not intended to be interpreted to be equivalent to “comprising.”
  • “corresponding to” or“corresponds to” means that when the amino acid sequences of variant or homolog Cry proteins are aligned with each other, the amino acids that“correspond to” certain enumerated positions in the variant or homolog protein are those that align with these positions in a reference protein but that are not necessarily in these exact numerical positions relative to the particular reference amino acid sequence of the invention.
  • SEQ ID NO:20 is the reference sequence and is aligned with SEQ ID NO:27
  • the Glnl5l of SEQ ID NO:27“corresponds to” Glnl44 of SEQ ID NO:20 or for example, the Asn30l of SEQ ID NO:27“corresponds to” the Thr294 of SEQ ID NO:20.
  • the term“Cry protein” means an insecticidal protein that may occur in crystalline form in Bacillus thuringiensis or related bacteria.
  • the term“Cry protein” can refer to the protoxin form or any insecticidal fragment or toxin thereof.
  • composition or toxic protein means that the composition or toxic
  • composition or toxic protein resulting in a toxic effect and control of the insect.
  • the composition or toxic protein can be delivered in many recognized ways, including but not limited to, transgenic plant expression, formulated protein composition(s), sprayable protein composition(s), a bait matrix, or any other art-recognized protein delivery system.
  • domain refers to a set of amino acids conserved at specific positions along an alignment of sequences of evolutionarily related proteins. While amino acids at other positions can vary between homologues, amino acids that are highly conserved at specific positions indicate amino acids that are likely essential in the structure, stability or function of a protein. Identified by their high degree of conservation in aligned sequences of a family of protein homologues, they can be used as identifiers to determine if any polypeptide in question belongs to a previously identified polypeptide group.
  • Effective insect-controlling amount means that concentration of a toxic protein that inhibits, through a toxic effect, the ability of insects to survive, grow, feed or reproduce, or limits insect-related damage or loss in crop plants or protects the yield potential of a crop when grown in the presence of insect pests.“Effective insect-controlling amount” may or may not mean killing the insects, although it preferably means killing the insects.
  • Expression cassette as used herein means a nucleic acid molecule capable of
  • an“expression cassette” also typically comprises additional polynucleotides required for proper translation of the polynucleotide of interest.
  • the expression cassette may also comprise other polynucleotides not necessary in the direct expression of a polynucleotide of interest but which are present due to convenient restriction sites for removal of the cassette from an expression vector.
  • the expression cassette comprising the polynucleotide(s) of interest may be chimeric, meaning that at least one of its components is heterologous with respect to at least one of its other components.
  • the expression cassette may also be one that is naturally occurring but has been obtained in a recombinant form useful for heterologous expression.
  • the expression cassette is heterologous with respect to the host, i.e. the polynucleotide of interest in the expression cassette does not occur naturally in the host cell and must have been introduced into the host cell or an ancestor of the host cell by a transformation process or a breeding process.
  • the expression of the polynucleotide(s) of interest in the expression cassette is generally under the control of a promoter.
  • the promoter can also be specific or preferential to a particular tissue, or organ, or stage of development.
  • An expression cassette, or fragment thereof, can also be referred to as "inserted polynucleotide” or “insertion polynucleotide” when transformed into a plant.
  • a " gene” is defined herein as a hereditary unit comprising one or more
  • polynucleotides that occupies a specific location on a chromosome or plasmid and that contains the genetic instruction for a particular characteristic or trait in an organism.
  • gut protease is a protease naturally found in the digestive tract of an insect. This protease is usually involved in the digestion of ingested proteins.
  • gut proteases include trypsin, which typically cleaves peptides on the C-terminal side of lysine (K) or arginine (R) residues, and chymotrypsin, which typically cleaves peptides on the C-terminal side of phenylalanine (F), tryptophan (W) or tyrosine (Y).
  • heterologous when used in reference to a gene or a polynucleotide or a polypeptide refers to a gene or a polynucleotide or a polypeptide that is or contains a part thereof not in its natural environment (i.e., has been altered by the hand of man).
  • a heterologous gene may include a polynucleotide from one species introduced into another species.
  • a heterologous gene may also include a polynucleotide native to an organism that has been altered in some way (e.g., mutated, added in multiple copies, linked to a non-native promoter or enhancer polynucleotide, etc.).
  • Heterologous genes further may comprise plant gene polynucleotides that comprise cDNA forms of a plant gene; the cDNAs may be expressed in either a sense (to produce mRNA) or anti-sense orientation (to produce an anti-sense RNA transcript that is complementary to the mRNA transcript).
  • heterologous genes are distinguished from endogenous plant genes in that the heterologous gene polynucleotide are typically joined to polynucleotides comprising regulatory elements such as promoters that are not found naturally associated with the gene for the protein encoded by the heterologous gene or with plant gene polynucleotide in the chromosome, or are associated with portions of the chromosome not found in nature (e.g., genes expressed in loci where the gene is not normally expressed).
  • a heterologous" polynucleotide refers to a polynucleotide not naturally associated with a host cell into which it is introduced, including non-naturally occurring multiple copies of a naturally occurring polynucleotide.
  • Homologous recombination is the exchange ("crossing over") of DNA fragments between two DNA molecules or chromatids of paired chromosomes in a region of identical polynucleotides.
  • a “recombination event” is herein understood to mean a meiotic crossing- over.
  • a nucleic acid sequence is "isocoding" with a reference nucleic acid sequence when the nucleic acid sequence encodes a polypeptide having the same amino acid sequence as the polypeptide encoded by the reference nucleic acid sequence.
  • SEQ ID NO:6 is isocoding with SEQ ID NO: 1 because they both encode the amino acid sequence represented by SEQ ID NO: 16.
  • isolated nucleic acid molecule, polynucleotide or protein is a nucleic acid molecule, polynucleotide or protein that no longer exists in its natural environment.
  • An isolated nucleic acid molecule, polynucleotide or protein of the invention may exist in a purified form or may exist in a recombinant host such as in a transgenic bacteria or a transgenic plant. Therefore, a claim to an“isolated” nucleic acid molecule, as enumerated herein, encompasses a nucleic acid molecule when the nucleic acid molecule is comprised within a transgenic plant genome.
  • a " nucleic acid molecule” is single- or double- stranded DNA or RNA that can be isolated from any source or can made synthetically. In the context of the present invention, the nucleic acid molecule is preferably a segment of DNA.
  • "Operably linked” refers to the association of polynucleotides on a single nucleic acid fragment so that the function of one affects the function of the other.
  • a promoter is operably linked with a coding polynucleotide or functional RNA when it is capable of affecting the expression of that coding polynucleotide or functional RNA (i.e., that the coding polynucleotide or functional RNA is under the transcriptional control of the promoter).
  • Coding polynucleotide in sense or antisense orientation can be operably linked to regulatory polynucleotides.
  • pesticidal refers to the ability of a Cry protein of the invention to control a pest organism or an amount of a Cry protein that can control a pest organism as defined herein.
  • a pesticidal Cry protein can kill or inhibit the ability of a pest organism (e.g., insect pest) to survive, grow, feed, or reproduce.
  • a "plant” is any plant at any stage of development, particularly a seed plant.
  • a "plant cell” is a structural and physiological unit of a plant, comprising a protoplast and a cell wall.
  • the plant cell may be in the form of an isolated single cell or a cultured cell, or as a part of a higher organized unit such as, for example, plant tissue, a plant organ, or a whole plant.
  • Plant cell culture means cultures of plant units such as, for example, protoplasts, cell culture cells, cells in plant tissues, pollen, pollen tubes, ovules, embryo sacs, zygotes and embryos at various stages of development.
  • Plant material refers to leaves, stems, roots, flowers or flower parts, fruits, pollen, egg cells, zygotes, seeds, cuttings, cell or tissue cultures, or any other part or product of a plant.
  • a "plant organ” is a distinct and visibly structured and differentiated part of a plant such as a root, stem, leaf, flower bud, or embryo.
  • Plant tissue as used herein means a group of plant cells organized into a structural and functional unit. Any tissue of a plant in planta or in culture is included. This term includes, but is not limited to, whole plants, plant organs, plant seeds, tissue culture and any groups of plant cells organized into structural or functional units. The use of this term in conjunction with, or in the absence of, any specific type of plant tissue as listed above or otherwise embraced by this definition is not intended to be exclusive of any other type of plant tissue.
  • A“polynucleotide” refers to a polymer composed of many nucleotide monomers covalently bonded in a chain.
  • Such“polynucleotides” includes DNA, RNA, modified oligo nucleotides (e.g., oligonucleotides comprising bases that are not typical to biological RNA or DNA, such as 2'-0-methylated oligonucleotides), and the like.
  • a nucleic acid or polynucleotide can be single-stranded, double- stranded, multi- stranded, or combinations thereof.
  • a particular nucleic acid or polynucleotide of the present invention optionally comprises or encodes complementary polynucleotides, in addition to any polynucleotide explicitly indicated.
  • Polynucleotide of interest refers to any polynucleotide which, when transferred to an organism, e.g., a plant, confers upon the organism a desired characteristic such as insect resistance, disease resistance, herbicide tolerance, antibiotic resistance, improved nutritional value, improved performance in an industrial process, production of commercially valuable enzymes or metabolites or altered reproductive capability.
  • promoter refers to a polynucleotide, usually upstream (5') of its coding polynucleotide, which controls the expression of the coding polynucleotide by providing the recognition for RNA polymerase and other factors required for proper transcription.
  • a "protoplast” is an isolated plant cell without a cell wall or with only parts of the cell wall.
  • a "recombinant nucleic acid molecule” is a nucleic acid molecule comprising a combination of polynucleotides that would not naturally occur together and is the result of human intervention, e.g., a nucleic acid molecule that is comprised of a combination of at least two polynucleotides heterologous to each other, or a nucleic acid molecule that is artificially synthesized, for example, a polynucleotide synthesize using an assembled nucleotide sequence, and comprises a polynucleotide that deviates from the polynucleotide that would normally exist in nature, or a nucleic acid molecule that comprises a transgene artificially incorporated into a host cell'
  • a recombinant nucleic acid molecule is a DNA molecule resulting from the insertion of a transgene into a planks genomic DNA, which may ultimately result in the expression of a recombinant RNA or protein molecule in that organism.
  • a "recombinant plant” is a plant that would not normally exist in nature, is the result of human intervention, and contains a transgene or heterologous nucleic acid molecule incorporated into its genome. As a result of such genomic alteration, the recombinant plant is distinctly different from the related wild-type plant.
  • regulatory elements refer to sequences involved in controlling the expression of a nucleotide sequence. Regulatory elements comprise a promoter operably linked to the nucleotide sequence of interest and termination signals. They also typically encompass sequences required for proper translation of the nucleotide sequence.
  • nucleic acid or amino acid sequences refers to two or more sequences or subsequences that have at least 60%, preferably at least 80%, more preferably 90%, even more preferably 95%, and most preferably at least 99% nucleotide or amino acid residue identity, when compared and aligned for maximum correspondence, as measured using one of the following sequence comparison algorithms or by visual inspection.
  • the substantial identity exists over a region of the sequences that is at least about 50 residues or bases in length, more preferably over a region of at least about 100 residues or bases, and most preferably the sequences are substantially identical over at least about 150 residues or bases.
  • the sequences are substantially identical over the entire length of the coding regions.
  • substantially identical nucleic acid or amino acid sequences perform substantially the same function.
  • sequence comparison typically one sequence acts as a reference sequence to which test sequences are compared.
  • test and reference sequences are input into a computer, subsequence coordinates are designated if necessary, and sequence algorithm program parameters are designated.
  • sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters.
  • Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2: 482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol.
  • BEAST algorithm which is described in Altschul et al., J. Mol. Biol. 215: 403-410 (1990).
  • Software for performing BEAST analyses is publicly available through the National Center for Biotechnology Information (National Center for Biotechnology Information, U.S. National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894 USA).
  • This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive- valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., 1990).
  • initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them.
  • the word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always>0) and N (penalty score for mismatching residues; always O). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when the cumulative alignment score falls off by the quantity X from its maximum achieved value, the cumulative score goes to zero or below due to the accumulation of one or more negative scoring residue alignments, or the end of either sequence is reached.
  • the BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment.
  • the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad Sci. USA 89: 10915 (1989)).
  • test nucleic acid sequence is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid sequence to the reference nucleic acid sequence is less than about 0.1, more preferably less than about 0.01, and most preferably less than about 0.001.
  • hybridizing specifically to refers to the binding, duplexing, or hybridizing of a molecule only to a particular nucleotide sequence under stringent conditions when that sequence is present in a complex mixture (e.g., total cellular) DNA or RNA.
  • Bod(s) substantially refers to complementary hybridization between a probe nucleic acid and a target nucleic acid and embraces minor mismatches that can be accommodated by reducing the stringency of the hybridization media to achieve the desired detection of the target nucleic acid sequence.
  • Stringent hybridization conditions and “stringent hybridization wash conditions” in the context of nucleic acid hybridization experiments such as Southern and Northern hybridizations are sequence dependent, and are different under different environmental parameters. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biology-Hybridization with Nucleic Acid Probes part I chapter 2 “Overview of principles of hybridization and the strategy of nucleic acid probe assays” Elsevier, New York. Generally, highly stringent hybridization and wash conditions are selected to be about 5°C lower than the thermal melting point (T m ) for the specific sequence at a defined ionic strength and pH.
  • T m thermal melting point
  • T m is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe.
  • Very stringent conditions are selected to be equal to the T m for a particular probe.
  • An example of stringent hybridization conditions for hybridization of complementary nucleic acids which have more than 100 complementary residues on a filter in a Southern or northern blot is 50% formamide with 1 mg of heparin at 42°C, with the hybridization being carried out overnight.
  • An example of highly stringent wash conditions is 0.15M NaCl at 72°C for about 15 minutes.
  • An example of stringent wash conditions is a 0.2x SSC wash at 65°C for 15 minutes (see, Sambrook, infra, for a description of SSC buffer). Often, a high stringency wash is preceded by a low stringency wash to remove background probe signal.
  • An example medium stringency wash for a duplex of, e.g., more than 100 nucleotides, is lx SSC at 45°C for 15 minutes.
  • An example low stringency wash for a duplex of, e.g., more than 100 nucleotides, is 4-6x SSC at 40°C for 15 minutes.
  • stringent conditions typically involve salt concentrations of less than about 1.0 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3, and the temperature is typically at least about 30°C.
  • Stringent conditions can also be achieved with the addition of destabilizing agents such as formamide.
  • a signal to noise ratio of 2x (or higher) than that observed for an unrelated probe in the particular hybridization assay indicates detection of a specific hybridization.
  • Nucleic acids that do not hybridize to each other under stringent conditions are still substantially identical if the proteins that they encode are substantially identical. This occurs, e.g., when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code.
  • a reference nucleotide sequence preferably hybridizes to the reference nucleotide sequence in 7% sodium dodecyl sulfate (SDS), 0.5 M NaP0 4 , 1 mM EDTA at 50°C with washing in 2x SSC, 0.1% SDS at 50°C, more desirably in 7% sodium dodecyl sulfate (SDS), 0.5 M NaP0 4 , 1 mM EDTA at 50°C with washing in lx SSC, 0.1% SDS at 50°C, more desirably still in 7% sodium dodecyl sulfate (SDS), 0.5 M NaP0 4 , 1 mM EDTA at 50°C with washing in 0.5x SSC, 0.1% SDS at 50°C,
  • a protein encoded by the first nucleic acid is immunologically cross reactive with, or specifically binds to, the protein encoded by the second nucleic acid.
  • a protein is typically substantially identical to a second protein, for example, where the two proteins differ only by conservative substitutions.
  • a "synthetic polynucleotide” refers to a polynucleotide comprising bases or structural features that are not present in a naturally occurring polynucleotide.
  • a synthetic polynucleotide encoding a Cry protein of the invention that comprises a nucleotide sequence that resembles more closely the G+C content and the normal codon distribution of dicot or monocot plant genes is said to be synthetic.
  • polynucleotide of the invention may also, for example, comprise an assembled nucleotide sequence of the invention.
  • a Cry protein that is“toxic” to an insect pest is meant that the Cry protein functions as an orally active insect control agent to kill the insect pest, or the Cry protein is able to disrupt or deter insect feeding, or causes growth inhibition to the insect pest, both of which may or may not cause death of the insect.
  • a Cry protein of the invention is delivered to an insect or an insect comes into oral contact with the Cry protein, the result is typically death of the insect, or the insect’s growth is slowed, or the insect stops feeding upon the source that makes the toxic Cry protein available to the insect.
  • Transformation is a process for introducing heterologous nucleic acid into a host cell or organism.
  • transformation means the stable integration of a DNA molecule into the genome of an organism of interest.
  • Transformed / transgenic / recombinant refer to a host organism such as a bacterium or a plant into which a heterologous nucleic acid molecule has been introduced.
  • the nucleic acid molecule can be stably integrated into the genome of the host or the nucleic acid molecule can also be present as an extrachromosomal molecule. Such an extrachromosomal molecule can be auto-replicating.
  • Transformed cells, tissues, or plants are understood to encompass not only the end product of a transformation process, but also transgenic progeny thereof.
  • non-transformed refers to a wild- type organism, e.g., a bacterium or plant, which does not contain the heterologous nucleic acid molecule.
  • Nucleotides are indicated herein by the following standard abbreviations: adenine (A), cytosine (C), thymine (T), and guanine (G).
  • Amino acids are likewise indicated by the following standard abbreviations: alanine (Ala; A), arginine (Arg; R), asparagine (Asn; N), aspartic acid (Asp; D), cysteine (Cys; C), glutamine (Gln; Q), glutamic acid (Glu; E), glycine (Gly; G), histidine (His; H), isoleucine (he; 1), leucine (Leu; L), lysine (Lys; K), methionine (Met; M), phenylalanine (Phe; F), proline (Pro; P), serine (Ser; S), threonine (Thr; T), tryptophan (Trp; W), tyrosine (Tyr; Y
  • This invention provides compositions and methods for controlling harmful plant pests.
  • the invention relates to Cry proteins that are encoded by nucleotides sequences assembled from genomic DNA isolated from bacteria, such as Bacillus
  • thuringiensis that are toxic to insect pests and to assembled polynucleotides and related polynucleotides that comprise nucleotide sequences that encode the Cry proteins, and to the making and using of the assembled polynucleotides and related polynucleotides and Cry proteins to control insect pests.
  • the invention provides a nucleic acid molecule or optionally an isolated nucleic acid molecule comprising, consisting essentially of or consisting of a nucleotide sequence encoding a Cry protein in its protoxin form or a biologically active or toxin fragment thereof, wherein the nucleotide sequence (a) has at least 80% to at least 99% sequence identity with an assembled sequence of any of SEQ ID NOs:l- 5 or a toxin-encoding fragment thereof; or (b) encodes a protein comprising an amino acid sequence that has at least 80% to at least 99% sequence identity with any of SEQ ID NOs: 16- 20 or an toxin fragment thereof; or (c) is an assembled nucleotide sequence of (a) or (b); or (d) is a synthetic sequence of (a), (b) or (c) that has codons optimized for expression in a transgenic organism.
  • the nucleotide sequence comprises SEQ ID NO:l, SEQ ID NO:2, SEQ ID NOG, SEQ ID NO:4, SEQ ID NOG, or any toxin-encoding fragments of any of SEQ ID NOs: 1-5.
  • the synthetic nucleotide sequence comprises SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, or any toxin-encoding fragments of any of SEQ ID NOs:6-l5.
  • fragments are also encompassed by the invention.
  • fragment is intended a portion of the nucleotide sequence encoding a Cry protein.
  • a fragment of a nucleotide sequence may encode a biologically active portion of a Cry protein, the so called“toxin fragment,” or it may be a fragment that can be used as a hybridization probe or PCR primer using methods disclosed below.
  • Nucleic acid molecules that are fragments of a Cry protein-encoding nucleotide sequence comprise at least about 15, 20, 50, 75, 100, 200, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450 contiguous nucleotides, or up to the number of nucleotides present in a full-length Cry protein encoding nucleotide sequence disclosed herein (for example, 3519 nucleotides for SEQ ID NO:l) depending upon the intended use.
  • nucleotide sequences of the invention will encode toxin fragments that retain the biological activity of the Cry protein and, hence, retain insecticidal activity.
  • insecticidal activity is intended that the fragment will have at least about 30%, preferably at least about 50%, more preferably at least about 70%, even more preferably at least about 80% of the insecticidal activity of the Cry protein.
  • Methods for measuring insecticidal activity are well known in the art. See, for example, Czapla and Lang (1990) J. Econ. Entomol. 83:2480-2485; Andrews et al. (1988) Biochem. J. 252:199-206; Marrone et al. (1985) J. of Economic Entomology 78:290-293; and U.S. Pat. No. 5,743,477, all of which are herein incorporated by reference in their entirety.
  • a toxin fragment of a Cry protein of the invention will encode at least about 15, 25, 30, 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, and 450 contiguous amino acids, or up to the total number of amino acids present in a full-length Cry protein of the invention (for example, 1173 amino acids for SEQ ID NO: 16).
  • a nucleic acid molecule of the invention comprises, consists essentially of or consists of a nucleotide sequence encoding a Cry protein comprising an amino acid sequence that has at least 80% to at least 99% sequence identity with any of SEQ ID NOs: 16-20 or a toxin fragment thereof.
  • the amino acid sequence comprises, consists essentially of or consists of any of SEQ ID NOs: 16-20 or a toxin fragment thereof.
  • Cry proteins which have been activated by means of proteolytic processing for example, by proteases prepared from the gut of an insect, may be characterized and the N-terminal or C-terminal amino acids of the activated toxin fragment identified.
  • the skilled person can determine that, for example, the toxin fragment of SEQ ID NO: 16 may comprise amino acids from about 26-605 or about 26-617 or about 26-628 of SEQ ID NO: 16, or the toxin fragment of SEQ ID NO: 17 may comprise amino acids from about 45 or from about 53 to about 622 or about 624 or to about 642 or to about 662 of SEQ ID NO: 17, or the toxin fragment of SEQ ID NO: 18 may comprise amino acids from about amino acid 11 or from about amino acid 13 or from about amino acid 35 or from about amino acid 47 to about amino acid 628, or to about amino acid 662 of SEQ ID NO: 18, or the toxin fragment of SEQ ID NO: 19 may comprise amino acids from about amino acid 24, or from amino acid 35, or from amino acid 47, or from amino acid 49 to about amino acid 660, or to amino acid 670 of SEQ ID NO: 19, or the toxin fragment of SEQ ID NO:20 may comprise amino acids from about amino acid 17, or from about amino acid 18, or from about
  • a chimeric gene comprises a heterologous promoter operably linked to a polynucleotide comprising, consisting essentially of or consisting of a nucleotide sequence that encodes a Cry protein toxic to a lepidopteran pest, wherein the nucleotide sequence (a) has at least 80% (e.g., 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9%) to at least 99% (99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9%) to at least 99% (99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%
  • the heterologous promoter is a plant-expressible promoter.
  • the plant-expressible promoter can be selected from the group of promoters consisting of ubiquitin, cestrum yellow virus, com TrpA, OsMADS 6, maize H3 histone, bacteriophage T3 gene 9 5' ETTR, com sucrose synthetase 1, corn alcohol dehydrogenase 1, corn light harvesting complex, com heat shock protein, maize mtl, pea small subunit RuBP carboxylase, rice actin, rice cyclophilin, Ti plasmid mannopine synthase, Ti plasmid nopaline synthase, petunia chalcone isomerase, bean glycine rich protein 1, potato patatin, lectin, CaMV 35S and S-E9 small subunit RuBP carboxylase promoter.
  • promoters consisting of ubiquitin, cestrum yellow virus, com TrpA, OsMADS 6, maize H3 histone, bacteriophage T3 gene 9 5' ETTR, com
  • the protein encoded by the chimeric gene is toxic to one or more lepidopteran pests selected from the group consisting of Asian corn borer ( Ostrinia furnacalis ), black cutworm ( Agrotis ipsilon ), cotton bollworm ( Helicoverpa armigera ), yellow peach borer ( Conogethes punctiferalis), oriental armyworm ( Mythimna sepatate), European com borer ( Ostrinia nubilalis ), fall armyworm (Spodoptera frugiperda), com earworm ⁇ Helicoverpa zea), sugarcane borer ( Diatraea saccharalis), velvetbean caterpillar ( Anticarsia gemmatalis ), soybean looper ( Chrysodeixis includes), southwest com borer ⁇ Diatraea grandio ella), western bean cutworm ⁇ Richia albicosta), tobacco budworms selected from the group consisting of Asian corn borer ( Ostrinia furnacalis
  • the polynucleotide comprises, consists essentially of or
  • the polynucleotide comprises, consists essentially of or consists of any one of SEQ ID NOs:l-5, or a toxin encoding fragment thereof
  • the polynucleotide comprises, consists essentially of or
  • nucleotide sequence that encodes a protein comprising, consisting essentially of or consisting of an amino acid sequence that has at least 80% to at least 99% sequence identity with any one of SEQ ID NOS: 16-20, or a toxin fragment thereof.
  • the amino acid sequence has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO: 16, or a toxin fragment thereof.
  • the amino acid sequence has at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO: 17, or a toxin fragment thereof.
  • the amino acid sequence has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO: 18, or a toxin fragment thereof.
  • the amino acid sequence has at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO: 19, or a toxin fragment thereof.
  • the amino acid sequence has at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO:20, or a toxin fragment thereof.
  • the chimeric gene of the invention comprises a polynucleotide comprising, consisting essentially of or consisting of a synthetic sequence of a nucleotide sequence that has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% with any of SEQ ID NOs:6-l5, or a toxin encoding
  • the chimeric gene of the invention comprises a polynucleotide comprising, consisting essentially of or consisting of a synthetic sequence of a nucleotide sequence that encodes a protein comprising an amino acid sequence that has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with any of SEQ ID NOs: 16-25,
  • the invention provides a synthetic polynucleotide comprising, consisting essentially of or consisting of a nucleotide sequence that encodes a protein that is toxic to a lepidopteran pest , wherein the nucleotide sequence has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with any one
  • the invention provides a synthetic polynucleotide comprising, consisting essentially of or consisting of a nucleotide sequence that encodes a protein that is toxic to a lepidopteran pest, wherein the nucleotide sequence encodes an amino acid sequence that has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.
  • Cry proteins of the invention may be assembled using genomes from Bacillus
  • Bt strains can be isolated by standard techniques and either tested for toxicity to a lepidopteran pest of the invention or used for isolation of genomic DNA without testing the Bt strain for toxicity to insects.
  • Bt strains can be isolated from any environmental sample, including soil, plant, insect, grain elevator dust, and other sample material, etc., by methods known in the art. See, for example, Travers et al. (1987) Appl. Environ. Microbiol. 53:1263-1266; Saleh et al. (1969) Can J. Microbiol. 15:1101-1104; DeLucca et al. (1981) Can J. Microbiol. 27:865-870; and Norris, et al.
  • the invention provides an isolated Bacillus thuringiensis (Bt) strain that produces a Cry protein or a recombinant Cry protein comprising, consisting essentially of or consisting of an amino acid sequence having at least 80% to at least 99% sequence identity to any of SEQ ID NOs: 16-25.
  • the Cry protein or recombinant Cry protein comprises, consists essentially of or consists of any of SEQ ID NOs: 16-25.
  • the invention provides a Cry protein, and optionally an isolated Cry protein, that is toxic to a lepidopteran pest, wherein the Cry protein comprises, consists essentially of or consists of (a) an amino acid sequence that has at least 80% sequence identity to at least 99% sequence identity with an amino acid sequence represented by any one of SEQ ID NOs: 16-25, or a toxin fragment thereof; or (b) an amino acid sequence that is encoded by a nucleotide sequence or an assembled nucleotide sequence that has at least 80% sequence identity to at least 99% sequence identity with a nucleotide sequence represented by any one of SEQ ID NOs:6-l5, or a toxin-encoding fragment thereof.
  • the Cry protein or isolated Cry protein comprises, consists essentially of or consists of an amino acid sequence that has at least 80% to at least 99% sequence identity with any one of SEQ ID NOs: 16-25, or a toxin fragment thereof.
  • the amino acid sequence has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO: 16, or a toxin fragment thereof.
  • the amino acid sequence has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO: 17, or a toxin fragment thereof.
  • the amino acid sequence has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO: 18, or a toxin fragment thereof.
  • the amino acid sequence has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO: 19, or a toxin fragment thereof.
  • the amino acid sequence has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO:20, or a toxin fragment thereof.
  • the amino acid sequence comprises, consists essentially of or consists of any one of SEQ ID NOs: 16-25, or a toxin fragment thereof.
  • the amino acid sequence is encoded by a nucleotide sequence comprising, consisting essentially of or consisting of any of SEQ ID NOs:6-l5, or a toxin-encoding fragment thereof.
  • the Cry proteins of the invention are toxic to a lepidopteran pest selected from the group consisting of Asian corn borer (Ostrinia furnacalis), black cutworm ( Agrotis ipsilon ), cotton bollworm ( Helicoverpa armigera ), yellow peach borer ( Conogethes punctiferalis ), oriental armyworm ( Mythimna sepatate), European corn borer (Ostrinia nubilalis), fall armyworm (Spodoptera frugiperda), corn earworm ( Helicoverpa zea), sugarcane borer ( Diatraea saccharalis ), velvetbean caterpillar (Anticarsia gemmatalis ), soybean looper ( Chrysodeixis includes), southwest corn bore
  • Asian corn borer Ostri
  • the invention encompasses a recombinant Cry protein that is toxic to a lepidopteran pest, wherein the recombinant Cry protein comprises, consists essentially of or consists of (a) an amino acid sequence that has at least 80% to at least 99% sequence identity with an amino acid sequence represented by any of SEQ ID NOs:2l-25, or a toxin fragment thereof; or (b) an amino acid sequence that is encoded by a nucleotide sequence that has at 80% to at least 99% sequence identity with a nucleotide sequence represented by any of SEQ ID NOs:l l-l5, or a toxin-encoding fragment thereof.
  • the recombinant Cry protein comprises, consists essentially of or consists of an amino acid sequence that has at least 80% to at least 99% sequence identity with any one of SEQ ID NOs:2l-25, or a toxin fragment thereof.
  • the amino acid sequence has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO:2l, or a toxin fragment thereof.
  • the amino acid sequence has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO:22, or a toxin fragment thereof.
  • the amino acid sequence has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO:23, or a toxin fragment thereof.
  • the amino acid sequence has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO:24, or a toxin fragment thereof.
  • the amino acid sequence has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO:25, or a toxin fragment thereof.
  • the recombinant Cry protein comprises, consists essentially of or consists of an amino acid sequence of any of SEQ ID NOs:2l-25, or a toxin fragment thereof.
  • the recombinant Cry protein is encoded by a nucleotide sequence that comprises, consists essentially of or consists of any of SEQ ID NOs:l l-l5, or a toxin-encoding fragment thereof.
  • Antibodies raised in response to immune challenge by an assembled or mutant BT- 0264, BT-0288, BT-0302, BT-0454 and BT-0485, or related Cry proteins, including a native Cry protein are also encompassed by the invention.
  • Such antibodies may be produced using standard immunological techniques for production of polyclonal antisera and, if desired, immortalizing the antibody-producing cells of the immunized host for sources of monoclonal antibody production. Techniques for producing antibodies to any substance of interest are well known, e.g., as in Harlow and Lane (1988. Antibodies a laboratory manual pp. 726. Cold Spring Harbor Laboratory) and as in Goding (Monoclonal Antibodies: Principles & practice.1986. Academic Press, Inc., Orlando, LL).
  • the present invention encompasses insecticidal proteins that cross-react with antibodies, particularly monoclonal antibodies, raised against one or more of the insecticidal Cry proteins of the present invention.
  • the antibodies produced in the invention are also useful in immunoassays for
  • Such assays are also useful in quality-controlled production of compositions containing one or more of the Cry proteins of the invention or related toxic proteins.
  • the antibodies can be used to assess the efficacy of recombinant production of one or more of the Cry proteins of the invention or a related protein, as well as for screening expression libraries for the presence of a nucleotide sequence encoding one or more of the Cry proteins of the invention or related protein coding sequences.
  • Antibodies are useful also as affinity ligands for purifying or isolating any one or more of the proteins of the invention and related proteins.
  • the Cry proteins of the invention and proteins containing related antigenic epitopes may be obtained by over expressing full or partial lengths of a sequence encoding all or part of a Cry protein of the invention or a related protein in a preferred host cell.
  • the invention may be altered by various methods, and that these alterations may result in DNA sequences encoding proteins with amino acid sequences different than that encoded by an assembled Cry protein of the invention.
  • the resulting mutant Cry protein may be altered in various ways including amino acid substitutions, deletions, truncations, and insertions of one or more amino acids of any of SEQ ID NOs: 16-20, including up to about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 15, about 20, about 25, about 30, about 35, about 40, about 45, about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 85, about 90, about 100, about 105, about 110, about 115, about 120, about 125, about 130, about 135, about 140, about 145, about 150, about 155, or more amino acid substitutions, deletions or insertions.
  • amino acid sequence variants of a native Cry protein can be prepared by mutations in a polynucleotide that encodes the protein. This may also be accomplished by one of several forms of mutagenesis or in directed evolution. In some aspects, the changes encoded in the amino acid sequence will not substantially affect the function of the protein. Such variants will possess the desired insecticidal activity.
  • nucleotide sequences represented by SEQ ID NOs: 1-5 are altered to introduce amino acid substitutions in the encoded protein.
  • the resulting mutant protein is encoded by a synthetic mutant polynucleotide comprising a nucleotide sequence represented by any one of SEQ ID NOs: 11- 15.
  • the mutant Cry proteins comprise, consist essentially of or consist of an amino acid sequence represented by any one of SEQ ID NOs:2l-25.
  • an insecticidal protein may be improved by the use of such techniques upon the compositions of this invention.
  • a Cry protein in host cells that exhibit high rates of base mis- incorporation during DNA replication, such as XL-l Red (Stratagene, La Jolla, CA). After propagation in such strains, one can isolate the DNA (for example by preparing plasmid DNA, or by amplifying by PCR and cloning the resulting PCR fragment into a vector), culture the Cry protein mutations in a non-mutagenic strain, and identify mutated genes with insecticidal activity, for example by performing an assay to test for insecticidal activity.
  • the protein is mixed and used in feeding assays. See, for example Marrone et al. (1985) J. of Economic Entomology 78:290-293.
  • assays can include contacting plants with one or more pests and determining the plant's ability to survive or cause the death of the pests. Examples of mutations that result in increased toxicity are found in Schnepf et al. (1998) Microbiol. Mol. Biol. Rev. 62:775-806.
  • alterations may be made to an amino acid sequence of the invention at the amino or carboxy terminus without substantially affecting activity.
  • This can include insertions, deletions, or alterations introduced by modem molecular methods, such as PCR, including PCR amplifications that alter or extend the protein coding sequence by virtue of inclusion of amino acid encoding sequences in the oligonucleotides utilized in the PCR amplification.
  • the protein sequences added can include entire protein-coding sequences, such as those used commonly in the art to generate protein fusions.
  • Such fusion proteins are often used to (1) increase expression of a protein of interest (2) introduce a binding domain, enzymatic activity, or epitope to facilitate either protein purification, protein detection, or other experimental uses known in the art (3) target secretion or translation of a protein to a subcellular organelle, such as the periplasmic space of Gram-negative bacteria, or the endoplasmic reticulum of eukaryotic cells, the latter of which often results in glycosylation of the protein.
  • a subcellular organelle such as the periplasmic space of Gram-negative bacteria, or the endoplasmic reticulum of eukaryotic cells, the latter of which often results in glycosylation of the protein.
  • a Cry protein of the invention can also be mutated to introduce an epitope to generate antibodies that recognize the mutated protein. Therefore, in some embodiments, the invention provides a mutated Cry protein, wherein an amino acid substitution in a native Cry protein produces a mutant Cry protein having an antigenic region that allows the mutant Cry protein to be distinguished from the native Cry protein in a protein detection assay.
  • the invention provides a method of making an antibody that differentially recognizes a mutated Cry protein from the assembled or related native Cry protein from which the mutated Cry protein is derived, the method comprising the steps of substituting amino acids in an antigenic loop of an assembled or native Cry protein and raising antibodies that specifically recognize the mutated antigenic loop in the mutated Cry protein and does not recognize the assembled or native Cry protein.
  • the antigenic loop is identified in non-conserved regions outside of domain I of the assembled or native Cry protein.
  • the antigenic loop is not a loop involved in the Cry protein’s insect gut receptor recognition or involved in the protease activation of the Cry protein.
  • Variant nucleotide and amino acid sequences of the invention also encompass sequences derived from mutagenic and recombinogenic procedures such as DNA shuffling. With such a procedure, one or more different toxic protein coding regions can be used to create a new toxic protein possessing the desired properties. In this manner, libraries of recombinant polynucleotides are generated from a population of related sequence
  • polynucleotides comprising sequence regions that have substantial sequence identity and can be homologously recombined in vitro or in vivo.
  • sequence motifs encoding a domain of interest may be shuffled between a pesticidal gene of the invention and other known pesticidal genes to obtain a new gene coding for a protein with an improved property of interest, such as an increased insecticidal activity.
  • Strategies for such DNA shuffling are known in the art. See, for example, Stemmer (1994) Proc. Natl. Acad. Sci. USA 91:10747-10751; Stemmer (1994) Nature 370:389-391; Crameri et al. (1997) Nature Biotech. 15:436-438; Moore et al. (1997) J. Mol. Biol. 272:336-347; Zhang et al. (1997)
  • Domains may be swapped between Cry proteins, resulting in hybrid or chimeric toxic proteins with improved pesticidal activity or target spectrum.
  • the invention encompasses a hybrid insecticidal protein comprising in an N-terminal to C-terminal direction a) an N-terminal region of a Cry54A protein fused to a C-terminal region of a Cry4A protein, wherein the crossover position between the Cry54A protein and the Cry4A protein is located between domain III of the Cry54A and the protoxin tail of Cry4A and wherein the hybrid insecticidal protein has at least 90% identity to SEQ ID NO: 17; or b) an N-terminal region of a Cry39A protein fused to a C-terminal region of a Cryl9C protein, wherein the crossover position between the Cry39A protein and the Cry 19 protein is located between domain III of the Cry39A and the protoxin tail of the Cryl9C and wherein the hybrid insecticidal protein has at least 90% identity to SEQ ID NO: 18; or c) an N-terminal region of a Cry50
  • the invention provides a recombinant vector comprising a polynucleotide, an assembled polynucleotide, a nucleic acid molecule, an expression cassette or a chimeric gene of the invention.
  • the vector is further defined as a plasmid, cosmid, phagemid, artificial chromosome, phage or viral vector. Certain vectors for use in transformation of plants and other organisms are known in the art.
  • expression cassette means a nucleic acid molecule having at least a control sequence operatively linked to a nucleotide sequence of interest, e.g. a nucleotide sequence of the invention encoding a Cry protein of the invention.
  • plant promoters operably linked to the nucleotide sequences to be expressed are provided in expression cassettes for expression in a plant, plant part or plant cell.
  • An expression cassette comprising a polynucleotide of interest may be chimeric, meaning that at least one of its components is heterologous with respect to at least one other of its other components.
  • An expression cassette may also be one that is naturally occurring but has been obtained in a recombinant form useful for heterologous expression. Typically, however, the expression cassette is heterologous with respect to the host, i.e., the particular nucleic acid sequence of the expression cassette does not occur naturally in the host cell and must have been introduced into the host cell or an ancestor of the host cell by a
  • an expression cassette of this invention also can include other regulatory sequences.
  • regulatory sequences means nucleotide sequences located upstream (5' non-coding sequences), within or downstream (3' non-coding sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences include, but are not limited to, enhancers, introns, translation leader sequences, termination signals, and polyadenylation signal sequences.
  • an expression cassette of the invention also can include
  • Such expression cassettes comprising the stacked traits may be used to create plants, plant parts or plant cells having a desired phenotype with the stacked traits (i.e., molecular stacking). Such stacked combinations in plants can also be created by other methods including, but not limited to, cross breeding plants by any conventional
  • the nucleotide sequences of interest can be combined at any time and in any order.
  • a transgenic plant comprising one or more desired traits can be used as the target to introduce further traits by subsequent transformation.
  • the additional nucleotide sequences can be introduced simultaneously in a co-transformation protocol with a nucleotide sequence, nucleic acid molecule, nucleic acid construct, or composition of this invention, provided by any combination of expression cassettes.
  • two nucleotide sequences will be introduced, they can be incorporated in separate cassettes ( trans ) or can be incorporated on the same cassette ( cis ).
  • Expression of polynucleotides can be driven by the same promoter or by different promoters.
  • polynucleotides can be stacked at a desired genomic location using a site-specific recombination system. See, e.g., Int'l Patent Application Publication Nos. WO 99/25821; WO 99/25854; WO 99/25840; WO 99/25855 and WO 99/25853.
  • the expression cassette also can include an additional coding sequence for one or more polypeptides or double stranded RNA molecules (dsRNA) of interest for agronomic traits that primarily are of benefit to a seed company, grower or grain processor.
  • a polypeptide of interest can be any polypeptide encoded by a nucleotide sequence of interest.
  • Non-limiting examples of polypeptides of interest that are suitable for production in plants include those resulting in agronomically important traits such as herbicide resistance (also sometimes referred to as“herbicide tolerance”), virus resistance, bacterial pathogen resistance, insect resistance, nematode resistance, or fungal resistance. See, e.g., U.S. Patent Nos.
  • the polypeptide also can be one that increases plant vigor or yield (including traits that allow a plant to grow at different temperatures, soil conditions and levels of sunlight and precipitation), or one that allows identification of a plant exhibiting a trait of interest (e.g., a selectable marker, seed coat color, etc.).
  • a trait of interest e.g., a selectable marker, seed coat color, etc.
  • growing point or meristem such as an imidazalinone or a sulfonylurea can also be suitable in some embodiments of the invention.
  • Exemplary polynucleotides in this category code for mutant ALS and AHAS enzymes as described, e.g., in U.S. Patent Nos. 5,767,366 and 5,928,937.
  • U.S. Patent Nos. 4,761,373 and 5,013,659 are directed to plants resistant to various imidazalinone or sulfonamide herbicides.
  • 4,975,374 relates to plant cells and plants containing a nucleic acid encoding a mutant glutamine synthetase (GS) resistant to inhibition by herbicides that are known to inhibit GS, e.g., phosphinothricin and methionine sulfoximine.
  • GS glutamine synthetase
  • U.S. Patent No. 5,162,602 discloses plants resistant to inhibition by cyclohexanedione and aryloxyphenoxypropanoic acid herbicides. The resistance is conferred by an altered acetyl coenzyme A carboxylase (ACCase).
  • glufosinate ammonium or phosphinothricin and pyridinoxy or phenoxy propionic acids and cyclohexones are also suitable. See, European Patent Application No. 0 242 246. See also, U.S. Patent Nos. 5,879,903, 5,276,268 and 5,561,236.
  • suitable polynucleotides include those coding for resistance to herbicides that inhibit photosynthesis, such as a triazine and a benzonitrile (nitrilase) See, U.S. Patent No. 4,810,648. Additional suitable polynucleotides coding for herbicide resistance include those coding for resistance to 2,2-dichloropropionic acid, sethoxydim, haloxyfop, imidazolinone herbicides, sulfonylurea herbicides, triazolopyrimidine herbicides, s-triazine herbicides and bromoxynil. Also suitable are polynucleotides conferring resistance to a protox enzyme, or that provide enhanced resistance to plant diseases; enhanced tolerance of adverse
  • Additional suitable polynucleotides include those coding for pesticidal (e.g., insecticidal) polypeptides. These polypeptides may be produced in amounts sufficient to control, for example, insect pests (i.e., insect controlling amounts). It is recognized that the amount of production of a pesticidal polypeptide in a plant necessary to control insects or other pests may vary depending upon the cultivar, type of pest, environmental factors and the like. Polynucleotides useful for additional insect or pest resistance include, for example, those that encode toxins identified in Bacillus organisms.
  • Bt insecticidal proteins include the Cry proteins such as CrylAa, CrylAb, Cry 1 Ac, Cry IB, Cry 1C, Cry ID, CrylEa, CrylFa, Cry3A, Cry9A, Cry9B, Cry9C, and the like, as well as vegetative insecticidal proteins such as Vipl, Vip2, Vip3, and the like.
  • Polypeptides that are suitable for production in plants further include those that improve or otherwise facilitate the conversion of harvested plants or plant parts into a commercially useful product, including, for example, increased or altered carbohydrate content or distribution, improved fermentation properties, increased oil content, increased protein content, improved digestibility, and increased nutraceutical content, e.g., increased phytosterol content, increased tocopherol content, increased stand content or increased vitamin content.
  • Polypeptides of interest also include, for example, those resulting in or contributing to a reduced content of an unwanted component in a harvested crop, e.g., phytic acid, or sugar degrading enzymes. By“resulting in” or“contributing to” is intended that the polypeptide of interest can directly or indirectly contribute to the existence of a trait of interest (e.g., increasing cellulose degradation by the use of a heterologous cellulase enzyme).
  • the polypeptide contributes to improved digestibility for food or feed.
  • Xylanases are hemicellulolytic enzymes that improve the breakdown of plant cell walls, which leads to better utilization of the plant nutrients by an animal. This leads to improved growth rate and feed conversion. Also, the viscosity of the feeds containing xylan can be reduced. Heterologous production of xylanases in plant cells also can facilitate lignocellulosic conversion to fermentable sugars in industrial processing.
  • a polypeptide useful for the invention can be a polysaccharide degrading enzyme. Plants of this invention producing such an enzyme may be useful for generating, for example, fermentation feedstocks for bioprocessing.
  • enzymes useful for a fermentation process include alpha amylases, proteases, pullulanases, isoamylases, cellulases, hemicellulases, xylanases, cyclodextrin
  • glycotransferases glycotransferases, lipases, phytases, laccases, oxidases, esterases, cutinases, granular starch hydrolyzing enzyme and other glucoamylases.
  • Polysaccharide-degrading enzymes include: starch degrading enzymes such as a- amylases (EC 3.2.1.1), glucuronidases (E.C. 3.2.1.131); exo-l,4-a- D glucanases such as amyloglucosidases and glucoamylase (EC 3.2.1.3), b-amylases (EC 3.2.1.2), a- glucosidases (EC 3.2.1.20), and other exo-amylases; starch debranching enzymes, such as a) isoamylase (EC 3.2.1.68), pullulanase (EC 3.2.1.41), and the like; b) cellulases such as exo-l,4-3- cellobiohydrolase (EC 3.2.1.91), exo-l,3b-D-glucanase (EC 3.2.1.39), b-glucosidase (EC 3.2.1.21); c) L
  • proteases such as fungal and bacterial proteases.
  • Fungal proteases include, but are not limited to, those obtained from Aspergillus, Trichoderma, Mucor and Rhizopus, such as A. niger, A. awamori, A. oryzae and M. miehei.
  • the polypeptides of this invention can be cellobiohydrolase (CBH) enzymes (EC 3.2.1.91).
  • the cellobiohydrolase enzyme can be CBH1 or CBH2.
  • hemicellulases such as mannases and arabinofuranosidases (EC 3.2.1.55); ligninases; lipases (e.g., E.C. 3.1.1.3), glucose oxidases, pectinases, xylanases, transglucosidases, alpha 1,6 glucosidases (e.g., E.C. 3.2.1.20); esterases such as ferulic acid esterase (EC 3.1.1.73) and acetyl xylan esterases (EC 3.1.1.72); and cutinases (e.g. E.C. 3.1.1.74).
  • hemicellulases such as mannases and arabinofuranosidases (EC 3.2.1.55); ligninases; lipases (e.g., E.C. 3.1.1.3), glucose oxidases, pectinases, xylanases, transglucosidases
  • Double stranded RNA molecules useful with the invention include, but are not
  • Gene suppression when taken together, are intended to refer to any of the well-known methods for reducing the levels of protein produced as a result of gene transcription to mRNA and subsequent translation of the mRNA. Gene suppression is also intended to mean the reduction of protein expression from a gene or a coding sequence including
  • Posttranscriptional gene suppression is mediated by the homology between of all or a part of a mRNA transcribed from a gene or coding sequence targeted for suppression and the corresponding double stranded RNA used for suppression, and refers to the substantial and measurable reduction of the amount of available mRNA available in the cell for binding by ribosomes.
  • the transcribed RNA can be in the sense orientation to effect what is called co-suppression, in the anti-sense orientation to effect what is called anti-sense suppression, or in both orientations producing a dsRNA to effect what is called RNA interference (RNAi).
  • Transcriptional suppression is mediated by the presence in the cell of a dsRNA, a gene suppression agent, exhibiting substantial sequence identity to a promoter DNA sequence or the complement thereof to effect what is referred to as promoter trans suppression.
  • Gene suppression may be effective against a native plant gene associated with a trait, e.g., to provide plants with reduced levels of a protein encoded by the native gene or with enhanced or reduced levels of an affected metabolite.
  • Gene suppression can also be effective against target genes in plant pests that may ingest or contact plant material containing gene suppression agents, specifically designed to inhibit or suppress the expression of one or more homologous or complementary sequences in the cells of the pest.
  • genes targeted for suppression can encode an essential protein, the predicted function of which is selected from the group consisting of muscle formation, juvenile hormone formation, juvenile hormone regulation, ion regulation and transport, digestive enzyme synthesis, maintenance of cell membrane potential, amino acid biosynthesis, amino acid degradation, sperm formation, pheromone synthesis, pheromone sensing, antennae formation, wing formation, leg formation, development and differentiation, egg formation, larval maturation, digestive enzyme formation, hemolymph synthesis, hemolymph maintenance, neurotransmission, cell division, energy metabolism, respiration, and apoptosis.
  • the invention provides a transgenic non-human host cell
  • the transgenic non-human host cell can include, but is not limited to, a plant cell, a yeast cell, a bacterial cell or an insect cell. Accordingly, in some embodiments, the invention provides a bacterial cell selected from the genera Bacillus, Brevibacillus, Clostridium, Xenorhabdus, Photorhabdus, Pasteuria, Escherichia,
  • the Cry proteins of the invention can be produced by expression of a chimeric gene encoding the Cry proteins of the invention in a bacterial cell.
  • a Bacillus thuringiensis cell comprising a chimeric gene of the invention is provided.
  • the invention provides a transgenic plant cell that is a dicot plant cell or a monocot plant cell.
  • the dicot plant cell is selected from the group consisting of a soybean cell, sunflower cell, tomato cell, cole crop cell, cotton cell, sugar beet cell and tobacco cell.
  • the monocot cell is selected from the group consisting of a barley cell, maize cell, oat cell, rice cell, sorghum cell, sugar cane cell and wheat cell.
  • the invention provides a plurality of dicot cells or monocot cells expressing a Cry protein of the invention encoded by a chimeric gene of the invention. In other embodiments the plurality of cells are juxtaposed to form an apoplast and are grown in natural sunlight.
  • an insecticidal Cry protein of the invention is expressed in a higher organism, for example, a plant.
  • transgenic plants expressing effective amounts of the insecticidal protein protect themselves from plant pests such as insect pests.
  • an insect starts feeding on such a transgenic plant it ingests the expressed insecticidal Cry protein. This can deter the insect from further biting into the plant tissue or may even harm or kill the insect.
  • a polynucleotide of the invention is inserted into an expression cassette, which is then stably integrated in the genome of the plant. In other embodiments, the polynucleotide is included in a non-pathogenic self-replicating virus.
  • Plants transformed in accordance with the invention may be monocots or dicots and include, but are not limited to, corn (maize), soybean, rice, wheat, barley, rye, oats, sorghum, millet, sunflower, safflower, sugar beet, cotton, sugarcane, oilseed rape, alfalfa, tobacco, peanuts, vegetables, including, sweet potato, bean, pea, chicory, lettuce, cabbage, cauliflower, broccoli, turnip, carrot, eggplant, cucumber, radish, spinach, potato, tomato, asparagus, onion, garlic, melons, pepper, celery, squash, pumpkin, zucchini, fruits, including, apple, pear, quince, plum, cherry, peach, nectarine, apricot, strawberry, grape, raspberry, blackberry, pineapple, avocado, papaya, mango, banana, and specialty plants, such as Arabidopsis, and woody plants such as coniferous and deciduous trees.
  • plants of the of the invention are crop plants such as maize, sorghum, wheat, sunflower, tomato, crucifers, peppers, potato, cotton, rice, soybean, sugar beet, sugarcane, tobacco, barley, oilseed rape, and the like.
  • a desired polynucleotide may be propagated in that species or moved into other varieties of the same species, particularly including commercial varieties, using traditional breeding techniques.
  • a polynucleotide of the invention is expressed in transgenic plants, thus causing the biosynthesis of the encoded Cry protein, either in protoxin or toxin form, in the transgenic plants.
  • transgenic plants with enhanced yield protection in the presence of insect pressure are generated.
  • the nucleotide sequences of the invention may require modification and optimization. Although in many cases genes from microbial organisms can be expressed in plants at high levels without modification, low expression in transgenic plants may result from microbial nucleotide sequences having codons that are not preferred in plants.
  • sequences can be modified to account for the specific codon preferences and GC content preferences of monocotyledons or dicotyledons as these preferences have been shown to differ (Murray et al. Nucl. Acids Res. 17:477-498 (1989)).
  • the nucleotide sequences are screened for the existence of illegitimate splice sites that may cause message truncation. All changes required to be made within the nucleotide sequences such as those described above are made using well known techniques of site directed mutagenesis, PCR, and synthetic gene construction using the methods described for example in US Patent Nos. 5,625,136; 5,500,365 and 6,013,523.
  • the invention provides synthetic coding sequences or
  • polynucleotide made according to the procedure disclosed in U.S. Pat. No. 5,625,136, herein incorporated by reference.
  • maize preferred codons i.e., the single codon that most frequently encodes that amino acid in maize
  • the maize preferred codon for a particular amino acid can be derived, for example, from known gene sequences from maize.
  • maize codon usage for 28 genes from maize plants is found in Murray et al., Nucleic Acids Research 17:477-498 (1989), the disclosure of which is incorporated herein by reference.
  • Specifically exemplified synthetic sequences of the present invention made with maize optimized codons are represented by any one of SEQ ID NOs: 6-15.
  • nucleotide sequences can be optimized for expression in any plant. It is recognized that all or any part of a nucleotide sequence may be optimized or synthetic. That is, a polynucleotide may comprise a nucleotide sequence that is part native sequence and part codon optimized sequence.
  • sequences adjacent to the initiating methionine may require modification.
  • they can be modified by the inclusion of sequences known to be effective in plants.
  • Joshi has suggested an appropriate consensus for plants (NAR 15:6643-6653 (1987)). These consensuses are suitable for use with the nucleotide sequences of this invention.
  • the sequences are incorporated into constructions comprising the nucleotide sequences, up to and including the ATG (while leaving the second amino acid unmodified), or alternatively up to and including the GTC subsequent to the ATG (with the possibility of modifying the second amino acid of the transgene).
  • novel Cry protein coding sequences of the invention can be operably fused to a variety of promoters for expression in plants including constitutive, inducible, temporally regulated, developmentally regulated, chemically regulated, tissue-preferred and tissue-specific promoters to prepare recombinant DNA molecules, i.e., chimeric genes.
  • promoters for expression in plants including constitutive, inducible, temporally regulated, developmentally regulated, chemically regulated, tissue-preferred and tissue-specific promoters to prepare recombinant DNA molecules, i.e., chimeric genes.
  • the choice of promoter will vary depending on the temporal and spatial requirements for expression, and also depending on the target species.
  • expression of the nucleotide sequences of this invention in leaves, in stalks or stems, in ears, in inflorescences e.g.
  • Suitable constitutive promoters include, for example, CaMV 35S promoter (SEQ ID NO:l546; Odell et ah, Nature 313:810-812, 1985); Arabidopsis At6669 promoter (SEQ ID NO: 1652; see PCT Publication No. W004081173A2); maize Ubi 1 (Christensen et ah, Plant Mol. Biol. 18:675-689, 1992); rice actin (McElroy et ah, Plant Cell 2:163-171, 1990); pEMU (Last et ah, Theor. Appl. Genet.
  • constitutive root tip CT2 promoter SEQ ID NO: 1535; see also PCT application No. IL/2005/000627) and Synthetic Super MAS (Ni et al., The Plant Journal 7: 661-76, 1995).
  • constitutive promoters include those in U.S. Pat. Nos. 5,659,026, 5,608,149; 5,608,144; 5,604,121; 5,569,597:
  • tissue-specific or tissue-preferential promoters useful for the expression of the novel cry protein coding sequences of the invention in plants, particularly maize are those that direct expression in root, pith, leaf or pollen.
  • tissue-specific promoters include, but not limited to, leaf-specific promoters [such as described, for example, by Yamamoto et al., Plant J. 12:255-265, 1997; Kwon et al., Plant Physiol. 105:357-67, 1994; Yamamoto et al., Plant Cell Physiol. 35:773-778, 1994; Gotor et al., Plant J. 3:509-18, 1993; Orozco et al., Plant Mol. Biol.
  • seed-preferred promoters e.g., from seed specific genes (Simon, et al., Plant Mol. Biol. 5. 191, 1985; Scofield, et al., J. Biol. Chem. 262: 12202, 1987; Baszczynski, et al., Plant Mol. Biol. 14: 633, 1990), Brazil Nut albumin (Pearson' et al., Plant Mol. Biol.
  • legumin Ellis, et al. Plant Mol. Biol. 10: 203-214, 1988
  • Glutelin ⁇ rice Glutelin ⁇ rice
  • endosperm specific promoters e.g., wheat LMW and HMW, glutenin-l (Mol Gen Genet 216:81-90, 1989; NAR 17:461-2), wheat a, b and g gliadins (EMB03: 1409-15, 1984), Barley ltrl promoter, barley Bl, C, D hordein (Theor Appl Gen 98:1253-62, 1999; Plant J 4:343-55, 1993; Mol Gen Genet
  • the nucleotide sequences of this invention can also be expressed under the regulation of promoters that are chemically regulated. This enables the Cry proteins of the invention to be synthesized only when the crop plants are treated with the inducing chemicals. Examples of such technology for chemical induction of gene expression is detailed in the published application EP 0 332 104 and US Patent No. 5,614,395.
  • the chemically regulated promoter is the tobacco PR- la promoter.
  • promoters of this kind include those described by Stanford et al. Mol. Gen. Genet. 215:200-208 (1989), Xu et al. Plant Molec. Biol. 22:573-588 (1993), Logemann et al. Plant Cell 1:151-158 (1989), Rohrmeier & Lehle, Plant Molec. Biol. 22:783-792 (1993), Firek et al. Plant Molec. Biol. 22:129-142 (1993), and Warner et al. Plant J. 3:191-201 (1993).
  • Non-limiting examples of promoters that cause tissue specific expression patterns that are useful in the invention include green tissue specific, root specific, stem specific, or flower specific. Promoters suitable for expression in green tissue include many that regulate genes involved in photosynthesis and many of these have been cloned from both
  • One such promoter is the maize PEPC promoter from the phosphoenol carboxylase gene (Hudspeth & Grula, Plant Molec. Biol. 12:579-589 (1989)).
  • Another promoter for root specific expression is that described by de Framond (FEBS 290:103-106 (1991) or US Patent No. 5,466,785).
  • Another promoter useful in the invention is the stem specific promoter described in U.S. Pat. No. 5,625,136, which naturally drives expression of a maize trpA gene.
  • constructs for expression of an insecticidal toxin in plants require an appropriate transcription terminator to be operably linked downstream of the heterologous nucleotide sequence.
  • an appropriate transcription terminator e.g. tml from CaMV, E9 from rbcS. Any available terminator known to function in plants can be used in the context of this invention.
  • sequences can be incorporated into expression cassettes described in this invention. These include sequences that have been shown to enhance expression such as intron sequences (e.g. from Adhl and bronzel) and viral leader sequences (e.g. from TMV, MCMV and AMV).
  • intron sequences e.g. from Adhl and bronzel
  • viral leader sequences e.g. from TMV, MCMV and AMV.
  • nucleotide sequences of the present invention may be preferable to target expression of the nucleotide sequences of the present invention to different cellular localizations in the plant. In some cases, localization in the cytosol may be desirable, whereas in other cases, localization in some subcellular organelle may be preferred. Any mechanism for targeting gene products, e.g., in plants, can be used to practice this invention, and such mechanisms are known to exist in plants and the sequences controlling the functioning of these mechanisms have been characterized in some detail.
  • Amino terminal sequences can be responsible for targeting a protein of interest to any cell compartment, such as, a vacuole, mitochondrion, peroxisome, protein bodies, endoplasmic reticulum, chloroplast, starch granule, amyloplast, apoplast or cell wall of a plant (e.g. Unger et. al. Plant Molec. Biol. 13: 411-418 (1989); Rogers et. al. (1985) Proc. Natl. Acad. Sci. USA 82: 6512-651; U.S. Pat. No. 7,102,057; WO 2005/096704, all of which are hereby incorporated by reference.
  • the signal sequence may be an N-terminal signal sequence from waxy, an N-terminal signal sequence from gamma- zein, a starch binding domain, a C-terminal starch binding domain, a chloroplast targeting sequence, which imports the mature protein to the chloroplast (Comai et. al. (1988) J. Biol. Chem. 263:
  • the signal sequence selected includes the known cleavage site, and the fusion constructed takes into account any amino acids after the cleavage site(s), which are required for cleavage.
  • this requirement may be fulfilled by the addition of a small number of amino acids between the cleavage site and the transgene ATG or, alternatively, replacement of some amino acids within the transgene sequence.
  • Procedures for transforming plants are well known and routine in the art and are described throughout the literature.
  • Non-limiting examples of methods for transformation of plants include transformation via bacterial-mediated nucleic acid delivery (e.g., via
  • Agrobacterium viral-mediated nucleic acid delivery, silicon carbide or nucleic acid whisker-mediated nucleic acid delivery, liposome mediated nucleic acid delivery, microinjection, microparticle bombardment, calcium-phosphate-mediated transformation, cyclodextrin-mediated transformation, electroporation, nanoparticle-mediated
  • binary vectors or vectors carrying at least one T-DNA border sequence are suitable, whereas for direct gene transfer (e.g., particle bombardment and the like) any vector is suitable and linear DNA containing only the construction of interest can be used.
  • direct gene transfer transformation with a single DNA species or co-transformation can be used (Schocher et ah, Biotechnology 4:1093- 1096 (1986)).
  • transformation is usually (but not necessarily) undertaken with a selectable marker that may be a positive selection (Phosphomannose Isomerase), provide resistance to an antibiotic (kanamycin, hygromycin or methotrexate) or a herbicide (glyphosate or glufosinate).
  • a selectable marker that may be a positive selection (Phosphomannose Isomerase)
  • antibiotic kanamycin, hygromycin or methotrexate
  • glyphosate or glufosinate glyphosate or glufosinate
  • selectable marker is not critical to the invention.
  • Agrobacterium- mediated transformation is a commonly used method for
  • Agrobacterium- mediated transformation typically involves transfer of the binary vector carrying the foreign DNA of interest to an appropriate Agrobacterium strain that may depend on the complement of vir genes carried by the host Agrobacterium strain either on a co-resident Ti plasmid or chromosomally (Uknes et al. (1993) Plant Cell 5:159-169). The transfer of the recombinant binary vector to
  • Agrobacterium can be accomplished by a triparental mating procedure using Escherichia coli carrying the recombinant binary vector, a helper E. coli strain that carries a plasmid that is able to mobilize the recombinant binary vector to the target Agrobacterium strain.
  • the recombinant binary vector can be transferred to Agrobacterium by nucleic acid transformation (Hofgen & Willmitzer (1988) Nucleic Acids Res. 16:9877).
  • Dicots as well as monocots may be transformed using Agrobacterium.
  • Methods for Agrobacterium-mediated transformation of rice include well known methods for rice transformation, such as those described in any of the following: European patent application EP 1198985 Al, Aldemita and Hodges (Planta 199: 612-617, 1996); Chan et al. (Plant Mol Biol 22 (3): 491-506, 1993), Hiei et al. (Plant J 6 (2): 271-282, 1994), which disclosures are incorporated by reference herein as if fully set forth.
  • the preferred method is as described in either Ishida et al. (Nat.
  • Agrobacterium tumefaciens for example pBinl9 (Bevan et al., Nucl. Acids Res. 12 (1984) 8711).
  • Agrobacteria transformed by such a vector can then be used in known manner for the transformation of plants, such as plants used as a model, like Arabidopsis or crop plants such as, by way of example, tobacco plants, for example by immersing bruised leaves or chopped leaves in an agrobacterial solution and then culturing them in suitable media.
  • the transformation of plants by means of Agrobacterium tumefaciens is described, for example, by Hagen and Willmitzer in Nucl. Acid Res. (1988) 16, 9877 or is known inter alia from F. F. White, Vectors for Gene Transfer in Higher Plants; in Transgenic Plants, Vol. 1, Engineering and Utilization, eds. S. D. Kung and R. Wu, Academic Press, 1993, pp. 15-38.
  • Transformation of a plant by recombinant Agrobacterium usually involves co cultivation of the Agrobacterium with explants from the plant and follows methods well known in the art. Transformed tissue is regenerated on selection medium carrying an antibiotic or herbicide resistance marker between the binary plasmid T-DNA borders.
  • the vector can be introduced into the cell by coating the particles with the vector containing the nucleic acid of interest.
  • a cell or cells can be surrounded by the vector so that the vector is carried into the cell by the wake of the particle.
  • Biologically active particles e.g., a dried yeast cell, a dried bacterium or a bacteriophage, each containing one or more nucleic acids sought to be introduced also can be propelled into plant tissue.
  • a polynucleotide of the invention can be directly
  • plastid transformation is that plastids are generally capable of expressing bacterial genes without substantial modification, and plastids are capable of expressing multiple open reading frames under control of a single promoter. Plastid transformation technology is extensively described in U.S. Patent Nos. 5,451,513, 5,545,817, and 5,545,818, in PCT application no. WO 95/16783, and in McBride et al. (1994) Proc. Nati. Acad. Sci. USA 91, 7301-7305.
  • the basic technique for chloroplast transformation involves introducing regions of cloned plastid DNA flanking a selectable marker together with the gene of interest into a suitable target tissue, e.g., using biolistics or protoplast transformation (e.g., calcium chloride or PEG mediated transformation).
  • a suitable target tissue e.g., using biolistics or protoplast transformation (e.g., calcium chloride or PEG mediated transformation).
  • the 1 to 1.5 kb flanking regions termed targeting sequences, facilitate homologous recombination with the plastid genome and thus allow the replacement or modification of specific regions of the plastome.
  • point mutations in the chloroplast 16S rRNA and rpsl2 genes conferring resistance to spectinomycin or streptomycin can be utilized as selectable markers for transformation (Svab, Z., Hajdukiewicz, P., and Maliga, P. (1990) Proc. Natl. Acad. Sci. USA 87, 8526-8530; Staub, J. M., and Maliga, P. (1992) Plant Cell 4, 39-45).
  • the presence of cloning sites between these markers allows creation of a plastid targeting vector for introduction of foreign genes (Staub, J.M., and Maliga, P. (1993) EMBO J. 12, 601-606).
  • Substantial increases in transformation frequency can be obtained by replacement of the recessive rRNA or r-protein antibiotic resistance genes with a dominant selectable marker, the bacterial aadA gene encoding the spectinomycin-cletoxifying enzyme aminoglycoside s'- adenyltransf erase (Svab, Z., and Maliga, P. (1993) Proc. Natl. Acad. Sci. USA 90, 913- 917).
  • this marker had been used successfully for high-frequency transformation of the plastid genome of the green alga Chlamydomonas reinhardtii (Goldschmidt-Clermont, M. (1991) Nucl. Acids Res. 19:4083-4089).
  • telomeres genes that are inserted by homologous recombination into all of the several thousand copies of the circular plastid genome present in each plant cell, takes advantage of the enormous copy number advantage over nuclear- expressed genes to permit expression levels that can readily exceed 10% of the total soluble plant protein.
  • a polynucleotide of the invention can be inserted into a plastid-targeting vector and transformed into the plastid genome of a desired plant host.
  • plants homoplastic for plastid genomes containing a nucleotide sequence of the invention can be obtained, which are capable of high expression of the polynucleotide.
  • a recombinant vector of the invention also can include an expression cassette comprising a nucleotide sequence for a selectable marker, which can be used to select a transformed plant, plant part or plant cell.
  • selectable marker means a nucleotide sequence that when expressed imparts a distinct phenotype to the plant, plant part or plant cell expressing the marker and thus allows such transformed plants, plant parts or plant cells to be distinguished from those that do not have the marker.
  • Such a nucleotide sequence may encode either a selectable or screenable marker, depending on whether the marker confers a trait that can be selected for by chemical means, such as by using a selective agent (e.g., an antibiotic, herbicide, or the like), or on whether the marker is simply a trait that one can identify through observation or testing, such as by screening (e.g., the R-locus trait).
  • a selective agent e.g., an antibiotic, herbicide, or the like
  • screening e.g., the R-locus trait
  • selectable markers include, but are not limited to, a nucleotide
  • neo or nptll which confers resistance to kanamycin, G418, and the like
  • a nucleotide sequence encoding bar which confers resistance to phosphinothricin
  • a nucleotide sequence encoding an altered 5- enolpyruvylshikimate-3-phosphate (EPSP) synthase which confers resistance to glyphosate
  • nucleotide sequence encoding a nitrilase such as bxn from Klebsiella ozaenae that confers resistance to bromoxynil (Stalker et al. (1988) Science 242:419-423); a nucleotide sequence encoding an altered acetolactate synthase (ALS) that confers resistance to imidazolinone, sulfonylurea or other ALS -inhibiting chemicals (EP Patent Application No. 154204); a nucleotide sequence encoding a methotrexate-resistant dihydrofolate reductase (DHFR) (Thillet et al. (1988) J. Biol. Chem.
  • DHFR methotrexate-resistant dihydrofolate reductase
  • nucleotide sequence encoding a dalapon dehalogenase that confers resistance to dalapon a nucleotide sequence encoding a mannose-6-phosphate isomerase (also referred to as phosphomannose isomerase (PMI)) that confers an ability to metabolize mannose
  • PMI phosphomannose isomerase
  • nucleotide sequence encoding an altered anthranilate synthase that confers resistance to 5-methyl tryptophan or a nucleotide sequence encoding hph that confers resistance to hygromycin.
  • One of skill in the art is capable of choosing a suitable selectable marker for use in an expression cassette of this invention.
  • Additional selectable markers include, but are not limited to, a nucleotide
  • nucleotide sequence encoding b-galactosidase an enzyme for which there are chromogenic substrates
  • nucleotide sequence encoding lucif erase (lux) that allows for bioluminescence detection Ow et al. (1986) Science 234:856-859
  • a nucleotide sequence encoding aequorin which may be employed in calcium-sensitive bioluminescence detection
  • transgenic plants can be regenerated from transformed plant cells, plant tissue culture or cultured protoplasts using any of a variety of known techniques. Plant regeneration from plant cells, plant tissue culture or cultured protoplasts is described, for example, in Evans et al. ⁇ Handbook of Plant Cell Cultures, Vol. 1, MacMilan Publishing Co. New York (1983)); and Vasil I. R. (ed.) ( Cell Culture and Somatic Cell Genetics of Plants, Acad. Press, Orlando, Vol. I (1984), and Vol. II (1986)).
  • the genetic properties engineered into the transgenic seeds and plants, plant parts, or plant cells of the invention described above can be passed on by sexual reproduction or vegetative growth and therefore can be maintained and propagated in progeny plants.
  • maintenance and propagation make use of known agricultural methods developed to fit specific purposes such as harvesting, sowing or tilling.
  • a polynucleotide therefore can be introduced into the plant, plant part or plant cell in any number of ways that are well known in the art, as described above. Therefore, no particular method for introducing one or more polynucleotides into a plant is relied upon, rather any method that allows the one or more polynucleotides to be stably integrated into the genome of the plant can be used. Where more than one polynucleotides is to be introduced, the respective polynucleotides can be assembled as part of a single nucleic acid molecule, or as separate nucleic acid molecules, and can be located on the same or different nucleic acid molecules. Accordingly, the polynucleotides can be introduced into the cell of interest in a single transformation event, in separate transformation events, or, for example, in plants, as part of a breeding protocol.
  • Additional embodiments of the invention include harvested products produced from the transgenic plants or parts thereof of the invention, as well as a processed product produced from the harvested products.
  • a harvested product can be a whole plant or any plant part, as described herein.
  • non-limiting examples of a harvested product include a seed, a fruit, a flower or part thereof (e.g., an anther, a stigma, and the like), a leaf, a stem, and the like.
  • a processed product includes, but is not limited to, a flour, meal, oil, starch, cereal, and the like produced from a harvested seed or other plant part of the invention, wherein said seed or other plant part comprises a nucleic acid molecule/polynucleotide/nucleotide sequence of this invention.
  • the invention provides an extract from a transgenic seed or a transgenic plant of the invention, wherein the extract comprises a nucleic acid molecule, a polynucleotide, a nucleotide sequence or a toxic protein of the invention.
  • Extracts from plants or plant parts can be made according to procedures well known in the art (See, de la Torre et al., Food, Agric. Environ. 2(l):84-89 (2004); Guidet, Nucleic Acids Res. 22(9): 1772-1773 (1994); Lipton et al., Food Agric. Immun. 12:153-164 (2000)).
  • the invention provides an insecticidal composition
  • an“agriculturally-acceptable carrier” can include natural or synthetic, organic or inorganic material which is combined with the active Cry protein to facilitate its application to or in the plant, or part thereof.
  • agriculturally acceptable carriers include, without limitation, powders, dusts, pellets, granules, sprays, emulsions, colloids, and solutions.
  • Agriculturally-acceptable carriers further include, but are not limited to, inert components, dispersants, surfactants, adjuvants, tackifiers, stickers, binders, or combinations thereof, that can be used in agricultural formulations.
  • compositions can be applied in any manner that brings the pesticidal proteins or other pest control agents in contact with the pests. Accordingly, the compositions can be applied to the surfaces of plants or plant parts, including seeds, leaves, flowers, stems, tubers, roots, and the like.
  • a plant producing a Cry protein of the invention in planta is an agricultural-carrier of the expressed Cry protein.
  • the insecticidal composition comprises a bacterial cell or a transgenic bacterial cell of the invention, wherein the bacterial cell or transgenic bacterial cell produces a Cry protein of the invention.
  • an insecticidal composition can be prepared by desiccation, lyophilization, homogenization, extraction, filtration, centrifugation, sedimentation, or concentration of a culture of Bacillus thuringiensis ( Bt ).
  • Bt cultures can be the naturally occurring Bt strains YN171-1, GX078-2 and GX435-1 described below in the Examples or transgenic Bt cultures.
  • the composition comprises from about 1% to about 99% by weight of the Cry protein of the invention.
  • the invention provides a composition that controls one or more plant pests, wherein the composition comprises a first Cry protein of the invention and a second pest control agent different from the first Cry protein.
  • the composition is a formulation for topical application to a plant.
  • the composition is a transgenic plant.
  • the composition is a combination of a formulation topically applied to a transgenic plant.
  • the formulation comprises the first Cry protein of the invention when the transgenic plant comprises the second pest control agent.
  • the formulation comprises the second pest control agent when the transgenic plant comprises the first Cry protein of the invention.
  • the second pest control agent can be an agent selected from the group consisting of a chemical pesticide, such as an insecticide, a Bacillus thuringiensis ( Bt ) insecticidal protein, a Xenorhabdus insecticidal protein, a Photorhabdus insecticidal protein, a Brevibacillus laterosporus insecticidal protein, a Bacillus sphaericus insecticidal protein, a protease inhibitors (both serine and cysteine types), lectins, alpha -amylase, peroxidase, cholesterol oxidase and a double stranded RNA (dsRNA) molecule.
  • a chemical pesticide such as an insecticide, a Bacillus thuringiensis ( Bt ) insecticidal protein, a Xenorhabdus insecticidal protein, a Photorhabdus insecticidal protein, a Brevibacillus laterosporus insecticidal protein, a Bacillus s
  • the second pest control agent is a chemical pesticide selected from the group consisting of pyrethroids, carbamates, neonicotinoids, neuronal sodium channel blockers, insecticidal macrocyclic lactones, gamma-aminobutyric acid (GABA) antagonists, insecticidal ureas and juvenile hormone mimics.
  • pyrethroids selected from the group consisting of pyrethroids, carbamates, neonicotinoids, neuronal sodium channel blockers, insecticidal macrocyclic lactones, gamma-aminobutyric acid (GABA) antagonists, insecticidal ureas and juvenile hormone mimics.
  • GABA gamma-aminobutyric acid
  • the chemical pesticide is selected from the group consisting of abamectin, acephate, acetamiprid, amidoflumet (S-1955), avermectin, azadirachtin, azinphos-methyl, bifenthrin, binfenazate, buprofezin, carbofuran, chlorfenapyr, chlorfluazuron, chlorpyrifos, chlorpyrifos-methyl, chromafenozide, clothianidin, cyfluthrin, beta-cyfluthrin, cyhalothrin, lambda-cyhalothrin, cypermethrin, cyromazine, deltamethrin, diafenthiuron, diazinon, diflubenzuron, dimethoate, diofenolan, emamectin, endosulfan, esfenvalerate, e
  • the chemical pesticide is selected from the group consisting of cypermethrin, cyhalothrin, cyfluthrin and beta-cyfluthrin, esfenvalerate, fenvalerate, tralomethrin, fenothicarb, methomyl, oxamyl, thiodicarb, clothianidin, imidacloprid, thiacloprid, indoxacarb, spinosad, abamectin, avermectin, emamectin, endosulfan, ethiprole, fipronil, flufenoxuron, triflumuron, diofenolan, pyriproxyfen, pymetrozine and amitraz.
  • the second pest control agent can be one or more of any number of Bacillus thuringiensis insecticidal proteins including but not limited to a Cry protein, a vegetative insecticidal protein (VIP) and insecticidal chimeras of any of the preceding insecticidal proteins.
  • Bacillus thuringiensis insecticidal proteins including but not limited to a Cry protein, a vegetative insecticidal protein (VIP) and insecticidal chimeras of any of the preceding insecticidal proteins.
  • the second pest control agent is a Cry protein selected from the group consisting of CrylAa, CrylAb, CrylAc, CrylAd, CrylAe, CrylAf, CrylAg, CrylAh, CrylAi, CrylAj, CrylBa, CrylBb, CrylBc, CrylBd, CrylBe, CrylBf, CrylBg, CrylBh, CrylBi, CrylCa, CrylCb, CrylDa, CrylDb, CrylDc, CrylDd, CrylEa, CrylEb, CrylFa, CrylFb, CrylGa, CrylGb, CrylGc, CrylHa, CrylHb, CrylHc, Crylla, Cryllb, Cryllc, Crylld, Crylle, Cryllf, Cryllg, CrylJa, CrylJb, CrylJc, CrylJd, CrylKa, C
  • the second pest control agent is a Vip3 vegetative
  • insecticidal protein selected from the group consisting of Vip3Aal, Vip3Aa2, Vip3Aa3, Vip3Aa4, Vip3Aa5, Vip3Aa6, Vip3Aa7, Vip3Aa8, Vip3Aa9, Vip3Aal0, Vip3Aal l, Vip3Aal2, Vip3Aal3, Vip3Aal4, Vip3Aal5, Vip3Aal6 , Vip3Aal7, Vip3Aal8, Vip3Aal9, Vip3Aa20, Vip3Aa2l, Vip3Aa22, Vip3Aa2 , Vip3Aa24, Vip3Aa25, Vip3Aa26, Vip3Aa27, Vip3Aa28, Vip3Aa29, Vip3Aa30, Vip3Aa3l, Vip3Aa32, Vip3Aa33 , Vip3Aa34, Vip3Aa35, Vip3
  • Vip3Ahl Vip3Bal, Vip3Ba2, Vip3Bbl, Vip3Bb2 and Vip3Bb3.
  • the first Cry protein of the invention and the second pest control agent are co-expressed in a transgenic plant.
  • This co-expression of more than one pesticidal principle in the same transgenic plant can be achieved by genetically engineering a plant to contain and express all the genes necessary.
  • a plant, Parent 1 can be genetically engineered for the expression of the Cry protein of the invention.
  • a second plant, Parent 2 can be genetically engineered for the expression of a second pest control agent. By crossing Parent 1 with Parent 2, progeny plants are obtained which express all the genes introduced into Parents 1 and 2.
  • the invention provides a stacked transgenic plant resistant to plant pest infestation comprising a DNA sequence encoding a dsRNA for suppression of an essential gene in a target pest and a DNA sequence encoding a Cry protein of the invention exhibiting biological activity against the target pest. It has been reported that dsRNAs are ineffective against certain lepidopteran pests (Rajagopol et al. 2002. J. Biol. Chem. 277:468- 494), likely due to the high pH of the midgut which destabilizes the dsRNA.
  • a Cry protein of the invention acts to transiently reduce the midgut pH which serves to stabilize the co-ingested dsRNA rendering the dsRNA effective in silencing the target genes.
  • the invention provides methods of
  • Such a method comprises, culturing a transgenic non-human host cell that comprises a polynucleotide or a chimeric gene or nucleic acid molecule or a recombinant vector of the invention under conditions in which the host cell produces a protein toxic to the lepidopteran pest.
  • the transgenic non-human host cell is a plant cell.
  • the plant cell is a maize cell.
  • the conditions under which the plant cell or maize cell are grown include natural sunlight.
  • the transgenic non-human host cell is a bacterial cell.
  • the transgenic non-human host cell is a yeast cell.
  • the lepidopteran pest is selected from the group consisting of Asian com borer (Ostrinia furnacalis), black cutworm ( Agrotis ipsilon ), cotton bollworm ( Helicoverpa armigera ), yellow peach borer ( Conogethes punctiferalis), oriental armyworm ( Mythimna sepatate), European com borer ( Ostrinia nubilalis ), fall armyworm (Spodoptera frugiperda), corn earworm ( Helicoverpa zea), sugarcane borer ( Diatraea saccharalis ), velvetbean caterpillar ( Anticarsia gemmatalis ), soybean looper ( Chrysodeixis includes), southwest corn borer ( Diatraea grandioselld), western bean cutworm ( Richia albicostd), tobacco budworm ( Heliothis virescens), striped stem borer ( Chile suppressalis), pink stem borer ( Sesamia cal
  • the chimeric gene comprises any of SEQ ID NOs:l-5.
  • the produced protein comprises an amino acid sequence of any of SEQ ID NOs: 16-25.
  • the chimeric gene comprises a nucleotide
  • the chimeric gene comprises any of SEQ ID NOs:6-lO.
  • the produced protein comprises an amino acid sequence of any of SEQ ID NOs: 16-25.
  • the invention provides a method of producing a pest-resistant (e.g., an insect-resistant) transgenic plant, comprising, introducing into a plant a pest-resistant (e.g., an insect-resistant) transgenic plant, comprising, introducing into a plant a pest-resistant (e.g., an insect-resistant) transgenic plant, comprising, introducing into a plant a pest-resistant (e.g., an insect-resistant) transgenic plant, comprising, introducing into a plant a pest-resistant (e.g., an insect-resistant) transgenic plant, comprising, introducing into a plant a pest-resistant (e.g., an insect-resistant) transgenic plant, comprising, introducing into a plant a pest-resistant (e.g., an insect-resistant) transgenic plant, comprising, introducing into a plant a pest-resistant (e.g., an insect-resistant) transgenic plant, comprising, introducing into a plant a pest-resistant (e.g., an insect-
  • a pest-resistant transgenic plant is resistant to a lepidopteran pest in the Genus Ostrinia as compared to a control plant lacking the
  • the introducing is achieved by transforming the plant. In other embodiments, the introducing is achieved by crossing a first plant comprising the chimeric gene, recombinant vector, expression cassette or nucleic acid molecule of the invention with a different second plant.
  • a transgenic plant of the invention that is resistant to at least Asian com borer is further resistant to at least one additional lepidopteran pest, wherein the additional lepidopteran pest includes, but is not limited to, black cutworm ( Agrotis ipsilon), fall army worm (Spodoptera frugiperda), corn earworm ( Helicoverpa zea), sugarcane borer ( Diatraea saccharalis), velvetbean caterpillar (.
  • a method of controlling a lepidopteran pest such as Asian com borer ⁇ Ostrinia furnacalis
  • the method comprising delivering to the insects an effective amount of a Cry protein of the invention.
  • the Cry protein is first orally ingested by the insect.
  • the Cry protein can be delivered to the insect in many recognized ways.
  • the ways to deliver a protein orally to an insect include, but are not limited to, providing the protein (1) in a transgenic plant, wherein the insect eats (ingests) one or more parts of the transgenic plant, thereby ingesting the polypeptide that is expressed in the transgenic plant; (2) in a formulated protein composition(s) that can be applied to or incorporated into, for example, insect growth media; (3) in a protein composition(s) that can be applied to the surface, for example, sprayed, onto the surface of a plant part, which is then ingested by the insect as the insect eats one or more of the sprayed plant parts; (4) a bait matrix; or (5) any other art-recognized protein delivery system.
  • any method of oral delivery to an insect can be used to deliver the toxic Cry proteins of the invention.
  • the Cry protein of the invention is delivered orally to an insect, wherein the insect ingests one or more parts of a transgenic plant.
  • the Cry protein of the invention is delivered orally to an insect, wherein the insect ingests one or more parts of a plant sprayed with a composition
  • Delivering the compositions of the invention to a plant surface can be done using any method known to those of skill in the art for applying compounds, compositions, formulations and the like to plant surfaces.
  • Some non-limiting examples of delivering to or contacting a plant or part thereof include spraying, dusting, sprinkling, scattering, misting, atomizing, broadcasting, soaking, soil injection, soil incorporation, drenching (e.g., root, soil treatment), dipping, pouring, coating, leaf or stem infiltration, side dressing or seed treatment, and the like, and combinations thereof.
  • the invention encompasses a method of providing a farmer with a means of controlling a lepidopteran pest, the method comprising supplying or selling to the farmer plant material such as a seed, the plant material comprising a polynucleotide, chimeric gene, expression cassette or a recombinant vector capable of expressing a Cry protein of the invention in a plant grown from the seed, as described above.
  • Bacillus thuringiensis (Bt) strains were isolated from soil samples collected in China.
  • Soil samples were suspended in LB+2.5M sodium acetate liquid media followed by 70°C heat treatment for about 20 mins. A one microliter suspension was then spread on T3 + penicillin agar plates and incubated at 28°C until colonies formed. Colonies with Bacillus like morphology were picked from the plates and re- streaked on T3 + penicillin agar plates until they had sporulated, typically for approximately three days. Bt strains were identified by staining the culture with Coomasie blue/acetic acid and visualization with a microscope.
  • genomic DNA was isolated as described below.
  • Bt cry genes of the invention were assembled from the genomes of the Bt strains isolated as described in Example 1 using a whole genome sequencing approach. Briefly, Bacillus DNA was sheared using a Covaris S2 ultrasonic device (Covaris, Inc., Wobum,
  • the library was size fractionated as follows: A 50 uL sample was mixed with 45 ul 75% bead mix (25% AMPure beads plus 75% NaCl/PEG solution TekNova cat # P4136).
  • the sized DNA library was amplified using KAPA Biosystem HiFi Hot Start (Kapa Biosystems, Inc., Wilmington, MA) using the following cycle conditions: [98°C, 45s]; 12 x [98°C, l5s, 60°C, 30s, 72°C, 30s]; [72°C, 1 min].
  • Each reaction contained: 5 ul DNA library, 1 uL Bioscience universal primer (25 uM), 18 uL sterile water, luL Bioscience indexed primer (25 uM), 25 ul 2X KAPA HiFi polymerase.
  • nucleotide sequences are referred to herein as“assembled sequences,” and the Cry proteins which they encode are derived from“assembled sequences.”
  • the nearest Cry family identified for the truncated BT288 Cry protein is Cry54Aa compared to the full-length BT288 (SEQ ID NO: 17) in which the nearest Cry family is Cry4Aa, which have 42% identity across their full-length.
  • BT288 Aligning BT288 with Cry54A and Cry4Aa revealed that the N-terminus of BT288 (SEQ ID NO:26) has 51% identity to a Cry54A protein (See Table 2) and the C-terminus of BT288 (SEQ ID NO:27) has 47% identity to a Cry4A protein (See Table 3), suggesting that the assembled BT288 nucleotide sequence is a hybrid between a Cry50A and a Cry4A protein.
  • BT302 is Cry39Aa compared to the full-length BT302 (SEQ ID NO: 18) in which the nearest Cry family is Cryl9Ca, which have 47% identity across their full-length. Aligning BT302 with Cry39A and Cryl9Ca revealed that the N-terminus of BT302 (SEQ ID NO:28) has 54% identity to Cry39A (See Table 4) and the C-terminus of BT302 (SEQ ID NO:29) has 53% identity to Cryl9Ca (See Table 5), suggesting that the assembled BT302 nucleotide sequence is a hybrid between a Cry39A and a Cryl9C protein.
  • BT485 nucleotide sequence appears to by a hybrid between a Cry50 and a Cry4.
  • Cry4B and Cry50 are known in the art to be active against Dipteran insects, particularly mosquitoes (Zhang et al. 2012. Characterization of a new highly mosquitocidal isolate of Bacillus thuringiensis— an alternative to Bti. J. Invertebr. Pathol. 109 (2), 217-222), and there is no apparent report of activity against lepidopteran insects.
  • Bacillus Expression The Cry proteins described in Example 2 were expressed in an crystal minus Bacillus thuringiensis (Bt) strain having no observable background insecticidal activity via a shuttle vector designated pCIB5634', designed for expression in both E. coli and Bt.
  • Vector pCIB5634' comprises a CrylAc promoter that drives expression of the cloned Bt Cry gene and a erythromycin resistance marker.
  • Expression cassettes comprising the Cry coding sequence of interest were transformed into the host Bt strain via electroporation and transgenic Bt strains were selected for on erythromycin containing agar plates.
  • Selected transgenic Bt strains were grown to the sporulation phase in T3 media at 28°C for 4-5 days. Cell pellets were harvested and washed iteratively before solubilization in high pH carbonate buffer (50mM) containing 2mM DTT.
  • E. coli Expression Cry proteins were expressed in E. coli strains using pET28a or pET29a vectors (Merck KGaA, Darmstadt, Germany). Constructs were transformed by electroporation and transgenic E. coli clones were selected for on kanamycin-containing agar plates. Selected transgenic E. coli strains were grown and Cry protein expression induced using IPTG induction at 28°C. Cells were resuspended in high pH carbonate buffer (50mM) containing 2mM DTT and then broken using a Microfluidics LV-l homogenizer.
  • high pH carbonate buffer 50mM
  • Example 3 The Cry proteins produced in Example 3 were tested against one or more of the following lepidopteran pest species using an art-recognized artificial diet bioassay method: Asian com borer (ACB; Ostrinia furnacalis), cotton bollworm (CBW; Helicoverpa armigera), black cutworm (BCW; Agrotis ipsilon ), European com borer (ECB; Ostrinia nubilalis), fall armyworm (FAW; Spodoptera frugiperda), corn earworm (CEW; Helicoverpa zea), sugarcane borer (SCB; Diatraea saccharlis), southwest com borer (SWCB; Diatraea grandio ella), soybean looper (SBL; Pseudoplusia includens) and tobacco budworm (TBW; Heliothis virescens).
  • ACB Asian com borer
  • CBW Cotton bollworm
  • CBW Helicoverpa armigera
  • Results are shown in Table 9, where a“-’’means no activity compared to the
  • a“+/-” means 0-10% activity compared to control group (this category also includes 0% mortality with strong larval growth inhibition), a“+” means 10-25% activity compared to control group, a“++” means 25-75% activity compared to control group, and a “+++” 75-100% activity compared to control group.
  • the designation“nt” in Table 2 means the indicated protein was not tested against that particular pest.
  • polynucleotides encoding Cry proteins Prior to expression in plants, polynucleotides encoding Cry proteins, BT264 (SEQ ID NO: 16), BT288 (SEQ ID NO: 17), BT302 (SEQ IDNO:l8), BT454 (SEQ ID NO: 19) or BT485 (SEQ ID NO:20) or mutant Cry proteins, mBT264 (SEQ ID NO:2l), mBT288 (SEQ ID NO:22), mBT302 (SEQ ID NO:23), mBT454 (SEQ ID NO;24) or mBT485 (SEQ ID NO:25) are synthesized on an automated gene synthesis platform (e.g., Genscript, Inc., Piscataway, NJ).
  • an automated gene synthesis platform e.g., Genscript, Inc., Piscataway, NJ.
  • a first expression cassette is made comprising a plant expressible promoter operably linked to a Cry protein coding sequence which is operably linked to a terminator and a second expression cassette is made comprising a plant expressible promoter operably linked to a selectable marker which is operably linked to a terminator. Expression of the selectable marker allows for identification of transgenic plants on selection media. Both expression cassettes are cloned into a suitable vector for
  • Transformation of immature maize embryos is performed essentially as described in Negrotto et al, 2000, Plant Cell Reports 19: 798 803. Briefly, Agrobacterium strain
  • LBA4404 comprising an expression vector described in Example 5 is grown on YEP (yeast extract (5 g/L), peptone (lOg/L), NaCl (5g/L), l5g/l agar, pH 6.8) solid medium for 2- 4 days at 28°C. Approximately 0.8X 10 9 Agrobacterium cells are suspended in LS-inf media supplemented with 100 mM As. Bacteria are pre-induced in this medium for approximately 30-60 minutes.
  • Immature embryos from an inbred maize line are excised from 8-12 day old ears into liquid LS-inf + 100 mM As. Embryos are rinsed once with fresh infection medium. Agrobacterium solution is then added and embryos are vortexed for 30 seconds and allowed to settle with the bacteria for 5 minutes. The embryos are then transferred scutellum side up to LSAs medium and cultured in the dark for two to three days. Subsequently, between approximately 20 and 25 embryos per petri plate are transferred to LSDc medium
  • cefotaxime 250 mg/l
  • silver nitrate 1.6 mg/l
  • Immature embryos, producing embryogenic callus are transferred to LSD1M0.5S medium.
  • the cultures are selected on this medium for approximately 6 weeks with a subculture step at about 3 weeks.
  • Surviving calli are transferred to Regl medium
  • Transgenic plants are evaluated for copy number (determined by Taqman analysis), protein expression level (determined by ELISA), and efficacy against insect species of interest in leaf excision bioassays.
  • plant tissue leaf or silks
  • leaf disks from transgenic plants expressing BT264, BT288, BT302, BT454, BT485, mBT264, mBT288, mBT302, mBT454 or mBT485 are tested against one or more lepidopteran pests such as Asian com borer ( Ostrinia furnacalis ).
  • Results of the transgenic plant tissue bioassay will confirm that the Cry proteins of the invention when expressed in transgenic plants are toxic to one or more of the target lepidopteran pests.

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Abstract

Novel insecticidal proteins that are toxic to lepidopteran pests are disclosed. The DNA encoding the insecticidal proteins can be used to transform prokaryotic and eukaryotic organisms to express the insecticidal proteins. The recombinant organisms or compositions containing the recombinant organisms or the insecticidal proteins alone or in combination with an appropriate agricultural carrier can be used to control lepidopteran pests in various environments.

Description

COMPOSITIONS AND METHODS FOR CONTROLLING PLANT PESTS
REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY
[0001] The official copy of the sequence listing is submitted electronically as an ASCII formatted sequence listing with a file named "81292-CN-REG-ORG- P_SeqList_ST25.txt", created on August 27, 2018, and having a size of 247 kilobytes and is filed concurrently with the specification. The sequence listing contained in this ASCII formatted document is part of the specification and is herein incorporated by reference in its entirety.
FIELD OF THE INVENTION
[0002] This invention relates to pesticidal proteins and the nucleic acid molecules that
encode them, as well as compositions and methods for controlling plant pests.
BACKGROUND
[0003] Bacillus thuringiensis ( Bt ) is a gram-positive spore forming soil bacterium
characterized by its ability to produce crystalline inclusions that are specifically toxic to certain orders and species of plant pests, including insects, but are harmless to plants and other non-target organisms. For this reason, compositions comprising Bacillus thuringiensis strains or their insecticidal proteins can be used as environmentally- acceptable insecticides to control agricultural insect pests or insect vectors of a variety of human or animal diseases.
[0004] Crystal (Cry) proteins from Bacillus thuringiensis have potent insecticidal activity against predominantly lepidopteran, dipteran, and coleopteran pest insects. These proteins also have shown activity against pests in the Orders Hymenoptera, Homoptera, Phthiraptera, Mallophaga, and Acari pest orders, as well as other invertebrate orders such as
Nemathelminthes, Platyhelminthes, and Sarcomastigorphora (Feitelson, J. 1993. The Bacillus Thuringiensis family tree. In Advanced Engineered Pesticides. Marcel Dekker, Inc., New York, N.Y.). These proteins were originally classified as Cryl to Cry VI based primarily on their insecticidal activity. The major classes were Lepidoptera- specific (I), Lepidoptera- and Dip tera- specific (II), Coleoptera- specific (III), Dip tera- specific (IV), and nematode- specific (V) and (VI). The proteins were further classified into subfamilies; more highly related proteins within each family were assigned divisional letters such as CrylA, Cry IB, CrylC, etc. Even more closely related proteins within each division were given names such as CrylC(a), CrylC(b), etc. The terms“Cry toxin” and“delta-endotoxin” have been used interchangeably with the term“Cry protein.” Current nomenclature for Cry proteins and genes is based upon amino acid sequence homology rather than insect target specificity (Crickmore el al. (1998) Microbiol. Mol. Biol. Rev. 62:807-813). In this more accepted classification, each toxin is assigned a unique name incorporating a primary rank (an Arabic number), a secondary rank (an uppercase letter), a tertiary rank (a lowercase letter), and a quaternary rank (another Arabic number). In the current classification, Roman numerals have been exchanged for Arabic numerals in the primary rank. For example,“CrylA(a)” under the older nomenclature is now“CrylAa” under the current nomenclature. According to Ibrahim et al. (2010, Bioeng. Bugs, 1:31-50), the Cry toxins can still be separated into six major classes according to their insect host specificities and include: Group 1— lepidopteran e.g., Cryl, Cry9 and Cryl5); group 2— lepidopteran and dipteran (e.g., Cry2); group 3— coleopteran (Cry3, Cry7 and Cry8); group 4— dipteran (Cry4, CrylO, Cryl l, Cryl6, Cryl7, Cry 19 and Cry 20); group 5— lepidopteran and coleopteran (Cryll); and group 6— nematodes (Cry6). The Cryll, Cry2, Cry3, CrylO and Cryl l toxins (73-82 kDa) are unique because they appear to be natural truncations of the larger Cryl and Cry4 proteins (130-140 kDa).
[0005] Cry proteins are globular protein molecules which accumulate as protoxins in
crystalline form during the sporulation stage of Bt. After ingestion by a pest, the crystals are typically solubilized to release protoxins, which can range in size, for example, from 130-140 kDa for many of the lepidopteran- active Cry proteins, such as Cryl and Cry9, and 60-80 kDa for the coleopteran- active Cry3 proteins and the lepidopteran/dipteran-active Cry2 proteins. After the crystals are solubilized by a susceptible insect the released protoxins are processed by proteases in the insect gut, for example trypsin and chymotrypsin, to produce a protease- resistant core Cry protein toxin. This proteolytic processing involves the removal of amino acids from different regions of the various Cry protoxins. For example, Cry protoxins that are 130-140 kDa are typically activated through the proteolytic removal of an N-terminal peptide of 25-30 amino acids and approximately half of the remaining protein from the C-terminus resulting in an approximately 60-70 kDa mature Cry toxin. The protoxins that are 60-80 kDa, e.g. Cry2 and Cry3, are also processed but not to the same extent as the larger protoxins. The smaller protoxins typically have equal or more amino acids removed from the N-terminus than the larger protoxins but less amino acids removed from the C-terminus. For example, proteolytic activation of Cry2 family members typically involves the removal of approximately 40-50 N-terminal amino acids. Many of the Cry proteins are quite toxic to specific target insects, but many have narrow spectrums of activity.
[0006] Cry proteins generally have five conserved sequence domains, and three conserved structural domains (see, for example, de Maagd et al. (2001) Trends Genetics 17:193-199). The first conserved structural domain, called Domain I, typically consists of seven alpha helices and is involved in membrane insertion and pore formation. Domain II typically consists of three beta- sheets arranged in a Greek key configuration, and domain III typically consists of two antiparallel beta-sheets in‘jelly-roll’ formation (de Maagd et ah, 2001, supra). Domains II and III are involved in receptor recognition and binding, and are therefore considered determinants of toxin specificity.
[0007] Numerous commercially valuable plants, including common agricultural crops, are susceptible to attack by plant pests including insect and nematode pests, causing substantial reductions in crop yield and quality. For example, plant pests are a major factor in the loss of the world's important agricultural crops. About 15-20 percent of harvestable grain in China is lost every year to insect pests and diseases. In addition, about $8 billion are lost every year in the United States alone due to infestations of invertebrate pests including insects. Insect pests are also a burden to vegetable and fruit growers, to producers of ornamental flowers, and to home gardeners.
[0008] Insect pests are mainly controlled by intensive applications of chemical pesticides, which are active through inhibition of insect growth, prevention of insect feeding or reproduction, or cause death. Biological pest control agents, such as Bacillus thuringiensis strains expressing pesticidal toxins such as Cry proteins, have also been applied to crop plants with satisfactory results, offering an alternative or compliment to chemical pesticides. The genes coding for some of these Cry proteins have been isolated and their expression in heterologous hosts such as transgenic plants have been shown to provide another tool for the control of economically important insect pests.
[0009] Good insect control can thus be reached, but certain chemicals can sometimes also affect non-target beneficial insects and certain biologicals have a very narrow spectrum of activity. In addition, the continued use of certain chemical and biological control methods heightens the chance for insect pests to develop resistance to such control measures. This has been partially alleviated by various resistance management practices, but there remains a need to develop new and effective pest control agents that provide an economic benefit to farmers and that are environmentally acceptable. Particularly needed are control agents that can target to a wider spectrum of economically important insect pests and that efficiently control insect strains that are or could become resistant to existing insect control agents.
SUMMARY
[0010] In view of these needs, it is an object of the present invention to provide new pest control agents by providing novel genes and pesticidal proteins that may be used to control a variety of plant pests.
[0011] The invention provides compositions and methods for conferring pesticidal activity to bacteria, plants, plant cells, tissues and seeds. In particular, chimeric genes comprising novel polynucleotides that encode Cry proteins derived from assembled polynucleotides and sequences substantially identical thereto, whose expression results in proteins with toxicity to economically important insect pests, particularly insect pests that infest plants, are provided. The invention is further drawn to novel Cry proteins resulting from the expression of the polynucleotides, and to compositions and formulations containing the Cry proteins, which are toxic to insects by inhibiting the ability of insect pests to survive, grow and reproduce, or of limiting insect-related damage or loss to crop plants. Cry proteins of the invention include Cry proteins derived from assembled polynucleotides and mutant or variant Cry proteins that have one or more amino acid substitutions, additions or deletions. Examples of mutant Cry proteins include without limitation those that are mutated to have a broader spectrum of activity or higher specific activity than native Cry protein counterparts, those mutated to introduce an epitope to generate antibodies that differentially recognize the mutated protein from a native protein or those mutated to modulate expression in a transgenic organism. The novel Cry proteins of the invention are highly toxic to insect pests. For example, the Cry proteins of the invention may be used to control one or more economically important insect pests such as Asian com borer {Ostrinia furnacalis), black cutworm ( Agrotis ipsilon ), cotton bollworm ( Helicoverpa armigera ), yellow peach borer ( Conogethes punctiferalis), Oriental armyworm ( Mythimna sepatate), European com borer ( Ostrinia nubilalis ), fall armyworm (Spodoptera frugiperda), corn earworm ( Helicoverpa zea), sugarcane borer ( Diatraea saccharalis ), velvetbean caterpillar ( Anticarsia gemmatalis ), soybean looper ( Chrysodeixis includes), southwest corn borer ( Diatraea grandio ella), western bean cutworm ( Richia albicosta), tobacco budworm ( Heliothis virescens), striped stem borer ( Chile suppressalis), pink stem borer ( Sesamia calamistis), rice leaffolder ( Cnaphalocrocis medinalis), and the like. [0012] The invention also provides synthetic polynucleotides that encode the Cry proteins of the invention that have one or more codons optimized for expression in transgenic organisms such as transgenic bacteria or transgenic plants.
[0013] The invention is further drawn to expression cassettes and recombinant vectors
comprising a polynucleotide that encodes a Cry protein of the invention. The invention also provides transformed bacteria, plants, plant cells, tissues, and seeds comprising a chimeric gene, or an expression cassette or a recombinant vector which are useful in expressing a Cry protein of the invention in the transformed bacteria, plants, plant cells, tissues and seeds.
[0014] The invention is also drawn to isolated Bacillus thuringiensis ( Bt ) strains that produce Cry proteins of the invention.
[0015] The invention is also drawn to methods of using the polynucleotides of the
invention, for example in DNA constructs or chimeric genes or expression cassettes or recombinant vectors for transformation and expression in organisms, including plants and microorganisms, such as bacteria. The nucleotide or amino acid sequences may be assembled, native or codon optimized sequences that have been designed for expression in an organism such as a plant or bacteria, or in making hybrid Cry toxins with enhanced pesticidal activity. The invention is further drawn to methods of making Cry proteins and to methods of using the polynucleotide sequences and Cry proteins, for example in microorganisms to control insects or in transgenic plants to confer protection from insect damage.
[0016] Another aspect of the invention includes insecticidal compositions and formulations comprising the Cry proteins or Bacillus thuringiensis strains of the invention, and methods of using the compositions or formulations to control insect populations, for example by applying the compositions or formulations to insect-infested areas, or to prophylactically treat insect-susceptible areas or plants to confer protection against the insect pests.
Optionally, the compositions or formulations of the invention may, in addition to the Cry protein or Bt strain of the invention, comprises other pesticidal agents such as chemical pesticides in order to augment or enhance the insect-controlling capability of the composition or formulation.
[0017] The compositions and methods of the invention are useful for controlling insect pests that attack plants, particularly crop plants. The compositions of the invention are also useful for generating altered or improved Cry proteins that have pesticidal activity, or for detecting the presence of a Cry protein or nucleic acids in commercial products or transgenic organisms.
[0018] These and other features, aspects, and advantages of the invention will become better understood with reference to the following detailed description and claims.
BRIEF DESCRIPTION OF THE SEQUENCES IN THE SEQUENCE FISTING
[0019] SEQ ID NO:l represents a nucleotide sequence encoding a BT264 protein.
[0020] SEQ ID NO:2 represents a nucleotide sequence encoding a BT288 protein.
[0021] SEQ ID NO:3 represents a nucleotide sequence encoding a BT302 protein.
[0022] SEQ ID NO:4 represents a nucleotide sequence encoding a BT454 protein.
[0023] SEQ ID NO:5 represents a nucleotide sequence encoding a BT485 protein.
[0024] SEQ ID NO:6 represents a codon optimized sequence encoding a BT264 protein.
[0025] SEQ ID NO:7 represents a codon optimized sequence encoding a BT288 protein.
[0026] SEQ ID NO:8 represents a codon optimized sequence encoding a BT302 protein.
[0027] SEQ ID NO:9 represents a codon optimized sequence encoding a BT454 protein.
[0028] SEQ ID NO: 10 represents a codon optimized sequence encoding a BT485 protein.
[0029] SEQ ID NO: 11 represents a nucleotide sequence encoding a mutant BT264 protein.
[0030] SEQ ID NO: 12 represents a nucleotide sequence encoding a mutant BT288 protein.
[0031] SEQ ID NO: 13 represents a nucleotide sequence encoding a mutant BT302 protein.
[0032] SEQ ID NO: 14 represents a nucleotide sequence encoding a mutant BT454 protein.
[0033] SEQ ID NO: 15 represents a nucleotide sequence encoding a mutant BT485 protein.
[0034] SEQ ID NO: 16 represents an amino acid sequence of a BT264 protein.
[0035] SEQ ID NO: 17 represents an amino acid sequence of a BT288 protein.
[0036] SEQ ID NO: 18 represents an amino acid sequence of a BT302 protein.
[0037] SEQ ID NO: 19 represents an amino acid sequence of a BT454 protein.
[0038] SEQ ID NO:20 represents an amino acid sequence of a BT485 protein.
[0039] SEQ ID NO:2l represents an amino acid sequence of a mutant BT264 protein.
[0040] SEQ ID NO:22 represents an amino acid sequence of a mutant BT288 protein.
[0041] SEQ ID NO:23 represents an amino acid sequence of a mutant BT302 protein. [0042] SEQ ID NO:24 represents an amino acid sequence of a mutant BT454 protein
[0043] SEQ ID NO:25 represents an amino acid sequence of a mutant BT485 protein.
[0044] SEQ ID NO:26 represents an N-terminus of SEQ ID NO: 17.
[0045] SEQ ID NO:27 represents a C-terminus of SEQ ID NO: 17.
[0046] SEQ ID NO:28 represents an N-terminus of SEQ ID NO: 18.
[0047] SEQ ID NO:29 represents a C-terminus of SEQ ID NO: 18.
[0048] SEQ ID NO:30 represents an N-terminus of SEQ ID NO:20.
[0049] SEQ ID NO:3l represents a C-terminus of SEQ ID NO:20.
[0050] SEQ ID NO:32 is an amino acid sequence of a Cry54Aa protein.
[0051] SEQ ID NO:33 is an amino acid sequence of a Cry4Aa protein.
[0052] SEQ ID NO:34 is an amino acid sequence of a Cry39Aa protein.
[0053] SEQ ID NO:35 is an amino acid sequence of a Cryl9Ca protein.
[0054] SEQ ID NO:36 is an amino acid sequence of a Cry50Ba protein.
[0055] SEQ ID NO:37 is an amino acid sequence of a Cry4Ba protein.
DETAILED DESCRIPTION
[0056] This description is not intended to be a detailed catalog of all the different ways in which the invention may be implemented, or all the features that may be added to the instant invention. For example, features illustrated with respect to one embodiment may be incorporated into other embodiments, and features illustrated with respect to a particular embodiment may be deleted from that embodiment. Thus, the invention contemplates that in some embodiments of the invention, any feature or combination of features set forth herein can be excluded or omitted. In addition, numerous variations and additions to the various embodiments suggested herein will be apparent to those skilled in the art in light of the instant disclosure, which do not depart from the instant invention. Hence, the following descriptions are intended to illustrate some particular embodiments of the invention, and not to exhaustively specify all permutations, combinations and variations thereof.
[0057] Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. The terminology used in the description of the invention herein is for the purpose of describing particular embodiments only and is not intended to be limiting of the invention.
Definitions
[0058] As used herein and in the appended claims, the singular forms "a," "an," and "the" include plural reference unless the context clearly dictates otherwise. Thus, for example, reference to "a plant" is a reference to one or more plants and includes equivalents thereof known to those skilled in the art, and so forth.
[0059] As used herein, the word "and/or" refers to and encompasses any and all possible combinations of one or more of the associated listed items, as well as the lack of
combinations when interpreted in the alternative,“or.”
[0060] The term "about" is used herein to mean approximately, roughly, around, or in the region of. When the term "about" is used in conjunction with a numerical range, it modifies that range by extending the boundaries above and below the numerical values set forth. In general, the term "about" is used herein to modify a numerical value above and below the stated value by a variance of 20 percent, preferably 10 percent up or down (higher or lower). With regard to a temperature the term“about” means ± 1 °C, preferably ± 0.5°C. Where the term“about” is used in the context of this invention (e.g., in combinations with temperature or molecular weight values) the exact value (i.e., without“about”) is preferred.
[0061] As used herein, the term "amplified" means the construction of multiple copies of a nucleic acid molecule or multiple copies complementary to the nucleic acid molecule using at least one of the nucleic acid molecules as a template. Amplification systems include the polymerase chain reaction (PCR) system, ligase chain reaction (LCR) system, nucleic acid sequence based amplification (NASBA, Cangene, Mississauga, Ontario), Q-Beta Replicase systems, transcription-based amplification system (TAS), and strand displacement amplification (SDA). See, e.g., Diagnostic Molecular Microbiology: Principles and
Applications, PERSING et ah, Ed., American Society for Microbiology, Washington, D.C. (1993). The product of amplification is termed an“amplicon.”
[0062] An“assembled sequence,”“assembled polynucleotide,”“assembled nucleotide
sequence,” and the like, according to the invention is a synthetic polynucleotide made by aligning overlapping sequences of polynucleotides or portions of sequenced polynucleotides, i.e. k-mers (all the possible subsequences of length k from a read obtained through DNA sequencing), that are determined from genomic DNA using DNA sequencing technology. Assembled sequences typically contain base-calling errors, which can be incorrectly determined bases, insertions and/or deletions compared to the native DNA sequence comprised in the genome from which the genomic DNA is obtained. Therefore, for example, an“assembled polynucleotide” may encode a protein and according to the invention both the polynucleotide and the protein are not products of nature, but exist only by human activity.
[0063] The term“chimeric construct” or“chimeric gene” or“chimeric polynucleotide” or “chimeric nucleic acid” (or similar terms) as used herein refers to a construct or molecule comprising two or more polynucleotides of different origin assembled into a single nucleic acid molecule. The term“chimeric construct”,“chimeric gene”,“chimeric polynucleotide” or “chimeric nucleic acid” refers to any construct or molecule that contains, without limitation, (1) polynucleotides (e.g., DNA) , including regulatory and coding polynucleotides that are not found together in nature (i.e., at least one of the polynucleotides in the construct is heterologous with respect to at least one of its other polynucleotides), or (2) polynucleotides encoding parts of proteins not naturally adjoined, or (3) parts of promoters that are not naturally adjoined. Further, a chimeric construct, chimeric gene, chimeric polynucleotide or chimeric nucleic acid may comprise regulatory polynucleotides and coding polynucleotides that are derived from different sources, or comprise regulatory polynucleotides and coding polynucleotides derived from the same source, but arranged in a manner different from that found in nature. In some embodiments of the invention, the chimeric construct, chimeric gene, chimeric polynucleotide or chimeric nucleic acid comprises an expression cassette comprising a polynucleotide of the invention under the control of regulatory polynucleotides, particularly under the control of regulatory polynucleotides functional in plants or bacteria.
[0064] A "coding sequence" is a nucleic acid sequence that is transcribed into RNA such as mRNA, rRNA, tRNA, snRNA, sense RNA or antisense RNA. Preferably the RNA is then translated in an organism to produce a protein.
[0065] As used herein, a“codon optimized” sequence means a nucleotide sequence wherein the codons are chosen to reflect the particular codon bias that a host cell or organism may have. This is typically done in such a way so as to preserve the amino acid sequence of the polypeptide encoded by the nucleotide sequence to be optimized. In certain embodiments, the DNA sequence of the recombinant DNA construct includes sequence that has been codon optimized for the cell (e.g., an animal, plant, or fungal cell) in which the construct is to be expressed. For example, a construct to be expressed in a plant cell can have all or parts of its sequence (e.g., the first gene suppression element or the gene expression element) codon optimized for expression in a plant. See, for example, U.S. Pat. No. 6,121,014, incorporated herein by reference.
[0066] To "control" insects means to inhibit, through a toxic effect, the ability of insect pests to survive, grow, feed, or reproduce, or to limit insect-related damage or loss in crop plants or to protect the yield potential of a crop when grown in the presence of insect pests. To "control" insects may or may not mean killing the insects, although it preferably means killing the insects.
[0067] The terms“comprises” or“comprising,” when used in this specification, specify the presence of stated features, integers, steps, operations, elements, or components, but do not preclude the presence or addition of one or more other features, integers, steps, operations, elements, components, or groups thereof.
[0068] As used herein, the transitional phrase“consisting essentially of’ (and grammatical variants) means that the scope of a claim is to be interpreted to encompass the specified materials or steps recited in the claim” and those that do not materially alter the basic and novel characteristic(s)” of the claimed invention. Thus, the term“consisting essentially of’ when used in a claim of this invention is not intended to be interpreted to be equivalent to “comprising.”
[0069] In the context of the invention,“corresponding to” or“corresponds to” means that when the amino acid sequences of variant or homolog Cry proteins are aligned with each other, the amino acids that“correspond to” certain enumerated positions in the variant or homolog protein are those that align with these positions in a reference protein but that are not necessarily in these exact numerical positions relative to the particular reference amino acid sequence of the invention. For example, if SEQ ID NO:20 is the reference sequence and is aligned with SEQ ID NO:27, the Glnl5l of SEQ ID NO:27“corresponds to” Glnl44 of SEQ ID NO:20, or for example, the Asn30l of SEQ ID NO:27“corresponds to” the Thr294 of SEQ ID NO:20.
[0070] As used herein, the term“Cry protein” means an insecticidal protein that may occur in crystalline form in Bacillus thuringiensis or related bacteria. The term“Cry protein” can refer to the protoxin form or any insecticidal fragment or toxin thereof.
[0071] To "deliver" a composition or toxic protein means that the composition or toxic
protein comes in contact with an insect, which facilitates the oral ingestion of the
composition or toxic protein, resulting in a toxic effect and control of the insect. The composition or toxic protein can be delivered in many recognized ways, including but not limited to, transgenic plant expression, formulated protein composition(s), sprayable protein composition(s), a bait matrix, or any other art-recognized protein delivery system.
[0072] The term "domain" refers to a set of amino acids conserved at specific positions along an alignment of sequences of evolutionarily related proteins. While amino acids at other positions can vary between homologues, amino acids that are highly conserved at specific positions indicate amino acids that are likely essential in the structure, stability or function of a protein. Identified by their high degree of conservation in aligned sequences of a family of protein homologues, they can be used as identifiers to determine if any polypeptide in question belongs to a previously identified polypeptide group.
[0073] “Effective insect-controlling amount” means that concentration of a toxic protein that inhibits, through a toxic effect, the ability of insects to survive, grow, feed or reproduce, or limits insect-related damage or loss in crop plants or protects the yield potential of a crop when grown in the presence of insect pests.“Effective insect-controlling amount” may or may not mean killing the insects, although it preferably means killing the insects.
[0074] "Expression cassette" as used herein means a nucleic acid molecule capable of
directing expression of at least one polynucleotide of interest, such as a polynucleotide that encodes a Cry protein of the invention, in an appropriate host cell, comprising a promoter operably linked to the polynucleotide of interest which is operably linked to a termination signal. An“expression cassette” also typically comprises additional polynucleotides required for proper translation of the polynucleotide of interest. The expression cassette may also comprise other polynucleotides not necessary in the direct expression of a polynucleotide of interest but which are present due to convenient restriction sites for removal of the cassette from an expression vector. The expression cassette comprising the polynucleotide(s) of interest may be chimeric, meaning that at least one of its components is heterologous with respect to at least one of its other components. The expression cassette may also be one that is naturally occurring but has been obtained in a recombinant form useful for heterologous expression. Typically, however, the expression cassette is heterologous with respect to the host, i.e. the polynucleotide of interest in the expression cassette does not occur naturally in the host cell and must have been introduced into the host cell or an ancestor of the host cell by a transformation process or a breeding process. The expression of the polynucleotide(s) of interest in the expression cassette is generally under the control of a promoter. In the case of a multicellular organism, such as a plant, the promoter can also be specific or preferential to a particular tissue, or organ, or stage of development. An expression cassette, or fragment thereof, can also be referred to as "inserted polynucleotide" or "insertion polynucleotide" when transformed into a plant.
[0075] A " gene" is defined herein as a hereditary unit comprising one or more
polynucleotides that occupies a specific location on a chromosome or plasmid and that contains the genetic instruction for a particular characteristic or trait in an organism.
[0076] A“gut protease” is a protease naturally found in the digestive tract of an insect. This protease is usually involved in the digestion of ingested proteins. Examples of gut proteases include trypsin, which typically cleaves peptides on the C-terminal side of lysine (K) or arginine (R) residues, and chymotrypsin, which typically cleaves peptides on the C-terminal side of phenylalanine (F), tryptophan (W) or tyrosine (Y).
[0077] The term "heterologous" when used in reference to a gene or a polynucleotide or a polypeptide refers to a gene or a polynucleotide or a polypeptide that is or contains a part thereof not in its natural environment (i.e., has been altered by the hand of man). For example, a heterologous gene may include a polynucleotide from one species introduced into another species. A heterologous gene may also include a polynucleotide native to an organism that has been altered in some way (e.g., mutated, added in multiple copies, linked to a non-native promoter or enhancer polynucleotide, etc.). Heterologous genes further may comprise plant gene polynucleotides that comprise cDNA forms of a plant gene; the cDNAs may be expressed in either a sense (to produce mRNA) or anti-sense orientation (to produce an anti-sense RNA transcript that is complementary to the mRNA transcript). In one aspect of the invention, heterologous genes are distinguished from endogenous plant genes in that the heterologous gene polynucleotide are typically joined to polynucleotides comprising regulatory elements such as promoters that are not found naturally associated with the gene for the protein encoded by the heterologous gene or with plant gene polynucleotide in the chromosome, or are associated with portions of the chromosome not found in nature (e.g., genes expressed in loci where the gene is not normally expressed). Further, a "heterologous" polynucleotide refers to a polynucleotide not naturally associated with a host cell into which it is introduced, including non-naturally occurring multiple copies of a naturally occurring polynucleotide.
[0078] "Homologous recombination" is the exchange ("crossing over") of DNA fragments between two DNA molecules or chromatids of paired chromosomes in a region of identical polynucleotides. A "recombination event" is herein understood to mean a meiotic crossing- over.
[0079] A nucleic acid sequence is "isocoding" with a reference nucleic acid sequence when the nucleic acid sequence encodes a polypeptide having the same amino acid sequence as the polypeptide encoded by the reference nucleic acid sequence. For example, SEQ ID NO:6 is isocoding with SEQ ID NO: 1 because they both encode the amino acid sequence represented by SEQ ID NO: 16.
[0080] The term "isolated" nucleic acid molecule, polynucleotide or protein is a nucleic acid molecule, polynucleotide or protein that no longer exists in its natural environment. An isolated nucleic acid molecule, polynucleotide or protein of the invention may exist in a purified form or may exist in a recombinant host such as in a transgenic bacteria or a transgenic plant. Therefore, a claim to an“isolated” nucleic acid molecule, as enumerated herein, encompasses a nucleic acid molecule when the nucleic acid molecule is comprised within a transgenic plant genome.
[0081] A " nucleic acid molecule" is single- or double- stranded DNA or RNA that can be isolated from any source or can made synthetically. In the context of the present invention, the nucleic acid molecule is preferably a segment of DNA. [0082] "Operably linked" refers to the association of polynucleotides on a single nucleic acid fragment so that the function of one affects the function of the other. For example, a promoter is operably linked with a coding polynucleotide or functional RNA when it is capable of affecting the expression of that coding polynucleotide or functional RNA (i.e., that the coding polynucleotide or functional RNA is under the transcriptional control of the promoter). Coding polynucleotide in sense or antisense orientation can be operably linked to regulatory polynucleotides.
[0083] As used herein“pesticidal,” insecticidal,” and the like, refer to the ability of a Cry protein of the invention to control a pest organism or an amount of a Cry protein that can control a pest organism as defined herein. Thus, a pesticidal Cry protein can kill or inhibit the ability of a pest organism (e.g., insect pest) to survive, grow, feed, or reproduce.
[0084] A "plant" is any plant at any stage of development, particularly a seed plant.
[0085] A "plant cell" is a structural and physiological unit of a plant, comprising a protoplast and a cell wall. The plant cell may be in the form of an isolated single cell or a cultured cell, or as a part of a higher organized unit such as, for example, plant tissue, a plant organ, or a whole plant.
[0086] Plant cell culture" means cultures of plant units such as, for example, protoplasts, cell culture cells, cells in plant tissues, pollen, pollen tubes, ovules, embryo sacs, zygotes and embryos at various stages of development.
[0087] Plant material" refers to leaves, stems, roots, flowers or flower parts, fruits, pollen, egg cells, zygotes, seeds, cuttings, cell or tissue cultures, or any other part or product of a plant.
[0088] A "plant organ" is a distinct and visibly structured and differentiated part of a plant such as a root, stem, leaf, flower bud, or embryo.
[0089] Plant tissue" as used herein means a group of plant cells organized into a structural and functional unit. Any tissue of a plant in planta or in culture is included. This term includes, but is not limited to, whole plants, plant organs, plant seeds, tissue culture and any groups of plant cells organized into structural or functional units. The use of this term in conjunction with, or in the absence of, any specific type of plant tissue as listed above or otherwise embraced by this definition is not intended to be exclusive of any other type of plant tissue.
[0090] A“polynucleotide” refers to a polymer composed of many nucleotide monomers covalently bonded in a chain. Such“polynucleotides” includes DNA, RNA, modified oligo nucleotides (e.g., oligonucleotides comprising bases that are not typical to biological RNA or DNA, such as 2'-0-methylated oligonucleotides), and the like. In some embodiments, a nucleic acid or polynucleotide can be single-stranded, double- stranded, multi- stranded, or combinations thereof. Unless otherwise indicated, a particular nucleic acid or polynucleotide of the present invention optionally comprises or encodes complementary polynucleotides, in addition to any polynucleotide explicitly indicated.
[0091] "Polynucleotide of interest" refers to any polynucleotide which, when transferred to an organism, e.g., a plant, confers upon the organism a desired characteristic such as insect resistance, disease resistance, herbicide tolerance, antibiotic resistance, improved nutritional value, improved performance in an industrial process, production of commercially valuable enzymes or metabolites or altered reproductive capability.
[0092] The term "promoter" refers to a polynucleotide, usually upstream (5') of its coding polynucleotide, which controls the expression of the coding polynucleotide by providing the recognition for RNA polymerase and other factors required for proper transcription.
[0093] A "protoplast" is an isolated plant cell without a cell wall or with only parts of the cell wall.
[0094] As used herein, the term "recombinant" refers to a form of nucleic acid (e.g., DNA or RNA) or protein or an organism that would not normally be found in nature and as such was created by human intervention. As used herein, a "recombinant nucleic acid molecule" is a nucleic acid molecule comprising a combination of polynucleotides that would not naturally occur together and is the result of human intervention, e.g., a nucleic acid molecule that is comprised of a combination of at least two polynucleotides heterologous to each other, or a nucleic acid molecule that is artificially synthesized, for example, a polynucleotide synthesize using an assembled nucleotide sequence, and comprises a polynucleotide that deviates from the polynucleotide that would normally exist in nature, or a nucleic acid molecule that comprises a transgene artificially incorporated into a host cell's genomic DNA and the associated flanking DNA of the host cell's genome. Another example of a recombinant nucleic acid molecule is a DNA molecule resulting from the insertion of a transgene into a planks genomic DNA, which may ultimately result in the expression of a recombinant RNA or protein molecule in that organism. As used herein, a "recombinant plant" is a plant that would not normally exist in nature, is the result of human intervention, and contains a transgene or heterologous nucleic acid molecule incorporated into its genome. As a result of such genomic alteration, the recombinant plant is distinctly different from the related wild-type plant.
[0095] “Regulatory elements" refer to sequences involved in controlling the expression of a nucleotide sequence. Regulatory elements comprise a promoter operably linked to the nucleotide sequence of interest and termination signals. They also typically encompass sequences required for proper translation of the nucleotide sequence.
[0096] The term“identity” or“identical” or "substantially identical," in the context of two nucleic acid or amino acid sequences, refers to two or more sequences or subsequences that have at least 60%, preferably at least 80%, more preferably 90%, even more preferably 95%, and most preferably at least 99% nucleotide or amino acid residue identity, when compared and aligned for maximum correspondence, as measured using one of the following sequence comparison algorithms or by visual inspection. Preferably, the substantial identity exists over a region of the sequences that is at least about 50 residues or bases in length, more preferably over a region of at least about 100 residues or bases, and most preferably the sequences are substantially identical over at least about 150 residues or bases. In an especially preferred embodiment, the sequences are substantially identical over the entire length of the coding regions. Furthermore, substantially identical nucleic acid or amino acid sequences perform substantially the same function.
[0097] For sequence comparison, typically one sequence acts as a reference sequence to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are input into a computer, subsequence coordinates are designated if necessary, and sequence algorithm program parameters are designated. The sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters. [0098] Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2: 482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48: 443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat'l. Acad Sci. USA 85: 2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by visual inspection (see generally, Ausubel et al., infra).
[0099] One example of an algorithm that is suitable for determining percent sequence
identity and sequence similarity is the BEAST algorithm, which is described in Altschul et al., J. Mol. Biol. 215: 403-410 (1990). Software for performing BEAST analyses is publicly available through the National Center for Biotechnology Information (National Center for Biotechnology Information, U.S. National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894 USA). This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive- valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., 1990). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always>0) and N (penalty score for mismatching residues; always O). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when the cumulative alignment score falls off by the quantity X from its maximum achieved value, the cumulative score goes to zero or below due to the accumulation of one or more negative scoring residue alignments, or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, a cutoff of 100, M=5, N=-4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad Sci. USA 89: 10915 (1989)).
[00100] In addition to calculating percent sequence identity, the BLAST algorithm also
performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Nat'l. Acad. Sci. USA 90: 5873-5787 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a test nucleic acid sequence is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid sequence to the reference nucleic acid sequence is less than about 0.1, more preferably less than about 0.01, and most preferably less than about 0.001.
[00101] Another indication that two nucleic acid sequences are substantially identical is that the two molecules hybridize to each other under stringent conditions. The phrase
"hybridizing specifically to" refers to the binding, duplexing, or hybridizing of a molecule only to a particular nucleotide sequence under stringent conditions when that sequence is present in a complex mixture (e.g., total cellular) DNA or RNA. "Bind(s) substantially" refers to complementary hybridization between a probe nucleic acid and a target nucleic acid and embraces minor mismatches that can be accommodated by reducing the stringency of the hybridization media to achieve the desired detection of the target nucleic acid sequence.
[00102] "Stringent hybridization conditions" and "stringent hybridization wash conditions" in the context of nucleic acid hybridization experiments such as Southern and Northern hybridizations are sequence dependent, and are different under different environmental parameters. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biology-Hybridization with Nucleic Acid Probes part I chapter 2 "Overview of principles of hybridization and the strategy of nucleic acid probe assays" Elsevier, New York. Generally, highly stringent hybridization and wash conditions are selected to be about 5°C lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. Typically, under "stringent conditions" a probe will hybridize to its target subsequence, but not to other sequences. [00103] The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Very stringent conditions are selected to be equal to the Tm for a particular probe. An example of stringent hybridization conditions for hybridization of complementary nucleic acids which have more than 100 complementary residues on a filter in a Southern or northern blot is 50% formamide with 1 mg of heparin at 42°C, with the hybridization being carried out overnight. An example of highly stringent wash conditions is 0.15M NaCl at 72°C for about 15 minutes. An example of stringent wash conditions is a 0.2x SSC wash at 65°C for 15 minutes (see, Sambrook, infra, for a description of SSC buffer). Often, a high stringency wash is preceded by a low stringency wash to remove background probe signal. An example medium stringency wash for a duplex of, e.g., more than 100 nucleotides, is lx SSC at 45°C for 15 minutes. An example low stringency wash for a duplex of, e.g., more than 100 nucleotides, is 4-6x SSC at 40°C for 15 minutes. For short probes (e.g., about 10 to 50 nucleotides), stringent conditions typically involve salt concentrations of less than about 1.0 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3, and the temperature is typically at least about 30°C. Stringent conditions can also be achieved with the addition of destabilizing agents such as formamide. In general, a signal to noise ratio of 2x (or higher) than that observed for an unrelated probe in the particular hybridization assay indicates detection of a specific hybridization. Nucleic acids that do not hybridize to each other under stringent conditions are still substantially identical if the proteins that they encode are substantially identical. This occurs, e.g., when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code.
[00104] The following are examples of sets of hybridization/wash conditions that may be used to clone homologous nucleotide sequences that are substantially identical to reference nucleotide sequences of the present invention: a reference nucleotide sequence preferably hybridizes to the reference nucleotide sequence in 7% sodium dodecyl sulfate (SDS), 0.5 M NaP04, 1 mM EDTA at 50°C with washing in 2x SSC, 0.1% SDS at 50°C, more desirably in 7% sodium dodecyl sulfate (SDS), 0.5 M NaP04, 1 mM EDTA at 50°C with washing in lx SSC, 0.1% SDS at 50°C, more desirably still in 7% sodium dodecyl sulfate (SDS), 0.5 M NaP04, 1 mM EDTA at 50°C with washing in 0.5x SSC, 0.1% SDS at 50°C, preferably in 7% sodium dodecyl sulfate (SDS), 0.5 M NaP04, 1 mM EDTA at 50°C with washing in O.lx SSC, 0.1% SDS at 50°C, more preferably in 7% sodium dodecyl sulfate (SDS), 0.5 M
NaP04, 1 mM EDTA at 50°C with washing in O.lx SSC, 0.1% SDS at 65°C.
[00105] A further indication that two nucleic acid sequences or proteins are substantially
identical is that the protein encoded by the first nucleic acid is immunologically cross reactive with, or specifically binds to, the protein encoded by the second nucleic acid. Thus, a protein is typically substantially identical to a second protein, for example, where the two proteins differ only by conservative substitutions.
[00106] As used herein, a "synthetic polynucleotide" refers to a polynucleotide comprising bases or structural features that are not present in a naturally occurring polynucleotide. For example, a synthetic polynucleotide encoding a Cry protein of the invention that comprises a nucleotide sequence that resembles more closely the G+C content and the normal codon distribution of dicot or monocot plant genes is said to be synthetic. A synthetic
polynucleotide of the invention may also, for example, comprise an assembled nucleotide sequence of the invention.
[00107] As used herein, a Cry protein that is“toxic” to an insect pest is meant that the Cry protein functions as an orally active insect control agent to kill the insect pest, or the Cry protein is able to disrupt or deter insect feeding, or causes growth inhibition to the insect pest, both of which may or may not cause death of the insect. When a Cry protein of the invention is delivered to an insect or an insect comes into oral contact with the Cry protein, the result is typically death of the insect, or the insect’s growth is slowed, or the insect stops feeding upon the source that makes the toxic Cry protein available to the insect.
[00108] " Transformation" is a process for introducing heterologous nucleic acid into a host cell or organism. In particular, "transformation" means the stable integration of a DNA molecule into the genome of an organism of interest.
[00109] " Transformed / transgenic / recombinant" refer to a host organism such as a bacterium or a plant into which a heterologous nucleic acid molecule has been introduced. The nucleic acid molecule can be stably integrated into the genome of the host or the nucleic acid molecule can also be present as an extrachromosomal molecule. Such an extrachromosomal molecule can be auto-replicating. Transformed cells, tissues, or plants are understood to encompass not only the end product of a transformation process, but also transgenic progeny thereof. A "non-transformed", "non-transgenic", or "non- recombinant" host refers to a wild- type organism, e.g., a bacterium or plant, which does not contain the heterologous nucleic acid molecule.
[00110] Nucleotides are indicated herein by the following standard abbreviations: adenine (A), cytosine (C), thymine (T), and guanine (G). Amino acids are likewise indicated by the following standard abbreviations: alanine (Ala; A), arginine (Arg; R), asparagine (Asn; N), aspartic acid (Asp; D), cysteine (Cys; C), glutamine (Gln; Q), glutamic acid (Glu; E), glycine (Gly; G), histidine (His; H), isoleucine (he; 1), leucine (Leu; L), lysine (Lys; K), methionine (Met; M), phenylalanine (Phe; F), proline (Pro; P), serine (Ser; S), threonine (Thr; T), tryptophan (Trp; W), tyrosine (Tyr; Y), and valine (Val; V).
[00111] This invention provides compositions and methods for controlling harmful plant pests. Particularly, the invention relates to Cry proteins that are encoded by nucleotides sequences assembled from genomic DNA isolated from bacteria, such as Bacillus
thuringiensis, that are toxic to insect pests and to assembled polynucleotides and related polynucleotides that comprise nucleotide sequences that encode the Cry proteins, and to the making and using of the assembled polynucleotides and related polynucleotides and Cry proteins to control insect pests.
[00112] According to some embodiments, the invention provides a nucleic acid molecule or optionally an isolated nucleic acid molecule comprising, consisting essentially of or consisting of a nucleotide sequence encoding a Cry protein in its protoxin form or a biologically active or toxin fragment thereof, wherein the nucleotide sequence (a) has at least 80% to at least 99% sequence identity with an assembled sequence of any of SEQ ID NOs:l- 5 or a toxin-encoding fragment thereof; or (b) encodes a protein comprising an amino acid sequence that has at least 80% to at least 99% sequence identity with any of SEQ ID NOs: 16- 20 or an toxin fragment thereof; or (c) is an assembled nucleotide sequence of (a) or (b); or (d) is a synthetic sequence of (a), (b) or (c) that has codons optimized for expression in a transgenic organism. In other embodiments, the nucleotide sequence comprises SEQ ID NO:l, SEQ ID NO:2, SEQ ID NOG, SEQ ID NO:4, SEQ ID NOG, or any toxin-encoding fragments of any of SEQ ID NOs: 1-5. In other embodiments, the synthetic nucleotide sequence comprises SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, or any toxin-encoding fragments of any of SEQ ID NOs:6-l5.
[00113] Polynucleotides that are fragments of Cry protein protoxin-encoding polynucleotides are also encompassed by the invention. By "fragment" is intended a portion of the nucleotide sequence encoding a Cry protein. A fragment of a nucleotide sequence may encode a biologically active portion of a Cry protein, the so called“toxin fragment,” or it may be a fragment that can be used as a hybridization probe or PCR primer using methods disclosed below. Nucleic acid molecules that are fragments of a Cry protein-encoding nucleotide sequence comprise at least about 15, 20, 50, 75, 100, 200, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450 contiguous nucleotides, or up to the number of nucleotides present in a full-length Cry protein encoding nucleotide sequence disclosed herein (for example, 3519 nucleotides for SEQ ID NO:l) depending upon the intended use. By "contiguous" nucleotides is intended nucleotide residues that are immediately adjacent to one another. Some fragments of the nucleotide sequences of the invention will encode toxin fragments that retain the biological activity of the Cry protein and, hence, retain insecticidal activity. By "retains insecticidal activity" is intended that the fragment will have at least about 30%, preferably at least about 50%, more preferably at least about 70%, even more preferably at least about 80% of the insecticidal activity of the Cry protein. Methods for measuring insecticidal activity are well known in the art. See, for example, Czapla and Lang (1990) J. Econ. Entomol. 83:2480-2485; Andrews et al. (1988) Biochem. J. 252:199-206; Marrone et al. (1985) J. of Economic Entomology 78:290-293; and U.S. Pat. No. 5,743,477, all of which are herein incorporated by reference in their entirety.
[00114] A toxin fragment of a Cry protein of the invention will encode at least about 15, 25, 30, 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, and 450 contiguous amino acids, or up to the total number of amino acids present in a full-length Cry protein of the invention (for example, 1173 amino acids for SEQ ID NO: 16).
[00115] In some embodiments, a nucleic acid molecule of the invention comprises, consists essentially of or consists of a nucleotide sequence encoding a Cry protein comprising an amino acid sequence that has at least 80% to at least 99% sequence identity with any of SEQ ID NOs: 16-20 or a toxin fragment thereof. In some other embodiments, the amino acid sequence comprises, consists essentially of or consists of any of SEQ ID NOs: 16-20 or a toxin fragment thereof. Thus, in some embodiments, Cry proteins which have been activated by means of proteolytic processing, for example, by proteases prepared from the gut of an insect, may be characterized and the N-terminal or C-terminal amino acids of the activated toxin fragment identified. In this aspect of the invention, the skilled person can determine that, for example, the toxin fragment of SEQ ID NO: 16 may comprise amino acids from about 26-605 or about 26-617 or about 26-628 of SEQ ID NO: 16, or the toxin fragment of SEQ ID NO: 17 may comprise amino acids from about 45 or from about 53 to about 622 or about 624 or to about 642 or to about 662 of SEQ ID NO: 17, or the toxin fragment of SEQ ID NO: 18 may comprise amino acids from about amino acid 11 or from about amino acid 13 or from about amino acid 35 or from about amino acid 47 to about amino acid 628, or to about amino acid 662 of SEQ ID NO: 18, or the toxin fragment of SEQ ID NO: 19 may comprise amino acids from about amino acid 24, or from amino acid 35, or from amino acid 47, or from amino acid 49 to about amino acid 660, or to amino acid 670 of SEQ ID NO: 19, or the toxin fragment of SEQ ID NO:20 may comprise amino acids from about amino acid 17, or from about amino acid 18, or from about amino acid 32, or from about amino acid 37 to about amino acid 610, or to about amino acid 636, or to about amino acid 652, or to about amino acid 657, or to about amino acid 660, or to about amino acid 671 or SEQ ID NO:20, or a toxin fragment of a Cry protein variant produced by introduction or elimination of protease processing sites at appropriate positions in the coding sequence to allow, or eliminate, proteolytic cleavage of a larger variant protein by insect, plant or microorganism proteases is also within the scope of the invention. The end result of such manipulation is understood to be the generation of toxin fragment molecules having the same or better activity as the intact Cry pro toxin protein.
[00116] In some embodiments of the invention, a chimeric gene is provided that comprises a heterologous promoter operably linked to a polynucleotide comprising, consisting essentially of or consisting of a nucleotide sequence that encodes a Cry protein toxic to a lepidopteran pest, wherein the nucleotide sequence (a) has at least 80% (e.g., 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9%) to at least 99% (99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9%) sequence identity with any one of SEQ ID NOs:l-5, or a toxin-encoding fragment thereof; or (b) encodes a protein comprising an amino acid sequence that has at least 80% (e.g., 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9%) to at least 99% (99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9%) sequence identity with any one of SEQ ID NOs: 16-20, or a toxin fragment thereof; or (c) is a synthetic sequence of (a) or (b) that has codons optimized for expression in a transgenic organism.
[00117] In other embodiments, the heterologous promoter is a plant-expressible promoter.
For example, without limitation, the plant-expressible promoter can be selected from the group of promoters consisting of ubiquitin, cestrum yellow virus, com TrpA, OsMADS 6, maize H3 histone, bacteriophage T3 gene 9 5' ETTR, com sucrose synthetase 1, corn alcohol dehydrogenase 1, corn light harvesting complex, com heat shock protein, maize mtl, pea small subunit RuBP carboxylase, rice actin, rice cyclophilin, Ti plasmid mannopine synthase, Ti plasmid nopaline synthase, petunia chalcone isomerase, bean glycine rich protein 1, potato patatin, lectin, CaMV 35S and S-E9 small subunit RuBP carboxylase promoter.
[00118] In additional embodiments, the protein encoded by the chimeric gene is toxic to one or more lepidopteran pests selected from the group consisting of Asian corn borer ( Ostrinia furnacalis ), black cutworm ( Agrotis ipsilon ), cotton bollworm ( Helicoverpa armigera ), yellow peach borer ( Conogethes punctiferalis), oriental armyworm ( Mythimna sepatate), European com borer ( Ostrinia nubilalis ), fall armyworm (Spodoptera frugiperda), com earworm {Helicoverpa zea), sugarcane borer ( Diatraea saccharalis), velvetbean caterpillar ( Anticarsia gemmatalis ), soybean looper ( Chrysodeixis includes), southwest com borer {Diatraea grandio ella), western bean cutworm {Richia albicosta), tobacco budworm
{Heliothis virescens), striped stem borer {Chile suppressalis), pink stem borer {Sesamia calamistis) and rice leaffolder {Cnaphalocrocis medinalis).
[00119] In further embodiments, the polynucleotide comprises, consists essentially of or
consists of a nucleotide sequence that has at least 85% to at least 99% sequence identity with SEQ ID NO:l, or a toxin-encoding fragment thereof, or has at least 95% to at least 99% sequence identity with SEQ ID NO:2, or a toxin-encoding fragment thereof, or has at least 90% to at least 99% sequence identity with SEQ ID NO:3, or a toxin-encoding fragment thereof, or has at least 90% to at least 99% sequence identity with SEQ ID NO:4, or a toxin encoding fragment thereof, or has at least 95% to at least 99% sequence identity with SEQ ID NO:5, or a toxin-encoding fragment thereof. In other embodiments, the polynucleotide comprises, consists essentially of or consists of any one of SEQ ID NOs:l-5, or a toxin encoding fragment thereof
[00120] In other embodiments, the polynucleotide comprises, consists essentially of or
consists of a nucleotide sequence that encodes a protein comprising, consisting essentially of or consisting of an amino acid sequence that has at least 80% to at least 99% sequence identity with any one of SEQ ID NOS: 16-20, or a toxin fragment thereof.
[00121] In still other embodiments, the amino acid sequence has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO: 16, or a toxin fragment thereof.
[00122] In further embodiments, the amino acid sequence has at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO: 17, or a toxin fragment thereof.
[00123] In still further embodiments, the amino acid sequence has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO: 18, or a toxin fragment thereof.
[00124] In other embodiments, the amino acid sequence has at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO: 19, or a toxin fragment thereof.
[00125] In still other embodiments, the amino acid sequence has at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO:20, or a toxin fragment thereof.
[00126] In some embodiments, the chimeric gene of the invention comprises a polynucleotide comprising, consisting essentially of or consisting of a synthetic sequence of a nucleotide sequence that has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% with any of SEQ ID NOs:6-l5, or a toxin encoding fragment thereof, wherein the synthetic sequence has codons optimized for expression is a transgenic organism. In other embodiments, the chimeric gene of the invention comprises a polynucleotide comprising, consisting essentially of or consisting of a synthetic sequence of a nucleotide sequence that encodes a protein comprising an amino acid sequence that has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with any of SEQ ID NOs: 16-25, or a toxin fragment thereof, wherein the synthetic sequence has codons optimized for expression is a transgenic organism. In further embodiments, the transgenic organism is a transgenic bacteria or a transgenic plant.
[00127] In some embodiments, the invention provides a synthetic polynucleotide comprising, consisting essentially of or consisting of a nucleotide sequence that encodes a protein that is toxic to a lepidopteran pest , wherein the nucleotide sequence has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with any one of SEQ ID NOs:6-l5, or a toxin-encoding fragment thereof.
[00128] In other embodiments, the invention provides a synthetic polynucleotide comprising, consisting essentially of or consisting of a nucleotide sequence that encodes a protein that is toxic to a lepidopteran pest, wherein the nucleotide sequence encodes an amino acid sequence that has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with any one of SEQ ID
NOs: 16-25, or a toxin fragment thereof.
[00129] Cry proteins of the invention may be assembled using genomes from Bacillus
thuringiensis ( Bt ) strains. Bt strains can be isolated by standard techniques and either tested for toxicity to a lepidopteran pest of the invention or used for isolation of genomic DNA without testing the Bt strain for toxicity to insects. Generally Bt strains can be isolated from any environmental sample, including soil, plant, insect, grain elevator dust, and other sample material, etc., by methods known in the art. See, for example, Travers et al. (1987) Appl. Environ. Microbiol. 53:1263-1266; Saleh et al. (1969) Can J. Microbiol. 15:1101-1104; DeLucca et al. (1981) Can J. Microbiol. 27:865-870; and Norris, et al. (1981) "The genera Bacillus and Sporolactobacillus." In Starr et al. (eds.), The Prokaryotes: A Handbook on Habitats, Isolation, and Identification of Bacteria, Vol. II, Springer- Verlog Berlin Heidelberg. After isolation, Bt strains may be tested for toxicity to an insect pest and Cry proteins encompassed by the invention can be identified. Therefore, in some embodiments, the invention provides an isolated Bacillus thuringiensis (Bt) strain that produces a Cry protein or a recombinant Cry protein comprising, consisting essentially of or consisting of an amino acid sequence having at least 80% to at least 99% sequence identity to any of SEQ ID NOs: 16-25. In still further embodiments, the Cry protein or recombinant Cry protein comprises, consists essentially of or consists of any of SEQ ID NOs: 16-25.
[00130] According to some embodiments, the invention provides a Cry protein, and optionally an isolated Cry protein, that is toxic to a lepidopteran pest, wherein the Cry protein comprises, consists essentially of or consists of (a) an amino acid sequence that has at least 80% sequence identity to at least 99% sequence identity with an amino acid sequence represented by any one of SEQ ID NOs: 16-25, or a toxin fragment thereof; or (b) an amino acid sequence that is encoded by a nucleotide sequence or an assembled nucleotide sequence that has at least 80% sequence identity to at least 99% sequence identity with a nucleotide sequence represented by any one of SEQ ID NOs:6-l5, or a toxin-encoding fragment thereof.
[00131] In other embodiments, the Cry protein or isolated Cry protein comprises, consists essentially of or consists of an amino acid sequence that has at least 80% to at least 99% sequence identity with any one of SEQ ID NOs: 16-25, or a toxin fragment thereof. In still other embodiments, the amino acid sequence has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO: 16, or a toxin fragment thereof.
[00132] In other embodiments, the amino acid sequence has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO: 17, or a toxin fragment thereof.
[00133] In further embodiments, the amino acid sequence has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO: 18, or a toxin fragment thereof.
[00134] In still further embodiments, the amino acid sequence has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO: 19, or a toxin fragment thereof.
[00135] In other embodiments, the amino acid sequence has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO:20, or a toxin fragment thereof.
[00136] In some embodiments, the amino acid sequence comprises, consists essentially of or consists of any one of SEQ ID NOs: 16-25, or a toxin fragment thereof. In other
embodiments, the amino acid sequence is encoded by a nucleotide sequence comprising, consisting essentially of or consisting of any of SEQ ID NOs:6-l5, or a toxin-encoding fragment thereof. [00137] In other embodiments, the Cry proteins of the invention are toxic to a lepidopteran pest selected from the group consisting of Asian corn borer (Ostrinia furnacalis), black cutworm ( Agrotis ipsilon ), cotton bollworm ( Helicoverpa armigera ), yellow peach borer ( Conogethes punctiferalis ), oriental armyworm ( Mythimna sepatate), European corn borer (Ostrinia nubilalis), fall armyworm (Spodoptera frugiperda), corn earworm ( Helicoverpa zea), sugarcane borer ( Diatraea saccharalis ), velvetbean caterpillar (Anticarsia gemmatalis ), soybean looper ( Chrysodeixis includes), southwest corn borer ( Diatraea grandio sella), western bean cutworm ( Richia albicosta), tobacco budworm (Heliothis virescens), striped stem borer ( Chile suppressalis), pink stem borer ( Sesamia calamistis) and rice leaffolder ( Cnaphalocrocis medinalis). In other embodiments, the Cry proteins of the invention are toxic to at least Asian com borer (Ostrinia furnacalis).
[00138] In some embodiments, the invention encompasses a recombinant Cry protein that is toxic to a lepidopteran pest, wherein the recombinant Cry protein comprises, consists essentially of or consists of (a) an amino acid sequence that has at least 80% to at least 99% sequence identity with an amino acid sequence represented by any of SEQ ID NOs:2l-25, or a toxin fragment thereof; or (b) an amino acid sequence that is encoded by a nucleotide sequence that has at 80% to at least 99% sequence identity with a nucleotide sequence represented by any of SEQ ID NOs:l l-l5, or a toxin-encoding fragment thereof.
[00139] In other embodiments, the recombinant Cry protein comprises, consists essentially of or consists of an amino acid sequence that has at least 80% to at least 99% sequence identity with any one of SEQ ID NOs:2l-25, or a toxin fragment thereof. In still other embodiments, the amino acid sequence has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO:2l, or a toxin fragment thereof.
[00140] In still other embodiments, the amino acid sequence has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO:22, or a toxin fragment thereof.
[00141] In still other embodiments, the amino acid sequence has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO:23, or a toxin fragment thereof.
[00142] In still other embodiments, the amino acid sequence has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO:24, or a toxin fragment thereof.
[00143] In still other embodiments, the amino acid sequence has at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequence identity with SEQ ID NO:25, or a toxin fragment thereof.
[00144] In still further embodiments, the recombinant Cry protein comprises, consists essentially of or consists of an amino acid sequence of any of SEQ ID NOs:2l-25, or a toxin fragment thereof. In other embodiments, the recombinant Cry protein is encoded by a nucleotide sequence that comprises, consists essentially of or consists of any of SEQ ID NOs:l l-l5, or a toxin-encoding fragment thereof.
[00145] Antibodies raised in response to immune challenge by an assembled or mutant BT- 0264, BT-0288, BT-0302, BT-0454 and BT-0485, or related Cry proteins, including a native Cry protein, are also encompassed by the invention. Such antibodies may be produced using standard immunological techniques for production of polyclonal antisera and, if desired, immortalizing the antibody-producing cells of the immunized host for sources of monoclonal antibody production. Techniques for producing antibodies to any substance of interest are well known, e.g., as in Harlow and Lane (1988. Antibodies a laboratory manual pp. 726. Cold Spring Harbor Laboratory) and as in Goding (Monoclonal Antibodies: Principles & practice.1986. Academic Press, Inc., Orlando, LL). The present invention encompasses insecticidal proteins that cross-react with antibodies, particularly monoclonal antibodies, raised against one or more of the insecticidal Cry proteins of the present invention.
[00146] The antibodies produced in the invention are also useful in immunoassays for
determining the amount or presence of an assembled or mutant BT-0264, BT-0288, BT- 0302, BT-0454 and BT-0485 Cry protein, or related Cry protein, including a native Cry protein, in a biological sample. Such assays are also useful in quality-controlled production of compositions containing one or more of the Cry proteins of the invention or related toxic proteins. In addition, the antibodies can be used to assess the efficacy of recombinant production of one or more of the Cry proteins of the invention or a related protein, as well as for screening expression libraries for the presence of a nucleotide sequence encoding one or more of the Cry proteins of the invention or related protein coding sequences. Antibodies are useful also as affinity ligands for purifying or isolating any one or more of the proteins of the invention and related proteins. The Cry proteins of the invention and proteins containing related antigenic epitopes may be obtained by over expressing full or partial lengths of a sequence encoding all or part of a Cry protein of the invention or a related protein in a preferred host cell.
[00147] It is recognized that assembled DNA sequences that encode a Cry protein of the
invention may be altered by various methods, and that these alterations may result in DNA sequences encoding proteins with amino acid sequences different than that encoded by an assembled Cry protein of the invention. The resulting mutant Cry protein may be altered in various ways including amino acid substitutions, deletions, truncations, and insertions of one or more amino acids of any of SEQ ID NOs: 16-20, including up to about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 15, about 20, about 25, about 30, about 35, about 40, about 45, about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 85, about 90, about 100, about 105, about 110, about 115, about 120, about 125, about 130, about 135, about 140, about 145, about 150, about 155, or more amino acid substitutions, deletions or insertions. Methods for such manipulations are generally known in the art. For example, amino acid sequence variants of a native Cry protein can be prepared by mutations in a polynucleotide that encodes the protein. This may also be accomplished by one of several forms of mutagenesis or in directed evolution. In some aspects, the changes encoded in the amino acid sequence will not substantially affect the function of the protein. Such variants will possess the desired insecticidal activity. In some embodiments of the invention, nucleotide sequences represented by SEQ ID NOs: 1-5 are altered to introduce amino acid substitutions in the encoded protein. In other embodiments, the resulting mutant protein is encoded by a synthetic mutant polynucleotide comprising a nucleotide sequence represented by any one of SEQ ID NOs: 11- 15. In other embodiments, the mutant Cry proteins comprise, consist essentially of or consist of an amino acid sequence represented by any one of SEQ ID NOs:2l-25.
[00148] It is understood that the ability of an insecticidal protein to confer insecticidal activity may be improved by the use of such techniques upon the compositions of this invention. For example, one may express a Cry protein in host cells that exhibit high rates of base mis- incorporation during DNA replication, such as XL-l Red (Stratagene, La Jolla, CA). After propagation in such strains, one can isolate the DNA (for example by preparing plasmid DNA, or by amplifying by PCR and cloning the resulting PCR fragment into a vector), culture the Cry protein mutations in a non-mutagenic strain, and identify mutated genes with insecticidal activity, for example by performing an assay to test for insecticidal activity. Generally, the protein is mixed and used in feeding assays. See, for example Marrone et al. (1985) J. of Economic Entomology 78:290-293. Such assays can include contacting plants with one or more pests and determining the plant's ability to survive or cause the death of the pests. Examples of mutations that result in increased toxicity are found in Schnepf et al. (1998) Microbiol. Mol. Biol. Rev. 62:775-806.
[00149] Alternatively, alterations may be made to an amino acid sequence of the invention at the amino or carboxy terminus without substantially affecting activity. This can include insertions, deletions, or alterations introduced by modem molecular methods, such as PCR, including PCR amplifications that alter or extend the protein coding sequence by virtue of inclusion of amino acid encoding sequences in the oligonucleotides utilized in the PCR amplification. Alternatively, the protein sequences added can include entire protein-coding sequences, such as those used commonly in the art to generate protein fusions. Such fusion proteins are often used to (1) increase expression of a protein of interest (2) introduce a binding domain, enzymatic activity, or epitope to facilitate either protein purification, protein detection, or other experimental uses known in the art (3) target secretion or translation of a protein to a subcellular organelle, such as the periplasmic space of Gram-negative bacteria, or the endoplasmic reticulum of eukaryotic cells, the latter of which often results in glycosylation of the protein.
[00150] A Cry protein of the invention can also be mutated to introduce an epitope to generate antibodies that recognize the mutated protein. Therefore, in some embodiments, the invention provides a mutated Cry protein, wherein an amino acid substitution in a native Cry protein produces a mutant Cry protein having an antigenic region that allows the mutant Cry protein to be distinguished from the native Cry protein in a protein detection assay.
[00151] In some embodiments, the invention provides a method of making an antibody that differentially recognizes a mutated Cry protein from the assembled or related native Cry protein from which the mutated Cry protein is derived, the method comprising the steps of substituting amino acids in an antigenic loop of an assembled or native Cry protein and raising antibodies that specifically recognize the mutated antigenic loop in the mutated Cry protein and does not recognize the assembled or native Cry protein. In one embodiment, the antigenic loop is identified in non-conserved regions outside of domain I of the assembled or native Cry protein. In another embodiment, the antigenic loop is not a loop involved in the Cry protein’s insect gut receptor recognition or involved in the protease activation of the Cry protein. [00152] Variant nucleotide and amino acid sequences of the invention also encompass sequences derived from mutagenic and recombinogenic procedures such as DNA shuffling. With such a procedure, one or more different toxic protein coding regions can be used to create a new toxic protein possessing the desired properties. In this manner, libraries of recombinant polynucleotides are generated from a population of related sequence
polynucleotides comprising sequence regions that have substantial sequence identity and can be homologously recombined in vitro or in vivo. For example, using this approach, sequence motifs encoding a domain of interest may be shuffled between a pesticidal gene of the invention and other known pesticidal genes to obtain a new gene coding for a protein with an improved property of interest, such as an increased insecticidal activity. Strategies for such DNA shuffling are known in the art. See, for example, Stemmer (1994) Proc. Natl. Acad. Sci. USA 91:10747-10751; Stemmer (1994) Nature 370:389-391; Crameri et al. (1997) Nature Biotech. 15:436-438; Moore et al. (1997) J. Mol. Biol. 272:336-347; Zhang et al. (1997)
Proc. Natl. Acad. Sci. USA 94:4504-4509; Crameri et al. (1998) Nature 391:288-291; and U.S. Pat. Nos. 5,605,793 and 5,837,458.
[00153] Domain swapping or shuffling is another mechanism for generating altered Cry
proteins of the invention. Domains may be swapped between Cry proteins, resulting in hybrid or chimeric toxic proteins with improved pesticidal activity or target spectrum.
Methods for generating recombinant proteins and testing them for pesticidal activity are well known in the art (see, for example, Naimov et al. (2001) Appl. Environ. Microbiol. 67:5328- 5330; de Maagd et al. (1996) Appl. Environ. Microbiol. 62:1537-1543; Ge et al. (1991) J. Biol. Chem. 266:17954-17958; Schnepf et al. (1990) J. Biol. Chem. 265:20923-20930; Rang et al. 91999) Appl. Environ. Microbiol. 65:2918-2925).
[00154] Thus, in some embodiments, the invention encompasses a hybrid insecticidal protein comprising in an N-terminal to C-terminal direction a) an N-terminal region of a Cry54A protein fused to a C-terminal region of a Cry4A protein, wherein the crossover position between the Cry54A protein and the Cry4A protein is located between domain III of the Cry54A and the protoxin tail of Cry4A and wherein the hybrid insecticidal protein has at least 90% identity to SEQ ID NO: 17; or b) an N-terminal region of a Cry39A protein fused to a C-terminal region of a Cryl9C protein, wherein the crossover position between the Cry39A protein and the Cry 19 protein is located between domain III of the Cry39A and the protoxin tail of the Cryl9C and wherein the hybrid insecticidal protein has at least 90% identity to SEQ ID NO: 18; or c) an N-terminal region of a Cry50B protein fused to a C- terminal region of a Cry4B protein, wherein the crossover position between the Cry50B protein and the Cry4B protein is located between domain III of the Cry50B and the protoxin tail of the Cry4B and wherein the hybrid insecticidal protein has at least 90% identity to SEQ ID NO:20. In other embodiments, the hybrid insecticidal protein is active against a lepidopteran insect pest. In one aspect of this embodiment the lepidopteran insect pest is Asian com borer (ACB; Ostrinia furnacalis).
[00155] In some embodiments, the invention provides a recombinant vector comprising a polynucleotide, an assembled polynucleotide, a nucleic acid molecule, an expression cassette or a chimeric gene of the invention. In other embodiments, the vector is further defined as a plasmid, cosmid, phagemid, artificial chromosome, phage or viral vector. Certain vectors for use in transformation of plants and other organisms are known in the art.
[00156] Thus, some embodiments of the invention are directed to expression cassettes
designed to express the polynucleotides and nucleic acid molecules of the invention. As used herein,“expression cassette” means a nucleic acid molecule having at least a control sequence operatively linked to a nucleotide sequence of interest, e.g. a nucleotide sequence of the invention encoding a Cry protein of the invention. In this manner, for example, plant promoters operably linked to the nucleotide sequences to be expressed are provided in expression cassettes for expression in a plant, plant part or plant cell.
[00157] An expression cassette comprising a polynucleotide of interest may be chimeric, meaning that at least one of its components is heterologous with respect to at least one other of its other components. An expression cassette may also be one that is naturally occurring but has been obtained in a recombinant form useful for heterologous expression. Typically, however, the expression cassette is heterologous with respect to the host, i.e., the particular nucleic acid sequence of the expression cassette does not occur naturally in the host cell and must have been introduced into the host cell or an ancestor of the host cell by a
transformation event. [00158] In addition to the promoters operatively linked to the nucleotide sequences of the invention, an expression cassette of this invention also can include other regulatory sequences. As used herein,“regulatory sequences” means nucleotide sequences located upstream (5' non-coding sequences), within or downstream (3' non-coding sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences include, but are not limited to, enhancers, introns, translation leader sequences, termination signals, and polyadenylation signal sequences.
[00159] In some embodiments, an expression cassette of the invention also can include
polynucleotides that encode other desired traits in addition to the Cry proteins of the invention. Such expression cassettes comprising the stacked traits may be used to create plants, plant parts or plant cells having a desired phenotype with the stacked traits (i.e., molecular stacking). Such stacked combinations in plants can also be created by other methods including, but not limited to, cross breeding plants by any conventional
methodology. If stacked by genetically transforming the plants, the nucleotide sequences of interest can be combined at any time and in any order. For example, a transgenic plant comprising one or more desired traits can be used as the target to introduce further traits by subsequent transformation. The additional nucleotide sequences can be introduced simultaneously in a co-transformation protocol with a nucleotide sequence, nucleic acid molecule, nucleic acid construct, or composition of this invention, provided by any combination of expression cassettes. For example, if two nucleotide sequences will be introduced, they can be incorporated in separate cassettes ( trans ) or can be incorporated on the same cassette ( cis ). Expression of polynucleotides can be driven by the same promoter or by different promoters. It is further recognized that polynucleotides can be stacked at a desired genomic location using a site-specific recombination system. See, e.g., Int'l Patent Application Publication Nos. WO 99/25821; WO 99/25854; WO 99/25840; WO 99/25855 and WO 99/25853.
[00160] The expression cassette also can include an additional coding sequence for one or more polypeptides or double stranded RNA molecules (dsRNA) of interest for agronomic traits that primarily are of benefit to a seed company, grower or grain processor. A polypeptide of interest can be any polypeptide encoded by a nucleotide sequence of interest. Non-limiting examples of polypeptides of interest that are suitable for production in plants include those resulting in agronomically important traits such as herbicide resistance (also sometimes referred to as“herbicide tolerance”), virus resistance, bacterial pathogen resistance, insect resistance, nematode resistance, or fungal resistance. See, e.g., U.S. Patent Nos. 5,569,823; 5,304,730; 5,495,071; 6,329,504; and 6,337,431. The polypeptide also can be one that increases plant vigor or yield (including traits that allow a plant to grow at different temperatures, soil conditions and levels of sunlight and precipitation), or one that allows identification of a plant exhibiting a trait of interest (e.g., a selectable marker, seed coat color, etc.). Various polypeptides of interest, as well as methods for introducing these polypeptides into a plant, are described, for example, in US Patent Nos. 4,761,373;
4,769,061; 4,810,648; 4,940,835; 4,975,374; 5,013,659; 5,162,602; 5,276,268; 5,304,730; 5,495,071; 5,554,798; 5,561,236; 5,569,823; 5,767,366; 5,879,903, 5,928,937; 6,084,155; 6,329,504 and 6,337,431; as well as US Patent Publication No. 2001/0016956. See also, on the World Wide Web at lifesci.sussex.ac.uk/home/Neil_Crickmore/Bt/.
[00161] Polynucleotides conferring resistance/tolerance to an herbicide that inhibits the
growing point or meristem, such as an imidazalinone or a sulfonylurea can also be suitable in some embodiments of the invention. Exemplary polynucleotides in this category code for mutant ALS and AHAS enzymes as described, e.g., in U.S. Patent Nos. 5,767,366 and 5,928,937. U.S. Patent Nos. 4,761,373 and 5,013,659 are directed to plants resistant to various imidazalinone or sulfonamide herbicides. U.S. Patent No. 4,975,374 relates to plant cells and plants containing a nucleic acid encoding a mutant glutamine synthetase (GS) resistant to inhibition by herbicides that are known to inhibit GS, e.g., phosphinothricin and methionine sulfoximine. U.S. Patent No. 5,162,602 discloses plants resistant to inhibition by cyclohexanedione and aryloxyphenoxypropanoic acid herbicides. The resistance is conferred by an altered acetyl coenzyme A carboxylase (ACCase).
[00162] Polypeptides encoded by nucleotides sequences conferring resistance to glyphosate are also suitable for the invention. See, e.g., U.S. Patent No. 4,940,835 and U.S. Patent No. 4,769,061. U.S. Patent No. 5,554,798 discloses transgenic glyphosate resistant maize plants, which resistance is conferred by an altered 5-enolpyruvyl-3-phosphoshikimate (EPSP) synthase gene.
[00163] Polynucleotides coding for resistance to phosphono compounds such as
glufosinate ammonium or phosphinothricin, and pyridinoxy or phenoxy propionic acids and cyclohexones are also suitable. See, European Patent Application No. 0 242 246. See also, U.S. Patent Nos. 5,879,903, 5,276,268 and 5,561,236.
[00164] Other suitable polynucleotides include those coding for resistance to herbicides that inhibit photosynthesis, such as a triazine and a benzonitrile (nitrilase) See, U.S. Patent No. 4,810,648. Additional suitable polynucleotides coding for herbicide resistance include those coding for resistance to 2,2-dichloropropionic acid, sethoxydim, haloxyfop, imidazolinone herbicides, sulfonylurea herbicides, triazolopyrimidine herbicides, s-triazine herbicides and bromoxynil. Also suitable are polynucleotides conferring resistance to a protox enzyme, or that provide enhanced resistance to plant diseases; enhanced tolerance of adverse
environmental conditions (abiotic stresses) including but not limited to drought, excessive cold, excessive heat, or excessive soil salinity or extreme acidity or alkalinity; and alterations in plant architecture or development, including changes in developmental timing. See, e.g., U.S. Patent Publication No. 2001/0016956 and U.S. Patent No. 6,084,155.
[00165] Additional suitable polynucleotides include those coding for pesticidal (e.g., insecticidal) polypeptides. These polypeptides may be produced in amounts sufficient to control, for example, insect pests (i.e., insect controlling amounts). It is recognized that the amount of production of a pesticidal polypeptide in a plant necessary to control insects or other pests may vary depending upon the cultivar, type of pest, environmental factors and the like. Polynucleotides useful for additional insect or pest resistance include, for example, those that encode toxins identified in Bacillus organisms. Polynucleotides comprising nucleotide sequences encoding Bacillus thuringiensis ( Bt ) Cry proteins from several subspecies have been cloned and recombinant clones have been found to be toxic to lepidopteran, dipteran and/or coleopteran insect larvae. Examples of such Bt insecticidal proteins include the Cry proteins such as CrylAa, CrylAb, Cry 1 Ac, Cry IB, Cry 1C, Cry ID, CrylEa, CrylFa, Cry3A, Cry9A, Cry9B, Cry9C, and the like, as well as vegetative insecticidal proteins such as Vipl, Vip2, Vip3, and the like. A full list of ///-derived proteins can be found on the worldwide web at Bacillus thuringiensis Toxin Nomenclature Database maintained by the University of Sussex (see also, Crickmore el al. (1998) Microbiol. Mol. Biol. Rev. 62:807-813).
[00166] Polypeptides that are suitable for production in plants further include those that improve or otherwise facilitate the conversion of harvested plants or plant parts into a commercially useful product, including, for example, increased or altered carbohydrate content or distribution, improved fermentation properties, increased oil content, increased protein content, improved digestibility, and increased nutraceutical content, e.g., increased phytosterol content, increased tocopherol content, increased stand content or increased vitamin content. Polypeptides of interest also include, for example, those resulting in or contributing to a reduced content of an unwanted component in a harvested crop, e.g., phytic acid, or sugar degrading enzymes. By“resulting in” or“contributing to” is intended that the polypeptide of interest can directly or indirectly contribute to the existence of a trait of interest (e.g., increasing cellulose degradation by the use of a heterologous cellulase enzyme).
[00167] In some embodiments, the polypeptide contributes to improved digestibility for food or feed. Xylanases are hemicellulolytic enzymes that improve the breakdown of plant cell walls, which leads to better utilization of the plant nutrients by an animal. This leads to improved growth rate and feed conversion. Also, the viscosity of the feeds containing xylan can be reduced. Heterologous production of xylanases in plant cells also can facilitate lignocellulosic conversion to fermentable sugars in industrial processing.
[00168] Numerous xylanases from fungal and bacterial microorganisms have been
identified and characterized (see, e.g., U.S. Patent No. 5,437,992; Coughlin et al. (1993) “Proceedings of the Second TRICEL Symposium on Trichoderma reesei Cellulases and Other Hydrolases” Espoo; Souminen and Reinikainen, eds. (1993) Foundation for
Biotechnical and Industrial Fermentation Research 8:125-135; U.S. Patent Publication No. 2005/0208178; and PCT Publication No. WO 03/16654). In particular, three specific xylanases (XYL-I, XYL-II, and XYL-III) have been identified in T. reesei (Tenkanen et al. (1992) Enzyme Microb. Technol. 14:566; Torronen et al. (1992) Bio/Technology 10:1461; and Xu et al. (1998) Appl. Microbiol. Biotechnol. 49:718). [00169] In other embodiments, a polypeptide useful for the invention can be a polysaccharide degrading enzyme. Plants of this invention producing such an enzyme may be useful for generating, for example, fermentation feedstocks for bioprocessing. In some embodiments, enzymes useful for a fermentation process include alpha amylases, proteases, pullulanases, isoamylases, cellulases, hemicellulases, xylanases, cyclodextrin
glycotransferases, lipases, phytases, laccases, oxidases, esterases, cutinases, granular starch hydrolyzing enzyme and other glucoamylases.
[00170] Polysaccharide-degrading enzymes include: starch degrading enzymes such as a- amylases (EC 3.2.1.1), glucuronidases (E.C. 3.2.1.131); exo-l,4-a- D glucanases such as amyloglucosidases and glucoamylase (EC 3.2.1.3), b-amylases (EC 3.2.1.2), a- glucosidases (EC 3.2.1.20), and other exo-amylases; starch debranching enzymes, such as a) isoamylase (EC 3.2.1.68), pullulanase (EC 3.2.1.41), and the like; b) cellulases such as exo-l,4-3- cellobiohydrolase (EC 3.2.1.91), exo-l,3b-D-glucanase (EC 3.2.1.39), b-glucosidase (EC 3.2.1.21); c) L-arabinases, such as endo-l,5-a-L-arabinase (EC 3.2.1.99), a- arabinosidases (EC 3.2.1.55) and the like; d) galactanases such as endo-l,4b-D-galactanase (EC 3.2.1.89), endo-l,3b-D-galactanase (EC 3.2.1.90), a- galactosidase (EC 3.2.1.22), b-galactosidase (EC 3.2.1.23) and the like; e) mannanases, such as endo-l,4b-D-mannanase (EC 3.2.1.78), b- mannosidase (EC 3.2.1.25), a- mannosidase (EC 3.2.1.24) and the like; f) xylanases, such as endo-l,4b-xylanase (EC 3.2.1.8), b-D-xylosidase (EC 3.2.1.37), l,3b-D-xylanase, and the like; and g) other enzymes such as a- L-fucosidase (EC 3.2.1.51), a-L-rhamnosidase (EC 3.2.1.40), levanase (EC 3.2.1.65), inulanase (EC 3.2.1.7), and the like. In one embodiment, the a- amylase is the synthetic a- amylase, Amy797E, described is US Patent No. 8,093,453, herein incorporated by reference in its entirety.
[00171] Further enzymes which may be used with the invention include proteases, such as fungal and bacterial proteases. Fungal proteases include, but are not limited to, those obtained from Aspergillus, Trichoderma, Mucor and Rhizopus, such as A. niger, A. awamori, A. oryzae and M. miehei. In some embodiments, the polypeptides of this invention can be cellobiohydrolase (CBH) enzymes (EC 3.2.1.91). In one embodiment, the cellobiohydrolase enzyme can be CBH1 or CBH2. [00172] Other enzymes useful with the invention include, but are not limited to, hemicellulases, such as mannases and arabinofuranosidases (EC 3.2.1.55); ligninases; lipases (e.g., E.C. 3.1.1.3), glucose oxidases, pectinases, xylanases, transglucosidases, alpha 1,6 glucosidases (e.g., E.C. 3.2.1.20); esterases such as ferulic acid esterase (EC 3.1.1.73) and acetyl xylan esterases (EC 3.1.1.72); and cutinases (e.g. E.C. 3.1.1.74).
[00173] Double stranded RNA molecules useful with the invention include, but are not
limited to those that suppress target insect genes. As used herein the words "gene
suppression", when taken together, are intended to refer to any of the well-known methods for reducing the levels of protein produced as a result of gene transcription to mRNA and subsequent translation of the mRNA. Gene suppression is also intended to mean the reduction of protein expression from a gene or a coding sequence including
posttranscriptional gene suppression and transcriptional suppression. Posttranscriptional gene suppression is mediated by the homology between of all or a part of a mRNA transcribed from a gene or coding sequence targeted for suppression and the corresponding double stranded RNA used for suppression, and refers to the substantial and measurable reduction of the amount of available mRNA available in the cell for binding by ribosomes. The transcribed RNA can be in the sense orientation to effect what is called co-suppression, in the anti-sense orientation to effect what is called anti-sense suppression, or in both orientations producing a dsRNA to effect what is called RNA interference (RNAi). Transcriptional suppression is mediated by the presence in the cell of a dsRNA, a gene suppression agent, exhibiting substantial sequence identity to a promoter DNA sequence or the complement thereof to effect what is referred to as promoter trans suppression. Gene suppression may be effective against a native plant gene associated with a trait, e.g., to provide plants with reduced levels of a protein encoded by the native gene or with enhanced or reduced levels of an affected metabolite. Gene suppression can also be effective against target genes in plant pests that may ingest or contact plant material containing gene suppression agents, specifically designed to inhibit or suppress the expression of one or more homologous or complementary sequences in the cells of the pest. Such genes targeted for suppression can encode an essential protein, the predicted function of which is selected from the group consisting of muscle formation, juvenile hormone formation, juvenile hormone regulation, ion regulation and transport, digestive enzyme synthesis, maintenance of cell membrane potential, amino acid biosynthesis, amino acid degradation, sperm formation, pheromone synthesis, pheromone sensing, antennae formation, wing formation, leg formation, development and differentiation, egg formation, larval maturation, digestive enzyme formation, hemolymph synthesis, hemolymph maintenance, neurotransmission, cell division, energy metabolism, respiration, and apoptosis.
[00174] In some embodiments, the invention provides a transgenic non-human host cell
comprising a polynucleotide, a nucleic acid molecule, a chimeric gene, an expression cassette or a recombinant vector of the invention. The transgenic non-human host cell can include, but is not limited to, a plant cell, a yeast cell, a bacterial cell or an insect cell. Accordingly, in some embodiments, the invention provides a bacterial cell selected from the genera Bacillus, Brevibacillus, Clostridium, Xenorhabdus, Photorhabdus, Pasteuria, Escherichia,
Pseudomonas, Erwinia, Serratia, Klebsiella, Salmonella, Pasteurella, Xanthomonas, Streptomyces, Rhizobium, Rhodopseudomonas, Methylophilius, Agrobacterium, Acetobacter, Lactobacillus, Arthrobacter, Azotobacter, Eeuconostoc, or Alcaligenes. Thus, for example, as biological insect control agents, the Cry proteins of the invention can be produced by expression of a chimeric gene encoding the Cry proteins of the invention in a bacterial cell. For example, in some embodiments, a Bacillus thuringiensis cell comprising a chimeric gene of the invention is provided.
[00175] In further embodiments, the invention provides a transgenic plant cell that is a dicot plant cell or a monocot plant cell. In additional embodiments, the dicot plant cell is selected from the group consisting of a soybean cell, sunflower cell, tomato cell, cole crop cell, cotton cell, sugar beet cell and tobacco cell. In further embodiments, the monocot cell is selected from the group consisting of a barley cell, maize cell, oat cell, rice cell, sorghum cell, sugar cane cell and wheat cell. In some embodiments, the invention provides a plurality of dicot cells or monocot cells expressing a Cry protein of the invention encoded by a chimeric gene of the invention. In other embodiments the plurality of cells are juxtaposed to form an apoplast and are grown in natural sunlight.
[00176] In other embodiments of the invention, an insecticidal Cry protein of the invention is expressed in a higher organism, for example, a plant. In this case, transgenic plants expressing effective amounts of the insecticidal protein protect themselves from plant pests such as insect pests. When an insect starts feeding on such a transgenic plant, it ingests the expressed insecticidal Cry protein. This can deter the insect from further biting into the plant tissue or may even harm or kill the insect. A polynucleotide of the invention is inserted into an expression cassette, which is then stably integrated in the genome of the plant. In other embodiments, the polynucleotide is included in a non-pathogenic self-replicating virus.
Plants transformed in accordance with the invention may be monocots or dicots and include, but are not limited to, corn (maize), soybean, rice, wheat, barley, rye, oats, sorghum, millet, sunflower, safflower, sugar beet, cotton, sugarcane, oilseed rape, alfalfa, tobacco, peanuts, vegetables, including, sweet potato, bean, pea, chicory, lettuce, cabbage, cauliflower, broccoli, turnip, carrot, eggplant, cucumber, radish, spinach, potato, tomato, asparagus, onion, garlic, melons, pepper, celery, squash, pumpkin, zucchini, fruits, including, apple, pear, quince, plum, cherry, peach, nectarine, apricot, strawberry, grape, raspberry, blackberry, pineapple, avocado, papaya, mango, banana, and specialty plants, such as Arabidopsis, and woody plants such as coniferous and deciduous trees. Preferably, plants of the of the invention are crop plants such as maize, sorghum, wheat, sunflower, tomato, crucifers, peppers, potato, cotton, rice, soybean, sugar beet, sugarcane, tobacco, barley, oilseed rape, and the like.
[00177] Once a desired polynucleotide has been transformed into a particular plant species, it may be propagated in that species or moved into other varieties of the same species, particularly including commercial varieties, using traditional breeding techniques.
[00178] A polynucleotide of the invention is expressed in transgenic plants, thus causing the biosynthesis of the encoded Cry protein, either in protoxin or toxin form, in the transgenic plants. In this way, transgenic plants with enhanced yield protection in the presence of insect pressure are generated. For their expression in transgenic plants, the nucleotide sequences of the invention may require modification and optimization. Although in many cases genes from microbial organisms can be expressed in plants at high levels without modification, low expression in transgenic plants may result from microbial nucleotide sequences having codons that are not preferred in plants. It is known in the art that living organisms have specific preferences for codon usage, and the codons of the nucleotide sequences described in this invention can be changed to conform with plant preferences, while maintaining the amino acids encoded thereby. Furthermore, high expression in plants, for example com plants, is best achieved from coding sequences that have at least about 35% GC content, or at least about 45%, or at least about 50%, or at least about 60%. Microbial nucleotide sequences that have low GC contents may express poorly in plants due to the existence of ATTTA motifs that may destabilize messages, and AATAAA motifs that may cause inappropriate polyadenylation. Although certain gene sequences may be adequately expressed in both monocotyledonous and dicotyledonous plant species, sequences can be modified to account for the specific codon preferences and GC content preferences of monocotyledons or dicotyledons as these preferences have been shown to differ (Murray et al. Nucl. Acids Res. 17:477-498 (1989)). In addition, the nucleotide sequences are screened for the existence of illegitimate splice sites that may cause message truncation. All changes required to be made within the nucleotide sequences such as those described above are made using well known techniques of site directed mutagenesis, PCR, and synthetic gene construction using the methods described for example in US Patent Nos. 5,625,136; 5,500,365 and 6,013,523.
[00179] In some embodiments, the invention provides synthetic coding sequences or
polynucleotide made according to the procedure disclosed in U.S. Pat. No. 5,625,136, herein incorporated by reference. In this procedure, maize preferred codons, i.e., the single codon that most frequently encodes that amino acid in maize, are used. The maize preferred codon for a particular amino acid can be derived, for example, from known gene sequences from maize. For example, maize codon usage for 28 genes from maize plants is found in Murray et al., Nucleic Acids Research 17:477-498 (1989), the disclosure of which is incorporated herein by reference. Specifically exemplified synthetic sequences of the present invention made with maize optimized codons are represented by any one of SEQ ID NOs: 6-15. In this manner, the nucleotide sequences can be optimized for expression in any plant. It is recognized that all or any part of a nucleotide sequence may be optimized or synthetic. That is, a polynucleotide may comprise a nucleotide sequence that is part native sequence and part codon optimized sequence.
[00180] For efficient initiation of translation, sequences adjacent to the initiating methionine may require modification. For example, they can be modified by the inclusion of sequences known to be effective in plants. Joshi has suggested an appropriate consensus for plants (NAR 15:6643-6653 (1987)). These consensuses are suitable for use with the nucleotide sequences of this invention. The sequences are incorporated into constructions comprising the nucleotide sequences, up to and including the ATG (while leaving the second amino acid unmodified), or alternatively up to and including the GTC subsequent to the ATG (with the possibility of modifying the second amino acid of the transgene).
[00181] The novel Cry protein coding sequences of the invention, either as their assembled sequence, native sequence or as synthetic sequences as described above, can be operably fused to a variety of promoters for expression in plants including constitutive, inducible, temporally regulated, developmentally regulated, chemically regulated, tissue-preferred and tissue-specific promoters to prepare recombinant DNA molecules, i.e., chimeric genes. The choice of promoter will vary depending on the temporal and spatial requirements for expression, and also depending on the target species. Thus, expression of the nucleotide sequences of this invention in leaves, in stalks or stems, in ears, in inflorescences (e.g. spikes, panicles, cobs, etc.), in roots, or seedlings is preferred. In many cases, however, protection against more than one type of insect pest is sought, and thus expression in multiple tissues is desirable. Although many promoters from dicotyledons have been shown to be operational in monocotyledons and vice versa, ideally dicotyledonous promoters are selected for expression in dicotyledons, and monocotyledonous promoters for expression in monocotyledons.
However, there is no restriction to the provenance of selected promoters; it is sufficient that they are operational in driving the expression of the nucleotide sequences in the desired cell.
[00182] Suitable constitutive promoters include, for example, CaMV 35S promoter (SEQ ID NO:l546; Odell et ah, Nature 313:810-812, 1985); Arabidopsis At6669 promoter (SEQ ID NO: 1652; see PCT Publication No. W004081173A2); maize Ubi 1 (Christensen et ah, Plant Mol. Biol. 18:675-689, 1992); rice actin (McElroy et ah, Plant Cell 2:163-171, 1990); pEMU (Last et ah, Theor. Appl. Genet. 81:581-588, 1991); CaMV 19S (Nilsson et ah, Physiol. Plant 100:456-462, 1997); GOS2 (de Pater et ah, Plant J November; 2(6):837-44, 1992); ubiquitin (Christensen et ah, Plant Mol. Biol. 18: 675-689, 1992); Rice cyclophilin (Bucholz et ah, Plant Mol Biol. 25(5):837-43, 1994); Maize H3 histone (Lepetit et ah, Mol. Gen. Genet. 231: 276-285, 1992); Actin 2 (An et ah, Plant J. 10(1); 107-121, 1996), constitutive root tip CT2 promoter (SEQ ID NO: 1535; see also PCT application No. IL/2005/000627) and Synthetic Super MAS (Ni et al., The Plant Journal 7: 661-76, 1995). Other constitutive promoters include those in U.S. Pat. Nos. 5,659,026, 5,608,149; 5,608,144; 5,604,121; 5,569,597:
5,466,785; 5,399,680; 5,268,463; and 5,608,142.
[00183] Tissue-specific or tissue-preferential promoters useful for the expression of the novel cry protein coding sequences of the invention in plants, particularly maize, are those that direct expression in root, pith, leaf or pollen. Suitable tissue-specific promoters include, but not limited to, leaf-specific promoters [such as described, for example, by Yamamoto et al., Plant J. 12:255-265, 1997; Kwon et al., Plant Physiol. 105:357-67, 1994; Yamamoto et al., Plant Cell Physiol. 35:773-778, 1994; Gotor et al., Plant J. 3:509-18, 1993; Orozco et al., Plant Mol. Biol. 23:1129-1138, 1993; and Matsuoka et al., Proc. Natl. Acad. Sci. USA 90:9586-9590, 1993], seed-preferred promoters [e.g., from seed specific genes (Simon, et al., Plant Mol. Biol. 5. 191, 1985; Scofield, et al., J. Biol. Chem. 262: 12202, 1987; Baszczynski, et al., Plant Mol. Biol. 14: 633, 1990), Brazil Nut albumin (Pearson' et al., Plant Mol. Biol.
18: 235-245, 1992), legumin (Ellis, et al. Plant Mol. Biol. 10: 203-214, 1988), Glutelin {rice) (Takaiwa, et al., Mol. Gen. Genet. 208: 15-22, 1986; Takaiwa, et al., FEBS Letts. 221: 43-47, 1987), Zein (Matzke et al., Plant Mol Biol, 143)323-32 1990), napA (Stalberg, et al., Planta 199: 515-519, 1996), Wheat SPA (Albanietal, Plant Cell, 9: 171-184, 1997), sunflower oleosin (Cummins, etak, Plant Mol. Biol. 19: 873-876, 1992)], endosperm specific promoters [e.g., wheat LMW and HMW, glutenin-l (Mol Gen Genet 216:81-90, 1989; NAR 17:461-2), wheat a, b and g gliadins (EMB03: 1409-15, 1984), Barley ltrl promoter, barley Bl, C, D hordein (Theor Appl Gen 98:1253-62, 1999; Plant J 4:343-55, 1993; Mol Gen Genet
250:750-60, 1996), Barley DOF (Mena et al., The Plant Journal, 116(1): 53-62, 1998), Biz2 (EP99106056.7), Synthetic promoter (Vicente-Carbajosa et al., Plant J. 13: 629-640, 1998), rice prolamin NRP33, rice -globulin Glb-l (Wu et al., Plant Cell Physiology 39(8) 885-889, 1998), rice alpha-globulin REB/OHP-l (Nakase et al. Plant Mol. Biol. 33: 513-S22, 1997), rice ADP-glucose PP (Trans Res 6:157-68, 1997), maize ESR gene family (Plant J 12:235- 46, 1997), sorgum gamma-kafirin (Plant Mol. Biol 32:1029-35, 1996)], embryo specific promoters [e.g., rice OSH1 (Sato et al., Proc. Nati. Acad. Sci. USA, 93: 8117-8122), KNOX (Postma-Haarsma of al, Plant Mol. Biol. 39:257-71, 1999), rice oleosin (Wu et at, J. Biochem., 123:386, 1998)], flower- specific promoters [e.g., AtPRP4, chalene synthase (chsA) (Van der Meer, et al., Plant Mol. Biol. 15, 95-109, 1990), LAT52 (Twell et al., Mol. Gen Genet. 217:240-245; 1989), apetala-3, plant reproductive tissues [e.g., OsMADS promoters (U.S. Patent Application 2007/0006344)].
[00184] The nucleotide sequences of this invention can also be expressed under the regulation of promoters that are chemically regulated. This enables the Cry proteins of the invention to be synthesized only when the crop plants are treated with the inducing chemicals. Examples of such technology for chemical induction of gene expression is detailed in the published application EP 0 332 104 and US Patent No. 5,614,395. In one embodiment, the chemically regulated promoter is the tobacco PR- la promoter.
[00185] Another category of promoters useful in the invention is that which is wound
inducible. Numerous promoters have been described which are expressed at wound sites and also at the sites of phytopathogen infection. Ideally, such a promoter should only be active locally at the sites of insect invasion, and in this way the insecticidal proteins only
accumulate in cells that need to synthesize the insecticidal proteins to kill the invading insect pest. Examples of promoters of this kind include those described by Stanford et al. Mol. Gen. Genet. 215:200-208 (1989), Xu et al. Plant Molec. Biol. 22:573-588 (1993), Logemann et al. Plant Cell 1:151-158 (1989), Rohrmeier & Lehle, Plant Molec. Biol. 22:783-792 (1993), Firek et al. Plant Molec. Biol. 22:129-142 (1993), and Warner et al. Plant J. 3:191-201 (1993).
[00186] Non-limiting examples of promoters that cause tissue specific expression patterns that are useful in the invention include green tissue specific, root specific, stem specific, or flower specific. Promoters suitable for expression in green tissue include many that regulate genes involved in photosynthesis and many of these have been cloned from both
monocotyledons and dicotyledons. One such promoter is the maize PEPC promoter from the phosphoenol carboxylase gene (Hudspeth & Grula, Plant Molec. Biol. 12:579-589 (1989)). Another promoter for root specific expression is that described by de Framond (FEBS 290:103-106 (1991) or US Patent No. 5,466,785). Another promoter useful in the invention is the stem specific promoter described in U.S. Pat. No. 5,625,136, which naturally drives expression of a maize trpA gene. [00187] In addition to the selection of a suitable promoter, constructs for expression of an insecticidal toxin in plants require an appropriate transcription terminator to be operably linked downstream of the heterologous nucleotide sequence. Several such terminators are available and known in the art (e.g. tml from CaMV, E9 from rbcS). Any available terminator known to function in plants can be used in the context of this invention.
[00188] Numerous other sequences can be incorporated into expression cassettes described in this invention. These include sequences that have been shown to enhance expression such as intron sequences (e.g. from Adhl and bronzel) and viral leader sequences (e.g. from TMV, MCMV and AMV).
[00189] It may be preferable to target expression of the nucleotide sequences of the present invention to different cellular localizations in the plant. In some cases, localization in the cytosol may be desirable, whereas in other cases, localization in some subcellular organelle may be preferred. Any mechanism for targeting gene products, e.g., in plants, can be used to practice this invention, and such mechanisms are known to exist in plants and the sequences controlling the functioning of these mechanisms have been characterized in some detail. Sequences have been characterized which cause the targeting of gene products to other cell compartments Amino terminal sequences can be responsible for targeting a protein of interest to any cell compartment, such as, a vacuole, mitochondrion, peroxisome, protein bodies, endoplasmic reticulum, chloroplast, starch granule, amyloplast, apoplast or cell wall of a plant (e.g. Unger et. al. Plant Molec. Biol. 13: 411-418 (1989); Rogers et. al. (1985) Proc. Natl. Acad. Sci. USA 82: 6512-651; U.S. Pat. No. 7,102,057; WO 2005/096704, all of which are hereby incorporated by reference. Optionally, the signal sequence may be an N-terminal signal sequence from waxy, an N-terminal signal sequence from gamma- zein, a starch binding domain, a C-terminal starch binding domain, a chloroplast targeting sequence, which imports the mature protein to the chloroplast (Comai et. al. (1988) J. Biol. Chem. 263:
15104-15109; van den Broeck, et. al. (1985) Nature 313: 358-363; U.S. Pat. No. 5,639,949) or a secretion signal sequence from aleurone cells (Koehler & Ho, Plant Cell 2: 769-783 (1990)). Additionally, amino terminal sequences in conjunction with carboxy terminal sequences are responsible for vacuolar targeting of gene products (Shinshi et. al. (1990) Plant Molec. Biol. 14: 357-368). In one embodiment, the signal sequence selected includes the known cleavage site, and the fusion constructed takes into account any amino acids after the cleavage site(s), which are required for cleavage. In some cases this requirement may be fulfilled by the addition of a small number of amino acids between the cleavage site and the transgene ATG or, alternatively, replacement of some amino acids within the transgene sequence. These construction techniques are well known in the art and are equally applicable to any cellular compartment.
[00190] It will be recognized that the above-described mechanisms for cellular targeting can be utilized not only in conjunction with their cognate promoters, but also in conjunction with heterologous promoters so as to effect a specific cell-targeting goal under the transcriptional regulation of a promoter that has an expression pattern different to that of the promoter from which the targeting signal derives.
Plant Transformation
[00191] Procedures for transforming plants are well known and routine in the art and are described throughout the literature. Non-limiting examples of methods for transformation of plants include transformation via bacterial-mediated nucleic acid delivery (e.g., via
Agrobacterium ), viral-mediated nucleic acid delivery, silicon carbide or nucleic acid whisker-mediated nucleic acid delivery, liposome mediated nucleic acid delivery, microinjection, microparticle bombardment, calcium-phosphate-mediated transformation, cyclodextrin-mediated transformation, electroporation, nanoparticle-mediated
transformation, sonication, infiltration, PEG-mediated nucleic acid uptake, as well as any other electrical, chemical, physical (mechanical) or biological mechanism that results in the introduction of nucleic acid into the plant cell, including any combination thereof. General guides to various plant transformation methods known in the art include Miki et al.
(“Procedures for Introducing Foreign DNA into Plants” in Methods in Plant Molecular Biology and Biotechnology , Glick, B. R. and Thompson, J. E., Eds. (CRC Press, Inc., Boca Raton, 1993), pages 67-88) and Rakowoczy-Trojanowska (Cell. Mol. Biol. Lett. 7:849-858 (2002)).
[00192] For Agrobacterium- mediated transformation, binary vectors or vectors carrying at least one T-DNA border sequence are suitable, whereas for direct gene transfer (e.g., particle bombardment and the like) any vector is suitable and linear DNA containing only the construction of interest can be used. In the case of direct gene transfer, transformation with a single DNA species or co-transformation can be used (Schocher et ah, Biotechnology 4:1093- 1096 (1986)). For both direct gene transfer and Agrobacterium- mediated transfer, transformation is usually (but not necessarily) undertaken with a selectable marker that may be a positive selection (Phosphomannose Isomerase), provide resistance to an antibiotic (kanamycin, hygromycin or methotrexate) or a herbicide (glyphosate or glufosinate).
However, the choice of selectable marker is not critical to the invention.
[00193] Agrobacterium- mediated transformation is a commonly used method for
transforming plants because of its high efficiency of transformation and because of its broad utility with many different species. Agrobacterium- mediated transformation typically involves transfer of the binary vector carrying the foreign DNA of interest to an appropriate Agrobacterium strain that may depend on the complement of vir genes carried by the host Agrobacterium strain either on a co-resident Ti plasmid or chromosomally (Uknes et al. (1993) Plant Cell 5:159-169). The transfer of the recombinant binary vector to
Agrobacterium can be accomplished by a triparental mating procedure using Escherichia coli carrying the recombinant binary vector, a helper E. coli strain that carries a plasmid that is able to mobilize the recombinant binary vector to the target Agrobacterium strain.
Alternatively, the recombinant binary vector can be transferred to Agrobacterium by nucleic acid transformation (Hofgen & Willmitzer (1988) Nucleic Acids Res. 16:9877).
[00194] Dicots as well as monocots may be transformed using Agrobacterium. Methods for Agrobacterium-mediated transformation of rice include well known methods for rice transformation, such as those described in any of the following: European patent application EP 1198985 Al, Aldemita and Hodges (Planta 199: 612-617, 1996); Chan et al. (Plant Mol Biol 22 (3): 491-506, 1993), Hiei et al. (Plant J 6 (2): 271-282, 1994), which disclosures are incorporated by reference herein as if fully set forth. In the case of com transformation, the preferred method is as described in either Ishida et al. (Nat. Biotechnol 14(6): 745-50, 1996) or Frame et al. (Plant Physiol 129(1): 13-22, 2002), which disclosures are incorporated by reference herein as if fully set forth. Said methods are further described by way of example in B. Jenes et al., Techniques for Gene Transfer, in: Transgenic Plants, Vol. 1, Engineering and Utilization, eds. S. D. Kung and R. Wu, Academic Press (1993) 128-143 and in Potrykus Annu. Rev. Plant Physiol. Plant Molec. Biol. 42 (1991) 205-225). The nucleic acids or the construct to be expressed is preferably cloned into a vector, which is suitable for
transforming Agrobacterium tumefaciens, for example pBinl9 (Bevan et al., Nucl. Acids Res. 12 (1984) 8711). Agrobacteria transformed by such a vector can then be used in known manner for the transformation of plants, such as plants used as a model, like Arabidopsis or crop plants such as, by way of example, tobacco plants, for example by immersing bruised leaves or chopped leaves in an agrobacterial solution and then culturing them in suitable media. The transformation of plants by means of Agrobacterium tumefaciens is described, for example, by Hagen and Willmitzer in Nucl. Acid Res. (1988) 16, 9877 or is known inter alia from F. F. White, Vectors for Gene Transfer in Higher Plants; in Transgenic Plants, Vol. 1, Engineering and Utilization, eds. S. D. Kung and R. Wu, Academic Press, 1993, pp. 15-38.
[00195] Transformation of a plant by recombinant Agrobacterium usually involves co cultivation of the Agrobacterium with explants from the plant and follows methods well known in the art. Transformed tissue is regenerated on selection medium carrying an antibiotic or herbicide resistance marker between the binary plasmid T-DNA borders.
[00196] As discussed previously, another method for transforming plants, plant parts and plant cells involves propelling inert or biologically active particles at plant tissues and cells. See, e.g., US Patent Nos. 4,945,050; 5,036,006 and 5,100,792. Generally, this method involves propelling inert or biologically active particles at the plant cells under conditions effective to penetrate the outer surface of the cell and afford incorporation within the interior thereof. When inert particles are utilized, the vector can be introduced into the cell by coating the particles with the vector containing the nucleic acid of interest. Alternatively, a cell or cells can be surrounded by the vector so that the vector is carried into the cell by the wake of the particle. Biologically active particles (e.g., a dried yeast cell, a dried bacterium or a bacteriophage, each containing one or more nucleic acids sought to be introduced) also can be propelled into plant tissue.
[00197] In other embodiments, a polynucleotide of the invention can be directly
transformed into the plastid genome. A major advantage of plastid transformation is that plastids are generally capable of expressing bacterial genes without substantial modification, and plastids are capable of expressing multiple open reading frames under control of a single promoter. Plastid transformation technology is extensively described in U.S. Patent Nos. 5,451,513, 5,545,817, and 5,545,818, in PCT application no. WO 95/16783, and in McBride et al. (1994) Proc. Nati. Acad. Sci. USA 91, 7301-7305. The basic technique for chloroplast transformation involves introducing regions of cloned plastid DNA flanking a selectable marker together with the gene of interest into a suitable target tissue, e.g., using biolistics or protoplast transformation (e.g., calcium chloride or PEG mediated transformation). The 1 to 1.5 kb flanking regions, termed targeting sequences, facilitate homologous recombination with the plastid genome and thus allow the replacement or modification of specific regions of the plastome. Initially, point mutations in the chloroplast 16S rRNA and rpsl2 genes conferring resistance to spectinomycin or streptomycin can be utilized as selectable markers for transformation (Svab, Z., Hajdukiewicz, P., and Maliga, P. (1990) Proc. Natl. Acad. Sci. USA 87, 8526-8530; Staub, J. M., and Maliga, P. (1992) Plant Cell 4, 39-45). The presence of cloning sites between these markers allows creation of a plastid targeting vector for introduction of foreign genes (Staub, J.M., and Maliga, P. (1993) EMBO J. 12, 601-606). Substantial increases in transformation frequency can be obtained by replacement of the recessive rRNA or r-protein antibiotic resistance genes with a dominant selectable marker, the bacterial aadA gene encoding the spectinomycin-cletoxifying enzyme aminoglycoside s'- adenyltransf erase (Svab, Z., and Maliga, P. (1993) Proc. Natl. Acad. Sci. USA 90, 913- 917). Previously, this marker had been used successfully for high-frequency transformation of the plastid genome of the green alga Chlamydomonas reinhardtii (Goldschmidt-Clermont, M. (1991) Nucl. Acids Res. 19:4083-4089). Other selectable markers useful for plastid transformation are known in the art and encompassed within the scope of the invention. Typically, approximately 15-20 cell division cycles following transformation are required to reach a homoplastidic state. Plastid expression, in which genes are inserted by homologous recombination into all of the several thousand copies of the circular plastid genome present in each plant cell, takes advantage of the enormous copy number advantage over nuclear- expressed genes to permit expression levels that can readily exceed 10% of the total soluble plant protein. In one embodiment, a polynucleotide of the invention can be inserted into a plastid-targeting vector and transformed into the plastid genome of a desired plant host. Thus, plants homoplastic for plastid genomes containing a nucleotide sequence of the invention can be obtained, which are capable of high expression of the polynucleotide.
[00198] Methods of selecting for transformed, transgenic plants, plant cells or plant tissue culture are routine in the art and can be employed in the methods of the invention provided herein. For example, a recombinant vector of the invention also can include an expression cassette comprising a nucleotide sequence for a selectable marker, which can be used to select a transformed plant, plant part or plant cell. As used herein,“selectable marker” means a nucleotide sequence that when expressed imparts a distinct phenotype to the plant, plant part or plant cell expressing the marker and thus allows such transformed plants, plant parts or plant cells to be distinguished from those that do not have the marker. Such a nucleotide sequence may encode either a selectable or screenable marker, depending on whether the marker confers a trait that can be selected for by chemical means, such as by using a selective agent (e.g., an antibiotic, herbicide, or the like), or on whether the marker is simply a trait that one can identify through observation or testing, such as by screening (e.g., the R-locus trait). Of course, many examples of suitable selectable markers are known in the art and can be used in the expression cassettes described herein.
[00199] Examples of selectable markers include, but are not limited to, a nucleotide
sequence encoding neo or nptll, which confers resistance to kanamycin, G418, and the like (Potrykus et al. (1985) Mol. Gen. Genet. 199:183-188); a nucleotide sequence encoding bar, which confers resistance to phosphinothricin; a nucleotide sequence encoding an altered 5- enolpyruvylshikimate-3-phosphate (EPSP) synthase, which confers resistance to glyphosate (Hinchee et al. (1988) Biotech. 6:915-922); a nucleotide sequence encoding a nitrilase such as bxn from Klebsiella ozaenae that confers resistance to bromoxynil (Stalker et al. (1988) Science 242:419-423); a nucleotide sequence encoding an altered acetolactate synthase (ALS) that confers resistance to imidazolinone, sulfonylurea or other ALS -inhibiting chemicals (EP Patent Application No. 154204); a nucleotide sequence encoding a methotrexate-resistant dihydrofolate reductase (DHFR) (Thillet et al. (1988) J. Biol. Chem. 263:12500-12508); a nucleotide sequence encoding a dalapon dehalogenase that confers resistance to dalapon; a nucleotide sequence encoding a mannose-6-phosphate isomerase (also referred to as phosphomannose isomerase (PMI)) that confers an ability to metabolize mannose (US Patent Nos. 5,767,378 and 5,994,629); a nucleotide sequence encoding an altered anthranilate synthase that confers resistance to 5-methyl tryptophan; or a nucleotide sequence encoding hph that confers resistance to hygromycin. One of skill in the art is capable of choosing a suitable selectable marker for use in an expression cassette of this invention.
[00200] Additional selectable markers include, but are not limited to, a nucleotide
sequence encoding b-glucuronidase or iiidA (GUS) that encodes an enzyme for which various chromogenic substrates are known; an R-locus nucleotide sequence that encodes a product that regulates the production of anthocyanin pigments (red color) in plant tissues (Dellaporta et al,“Molecular cloning of the maize R-nj allele by transposon-tagging with Ac” 263-282 In: Chromosome Structure and Function: Impact of New Concepts, 18th Stadler Genetics Symposium (Gustafson & Appels eds., Plenum Press 1988)); a nucleotide sequence encoding b-lactamase, an enzyme for which various chromogenic substrates are known (e.g., PAD AC, a chromogenic cephalosporin) (Sutcliffe (1978) Proc. Natl. Acad. Sci. USA 75:3737-3741); a nucleotide sequence encoding xylE that encodes a catechol dioxygenase (Zukowsky et al. (1983) Proc. Natl. Acad. Sci. USA 80:1101-1105); a nucleotide sequence encoding tyrosinase, an enzyme capable of oxidizing tyrosine to DOPA and dopaquinone, which in turn condenses to form melanin (Katz et al. (1983) J. Gen. Microbiol. 129:2703-2714); a nucleotide sequence encoding b-galactosidase, an enzyme for which there are chromogenic substrates; a nucleotide sequence encoding lucif erase (lux) that allows for bioluminescence detection (Ow et al. (1986) Science 234:856-859); a nucleotide sequence encoding aequorin which may be employed in calcium-sensitive bioluminescence detection (Prasher et al.
(1985) Biochem. Biophys. Res. Comm. 126:1259-1268); or a nucleotide sequence encoding green fluorescent protein (Niedz et al. (1995) Plant Cell Reports 14:403-406). One of skill in the art is capable of choosing a suitable selectable marker for use in an expression cassette of this invention.
[00201] Further, as is well known in the art, intact transgenic plants can be regenerated from transformed plant cells, plant tissue culture or cultured protoplasts using any of a variety of known techniques. Plant regeneration from plant cells, plant tissue culture or cultured protoplasts is described, for example, in Evans et al. {Handbook of Plant Cell Cultures, Vol. 1, MacMilan Publishing Co. New York (1983)); and Vasil I. R. (ed.) ( Cell Culture and Somatic Cell Genetics of Plants, Acad. Press, Orlando, Vol. I (1984), and Vol. II (1986)).
[00202] Additionally, the genetic properties engineered into the transgenic seeds and plants, plant parts, or plant cells of the invention described above can be passed on by sexual reproduction or vegetative growth and therefore can be maintained and propagated in progeny plants. Generally, maintenance and propagation make use of known agricultural methods developed to fit specific purposes such as harvesting, sowing or tilling.
[00203] A polynucleotide therefore can be introduced into the plant, plant part or plant cell in any number of ways that are well known in the art, as described above. Therefore, no particular method for introducing one or more polynucleotides into a plant is relied upon, rather any method that allows the one or more polynucleotides to be stably integrated into the genome of the plant can be used. Where more than one polynucleotides is to be introduced, the respective polynucleotides can be assembled as part of a single nucleic acid molecule, or as separate nucleic acid molecules, and can be located on the same or different nucleic acid molecules. Accordingly, the polynucleotides can be introduced into the cell of interest in a single transformation event, in separate transformation events, or, for example, in plants, as part of a breeding protocol.
[00204] Additional embodiments of the invention include harvested products produced from the transgenic plants or parts thereof of the invention, as well as a processed product produced from the harvested products. A harvested product can be a whole plant or any plant part, as described herein. Thus, in some embodiments, non-limiting examples of a harvested product include a seed, a fruit, a flower or part thereof (e.g., an anther, a stigma, and the like), a leaf, a stem, and the like. In other embodiments, a processed product includes, but is not limited to, a flour, meal, oil, starch, cereal, and the like produced from a harvested seed or other plant part of the invention, wherein said seed or other plant part comprises a nucleic acid molecule/polynucleotide/nucleotide sequence of this invention.
[00205] In other embodiments, the invention provides an extract from a transgenic seed or a transgenic plant of the invention, wherein the extract comprises a nucleic acid molecule, a polynucleotide, a nucleotide sequence or a toxic protein of the invention. Extracts from plants or plant parts can be made according to procedures well known in the art (See, de la Torre et al., Food, Agric. Environ. 2(l):84-89 (2004); Guidet, Nucleic Acids Res. 22(9): 1772-1773 (1994); Lipton et al., Food Agric. Immun. 12:153-164 (2000)).
Insecticidal Compositions
[00206] In some embodiments, the invention provides an insecticidal composition
comprising a Cry protein of the invention in an agriculturally acceptable carrier. As used herein an“agriculturally-acceptable carrier” can include natural or synthetic, organic or inorganic material which is combined with the active Cry protein to facilitate its application to or in the plant, or part thereof. Examples of agriculturally acceptable carriers include, without limitation, powders, dusts, pellets, granules, sprays, emulsions, colloids, and solutions. Agriculturally-acceptable carriers further include, but are not limited to, inert components, dispersants, surfactants, adjuvants, tackifiers, stickers, binders, or combinations thereof, that can be used in agricultural formulations. Such compositions can be applied in any manner that brings the pesticidal proteins or other pest control agents in contact with the pests. Accordingly, the compositions can be applied to the surfaces of plants or plant parts, including seeds, leaves, flowers, stems, tubers, roots, and the like. In other embodiments, a plant producing a Cry protein of the invention in planta is an agricultural-carrier of the expressed Cry protein.
[00207] In further embodiments, the insecticidal composition comprises a bacterial cell or a transgenic bacterial cell of the invention, wherein the bacterial cell or transgenic bacterial cell produces a Cry protein of the invention. Such an insecticidal composition can be prepared by desiccation, lyophilization, homogenization, extraction, filtration, centrifugation, sedimentation, or concentration of a culture of Bacillus thuringiensis ( Bt ). Such Bt cultures can be the naturally occurring Bt strains YN171-1, GX078-2 and GX435-1 described below in the Examples or transgenic Bt cultures. In additional embodiments, the composition comprises from about 1% to about 99% by weight of the Cry protein of the invention.
[00208] The Cry proteins of the invention can be used in combination with other pest control agents to increase pest target range or for the prevention or management of insect resistance. Therefore, in some embodiments, the invention provides a composition that controls one or more plant pests, wherein the composition comprises a first Cry protein of the invention and a second pest control agent different from the first Cry protein. In other embodiments, the composition is a formulation for topical application to a plant. In still other embodiments, the composition is a transgenic plant. In further embodiments, the composition is a combination of a formulation topically applied to a transgenic plant. In some embodiments, the formulation comprises the first Cry protein of the invention when the transgenic plant comprises the second pest control agent. In other embodiments, the formulation comprises the second pest control agent when the transgenic plant comprises the first Cry protein of the invention.
[00209] In some embodiments, the second pest control agent can be an agent selected from the group consisting of a chemical pesticide, such as an insecticide, a Bacillus thuringiensis ( Bt ) insecticidal protein, a Xenorhabdus insecticidal protein, a Photorhabdus insecticidal protein, a Brevibacillus laterosporus insecticidal protein, a Bacillus sphaericus insecticidal protein, a protease inhibitors (both serine and cysteine types), lectins, alpha -amylase, peroxidase, cholesterol oxidase and a double stranded RNA (dsRNA) molecule.
[00210] In other embodiments, the second pest control agent is a chemical pesticide selected from the group consisting of pyrethroids, carbamates, neonicotinoids, neuronal sodium channel blockers, insecticidal macrocyclic lactones, gamma-aminobutyric acid (GABA) antagonists, insecticidal ureas and juvenile hormone mimics. In other embodiments, the chemical pesticide is selected from the group consisting of abamectin, acephate, acetamiprid, amidoflumet (S-1955), avermectin, azadirachtin, azinphos-methyl, bifenthrin, binfenazate, buprofezin, carbofuran, chlorfenapyr, chlorfluazuron, chlorpyrifos, chlorpyrifos-methyl, chromafenozide, clothianidin, cyfluthrin, beta-cyfluthrin, cyhalothrin, lambda-cyhalothrin, cypermethrin, cyromazine, deltamethrin, diafenthiuron, diazinon, diflubenzuron, dimethoate, diofenolan, emamectin, endosulfan, esfenvalerate, ethiprole, fenothicarb, fenoxycarb, fenpropathrin, fenproximate, fenvalerate, fipronil, flonicamid, flucythrinate, tau-fluvalinate, flufenerim (UR-50701), flufenoxuron, fonophos, halofenozide, hexaflumuron, imidacloprid, indoxacarb, isofenphos, lufenuron, malathion, metaldehyde, methamidophos, methidathion, methomyl, methoprene, methoxychlor, monocrotophos, methoxyfenozide, nithiazin, novaluron, noviflumuron (XDE-007), oxamyl, parathion, parathion-methyl, permethrin, phorate, phosalone, phosmet, phosphamidon, pirimicarb, profenofos, pymetrozine, pyridalyl, pyriproxyfen, rotenone, spinosad, spiromesifin (BSN 2060), sulprofos, tebufenozide, teflubenzuron, tefluthrin, terbufos, tetrachlorvinphos, thiacloprid, thiamethoxam, thiodicarb, thiosultap-sodium, tralomethrin, trichlorfon and triflumuron, aldicarb, oxamyl, fenamiphos, amitraz, chinomethionat, chlorobenzilate, cyhexatin, dicofol, dienochlor, etoxazole, fenazaquin, fenbutatin oxide, fenpropathrin, fenpyroximate, hexythiazox, propargite, pyridaben and tebufenpyrad. In still other embodiments, the chemical pesticide is selected from the group consisting of cypermethrin, cyhalothrin, cyfluthrin and beta-cyfluthrin, esfenvalerate, fenvalerate, tralomethrin, fenothicarb, methomyl, oxamyl, thiodicarb, clothianidin, imidacloprid, thiacloprid, indoxacarb, spinosad, abamectin, avermectin, emamectin, endosulfan, ethiprole, fipronil, flufenoxuron, triflumuron, diofenolan, pyriproxyfen, pymetrozine and amitraz.
[00211] In additional embodiments, the second pest control agent can be one or more of any number of Bacillus thuringiensis insecticidal proteins including but not limited to a Cry protein, a vegetative insecticidal protein (VIP) and insecticidal chimeras of any of the preceding insecticidal proteins. In other embodiments, the second pest control agent is a Cry protein selected from the group consisting of CrylAa, CrylAb, CrylAc, CrylAd, CrylAe, CrylAf, CrylAg, CrylAh, CrylAi, CrylAj, CrylBa, CrylBb, CrylBc, CrylBd, CrylBe, CrylBf, CrylBg, CrylBh, CrylBi, CrylCa, CrylCb, CrylDa, CrylDb, CrylDc, CrylDd, CrylEa, CrylEb, CrylFa, CrylFb, CrylGa, CrylGb, CrylGc, CrylHa, CrylHb, CrylHc, Crylla, Cryllb, Cryllc, Crylld, Crylle, Cryllf, Cryllg, CrylJa, CrylJb, CrylJc, CrylJd, CrylKa, CrylLa, CrylMa, CrylNa, CrylNb, Cry2Aa, Cry2Ab, Cry2Ac, Cry2Ad, Cry2Ae, Cry2Af, Cry2Ag, Cry2Ah, Cry2Ai, Cry2Aj, Cry2Ak,Cry2Al, Cry2Ba, Cry3Aa, Cry3Ba, Cry3Bb, Cry3Ca, Cry4Aa, Cry4Ba, Cry4Ca, Cry4Cb, Cry4Cc, Cry5Aa, Cry5Ab, Cry5Ac, Cry5Ad, Cry5Ba, Cry5Ca, Cry5Da, Cry5Ea, Cry6Aa, Cry6Ba, Cry7Aa, Cry7Ab, Cry7Ac, Cry7Ba, Cry7Bb, Cry7Ca, Cry7Cb, Cry7Da, Cry7Ea, Cry7Fa, Cry7Fb, Cry7Ga, Cry7Gb, Cry7Gc, Cry7Gd, Cry7Ha, Cry7Ia, Cry7Ja, Cry7Ka, Cry7Kb, Cry7La, Cry8Aa, Cry8Ab, Cry8Ac, Cry8Ad, Cry8Ba, Cry8Bb, Cry8Bc, Cry8Ca, Cry8Da, Cry8Db, Cry8Ea, Cry8Fa, Cry8Ga, Cry8Ha, Cry8Ia, Cry8Ib, Cry8Ja, Cry8Ka, Cry8Kb, Cry8La, Cry8Ma, Cry8Na, Cry8Pa, Cry8Qa, Cry8Ra, Cry8Sa, Cry8Ta, Cry9Aa, Cry9Ba, Cry9Bb, Cry9Ca, Cry9Da, Cry9Db, Cry9Dc, Cry9Ea, Cry9Eb, Cry9Ec, Cry9Ed, Cry9Ee, Cry9Fa, Cry9Ga, CrylOAa, Cryl lAa, Cryl lBa, Cryl lBb, Cryl2Aa,Cryl3Aa, Cryl4Aa, Cryl4Ab, Cryl5Aa, Cryl6Aa, Cryl7Aa, Cryl8Aa, Cryl8Ba, Cryl8Ca, Cryl9Aa, Cryl9Ba, Cryl9Ca, Cry20Aa, Cry20Ba, Cry2lAa, Cry2lBa, Cry2lCa, Cry2lDa, Cry2lEa, Cry2lFa, Cry2lGa, Cry2lHa, Cry22Aa, Cry22Ab, Cry22Ba, Cry22Bb, Cry23Aa, Cry24Aa, Cry24Ba, Cry24Ca, Cry25Aa, Cry26Aa, Cry27Aa, Cry28Aa, Cry29Aa, Cry29Ba, Cry30Aa, Cry30Ba, Cry30Ca, Cry30Da, Cry30Db, Cry30Ea, Cry30Fa, Cry30Ga,Cry3lAa, Cry3lAb, Cry3lAc, Cry3lAd, Cry32Aa, Cry32Ab, Cry32Ba, Cry32Ca, Cry32Cb, Cry32Da, Cry32Ea, Cry32Eb, Cry32Fa, Cry32Ga, Cry32Ha, Cry32Hb, Cry32Ia, Cry32Ja, Cry32Ka, Cry32La, Cry32Ma, Cry32Mb, Cry32Na, Cry320a, Cry32Pa, Cry32Qa, Cry32Ra, Cry32Sa, Cry32Ta, Cry32Ua, Cry33Aa, Cry34Aa, Cry34Ab, Cry34Ac, Cry34Ba, Cry35Aa, Cry35Ab, Cry35Ac, Cry35Ba, Cry36Aa, Cry37Aa, Cry38Aa, Cry39Aa, Cry40Aa, Cry40Ba, Cry40Ca, Cry40Da, Cry4lAa, Cry4lAb, Cry4lBa, Cry42Aa, Cry43Aa, Cry43Ba, Cry43Ca, Cry43Cb, Cry43Cc, Cry44Aa, Cry45Aa, Cry46Aa Cry46Ab, Cry47Aa, Cry48Aa, Cry48Ab, Cry49Aa, Cry49Ab, Cry50Aa, Cry50Ba, Cry5lAa, Cry52Aa, Cry52Ba, Cry53Aa, Cry53Ab, Cry54Aa, Cry54Ab, Cry54Ba, Cry55Aa, Cry56Aa, Cry57Aa, Cry57Ab, Cry58Aa, Cry59Aa, Cry59Ba, Cry60Aa, Cry60Ba, Cry6lAa, Cry62Aa, Cry63Aa, Cry64Aa, Cry65Aa, Cry66Aa, Cry67Aa, Cry68Aa, Cry69Aa, Cry69Ab, Cry70Aa, Cry70Ba, Cry70Bb, Cry7lAa, Cry72Aa and Cry73Aa.
[00212] In further embodiments, the second pest control agent is a Vip3 vegetative
insecticidal protein selected from the group consisting of Vip3Aal, Vip3Aa2, Vip3Aa3, Vip3Aa4, Vip3Aa5, Vip3Aa6, Vip3Aa7, Vip3Aa8, Vip3Aa9, Vip3Aal0, Vip3Aal l, Vip3Aal2, Vip3Aal3, Vip3Aal4, Vip3Aal5, Vip3Aal6 , Vip3Aal7, Vip3Aal8, Vip3Aal9, Vip3Aa20, Vip3Aa2l, Vip3Aa22, Vip3Aa2 , Vip3Aa24, Vip3Aa25, Vip3Aa26, Vip3Aa27, Vip3Aa28, Vip3Aa29, Vip3Aa30, Vip3Aa3l, Vip3Aa32, Vip3Aa33 , Vip3Aa34, Vip3Aa35, Vip3Aa36, Vip3Aa37, Vip3Aa38, Vip3Aa39, Vip3Aa40, Vip3Aa4l, Vip3Aa42, Vip3Aa43, Vip3Aa44, Vip3Abl, Vip3Ab2, Vip3Acl, Vip3Adl, Vip3Ad2, Vip3Ael, Vip3Afl,
Vip3Af2, Vip3Af3, Vip3Agl,Vip3Ag2,Vip3Ag3 HM117633, Vip3Ag4, Vip3Ag5,
Vip3Ahl, Vip3Bal, Vip3Ba2, Vip3Bbl, Vip3Bb2 and Vip3Bb3.
[00213] In still further embodiments, the first Cry protein of the invention and the second pest control agent are co-expressed in a transgenic plant. This co-expression of more than one pesticidal principle in the same transgenic plant can be achieved by genetically engineering a plant to contain and express all the genes necessary. Alternatively, a plant, Parent 1, can be genetically engineered for the expression of the Cry protein of the invention. A second plant, Parent 2, can be genetically engineered for the expression of a second pest control agent. By crossing Parent 1 with Parent 2, progeny plants are obtained which express all the genes introduced into Parents 1 and 2.
[00214] In other embodiments, the invention provides a stacked transgenic plant resistant to plant pest infestation comprising a DNA sequence encoding a dsRNA for suppression of an essential gene in a target pest and a DNA sequence encoding a Cry protein of the invention exhibiting biological activity against the target pest. It has been reported that dsRNAs are ineffective against certain lepidopteran pests (Rajagopol et al. 2002. J. Biol. Chem. 277:468- 494), likely due to the high pH of the midgut which destabilizes the dsRNA. Therefore, in some embodiments where the target pest is a lepidopteran pest, a Cry protein of the invention acts to transiently reduce the midgut pH which serves to stabilize the co-ingested dsRNA rendering the dsRNA effective in silencing the target genes.
[00215] In addition to providing compositions, the invention provides methods of
producing a Cry protein toxic to a lepidopteran pest. Such a method comprises, culturing a transgenic non-human host cell that comprises a polynucleotide or a chimeric gene or nucleic acid molecule or a recombinant vector of the invention under conditions in which the host cell produces a protein toxic to the lepidopteran pest. In some embodiments, the transgenic non-human host cell is a plant cell. In some other embodiments, the plant cell is a maize cell. In other embodiments, the conditions under which the plant cell or maize cell are grown include natural sunlight. In other embodiments, the transgenic non-human host cell is a bacterial cell. In still other embodiments, the transgenic non-human host cell is a yeast cell.
[00216] In other embodiments of the method, the lepidopteran pest is selected from the group consisting of Asian com borer (Ostrinia furnacalis), black cutworm ( Agrotis ipsilon ), cotton bollworm ( Helicoverpa armigera ), yellow peach borer ( Conogethes punctiferalis), oriental armyworm ( Mythimna sepatate), European com borer ( Ostrinia nubilalis ), fall armyworm (Spodoptera frugiperda), corn earworm ( Helicoverpa zea), sugarcane borer ( Diatraea saccharalis ), velvetbean caterpillar ( Anticarsia gemmatalis ), soybean looper ( Chrysodeixis includes), southwest corn borer ( Diatraea grandioselld), western bean cutworm ( Richia albicostd), tobacco budworm ( Heliothis virescens), striped stem borer ( Chile suppressalis), pink stem borer ( Sesamia calamistis ) and rice leaffolder ( Cnaphalocrocis medinalis), and any combination thereof.
[00217] In further embodiments of the method, the chimeric gene comprises any of SEQ ID NOs:l-5. In still other embodiments, the produced protein comprises an amino acid sequence of any of SEQ ID NOs: 16-25.
[00218] In some embodiments of the method, the chimeric gene comprises a nucleotide
sequence that is codon optimized for expression in a plant. In other embodiments, the chimeric gene comprises any of SEQ ID NOs:6-lO. In further embodiments, the produced protein comprises an amino acid sequence of any of SEQ ID NOs: 16-25.
[00219] In further embodiments, the invention provides a method of producing a pest-resistant (e.g., an insect-resistant) transgenic plant, comprising, introducing into a plant a
polynucleotide, a chimeric gene, a recombinant vector, an expression cassette or a nucleic acid molecule of the invention comprising a nucleotide sequence that encodes a Cry protein of the invention, wherein the nucleotide sequence is expressed in the plant, thereby conferring to the plant resistance to a lepidopteran pest, and producing an insect-resistant transgenic plant. In some embodiments, a pest-resistant transgenic plant is resistant to a lepidopteran pest in the Genus Ostrinia as compared to a control plant lacking the
polynucleotide, chimeric gene, recombinant vector, expression cassette or nucleic acid molecule of the invention. In other embodiments, the insect in the Genus Ostrinia is an Asian com borer {Ostrinia furnacalis). In some embodiments, the introducing is achieved by transforming the plant. In other embodiments, the introducing is achieved by crossing a first plant comprising the chimeric gene, recombinant vector, expression cassette or nucleic acid molecule of the invention with a different second plant.
[00220] In some embodiments, a transgenic plant of the invention that is resistant to at least Asian com borer (Ostrinia furnacalis) is further resistant to at least one additional lepidopteran pest, wherein the additional lepidopteran pest includes, but is not limited to, black cutworm ( Agrotis ipsilon), fall army worm (Spodoptera frugiperda), corn earworm ( Helicoverpa zea), sugarcane borer ( Diatraea saccharalis), velvetbean caterpillar (. Anticar sia gemmatalis), soybean looper ( Chrysodeixis includes), southwest corn borer ( Diatraea grandio ella), western bean cutworm ( Richia albicosta), tobacco budworm ( Heliothis virescens), cotton bollworm ( Helicoverpa armigera), striped stem borer ( Chile suppressalis), pink stem borer ( Sesamia calamistis) or rice leaffolder ( Cnaphalocrocis medinalis), and any combination thereof.
[00221] In further embodiments, a method of controlling a lepidopteran pest such as Asian com borer {Ostrinia furnacalis) is provided, the method comprising delivering to the insects an effective amount of a Cry protein of the invention. To be effective, the Cry protein is first orally ingested by the insect. However, the Cry protein can be delivered to the insect in many recognized ways. The ways to deliver a protein orally to an insect include, but are not limited to, providing the protein (1) in a transgenic plant, wherein the insect eats (ingests) one or more parts of the transgenic plant, thereby ingesting the polypeptide that is expressed in the transgenic plant; (2) in a formulated protein composition(s) that can be applied to or incorporated into, for example, insect growth media; (3) in a protein composition(s) that can be applied to the surface, for example, sprayed, onto the surface of a plant part, which is then ingested by the insect as the insect eats one or more of the sprayed plant parts; (4) a bait matrix; or (5) any other art-recognized protein delivery system. Thus, any method of oral delivery to an insect can be used to deliver the toxic Cry proteins of the invention. In some particular embodiments, the Cry protein of the invention is delivered orally to an insect, wherein the insect ingests one or more parts of a transgenic plant.
[00222] In other embodiments, the Cry protein of the invention is delivered orally to an insect, wherein the insect ingests one or more parts of a plant sprayed with a composition
comprising the Cry proteins of the invention. Delivering the compositions of the invention to a plant surface can be done using any method known to those of skill in the art for applying compounds, compositions, formulations and the like to plant surfaces. Some non-limiting examples of delivering to or contacting a plant or part thereof include spraying, dusting, sprinkling, scattering, misting, atomizing, broadcasting, soaking, soil injection, soil incorporation, drenching (e.g., root, soil treatment), dipping, pouring, coating, leaf or stem infiltration, side dressing or seed treatment, and the like, and combinations thereof. These and other procedures for contacting a plant or part thereof with compound(s), composition(s) or formulation(s) are well-known to those of skill in the art.
[00223] In some embodiments, the invention encompasses a method of providing a farmer with a means of controlling a lepidopteran pest, the method comprising supplying or selling to the farmer plant material such as a seed, the plant material comprising a polynucleotide, chimeric gene, expression cassette or a recombinant vector capable of expressing a Cry protein of the invention in a plant grown from the seed, as described above.
[00224] Embodiments of this invention can be better understood by reference to the following examples. The foregoing and following description of embodiments of the invention and the various embodiments are not intended to limit the claims, but are rather illustrative thereof. Therefore, it will be understood that the claims are not limited to the specific details of these examples. It will be appreciated by those skilled in the art that other embodiments of the invention may be practiced without departing from the spirit and the scope of the disclosure, the scope of which is defined by the appended claims.
EXAMPLES
Example 1. Identification of Bt Strains for Genome Sequencing
[00225] Bacillus thuringiensis (Bt) strains were isolated from soil samples collected in China.
Soil samples were suspended in LB+2.5M sodium acetate liquid media followed by 70°C heat treatment for about 20 mins. A one microliter suspension was then spread on T3 + penicillin agar plates and incubated at 28°C until colonies formed. Colonies with Bacillus like morphology were picked from the plates and re- streaked on T3 + penicillin agar plates until they had sporulated, typically for approximately three days. Bt strains were identified by staining the culture with Coomasie blue/acetic acid and visualization with a microscope.
After identification of the Bt strain, genomic DNA was isolated as described below.
Example 2. Genome Assembly and Analysis [00226] Bt cry genes of the invention were assembled from the genomes of the Bt strains isolated as described in Example 1 using a whole genome sequencing approach. Briefly, Bacillus DNA was sheared using a Covaris S2 ultrasonic device (Covaris, Inc., Wobum,
MA) with the program DNA_400bp set at duty cycle: 10%; intensity: 4; cycles/burst: 200. The DNA was treated with the NEBNext® Ultra™ End Repair/dA-tailing module (New England Biolabs, Inc. Ipswich, MA). Biooscience indexes 1-57 adapters (1-27 Brazil, 28-57 USA, UK and Switzerland) were ligated using NEB Quick Ligation™ as described by the supplier (New England Biolabs, Inc. Ipswich, MA). Ligations were cleaned up using Agencourt AMPure XP beads as described by the supplier (Beckman Coulter, Inc.,
Indianapolis, IN).
[00227] The library was size fractionated as follows: A 50 uL sample was mixed with 45 ul 75% bead mix (25% AMPure beads plus 75% NaCl/PEG solution TekNova cat # P4136).
The mix was stirred and placed on magnetic rack. The resulting supernatant was transferred to a new well and 45 ul 50% bead mix (50% AMPure beads plus 50% NaCl/PEG solution TekNova cat # P4136) was added. This mix was stirred and placed on a magnetic rack. The resulting supernatant was removed and the beads were washed with 80% ethanol. 25 uL of elution buffer (EB) buffer was added and the mix placed on a magnetic rack. The final resulting supernatant was removed and placed in 1.5 mL tube. This method yielded libraries in the 525 DNA base pairs (bp) (insert plus adapter) size range.
[00228] The sized DNA library was amplified using KAPA Biosystem HiFi Hot Start (Kapa Biosystems, Inc., Wilmington, MA) using the following cycle conditions: [98°C, 45s]; 12 x [98°C, l5s, 60°C, 30s, 72°C, 30s]; [72°C, 1 min]. Each reaction contained: 5 ul DNA library, 1 uL Bioscience universal primer (25 uM), 18 uL sterile water, luL Bioscience indexed primer (25 uM), 25 ul 2X KAPA HiFi polymerase.
[00229] Libraries were run on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) using High Sensitivity chips to determine the library size range and average insert size. All libraries were processed for paired end (PE) sequencing (100 cycles per read; 12-24 libraries per lane) on a HiSeq 2500 sequencing system using standard manufacturer’s sequencing protocols (Illumina, Inc., San Diego, CA). [00230] A Bacillus computational analysis tool developed to identify and characterize likely Cry-like genes was used for prioritization of leads for further laboratory testing.
[00231] The genome assembly and analysis described above led to the identification of five Cry-like genes, designated herein as BT264, BT288, BT302, BT454 and BT485, encoding proteins comprising 1173 amino acids, 1190 amino acids, 1192 amino acids, 1201 amino acids and 1146 amino acids, respectively, and having molecular weights of 132.1 kD, 135.8 kD, 135.6 kD, 134.1 kD and 129.3 kD, respectively. The skilled person will recognize that due to the genome sequencing and gene assembly process, it is unlikely that the assembled nucleotide sequences and the amino acid sequences derived therefrom are naturally occurring since assembly of sequences is known in the art not to be 100% accurate and likely introduces bases different than a native nucleotide sequence. Therefore, the nucleotide sequences are referred to herein as“assembled sequences,” and the Cry proteins which they encode are derived from“assembled sequences.”
[00232] Sequence homology searches were carried out on both the full-length and truncated Cry protein amino acid sequences derived from the assembled nucleotide sequences. The truncated sequence approximated the size of the mature toxin, i.e. approximately 67 kD. Homology was determined using the NCBI protein-protein BLAST program on the worldwide web at ncbi.nlm.nih.gov/ BLAST. Known Cry proteins with the highest homology to each of the assembled Cry proteins indicated the nearest Cry family to which the assembled Cry protein belongs. Identifying characteristics of the assembled Cry coding sequences and proteins are shown in Table 1.
Table 1. Assembled Cry genes/proteins identified in Bacillus thuringiensis strains.
Figure imgf000068_0001
Figure imgf000069_0001
[00233] Surprisingly, a different nearest Cry family member was identified depending on whether the search was carried out on the full-length vs. the truncated amino acid sequence for three of the assembled Cry proteins, BT288, BT302 and BT485. As shown in Table 1, the nearest Cry family identified for the truncated BT288 Cry protein (SEQ ID NO:26) is Cry54Aa compared to the full-length BT288 (SEQ ID NO: 17) in which the nearest Cry family is Cry4Aa, which have 42% identity across their full-length. Aligning BT288 with Cry54A and Cry4Aa revealed that the N-terminus of BT288 (SEQ ID NO:26) has 51% identity to a Cry54A protein (See Table 2) and the C-terminus of BT288 (SEQ ID NO:27) has 47% identity to a Cry4A protein (See Table 3), suggesting that the assembled BT288 nucleotide sequence is a hybrid between a Cry50A and a Cry4A protein.
Table 2. Alignment of N-terminus of BT288 (SEQ ID NO:26) with Cry54Aa (SEQ ID NO:32).
Figure imgf000069_0002
Figure imgf000070_0001
Table 3. Alignment of C-terminus of BT0288 (SEQ ID NO:27) with Cry4Aa (SEQ ID NO:33).
Pos Sequence Start End Length Matches % Identity
Ref 1 BTO288 ( SEQ ID NO:27) 670 1190 521 aa
2 Cry4Aa ( SEQ ID NO:33) 679 1180 502 aa 254 47
Figure imgf000070_0002
[00234] The nearest Cry family identified for the truncated BT302 Cry protein (SEQ ID
NO:28) is Cry39Aa compared to the full-length BT302 (SEQ ID NO: 18) in which the nearest Cry family is Cryl9Ca, which have 47% identity across their full-length. Aligning BT302 with Cry39A and Cryl9Ca revealed that the N-terminus of BT302 (SEQ ID NO:28) has 54% identity to Cry39A (See Table 4) and the C-terminus of BT302 (SEQ ID NO:29) has 53% identity to Cryl9Ca (See Table 5), suggesting that the assembled BT302 nucleotide sequence is a hybrid between a Cry39A and a Cryl9C protein.
Table 4. Alignment of N-terminus odBT0302 (SEQ ID NO:28) with Cry39Aa (SEQ ID NO:34).
Figure imgf000071_0001
Table 5. Alignment of C-terminus of BT0302 (SEQ ID NO:29) with Cryl9Ca (SEQ ID NO:35).
Figure imgf000072_0001
[00235] The nearest Cry family identified for the truncated BT485 Cry protein (SEQ ID
NO:30) is Cry50B compared to the full-length (SEQ ID NO:20) in which the nearest Cry family is Cry4Ba, which have 62% identity across their full-length. Aligning BT485 with Cry50B and Cry4B revealed that the N-terminus of BT485 (SEQ ID NO:30) has 70% identity to Cry50B (See Table 6) and the C-terminus of BT485 (SEQ ID NO:3l) has 75% identity to Cry4B (See Table 7). Cry50B and Cry4B have only 51% identity across their full- length (See Table 8). Therefore, the assembled BT485 nucleotide sequence appears to by a hybrid between a Cry50 and a Cry4. Cry4B and Cry50 are known in the art to be active against Dipteran insects, particularly mosquitoes (Zhang et al. 2012. Characterization of a new highly mosquitocidal isolate of Bacillus thuringiensis— an alternative to Bti. J. Invertebr. Pathol. 109 (2), 217-222), and there is no apparent report of activity against lepidopteran insects.
Table 6. Alignment of N-terminus of BT485 (SEQ ID NO:30) with Cry50Ba (SEQ ID NO:36).
Figure imgf000073_0001
Table 7. Alignment of C-terminus of BT485 (SEQ ID NO:3l) with Cry4Ba (SEQ ID NO:37).
Figure imgf000073_0002
Figure imgf000074_0001
Table 8. Alignment of Cry4Ba (SEQ ID NO:37) with Cry50Ba (SEQ ID NO:36).
Figure imgf000074_0002
Figure imgf000075_0001
Example 3. Bt Protein Expression in Recombinant Host Cells
[00236] Bacillus Expression. The Cry proteins described in Example 2 were expressed in an crystal minus Bacillus thuringiensis (Bt) strain having no observable background insecticidal activity via a shuttle vector designated pCIB5634', designed for expression in both E. coli and Bt. Vector pCIB5634' comprises a CrylAc promoter that drives expression of the cloned Bt Cry gene and a erythromycin resistance marker. Expression cassettes comprising the Cry coding sequence of interest were transformed into the host Bt strain via electroporation and transgenic Bt strains were selected for on erythromycin containing agar plates. Selected transgenic Bt strains were grown to the sporulation phase in T3 media at 28°C for 4-5 days. Cell pellets were harvested and washed iteratively before solubilization in high pH carbonate buffer (50mM) containing 2mM DTT.
[00237] E. coli Expression. Cry proteins were expressed in E. coli strains using pET28a or pET29a vectors (Merck KGaA, Darmstadt, Germany). Constructs were transformed by electroporation and transgenic E. coli clones were selected for on kanamycin-containing agar plates. Selected transgenic E. coli strains were grown and Cry protein expression induced using IPTG induction at 28°C. Cells were resuspended in high pH carbonate buffer (50mM) containing 2mM DTT and then broken using a Microfluidics LV-l homogenizer.
[00238] Expression Analysis. Resulting cell lysates from either transgenic Bt or E. coli strains were then clarified via centrifugation and samples were analyzed for purity via SDS- PAGE and electropherogram using a BioRad Experion system (Biorad, Hercules, CA).
Total protein concentrations were determined via Bradford or Thermo 660 assay. Purified Cry proteins were then tested in bioassays described below. Example 4. Activity of Cry Proteins in Bioassays
[00239] The Cry proteins produced in Example 3 were tested against one or more of the following lepidopteran pest species using an art-recognized artificial diet bioassay method: Asian com borer (ACB; Ostrinia furnacalis), cotton bollworm (CBW; Helicoverpa armigera), black cutworm (BCW; Agrotis ipsilon ), European com borer (ECB; Ostrinia nubilalis), fall armyworm (FAW; Spodoptera frugiperda), corn earworm (CEW; Helicoverpa zea), sugarcane borer (SCB; Diatraea saccharlis), southwest com borer (SWCB; Diatraea grandio ella), soybean looper (SBL; Pseudoplusia includens) and tobacco budworm (TBW; Heliothis virescens).
[00240] An equal amount of protein in solution was applied to the surface of an artifical insect diet (Bioserv, Inc., Frenchtown, NJ) in 24 well plates. After the diet surface dried, larvae of the insect species being tested were added to each well. The plates were sealed and maintained at ambient laboratory conditions with regard to temperature, lighting and relative himidity. A positive-control group consisted of larvae exposed to a very active and broad- spectrum wild-type Bacillus strain. Negative control groups consisted of larvae exposed to insect diet treated with only the buffer solution and larvae on untreated insect diet; i.e. diet alone. Mortality was assessed after about 120 hours and scored relative to the controls.
[00241] Results are shown in Table 9, where a“-’’means no activity compared to the
control group, a“+/-” means 0-10% activity compared to control group (this category also includes 0% mortality with strong larval growth inhibition), a“+” means 10-25% activity compared to control group, a“++” means 25-75% activity compared to control group, and a “+++” 75-100% activity compared to control group. The designation“nt” in Table 2 means the indicated protein was not tested against that particular pest.
Table 9. Results of bioassays with Cry Proteins.
Figure imgf000076_0001
Figure imgf000077_0001
Example 5. Vectoring of Genes for Plant Expression
[00242] Prior to expression in plants, polynucleotides encoding Cry proteins, BT264 (SEQ ID NO: 16), BT288 (SEQ ID NO: 17), BT302 (SEQ IDNO:l8), BT454 (SEQ ID NO: 19) or BT485 (SEQ ID NO:20) or mutant Cry proteins, mBT264 (SEQ ID NO:2l), mBT288 (SEQ ID NO:22), mBT302 (SEQ ID NO:23), mBT454 (SEQ ID NO;24) or mBT485 (SEQ ID NO:25) are synthesized on an automated gene synthesis platform (e.g., Genscript, Inc., Piscataway, NJ). For this example, a first expression cassette is made comprising a plant expressible promoter operably linked to a Cry protein coding sequence which is operably linked to a terminator and a second expression cassette is made comprising a plant expressible promoter operably linked to a selectable marker which is operably linked to a terminator. Expression of the selectable marker allows for identification of transgenic plants on selection media. Both expression cassettes are cloned into a suitable vector for
Agrobacterium- mediated rice or maize transformation.
Example 6. Expression and Activity of Cry Proteins in Maize Plants
[00243] Transformation of immature maize embryos is performed essentially as described in Negrotto et al, 2000, Plant Cell Reports 19: 798 803. Briefly, Agrobacterium strain
LBA4404 (pSBl) comprising an expression vector described in Example 5 is grown on YEP (yeast extract (5 g/L), peptone (lOg/L), NaCl (5g/L), l5g/l agar, pH 6.8) solid medium for 2- 4 days at 28°C. Approximately 0.8X 109 Agrobacterium cells are suspended in LS-inf media supplemented with 100 mM As. Bacteria are pre-induced in this medium for approximately 30-60 minutes.
[00244] Immature embryos from an inbred maize line are excised from 8-12 day old ears into liquid LS-inf + 100 mM As. Embryos are rinsed once with fresh infection medium. Agrobacterium solution is then added and embryos are vortexed for 30 seconds and allowed to settle with the bacteria for 5 minutes. The embryos are then transferred scutellum side up to LSAs medium and cultured in the dark for two to three days. Subsequently, between approximately 20 and 25 embryos per petri plate are transferred to LSDc medium
supplemented with cefotaxime (250 mg/l) and silver nitrate (1.6 mg/l) and cultured in the dark at approximately 28°C for 10 days.
[00245] Immature embryos, producing embryogenic callus are transferred to LSD1M0.5S medium. The cultures are selected on this medium for approximately 6 weeks with a subculture step at about 3 weeks. Surviving calli are transferred to Regl medium
supplemented with mannose. Following culturing in the light (16 hour light/ 8 hour dark regiment), green tissues are then transferred to Reg2 medium without growth regulators and incubated for about 1-2 weeks. Plantlets are transferred to Magenta GA-7 boxes (Magenta Corp, Chicago Ill.) containing Reg3 medium and grown in the light. After about 2-3 weeks, plants are tested for the presence of the selectable marker gene and the Bt cry gene by PCR. Positive plants from the PCR assay are transferred to a greenhouse for further evaluation.
[00246] Transgenic plants are evaluated for copy number (determined by Taqman analysis), protein expression level (determined by ELISA), and efficacy against insect species of interest in leaf excision bioassays. Specifically, plant tissue (leaf or silks) is excised from single copy events (V3-V4 stage) and infested with neonate larvae of a target pest, then incubated at room temperature for 5 days. Leaf disks from transgenic plants expressing BT264, BT288, BT302, BT454, BT485, mBT264, mBT288, mBT302, mBT454 or mBT485 are tested against one or more lepidopteran pests such as Asian com borer ( Ostrinia furnacalis ). Results of the transgenic plant tissue bioassay will confirm that the Cry proteins of the invention when expressed in transgenic plants are toxic to one or more of the target lepidopteran pests.

Claims

What is claimed is:
1. A nucleic acid molecule comprising a nucleotide sequence that encodes a Cry protein that is toxic to a lepidopteran pest, wherein the nucleotide sequence (a) has at least 80% to at least 99% sequence identity with any of SEQ ID NOs:l-5, or a toxin-encoding fragment thereof; or (b) encodes a Cry protein comprising an amino acid sequence that has at least 80% to at least 99% sequence identity with any of SEQ ID NOs: 16-25, or a toxin fragment thereof; or (c) is an assembled nucleotide sequence of (a) or (b); or (d) is a synthetic sequence of (a), (b) or (c) that has codons optimized for expression in a transgenic organism.
2. The nucleic acid molecule of claim 1, wherein the nucleotide sequence comprises any of SEQ ID NOs: 1-5, or a toxin-encoding fragment thereof.
3. The nucleic acid molecule of claim 1, wherein the Cry protein comprises an amino acid sequence of any of SEQ ID NOs: 16-25, or a toxic fragment thereof.
4. The nucleic acid molecule of claim 1, wherein the synthetic nucleotide sequence comprises any of SEQ ID NOs:6-l5, or a toxin-encoding fragment thereof.
5. A chimeric gene comprising a heterologous promoter operably linked to the nucleic acid molecule of any one of claims 1-4.
6. The chimeric gene of claim 5, wherein the heterologous promoter is a plant expressible promoter.
7. The chimeric gene of claim 6, wherein the plant expressible promoter is selected from the group of promoters consisting of ubiquitin, cestrum yellow virus, corn TrpA, OsMADS 6, maize H3 histone, bacteriophage T3 gene 9 5' EiTR, com sucrose synthetase 1, corn alcohol dehydrogenase 1, corn light harvesting complex, com heat shock protein, maize mtl, pea small subunit RuBP carboxylase, rice actin, rice cyclophilin, Ti plasmid mannopine synthase, Ti plasmid nopaline synthase, petunia chalcone isomerase, bean glycine rich protein 1, potato patatin, lectin, CaMV 35S and S-E9 small subunit RuBP carboxylase promoter.
8. The chimeric gene of claim 5, wherein the lepidopteran pest is selected from the group consisting of Asian corn borer (Ostrinia furnacalis), cotton bollworm ( Helicoverpa armigera), European com borer ( Ostrinia nubilalis ) and fall army worm (Spodoptera frugiperdd).
9. The chimeric gene of claim 5, wherein the transgenic organism is a bacterium.
10. A Cry protein, and optionally an isolated Cry protein, that is toxic to a lepidopteran pest, wherein the Cry protein or isolated Cry protein comprises (a) an amino acid sequence that has at least 80% to at least 99% sequence identity with an amino acid sequence of any of SEQ ID NOs: 16-25, or a toxin fragment thereof; or (b) an amino acid sequence that is encoded by a nucleotide sequence or an assembled nucleotide sequence that has at least 80% to at least 99% sequence identity with a nucleotide sequence of any of SEQ ID NOs:6-l5, or a toxin-encoding fragment thereof.
11. The Cry protein of claim 10, wherein the amino acid sequence comprises any of SEQ ID NOs: 16-25, or a toxin fragment thereof.
12. The Cry protein of claim 10, wherein the amino acid sequence is encoded by a nucleotide sequence comprising any of SEQ ID NOs:6-l5, or a toxin-encoding fragment thereof.
13. The Cry protein of any of claims 10-12 wherein the lepidopteran pest is selected from the group consisting of Asian com borer (Ostrinia furnacalis), cotton bollworm ( Helicoverpa armigera ), European corn borer ( Ostrinia nubilalis) and fall armyworm (Spodoptera frugiperdd).
14. An isolated Bacillus thuringiensis strain that produces the Cry protein of claim 11.
15. An insecticidal composition comprising the Cry protein of claim 10 and an agriculturally acceptable carrier.
16. The composition of claim 15, wherein the agriculturally acceptable carrier is selected from the group consisting of a powder, dust, pellet, granule, spray, emulsion, colloid, and solution.
17. The composition of claim 10, wherein the composition is prepared by desiccation, lyophilization, homogenization, extraction, filtration, centrifugation, sedimentation, or concentration of a culture of a strain of Bacillus thuringiensis.
18. The composition of claim 17, wherein the strain of Bacillus thuringiensis is the Bacillus thuringiensis strain of claim 14.
19. The composition of claim 10, wherein the composition comprises a transgenic bacterial cell that produces the Cry protein.
20. The composition of claim 10, comprising from about 1% to about 99% by weight of the Cry protein.
21. A recombinant vector comprising the nucleic acid molecule of claim 1 or the chimeric gene of claim 5.
22. A transgenic bacterial cell or plant cell comprising the recombinant vector of claim 21.
23. The transgenic bacterial cell of claim 22, wherein the bacterial cell is in the genus Bacillus, Clostridium, Xenorhabdus, Photorhabdus, Pasteuria, Escherichia, Pseudomonas, Erwinia, Serratia, Klebsiella, Salmonella, Pasteurella, Xanthomonas, Streptomyces, Rhizobium, Rhodopseudomonas, Methylophilius, Agrobacterium, Acetobacter, Lactobacillus, Arthrobacter, Azotobacter, Eeuconostoc, or Alcaligenes.
24. The transgenic Bacillus cell of claim 23, wherein the Bacillus cell is a Bacillus thuringiensis cell.
25. The transgenic plant cell of claim 22, wherein the plant cell is a dicot plant cell or a monocot plant cell.
26. The dicot plant cell of claim 25, wherein the dicot plant cell is selected from the group consisting of a soybean cell, sunflower cell, tomato cell, cole crop cell, cotton cell, sugar beet cell and tobacco cell.
27. The monocot plant cell of claim 25, wherein the monocot plant cell is selected from the group consisting of a barley cell, maize cell, oat cell, rice cell, sorghum cell, sugar cane cell and wheat cell.
28. A harvested product derived from the transgenic plant cell of any of claims 25-27, wherein the harvested product comprises the protein.
29. A processed product derived from the harvested product of claim 28, wherein the processed product is selected from the group consisting of flour, meal, oil, and starch, or a product derived therefrom.
30. A harvested product derived from a transgenic plant comprising the plant cell of claim 25, wherein the harvested product comprises the protein.
31. A processed product derived from the harvested product of claim 30, wherein the processed product is selected from the group consisting of flour, meal, oil, and starch, or a product derived therefrom.
32. A method of producing a Cry protein that is toxic to a lepidopteran pest comprising: culturing the transgenic cell of claim 22 under conditions in which the transgenic cell produces the Cry protein.
33. The method of claim 32, wherein the lepidopteran pest is selected from the group consisting of Asian corn borer (Ostrinia furnacalis), cotton bollworm ( Helicoverpa armigera), European com borer ( Ostrinia nubilalis ) and fall army worm (Spodoptera frugiperda), or any combination thereof.
34. The method of claim 32, wherein the nucleotide sequence is codon optimized for expression in a plant.
35. The method of claim 32, wherein the nucleic acid molecule or the chimeric gene comprises any of SEQ ID NOs:l-l5, or a toxin-encoding fragment thereof.
36. The method of claim 32, wherein the Cry protein comprises an amino acid sequence of any of SEQ ID NOs: 16-25, or a toxin fragment.
37. A method of producing an insect-resistant transgenic plant, comprising: introducing into a plant the chimeric gene of claim 6, wherein the Cry protein is expressed in the plant, thereby producing an insect-resistant transgenic plant.
38. The method of claim 37, wherein the introducing step is achieved by a) transforming the plant; or b) crossing a first plant comprising the chimeric gene with a different second plant.
39. The method of claim 37 or 38, wherein the plant is a rice plant or maize plant.
40. A method of controlling a lepidopteran pest, comprising delivering to the lepidopteran pest or an environment thereof an insecticidal composition comprising an effective amount of the Cry protein of claim 10.
41. The method of claim 40, wherein the lepidopteran pest is selected from the group consisting of Asian corn borer (Ostrinia furnacalis), cotton bollworm (Helicoverpa armigera), European com borer (Ostrinia nubilalis) and fall army worm (Spodoptera frugiperda), or any combination thereof.
42. The method of claim 40, wherein the composition is a transgenic plant.
43. A hybrid insecticidal protein comprising in an N-terminal to C-terminal direction a) an N-terminal region of a Cry54A protein fused to a C-terminal region of a Cry4A protein, wherein the crossover position between the Cry54A protein and the Cry4A protein is located between domain III of the Cry54A and the protoxin tail of Cry4A and wherein the hybrid insecticidal protein has at least 90% identity to SEQ ID NO: 17; or b) an N-terminal region of a Cry39A protein fused to a C-terminal region of a Cryl9C protein, wherein the crossover position between the Cry39A protein and the Cry 19 protein is located between domain III of the Cry39A and the protoxin tail of the Cryl9C and wherein the hybrid insecticidal protein has at least 90% identity to SEQ ID NO: 18; or c) an N-terminal region of a Cry50B protein fused to a C-terminal region of a Cry4B protein, wherein the crossover position between the Cry50B protein and the Cry4B protein is located between domain III of the Cry50B and the protoxin tail of the Cry4B and wherein the hybrid insecticidal protein has at least 90% identity to SEQ ID NO:20; and wherein the hybrid insecticidal protein is active against a lepidopteran insect pest.
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