EP1257640A2 - Nukleinsäuren und polypeptide von drosophila melanogaster snf natrium-neurotransmitter symporter zelloberfächerezeptorfamilie und verwendungsverfahren - Google Patents

Nukleinsäuren und polypeptide von drosophila melanogaster snf natrium-neurotransmitter symporter zelloberfächerezeptorfamilie und verwendungsverfahren

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Publication number
EP1257640A2
EP1257640A2 EP00989575A EP00989575A EP1257640A2 EP 1257640 A2 EP1257640 A2 EP 1257640A2 EP 00989575 A EP00989575 A EP 00989575A EP 00989575 A EP00989575 A EP 00989575A EP 1257640 A2 EP1257640 A2 EP 1257640A2
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EP
European Patent Office
Prior art keywords
nucleic acid
protein
sequence
seq
subject
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
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EP00989575A
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English (en)
French (fr)
Inventor
Kathryn A. Kellerman
Kevin Patrick Keegan
Allen James Ebens, Jr.
Justin Torpey
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Genoptera LLC
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Genoptera LLC
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Application filed by Genoptera LLC filed Critical Genoptera LLC
Priority to EP05006787A priority Critical patent/EP1561818A1/de
Publication of EP1257640A2 publication Critical patent/EP1257640A2/de
Withdrawn legal-status Critical Current

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/43504—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from invertebrates
    • C07K14/43563—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from invertebrates from insects
    • C07K14/43577—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from invertebrates from insects from flies
    • C07K14/43581—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from invertebrates from insects from flies from Drosophila
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2217/00—Genetically modified animals
    • A01K2217/05—Animals comprising random inserted nucleic acids (transgenic)
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2217/00—Genetically modified animals
    • A01K2217/07—Animals genetically altered by homologous recombination
    • A01K2217/075—Animals genetically altered by homologous recombination inducing loss of function, i.e. knock out

Definitions

  • the sodium/neurotransmitter family (SNF) of symporter cell surface receptors is implicated in neuroregulation and brain development. These molecules are targets of antidepressant medicines and other drugs (e.g. amphetamines, cocaine). Most members of this family function in the brain to terminate neurotransmitter activity by mediating neurotransmitter re-uptake into pre-synaptic terminals (Reizer et ⁇ /., Biochim. Biophys. Acta (1994) 1197:133-136).
  • the SNF family also includes members that function outside the brain, orphan transporters of unknown function, and hypothetical transporters from bacteria. Solutes transported by members of this family include serotonin, GABA, noradrenaline, dopamine, glycine, possibly proline, acetylcholine, choline, taurine, betaine and creatine.
  • the NTT4 subclass of SNFs is comprised of orphan receptors most closely related to serotonin porters, i rat, the liming and localization of NTT4 expression suggests a role in central nervous system maturation (Jursky and Nelson, J. Neurosci. Res. (1999) 55(l):24-35).
  • Others members of the SNF family include K + -coupled amino acid transporters from insects. These transporters are related to members of the sodium/neurotransmitter symporter family (SNF), but transport is driven by K + and ⁇ gradients rather than Na + and H 4" gradients.
  • Lepidopteran insect larvae have a high K + and a low Na + content, and their midgut cells lack Na + /K + ATPase. Instead, an let translocating, vacuolar-type ATPase generates a voltage of approximately -240 mV across the apical membrane of the gut goblet cells, which drives ⁇ back into the cells in exchange for K + , resulting in net K + secretion into the lumen. The resulting inwardly directed K + electrochemical gradient serves as a driving force for active amino acid uptake into adjacent columnar cells.
  • the KAAT1 gene was cloned from aManduca sexta larval midgut library using expression Xenopus laevis oocytes. It is expressed in absorptive columnar cells of the midgut and in labial glands (Castagna et al, Proc Natl Acad Sci USA (1998) 95:5395-5400).
  • the transporters are responsible for re-uptake of neurotransmitters.
  • the Manduca sexta GABA transporter, MasGAT has been shown to be pharmacologically distinct from known mammalian GABA transporters (Mbungu et al., Arch Biochem Biophys 1995, 318:489-497).
  • TrnGAT has been cloned from the Cabbage looper, Trichoplusia ni (Gao,X. et al., Insect Biochem Mol Biol 1999 Jul;29(7):609-23).
  • TM domains 12 putative transmembrane (TM) domains with a hydrophillic extracellular loop between the third and fourth TM domains. They share significant sequence similarity, particularly in the putative membrane- spanning domains.
  • Pesticide development has traditionally focused on the chemical and physical properties of the pesticide itself, a relatively time-consuming and expensive process. As a consequence, efforts have been concentrated on the modification of pre-existing, well-validated compounds, rather than on the development of new pesticides. There is a need in the art for new pesticidal compounds that are safer, more selective, and more efficient than currently available pesticides.
  • the present invention addresses this need by providing novel pesticide targets from invertebrates such as the fruit fly Drosophila melanogaster, and by providing methods of identifying compounds that bind to and modulate the activity of such targets.
  • the isolated insect nucleic acid molecules provided herein are useful for producing insect proteins encoded thereby.
  • the insect proteins are useful in assays to identify compounds that modulate a biological activity of the proteins, which assays identify compounds that may have utility as pesticides.
  • It is an object of the present invention to provide invertebrate homologs of SNF genes that can be used in genetic screening methods to characterize pathways that such genes may be involved in, as well as other interacting genetic pathways. It is also an object of the invention to provide methods for screening compounds that interact with a subject SNF. Compounds that interact with a subject SNF may have utility as therapeutics or pesticides.
  • the subject proteins are SNFs from Drosophila melanogaster; particular embodiments are referred to herein as dmSNF, dmSNF2, and dmSNF3.
  • the subject proteins are members of the NTT4 subclass of SNFs.
  • the subject proteins are NTT4 proteins from Drosophila melanogaster, referred to herein as dmNTT4.
  • the subject proteins are K + - coupled amino acid transporters.
  • the subject proteins are K + -coupled amino acid transporters from Drosophila melanogaster, referred to herein as dmKSNF.
  • the subject proteins are ⁇ -amino butyric acid (GABA) transporters (GAT).
  • GABA ⁇ -amino butyric acid
  • the subject proteins are GAT from Drosophila melanogaster, referred to herein as dmGAT.
  • Isolated nucleic acid molecules are provided that comprise nucleic acid sequences encoding subject proteins as well as novel fragments and derivatives thereof.
  • Methods of using the isolated nucleic acid molecules and fragments of the invention as biopesticides are described, such as use of RNA interference methods that block a biological activity of a subject protein.
  • Vectors and host cells comprising the subject nucleic acid molecules are also described, as well as metazoan invertebrate organisms (e.g. insects, coelomates and pseudocoelomates) that are genetically modified to express or mis-express a subject protein.
  • an important utility of the subject nucleic acids and proteins is that they can be used in screening assays to identify candidate compounds which are potential pesticidal agents or therapeutics that interact with subject proteins.
  • Such assays typically comprise contacting a subject protein or fragment with one or more candidate molecules, and detecting any interaction between the candidate compound and the subject protein.
  • the assays may comprise adding the candidate molecules to cultures of cells genetically engineered to express subject proteins, or alternatively, administering the candidate compound to a metazoan invertebrate organism genetically engineered to express a subject protein.
  • the genetically engineered metazoan invertebrate animals of the invention can also be used in methods for studying a biological activity of a subject protein.
  • the methods typically involve detecting the phenotype caused by the expression or mis-expression of the subject protein.
  • the methods may additionally comprise observing a second animal that has the same genetic modification as the first animal and, additionally has a mutation in a gene of interest. Any difference between the phenotypes of the two animals identifies the gene of interest as capable of modifying the function of the gene encoding the subject protein.
  • Drosophila melanogaster Drosophila melanogaster
  • SNF sodium neurotransmitter family
  • Novel SNF nucleic acids, and the encoded proteins are identified herein.
  • the newly identified subject nucleic acid can be used for the generation of mutant phenotypes in animal models or in living cells that can be used to study regulation of genes encoding the subject proteins, and the use of subject proteins as a pesticide or drug target. Due to the ability to rapidly carry out large-scale, systematic genetic screens, the use of invertebrate model organisms such as Drosophila has great utility for analyzing the expression and mis-expression of a subject protein.
  • the invention provides a superior approach for identifying other components involved in the synthesis, activity, and regulation of subject proteins.
  • Model organisms or cultured cells that have been genetically engineered to express a subject protein can be used to screen candidate compounds for their ability to modulate expression or activity of a subject nucleic acid and/or protein, and thus are useful in the identification of new drug targets, therapeutic agents, diagnostics and prognostics useful in the treatment of disorders associated with ion channels. Additionally, these invertebrate model organisms can be used for the identification and screening of pesticide targets directed to components of pathways involving subject proteins.
  • the term “isolated” is meant to describe a polynucleotide, a polypeptide, an antibody, or a host cell that is in an environment different from that in which the polynucleotide, the polypeptide, the antibody, or the host cell naturally occurs.
  • the term “substantially purified” refers to a compound (e.g., either a polynucleotide or a polypeptide or an antibody) that is removed from its natural environment and is at least 60% ⁇ free, preferably 75% free, and most preferably 90% free from other components with which it is naturally associated.
  • polypeptide and protein refer to a polymeric form of amino acids of any length, which can include coded and non-coded amino acids, chemically or biochemically modified or derivatized amino acids, and polypeptides having modified peptide backbones.
  • the term includes fusion proteins, including, but not limited to, fusion proteins with a heterologous amino acid sequence, fusions with heterologous and homologous leader sequences, with or without N-terminal methionine residues; irnmunologically tagged proteins; and the like.
  • a "host cell”, as used herein, denotes microorganisms or eukaryotic cells or cell lines cultured as unicellular entities which can be, or have been, used as recipients for recombinant vectors or other transfer polynucleotides, and include the progeny of the original cell which has been transfected. It is understood that the progeny of a single cell may not necessarily be completely identical in morphology or in genomic or total DNA complement as the original parent, due to natural, accidental, or deliberate mutation.
  • transformation is meant a permanent or transient genetic change induced in a cell following incorporation of new DNA (i.e., DNA exogenous to the cell). Genetic change can be accomplished either by incorporation of the new DNA into the genome of the host cell, or by transient or stable maintenance of the new DNA as an episomal element. Where the cell is a eukaryotic cell, a permanent genetic change is generally achieved by introduction of the DNA into the genome of the cell.
  • the invention provides isolated insect nucleic acid molecules comprising nucleotide sequences of SNFs, and more particularly SNF nucleic acid sequences of Drosophila, and methods of using these nucleic acid molecules.
  • the present invention provides isolated nucleic acid molecules that comprise nucleotide sequences encoding insect proteins that are potential pesticide targets.
  • the isolated nucleic acid molecules have a variety of uses, e.g., as hybridization probes, e.g., to identify nucleic acid molecules that share nucleotide sequence identify; in expression vectors to produce the polypeptides encoded by the nucleic acid molecules; and to modify a host cell or animal for use in assays described hereinbelow.
  • isolated nucleic acid sequence includes the reverse complement, RNA equivalent, DNA or RNA single- or double-stranded sequences, and DNA/RNA hybrids of the sequence being described, unless otherwise indicated.
  • polynucleotide and nucleic acid molecule used interchangeably herein, refer to a polymeric forms of nucleotides of any length, either ribonucleotides or deoxynucleotides.
  • this tern includes, but is not limited to, single-, double-, or multi-stranded DNA or RNA, genomic DNA, cDNA, DNA-RNA hybrids, or a polymer comprising purine and pyrimidine bases or other natural, chemically or biochemically modified, non-natural, or derivatized nucleotide bases.
  • the backbone of the polynucleotide can comprise sugars and phosphate groups (as may typically be found in RNA or DNA), or modified or substituted sugar or phosphate groups.
  • the backbone of the polynucleotide can comprise a polymer of synthetic subunits such as phosphoramidites and thus can be an oligodeoxynucleoside phosphoramidate or a mixed phosphoramidate-phosphodiester oligomer.
  • a polynucleotide may comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs, uracyl, other sugars, and linking groups such as fluororibose and thioate, and nucleotide branches.
  • the sequence of nucleotides may be interrupted by non-nucleotide components.
  • a polynucleotide may be further modified after polymerization, such as by conjugation with a labeling component. Other types of modifications included in this definition are caps, substitution of one or more of the naturally occurring nucleotides with an analog, and introduction of means for attaching the polynucleotide to proteins, metal ions, labeling components, other polynucleotides, or a solid support.
  • nucleic acid analogs For hybridization probes, it may be desirable to use nucleic acid analogs, in order to improve the stability and binding affinity.
  • a number of modifications have been described that alter the chemistry of the phosphodiester backbone, sugars or heterocyclic bases. Among useful changes in the backbone chemistry are phosphorothioates; phosphorodithioates, where both of the non-bridging oxygens are substituted with sulfur; phosphoroamidites; alkyl phosphotriesters and boranophosphates.
  • Peptide nucleic acids replace the entire phosphodiester backbone with a peptide linkage.
  • Sugar modifications are also used to enhance stability and affinity.
  • the ⁇ -anomer of deoxyribose may be used, where the base is inverted with respect to the natural ⁇ -anomer.
  • the 2'-OH of the ribose sugar may be altered to form 2'-0-methyl or 2'-0-allyl sugars, which provides resistance to degradation without compromising affinity.
  • Modification of the heterocyclic bases must maintain proper base pairing.
  • Some useful substitutions include deoxyuridine for deoxythymidine; 5-methyl-2'- deoxycytidine and 5-bromo-2'-deoxycytidine for deoxycytidine.
  • 5- propynyl-2'-deoxyuridine and 5- propynyl-2'-deoxycytidine have been shown to increase affinity and biological activity when substituted for deoxythymidine and deoxycytidine, respectively.
  • the invention includes the reverse complements thereof.
  • the subject nucleic acid sequences, derivatives and fragments thereof may be RNA molecules comprising the nucleotide sequence of SEQ ID NOS: 1, 3, 5, 7, 9, and 11 (or derivative or fragment thereof) wherein the base U (uracil) is substituted for the base T (thymine).
  • the DNA and RNA sequences of the invention can be single- or double-stranded.
  • isolated nucleic acid sequence includes the reverse complement, RNA equivalent, DNA or RNA single- or double-stranded sequences, and DNA/RNA hybrids of the sequence being described, unless otherwise indicated.
  • RNAi Interfering RNA
  • ds double-stranded
  • biopesticides discussed further below
  • the subject nucleic acid fragments are also useful as nucleic acid hybridization probes and replication/amplification primers.
  • Certain "antisense" fragments i.e. that are reverse complements of portions of the coding sequence of an one ofSEQ ID NOS:l, 3, 5, 7, 9, and 1 lhave utility in inhibiting the function of a subject protein.
  • the fragments are of length sufficient to specifically hybridize with the corresponding any one of SEQ ID OS:l, 3, 5, 1, 9, and 11.
  • the fragments consist of or comprise at least 12, preferably at least 24, more preferably at least 36, and more preferably at least 96 contiguous nucleotides of any one of SEQ ID NOS:l, 3, 5, 7, 9, and 11.
  • the total length of the combined nucleic acid sequence is less than 15 kb, preferably less than 10 kb or less than 5kb, and more preferably less than 2 kb.
  • the subject nucleic acid sequences may consist solely of any one of SEQ ID NOS:l, 3, 5, 7, 9, and 11 or fragments thereof.
  • the subject nucleic acid sequences and fragments thereof may be joined to other components such as labels, peptides, agents that facilitate transport across cell membranes, hybridization-triggered cleavage agents or intercalating agents.
  • the subject nucleic acid sequences and fragments thereof may also be joined to other nucleic acid sequences (i.e. they may comprise part of larger sequences) and are of synthetic/non-natural sequences and/or are isolated and/or are purified, i.e. unaccompanied by at least some of the material with which it is associated in its natural state.
  • the isolated nucleic acids constitute at least about 0.5%, and more preferably at least about 5% by weight of the total nucleic acid present in a given fraction, and are preferably recombinant, meaning that they comprise a non-natural sequence or a natural sequence joined to nucleotide(s) other than that which it is joined to on a natural chromosome.
  • Derivative nucleic acid molecules of the subject nucleic acid molecules include sequences that hybridize to the nucleic acid sequence of anyone of SEQ ID NOS:l, 3, 5, 7, 9, and 11 under stringency conditions such that the hybridizing derivative nucleic acid is related to the subject nucleic acid by a certain degree of sequence identity.
  • a nucleic acid molecule is "hybridizable" to another nucleic acid molecule, such as a cDNA, genomic DNA, or RNA, when a single stranded form of the nucleic acid molecule can anneal to the other nucleic acid molecule.
  • Stringency of hybridization refers to conditions under which nucleic acids are hybridizable. The degree of stringency can be controlled by temperature, ionic strength, pH, and the presence of denaturing agents such as formamide during hybridization and washing.
  • stringent hybridization conditions are those normally used by one of skill in the art to establish at least a 90% sequence identify between complementary pieces of DNA or DNA and RNA.
  • “Moderately stringent hybridization conditions” are used to find derivatives having at least 70% sequence identify.
  • “low-stringency hybridization conditions” are used to isolate derivative nucleic acid molecules that share at least about 50% sequence identify with the subject nucleic acid sequence.
  • the ultimate hybridization stringency reflects both the actual hybridization conditions as well as the washing conditions following the hybridization, and it is well known in the art how to vary the conditions to obtain the desired result.
  • Conditions routinely used are set out in readily available procedure texts (e.g., Current Protocol in Molecular Biology, Vol. 1, Chap. 2.10, John Wiley & Sons, Publishers (1994); Sambrook et al, Molecular Cloning, Cold Spring Harbor (1989)).
  • a preferred derivative nucleic acid is capable of hybridizing to any one of SEQ ID NOS: 1, 3, 5, 7, 9, and 11 under stringent hybridization conditions that comprise: prehybridization of filters containing nucleic acid for 8 hours to overnight at 65° C in a solution comprising 6X single strength citrate (SSC) (IX SSC is 0.15 M NaCl, 0.015 M Na citrate; pH 7.0), 5X Denhardt's solution, 0.05% sodium pyrophosphate and 100 ⁇ g/ml herring sperm DNA; hybridization for 18-20 hours at 65° C in a solution containing 6X SSC, IX Denhardt's solution, 100 ⁇ g/ml yeast tRNA and 0.05% sodium pyrophosphate; and washing of filters at 65° C for 1 h in a solution containing 0.2X SSC and 0.1% SDS (sodium dodecyl sulfate).
  • SSC single strength citrate
  • Derivative nucleic acid sequences that have at least about 70% sequence identify with any one of SEQ ID NOS:l, 3, 5, 7, 9, and 11 are capable of hybridizing to any one of SEQ ID NOS:l, 3, 5, 1, 9, and 11 under moderately stringent conditions that comprise: pretreatment of filters containing nucleic acid for 6 h at 40° C in a solution containing 35% formamide, 5X SSC, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, 0.1% PVP, 0.1% Ficoll, 1% BSA, and 500 ⁇ g/ml denatured salmon sperm DNA; hybridization for 18-20 h at 40° C in a solution containing 35% formamide, 5X SSC, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.2% BSA, 100 ⁇ g/ml salmon sperm DNA, and 10% (wt/vol) dextran sulfate
  • ID NOS: 1, 3, 5, 7, 9, and 11 under low stringency conditions that comprise: incubation for 8 hours to overnight at 37° C in a solution comprising 20% formamide, 5 x SSC, 50 mM sodium phosphate (pH 7.6), 5X Denhardt's solution, 10% dextran sulfate, and 20 ⁇ g/ml denatured sheared salmon sperm DNA; hybridization in the same buffer for 18 to 20 hours; and washing of filters in l x SSC at about 37° C for 1 hour.
  • percent (%) nucleic acid sequence identify with respect to a subject sequence, or a specified portion of a subject sequence, is defined as the percentage of nucleotides in the candidate derivative nucleic acid sequence identical with the nucleotides in the subject sequence (or specified portion thereof), after aligning the sequences and introducing gaps, if necessary to achieve the maximum percent sequence identify, as generated by the program WU-BLAST-2.0al9 (Altschul et al., J. Mol.
  • HSP S and HSP S2 parameters are dynamic values and are established by the program itself depending upon the composition of the particular sequence and composition of the particular database against which the sequence of interest is being searched.
  • a percent (%) nucleic acid sequence identify value is determined by the number of matching identical nucleotides divided by the sequence length for which the percent identity is being reported.
  • Derivatives of a subject nucleic acid molecule usually have at least 70% sequence identify, preferably at least 80% sequence identity, more preferably at least 85% sequence identity, still more preferably at least 90%> sequence identity, and most preferably at least 95%> sequence identify with any one of SEQ ID NOS : 1, 3, 5, 7, 9, and 11, or domain-encoding regions thereof.
  • the derivative nucleic acid encodes a polypeptide comprising an amino acid sequence set forth in any one of SEQ ID NOS:2, 4, 6, 8, 10, and 12, or a fragment or derivative thereof as described further below.
  • a derivative of a subject nucleic acid molecule, or fragment thereof may comprise 100% sequence identify with any one of SEQ ID NOS:l, 3, 5, 7, 9, and 11, but be a derivative thereof in the sense that it has one or more modifications at the base or sugar moiety, or phosphate backbone. Examples of modifications are well known in the art (Bailey, Ullmann's Encyclopedia of Industrial Chemistry (1998), 6th ed. Wiley and Sons). Such derivatives may be used to provide modified stability or any other desired property.
  • a humanized nucleic acid sequence is one in which one or more codons has been substituted with a codon that is more commonly used in human genes. Preferably, a sufficient number of codons have been substituted such that a higher level expression is achieved in mammalian cells than what would otherwise be achieved without the substitutions. Tables are available in the art that show, for each amino acid, the calculated codon frequency in humans genes for 1000 codons (Wada et al.,
  • other nucleic acid derivatives can be generated with codon usage optimized for expression in other organisms, such as yeasts, bacteria, and plants, where it is desired to engineer the expression of receptor proteins by using specific codons chosen according to the preferred codons used in highly expressed genes in each organism.
  • a subject nucleic acid molecule in which the glutamic acid codon, GAA has been replaced with the codon GAG, which is more commonly used in human genes is an example of a humanized nucleic acid molecule.
  • a detailed discussion of the humanization of nucleic acid sequences is provided in U.S. Pat. No. 5,874,304 to Zolotukhin et al.
  • the invention provides isolated nucleic acid molecules comprising nucleotide sequences encoding a dmNTT4 SNF.
  • a nucleic acid sequence (SEQ ID NO: 1) was isolated from Drosophila that encodes an SNF omolog, hereinafter referred to as dmNTT4.
  • a dmNTT4 nucleic acid molecule comprises a nucleotide sequence of at least about 50, at least about 75, at least about 100, at least about 150, at least about 200, at least about 300, at least about 400, at least about 500, at least about 600, at least about 700, at least about 800, at least about 900, at least about 1000, at least about 1100, at least about 1200, at least about 1300, at least about 1400, at least about 1500, at least about 1600, at least about 1700, at least about at least about 1800, at least about 1900, at least about 2000, at least about 2100, at least about 2200, at least about 2300 at least about 2400, at least about 2500, at least about 2600, at least about 2700, at least about 2800, at least about 2900, at least about 3000, at least about 3100, at least about 3200, at least about 3300, at least about 3400, at least about 3500, at least about 3600, at least about 3700, at least about 3500
  • a dmNTT4 nucleic acid molecule of the invention comprises a nucleotide sequence that encodes a polypeptide comprising at least about 6, at least about 10, at least about 20, at least about 50, at least about 75, at least about 100, at least about 150, at least about 200, at least about 250, at least about 300, at least about 350, at least about 400, at least about 450, at least about 500, at least about 550, at least about 600, at least about 650, or at least about 670 contiguous amino acids of the sequence set forth in SEQ ID NO:2, up to the entire amino acid sequence as set forth in SEQ ID NO:2.
  • Additional preferred fragments of SEQ ID NO: 1 encode intracellular or extracellular domains, which are located at approximately nucleotides 239-412, 476-508, 572-631, 695-886, 950-967, 1031- 1117, 1181-1222, 1286-1519, 1583-1657, 1721-1753, 1817-1891, 1955-2023, 2087-2263, respectively. Further additional preferred fragments encode the SNF domains, located at approximately nucleotides 403-1294, and 1423-2089. Another preferred fragment is the ORF located at approximately nucleotides 239-2263 of SEQ ID NO:l. More specific embodiments of preferred dmNTT4 protein fragments and derivatives are discussed further below in connection with specific dmNTT4 proteins.
  • the invention provides isolated nucleic acid molecules comprising nucleotide sequence encoding K + coupled amino acid transporters of the SNF family of cell surface transporters, and more particularly SNF nucleic acid sequences of Drosophila, and methods of using these sequences.
  • SEQ ID NO:3 a nucleic acid sequence (SEQ ID NO:3) was isolated from Drosophila that encodes an SNF homolog, hereinafter referred to as dmKSNF.
  • a dmKSNF nucleic acid molecule comprises a nucleotide sequence of at least about 50, at least about 75, at least about 100, at least about 150, at least about 200, at least about 300, at least about 400, at least about 500, at least about 600, at least about 700, at least about 800, at least about 900, at least about 1000, at least about 1100, at least about 1200, at least about 1300, at least about 1400, at least about 1500, at least about 1600, at least about 1700, at least about at least about 1800, at least about 1900, at least about 2000, at least about 2100, at least about 2200, at least about 2300, or at least about 2400 contiguous nucleotides of the sequence set forth in SEQ ID NO:3, up to the entire sequence set forth in SEQ ID NO:3.
  • a dmKSNF nucleic acid molecule of the invention comprises a nucleotide sequence that encodes a polypeptide comprising at least about 6, at least about 10, at least about 20, at least about 50, at least about 75, at least about 100, at least about 150, at least about 200, at least about 250, at least about 300, at least about 350, at least about 400, at least about 450, at least about 500, at least about 550, at least about 600, or at least about 630 contiguous amino acids of the sequence set forth in SEQ ID NO:4, up to the entire amino acid sequence as set forth in SEQ ID NO:4.
  • Additional preferred fragments of SEQ ID NO:3 encode extracellular or intracellular domains, which are located at approximately nucleotides 249-371, 435-461, 522-617, 681-938, 1002-1019, 1083-1269, 1233-1283, 1347-1448, 1512-1568, 1632-1664, 1730-1790, 1854-1901, and 1965-2173. More specific embodiments of preferred dmKSNF protein fragments and derivatives are discussed further below in connection with specific dmKSNF proteins.
  • the invention provides isolated nucleic acid molecules comprising nucleotide sequences of SNF transporters, and more particularly SNF transporter nucleic acid sequences of Drosophila, and methods of using these sequences.
  • SNF sodium neurotransmitter symporter
  • a dmSNF nucleic acid molecule comprises a nucleotide sequence of at least about 50, at least about 75, at least about 100, at least about 150, at least about 200, at least about 300, at least about 400, at least about 500, at least about 600, at least about 700, at least about 800, at least about 900, at least about 1000, at least about 1100, at least about 1200, at least about 1300, at least about 1400, at least about 1500, at least about 1600, at least about 1700, at least about at least about 1800, or at least about 1900, contiguous nucleotides of the sequence set forth in SEQ ID NO:5, up to the entire sequence set forth in SEQ ID NO:5.
  • a dmSNF nucleic acid molecule of the invention comprises a nucleotide sequence that encodes a polypeptide comprising at least about 6, at least about 10, at least about 20, at least about 50, at least about 75, at least about 100, at least about 150, at least about 200, at least about 250, at least about 300, at least about 350, or at least about 400 contiguous amino acids of the sequence set forth in SEQ ID NO: 6, up to the entire amino acid sequence as set forth in SEQ ID NO:6.
  • SEQ ID NO: 5 encodes the signature motif of the sodium neurotransmitter symporter (SNF) family which are located at approximately nucleotides 864-1139. More specific embodiments of preferred dmSNF protein fragments and derivatives are discussed further below in connection with specific dmSNF proteins.
  • SNF sodium neurotransmitter symporter
  • the invention provides isolated nucleic acid molecules comprising nucleotide sequences of SNF transporters , and more particularly SNF transporter nucleic acid sequences of Drosophila, and methods of using these sequences.
  • SNF transporter SNF transporter nucleic acid sequences of Drosophila
  • dmSNF2 sodium neurotransmitter symporter family homolog
  • a dmSNF2 nucleic acid molecule comprises a nucleotide sequence of at least about 50, at least about 75, at least about 100, at least about 150, at least about 200, at least about 300, at least about 400, at least about 500, at least about 600, at least about 700, at least about 800, at least about 900, at least about 1000, at least about 1100, at least about 1200, at least about 1300, at least about 1400, at least about 1500, at least about 1600, at least about 1700, at least about at least about 1800, at least about 1900, or at least about 2000 contiguous nucleotides of the sequence set forth in SEQ ID NO:7, up to the entire sequence set forth in SEQ ID NO:7.
  • a dmSNF2 nucleic acid molecule of the invention comprises a nucleotide sequence that encodes a polypeptide comprising at least about 6, at least about 10, at least about 20, at least about 50, at least about 75, at least about 100, at least about 150, at least about 200, at least about 250, at least about 300, at least about 350, at least about 400, at least about 500, at least about 550, or at least about 575 contiguous amino acids of the sequence set forth in SEQ ID NO: 8, up to the entire amino acid sequence as set forth in SEQ ID NO: 8.
  • SEQ ID NO:7 encodes the signature motif of the sodium neurotransmitter symporter (SNF) family which is located at approximately nucleotides 99-1700.
  • Other preferred fragments encode the transmembrane domains, which are located at approximately nucleotides 120 - 170, 210 - 260, 357 - 407, 624 - 674, 702 - 752, 849 - 899, 969 - 1019, 1128 - 1178, 1242 - 1292, 1350 - 1400, 1482 - 1532, and 1563 - 1613.
  • dmSNF3 Nucleic Acid Molecules
  • the invention provides isolated nucleic acid molecules comprising nucleotide sequences of dmSNF3s, and more particularly dmSNF3 nucleic acid sequences of Drosophila, and methods of using these sequences.
  • dmSNF3s nucleotide sequences of dmSNF3s
  • dmSNF3 nucleic acid sequences of Drosophila methods of using these sequences.
  • SEQ ID NO: 9 was isolated from Drosophila that encodes a dmSNF3 homolog.
  • a dmSNF3 nucleic acid molecule comprises a nucleotide sequence of at least about 50, at least about 75, at least about 100, at least about 150, at least about 200, at least about 300, at least about 400, at least about 500, at least about 600, at least about 700, at least about 800, at least about 900, at least about 1000, at least about 1100, at least about 1200, at least about 1300, at least about 1400, at least about 1500, at least about 1600, at least about 1700, at least about at least about 1800, at least about 1900, at least about 2000, or at least about 2100 contiguous nucleotides of the sequence set forth in SEQ ID NO:9, up to the entire sequence set forth in SEQ ID NO:9.
  • a dmSNF3 nucleic acid molecule of the invention comprises a nucleotide sequence that encodes a polypeptide comprising at least about 6, at least about 10, at least about 20, at least about 50, at least about 75, at least about 100, at least about 150, at least about 200, at least about 250, at least about 300, at least about 350, at least about 400, at least about 500, at least about 550, at least about 600, or at least about 625 contiguous amino acids of the sequence set forth in SEQ ID NO : 10, up to the entire amino acid sequence as set forth in SEQ ID NO : 10.
  • SEQ ID NO:9 encodes the signature motif of the sodium neurotransmitter symporter (SNF) family which is located at approximately nucleotides 197-1843.
  • Other preferred fragments encode the transmembrane domains, which are located at approximately nucleotides 208 - 268; 308 - 368; 458 - 518; 764 - 824; 854 - 914; 1112 - 1172; 1274 - 1334; 1391 - 1451; 1469 - 1529; 1613 - 1673; and 1739 - 1799.
  • dmSNF3 protein fragments and derivatives are discussed further below in connection with specific dmSNF3 proteins.
  • the invention provides isolated nucleic acid molecules comprising nucleotide sequences of GABA transporters, and more particularly GABA transporter nucleic acid sequences of Drosophila, and methods of using these sequences.
  • a nucleic acid sequence SEQ ID NO: 11
  • dmGAT a nucleic acid sequence
  • a dmGAT nucleic acid molecule comprises a nucleotide sequence of at least about 50, at least about 75, at least about 100, at least about 150, at least about 200, at least about 300, at least about 400, at least about 500, at least about 600, at least about 700, at least about 800, at least about 900, at least about 1000, at least about 1100, at least about 1200, at least about 1300, at least about 1400, at least about 1500, at least about 1600, at least about 1700, at least about at least about 1800, at least about 1900, at least about 2000, at least about 2100, at least about 2200, at least about 2300 at least about 2400, at least about 2500, at least about 2600, at least about 2700, at least about 2800, at least about 2900, at least about 3000, at least about 3100, at least about 3200, at least about 3300, at least about 3400, at least about 3500, at least about 3600, at least about 3700, at least
  • a dmGAT nucleic acid molecule of the invention comprises a nucleotide sequence that encodes a polypeptide comprising at least about 6, at least about 10, at least about 20, at least about 50, at least about 75, at least about 100, at least about 150, at least about 200, at least about 250, at least about 300, at least about 350, at least about 400, at least about 450, at least about 500, at least about 550, at least about 600, at least about 650, or at least about 670 contiguous amino acids of the sequence set forth in SEQ ID NO: 12, up to the entire amino acid sequence as set forth in SEQ ID NO: 12.
  • SEQ ID NO: 11 encodes the transmembrane domains, which are located at approximately nucleotides 293-355, 386-448, 554-616, 857-919, 929-991, 1082-1144, 1199-1261, 1343-1405, 1481-1543, 1580-1642, 1712-1774, and 1823-1885.
  • Another preferred domain encodes the signature motif of the sodium neurotransmitter symporter (SNF) family, which is located at approximately nucleotides 278-1939.
  • SNF sodium neurotransmitter symporter
  • dmGAT protein fragments and derivatives are discussed further below in connection with specific dmGAT proteins.
  • the subject nucleic acid molecules, or fragments or derivatives thereof may be obtained from an appropriate cDNA library prepared from any eukaryotic species that encodes a subject protein, such as vertebrates, preferably mammalian (e.g. primate, porcine, bovine, feline, equine, and canine species, etc.) and invertebrates, such as arthropods, particularly insects species (preferably Drosophila), acarids, crustacea, molluscs, nematodes, and other worms.
  • An expression library can be constructed using known methods.
  • mRNA can be isolated to make cDNA which is ligated into a suitable expression vector for expression in a host cell into which it is introduced.
  • Various screening assays can then be used to select for the gene or gene product (e.g. oligonucleotides of at least about 20 to 80 bases designed to identify the gene of interest, or labeled antibodies that specifically bind to the gene product).
  • the gene and/or gene product can then be recovered from the host cell using known techniques.
  • PCR Polymerase chain reaction
  • oligonucleotide primers representing fragmentary sequences of interest amplify RNA or DNA sequences from a source such as a genomic or cDNA library (as described by Sambrook et al, supra). Additionally, degenerate primers for amplifying homologs from any species of interest may be used.
  • a PCR product of appropriate size and sequence is obtained, it may be cloned and sequenced by standard techniques, and utilized as a probe to isolate a complete cDNA or genomic clone.
  • Fragmentary sequences of the subject nucleic acid molecules and derivatives thereof may be synthesized by known methods.
  • oligonucleotides may be synthesized using an automated DNA synthesizer available from commercial suppliers (e.g. Biosearch, Novato, CA; Perkin-Elmer Applied Biosystems, Foster Cify, CA).
  • Antisense RNA sequences can be produced intracellularly by transcription from an exogenous sequence, e.g. from vectors that contain subject antisense nucleic acid sequences. Newly generated sequences may be identified and isolated using standard methods.
  • An isolated subject nucleic acid molecule can be inserted into any appropriate cloning vector, for example bacteriophages such as lambda derivatives, or plasmids such as PBR322, pUC plasmid derivatives and the Bluescript vector (Stratagene, San Diego, CA). Recombinant molecules can be introduced into host cells via transformation, transfection, infection, electroporation, etc., or into a transgenic animal such as a fly. The transformed cells can be cultured to generate large quantities of the subject nucleic acid. Suitable methods for isolating and producing the subject nucleic acid sequences are well known in the art (Sambrook et al, supra; DNA Cloning: A Practical Approach, Vol. 1, 2, 3, 4, (1995) Glover, ed., MRL Press, Ltd., Oxford, U.K.).
  • the nucleotide sequence encoding a subject protein or fragment or derivative thereof can be inserted into any appropriate expression vector for the transcription and translation of the inserted protein-coding sequence.
  • the necessary transcriptional and translational signals can be supplied by the native subject gene and/or its flanking regions.
  • a variety of host-vector systems may be utilized to express the protein-coding sequence such as mammalian cell systems infected with virus (e.g. vaccinia virus, adenovirus, etc); insect cell systems infected with virus (e.g. baculovirus); microorganisms such as yeast containing yeast vectors, or bacteria transformed with bacteriophage, DNA, plasmid DNA, or cosmid DNA.
  • Expression of a subject protein may be controlled by a suitable promoter/enhancer element.
  • a host cell strain may be selected which modulates the expression of the inserted sequences, or modifies and processes the gene product in the specific fashion desired.
  • the expression vector can comprise a promoter operably linked to a subject nucleic acid molecule, one or more origins of replication, and, one or more selectable markers (e.g. thymidine kinase activity, resistance to antibiotics, etc).
  • selectable markers e.g. thymidine kinase activity, resistance to antibiotics, etc.
  • recombinant expression vectors can be identified by assaying for the expression of a subj ect gene product based on the physical or functional properties of a subject protein in in vitro assay systems (e.g. immunoassays).
  • a subject protein, fragment, or derivative maybe optionally expressed as a fusion, or chimeric protein product (i.e. it is joined via a peptide bond to a heterologous protein sequence of a different protein).
  • a chimeric product can be made by ligating the appropriate nucleic acid sequences encoding the desired amino acid sequences to each other in the proper coding frame using standard methods and expressing the chimeric product.
  • a chimeric product may also be made by protein synthetic techniques, e.g. by use of a peptide synthesizer.
  • the gene product can be isolated and purified using standard methods (e.g. ion exchange, affinity, and gel exclusion chromatography; centrifugation; differential solubility; electrophoresis).
  • the amino acid sequence of the protein can be deduced from the nucleotide sequence of the chimeric gene contained in the recombinant and can thus be synthesized by standard chemical methods (Hunkapiller et al., Nature (1984) 310: 105- 111).
  • native subject proteins can be purified from natural sources, by standard methods (e.g. immunoaffinify purification).
  • the invention further provides isolated polypeptides comprising or consisting of an amino acid sequence of any of SEQ ID NOS:2, 4, 6, 8, 10, or 12, or fragments or derivatives thereof.
  • Compositions comprising any of these proteins may consist essentially of a subject protein, fragments, or derivatives, or may comprise additional components (e.g. pharmaceutically acceptable carriers or excipients, culture media, carriers used in pesticide formulations, etc).
  • a derivative of a subject protein typically shares a certain degree of sequence identify or sequence similarity with any one of SEQ IDNOS:2, 4, 6, 8, 10, or 12, or a fragment thereof.
  • percent (%) amino acid sequence identify with respect to a subject sequence, or a specified portion of a subject sequence, is defined as the percentage of a ino acids in the candidate derivative amino acid sequence identical with the amino acid in the subject sequence (or specified portion thereof), after aligning the sequences and introducing gaps, if necessary to achieve the maximum percent sequence identify, as generated by BLAST (Altschul et al, supra) using the same parameters discussed above for derivative nucleic acid sequences.
  • a %> amino acid sequence identify value is determined by the number of matching identical amino acids divided by the sequence length for which the percent identity is being reported. "Percent (%) amino acid sequence similarity" is determined by doing the same calculation as for determining %> amino acid sequence identify, but including conservative amino acid substitutions in addition to identical amino acids in the computation. A conservative amino acid substitution is one in which an amino acid is substituted for another amino acid having similar properties such that the folding or activity of the protein is not significantly affected.
  • Aromatic amino acids that can be substituted for each other are phenylalanine, tryptophan, and tyrosine; interchangeable hydrophobic amino acids are leucine, isoleucine, methionine, and valine; interchangeable polar amino acids are glutamine and asparagine; interchangeable basic amino acids are arginine, lysine and histidine; interchangeable acidic amino acids are aspartic acid and glutamic acid; and interchangeable small amino acids are alanine, serine, threonine, cysteine, and glycine.
  • a subject protein derivative shares at least 80% sequence identity or similarity, preferably at least 85%, more preferably at least 90%>, and most preferably at least 95% sequence identify or similarity with a contiguous stretch of at least 25 amino acids, preferably at least 50 amino acids, more preferably at least 100 amino acids, and in some cases, the entire length of any one of SEQ ID NOS:2, 4, 6, 8, 10, or 12.
  • the fragment or derivative of a subject protein is preferably "functionally active" meaning that the subject protein derivative or fragment exhibits one or more functional activities associated with a full-length, wild-type subject protein comprising the amino acid sequence of any one of SEQ ID NOS:2, 4, 6, 8, 10, or 12.
  • a fragment or derivative may have antigenicity such that it can be used in immunoassays, for immunization, for inhibition of activity of a subject protein, etc, as discussed further below regarding generation of antibodies to subject proteins.
  • a functionally active fragment or derivative of a subject protein is one that displays one or more biological activities associated with a subject protein, such as transport, ion conductance, etc.
  • functionally active fragments also include those fragments that exhibit one or more structural features of a subject protein, such as transmembrane or SNF domains.
  • the functional activity of the subject proteins, derivatives and fragments can be assayed by various methods known to one skilled in the art (Current Protocols in Protein Science (1998) Coligan et al, eds., John Wiley & Sons, Inc., Somerset, New Jersey).
  • a model organism such as Drosophila, is used in genetic studies to assess the phenofypic effect of a fragment or derivative (i.e. a mutant of a subject protein).
  • a derivative of a subject protein can be produced by various methods known in the art. The manipulations which result in their production can occur at the gene or protein level. For example, a cloned subject gene sequence can be cleaved at appropriate sites with restriction endonuclease(s) (Wells et al, Philos. Trans. R. Soc. London SerA (1986) 317:415), followed by further enzymatic modification if desired, isolated, and ligated in vitro, and expressed to produce the desired derivative.
  • a subject gene can be mutated in vitro or in vivo, to create and/or destroy translation, initiation, and/or termination sequences, or to create variations in coding regions and/or to form new restriction endonuclease sites or destroy preexisting ones, to facilitate further in vitro modification.
  • a variety of mutagenesis techniques are known in the art such as chemical mutagenesis, in vitro site-directed mutagenesis (Carter et al, Nucl. Acids Res. (1986) 13:4331), use of TAB ® linkers (available from Pharmacia and Upjohn, Kalamazoo, MI), etc.
  • manipulations include post translational modification, e.g. glycosylation, acetylation, phosphorylation, amidation, derivatization by known protecting/blocking groups, proteolytic cleavage, linkage to an antibody molecule or other cellular ligand, etc.
  • Any of numerous chemical modifications may be carried out by known technique (e.g. specific chemical cleavage by cyanogen bromide, trypsin, chymotrypsin, papain, V8 protease, NaBtL, acetylation, formylation, oxidation, reduction, metabolic synthesis in the presence of tunicamycin, etc).
  • Derivative proteins can also be chemically synthesized by use of a peptide synthesizer, for example to introduce nonclassical amino acids or chemical amino acid analogs as substitutions or additions into the subject protein sequence.
  • Chimeric or fusion proteins can be made comprising a subject protein or fragment thereof (preferably comprising one or more structural or functional domains of the subject protein) joined at its amino- or carboxy-terminus via a peptide bond to an amino acid sequence of a different protein.
  • Chimeric proteins can be produced by any known method, including: recombinant expression of a nucleic acid encoding the protein (comprising an amino acid sequence encoding a subject protein joined in-frame to a coding sequence for a different protein); ligating the appropriate nucleic acid sequences encoding the desired amino acid sequences to each other in the proper coding frame, and expressing the chimeric product; and protein synthetic techniques, e.g. by use of a peptide synthesizer. Specific subject proteins are discussed below.
  • the invention provides isolated dmNTT4 polypeptides.
  • isolated dmNTT4 polypeptides comprise or consist of an amino acid sequence of SEQ ID NO:2, or fragments or derivatives thereof.
  • a dmNTT4 polypeptide of the invention comprises an amino acid sequence of at least about 6, at least about 10, at least about 20, at least about 50, at least about 75, at least about 100, at least about 150, at least about 200, at least about 250, at least about 300, at least about 350, at least about 400, at least about 450, at least about 500, at least about 550, at least about 600, at least about 650, or at least about 670 contiguous amino acids of the sequence set forth in SEQ ID NO:2, up to the entire amino acid sequence as set forth in SEQ ID NO:2.
  • a dmNTT4 protein derivative may consist of or comprise a sequence that shares 100% similarity with any contiguous stretch of at least 35 amino acids, preferably at least 37 amino acids, more preferably at least 40 amino acids, and most preferably at least 45 amino acids of SEQ ID NO:2.
  • Preferred derivatives of dmNTT4 consist of or comprise an amino acid sequence that has at least 80%, preferably at least 85%, more preferably at least 90%, and most preferably at least 95% sequence identity or sequence similarity with any of amino acid residues 55-352, or 395-617, which code for the putative SNF domains, or residues 153-216, which code for the extracellular loop.
  • Preferred fragments of dmNTT4 proteins consist or comprise at least 15, preferably at least 17, more preferably at least 20, and most preferably at least 25 contiguous amino acids of SEQ ID NO:2.
  • the invention provides isolated dmKSNF polypeptides.
  • isolated dmKSNF proteins of the invention comprise or consist of an amino acid sequence of SEQ ID NO:4, or fragments or derivatives thereof.
  • an isolated dmKSNF polypeptide of the invention comprises an amino acid sequence of at least about 6, at least about 10, at least about 20, at least about 50, at least about 75, at least about 100, at least about 150, at least about 200, at least about 250, at least about 300, at least about 350, at least about 400, at least about 450, at least about 500, at least about 550, at least about 600, or at least about 630 contiguous amino acids of the sequence set forth in SEQ ID NO:4, up to the entire amino acid sequence as set forth in SEQ ID NO:4.
  • the dmKSNF protein derivative may consist of or comprise a sequence that shares 100% similarity with any contiguous stretch of at least 29 amino acids, preferably at least 31 amino acids, more preferably at least 34 amino acids, and most preferably at least 39 amino acids of SEQ ID NO:4.
  • Preferred derivatives of dmKSNF consist of or comprise an amino acid sequence that has at least 80%>, preferably at least 85%, more preferably at least 90%, and most preferably at least
  • Preferred fragments of dmKSNF proteins consist or comprise at least 20, preferably at least 22, more preferably at least 25, and most preferably at least 30 contiguous amino acids of SEQ ID NO:4.
  • the invention provides isolated dmSNF polypeptides.
  • isolated dmSNF proteins of the invention comprise or consist of an amino acid sequence of SEQ ID NO : 6, or fragments or derivatives thereof.
  • an isolated dmSNF polypeptide comprises at least about 6, at least about 10, at least about 20, at least about 50, at least about 75, at least about 100, at least about 150, at least about 200, at least about 250, at least about 300, at least about 350, or at least about 400 contiguous amino acids of the sequence set forth in SEQ ID NO: 6, up to the entire amino acid sequence as set forth in SEQ ID NO:6.
  • a dmSNF protein derivative shares at least 70% sequence identity or similarity, preferably at least 75%, more preferably at least 80%, still more preferably at least 85%, more preferably at least 90%, and most preferably at least 95%> sequence identity or similarity with a contiguous stretch of at least 25 amino acids, preferably at least 50 amino acids, more preferably at least 100 amino acids, and in some cases, the entire length of SEQ ID NO:6.
  • dmSNF preferred derivatives of dmSNF consist of or comprise an amino acid sequence that has the above-specified percent similarity or identity with amino acid residues 123-214, which comprise the SNF domain, or any of amino acid residues 1-119, 137-158, 176-221, 239-291, or 209-403, which are extra- or intracellular domains.
  • the dmSNF protein derivative may consist of or comprise a sequence that shares 100% similarity with any contiguous stretch of at least 23 amino acids, preferably at least 25 amino acids, more preferably at least 28 amino acids, and most preferably at least 33 amino acids of SEQ ID NO:6.
  • Preferred fragments of dmSNF proteins consist or comprise at least 19, preferably at least 21, more preferably at least 24, and most preferably at least 29 contiguous amino acids of SEQ ID NO:6.
  • the invention provides isolated dmSNF2 polypeptides.
  • isolated dmSNF2 proteins of the invention comprise or consist of an amino acid sequence of SEQ ID NO: 8, or fragments or derivatives thereof.
  • an isolated dmSNF2 polypeptide comprises at least about 6, at least about 10, at least about 20, at least about 50, at least about 75, at least about 100, at least about 150, at least about 200, at least about 250, at least about 300, at least about 350, at least about 400, at least about 500, at least about 550, or at least about 575 contiguous amino acids of the sequence set forth in SEQ ID NO:8, up to the entire amino acid sequence as set forth in SEQ ID NO:8.
  • a dmSNF2 protein derivative shares at least 70% sequence identity or similarity, preferably at least 75%, more preferably at least 80%, still more preferably at least 85%, more preferably at least 90%>, and most preferably at least 95%> sequence identity or similarity with a contiguous stretch of at least 25 amino acids, preferably at least 50 amino acids, more preferably at least 100 amino acids, and in some cases, the entire length of SEQ ID NO:8.
  • dmSNF2 consist of or comprise an amino acid sequence that shares the above sequence identities or similarities with amino acid residues 15-548 of SEQ ID NO:8, which comprise the SNF domain, or with any of amino acid residues 1-21, 69-100, 118-189, 233-264, 282-304, 322-357, 375- 395, 449-475, and 519-592 of SEQ ID NO:8, which are intracellular or extracellular domains.
  • the dmSNF2 protein derivative may consist of or comprise a sequence that shares 100% similarity with any contiguous stretch of at least 19 amino acids, preferably at least 21 amino acids, more preferably at least 24 amino acids, and most preferably at least 29 amino acids of SEQ ID NO:8.
  • Preferred fragments of dmSNF2 proteins consist or comprise at least 12, preferably at least 14, more preferably at least 17, and most preferably at least 22 contiguous amino acids of SEQ ID NO : 8. Further preferred fragments consist of or comprise dmSNF2 transmembrane domains.
  • the invention provides isolated dmSNF3 polypeptides.
  • isolated dmSNF3 proteins of the invention comprise or consist of an amino acid sequence of SEQ ID NO : 10, or fragments or derivatives thereof.
  • an isolated dmSNF3 polypeptide comprises at least about 6, at least about 10, at least about 20, at least about 50, at least about 75, at least about 100, at least about 150, at least about 200, at least about 250, at least about 300, at least about 350, at least about 400, at least about 500, at least about 550, at least about 600, or at least about 625 contiguous amino acids of the sequence set forth in SEQ ID NO: 10, up to the entire amino acid sequence as set forth in SEQ ID NO.10.
  • a dmSNF3 protein derivative shares at least 70% sequence identity or similarity, preferably at least 75%, more preferably at least 80%, still more preferably at least 85%, more preferably at least 90%, and most preferably at least 95% sequence identity or similarity with a contiguous stretch of at least 25 amino acids, preferably at least 50 amino acids, more preferably at least 100 amino acids, and in some cases, the entire length of SEQ ID NO: 10.
  • dmSNF3 consist of or comprise an amino acid sequence that shares the above sequence identities or similarities with amino acid residues 50-598 of SEQ ID NO: 10, which comprise the SNF domain, or with amino acids 57-73; 87-103; 137-153; 239-255; 269-285; 355-371; 408-424; 448-464; 474-490; 522-538; and 564-580, which are the transmembrane domains.
  • extracellular or intracellular domain-encoding regions between the transmembrane domains e.g. residues 1-56, 74-86, etc
  • the dmSNF3 protein derivative may consist of or comprise a sequence that shares 100% similarity with any contiguous stretch of at least 21 amino acids, preferably at least 23 amino acids, more preferably at least 26 amino acids, and most preferably at least 31 amino acids of SEQ ID NO:10.
  • Preferred fragments of dmSNF3 proteins consist or comprise at least 12 preferably at least 14, more preferably at least 17, and most preferably at least 22 contiguous amino acids of SEQ ID NO:10.
  • the invention provides isolated dmGAT polypeptides.
  • isolated dmGAT proteins of the invention comprise or consist of an amino acid sequence of SEQ ID NO: 12, or fragments or derivatives thereof.
  • an isolated dmGAT polypeptide comprises at least about 6, at least about
  • a dmGAT protein derivative shares at least 80% sequence identity or similarity, preferably at least 85%, more preferably at least 90%, and most preferably at least 95% sequence identity or similarity with a contiguous stretch of at least 25 amino acids, preferably at least 50 amino acids, more preferably at least 100 amino acids, and in some cases, the entire length of SEQ ID NO : 12.
  • the derivative dmGAT protein has the biological activity of a dmGAT protein.
  • the dmGAT protein derivative may consist of or comprise a sequence that shares 100% similarity with any contiguous stretch of at least 85 amino acids, preferably at least 87 amino acids, more preferably at least 90 amino acids, and most preferably at least 95 amino acids of SEQ ID NO:12.
  • Preferred derivatives of dmGAT consist of or comprise an amino acid sequence that has at least 80%, preferably at least 85%, more preferably at least 90%, and most preferably at least 95% sequence identity or sequence similarity with any of amino acid residues 58-611, which comprise the SNF domain, or with amino acids 63-83, 94-114, 150-170, 251-271, 275-295, 326-346, 365-385, 413-433, 459-479, 492-512, 536-556, and 573-593, which are the likely transmembrane domains. Other preferred derivatives share these % identities or similarities with intra- or extracellular domains of dmGAT that reside between the transmembrane domains (i.e. residues 1-57, 84-93, etc.).
  • Preferred fragments of dmGAT proteins consist or comprise at least 43, preferably at least 45, more preferably at least 48, and most preferably at least 53 contiguous amino acids of SEQ ID NO: 12.
  • the invention further provides gene regulatory DNA elements, such as enhancers or promoters that control transcription of the subject nucleic acid molecules.
  • gene regulatory DNA elements such as enhancers or promoters that control transcription of the subject nucleic acid molecules.
  • Such regulatory elements can be used to identify tissues, cells, genes and factors that specifically control production of a subject protein. Analyzing components that are specific to a particular subject protein function can lead to an understanding of how to manipulate these regulatory processes, especially for pesticide and therapeutic applications, as well as an understanding of how to diagnose dysfunction in these processes.
  • Gene fusions with the subject regulatory elements can be made. For compact genes that have relatively few and small intervening sequences, such as those described herein for Drosophila, it is typically the case that the regulatory elements that control spatial and temporal expression patterns are found in the DNA immediately upstream of the coding region, extending to the nearest neighboring gene. Regulatory regions can be used to construct gene fusions where the regulatory DNAs are operably fused to a coding region for a reporter protein whose expression is easily detected, and these constructs are introduced as transgenes into the animal of choice. An entire regulatory DNA region can be used, or the regulatory region can be divided into smaller segments to identify sub-elements that might be specific for controlling expression a given cell type or stage of development.
  • Reporter proteins that can be used for construction of these gene fusions include E. coli beta-galactosidase and green fluorescent protein (GFP). These can be detected readily in situ, and thus are useful for histological studies and can be used to sort cells that express a subject protein (O'Kane and Gehring PNAS (1987) 84(24):9123-9127; Chalfie et al, Science (1994) 263:802-805; and Cumberledge and Krasnow (1994) Methods in Cell Biology 44:143-159).
  • E. coli beta-galactosidase and green fluorescent protein (GFP). These can be detected readily in situ, and thus are useful for histological studies and can be used to sort cells that express a subject protein (O'Kane and Gehring PNAS (1987) 84(24):9123-9127; Chalfie et al, Science (1994) 263:802-805; and Cumberledge and Krasnow (1994) Methods in Cell Biology 44:143-159).
  • Recombinase proteins such as FLP or ere
  • Recombinase proteins can be used in controlling gene expression through site-specific recombination (Golic and Lindquist (1989) Cell 59(3):499-509; White et al, Science (1996) 271 :805-807).
  • Toxic proteins such as the reaper and hid cell death proteins, are useful to specifically ablate cells that normally express a subject protein in order to assess the physiological function of the cells (Kingston, In Current Protocols in Molecular Biology (1998) Ausubel et al, John Wiley & Sons, Inc. sections 12.0.3-12.10) or any other protein where it is desired to examine the function this particular protein specifically in cells that synthesize a subject protein.
  • a binary reporter system can be used, similar to that described further below, where a subject regulatory element is operably fused to the coding region of an exogenous transcriptional activator protein, such as the GAL4 or tTA activators described below, to create a subject regulatory element "driver gene".
  • an exogenous transcriptional activator protein such as the GAL4 or tTA activators described below
  • the exogenous activator controls a separate "target gene” containing a coding region of a reporter protein operabfy fused to a cognate regulatory element for the exogenous activator protein, such as UAS G or a tTA-response element, respectively.
  • Subject regulatory element-reporter gene fusions are also useful for tests of genetic interactions, where the objective is to identify those genes that have a specific role in controlling the expression of subject genes, or promoting the growth and differentiation of the tissues that expresses a subject protein.
  • Subject gene regulatory DNA elements are also useful in protein-DNA binding assays to identify gene regulatory proteins that control the expression of subject genes.
  • the gene regulatory proteins can be detected using a variety of methods that probe specific protein-DNA interactions well known to those skilled in the art (Kingston, supra) including in vivo footprinting assays based on protection of DNA sequences from chemical and enzymatic modification within living or permeabilized cells; and in vitro footprinting assays based on protection of DNA sequences from chemical or enzymatic modification using protein extracts, nitrocellulose filter-binding assays and gel electrophoresis mobility shift assays using radioactively labeled regulatory DNA elements mixed with protein extracts.
  • Candidate gene regulatory proteins can be purified using a combination of conventional and DNA-affinity purification techniques. Molecular cloning strategies can also be used to identify proteins that specifically bind subject gene regulatory DNA elements.
  • a Drosophila cDNA library in an expression vector can be screened for cDNAs that encode subject gene regulatory element DNA-binding activity.
  • yeast "one-hybrid" system can be used (Li and Herskowitz, Science (1993) 262:1870- 1874; Luo et al, Biotechniques (1996) 20(4):564-568; Vidal et al, PNAS (1996) 93(19):10315- 10320).
  • dnNTT4 regulatory elements are provided.
  • dmNTT4 regulatory DNA elements such as enhancers or promoters that reside within nucleotides 1 to 238, can be used to identify tissues, cells, genes and factors that specifically control dmNTT4 protein production.
  • Preferably at least 20, more preferably at least 25, and most preferably at least 50 contiguous nucleotides within nucleotides 1 to 238 of SEQ ID NO:l are used. Analyzing components that are specific to dmNTT4 protein function can lead to an understanding of how to manipulate these regulatory processes, especially for pesticide and therapeutic applications, as well as an understanding of how to diagnose dysfunction in these processes.
  • dmKSNF regulatory elements are provided.
  • dmKSNF gene regulatory DNA elements such as enhancers or promoters that reside within nucleotides 1 to 248, can be used to identify tissues, cells, genes and factors that specifically control dmKSNF protein production.
  • dmSNF Gene Regulatory Elements are provided.
  • dmSNF regulatory elements are provided.
  • dmSNF gene regulatory DNA elements such as enhancers or promoters that reside within nucleotides 1 to 497, can be used to identify tissues, cells, genes and factors that specifically control dmSNF protein production.
  • Preferably at least 20, more preferably at least 25, and most preferably at least 50 contiguous nucleotides within nucleotides 1 to 497. of SEQ ID NO:5 are used. Analyzing components that are specific to dmSNF protein function can lead to an understanding of how to manipulate these regulatory processes, especially for pesticide and therapeutic applications, as well as an understanding of how to diagnose dysfunction in these processes.
  • dmSNF2 regulatory elements are provided.
  • dmSNF2 gene regulatory DNA elements such as enhancers or promoters that reside within nucleotides 1 to 56, can be used to identify tissues, cells, genes and factors that specifically control dmSNF2 protein production.
  • Preferably at least 20, more preferably at least 25, and most preferably at least 50 contiguous nucleotides within nucleotides 1 to 56 of SEQ ID NO:7 are used. Analyzing components that are specific to dmSNF2 protein function can lead to an understanding of how to manipulate these regulatory processes, especially for pesticide and therapeutic applications, as well as an understanding of how to diagnose dysfunction in these processes.
  • dmSNF3 regulatory elements are provided.
  • dmSNF3 gene regulatory DNA elements such as enhancers or promoters that reside within nucleotides 1 to 49, can be used to identify tissues, cells, genes and factors that specifically control dmSNF3 protein production.
  • Preferably at least 20, more preferably at least 25, and most preferably at least 40 contiguous nucleotides within nucleotides 1 to 49 of SEQ ID NO:9 are used. Analyzing components that are specific to dmSNF3 protein function can lead to an understanding of how to manipulate these regulatory processes, especially for pesticide and therapeutic applications, as well as an understanding of how to diagnose dysfunction in these processes.
  • dmGAT regulatory elements are provided.
  • dmGAT gene regulatory DNA elements such as enhancers or promoters that reside within nucleotides 1 to 106, can be used to identify tissues, cells, genes and factors that specifically control dmGAT protein production.
  • the present invention provides antibodies, which may be isolated antibodies, that bind specifically to a subject protein.
  • the subject proteins, fragments thereof, and derivatives thereof may be used as an immunogen to generate monoclonal or polyclonal antibodies and antibody fragments or derivatives (e.g. chimeric, single chain, Fab fragments).
  • fragments of a subject protein preferably those identified as hydrophilic, are used as immunogens for antibody production using art- known methods such as by hybridomas; production of monoclonal antibodies in germ-free animals (PCT US90/02545); the use of human hybridomas (Cole et al, PNAS (1983) 80:2026-2030; Cole et al, in Monoclonal Antibodies and Cancer Therapy (1985) Alan R.
  • subject polypeptide fragments provide specific antigens and/or immunogens, especially when coupled to carrier proteins.
  • peptides are covalently coupled to keyhole limpet antigen (KLH) and the conjugate is emulsified in Freund's complete adjuvant.
  • KLH keyhole limpet antigen
  • Laboratory rabbits are immunized according to conventional protocol and bled. The presence of specific antibodies is assayed by solid phase immunosorbent assays using immobilized corresponding polypeptide.
  • Binding affinity may be assayed by determination of equilibrium constants of antigen-antibody association (usually at least about 10 7 M _1 , preferably at least about 10 8 M "1 , more preferably at least about 10 9 M "1 ).
  • a variety of methods can be used to identify or screen for molecules, such as proteins or other molecules, that interact with a subject protein, or derivatives or fragments thereof.
  • the assays may employ purified protein, or cell lines or model organisms such as Drosophila and C. elegans, that have been genetically engineered to express a subject protein. Suitable screening methodologies are well known in the art to test for proteins and other molecules that interact with a subject gene and protein (see e.g., PCT International Publication No. WO 96/34099).
  • the newly identified interacting molecules may provide new targets for pharmaceutical or pesticidal agents. Any of a variety of exogenous molecules, both naturally occurring and/or synthetic (e.g.
  • libraries of small molecules or peptides, or phage display libraries may be screened for binding capacity, hi a typical binding experiment, a subject protein or fragment is mixed with candidate molecules under conditions conducive to binding, sufficient time is allowed for any binding to occur, and assays are performed to test for bound complexes.
  • Assays to find interacting proteins can be performed by any method known in the art, for example, immunoprecipitation with an antibody that binds to the protein in a complex followed by analysis by size fractionation of the immunoprecipitated proteins (e.g.
  • Immunoassays can be used to identify proteins that interact with or bind to a subject protein.
  • Various assays are available for testing the ability of a protein to bind to or compete with binding to a wild-type subject protein or for binding to an anti- subject protein antibody.
  • Suitable assays include radioimmunoassays, ELISA (enzyme linked immunosorbent assay), immunoradiometric assays, gel diffusion precipitin reactions, immunodiffusion assays, in situ immunoassays (e.g., using colloidal gold, enzyme or radioisotope labels), western blots, precipitation reactions, agglutination assays (e.g., gel agglutination assays, hemagglutination assays), complement fixation assays, immunofluorescence assays, protein A assays, immunoelectrophoresis assays, etc.
  • radioimmunoassays e.g., ELISA (enzyme linked immunosorbent assay), immunoradiometric assays, gel diffusion precipitin reactions, immunodiffusion assays, in situ immunoassays (e.g., using colloidal gold, enzyme or radioisotope labels), western blots, precipitation reactions, agglutin
  • new target genes or target interacting genes can be assessed as potential pesticide or drug targets, or as potential biopesticides.
  • transgenic plants that express subject proteins can be tested for activity against insect pests (Estruch et al, Nat. Biotechnol (1997) 15(2):137-141).
  • the subject proteins are validated pesticide targets, since disruption of the Drosophila the subject genes results in lethality when homozygous.
  • the mutation to lethality of these gene indicates that drugs that agonize or antagonize the gene product may be effective pesticidal agents.
  • pesticide refers generally to chemicals, biological agents, and other compounds that il, paralyze, sterilize or otherwise disable pest species in the areas of agricultural crop protection, human and animal health.
  • exemplary pest species include parasites and disease vectors such as mosquitoes, fleas, ticks, parasitic nematodes, chiggers, mites, etc.
  • Pest species also include those that are eradicated for aesthetic and hygienic purposes (e.g. ants, cockroaches, clothes moths, flour beetles, etc), home and garden applications, and protection of structures (including wood boring pests such as termites, and marine surface fouling organisms).
  • Pesticidal compounds can include traditional small organic molecule pesticides (typified by compound classes such as the organophosphates, pyrethroids, carbamates, and organochlorines, benzoylureas, etc).
  • Other pesticides include proteinaceous toxins such as the Bacillus thuringiensis Crytoxins (Gill et al, Annu Rev Entomol (1992) 37:615-636) and Photorabdus luminescens toxins (Bowden et al, Science (1998) 280:2129-2132); and nucleic acids such as subject dsRNA or antisense nucleic acids that interfere with activity of a subject nucleic acid molecule.
  • Pesticides can be delivered by a variety of means including direct application to pests or to their food source.
  • toxic proteins and pesticidal nucleic acids e.g. dsRNA
  • biopesticidal methods for example, by viral infection with nucleic acid or by transgenic plants that have been engineered to produce interfering nucleic acid sequences or encode the toxic protein, which are ingested by plant-eating pests.
  • Putative pesticides, drugs, and molecules can be applied onto whole insects, nematodes, and other small invertebrate metazoans, and the ability of the compounds to modulate (e.g. block or enhance) activity of a subject protein can be observed.
  • the effect of various compounds on a subject protein can be assayed using cells that have been engineered to express one or more subject proteins and associated proteins.
  • the compounds to be tested are dissolved in DMSO or other organic solvent, mixed with a bacterial suspension at various test concentrations, preferably OP50 strain of bacteria (Brenner, Genetics (1974) 110:421-440), and supplied as food to the worms.
  • the population of worms to be treated can be synchronized larvae (Sulston and Hodgkin, in the nematode C. elegans (1988), supra) or adults or a mixed-stage population of animals.
  • Ratios are treated with different concentrations of compounds, typically ranging from 1 mg/ml to 0.001 mg/ml. Behavioral aberrations, such as a decrease in motility and growth, and morphological aberrations, sterility, and death are examined in both acutely and chronically treated adult and larval worms.
  • larval and adult worms are examined immediately after application of the compound and re-examined periodically (every 30 minutes) for 5-6 hours.
  • Chronic or long-term assays are performed on worms and the behavior of the treated worms is examined every 8-12 hours for 4-5 days . In some circumstances, it is necessary to reapply the pesticide to the treated worms every 24 hours for maximal effect.
  • Potential insecticidal compounds can be administered to insects in a variety of ways, including orally (including addition to synthetic diet, application to plants or prey to be consumed by the test organism), topically (including spraying, direct application of compound to animal, allowing animal to contact a treated surface), or by injection.
  • Insecticides are typically very hydrophobic molecules and must commonly be dissolved in organic solvents, which are allowed to evaporate in the case of methanol or acetone, or at low concentrations can be included to facilitate uptake (ethanol, dimethyl sulfoxide).
  • the first step in an insect assay is usually the determination of the minimal lethal dose (MLD) on the insects after a chronic exposure to the compounds.
  • MLD minimal lethal dose
  • the compounds are usually diluted in DMSO, and applied to the food surface bearing 0-48 hour old embryos and larvae.
  • this step allows the determination of the fraction of eggs that hatch, behavior of the larvae, such as how they move /feed compared to untreated larvae, the fraction that survive to pupate, and the fraction that eclose (emergence of the adult insect frompuparium). Based on these results more detailed assays with shorter exposure times may be designed, and larvae might be dissected to look for obvious morphological defects. Once the MLD is determined, more specific acute and chronic assays can be designed.
  • compounds are applied to the food surface for embryos, larvae, or adults, and the animals are observed after 2 hours and after an overnight incubation.
  • embryos defects in development and the percent that survive to adulthood are determined.
  • larvae defects in behavior, locomotion, and molting may be observed.
  • behavior and neurological defects are observed, and effects on fertility are noted.
  • Compounds that modulate (e.g. block or enhance) a subject protein's activity may also be assayed using cell culture.
  • various compounds added to cells expressing a subject protein may be screened for their ability to modulate the activity of subject genes based upon measurements of a biological activity of a subject protein.
  • Assays for changes in a biological activity of a subject protein can be performed on cultured cells expressing endogenous normal or mutant subject protein. Such studies also can be performed on cells transfected with vectors capable of expressing the subject protein, or functional domains of one of the subject protein, in normal or mutant form.
  • cells may be cotransfected with genes encoding a subject protein.
  • cells expressing a subject protein may be lysed, the subject protein purified, and tested in vitro using methods known in the art (Kanemaki M., et al., J Biol Chem, 1999 274:22437- 22444).
  • Subject Nucleic Acids as Biopesticides Subject nucleic acids and fragments thereof, such as antisense sequences or double-stranded
  • RNA can be used to inhibit subject nucleic acid molecule function, and thus can be used as biopesticides. Methods of using dsRNA interference are described in published PCT application WO 99/32619.
  • the biopesticides may comprise the nucleic acid molecule itself, an expression construct capable of expressing the nucleic acid, or organisms transfected with the expression construct.
  • the biopesticides may be applied directly to plant parts or to soil surrounding the plants (e.g. to access plant parts growing beneath ground level), or directly onto the pest.
  • Biopesticides comprising a subject nucleic acid may be prepared in a suitable vector for delivery to a plant or animal.
  • suitable vectors include Agrobacterium tumefaciens Ti plasmid-based vectors (Horsch et ⁇ /., Science (1984) 233:496-89; Fraley et al, Proc. Natl. Acad. Sci. USA (1983) 80:4803), and recombinant cauliflower mosaic virus (Hohn et al, 1982, In Molecular Biology of Plant Tumors, Academic Press, New York, pp 549-560; U.S. Patent No. 4,407,956 to Howell).
  • Retrovirus based vectors are useful for the introduction of genes into vertebrate animals (Burns et al, Proc. Natl. Acad. Sci. USA (1993) 90:8033-37).
  • Transgenic insects can be generated using a transgene comprising a subject gene operably fused to an appropriate inducible promoter.
  • a tTA-responsive promoter may be used in order to direct expression of a subject protein at an appropriate time in the life cycle of the insect, i this way, one may test efficacy as an insecticide in, for example, the larval phase of the life cycle (i.e. when feeding does the greatest damage to crops).
  • Vectors for the introduction of genes into insects include P element (Rubin and Spradling, Science (1982) 218:348-53; U.S. Pat. No.
  • Recombinant virus systems for expression of toxic proteins in infected insect cells are well known and include Semliki Forest virus (DiCiommo and Bremner, J. Biol. Chem. (1998) 273:18060-66), recombinant Sindbis virus (Higgs et al, Insect Mol. Biol. (1995) 4:97- 103; Seabaugh et al, Virology (1998) 243:99-112), recombinant pantropic retrovirus (Matsubara et al, Proc. Natl. Acad. Sci. USA (1996) 93:6181-85; Jordan et al, Insect Mol. Biol.
  • mis-expressed subject pathway protein may be one having an amino acid sequence that differs from wild-type (i.e. it is a derivative of the normal protein).
  • a mis-expressed subject pathway protein may also be one in which one or more amino acids have been deleted, and thus is a "fragment" of the normal protein.
  • mis-expression also includes ectopic expression (e.g. by altering the normal spatial or temporal expression), over-expression (e.g. by multiple gene copies), underexpression, non-expression (e.g. by gene knockout or blocking expression that would otherwise normally occur), and further, expression in ectopic tissues.
  • the term “gene of interest” refers to a subject pathway gene, or any other gene involved in regulation or modulation, or downstream effector of the subject pathway.
  • the in vivo and in vitro models may be genetically engineered or modified so that they 1) have deletions and/or insertions of one or more subject pathway genes, 2) harbor interfering RNA sequences derived from subject pathway genes, 3) have had one or more endogenous subject pathway genes mutated (e.g. contain deletions, insertions, rearrangements, or point mutations in subject gene or other genes in the pathway), and/or 4) contain transgenes for mis-expression of wild-type or mutant forms of such genes.
  • Such genetically modified in vivo and in vitro models are useful for identification of genes and proteins that are involved in the synthesis, activation, control, etc. of subject pathway gene and/or gene products, and also downstream effectors of subject function, genes regulated by subject, etc.
  • the newly identified genes could constitute possible pesticide targets (as judged by animal model phenotypes such as non-viability, block of normal development, defective feeding, defective movement, or defective reproduction).
  • the model systems can also be used for testing potential pesticidal or pharmaceutical compounds that interact with the subject pathway, for example by administering the compound to the model system using any suitable method (e.g. direct contact, ingestion, injection, etc) and observing any changes in phenotype, for example defective movement, lethality, etc.
  • suitable method e.g. direct contact, ingestion, injection, etc
  • Various genetic engineering and expression modification methods which can be used are well-known in the art, including chemical mutagenesis, transposon mutagenesis, antisense RNAi, dsRNAi, and transgene-mediated mis- expression.
  • Loss-of-function mutations in an invertebrate metazoan subject gene can be generated by any of several mutagenesis methods known in the art (Ashburner, In Drosophila melanogaster: A Laboratory Manual (1989) , Cold Spring Harbor, NY, Cold Spring Harbor Laboratory Press: pp. 299-418; Fly pushing: The Theory and Practice of Drosophila melanogaster Genetics (1997) Cold Spring Harbor Press, Plainview, NY; The nematode C. elegans (1988) Wood, Ed., Cold Spring Harbor Laboratory Press, Cold Spring harbor, New York).
  • Techniques for producing mutations in a gene or genome include use of radiation (e.g., X-ray, UV, or gamma ray); chemicals (e.g., EMS, MMS, ENU, formaldehyde, etc); and insertional mutagenesis by mobile elements including dysgenesis induced by transposon insertions, or transposon-mediated deletions, for example, male recombination, as described below.
  • radiation e.g., X-ray, UV, or gamma ray
  • chemicals e.g., EMS, MMS, ENU, formaldehyde, etc
  • insertional mutagenesis by mobile elements including dysgenesis induced by transposon insertions, or transposon-mediated deletions, for example, male recombination, as described below.
  • transposons e.g., P element, EP-type "overexpression trap” element, mariner element, piggyBac transposon, her es, minos, sleeping beauty, etc
  • transposons e.g., P element, EP-type "overexpression trap” element, mariner element, piggyBac transposon, her es, minos, sleeping beauty, etc
  • antisense double-stranded RNA interference
  • peptide and RNA aptamers directed deletions
  • homologous recombination dominant negative alleles
  • intrabodies e.g., a transposons, e.g., P element, EP-type "overexpression trap” element, mariner element, piggyBac transposon, her es, minos, sleeping beauty, etc
  • Transposon insertions lying adjacent to a gene of interest can be used to generate deletions of flanking genomic DNA, which if induced in the germline, are stably propagated in subsequent generations.
  • the utility of this technique in generating deletions has been demonstrated and is well- known in the art.
  • One version of the technique using collections of P element transposon induced recessive lethal mutations (P lethals) is particularly suitable for rapid identification of novel, essential genes ⁇ nDrosophila (Cooley et al, Science (1988) 239:1121-1128; Spralding et al, PNAS (1995) 92:0824-10830).
  • the subject genes may be identified and/or characterized by generating loss-of-function phenotypes in animals of interest through RNA-based methods, such as antisense RNA (Schubiger and Edgar, Methods in Cell Biology (1994) 44:697-713).
  • RNA-based methods such as antisense RNA (Schubiger and Edgar, Methods in Cell Biology (1994) 44:697-713).
  • One form of the antisense RNA method involves the injection of embryos with an antisense RNA that is partially homologous to the gene of interest (in this case the subject gene).
  • Another form of the antisense RNA method involves expression of an antisense RNA partially homologous to the gene of interest by operably joining a portion of the gene of interest in the antisense orientation to a powerful promoter that can drive the expression of large quantities of antisense RNA, either generally throughout the animal or in specific tissues.
  • RNA-generated loss-of-function phenotypes have been reported previously for several Drosophila genes including cactus, pecanex, and Kriippel (LaBonne et al, Dev. Biol. (1989) 136(1):1-16; Schuh and Jackie, Genome (1989) 31(l):422-425; Geisler et al, Cell (1992) 71(4):613-621).
  • Loss-of-function phenotypes can also be generated by cosuppression methods (Bingham Cell
  • Cosuppression is a phenomenon of reduced gene expression produced by expression or injection of a sense strand RNA corresponding to a partial segment of the gene of interest. Cosuppression effects have been employed extensively in plants and C. elegans to generate loss-of- function phenotypes, and there is a single report of cosuppression in Drosophila, where reduced expression of the Adh gene was induced from a white-Adh transgene using cosuppression methods (Pal- Bhadra et al, Cell (1997) 90(3):479-490). Another method for generating loss-of-function phenotypes is by double-stranded RNA interference (dsRNAi).
  • dsRNAi double-stranded RNA interference
  • This method is based on the interfering properties of double-stranded RNA derived from the coding regions of gene, and has proven to be of great utility in genetic studies of C. elegans (Fire et al, Nature (1998) 391:806-811), and can also be used to generate loss-of-function phenotypes Drosophila (Kennerdell and Carthew, Cell (1998) 95:1017-1026; Misquitta and Patterson PNAS (1999) 96:1451-1456).
  • complementary sense and antisense RNAs derived from a substantial portion of a gene of interest, such as a subject gene are synthesized in vitro.
  • RNAs are annealed in an injection buffer, and the double-stranded RNA injected or otherwise introduced into animals (such as in their food or by soaking in the buffer containing the RNA). Progeny of the injected animals are then inspected for phenotypes of interest (PCT publication no. W099/32619).
  • the dsRNA can be delivered to the animal by bathing the animal in a solution containing a sufficient concentration of the dsRNA.
  • dsRNA derived from the subject genes can be generated in vivo by simultaneous expression of both sense and antisense RNA from appropriately positioned promoters operably fused to subject sequences in both sense and antisense orientations, hi yet another embodiment of the method the dsRNA can be delivered to the animal by engineering expression of dsRNA vrithin cells of a second organism that serves as food for the animal, for example engineering expression of dsRNA inE. coli bacteria which are fed to C. elegans, or engineering expression of dsRNA in baker's yeast which are fed to Drosophila, or engineering expression of dsRNA in transgenic plants which are fed to plant eating insects such as Leptinotarsa or Heliothis. Recently, RNAi has been successfully used in cultured
  • Drosophila cells to inhibit expression of targeted proteins Clemens, J.C., et al, Proc Natl Acad Sci U S A 2000 Jun 6;97(12):6499-503.
  • RNAi RNAi both to perturb and study the function of the subject gene pathway components and to validate the efficacy of therapeutic or pesticidal strategies that involve the manipulation of this pathway.
  • Intracellularly expressed antibodies, or intrabodies are single-chain antibody molecules designed to specifically bind and inactivate target molecules inside cells. Intrabodies have been used in cell assays and in whole organisms such as Drosophila (Chen et al, Hum. Gen. Ther. (1994) 5:595- 601; Hassanzadeh et al, Febs Lett. (1998) 16(1, 2):75-80 and 81-86). Inducible expression vectors can be constructed with intrabodies that react specifically with a subject protein. These vectors can be introduced into model organisms and studied in the same manner as described above for aptamers.
  • transgenic animals are created that contain gene fusions of the coding regions of a subject gene (from either genomic DNA or cDNA) or genes engineered to encode antisense RNAs, cosuppression RNAs, interfering dsRNA, RNA aptamers, peptide aptamers, or intrabodies operably joined to a specific promoter and transcriptional enhancer whose regulation has been well characterized, preferably heterologous promoters/enhancers (i.e. promoters/enhancers that are non-native to a subject pathway genes being expressed).
  • Methods are well known for incorporating exogenous nucleic acid sequences into the genome of animals or cultured cells to create transgenic animals or recombinant cell lines.
  • fransposable elements For invertebrate animal models, the most common methods involve the use of fransposable elements. There are several suitable fransposable elements that can be used to incorporate nucleic acid sequences into the genome of model organisms. Transposable elements are particularly useful for inserting sequences into a gene of interest so that the encoded protein is not properly expressed, creating a "knock-out" animal having a loss-of- function phenotype. Techniques are well-established for the use of P element in Drosophila (Rubin and Spradling, Science (1982) 218:348-53; U.S. Pat. No. 4,670,388) and Tel in C. elegans (Zwaal et al, Proc. Natl. Acad. Sci.
  • P elements or marked P elements, are preferred for the isolation of loss-of-function mutations in Drosophila genes because of the precise molecular mapping of these genes, depending on the availability and proximity of preexisting P element insertions for use as a localized transposon source (Hamilton and Zinn, Methods in Cell Biology (1994) 44:81-94; and Wolfher and Goldberg, Methods in Cell Biology (1994) 44:33-80).
  • modified P elements are used which contain one or more elements that allow detection of animals containing the P element.
  • marker genes are used that affect the eye color of Drosophila, such as derivatives of the Drosophila white or rosy genes (Rubin and Spradling, Science (1982) 218(4570):348-353; and Klemenz et al, Nucleic Acids Res. (1987) 15(10):3947-3959).
  • any gene can be used as a marker that causes a reliable and easily scored phenotypic change in transgenic animals.
  • markers include bacterial plasmid sequences having selectable markers such as ampicillin resistance (Steller and Pirrotta, EMBO. J.
  • Preferred methods of transposon mutagenesis in Drosophila employ the "local hopping" method described by Tower et al (Genetics (1993) 133:347-359) or generation of localized deletions from Drosophila lines carrying P insertions in the gene of interest using known methods (Kaiser, Bioassays (1990) 12(6);297-301; Harnessing the power of Drosophila genetics, In Drosophila melanogaster: Practical Uses in Cell and Molecular Biology, Goldstein and Fyrberg, Eds., Academic Press, Inc., San Diego, California). The preferred method of transposon mutagenesis in C.
  • transposable elements can be used to incorporate the gene of interest, or mutant or derivative thereof, as an additional gene into any region of an animal's genome resulting in mis-expression (including over-expression) of the gene.
  • a preferred vector designed specifically for misexpression of genes in transgenic Drosophila is derived from pGMR (Hay et al, Development (1994) 120:2121-2129), is 9Kb long, and contains: an origin of replication for E.
  • the expression unit contains a first multiple cloning site (MCS) designed for insertion of an enhancer and a second MCS located 500 bases downstream, designed for the insertion of a gene of interest.
  • MCS multiple cloning site
  • homologous recombination or gene targeting techniques can be used to substitute a gene of interest for one or both copies of the animal's homologous gene.
  • the transgene can be under the regulation of either an exogenous or an endogenous promoter element, and be inserted as either a minigene or a large genomic fragment.
  • gene function can be analyzed by ectopic expression, using, for example, Drosophila (Brand et al, Methods in Cell Biology (1994) 44:635- 654) or C. elegans (Mello and Fire, Methods in Cell Biology (1995) 48:451-482).
  • heterologous promoters examples include heat shock promoters/enhancers, which are useful for temperature induced mis-expression.
  • heat shock promoters/enhancers include the hsp70 and hsp83 genes, and in C. elegans, include hsp 16-2 and hsp 16-41.
  • Tissue specific promoters/enhancers are also useful, and in Drosophila, include eyeless (Mozer and Benzer, Development (1994) 120: 1049-1058), sevenless (Bowtell et al, PNAS (1991) 88(15):6853-6857), and g/ ⁇ rc-responsive promoters/enhancers (Quiring et al, Science (1994) 265:785-789) which are useful for expression in the eye; and enhancers/promoters derived from the dpp or vestigal genes which are useful for expression in the wing (Staehling-Hampton et al, Cell Growth Differ.
  • tissue specific promoters/enhancers include the myo-2 gene promoter, useful for pharyngeal muscle-specific expression; the hlh-1 gene promoter, useful for body- muscle-specific expression; and the gene promoter, useful for touch-neuron-specific gene expression.
  • gene fusions for directing the mis-expression of a subject pathway gene are incorporated into a transformation vector which is injected into nematodes along with a plasmid containing a dominant selectable marker, such as rol-6.
  • Transgenic animals are identified as those exhibiting a roller phenotype, and the transgenic animals are inspected for additional phenotypes of interest created by mis-expression of a subject pathway gene.
  • binary control systems that employ exogenous DNA are useful when testing the mis-expression of genes in a wide variety of developmental stage-specific and tissue-specific patterns.
  • Two examples of binary exogenous regulatory systems include the UAS/GAL4 system from yeast (Hay et al, PNAS (1997) 94(10):5195-5200; Ellis et al, Development (1993) 119(3):855-865); Brand and Perrimon (1993) Development 118(2):401-415), and the "Tet system” derived from£. coli (Bello et al., Development (1998) 125:2193-2202).
  • Dominant negative mutations by which the mutation causes a protein to interfere with the normal function of a wild-type copy of the protein, and which can result in loss-of-function or reduced- function phenotypes in the presence of a normal copy of the gene, can be made using known methods (Hershkowitz, Nature (1987) 329:219-222).
  • Various expression analysis techniques may be used to identify genes which are differentially expressed between a cell line or an animal expressing a wild type subject gene compared to another cell line or animal expressing a mutant subject gene.
  • Such expression profiling techniques include differential display, serial analysis of gene expression (SAGE), transcript profiling coupled to a gene database query, nucleic acid array technology, subtractive hybridization, and proteome analysis (e.g. mass-spectrometiy and two-dimensional protein gels).
  • Nucleic acid array technology may be used to determine a global (i.e., genome-wide) gene expression pattern in a normal animal for comparison with an animal having a mutation in a subject gene.
  • Gene expression profiling can also be used to identify other genes (or proteins) that may have a functional relation to a subject (e.g. may participate in a signaling pathway with a subject gene). The genes are identified by detecting changes in their expression levels following mutation, i.e., insertion, deletion or substitution in, or over-expression, under- expression, mis-expression or
  • mice After isolation of model animals carrying mutated or mis-expressed subject pathway genes or inhibitory RNAs, animals are carefully examined for phenotypes of interest.
  • subject pathway genes that have been mutated (i.e. deletions, insertions, and/or point mutations) animal models that are both homozygous and heterozygous for the altered subject pathway gene are analyzed. Examples of specific phenotypes that may be investigated include lethality; sterility; feeding behavior, perturbations in neuromuscular function including alterations in motility, and alterations in sensitivity to pesticides and pharmaceuticals.
  • Some phenotypes more specific to flies include alterations in: adult behavior such as, flight ability, walking, grooming, phototaxis, mating or egg-laying; alterations in the responses of sensory organs, changes in the morphology, size or number of adult tissues such as, eyes, wings, legs, bristles, antennae, gut, fat body, gonads, and musculature; larval tissues such as mouth parts, cuticles, internal tissues or imaginal discs; or larval behavior such as feeding, molting, crawling, or puparian formation; or developmental defects in any germline or embryonic tissues.
  • adult behavior such as, flight ability, walking, grooming, phototaxis, mating or egg-laying
  • alterations in the responses of sensory organs changes in the morphology, size or number of adult tissues such as, eyes, wings, legs, bristles, antennae, gut, fat body, gonads, and musculature
  • larval tissues such as mouth parts, cuticles, internal tissues or imaginal disc
  • phenotypes more specific to nematodes include: locomotory, egg laying, chemosensation, male mating, and intestinal expulsion defects.
  • locomotory egg laying, chemosensation, male mating, and intestinal expulsion defects.
  • single phenotypes or a combination of specific phenotypes in model organisms might point to specific genes or a specific pathway of genes, which facilitate the cloning process.
  • Genomic sequences containing a subject pathway gene can be used to confirm whether an existing mutant insect or worm line corresponds to a mutation in one or more subject pathway genes, by rescuing the mutant phenotype.
  • a genomic fragment containing the subject pathway gene of interest and potential flanking regulatory regions can be subcloned into any appropriate insect (such as Drosophila) or worm (such as C. elegans) transformation vector, and injected into the animals.
  • an appropriate helper plasmid is used in the injections to supply transposase for transposon- based vectors. Resulting germline transformants are crossed for complementation testing to an existing or newly created panel of Drosophila or C.
  • elegans lines whose mutations have been mapped to the vicinity of the gene of interest (Fly Pushing: The Theory and Practice of Drosophila Genetics, supra; and Caenorhabditis elegans: Modern Biological Analysis of an Organism (1995), Epstein and Shakes, eds.). If a mutant line is discovered to be rescued by this genomic fragment, as judged by complementation of the mutant phenotype, then the mutant line likely harbors a mutation in the subject pathway gene. This prediction can be further confirmed by sequencing the subject pathway gene from the mutant line to identify the lesion in the subject pathway gene.
  • RNAi methods can be used to simulate loss-of-function mutations in the genes being analyzed. It is of particular interest to investigate whether there are any interactions of subject genes with other well- characterized genes, particularly genes involved in DNA unwinding. Genetic Modifier Screens
  • a genetic modifier screen using invertebrate model organisms is a particularly preferred method for identifying genes that interact with subject genes, because large numbers of animals can be systematically screened making it more possible that interacting genes will be identified.
  • a screen of up to about 10,000 animals is considered to be a pilot-scale screen.
  • Moderate-scale screens usually employ about 10,000 to about 50,000 flies, and large-scale screens employ greater than about 50,000 flies.
  • animals having a mutant phenotype due to a mutation in or misexpression of one or more subject genes are further mutagenized, for example by chemical mutagenesis or transposon mutagenesis.
  • the procedures involved in typical Drosophila genetic modifier screens are well nown in the art
  • mutant allele is genetically recessive, as is commonly the situation for a loss-of-function allele, then most typically males, or in some cases females, which carry one copy of the mutant allele are exposed to an effective mutagen, such as EMS, MMS, ENU, triethylamine, diepoxyalkanes, ICR-170, formaldehyde, X-rays, gamma rays, or ultraviolet radiation.
  • an effective mutagen such as EMS, MMS, ENU, triethylamine, diepoxyalkanes, ICR-170, formaldehyde, X-rays, gamma rays, or ultraviolet radiation.
  • the mutagenized animals are crossed to animals of the opposite sex that also carry the mutant allele to be modified.
  • mutant allele being modified is genetically dominant, as is commonly the situation for ectopically expressed genes
  • wild type males are mutagenized and crossed to females carrying the mutant allele to be modified.
  • the progeny of the mutagenized and crossed flies that exhibit either enhancement or suppression of the original phenotype are presumed to have mutations in other genes, called "modifier genes", that participate in the same phenotype-generating pathway.
  • progeny are immediately crossed to adults containing balancer chromosomes and used as founders of a stable genetic line, hi addition, progeny of the founder adult are retested under the original screening conditions to ensure stability and reproducibility of the phenotype. Additional secondary screens may be employed, as appropriate, to confirm the suitability of each new modifier mutant line for further analysis.
  • Standard techniques used for the mapping of modifiers that come from a genetic screen in Drosophila include meiotic mapping with visible or molecular genetic markers; male-specific recombination mapping relative to P-element insertions; complementation analysis with deficiencies, duplications, and lethal P-element insertions; and cytological analysis of chromosomal aberrations (Fly Pushing: Theory and Practice of Drosophila Genetics, supra; Drosophila: A Laboratory Handbook, supra). Genes corresponding to modifier mutations that fail to complement a lethal P-element may be cloned by plasmid rescue of the genomic sequence surrounding that P-element.
  • modifier genes may be mapped by phenotype rescue and positional cloning (Sambrook et al, supra). Newly identified modifier mutations can be tested directly for interaction with other genes of interest known to be involved or implicated with a subject gene using methods described above. Also, the new modifier mutations can be tested for interactions with genes in other pathways that are not believed to be related to neuronal signaling (e.g. nanos in Drosophila). New modifier mutations that exhibit specific genetic interactions with other genes implicated in neuronal signaling, but not interactions with genes in unrelated pathways, are of particular interest.
  • the modifier mutations may also be used to identify "complementation groups". Two modifier mutations are considered to fall within the same complementation group if animals carrying both mutations in trans exhibit essentially the same phenotype as animals that are homozygous for each mutation individually and, generally are lethal when in trans to each other (Fly Pushing: The Theory and Practice of Drosophila Genetics, supra). Generally, individual complementation groups defined in this way correspond to individual genes.
  • homologous genes in other species can be isolated using procedures based on cross-hybridization with modifier gene DNA probes, PCR-based strategies with primer sequences derived from the modifier genes, and/or computer searches of sequence databases.
  • human and rodent homologs of the modifier genes are of particular interest.
  • homologs of modifier genes in insects and arachnids are of particular interest.
  • Insects, arachnids, and other organisms of interest include, among others, Isopoda; Diplopoda; Chilopoda; Symphyla; Thysanura; Collembola; Orthoptera, such as Scistocerca spp; Blattoidea, such as Blattella germanica; Dermaptera; Isoptera; Anoplura; Mallophaga; Thysanoptera; Heteroptera; Homoptera, including Bemisia tabaci, wAMyzus spp.; Lepidoptera including Plodia inter punctella, Pectinophora gossypiella, Plutella spp., Heliothis spp., and Spodoptera species; Coleoptera such as Leptinotarsa, Diabrotica spp.,Anthonomus spp., and Tribolium spp.; Hymenoptera; Diptera, including Anopheles spp.; Siphonapt
  • Drosophila genetic modifier screens are quite powerful and sensitive, some genes that interact with subject genes may be missed in this approach, particularly if there is functional redundancy of those genes. This is because the vast majority of the mutations generated in the standard mutagenesis methods will be loss-of-function mutations, whereas gain-of- function mutations that could reveal genes with functional redundancy will be relatively rare.
  • Another method of genetic screening in Drosophila has been developed that focuses specifically on systematic gain-of-function genetic screens (Rorth et al, Development (1998) 125:1049-1057).
  • This method is based on a modular mis-expression system utilizing components of the GAL4/UAS system (described above) where a modified P element, termed an "enhanced P” (EP) element, is genetically engineered to contain a GAL4-responsive UAS element and promoter. Any other transposons can also be used for this system.
  • the resulting transposon is used to randomly tag genes by insertional mutagenesis (similar to the method of P element mutagenesis described above).
  • Thousands of transgenic Drosophila strains, termed EP lines can be generated, each containing a specific UAS-tagged gene. This approach takes advantage of the preference of P elements to insert at the 5'-ends of genes. Consequently, many of the genes that are tagged by insertion of EP elements become operably fused to a GAL4-regulated promoter, and increased expression or mis-expression of the randomly tagged gene can be induced by crossing in a GAL4 driver gene.
  • Systematic gain-of-function genetic screens for modifiers of phenotypes induced by mutation or mis-expression of a subject gene can be performed by crossing several thousand Drosophila EP lines individually into a genetic background containing a mutant or mis-expressed subject gene, and further containing an appropriate GAL4 driver transgene. It is also possible to remobilize the EP elements to obtain novel insertions. The progeny of these crosses are then analyzed for enhancement or suppression of the original mutant phenotype as described above. Those identified as having mutations that interact with the subject gene can be tested further to verify the reproducibilify and specificity of this genetic interaction.
  • EP insertions that demonstrate a specific genetic interaction with a mutant or mis-expressed subject gene, have a physically tagged new gene which can be identified and sequenced using PCR or hybridization screening methods, allowing the isolation of the genomic DNA adjacent to the position of the EP element insertion.
  • a Drosophila expressed sequence tag (EST) cDNA library was prepared as follows. Tissue from mixed stage embryos (0-20 hour), imaginal disks and adult fly heads were collected and total RNA was prepared. Mitochondrial rRNA was removed from the total RNA by hybridization with biotinylated rRNA specific oligonucleotides and the resulting RNA was selected for polyadenylated mRNA. The resulting material was then used to construct a random primed Hbrary. First strand cDNA synthesis was primed using a six nucleotide random primer. The first strand cDNA was then tailed with terminal transferase to add approximately 15 dGTP molecules.
  • EST Drosophila expressed sequence tag
  • the second strand was primed using a primer which contained a Notl site followed by a 13 nucleotide C-tail to hybridize to the G-tailed first strand cDNA.
  • the double stranded cDNA was ligated with BstXl adaptors and digested with Notl .
  • the cDNA was then fractionated by size by elecfrophoresis on an agarose gel and the cDNA greater than 700 bp was purified.
  • the cDNA was ligated with Notl, BstXl digested pCDNA-sk+ vector (a derivative of pBluescript, Stratagene) and used to transform E. coli (XLlblue).
  • the final complexity of the library was 6 X 10 6 independent clones.
  • the cDNA library was normalized using a modification of the method described by Bonaldo et al. (Genome Research (1996) 6:791-806).
  • Biotinylated driver was prepared from the cDNA by PCR amplification of the inserts and allowed to hybridize with single stranded plasmids of the same library.
  • the resulting double-stranded forms were removed using sfrepavidin magnetic beads, the remaining single stranded plasmids were converted to double stranded molecules using Sequenase (Amersham, Arlington Hills, IL), and the plasmid DNA stored at -20°C prior to transformation. Aliquots of the normalized plasmid library were used to transform E.
  • coli XL lblue or DH 10B
  • the clones were allowed to grow for 24 hours at 37° C then the master plates were frozen at -80° C for storage.
  • the total number of colonies picked for sequencing from the normalized library was 240,000.
  • the master plates were used to inoculate media for growth and preparation of DNA for use as template in sequencing reactions. The reactions were primarily carried out with primer that initiated at the 5' end of the cDNA inserts. However, a minor percentage of the clones were also sequenced from the 3' end.
  • Clones were selected for 3' end sequencing based on either further biological interest or the selection of clones that could extend assemblies of contiguous sequences ("contigs") as discussed below.
  • DNA sequencing was carried out using ABI377 automated sequencers and used either ABI FS, dirhodamine or BigDye chemistries (Applied Biosystems, Inc., Foster City, CA).
  • PCR conditions used for cloning the subject nucleic acid molecules were as follows: A denaturation step of 94° C, 5 min; followed by 35 cycles of: 94° C, 1 minute; 55° C, 1 minute; 72° C, 1 minute; then, a final extension at 72° C, 10 minutes.
  • primers were designed to the known DNA sequences in the clones, using the Primer-3 software (Steve Rozen, Helen J. Skaletsky (1998) Primer3. Code available athttp://www- genome.wi.mit.edu/genome_software/other/primer3 html.). These primers were then used in sequencing reactions to extend the sequence until the full sequence of the insert was determined.
  • the GPS-1 Genome Priming System in vitro transposon kit (New England Biolabs, Inc., Beverly, MA) was used for fransposon-based sequencing, following manufacturer's protocols. Briefly, multiple DNA templates with randomly interspersed primer-binding sites were generated. These clones were prepared by picking 24 colonies/clone into a Qiagen REAL Prep to purify DNA and sequenced by using supplied primers to perform bidirectional sequencing from both ends of transposon insertion.
  • a dmNTT4 nucleic acid molecule was identified in a contiguous nucleotide sequence of 3977 bases in length, encompassing an open reading frame (ORF) of 2025 nucleotides encoding a predicted protein of 675 amino acids.
  • the ORF extends from base 239-2263 of SEQ ID NO:l.
  • dmKSNF nucleic acid molecule was identified in a contiguous nucleotide sequence of 2473 bases in length, encompassing an open reading frame (ORF) of 1923 nucleotides encoding a predicted protein of 641 amino acids.
  • the ORF extends from base 249-2173 of SEQ ID NO:3.
  • a dmSNF nucleic acid molecule was identified in a contiguous nucleotide sequence of 1.969 kilobases in length, encompassing an open reading frame (ORF) of 1209 nucleotides encoding a predicted protein of 403 amino acids.
  • the ORF extends from base 498-1706 of SEQ ID NO:5.
  • dmSNF2 A dmSNF2 nucleic acid molecule was identified in a contiguous nucleotide sequence of 2.03 kilobases in length, encompassing an open reading frame (ORF) of 1779 nucleotides encoding a predicted protein of 593 amino acids.
  • the ORF extends from base 57-1838 of SEQ ID NO:7.
  • a dmSNF3 nucleic acid molecule was identified in a contiguous nucleotide sequence of 2.108 kilobases in length, encompassing an open reading frame (ORF) of 1917 nucleotides encoding a predicted protein of 639 amino acids.
  • the ORF extends from base 50-1969 of SEQ ID NO:9.
  • a dmGAT nucleic acid molecule was identified in a contiguous nucleotide sequence of 2.874 kilobases in length, encompassing an open reading frame (ORF) of 1908 nucleotides encoding a predicted protein of 636 amino acids.
  • the ORF begins at base 107-109 of SEQ ID NO: 11.
  • TopPred predicted 12 transmembrane domains at amino acids 59-79, 91-111, 132-152, 217- 237, 244-264, 294-314, 329-349, 428-448, 474-494, 506-526, 552-572,, and 596-616, corresponding to nucleotides 413-475, 509-571, 632-694, 887-949, 968-1030, 1118-1180, 1223-1285, 1520-1582, 1658-1720, 1754-1816, 1892-1954, and 2024-2086, respectively.
  • nucleotide and amino acid sequences for dmNTT4 nucleic acid sequence and its encoded protein were searched against all available nucleotide and amino acid sequences in the public databases, using BLAST (Altschul et al, supra). Table 1 below summarizes the results. The 5 most similar sequences are listed.
  • dmNTT4 is also a drug and/or pesticide target as well.
  • BLAST results for the dmNTT4 amino acid sequence indicate 15 amino acid residues as the shortest stretch of contiguous amino acids that is novel with respect to prior art sequences and 35 amino acids as the shortest sfretch of contiguous amino acids for which there are no sequences contained within public database sharing 100% sequence similarity. dmKSNF
  • PFAM also predicted an SNF (sodium neurotransmitter family) domain (PF00209) at amino acids 38-591 (nucleotides 355-2024).
  • nucleotide and amino acid sequences for the dmKSNF nucleic acid sequences and their encoded proteins were searched against all available nucleotide and amino acid sequences in the public databases, using BLAST (Altschul et al, supra). Table 2 below summarizes the results. The 5 most similar sequences are listed.
  • the closest homolog predicted by BLAST analysis is a potassium/sodium dependent amino acid transporter from w duca sexta with 48% identity and 63% sequence homology with dmKSNF.
  • the BLAST analysis also revealed several other transporter proteins that share significant amino acid homology dmKSNF.
  • BLAST results for the dmKSNF amino acid sequence indicate 20 amino acid residues as the shortest stretch of contiguous amino acids that is novel with respect to published sequences and 29 amino acids as the shortest stretch of contiguous amino acids for which there are no sequences contained within public database sharing 100% sequence similarity. dmSNF
  • PSORT predicted four transmembrane domains at amino acids 120-136, 159-175, 222-238, and 292-308 (nucleotides 855-905, 972-1022, 1161-1211, and 1371-1421, respectively). Pfam also predicted a SNF (sodium neurotransmitter family) domain (PF00209) at amino acids 123-214 (nucleotides 864-1139).
  • SNF sodium neurotransmitter family domain
  • Nucleotide and amino acid sequences for each of the dmSNF nucleic acid sequences and their encoded proteins were searched against all available nucleotide and amino acid sequences in the public databases, using BLAST (Altschul et al, supra). Table 3 below summarizes the results. The 5 most similar sequences are listed.
  • the closest homolog predicted by BLAST analysis is a glycine transporter from human, described in Patent WO 9807854-A1 (Example 1A), with 35% identity and 51% similarity to dmSNF.
  • the BLAST analysis also revealed several other cation-dependent transporter neurotransmitter proteins of the sodium:neurotransmitter symporter family(SNF), from many vertebrate and invertebrate species, that share homologies throughout the SNF domain.
  • SNF sodium:neurotransmitter symporter family
  • BLAST results for the dmSNF amino acid sequence indicate 19 amino acid residues as the shortest stretch of contiguous amino acids that is novel with respect to published sequences and 23 amino acids as the shortest stretch of contiguous amino acids for which there are no sequences contained within public database sharing 100% sequence similarity. dmSNF2
  • PSORT predicted 12 transmembrane domains, located at amino acids 22-38; 52-68; 101-117; 190-206; 216-232; 265-281; 305-321; 358-374; 396-412; 432-448; 476-492; and 503-519 (nucleotides 120-170, 210-260, 357-407, 624-674, 702-752, 849-899, 969-1019, 1128-1178, 1242- 1292, 1350-1400, 1482-1532, and 1563-1613, respectively). Additionally, Pfam predicted a SNF (sodium neurofransmitter family) domain (PF00209) at amino acids 15-548 (nucleotides 99-1700).
  • SNF sodium neurofransmitter family domain
  • nucleotide and amino acid sequences for each of the dmSNF2 nucleic acid sequences and their encoded proteins were searched against all available nucleotide and amino acid sequences in the public databases, using BLAST (Altschul et al, supra). Table 4 below summarizes the results. The 5 most similar sequences are listed.
  • the closest homolog predicted by BLAST analysis is a potassium/sodium dependent amino acid fransporter fromManduca sexta, with 47% identity and 62% sequence homology to dmSNF2.
  • the BLAST analysis also revealed several other cation-dependent fransporter neurofransmitter proteins of the sodium:neurotransmitter symporter family(SNF), from many vertebrate and invertebrate species, that share homologies throughout the SNF domain.
  • SNF sodium:neurotransmitter symporter family
  • BLAST results for the dmSNF2 amino acid sequence indicate 12 amino acid residues as the shortest stretch of contiguous amino acids that is novel with respect to published sequences and 19 amino acids as the shortest sfretch of contiguous amino acids for which there are no sequences contained within public database sharing 100% sequence similarity. dmSNF3
  • PSORT predicted 11 transmembrane domains, located at amino acids 57-73; 87-103; 137-153; 239-255; 269-285; 355-371; 408-424; 448-464; 474-490; 522-538; and 564-580 (nucleotides 208- 268; 308-368; 458-518; 764-824; 854-914; 1112-1172; 1274-1334; 1391-1451; 1469-1529; 1613- 1673; and 1739-1799, respectively). Additionally, Pfam predicted a SNF (sodium neurofransmitter family) domain (PF00209) at amino acids 50-598 (nucleotides 197-1843).
  • SNF sodium neurofransmitter family domain
  • Nucleotide and amino acid sequences for each of the dmSNF3 nucleic acid sequences and their encoded proteins were searched against all available nucleotide and amino acid sequences in the public databases, using BLAST (Altschul et al, supra). Table 5 below summarizes the results. The 5 most similar sequences are listed.
  • the closest homolog predicted by BLAST analysis is a potassium coupled amino acid transporter fromManduca sexta with 43% identity and 58% sequence homology to dmSNF3.
  • the BLAST analysis also revealed several other cation-dependent neurotransmitter fransporter proteins of the sodium neurofransmitter symporter family(SNF), from many vertebrate and invertebrate species, that share homologies throughout the conserved SNF domain. Taken together, this suggests that dmSNF3 functions as a SNF transporter and thus could be exploited as a target to control disease vectors and insect pests.
  • BLAST results for the dmSNF3 amino acid sequence indicate 12 amino acid residues as the shortest sfretch of contiguous amino acids that is novel with respect to published sequences and 21 amino acids as the shortest stretch of contiguous amino acids for which there are no sequences contained within public database sharing 100% sequence similarity.
  • dmGAT TopPredll predicted 12 transmembrane domains, located at amino acids 63-83, 94-114, 150-170, 251- 271, 275-295, 326-346, 365-385, 413-433, 459-479, 492-512, 536-556, and 573-593 (nucleotides 293- 355, 386-448, 554-616, 857-919, 929-991, 1082-1144, 1199-1261, 1343-1405, 1481-1543, 1580- 1642, 1712-1774, and 1823-1885, respectively). Additionally, Pfam predicted a SNF (sodium neurofransmitter family) domain (PF00209) at amino acids 58-611 (nucleotides 278-1939).
  • SNF sodium neurofransmitter family domain
  • Nucleotide and amino acid sequences for each of the dmGAT nucleic acid sequences and their encoded proteins were searched against all available nucleotide and amino acid sequences in the public databases, using BLAST (Altschul et al, supra). Table 6 below summarizes the results. The 5 most similar sequences are listed.
  • the closest homolog predicted by BLAST analysis is a GABA neurofransmitter fransporter fromManduca sexta which shares 79% sequence identity and 89%> homology with dmGAT protein.
  • the BLAST analysis also revealed several GABA neurotransmitter fransporter proteins, from many vertebrate and invertebrate species, that share a high degree of homology with dmGAT. Additionally, dmGAT shares homology with many other members of the sodium neurotransmitter symporter family (SNF). Taken together, this suggests that dmGAT functions as a GABA transporter and thus could be exploited as a target to confrol disease vectors and insect pests.
  • SNF sodium neurotransmitter symporter family
  • BLAST results for the dmGAT amino acid sequence indicate 43 amino acid residues as the shortest stretch of contiguous amino acids that is novel with respect to published sequences and 85 amino acids as the shortest stretch of contiguous amino acids for which there are no sequences contained within public database sharing 100% sequence similarity.
  • Example 4 Testing of Pesticide Compounds for Activity against a Subject Protein cDNAs encoding any one of the subject proteins are cloned into mammalian cell culture- compatible vectors (e.g. pCDNA, Invifrogen, Carlsbad, CA), and the resultant constructs are fransiently transfected into mammalian cells.
  • the transiently transfected cell lines are typically used 24 to 48 hours following fransfection for elecfrophysiology studies. Whole cell recordings, using the voltage clamp technique, are taken on the transfected cells versus cells transfected with vector only.
  • Cells are voltage- clamped at 60 mV and continuously superfused withND96 (96mM NaCl, 2mM KC1, 1.8mM CaCl 2 ImM MgCl 2 , 5mM HEPES, pH 7.5) containing varying concentrations of compounds. Current and fluxes are then measured.
  • ND96 96mM NaCl, 2mM KC1, 1.8mM CaCl 2 ImM MgCl 2 , 5mM HEPES, pH 7.5
  • Cell lines transiently transfected with dmKSNF can be assayed for uptake of radioactive or fluorescent bioamines such as glycine.
  • radioactive or fluorescent bioamines such as glycine.
  • cells are incubated in 0.5 ⁇ m radioactive (e.g., 3 H-, or 14 C-)glycine for 1 hour, washed with saline, and then assayed for compound uptake using a scintillation counter.
  • Appropriate confrols are comparison of this uptake to uptake in cells injected with water, or noninjected cells.
  • Cell lines transiently transfected with dmSNF, dmSNF2, or dmSNF3 can be assayed for uptake of radioactive or fluorescent neurofransmitter.
  • radioactive compounds cells are incubated in 0.5 ⁇ m radioactive ( 3 H-, or 14 C-) neurofransmitter for 1 hour, washed with saline, and then assayed for compound uptake using a scintillation counter. Appropriate confrols are comparison of this uptake to uptake in cells injected with water, or noninjected cells.
  • Cell lines transiently transfected with dmGAT can be assayed for uptake of radioactive or fluorescent GABA.
  • radioactive compounds cells are incubated in 0.5 ⁇ m radioactive ( 3 H-, or 14 C-) GABA for 1 hour, washed with saline, and then assayed for compound uptake using a scintillation counter. Appropriate controls are comparison of this uptake to uptake in cells injected with water, or noninjected cells.

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