US20080070829A1 - Family of pesticidal proteins and methods for their use - Google Patents

Family of pesticidal proteins and methods for their use Download PDF

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US20080070829A1
US20080070829A1 US11/763,947 US76394707A US2008070829A1 US 20080070829 A1 US20080070829 A1 US 20080070829A1 US 76394707 A US76394707 A US 76394707A US 2008070829 A1 US2008070829 A1 US 2008070829A1
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seq
sequence
nucleotide sequence
amino acid
polypeptide
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Nadine Carozzi
Michael Koziel
Nicholas Duck
Nalini Desai
Rong Guo
Daniel Tomso
Rebekah Deter
Tracy Hargiss
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Athenix Corp
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Athenix Corp
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Assigned to ATHENIX CORPORATION reassignment ATHENIX CORPORATION ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: HARGISS, TRACY, TOMSO, DANIEL JOHN, DUCK, NICHOLAS, CAROZZI, NADINE, DESAI, NALINI M., DETER, REBEKAH, KOZIEL, MICHAEL G., GUO, RONG
Publication of US20080070829A1 publication Critical patent/US20080070829A1/en
Priority to US13/168,454 priority patent/US8829279B2/en
Priority to US14/451,659 priority patent/US20140344999A1/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
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01N—PRESERVATION OF BODIES OF HUMANS OR ANIMALS OR PLANTS OR PARTS THEREOF; BIOCIDES, e.g. AS DISINFECTANTS, AS PESTICIDES OR AS HERBICIDES; PEST REPELLANTS OR ATTRACTANTS; PLANT GROWTH REGULATORS
    • A01N37/00—Biocides, pest repellants or attractants, or plant growth regulators containing organic compounds containing a carbon atom having three bonds to hetero atoms with at the most two bonds to halogen, e.g. carboxylic acids
    • A01N37/44—Biocides, pest repellants or attractants, or plant growth regulators containing organic compounds containing a carbon atom having three bonds to hetero atoms with at the most two bonds to halogen, e.g. carboxylic acids containing at least one carboxylic group or a thio analogue, or a derivative thereof, and a nitrogen atom attached to the same carbon skeleton by a single or double bond, this nitrogen atom not being a member of a derivative or of a thio analogue of a carboxylic group, e.g. amino-carboxylic acids
    • 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
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P21/00—Preparation of peptides or proteins
    • C12P21/02—Preparation of peptides or proteins having a known sequence of two or more amino acids, e.g. glutathione
    • 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 via EFS-Web as an ASCII formatted sequence listing with a file named “329211_SequenceListing.txt”, created on Jun. 14, 2007, and having a size of 305 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 the field of molecular biology. Provided are novel genes that encode pesticidal proteins. These proteins and the nucleic acid sequences that encode them are useful in preparing pesticidal formulations and in the production of transgenic pest-resistant plants.
  • Bacillus thuringiensis 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 insects, but are harmless to plants and other non-targeted organisms. For this reason, compositions including Bacillus thuringiensis strains or their insecticidal proteins can be used as environmentally-acceptable insecticides to control agricultural insect pests or insect vectors for a variety of human or animal diseases.
  • Crystal (Cry) proteins (delta-endotoxins) from Bacillus thuringiensis have potent insecticidal activity against predominantly Lepidopteran, Dipteran, and Coleopteran larvae. These proteins also have shown activity against Hymenoptera, Homoptera, Phthiraptera, Mallophaga, and Acari pest orders, as well as other invertebrate orders such as Nemathelminthes, Platyhelminthes, and Sarcomastigorphora (Feitelson (1993) The Bacillus Thuringiensis family tree. In Advanced Engineered Pesticides , Marcel Dekker, Inc., New York, N.Y.) These proteins were originally classified as CryI to CryV based primarily on their insecticidal activity.
  • the major classes were Lepidoptera-specific (I), Lepidoptera- and Diptera-specific (II), Coleoptera-specific (III), Diptera-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 Cry1A, Cry1B, Cry1C, etc. Even more closely related proteins within each division were given names such as Cry1C1, Cry1C2, etc.
  • 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
  • a secondary rank an uppercase letter
  • a tertiary rank a lowercase letter
  • a quaternary rank another Arabic number.
  • Roman numerals have been exchanged for Arabic numerals in the primary rank. Proteins with less than 45% sequence identity have different primary ranks, and the criteria for secondary and tertiary ranks are 78% and 95%, respectively.
  • the crystal protein does not exhibit insecticidal activity until it has been ingested and solubilized in the insect midgut.
  • the ingested protoxin is hydrolyzed by proteases in the insect digestive tract to an active toxic molecule. (Höfte and Whiteley (1989) Microbiol. Rev. 53:242-255). This toxin binds to apical brush border receptors in the midgut of the target larvae and inserts into the apical membrane creating ion channels or pores, resulting in larval death.
  • Delta-endotoxins 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 consists of seven alpha helices and is involved in membrane insertion and pore formation.
  • Domain II consists of three beta-sheets arranged in a Greek key configuration, and domain III consists of two antiparallel beta-sheets in “jelly-roll” formation (de Maagd et al., 2001, supra). Domains II and III are involved in receptor recognition and binding, and are therefore considered determinants of toxin specificity.
  • compositions and methods for conferring pesticidal activity to bacteria, plants, plant cells, tissues and seeds are provided.
  • Compositions include nucleic acid molecules encoding sequences for pesticidal and insectidal polypeptides, vectors comprising those nucleic acid molecules, and host cells comprising the vectors.
  • Compositions also include the pesticidal polypeptide sequences and antibodies to those polypeptides.
  • the nucleotide sequences can be used in DNA constructs or expression cassettes for transformation and expression in organisms, including microorganisms and plants.
  • the nucleotide or amino acid sequences may be synthetic sequences that have been designed for expression in an organism including, but not limited to, a microorganism or a plant.
  • Compositions also comprise transformed bacteria, plants, plant cells, tissues, and seeds.
  • isolated nucleic acid molecules are provided that encode a pesticidal protein.
  • amino acid sequences corresponding to the pesticidal protein are encompassed.
  • the present invention provides for an isolated nucleic acid molecule comprising a nucleotide sequence encoding the amino acid sequence shown in SEQ ID NO:2, 4, 6, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37 or 61, a nucleotide sequence set forth in SEQ ID NO:1, 3, 5, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, or 60, or the delta-endotoxin nucleotide sequence of the DNA insert of the plasmid deposited in a bacterial host as Accession No.
  • Nucleotide sequences that are complementary to a nucleotide sequence of the invention, or that hybridize to a sequence of the invention are also encompassed.
  • Methods are provided for producing the polypeptides of the invention, and for using those polypeptides for controlling or killing a lepidopteran, coleopteran, nematode, or dipteran pest. Methods and kits for detecting the nucleic acids and polypeptides of the invention in a sample are also included.
  • compositions and methods of the invention are useful for the production of organisms with enhanced pest resistance or tolerance. These organisms and compositions comprising the organisms are desirable for agricultural purposes.
  • compositions of the invention are also useful for generating altered or improved proteins that have pesticidal activity, or for detecting the presence of pesticidal proteins or nucleic acids in products or organisms.
  • FIG. 1 shows an alignment of AXMI-022 with the Iota1b from Clostridium perfringens (SEQ ID NO:49), Isp1A from Brevibacillus laterosporus (SEQ ID NO:50), Isp1B from Brevibacillus laterosporus (SEQ ID NO:51), Vip1Ab from Bacillus thuringiensis (SEQ ID NO:52), and Vip1Ac from Bacillus thuringiensis (SEQ ID NO:53).
  • the alignment shows the most highly conserved amino acid residues highlighted in black, and highly conserved amino acid residues highlighted in gray.
  • FIG. 2 shows an alignment of AXMI-022 with Vip1Ab (SEQ ID NO:52). The alignment shows the most highly conserved amino acid residues highlighted in black, and highly conserved amino acid residues highlighted in gray.
  • FIG. 3 shows an alignment of AXMI-022 with Cry 37Aa1 from Bacillus thuringiensis (SEQ ID NO:54). The alignment shows the most highly conserved amino acid residues highlighted in black, and highly conserved amino acid residues highlighted in gray.
  • FIG. 4 shows an alignment of AXMI-023 with the Vip2 pesticidal protein (SEQ ID NO:55), Isp2a from Brevibacillus laterosporus (SEQ ID NO:56) and Iota toxin component Ia from Clostridium perfringens (SEQ ID NO:57).
  • the alignment shows the most highly conserved amino acid residues highlighted in black, and highly conserved amino acid residues highlighted in gray.
  • the present invention is drawn to compositions and methods for regulating pest resistance or tolerance in organisms, particularly plants or plant cells.
  • resistance is intended that the pest (e.g., insect) is killed upon ingestion or other contact with the polypeptides of the invention.
  • tolerance is intended an impairment or reduction in the movement, feeding, reproduction, or other functions of the pest.
  • the methods involve transforming organisms with a nucleotide sequence encoding a pesticidal protein of the invention.
  • the nucleotide sequences of the invention are useful for preparing plants and microorganisms that possess pesticidal activity.
  • transformed bacteria, plants, plant cells, plant tissues and seeds are provided.
  • compositions are pesticidal nucleic acids and proteins of Bacillus or other species.
  • the sequences find use in the construction of expression vectors for subsequent transformation into organisms of interest, as probes for the isolation of other homologous (or partially homologous) genes, and for the generation of altered pesticidal proteins by methods known in the art, such as domain swapping or DNA shuffling.
  • the proteins find use in controlling or killing lepidopteran, coleopteran, dipteran, and nematode pest populations and for producing compositions with pesticidal activity.
  • Plasmids containing the nucleotide sequences of the invention were deposited in the permanent collection of the Agricultural Research Service Culture Collection, Northern Regional Research Laboratory (NRRL), 1815 North University Street, Peoria, Ill. 61604, United States of America, in accordance with Table 1. This deposit will be maintained under the terms of the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure. This deposit was made merely as a convenience for those of skill in the art and is not an admission that a deposit is required under 35 U.S.C. ⁇ 112. TABLE 1 Microorganism Deposit NRRL Gene Strain Clone number Deposit Date axmi-011 ATX13026 pAX4600 B-30961 Jul.
  • Pesticidal toxin or “pesticidal protein” is intended a toxin that has toxic activity against one or more pests, including, but not limited to, members of the Lepidoptera, Diptera, and Coleoptera orders, or the Nematoda phylum, or a protein that has homology to such a protein. Pesticidal proteins have been isolated from organisms including, for example, Bacillus sp., Clostridium bifermentans and Paenibacillus popilliae .
  • Pesticidal proteins include amino acid sequences deduced from the full-length nucleotide sequences disclosed herein, and amino acid sequences that are shorter than the full-length sequences, either due to the use of an alternate downstream start site, or due to processing that produces a shorter protein having pesticidal activity. Processing may occur in the organism the protein is expressed in, or in the pest after ingestion of the protein.
  • Pesticidal proteins encompass delta-endotoxins.
  • Delta-endotoxins include proteins identified as cry1 through cry43, cyt1 and cyt2, and Cyt-like toxin.
  • nucleotide sequences encoding polypeptides with homology to several other known classes of pesticidal protein toxins For example, axmi-011, axmi-012, axmi-015, axmi-032, axmi-044, axmi-033, axmi-034, axmi-022, axmi-063, and axmi-064 demonstrate homology to pesticidal binary toxins such as VIP, Bin, and MTX toxins.
  • the VIP1/VIP2 toxins see, for example, U.S. Pat. No.
  • A/B toxins such as VIP, C2, CDT, CST, or the B. anthracis edema and lethal toxins initially interact with target cells via a specific, receptor-mediated binding of “B” components as monomers. These monomers then form homoheptamers.
  • the “B” heptamer-receptor complex then acts as a docking platform that subsequently binds and allows the translocation of an enzymatic “A” component(s) into the cytosol via receptor-mediated endocytosis.
  • A enzymatic component(s) into the cytosol via receptor-mediated endocytosis.
  • A enzymatic component(s) into the cytosol via receptor-mediated endocytosis.
  • “A” components inhibit normal cell function by, for example, ADP-ribosylation of G-actin, or increasing intracellular levels of cyclic AMP (cAMP). See Barth et al. (2004) Microbiol Mol Biol Rev 68:373-402, herein incorporated by reference in its entirety.
  • Cry34Ab1 and Cry35Ab1 comprise a binary toxin with pesticidal activity that was identified from strain PS149B1 (Ellis et al. (2002) Appl Environ Microbiol. 68:1137-45, herein incorporated by reference in its entirety). These toxins have molecular masses of approximately 14 and 44 kDa, respectively. Other binary toxins with similar organization and homology to Cry34Aa and Cry34Ab have been identified (Baum et al. (2004) Appl Environ Microbiol. 70:4889-98, herein incorporated by reference in its entirety).
  • BinA and BinB are proteins from Bacillus sphaericus that comprise a mosquitocidal binary toxin protein (Baumann et al. (1991) Micriobiol. Rev. 55:425-36). Cry35 exhibits amino acid similarity to these BinA and BinB proteins. Cry36 (ET69) and Cry38 (ET75) (International Patent Application No. WO/00/66742-B, herein incorporated by reference in its entirety) are independently isolated peptides that also exhibit amino acid similarity to BinA and BinB, and thus are likely to comprise binary toxins.
  • Cry23 also known as cryET33; U.S. Pat. No. 6,063,756, herein incorporated by reference in its entirety
  • Cry37 also known as cryET34; U.S. Pat. No. 6,063,756, herein incorporated by reference in its entirety
  • MTX is used in the art to delineate a set of pesticidal proteins that are produced by Bacillus sphaericus . The first of these, often referred to in the art as MTX1, is synthesized as a parasporal crystal which is toxic to mosquitoes.
  • MTX1 is considered a “binary” toxin (Baumann et al. (1991) Microbiol. Rev. 55:425-436).
  • MTX2 and MTX3 represent separate, related classes of pesticidal toxins that exhibit pesticidal activity. See, for example, Baumann et al. (1991) Microbiol. Rev. 55:425-436, herein incorporated by reference in its entirety.
  • MTX2 is a 100-kDa toxin.
  • More recently MTX3 has been identified as a separate toxin, though the amino acid sequence of MTX3 from B. sphaericus is 38% identical to the MTX2 toxin of B. sphaericus SSII-1 (Liu, et al. (1996) Appl. Environ. Microbiol. 62: 2174-2176).
  • novel isolated nucleotide sequences that confer pesticidal activity. These isolated nucleotide sequences encode polypeptides with homology to known delta-endotoxins or binary toxins. Also provided are the amino acid sequences of the pesticidal proteins. The protein resulting from translation of this gene allows cells to control or kill pests that ingest it.
  • nucleic acid molecule is intended to include DNA molecules (e.g., recombinant DNA, cDNA or genomic DNA) and RNA molecules (e.g., mRNA) and analogs of the DNA or RNA generated using nucleotide analogs.
  • the nucleic acid molecule can be single-stranded or double-stranded, but preferably is double-stranded DNA.
  • nucleic acid molecule or protein is substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized.
  • an “isolated” nucleic acid is free of sequences (preferably protein encoding sequences) that naturally flank the nucleic acid (i.e., sequences located at the 5′ and 3′ ends of the nucleic acid) in the genomic DNA of the organism from which the nucleic acid is derived.
  • isolated when used to refer to nucleic acid molecules excludes isolated chromosomes.
  • the isolated nucleic acid molecule encoding a pesticidal protein can contain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb, or 0.1 kb of nucleotide sequences that naturally flank the nucleic acid molecule in genomic DNA of the cell from which the nucleic acid is derived.
  • a pesticidal protein that is substantially free of cellular material includes preparations of protein having less than about 30%, 20%, 10%, or 5% (by dry weight) of non-pesticidal protein (also referred to herein as a “contaminating protein”).
  • Nucleotide sequences encoding the proteins of the present invention include the sequence set forth in SEQ ID NO:1, 3, 5, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, or 60, or the nucleotide sequence deposited in a bacterial host as Accession No. NRRL B-30961, B-30955, B-30956, B-30957, B-30958, B-30942, B-30939, B-30941, B-50047, B-50047, B-30959, B-30960, B-30943, B-50048, or B-50048, and variants, fragments, and complements thereof.
  • complement is intended a nucleotide sequence that is sufficiently complementary to a given nucleotide sequence such that it can hybridize to the given nucleotide sequence to thereby form a stable duplex.
  • the corresponding amino acid sequence for the pesticidal protein encoded by this nucleotide sequence are set forth in SEQ ID NO:2, 4, 6, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37 or 61.
  • nucleic acid molecules that are fragments of these nucleotide sequences encoding pesticidal proteins are also encompassed by the present invention.
  • fragment is intended a portion of the nucleotide sequence encoding a pesticidal protein.
  • a fragment of a nucleotide sequence may encode a biologically active portion of a pesticidal protein, 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 nucleotide sequence encoding a pesticidal protein comprise at least about 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1350, 1400 contiguous nucleotides, or up to the number of nucleotides present in a full-length nucleotide sequence encoding a pesticidal protein disclosed herein (for example, 957 nucleotides for SEQ ID NO:1; 927 nucleotides for SEQ ID NO:3, 1017 nucleotides for SEQ ID NO:5; 1422 nucleotides for SEQ ID NO:8, 1053 nucleotides for SEQ ID NO:10; 1062 nucleotides for SEQ ID NO:12, 942 nucleotides for SEQ ID NO:14, etc.) depending upon the intended use.
  • nucleotide sequences of the present invention will encode protein fragments that retain the biological activity of the pesticidal protein and, hence, retain pesticidal activity.
  • contains activity is intended that the fragment will have at least about 30%, at least about 50%, at least about 70%, 80%, 90%, 95% or higher of the pesticidal activity of the pesticidal protein.
  • Methods for measuring pesticidal 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 fragment of a nucleotide sequence encoding a pesticidal protein that encodes a biologically active portion of a protein of the invention will encode at least about 15, 25, 30, 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, 450 contiguous amino acids, or up to the total number of amino acids present in a full-length pesticidal protein of the invention (for example, 318 amino acids for SEQ ID NO:2, 308 amino acids for SEQ ID NO:4, 338 amino acids for SEQ ID NO:6, 296 amino acids for SEQ ID NO:7, 473 amino acids for SEQ ID NO:9, 351 amino acids for SEQ ID NO:11, 353 amino acids for SEQ ID NO:13, and 314 amino acids for SEQ ID NO:15, etc.).
  • Preferred pesticidal proteins of the present invention are encoded by a nucleotide sequence sufficiently identical to the nucleotide sequence of SEQ ID NO:1, 3, 5, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, or 60.
  • a nucleotide sequence sufficiently identical is intended an amino acid or nucleotide sequence that has at least about 60% or 65% sequence identity, about 70% or 75% sequence identity, about 80% or 85% sequence identity, about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or greater sequence identity compared to a reference sequence using one of the alignment programs described herein using standard parameters.
  • these values can be appropriately adjusted to determine corresponding identity of proteins encoded by two nucleotide sequences by taking into account codon degeneracy, amino acid similarity, reading frame positioning, and the like.
  • the sequences are aligned for optimal comparison purposes.
  • the two sequences are the same length.
  • the percent identity between two sequences can be determined using techniques similar to those described below, with or without allowing gaps. In calculating percent identity, typically exact matches are counted.
  • the determination of percent identity between two sequences can be accomplished using a mathematical algorithm.
  • a nonlimiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin and Altschul (1990) Proc. Natl. Acad. Sci. USA 87:2264, modified as in Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-5877. Such an algorithm is incorporated into the BLASTN and BLASTX programs of Altschul et al. (1990) J. Mol. Biol. 215:403.
  • Gapped BLAST in BLAST 2.0
  • PSI-Blast can be used to perform an iterated search that detects distant relationships between molecules. See Altschul et al. (1997) supra.
  • the default parameters of the respective programs e.g., BLASTX and BLASTN
  • Alignment may also be performed manually by inspection.
  • ClustalW compares sequences and aligns the entirety of the amino acid or DNA sequence, and thus can provide data about the sequence conservation of the entire amino acid sequence.
  • the ClustalW algorithm is used in several commercially available DNA/amino acid analysis software packages, such as the ALIGNX module of the Vector NTI Program Suite (Invitrogen Corporation, Carlsbad, Calif.). After alignment of amino acid sequences with ClustalW, the percent amino acid identity can be assessed.
  • GENEDOCTM A non-limiting example of a software program useful for analysis of ClustalW alignments.
  • GENEDOCTM (Karl Nicholas) allows assessment of amino acid (or DNA) similarity and identity between multiple proteins.
  • Another non-limiting example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller (1988) CABIOS 4:11-17. Such an algorithm is incorporated into the ALIGN program (version 2.0), which is part of the GCG Wisconsin Genetics Software Package, Version 10 (available from Accelrys, Inc., 9685 Scranton Rd., San Diego, Calif., USA).
  • ALIGN program version 2.0
  • a PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used.
  • GAP Version 10 which uses the algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48(3):443-453, will be used to determine sequence identity or similarity using the following parameters: % identity and % similarity for a nucleotide sequence using GAP Weight of 50 and Length Weight of 3, and the nwsgapdna.cmp scoring matrix; % identity or % similarity for an amino acid sequence using GAP weight of 8 and length weight of 2, and the BLOSUM62 scoring program. Equivalent programs may also be used.
  • Equivalent program is intended any sequence comparison program that, for any two sequences in question, generates an alignment having identical nucleotide residue matches and an identical percent sequence identity when compared to the corresponding alignment generated by GAP Version 10.
  • the invention also encompasses variant nucleic acid molecules.
  • “Variants” of the pesticidal protein encoding nucleotide sequences include those sequences that encode the pesticidal proteins disclosed herein but that differ conservatively because of the degeneracy of the genetic code as well as those that are sufficiently identical as discussed above.
  • Naturally occurring allelic variants can be identified with the use of well-known molecular biology techniques, such as polymerase chain reaction (PCR) and hybridization techniques as outlined below.
  • Variant nucleotide sequences also include synthetically derived nucleotide sequences that have been generated, for example, by using site-directed mutagenesis but which still encode the pesticidal proteins disclosed in the present invention as discussed below.
  • Variant proteins encompassed by the present invention are biologically active, that is they continue to possess the desired biological activity of the native protein, that is, pesticidal activity.
  • By “retains activity” is intended that the variant will have at least about 30%, at least about 50%, at least about 70%, or at least about 80% of the pesticidal activity of the native protein.
  • Methods for measuring pesticidal 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.
  • variant isolated nucleic acid molecules can be created by introducing one or more nucleotide substitutions, additions, or deletions into the corresponding nucleotide sequence disclosed herein, such that one or more amino acid substitutions, additions or deletions are introduced into the encoded protein. Mutations can be introduced by standard techniques, such as site-directed mutagenesis and PCR-mediated mutagenesis. Such variant nucleotide sequences are also encompassed by the present invention.
  • conservative amino acid substitutions may be made at one or more, predicted, nonessential amino acid residues.
  • a “nonessential” amino acid residue is a residue that can be altered from the wild-type sequence of a pesticidal protein without altering the biological activity, whereas an “essential” amino acid residue is required for biological activity.
  • a “conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined in the art.
  • amino acids with basic side chains e.g., lysine, arginine, histidine
  • acidic side chains e.g., aspartic acid, glutamic acid
  • uncharged polar side chains e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine
  • nonpolar side chains e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan
  • beta-branched side chains e.g., threonine, valine, isoleucine
  • aromatic side chains e.g., tyrosine, phenylalanine, tryptophan, histidine
  • Delta-endotoxins 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 consists of seven alpha helices and is involved in membrane insertion and pore formation.
  • Domain II consists of three beta-sheets arranged in a Greek key configuration, and domain III consists of two antiparallel beta-sheets in “jelly-roll” formation (de Maagd et al., 2001, supra). Domains II and III are involved in receptor recognition and binding, and are therefore considered determinants of toxin specificity.
  • amino acid substitutions may be made in nonconserved regions that retain function. In general, such substitutions would not be made for conserved amino acid residues, or for amino acid residues residing within a conserved motif, where such residues are essential for protein activity. Examples of residues that are conserved and that may be essential for protein activity include, for example, residues that are identical between all proteins contained in an alignment of similar or related toxins to the sequences of the invention (e.g., residues that are identical between all proteins contained in the alignment in FIG. 1, 2 , 3 , or 4 ).
  • residues that are conserved but that may allow conservative amino acid substitutions and still retain activity include, for example, residues that have only conservative substitutions between all proteins contained in an alignment of similar or related toxins to the sequences of the invention (e.g., residues that have only conservative substitutions between all proteins contained in the alignment in FIG. 1, 2 , 3 , or 4 ).
  • residues that have only conservative substitutions between all proteins contained in an alignment of similar or related toxins to the sequences of the invention e.g., residues that have only conservative substitutions between all proteins contained in the alignment in FIG. 1, 2 , 3 , or 4 .
  • functional variants may have minor conserved or nonconserved alterations in the conserved residues.
  • variant nucleotide sequences can be made by introducing mutations randomly along all or part of the coding sequence, such as by saturation mutagenesis, and the resultant mutants can be screened for ability to confer pesticidal activity to identify mutants that retain activity.
  • the encoded protein can be expressed recombinantly, and the activity of the protein can be determined using standard assay techniques.
  • hybridization probes may be genomic DNA fragments, cDNA fragments, RNA fragments, or other oligonucleotides, and may be labeled with a detectable group such as 32 P, or any other detectable marker, such as other radioisotopes, a fluorescent compound, an enzyme, or an enzyme co-factor.
  • Probes for hybridization can be made by labeling synthetic oligonucleotides based on the known pesticidal protein-encoding nucleotide sequence disclosed herein. Degenerate primers designed on the basis of conserved nucleotides or amino acid residues in the nucleotide sequence or encoded amino acid sequence can additionally be used.
  • the probe typically comprises a region of nucleotide sequence that hybridizes under stringent conditions to at least about 12, at least about 25, at least about 50, 75, 100, 125, 150, 175, or 200 consecutive nucleotides of nucleotide sequence encoding a pesticidal protein of the invention or a fragment or variant thereof. Methods for the preparation of probes for hybridization are generally known in the art and are disclosed in Sambrook and Russell, 2001, supra herein incorporated by reference.
  • an entire pesticidal protein sequence disclosed herein, or one or more portions thereof may be used as a probe capable of specifically hybridizing to corresponding pesticidal protein-like sequences and messenger RNAs.
  • probes include sequences that are unique and are preferably at least about 10 nucleotides in length, or at least about 20 nucleotides in length.
  • Such probes may be used to amplify corresponding pesticidal sequences from a chosen organism by PCR. This technique may be used to isolate additional coding sequences from a desired organism or as a diagnostic assay to determine the presence of coding sequences in an organism.
  • Hybridization techniques include hybridization screening of plated DNA libraries (either plaques or colonies; see, for example, Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.).
  • Hybridization of such sequences may be carried out under stringent conditions.
  • stringent conditions or “stringent hybridization conditions” is intended conditions under which a probe will hybridize to its target sequence to a detectably greater degree than to other sequences (e.g., at least 2-fold over background).
  • Stringent conditions are sequence-dependent and will be different in different circumstances.
  • target sequences that are 100% complementary to the probe can be identified (homologous probing).
  • stringency conditions can be adjusted to allow some mismatching in sequences so that lower degrees of similarity are detected (heterologous probing).
  • a probe is less than about 1000 nucleotides in length, preferably less than 500 nucleotides in length.
  • stringent conditions will be those in which the salt concentration is less than about 1.5 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 at least about 30° C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C. for long probes (e.g., greater than 50 nucleotides).
  • Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide.
  • Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37° C., and a wash in 0.5 ⁇ to 1 ⁇ SSC at 55 to 60° C.
  • Exemplary high stringency conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 0.1 ⁇ SSC at 60 to 65° C.
  • wash buffers may comprise about 0.1% to about 1% SDS. Duration of hybridization is generally less than about 24 hours, usually about 4 to about 12 hours.
  • T m 81.5° C.+16.6 (log M)+0.41 (% GC) ⁇ 0.61 (% form) ⁇ 500/L; where M is the molarity of monovalent cations, % GC is the percentage of guanosine and cytosine nucleotides in the DNA, % form is the percentage of formamide in the hybridization solution, and L is the length of the hybrid in base pairs.
  • the T m is the temperature (under defined ionic strength and pH) at which 50% of a complementary target sequence hybridizes to a perfectly matched probe. T m is reduced by about 1° C. for each 1% of mismatching; thus, T m , hybridization, and/or wash conditions can be adjusted to hybridize to sequences of the desired identity. For example, if sequences with >90% identity are sought, the T m can be decreased 10° C.
  • stringent conditions are selected to be about 5° C. lower than the thermal melting point (T m ) for the specific sequence and its complement at a defined ionic strength and pH. However, severely stringent conditions can utilize a hybridization and/or wash at 1, 2, 3, or 4° C.
  • T m thermal melting point
  • moderately stringent conditions can utilize a hybridization and/or wash at 6, 7, 8, 9, or 10° C. lower than the thermal melting point (T m ); low stringency conditions can utilize a hybridization and/or wash at 11, 12, 13, 14, 15, or 20° C. lower than the thermal melting point (T m ).
  • T m thermal melting point
  • Pesticidal proteins are also encompassed within the present invention.
  • pesticidal protein is intended a protein having the amino acid sequence set forth in SEQ ID NO:2, 4, 6, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37 or 61. Fragments, biologically active portions, and variants thereof are also provided, and may be used to practice the methods of the present invention.
  • “Fragments” or “biologically active portions” include polypeptide fragments comprising amino acid sequences sufficiently identical to the amino acid sequence set forth in SEQ ID NO:2, 4, 6, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37 or 61, and that exhibit pesticidal activity (for example, SEQ ID NO:7).
  • a biologically active portion of a pesticidal protein can be a polypeptide that is, for example, 10, 25, 50, 100, 150, 200, 250 or more amino acids in length.
  • Such biologically active portions can be prepared by recombinant techniques and evaluated for pesticidal activity. Methods for measuring pesticidal activity are well known in the art. See, for example, Czapla and Lang (1990) J. Econ. Entomol.
  • a fragment comprises at least 8 contiguous amino acids of SEQ ID NO:2, 4, 6, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37 or 61.
  • the invention encompasses other fragments, however, such as any fragment in the protein greater than about 10, 20, 30, 50, 100, 150, 200, 250, or 300 amino acids.
  • variants proteins or polypeptides having an amino acid sequence that is at least about 60%, 65%, about 70%, 75%, about 80%, 85%, about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to the amino acid sequence of SEQ ID NO:2, 4, 6, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37 or 61.
  • variantants also include polypeptides encoded by a nucleic acid molecule that hybridizes to the nucleic acid molecule of SEQ ID NO:1, 3, 5, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, or 60, or a complement thereof, under stringent conditions.
  • Variants include polypeptides that differ in amino acid sequence due to mutagenesis.
  • Variant proteins encompassed by the present invention are biologically active, that is they continue to possess the desired biological activity of the native protein, that is, retaining pesticidal activity. Methods for measuring pesticidal 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.
  • Bacterial genes such as the axmi genes of this invention, quite often possess multiple methionine initiation codons in proximity to the start of the open reading frame. Often, translation initiation at one or more of these start codons will lead to generation of a functional protein. These start codons can include ATG codons. However, bacteria such as Bacillus sp. also recognize the codon GTG as a start codon, and proteins that initiate translation at GTG codons contain a methionine at the first amino acid. Furthermore, it is not often determined a priori which of these codons are used naturally in the bacterium. Thus, it is understood that use of one of the alternate methionine codons may also lead to generation of pesticidal proteins. These pesticidal proteins are encompassed in the present invention and may be used in the methods of the present invention.
  • Antibodies to the polypeptides of the present invention, or to variants or fragments thereof, are also encompassed. Methods for producing antibodies are well known in the art (see, for example, Harlow and Lane (1988) Antibodies: A Laboratory Manual , Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.; U.S. Pat. No. 4,196,265).
  • DNA sequences of a pesticidal protein 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 a pesticidal protein of the present invention.
  • This protein may be altered in various ways including amino acid substitutions, deletions, truncations, and insertions of one or more amino acids of SEQ ID NO:2, 4, 6, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37 or 61, 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 pesticidal protein can be prepared by mutations in the DNA. This may also be accomplished by one of several forms of mutagenesis and/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 pesticidal activity. However, it is understood that the ability of a pesticidal protein to confer pesticidal activity may be improved by the use of such techniques upon the compositions of this invention. For example, one may express a pesticidal protein in host cells that exhibit high rates of base misincorporation during DNA replication, such as XL-1 Red (Stratagene, La Jolla, Calif.).
  • the DNA for example by preparing plasmid DNA, or by amplifying by PCR and cloning the resulting PCR fragment into a vector
  • culture the pesticidal protein mutations in a non-mutagenic strain and identify mutated genes with pesticidal activity, for example by performing an assay to test for pesticidal activity.
  • 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 and/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 the protein sequence of many proteins at the amino or carboxy terminus without substantially affecting activity.
  • This can include insertions, deletions, or alterations introduced by modern 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.
  • Variant nucleotide and amino acid sequences of the present invention also encompass sequences derived from mutagenic and recombinogenic procedures such as DNA shuffling. With such a procedure, one or more different pesticidal protein coding regions can be used to create a new pesticidal 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) 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.
  • Domain swapping or shuffling is another mechanism for generating altered pesticidal proteins. Domains may be swapped between pesticidal proteins, resulting in hybrid or chimeric toxins 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).
  • a pesticidal sequence of the invention may be provided in an expression cassette for expression in a plant of interest.
  • plant expression cassette is intended a DNA construct that is capable of resulting in the expression of a protein from an open reading frame in a plant cell. Typically these contain a promoter and a coding sequence. Often, such constructs will also contain a 3′ untranslated region. Such constructs may contain a “signal sequence” or “leader sequence” to facilitate co-translational or post-translational transport of the peptide to certain intracellular structures such as the chloroplast (or other plastid), endoplasmic reticulum, or Golgi apparatus.
  • signal sequence is intended a sequence that is known or suspected to result in cotranslational or post-translational peptide transport across the cell membrane. In eukaryotes, this typically involves secretion into the Golgi apparatus, with some resulting glycosylation. Insecticidal toxins of bacteria are often synthesized as protoxins, which are protolytically activated in the gut of the target pest (Chang (1987) Methods Enzymol. 153:507-516). In some embodiments of the present invention, the signal sequence is located in the native sequence, or may be derived from a sequence of the invention.
  • leader sequence is intended any sequence that when translated, results in an amino acid sequence sufficient to trigger co-translational transport of the peptide chain to a subcellular organelle. Thus, this includes leader sequences targeting transport and/or glycosylation by passage into the endoplasmic reticulum, passage to vacuoles, plastids including chloroplasts, mitochondria, and the like.
  • plant transformation vector is intended a DNA molecule that is necessary for efficient transformation of a plant cell. Such a molecule may consist of one or more plant expression cassettes, and may be organized into more than one “vector” DNA molecule.
  • binary vectors are plant transformation vectors that utilize two non-contiguous DNA vectors to encode all requisite cis- and trans-acting functions for transformation of plant cells (Hellens and Mullineaux (2000) Trends in Plant Science 5:446-451).
  • Vector refers to a nucleic acid construct designed for transfer between different host cells.
  • Expression vector refers to a vector that has the ability to incorporate, integrate and express heterologous DNA sequences or fragments in a foreign cell.
  • the cassette will include 5′ and 3′ regulatory sequences operably linked to a sequence of the invention.
  • operably linked is intended a functional linkage between a promoter and a second sequence, wherein the promoter sequence initiates and mediates transcription of the DNA sequence corresponding to the second sequence.
  • operably linked means that the nucleic acid sequences being linked are contiguous and, where necessary to join two protein coding regions, contiguous and in the same reading frame.
  • the cassette may additionally contain at least one additional gene to be cotransformed into the organism. Alternatively, the additional gene(s) can be provided on multiple expression cassettes.
  • Promoter refers to a nucleic acid sequence that functions to direct transcription of a downstream coding sequence.
  • the promoter together with other transcriptional and translational regulatory nucleic acid sequences are necessary for the expression of a DNA sequence of interest.
  • Such an expression cassette is provided with a plurality of restriction sites for insertion of the pesticidal sequence to be under the transcriptional regulation of the regulatory regions.
  • the expression cassette will include in the 5′-3′ direction of transcription, a transcriptional and translational initiation region (i.e., a promoter), a DNA sequence of the invention, and a translational and transcriptional termination region (i.e., termination region) functional in plants.
  • the promoter may be native or analogous, or foreign or heterologous, to the plant host and/or to the DNA sequence of the invention. Additionally, the promoter may be the natural sequence or alternatively a synthetic sequence. Where the promoter is “native” or “homologous” to the plant host, it is intended that the promoter is found in the native plant into which the promoter is introduced. Where the promoter is “foreign” or “heterologous” to the DNA sequence of the invention, it is intended that the promoter is not the native or naturally occurring promoter for the operably linked DNA sequence of the invention.
  • the termination region may be native with the transcriptional initiation region, may be native with the operably linked DNA sequence of interest, may be native with the plant host, or may be derived from another source (i.e., foreign or heterologous to the promoter, the DNA sequence of interest, the plant host, or any combination thereof).
  • Convenient termination regions are available from the Ti-plasmid of A. tumefaciens , such as the octopine synthase and nopaline synthase termination regions. See also Guerineau et al. (1991) Mol. Gen. Genet. 262:141-144; Proudfoot (1991) Cell 64:671-674; Sanfacon et al. (1991) Genes Dev.
  • the gene(s) may be optimized for increased expression in the transformed host cell. That is, the genes can be synthesized using host cell-preferred codons for improved expression, or may be synthesized using codons at a host-preferred codon usage frequency. Generally, the GC content of the gene will be increased. See, for example, Campbell and Gowri (1990) Plant Physiol. 92:1-11 for a discussion of host-preferred codon usage. Methods are available in the art for synthesizing plant-preferred genes. See, for example, U.S. Pat. Nos. 5,380,831, and 5,436,391, and Murray et al. (1989) Nucleic Acids Res. 17:477-498, herein incorporated by reference.
  • the pesticidal protein is targeted to the chloroplast for expression.
  • the expression cassette will additionally contain a nucleic acid encoding a transit peptide to direct the pesticidal protein to the chloroplasts.
  • transit peptides are known in the art. See, for example, Von Heijne et al. (1991) Plant Mol. Biol. Rep. 9:104-126; Clark et al. (1989) J. Biol. Chem. 264:17544-17550; Della-Cioppa et al. (1987) Plant Physiol. 84:965-968; Romer et al. (1993) Biochem. Biophys. Res. Commun. 196:1414-1421; and Shah et al. (1986) Science 233:478-481.
  • the pesticidal gene to be targeted to the chloroplast may be optimized for expression in the chloroplast to account for differences in codon usage between the plant nucleus and this organelle.
  • the nucleic acids of interest may be synthesized using chloroplast-preferred codons. See, for example, U.S. Pat. No. 5,380,831, herein incorporated by reference.
  • Methods of the invention involve introducing a nucleotide construct into a plant.
  • introducing is intended to present to the plant the nucleotide construct in such a manner that the construct gains access to the interior of a cell of the plant.
  • the methods of the invention do not require that a particular method for introducing a nucleotide construct to a plant is used, only that the nucleotide construct gains access to the interior of at least one cell of the plant.
  • Methods for introducing nucleotide constructs into plants are known in the art including, but not limited to, stable transformation methods, transient transformation methods, and virus-mediated methods.
  • plant is intended whole plants, plant organs (e.g., leaves, stems, roots, etc.), seeds, plant cells, propagules, embryos and progeny of the same.
  • Plant cells can be differentiated or undifferentiated (e.g. callus, suspension culture cells, protoplasts, leaf cells, root cells, phloem cells, pollen).
  • Transgenic plants or “transformed plants” or “stably transformed” plants or cells or tissues refers to plants that have incorporated or integrated exogenous nucleic acid sequences or DNA fragments into the plant cell. These nucleic acid sequences include those that are exogenous, or not present in the untransformed plant cell, as well as those that may be endogenous, or present in the untransformed plant cell. “Heterologous” generally refers to the nucleic acid sequences that are not endogenous to the cell or part of the native genome in which they are present, and have been added to the cell by infection, transfection, microinjection, electroporation, microprojection, or the like.
  • Transformation of plant cells can be accomplished by one of several techniques known in the art.
  • the pesticidal gene of the invention may be modified to obtain or enhance expression in plant cells.
  • a construct that expresses such a protein would contain a promoter to drive transcription of the gene, as well as a 3′ untranslated region to allow transcription termination and polyadenylation.
  • the organization of such constructs is well known in the art.
  • the gene can be engineered to contain a signal peptide to facilitate transfer of the peptide to the endoplasmic reticulum.
  • This “plant expression cassette” will be inserted into a “plant transformation vector”.
  • This plant transformation vector may be comprised of one or more DNA vectors needed for achieving plant transformation.
  • DNA vectors needed for achieving plant transformation.
  • Binary vectors as well as vectors with helper plasmids are most often used for Agrobacterium -mediated transformation, where the size and complexity of DNA segments needed to achieve efficient transformation is quite large, and it is advantageous to separate functions onto separate DNA molecules.
  • Binary vectors typically contain a plasmid vector that contains the cis-acting sequences required for T-DNA transfer (such as left border and right border), a selectable marker that is engineered to be capable of expression in a plant cell, and a “gene of interest” (a gene engineered to be capable of expression in a plant cell for which generation of transgenic plants is desired). Also present on this plasmid vector are sequences required for bacterial replication. The cis-acting sequences are arranged in a fashion to allow efficient transfer into plant cells and expression therein. For example, the selectable marker gene and the pesticidal gene are located between the left and right borders.
  • a second plasmid vector contains the trans-acting factors that mediate T-DNA transfer from Agrobacterium to plant cells.
  • This plasmid often contains the virulence functions (Vir genes) that allow infection of plant cells by Agrobacterium , and transfer of DNA by cleavage at border sequences and vir-mediated DNA transfer, as is understood in the art (Hellens and Mullineaux (2000) Trends in Plant Science 5:446-451).
  • Several types of Agrobacterium strains e.g. LBA4404, GV3101, EHA101, EHA105, etc.
  • the second plasmid vector is not necessary for transforming the plants by other methods such as microprojection, microinjection, electroporation, polyethylene glycol, etc.
  • plant transformation methods involve transferring heterologous DNA into target plant cells (e.g. immature or mature embryos, suspension cultures, undifferentiated callus, protoplasts, etc.), followed by applying a maximum threshold level of appropriate selection (depending on the selectable marker gene) to recover the transformed plant cells from a group of untransformed cell mass.
  • Explants are typically transferred to a fresh supply of the same medium and cultured routinely.
  • the transformed cells are differentiated into shoots after placing on regeneration medium supplemented with a maximum threshold level of selecting agent.
  • the shoots are then transferred to a selective rooting medium for recovering rooted shoot or plantlet.
  • the transgenic plantlet then grows into a mature plant and produces fertile seeds (e.g. Hiei et al.
  • Transformation protocols as well as protocols for introducing nucleotide sequences into plants may vary depending on the type of plant or plant cell, i.e., monocot or dicot, targeted for transformation.
  • Generation of transgenic plants may be performed by one of several methods, including, but not limited to, microinjection, electroporation, direct gene transfer, introduction of heterologous DNA by Agrobacterium into plant cells ( Agrobacterium -mediated transformation), bombardment of plant cells with heterologous foreign DNA adhered to particles, ballistic particle acceleration, aerosol beam transformation (U.S. Published Application No. 20010026941; U.S. Pat. No. 4,945,050; International Publication No. WO 91/00915; U.S. Published Application No. 2002015066), Lec1 transformation, and various other non-particle direct-mediated methods to transfer DNA.
  • plastid transformation can be accomplished by transactivation of a silent plastid-borne transgene by tissue-preferred expression of a nuclear-encoded and plastid-directed RNA polymerase.
  • tissue-preferred expression of a nuclear-encoded and plastid-directed RNA polymerase Such a system has been reported in McBride et al. (1994) Proc. Natl. Acad. Sci. USA 91:7301-7305.
  • heterologous foreign DNA Following integration of heterologous foreign DNA into plant cells, one then applies a maximum threshold level of appropriate selection in the medium to kill the untransformed cells and separate and proliferate the putatively transformed cells that survive from this selection treatment by transferring regularly to a fresh medium. By continuous passage and challenge with appropriate selection, one identifies and proliferates the cells that are transformed with the plasmid vector. Molecular and biochemical methods can then be used to confirm the presence of the integrated heterologous gene of interest into the genome of the transgenic plant.
  • the cells that have been transformed may be grown into plants in accordance with conventional ways. See, for example, McCormick et al. (1986) Plant Cell Reports 5:81-84. These plants may then be grown, and either pollinated with the same transformed strain or different strains, and the resulting hybrid having constitutive expression of the desired phenotypic characteristic identified. Two or more generations may be grown to ensure that expression of the desired phenotypic characteristic is stably maintained and inherited and then seeds harvested to ensure expression of the desired phenotypic characteristic has been achieved. In this manner, the present invention provides transformed seed (also referred to as “transgenic seed”) having a nucleotide construct of the invention, for example, an expression cassette of the invention, stably incorporated into their genome.
  • heterologous foreign DNA Following introduction of heterologous foreign DNA into plant cells, the transformation or integration of heterologous gene in the plant genome is confirmed by various methods such as analysis of nucleic acids, proteins and metabolites associated with the integrated gene.
  • PCR analysis is a rapid method to screen transformed cells, tissue or shoots for the presence of incorporated gene at the earlier stage before transplanting into the soil (Sambrook and Russell (2001) Molecular Cloning: A Laboratory Manual . Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.). PCR is carried out using oligonucleotide primers specific to the gene of interest or Agrobacterium vector background, etc.
  • Plant transformation may be confirmed by Southern blot analysis of genomic DNA (Sambrook and Russell, 2001, supra). In general, total DNA is extracted from the transformant, digested with appropriate restriction enzymes, fractionated in an agarose gel and transferred to a nitrocellulose or nylon membrane. The membrane or “blot” is then probed with, for example, radiolabeled 32 P target DNA fragment to confirm the integration of introduced gene into the plant genome according to standard techniques (Sambrook and Russell, 2001, supra).
  • RNA is isolated from specific tissues of transformant, fractionated in a formaldehyde agarose gel, and blotted onto a nylon filter according to standard procedures that are routinely used in the art (Sambrook and Russell, 2001, supra). Expression of RNA encoded by the pesticidal gene is then tested by hybridizing the filter to a radioactive probe derived from a pesticidal gene, by methods known in the art (Sambrook and Russell, 2001, supra).
  • Western blot, biochemical assays and the like may be carried out on the transgenic plants to confirm the presence of protein encoded by the pesticidal gene by standard procedures (Sambrook and Russell, 2001, supra) using antibodies that bind to one or more epitopes present on the pesticidal protein.
  • Methods described above by way of example may be utilized to generate transgenic plants, but the manner in which the transgenic plant cells are generated is not critical to this invention. Methods known or described in the art such as Agrobacterium -mediated transformation, biolistic transformation, and non-particle-mediated methods may be used at the discretion of the experimenter.
  • Plants expressing a pesticidal protein may be isolated by common methods described in the art, for example by transformation of callus, selection of transformed callus, and regeneration of fertile plants from such transgenic callus. In such process, one may use any gene as a selectable marker so long as its expression in plant cells confers ability to identify or select for transformed cells.
  • markers have been developed for use with plant cells, such as resistance to chloramphenicol, the aminoglycoside G418, hygromycin, or the like.
  • Other genes that encode a product involved in chloroplast metabolism may also be used as selectable markers.
  • genes that provide resistance to plant herbicides such as glyphosate, bromoxynil, or imidazolinone may find particular use.
  • Such genes have been reported (Stalker et al. (1985) J. Biol. Chem. 263:6310-6314 (bromoxynil resistance nitrilase gene); and Sathasivan et al. (1990) Nucl. Acids Res. 18:2188 (AHAS imidazolinone resistance gene).
  • genes disclosed herein are useful as markers to assess transformation of bacterial or plant cells.
  • Methods for detecting the presence of a transgene in a plant, plant organ (e.g., leaves, stems, roots, etc.), seed, plant cell, propagule, embryo or progeny of the same are well known in the art.
  • the presence of the transgene is detected by testing for pesticidal activity.
  • Fertile plants expressing a pesticidal protein may be tested for pesticidal activity, and the plants showing optimal activity selected for further breeding. Methods are available in the art to assay for pest 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.
  • the present invention may be used for transformation of any plant species, including, but not limited to, monocots and dicots.
  • plants of interest include, but are not limited to, corn (maize), sorghum , wheat, sunflower, tomato, crucifers, peppers, potato, cotton, rice, soybean, sugarbeet, sugarcane, tobacco, barley, and oilseed rape, Brassica sp., alfalfa, rye, millet, safflower, peanuts, sweet potato, cassaya, coffee, coconut, pineapple, citrus trees, cocoa, tea, banana, avocado, fig, guava, mango, olive, papaya, cashew, macadamia, almond, oats, vegetables, ornamentals, and conifers.
  • Vegetables include, but are not limited to, tomatoes, lettuce, green beans, lima beans, peas, and members of the genus Curcumis such as cucumber, cantaloupe, and musk melon.
  • Ornamentals include, but are not limited to, azalea, hydrangea, hibiscus, roses, tulips, daffodils, petunias, carnation, poinsettia, and chrysanthemum.
  • plants of the present invention are crop plants (for example, maize, sorghum , wheat, sunflower, tomato, crucifers, peppers, potato, cotton, rice, soybean, sugarbeet, sugarcane, tobacco, barley, oilseed rape, etc.).
  • crop plants for example, maize, sorghum , wheat, sunflower, tomato, crucifers, peppers, potato, cotton, rice, soybean, sugarbeet, sugarcane, tobacco, barley, oilseed rape, etc.
  • Bacillus strains containing a nucleotide sequence of the present invention, or a variant thereof, or the microorganisms that have been genetically altered to contain a pesticidal gene and protein may be used for protecting agricultural crops and products from pests.
  • whole, i.e., unlysed, cells of a toxin (pesticide)-producing organism are treated with reagents that prolong the activity of the toxin produced in the cell when the cell is applied to the environment of target pest(s).
  • the pesticide is produced by introducing a pesticidal gene into a cellular host. Expression of the pesticidal gene results, directly or indirectly, in the intracellular production and maintenance of the pesticide. In one aspect of this invention, these cells are then treated under conditions that prolong the activity of the toxin produced in the cell when the cell is applied to the environment of target pest(s). The resulting product retains the toxicity of the toxin.
  • These naturally encapsulated pesticides may then be formulated in accordance with conventional techniques for application to the environment hosting a target pest, e.g., soil, water, and foliage of plants. See, for example EPA 0192319, and the references cited therein. Alternatively, one may formulate the cells expressing a gene of this invention such as to allow application of the resulting material as a pesticide.
  • the active ingredients of the present invention are normally applied in the form of compositions and can be applied to the crop area or plant to be treated, simultaneously or in succession, with other compounds.
  • These compounds can be fertilizers, weed killers, cryoprotectants, surfactants, detergents, pesticidal soaps, dormant oils, polymers, and/or time-release or biodegradable carrier formulations that permit long-term dosing of a target area following a single application of the formulation.
  • Suitable carriers and adjuvants can be solid or liquid and correspond to the substances ordinarily employed in formulation technology, e.g. natural or regenerated mineral substances, solvents, dispersants, wetting agents, tackifiers, binders or fertilizers.
  • the formulations may be prepared into edible “baits” or fashioned into pest “traps” to permit feeding or ingestion by a target pest of the pesticidal formulation.
  • Methods of applying an active ingredient of the present invention or an agrochemical composition of the present invention that contains at least one of the pesticidal proteins produced by the bacterial strains of the present invention include leaf application, seed coating and soil application. The number of applications and the rate of application depend on the intensity of infestation by the corresponding pest.
  • the composition may be formulated as a powder, dust, pellet, granule, spray, emulsion, colloid, solution, or such like, and may be prepared by such conventional means as desiccation, lyophilization, homogenation, extraction, filtration, centrifugation, sedimentation, or concentration of a culture of cells comprising the polypeptide.
  • the polypeptide may be present in a concentration of from about 1% to about 99% by weight.
  • Lepidopteran, dipteran, or coleopteran pests may be killed or reduced in numbers in a given area by the methods of the invention, or may be prophylactically applied to an environmental area to prevent infestation by a susceptible pest.
  • the pest ingests, or is contacted with, a pesticidally-effective amount of the polypeptide.
  • pesticidally-effective amount is intended an amount of the pesticide that is able to bring about death to at least one pest, or to noticeably reduce pest growth, feeding, or normal physiological development.
  • the formulations may also vary with respect to climatic conditions, environmental considerations, and/or frequency of application and/or severity of pest infestation.
  • the pesticide compositions described may be made by formulating either the bacterial cell, crystal and/or spore suspension, or isolated protein component with the desired agriculturally-acceptable carrier.
  • the compositions may be formulated prior to administration in an appropriate means such as lyophilized, freeze-dried, desiccated, or in an aqueous carrier, medium or suitable diluent, such as saline or other buffer.
  • the formulated compositions may be in the form of a dust or granular material, or a suspension in oil (vegetable or mineral), or water or oil/water emulsions, or as a wettable powder, or in combination with any other carrier material suitable for agricultural application.
  • Suitable agricultural carriers can be solid or liquid and are well known in the art.
  • agriculturally-acceptable carrier covers all adjuvants, inert components, dispersants, surfactants, tackifiers, binders, etc. that are ordinarily used in pesticide formulation technology; these are well known to those skilled in pesticide formulation.
  • the formulations may be mixed with one or more solid or liquid adjuvants and prepared by various means, e.g., by homogeneously mixing, blending and/or grinding the pesticidal composition with suitable adjuvants using conventional formulation techniques. Suitable formulations and application methods are described in U.S. Pat. No. 6,468,523, herein incorporated by reference.
  • Pests includes but is not limited to, insects, fungi, bacteria, nematodes, mites, ticks, and the like.
  • Insect pests include insects selected from the orders Coleoptera, Diptera, Hymenoptera, Lepidoptera, Mallophaga, Homoptera, Hemiptera, Orthroptera, Thysanoptera, Dermaptera, Isoptera, Anoplura, Siphonaptera, Trichoptera, etc., particularly Coleoptera, Lepidoptera, and Diptera.
  • the order Coleoptera includes the suborders Adephaga and Polyphaga.
  • Suborder Adephaga includes the superfamilies Caraboidea and Gyrinoidea
  • suborder Polyphaga includes the superfamilies Hydrophiloidea, Staphylinoidea, Cantharoidea, Cleroidea, Elateroidea, Dascilloidea, Dryopoidea, Byrrhoidea, Cucujoidea, Meloidea, Mordelloidea, Tenebrionoidea, Bostrichoidea, Scarabaeoidea, Cerambycoidea, Chrysomeloidea, and Curculionoidea.
  • Superfamily Caraboidea includes the families Cicindelidae, Carabidae, and Dytiscidae.
  • Superfamily Gyrinoidea includes the family Gyrinidae.
  • Superfamily Hydrophiloidea includes the family Hydrophilidae.
  • Superfamily Staphylinoidea includes the families Silphidae and Staphylinidae.
  • Superfamily Cantharoidea includes the families Cantharidae and Lampyridae.
  • Superfamily Cleroidea includes the families Cleridae and Dermestidae.
  • Superfamily Elateroidea includes the families Elateridae and Buprestidae.
  • Superfamily Cucujoidea includes the family Coccinellidae.
  • Superfamily Meloidea includes the family Meloidae.
  • Superfamily Tenebrionoidea includes the family Tenebrionidae.
  • Superfamily Scarabaeoidea includes the families Passalidae and Scarabaeidae.
  • Superfamily Cerambycoidea includes the family Cerambycidae.
  • Superfamily Chrysomeloidea includes the family Chrysomelidae.
  • Superfamily Curculionoidea includes the families Curculionidae and Scolytidae.
  • the order Diptera includes the Suborders Nematocera, Brachycera, and Cyclorrhapha.
  • Suborder Nematocera includes the families Tipulidae, Psychodidae, Culicidae, Ceratopogonidae, Chironomidae, Simuliidae, Bibionidae, and Cecidomyiidae.
  • Suborder Brachycera includes the families Stratiomyidae, Tabanidae, Therevidae, Asilidae, Mydidae, Bombyliidae, and Dolichopodidae.
  • Suborder Cyclorrhapha includes the Divisions Aschiza and Aschiza.
  • Division Aschiza includes the families Phoridae, Syrphidae, and Conopidae.
  • Division Aschiza includes the Sections Acalyptratae and Calyptratae.
  • Section Acalyptratae includes the families Otitidae, Tephritidae, Agromyzidae, and Drosophilidae.
  • Section Calyptratae includes the families Hippoboscidae, Oestridae, Tachinidae, Anthomyiidae, Muscidae, Calliphoridae, and Sarcophagidae.
  • the order Lepidoptera includes the families Papilionidae, Pieridae, Lycaenidae, Nymphalidae, Danaidae, Satyridae, Hesperiidae, Sphingidae, Saturniidae, Geometridae, Arctiidae, Noctuidae, Lymantriidae, Sesiidae, and Tineidae.
  • Insect pests of the invention for the major crops include: Maize: Ostrinia nubilalis , European corn borer; Agrotis ipsilon , black cutworm; Helicoverpa zea , corn earworm; Spodoptera frugiperda , fall armyworm; Diatraea grandiosella , southwestern corn borer; Elasmopalpus lignosellus , lesser cornstalk borer; Diatraea saccharalis , surgarcane borer; Diabrotica virgifera , western corn rootworm; Diabrotica longicornis barberi, northern corn rootworm; Diabrotica undecimpunctata howardi, southern corn rootworm; Melanotus spp., wireworms; Cyclocephala borealis , northern masked chafer (white grub); Cyclocephala immaculata , southern masked chafer (white grub); Popillia japonica , Japanese beet
  • Nematodes include parasitic nematodes such as root-knot, cyst, and lesion nematodes, including Heterodera spp., Meloidogyne spp., and Globodera spp.; particularly members of the cyst nematodes, including, but not limited to, Heterodera glycines (soybean cyst nematode); Heterodera schachtii (beet cyst nematode); Heterodera avenae (cereal cyst nematode); and Globodera rostochiensis and Globodera pailida (potato cyst nematodes).
  • Lesion nematodes include Pratylenchus spp.
  • Methods for increasing plant yield comprise introducing into a plant or plant cell a polynucleotide comprising a pesticidal sequence disclosed herein.
  • the “yield” of the plant refers to the quality and/or quantity of biomass produced by the plant.
  • biomass is intended any measured plant product.
  • An increase in biomass production is any improvement in the yield of the measured plant product.
  • Increasing plant yield has several commercial applications. For example, increasing plant leaf biomass may increase the yield of leafy vegetables for human or animal consumption. Additionally, increasing leaf biomass can be used to increase production of plant-derived pharmaceutical or industrial products.
  • An increase in yield can comprise any statistically significant increase including, but not limited to, at least a 1% increase, at least a 3% increase, at least a 5% increase, at least a 10% increase, at least a 20% increase, at least a 30%, at least a 50%, at least a 70%, at least a 100% or a greater increase in yield compared to a plant not expressing the pesticidal sequence.
  • strains ATX14759, ATX14875, ATX13026, ATX13002, ATX9387, ATX13045, ATX21738, ATX14833, ATX1489, ATX15398 and ATX12972 were selected for analysis. Pure cultures of each strain were grown in large quantities of rich media. The cultures were centrifuged to harvest the cell pellet. The cell pellet was then prepared by treatment with SDS by methods known in the art, resulting in breakage of the cell wall and release of DNA. Proteins and large genomic DNA were then precipitated by a high salt concentration. The plasmid DNA was then precipitated with ethanol. In several instances, the plasmid DNA was separated from any remaining chromosomal DNA by high-speed centrifugation through a cesium chloride gradient. Alternatively, the plasmid DNA was purified by binding to a resin, as known in the art. For each strain, the quality of the DNA was checked by visualization on an agarose gel by methods known in the art.
  • DNA libraries were prepared from the plasmid DNA or each strain. This may be achieved in many ways as known in the art. For, example, the purified plasmid DNA can be sheared into 5-10 kb sized fragments and the 5′ and 3′ single stranded overhangs repaired using T4 DNA polymerase and Klenow fragment in the presence of all four dNTPs, as known in the art. Phosphates can then be attached to the 5′ ends by treatment with T4 polynucleotide kinase, as known in the art. The repaired DNA fragments can then be ligated overnight into a standard high copy vector (i.e. pBLUESCRIPTTM SK+), suitably prepared to accept the inserts as known in the art (for example by digestion with a restriction enzyme producing blunt ends).
  • pBLUESCRIPTTM SK+ a standard high copy vector
  • the quality of the resulting DNA libraries was analyzed by digesting a subset of clones with a restriction enzyme known to have a cleavage site flanking the cloning site. A high percentage of clones were determined to contain inserts, ideally with an average insert size of 5-6 kb.
  • colonies were grown in a rich broth in 2 ml 96-well blocks overnight at 37° C., typically at a shaking speed of 350 rpm.
  • the blocks were centrifuged to harvest the cells to the bottom of the block.
  • the blocks were then prepared by standard alkaline lysis prep in a high throughput format.
  • the end sequences of clones from this library were then determined for a large number of clones from each block in the following manner:
  • the DNA sequence of each clone chosen for analysis was determined using the fluorescent dye terminator sequencing technique (Applied Biosystems), by methods known in the art using an automated DNA sequencing machine, and standard oligonucleotide primers that anneal to the plasmid vector in the region flanking the insert.
  • DNA sequences obtained were compiled into an assembly project and aligned together to form contigs. This can be done efficiently using a computer program, such as Vector NTI, or alternatively by using the Phred/Phrap suite of DNA alignment and analysis programs. These contigs, along with any individual read that may not have been added to a contig, were compared to a compiled database of all classes of known pesticidal genes. Contigs or individual reads identified as having identity to a known endotoxin or pesticidal gene were analyzed further.
  • clone pAX2558 was found to contain an open reading frame with homology to “cry” type delta-endotoxins. This open reading frame was designated as axmi-037 (SEQ ID NO:16). Inspection of the axmi-037 open reading frame suggests that more than one start codon may be present. The two predicted start codons are the ATG codon beginning at nucleotide position 1 of SEQ ID NO:16, and a downstream ATG codon (represented by SEQ ID NO:18).
  • the ATG at nucleotide 77 of SEQ ID NO:16 has a ribosome binding site sequence (5′-G-G-A-G-G-3′), located at nucleotide positions 63-67 of SEQ ID NO:16. Based on the presence of this strong ribosome binding consensus sequence immediately upstream of this second start site, and the homology of the two predicted proteins to other endotoxins, the translation product of the downstream start site is herein designated AXMI-037 (SEQ ID NO:19). The longer translation product, beginning at the ATG at nucleotide position 1 of SEQ ID NO:16, is designated AXMI-37-2 (and set forth in SEQ ID NO:17).
  • pAX2558 was deposited with the ARS Patent Strain Collection on Jun. 15, 2006, and assigned NRRL B-30939. AXMI-37-2 exhibits 60% amino acid identity to the Cry7Aa1 endotoxin.
  • the C-terminal region of AXMI-019 (starting at approximately amino acid 123 of SEQ ID NO:11) was found to have low homology to a class of toxins including Bacillus thuringiensis serovar darmstadiensis Cry14-4 toxin (SEQ ID NO:42; encoded by GENBANK® ID AAV70918.1), and the Bacillus sphaericus MTX2 protein (SEQ ID NO:16, GENBANK® ID AAC44124.1).
  • AXMI-011 was found to have low homology to a class of toxins including MTX2 (SEQ ID NO:16); AXMI-015 was found to have low homology (about 35% amino acid identify over 178 amino acids) to a mosquitocidal toxin from Bacillus thuringiensis israelensis RBTH — 02046 (SEQ ID NO:41, GENBANK® ID gi/75761628:1-79; AXMI-012 was found to have homology (29% over 217 amino acids) to a class of toxins including the p42 binary toxin of Bacillus sphaericus (SEQ ID NO:39; GENBANK® ID CAA73761).
  • axmi-011 Inspection of the axmi-011 coding region reveals the existence of an alternate translational start site 12 nucleotides upstream of the ATG start of axmi-011.
  • This open reading frame contains a 5′ extension of the following twelve nucleotides 5′-G-T-G-A-T-G-A-A-A-A-A-3′ (SEQ ID NO:59) immediately upstream and adjacent to the axmi-11 open reading frame.
  • This open reading frame is herein designated as axmi-011(long) (SEQ ID NO:60).
  • Translation of axmi-011 utilizing the putative GTG start would result in a modified AXMI-011 protein that contains an N-terminal extension of four amino acids (amino acid residues 1 through 4 of SEQ ID NO:61).
  • a plasmid was found to contain an open reading frame with homology to pesticidal toxins. This open reading frame was designated as axmi-032 (SEQ ID NO:12), and the encoded protein was designated AXMI-032 (SEQ ID NO:13).
  • GenPept database By searching of public databases of protein sequences, such as the GenPept database, AXMI-032 was found to have homology to a class of toxins including a presumed binary toxin from Bacillus thuringiensis (SEQ ID NO:43; GENBANK® Accession No. CAD30104.1) which is a possible two-domain toxin from Bacillus thuringiensis serovar israelensis.
  • the insecticidal AXMI-013 gene is amplified by PCR and cloned into the Bacillus expression vector pAX916 by methods well known in the art. The resulting clone is assayed for expression of AXMI-013 protein after transformation into cells of a cry( ⁇ ) Bacillus thuringiensis strain.
  • a Bacillus strain containing the axmi-013 clone and expressing the AXMI-013 insecticidal protein is grown in, for example, CYS media (10 g/l Bacto-casitone; 3 g/l yeast extract; 6 g/l KH 2 PO 4 ; 14 g/l K 2 HPO 4 ; 0.5 mM MgSO 4 ; 0.05 mM MnCl 2 ; 0.05 mM FeSO 4 ), until sporulation is evident by microscopic examination. Samples are prepared, and analyzed by polyacrylamide gel electrophoresis (PAGE). AXMI-013 is tested for insecticidal activity in bioassays against important insect pests.
  • CYS media 10 g/l Bacto-casitone; 3 g/l yeast extract; 6 g/l KH 2 PO 4 ; 14 g/l K 2 HPO 4 ; 0.5 mM MgSO 4 ; 0.05 mM MnCl 2 ;
  • AXMI-013 (SEQ ID NO:6)
  • the N-terminus of the full-length AXMI-013 protein may comprise a signal peptide for secretion.
  • the predicted site of cleavage was estimated to be between the alanine at position 27 and lysine at position 28 of SEQ ID NO:6.
  • MTX3 (SEQ ID NO:40) is predicted to possess a secretion signal peptide at its N-terminus (Liu, et al. (1996) Appl. Environ. Microbiol. 62:2174-2176).
  • the expressed AXMI-013 protein was excised from a polyacrylamide gel and subjected to N-terminal sequence analysis as known in the art.
  • the N-terminal sequence identified by this analysis corresponded to a N-terminal truncation of the AXMI-013 protein, resulting in a truncated peptide with an N-terminus corresponding to the glutamine (Q) at amino acid position 40 of SEQ ID NO:6.
  • This truncated protein is referred to herein as AXMI-013(Q), and the amino acid sequence of this protein is provided in SEQ ID NO:7.
  • prediction of the exact site of cleavage is somewhat difficult.
  • AXMI-013 is further processed after initial cleavage at amino acid positions 27/28, or AXMI-013 has a novel secretion signal.
  • AXMI-013 has a novel secretion signal.
  • one skilled in the art may make gene fusion constructs utilizing (1) a heterologous protein and (2) using increasing length portions of AXMI-013.
  • a plasmid clone was found to contain an open reading frame with homology to “cry” type delta-endotoxins. This open reading frame was designated as axmi-023 (SEQ ID NO:30), and the encoded protein was designated AXMI-023 (SEQ ID NO:31).
  • BLAST search of the non-redundant ‘nr’ database demonstrates that AXMI-023 has low amino acid identity (less than 30% amino acid identity) with the VIP2 protein toxin, as well as several other presumed or known toxins. (GENBANK® Accession No. AA086513.1, SEQ ID NO:55)
  • a plasmid clone was found to contain an open reading frame with homology to “cry” type delta-endotoxins. This open reading frame was designated as axmi-041 (SEQ ID NO:32), and the encoded protein was designated AXMI-041 (SEQ ID NO:33).
  • pAX4310 was deposited with the ARS Patent Strain Collection on Jun. 15, 2006, and assigned NRRL B-30943.
  • AXMI-041 is 21% identical to AXMI-023, and similarly exhibits low amino acid identity (less than 30% amino acid identity) with the VIP2 protein toxin, as well as several other presumed or known toxins.
  • FIG. 4 shows an alignment of AXMI-023 with the Vip2 pesticidal protein (SEQ ID NO:55), and several related toxins.
  • AXMI-041 also shows homology with this class of toxins.
  • AXMI-022 Defines a Novel Class of Pesticidal Proteins
  • a plasmid clone was found to contain an open reading frame with homology to known insect toxins. This open reading frame was designated as axmi-022 (SEQ ID NO:28), and the encoded protein was designated AXMI-022 (SEQ ID NO:29).
  • AXMI-022 The amino acid sequence of AXMI-022 is 64.9% identical to Vip1A(b) (SEQ ID NO:52; see also U.S. Pat. No. 5,770,696, herein incorporated by reference in its entirety) throughout the length of Vip1A(b), and has significant amino acid identity with several other binary protein toxins. Further analysis of AXMI-022 revealed the following features of this polypeptide:
  • AXMI-022 is significantly longer than other binary proteins to which it shares homology, and encodes a peptide of 1,003 amino acids.
  • the Vip1A(b) protein is 834 amino acids in length;
  • the receptor binding region of AXMI-022 (from about amino acid 640 to about amino acid 770 of SEQ ID NO:29) is different from other binary toxins.
  • the region of AXMI-022 corresponding to the region of binary proteins involved in receptor binding is quite different in AXMI-022 compared to other binary proteins. This is suggestive that AXMI-022 binds to a different receptor than other binary proteins
  • the C-terminal 133 amino acids of AXMI-022 show amino acid homology to the Cry37Aa binary protein (SEQ ID NO:54; GENBANK® Accession No. AAF76376; U.S. Pat. No. 6,063,756, herein incorporated by reference in its entirety). This region has homology to Cry37Aa at a sequence identity of about 36%.
  • Cry37Aa is in a different class of binary toxins than the Vip1-type toxins.
  • Cry37Aa belongs to the Cry34 family, which forms a binary toxin with the Cry35 family.
  • Cry34Ab1 is principally responsible for forming pores in lipid membranes, while Cry35Ab1 enhances the formation of pores (Masson, et al. (2004) Biochemistry 43:12349-57).
  • AXMI-022 appears to be a novel type of “single peptide” binary toxin, having homology to multiple classes of binary proteins, with a receptor-binding component from one class of binary toxins directly fused to a toxin component from a different class of binary toxins. This organization of domains has not been previously predicted in the art.
  • pAX2597 was found to contain an open reading frame with homology to “cry” type delta-endotoxins. This open reading frame was designated as axmi-043. pAX2597 was deposited with the ARS Patent Strain Collection on Jun. 15, 2006, and assigned NRRL B-30941. Inspection of the axmi-043 open reading frame suggests that more than one start codon may be present.
  • the ATG at position 46 of SEQ ID NO:20 has a ribosome binding site (5′ G-G-A-G-A-3′) (SEQ ID NO:63) starting at nucleotide 33 of SEQ ID NO:20.
  • AXMI-043 (SEQ ID NO:23), and the longer protein as AXMI-043-2 (SEQ ID NO:21).
  • AXMI-043 exhibits 93% amino acid identity to the AXMI-028 endotoxin
  • AXMI-43-2 is 90% identical to AXMI-028 (SEQ ID NO:45 of this application, see also U.S. patent application Ser. No. 11/416,261, herein incorporated by reference in its entirety).
  • AXMI-043 appears to be a “full-length endotoxin,” and contains a C-terminal region (after the aspartic residue at position 629 of the AXMI-043 amino acid sequence) often referred to in the art as a non-toxic domain or a “crystal domain.”
  • AXMI-043 exhibits 54% amino acid identity with the Cry7Aa1 endotoxin (SEQ ID NO:46) throughout the full length of the protein.
  • pAX2599 was found to contain an open reading frame with homology to “cry” type delta-endotoxins. This open reading frame was designated as axmi-044 (SEQ ID NO:14), and the encoded protein was designated AXMI-044 (SEQ ID NO:15). pAX2599 was deposited with the ARS Patent Strain Collection on Jun. 15, 2006, and assigned Accession No. NRRL B-30942.
  • GenPept database maintained by the NCBI (National Center for Biotechnology Information) AXMI-044 was found to have low homology to the cry-15Aa/cry33 family of toxins (SEQ ID NO:44, GENBANK® ID 8928022), and to MTX2 (SEQ ID NO:38).
  • AXMI-033 exhibits 61% amino acid identity to the 326 amino acid CryC35 insect toxin (SEQ ID NO:47, encoded by GENBANK® reference CAA63374).
  • the second open reading frame was designated as axmi-034 (SEQ ID NO:26), and the encoded protein was designated AXMI-034 (SEQ ID NO:27).
  • AXMI-34 exhibits 45% amino acid identity with the CryC53 endotoxin. (SEQ ID NO:48, encoded by GENBANK® reference CAA67205).
  • axmi-033 and axmi-034 appear to comprise an operon.
  • the ATG start of axmi-034 is immediately 3′ to, and in close proximity of (15 nucleotides immediately downstream of), the TAA stop codon of axmi-033.
  • This organization is well known in the art to suggest that two genes comprise an operon.
  • the AXMI-033 and AXMI-034 proteins are likely to be co-expressed in their native strain. It is likely that the activities of the two proteins expressed together may be synergistic and superior to the activity of the proteins expressed separately.
  • pAX4341 a clone containing both axmi-033 and axmi-034 open reading frames, was deposited with the ARS Patent Strain Collection on May 29, 2007, and assigned accession number NRRL B-50047.
  • a plasmid clone was found to contain two open reading frames with homology to insect toxins.
  • the first open reading frame was designated as axmi-063 (SEQ ID NO:34), and the encoded protein was designated AXMI-063 (SEQ ID NO:35).
  • AXMI-63 exhibits 53.1% amino acid identity to the CryC35 insect toxin (SEQ ID NO:47, encoded by GENBANK® reference CAA63374).
  • the second open reading frame was designated as axmi-064 (SEQ ID NO:36), and the encoded protein was designated AXMI-064 (SEQ ID NO:37).
  • AXMI-64 exhibits 44.3% amino acid identity with the CryC53 endotoxin (SEQ ID NO:48, encoded by GENBANK® reference CAA67205).
  • axmi-063 and axmi-064 appear to comprise an operon.
  • the ATG start of axmi-064 is immediately 3′ to, and in close proximity of, the TAA stop codon of axmi-063.
  • the AXMI-063 and AXMI-064 proteins are likely to be co-expressed in their native strain. It is likely that the activities of the two proteins expressed together may be synergistic and superior to the activity of the proteins expressed separately.
  • pAX5036 a clone containing both axmi-063 and axmi-064 open reading frames, was deposited with the ARS Patent Strain Collection on May 29, 2007, and assigned NRRL B-50048.
  • AXMI-033/AXMI-034 are similar to AXMI-063/AXMI-064.
  • Analysis of the amino acid sequence of AXMI-033, AXMI-043, AXMI-063, and AXMI-064 reveals that AXMI-033 and AXMI-063 share significant amino acid identity, and are 69% identical.
  • AXMI-034 and AXMI-064 share significant amino acid similarity (52% identical).
  • the proteins of the invention are “pesticidal proteins.” TABLE 2 Amino Acid Identity of AXMI-011, AXMI-012, AXMI-013, AXMI-015, AXMI-032, and AXMI-044 to mosquito toxins in public databases % Identity in PROTEIN Highest Blast Hit (nr) block AXMI-011 MTX2 28% AXMI-012 P42 component of binary toxin 29% AXMI-013 MTX3 52% AXMI-015 RBTH_02046 35% AXMI-019 Cry14-4, MTX2 35%, 30% AXMI-032 GENBANK ® ID CAD30104.1 19% AXMI-044 cry15Aa, MTX2 30%, 30%
  • the ability of a pesticidal protein to act as a pesticide upon a pest is often assessed in a number of ways.
  • One way well known in the art is to perform a feeding assay. In such a feeding assay, one exposes the pest to a sample containing either compounds to be tested, or control samples. Often this is performed by placing the material to be tested, or a suitable dilution of such material, onto a material that the pest will ingest, such as an artificial diet.
  • the material to be tested may be composed of a liquid, solid, or slurry. The material to be tested may be placed upon the surface and then allowed to dry. Alternatively, the material to be tested may be mixed with a molten artificial diet, then dispensed into the assay chamber.
  • the assay chamber may be, for example, a cup, a dish, or a well of a microtiter plate.
  • Assays for sucking pests may involve separating the test material from the insect by a partition, ideally a portion that can be pierced by the sucking mouth parts of the sucking insect, to allow ingestion of the test material. Often the test material is mixed with a feeding stimulant, such as sucrose, to promote ingestion of the test compound.
  • a feeding stimulant such as sucrose
  • test material can include microinjection of the test material into the mouth, or gut of the pest, as well as development of transgenic plants, followed by test of the ability of the pest to feed upon the transgenic plant.
  • Plant testing may involve isolation of the plant parts normally consumed, for example, small cages attached to a leaf, or isolation of entire plants in cages containing insects.
  • the coding regions of the invention are connected with appropriate promoter and terminator sequences for expression in plants.
  • Such sequences are well known in the art and may include the rice actin promoter or maize ubiquitin promoter for expression in monocots, the Arabidopsis UBQ3 promoter or CaMV 35S promoter for expression in dicots, and the nos or PinII terminators.
  • Techniques for producing and confirming promoter-gene-terminator constructs also are well known in the art.
  • synthetic DNA sequences are designed and generated. These synthetic sequences have altered nucleotide sequence relative to the parent sequence, but encode proteins that are essentially identical to the parent AXMI protein.
  • modified versions of the synthetic genes are designed such that the resulting peptide is targeted to a plant organelle, such as the endoplasmic reticulum or the apoplast.
  • a plant organelle such as the endoplasmic reticulum or the apoplast.
  • Peptide sequences known to result in targeting of fusion proteins to plant organelles are known in the art.
  • the N-terminal region of the acid phosphatase gene from the White Lupin Lupinus albus (GENEBANK® ID GI: 14276838, Miller et al. (2001) Plant Physiology 127: 594-606) is known in the art to result in endoplasmic reticulum targeting of heterologous proteins.
  • the resulting fusion protein also contains an endoplasmic reticulum retention sequence comprising the peptide N-terminus-lysine-aspartic acid-glutamic acid-leucine (i.e., the “KDEL” motif (SEQ ID NO:58)) at the C-terminus, the fusion protein will be targeted to the endoplasmic reticulum. If the fusion protein lacks an endoplasmic reticulum targeting sequence at the C-terminus, the protein will be targeted to the endoplasmic reticulum, but will ultimately be sequestered in the apoplast.
  • an endoplasmic reticulum retention sequence comprising the peptide N-terminus-lysine-aspartic acid-glutamic acid-leucine (i.e., the “KDEL” motif (SEQ ID NO:58)
  • this gene encodes a fusion protein that contains the N-terminal thirty-one amino acids of the acid phosphatase gene from the White Lupin Lupinus albus (GENBANK® ID GI: 14276838, Miller et al., 2001, supra) fused to the N-terminus of the AXMI sequence, as well as the KDEL sequence at the C-terminus.
  • the resulting protein is predicted to be targeted the plant endoplasmic reticulum upon expression in a plant cell.
  • the plant expression cassettes described above are combined with an appropriate plant selectable marker to aid in the selection of transformed cells and tissues, and ligated into plant transformation vectors.
  • plant transformation vectors may include binary vectors from Agrobacterium -mediated transformation or simple plasmid vectors for aerosol or biolistic transformation.
  • the coding region DNA of the axmi genes of the invention are operably connected with appropriate promoter and terminator sequences for expression in plants.
  • appropriate promoter and terminator sequences for expression in plants.
  • Such sequences are well known in the art and may include the rice actin promoter or maize ubiquitin promoter for expression in monocots, the Arabidopsis UBQ3 promoter or CaMV 35S promoter for expression in dicots, and the nos or PinII terminators. Techniques for producing and confirming promoter-gene-terminator constructs also are well known in the art.
  • the plant expression cassettes described above are combined with an appropriate plant selectable marker to aid in the selections of transformed cells and tissues, and ligated into plant transformation vectors.
  • plant transformation vectors may include binary vectors from Agrobacterium -mediated transformation or simple plasmid vectors for aerosol or biolistic transformation.
  • Embryos are isolated from the ears, and those embryos 0.8-1.5 mm in size are preferred for use in transformation. Embryos are plated scutellum side-up on a suitable incubation media, such as DN62A5S media (3.98 g/L N6 Salts; 1 mL/L (of 1000 ⁇ Stock) N6 Vitamins; 800 mg/L L-Asparagine; 100 mg/L Myo-inositol; 1.4 g/L L-Proline; 100 mg/L Casamino acids; 50 g/L sucrose; 1 mL/L (of 1 mg/mL Stock) 2,4-D). However, media and salts other than DN62A5S are suitable and are known in the art. Embryos are incubated overnight at 25° C. in the dark. However, it is not necessary per se to incubate the embryos overnight.
  • DN62A5S media 3.98 g/L N6 Salts; 1 mL/L (
  • the resulting explants are transferred to mesh squares (30-40 per plate), transferred onto osmotic media for about 30-45 minutes, then transferred to a beaming plate (see, for example, PCT Publication No. WO/0138514 and U.S. Pat. No. 5,240,842).
  • DNA constructs designed to the genes of the invention in plant cells are accelerated into plant tissue using an aerosol beam accelerator, using conditions essentially as described in PCT Publication No. WO/0138514.
  • embryos are incubated for about 30 min on osmotic media, and placed onto incubation media overnight at 25° C. in the dark.
  • incubation media For avoid unduly damaging beamed explants, they are incubated for at least 24 hours prior to transfer to recovery media.
  • Embryos are then spread onto recovery period media, for about 5 days, 25° C. in the dark, then transferred to a selection media. Explants are incubated in selection media for up to eight weeks, depending on the nature and characteristics of the particular selection utilized.
  • the resulting callus is transferred to embryo maturation media, until the formation of mature somatic embryos is observed.
  • the resulting mature somatic embryos are then placed under low light, and the process of regeneration is initiated by methods known in the art.
  • the resulting shoots are allowed to root on rooting media, and the resulting plants are transferred to nursery pots and propagated as transgenic plants.
  • the pH of the solution is adjusted to pH 5.8 with 1N KOH/1N KCl, Gelrite (Sigma) is added at a concentration up to 3 g/L, and the media is autoclaved. After cooling to 50° C., 2 ml/L of a 5 mg/ml stock solution of silver nitrate (Phytotechnology Labs) is added.
  • Ears are best collected 8-12 days after pollination. Embryos are isolated from the ears, and those embryos 0.8-1.5 mm in size are preferred for use in transformation. Embryos are plated scutellum side-up on a suitable incubation media, and incubated overnight at 25° C. in the dark. However, it is not necessary per se to incubate the embryos overnight. Embryos are contacted with an Agrobacterium strain containing the appropriate vectors for Ti plasmid mediated transfer for about 5-10 min, and then plated onto co-cultivation media for about 3 days (25° C. in the dark). After co-cultivation, explants are transferred to recovery period media for about five days (at 25° C. in the dark).
  • Explants are incubated in selection media for up to eight weeks, depending on the nature and characteristics of the particular selection utilized. After the selection period, the resulting callus is transferred to embryo maturation media, until the formation of mature somatic embryos is observed. The resulting mature somatic embryos are then placed under low light, and the process of regeneration is initiated as known in the art.
  • Transgenic plants containing an axmi gene of the invention under the control of a plant promoter are tested for resistance to infestation by Western corn rootworm (WCRW).
  • Plantlets are transplanted from tissue culture media to root trainer (clamshell) pots known in the art to be useful for growth of plantlets in soil. Plants are grown for about 2 weeks in a greeenhouse.
  • Transgenic plants, as well as untransformed controls are infested with approximately 1,000 WCRW eggs. WCRW eggs are preincubated such that eggs are at the point of hatching when infested onto the plants. Plants are held for about four weeks, or until controls exhibited obvious damage due to the rootworms. At this stage, plants are pulled from pots, roots are washed, and damage evaluated. Several independent events are examined for reduced damage from WCRW infestation relative to non-transformed control plants.
  • the resulting shoots are allowed to root on rooting media, and the resulting plants are transferred to nursery pots and propagated as transgenic plants.

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US20110263488A1 (en) 2011-10-27
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