# Patent

## Title
Genes encoding nematode toxins

## Abstract

Compositions and methods for conferring nematicidal activity to bacteria, plants, plant cells, tissues and seeds are provided. Compositions including a coding sequence for nematicidal polypeptides are provided. The coding sequences can be used in DNA constructs or expression cassettes for transformation and expression in plants and bacteria. Compositions also include transformed bacteria, plants, plant cells, tissues, and seeds. In particular, isolated nematicidal nucleic acid molecules are provided. Additionally, amino acid sequences corresponding to the polynucleotides are encompassed. In particular, the present invention provides for isolated nucleic acid molecules including nucleotide sequences encoding the amino acid sequence shown in SEQ ID NO:4, 5, 8, 9, 13, 14, 47, 48, or 49, the nucleotide sequence set forth in SEQ ID NO:1, 2, 3, 6, 7, 10, 11, 12, 15, 45, or 46, as well as variants and fragments thereof.

## Background
CROSS REFERENCE TO RELATED APPLICATION
This application is a divisional of U.S. patent application Ser. No. 12/638,591, filed Dec. 15, 2009, which claims the benefit of U.S. Provisional Application Ser. No. 61/122,674, filed Dec. 15, 2008 and U.S. Provisional Application Ser. No. 61/224,811, filed Jul. 10, 2009, the contents of which are herein incorporated by reference in their entirety.


REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY
The official copy of the sequence listing is submitted electronically via EFS-Web as an ASCII formatted sequence listing with a file named “APA060US02DSEQLIST.txt”, created on Jan. 14, 2013, and having a size of 165 kilobytes and is filed concurrently with the specification. The sequence listing contained in this ASCII formatted document is part of the specification and is herein incorporated by reference in its entirety.
FIELD OF THE INVENTION
This invention relates to the field of molecular biology. Provided are novel genes that encode nematicidal proteins. These proteins and the nucleic acid sequences that encode them are useful in preparing nematicidal formulations and in the production of transgenic pest-resistant plants.
BACKGROUND OF THE INVENTION
Nematodes (derived from the Greek word for thread) are active, flexible, elongate, organisms that live on moist surfaces or in liquid environments, including films of water within soil and moist tissues within other organisms. While only 20,000 species of nematode have been identified, it is estimated that 40,000 to 10 million actually exist. Some species of nematodes have evolved to be very successful parasites of both plants and animals and are responsible for significant economic losses in agriculture and livestock and for morbidity and mortality in humans (Whitehead (1998) Plant Nematode Control. CAB International, New York).
It is estimated that parasitic nematodes cost the horticulture and agriculture industries in excess of $78 billion worldwide a year, based on an estimated average 12% annual loss spread across all major crops. For example, it is estimated that nematodes cause soybean losses of approximately $3.2 billion annually worldwide (Barker et al. (1994) Plant and Soil Nematodes: Societal Impact and Focus for the Future. The Committee on National Needs and Priorities in Nematology. Cooperative State Research Service, US Department of Agriculture and Society of Nematologists).
There are a very small array of chemicals available to control nematodes (Becker (1999) Agricultural Research Magazine 47(3):22-24; U.S. Pat. No. 6,048,714). Nevertheless, the application of chemical nematicides remains the major means of nematode control. In general, chemical nematicides are highly toxic compounds known to cause substantial environmental impact and are increasingly restricted in the amounts and locations in which then can be used.
The macrocyclic lactones (e.g., avermectins and milbemycins) are chemicals that in principle provide excellent specificity and efficacy and should allow environmentally safe control of plant parasitic nematodes. Unfortunately, in practice, these two nematicidal agents have proven less effective in agricultural applications against root pathogens. Although certain avermectins show exquisite activity against plant parasitic nematodes these chemicals are hampered by poor bioavailability due to their light sensitivity, degradation by soil microorganisms and tight binding to soil particles (Lasota & Dybas (1990) Acta Leiden 59(1-2):217-225; Wright & Perry (1998) Musculature and Neurobiology. In: The Physiology and Biochemistry of Free-Living and Plant-parasitic Nematodes (eds R. N. Perry & D. J. Wright), CAB International 1998). Consequently despite years of research and extensive use against animal parasitic nematodes, mites and insects (plant and animal applications), macrocyclic lactones (e.g., avermectins and milbemycins) have never been commercially developed to control plant parasitic nematodes in the soil.
SUMMARY OF INVENTION
Compositions and methods for conferring nematode tolerance activity to plants, plant cells, tissues and seeds are provided. Compositions include nucleic acid molecules encoding sequences for nematicidal polypeptides, vectors comprising those nucleic acid molecules, and host cells comprising the vectors. Compositions also include the nematicidal polypeptide sequences and antibodies to those polypeptides. The nucleotide sequences can be used in DNA constructs or expression cassettes for transformation and expression in organisms, including microorganisms and plants. The nucleotide or amino acid sequences may be synthetic sequences that have been designed for expression in an organism including, but not limited to, a microorganism or a plant. Compositions also comprise transformed bacteria, plants, plant cells, tissues, and seeds.
In particular, isolated nucleic acid molecules are provided that encode nematicidal proteins. Additionally, amino acid sequences corresponding to the nematicidal protein are encompassed. In particular, the present invention provides for an isolated nucleic acid molecule comprising a nucleotide sequence encoding the amino acid sequence shown in SEQ ID NO:4, 5, 8, 9, 13, 14, 47, 48, or 49, the nucleotide sequence set forth in SEQ ID NO:1, 2, 3, 6, 7, 10, 11, 12, 15, 45, or 46, as well as variants and fragments thereof. Nucleotide sequences that are complementary to a nucleotide sequence of the invention, or that hybridize to a sequence of the invention are also encompassed.
Methods are provided for producing the polypeptides of the invention, and for using those polypeptides for controlling or killing a nematode pest. Methods and kits for detecting the nucleic acids and polypeptides of the invention in a sample are also included.
The compositions and methods of the invention are useful for the production of organisms with enhanced nematode resistance or tolerance. These organisms and compositions comprising the organisms are desirable for agricultural purposes. The compositions of the invention are useful for identifying and generating plant populations having improved nematode resistance, as well as in the identification of Quantitative Trait Loci (QTLs) useful in marker-assisted breeding of plants having nematode resistance or tolerance.



DESCRIPTION OF FIGURES
FIG. 1 shows the enzymatic action of polyphenol oxidases.
FIG. 2 shows the AXN-1 precursor protein (SEQ ID NO:13) with the mass spectroscopy peaks mapped.
FIGS. 3A and 3B show an alignment of AXN-1 (SEQ ID NO:4) with polyphenol oxidases from Neurospora crassa (SEQ ID NO:31), Pyrenophora tritici-repentis (SEQ ID NO:32), Podospora anserina (SEQ ID NO:33), Lentinula edodes (SEQ ID NO:34), Pycnoporus sanguineus (SEQ ID NO:35), Pholio nameko (SEQ ID NO:36), Tuber melanosporum (SEQ ID NO:37), and Aspergillus fumigatus (SEQ ID NO:38).
FIG. 4 shows an alignment of AXN-8 (SEQ ID NO:13) with polyphenol oxidases from Agaricus bisporus (SEQ ID NO:39), Neurospora crassa (SEQ ID NO:31), and Streptomyces castaneglobisporus (SEQ ID NO:40). Putative copper binding histidines are found at amino acid positions 47, 81, 90, 208, 212, and 235 of SEQ ID NO:13. The protease activation site is located at position 377 of SEQ ID NO:39 and position 403 of SEQ ID NO:31. Copper binding histidines are located at amino acid position 58 of SEQ ID NO:39, position 67 of SEQ ID NO:31, and positions 38, 54, 63, 190, 194, and 216 of SEQ ID NO:40.
FIG. 5 shows an alignment of AXN-9 (SEQ ID NO:48) with AXN-8 (SEQ ID NO:13).
FIG. 6 shows a Western blot of soybean hairy root tissue incubated with anti-AXN-1 antibody. Lane A is root tissue from transgenic root tissue containing the AXN-1 gene, and Lane B is from a control line lacking the AXN-1 gene.



DETAILED DESCRIPTION
Overview
Nematodes cause a substantial loss in agricultural products including food and industrial crops and have primarily been combated with chemical compounds having nematicidal activity. Nematodes are microscopic wormlike animals that feed on roots, leaves, and stems of more than 2,000 vegetables, fruits, and ornamental plants. One common type of nematode is the root-knot nematode, whose feeding causes the characteristic galls on roots. Other root-feeding nematodes are the cyst- and lesion-type, which are more host specific. Soybean cyst nematode (SCN) can decrease the number of nitrogen-fixing nodules on the roots, and may make the roots more susceptible to attacks by other soil-borne plant pathogens. Due to the toxicity (and in many cases, poor efficacy) of existing nematode control methods, it would be desirable to develop safe and effective alternatives for nematode control.
The present invention is drawn to compositions and methods for regulating nematode resistance or tolerance in organisms, particularly plants or plant cells. By “resistance” is intended that the nematode is killed upon ingestion or other contact with the polypeptides of the invention. By “tolerance” is intended an impairment or reduction in the movement, feeding, reproduction, or other functions of the nematode. The methods involve transforming organisms with a nucleotide sequence encoding a nematicidal protein of the invention. In particular, the nucleotide sequences of the invention are useful for preparing plants and microorganisms that possess nematicidal activity. Thus, transformed bacteria, plants, plant cells, plant tissues and seeds are provided.
Compositions include nematicidal nucleic acids and proteins of bacterial, fungal, or plant origin. The nematicidal nucleic acid sequences described herein encode polyphenol oxidase enzymes. Polyphenol oxidases are believed to play key physiological roles both in preventing insects and microorganisms from attacking plants and as part of the wound response of plants and plant products to insects, microorganisms and bruising (reviewed in Marshall et al. (2000) “Enzymatic Browning in Fruits, Vegetables and Seafoods” Food and Agricultural Organization of the United Nations at www.fao.org). As fruits and vegetables ripen, their susceptibility to disease and infestation is increased due to a decline in their phenolic content. Phenoloxidase enzymes endogenous to fruits and vegetables catalyze the production of quinones from their phenolic constituents. Once formed, these quinones undergo polymerization reactions, leading to the production of melanins, which exhibit both antibacterial and antifungal activity and assist in keeping the fruit and/or vegetable physiologically wholesome. However, the use of polyphenol oxidase activity for nematode control has not previously been discovered.
The polyphenol oxidase enzymes encompassed herein include novel sequences as well as polyphenol oxidase sequences known in the art. The sequences find use in the construction of expression vectors for subsequent transformation into organisms of interest, as probes for the isolation of other homologous (or partially homologous) genes, and for the generation of altered nematicidal proteins by methods known in the art, such as domain swapping or DNA shuffling. The proteins find use in controlling or killing nematode pest populations and for producing compositions with nematicidal activity.
By “nematicidal toxin” or “nematicidal protein” is intended a toxin that has toxic activity against one or more nematode pests, including, but not limited to, the nematicidal toxins set forth in SEQ ID NO:4, 5, 8, 9, 13, 14, 18, 20, 22, 47, 48, or 49, or a protein that has homology to such a protein. Nematicidal proteins include amino acid sequences deduced from the full-length nucleotide sequences disclosed herein, and amino acid sequences that are shorter than the full-length sequences, either due to the use of an alternate downstream start site, or due to processing (e.g., proteolytic cleavage, alternative splicing, and the like) that produces a shorter protein having nematicidal activity. Processing may occur in the organism the protein is expressed in, or in the pest after ingestion of the protein.
Nematode Pests
The compositions and methods of the present invention are useful for developing transgenic plants that are tolerant to nematode pests, particularly plant-parasitic nematodes. Nematode parasites of plants can inhabit all parts of plants, including roots, developing flower buds, leaves, and stems. Plant parasites are classified on the basis of their feeding habits into the broad categories: migratory ectoparasites, migratory endoparasites, and sedentary endoparasites. Sedentary endoparasites, which include the root knot nematodes (Meloidogyne) and cyst nematodes (Globodera and Heterodera) induce feeding sites and establish long-term infections within roots that are often very damaging to crops (Whitehead (1998) Plant Nematode Control. CAB International, New York). Exemplary plant-parasitic nematodes include, but are not limited to, Aphelenchoides spp. (Foliar nematodes), Belonolaimus spp. (The Sting nematode), Bursaphelenchus xylophilus (Pine wilt nematode), Criconemoides species (Ring Nematode), Ditylenchus destructor (Potato Rot Nematode), Ditylenchus dipsaci (Stem and bulb nematode), Globodera pallida (Pale Potato Cyst Nematode), Globodera rostochiensis (Golden Nematode), Helicotylenchus (Spiral Nematodes), Heterodera glycines (Soybean cyst nematode, Heterodera schachtii (Sugar beet cyst nematode), Heterodera zeae (The Corn Cyst Nematode), Heterodera avenae (cereal cyst nematode), Hoplolaimus (The Lance Nematode), Meloidogyne spp. (Root-knot nematodes), Mesocriconema xenoplax (Ring nematode), Nacobbus aberrans (False root-knot nematode), Paratrichodorus (Stubby-Root Nematodes), Pratylenchus spp (Lesion nematode), Radopholus similis (Burrowing nematode), Rotylenchulus spp. (Reniform nematode), Tylenchorhynchus spp. (Stunt nematodes), Tylenchulus semipenetrans (The Citrus nematode), and Xiphinema (The Dagger Nematode).
Polyphenol Oxidases
The nematicidal compositions disclosed herein comprise polyphenol oxidase nucleic acid and amino acid sequences, as well as variants and fragments thereof. In various embodiments, the compositions comprise transgenic plants or pesticidal formulations expressing or comprising a polyphenol oxidase. The compositions are useful for controlling or killing plant-parasitic nematodes in an area susceptible to nematode infestation, particularly plant-parasitic nematode infestation.
For the purposes of the present invention, a “polyphenol oxidase” refers to a class of copper-containing oxidase enzymes that includes, for example, monophenol monooxidases such as tyrosinase, diphenol oxidases such as catechol oxidase and laccase, hemocyanins, and the like. In various embodiments, the polyphenol oxidase enzymes encompassed herein are members of the type 3 copper protein family.
Polyphenol oxidases are enzymes with a dinuclear copper center, with the copper ions serving to bind a molecular oxygen atom within the active site of the enzyme to allow catalysis. The oxidation state of each copper atom influences oxygen binding and thus oxidase activity at each step. In the case of a monophenol monooxidase, copper ions in the +2 oxidation state guide the addition of a hydroxyl group in the ortho-position on an existing phenol ring. Subsequently, a diphenol oxidase can bind this diphenol product and oxidize both hydroxyl moieties to generate the corresponding quinone. The diphenol oxidase activity takes place by reduction of the copper ions to the +1 state and binding to a molecular oxygen atom. While some organisms possess only a single polyphenol oxidase activity (notably plants, which carry out the diphenol oxidase step), other enzymes perform both the monooxidase and diphenol oxidase reactions. Several x-ray structures have been solved for type 3 copper enzymes, and distinct structural motifs are conserved among the enzymes. Notable is the active site of these enzymes, in which copper is bound by six or seven histidine residues and a single cysteine residue is highly conserved. The structural data also suggests most polyphenol oxidase enzymes have somewhat relaxed specificity for their substrates, and that the active site of the enzymes is flexible during catalysis.
The enzyme seems to be of almost universal distribution in animals, plants, fungi and bacteria. Primary protein sequences of polyphenol oxidases from Streptomyces glaucescens (Huber et al. 1985), Streptomyces antibioticus (Bernan et al. 1985) and Neurospora crassa (Lerch, 1982), tomato (Shahar et al. 1992; Newman et al. 1993), broad bean (Cary et al. 1992) potato (Hunt et al. 1993), mice (Shibahara et al. 1986) and humans (Kwon et al. 1987; Giebel et al. 1991) have been determined using cDNA sequencing techniques. Polyphenol oxidases of closely related plants, such as tomato and potato, show approximately 91 percent sequence homology, while those of tomato and fava bean show only 40 percent exact homology (Wong, 1995).
Despite low sequence identity amongst polyphenol oxidase enzymes derived from different species, they all have at their active site a dinuclear copper center, in which type 3 copper is bound to histidine residues, and this structure is highly conserved. Marusek et al. show that a number of important structural features are conserved in the N-terminal domains of polyphenol oxidases from various plants and fungi, including a tyrosine motif which can be considered a landmark indicating the beginning of the linker region connecting the N- and C-terminal domains. Sequence alignments and secondary structure predictions indicate that the C-terminal domains of polyphenol oxidases are likely to be similar in tertiary structure to that of hemocyanin (Marusek et al. (2006) J Inorg Biochem. 100(1):108-23, herein incorporated by reference in its entirety, particularly with respect to the description of conserved structural features of polyphenol oxidases).
The amino acid sequence of a considerable number of PPOs, on plants, fungi and other organisms derived from cloning of the enzyme, has now been published and many of the reports and reviews give such comparative information, e.g. van Gelder et al. (1997) Phytochemistry 45:1309-1323; Wichers et al. (2003) Appl. Microbiol. Biotechnol. 61:336-341; Cho et al. (2003) Proc. Nat. Acad. Sci. USA 100:10641-10646; Marusek et al. (2006) J Inorg Biochem. 100(1):108-23; Halaouili et al. (2006) J. Appl. Microbiol. 100:219-232; Hernandez-Romero et al. (2006) FEBS J. 273:257-270; Nakamura et al. (2000) Biochem. J. 350:537-545; and, Matoba et al. (2006) J. Biol. Chem. 281:8981-8990, each of which is herein incorporated by reference in its entirety. Polyphenol oxidase enzymes have been isolated from mammals, birds, fish, insects, reptiles, amphibians, fungi and bacteria.
Polyphenol oxidase exists in certain species as a zymogen or propolyphenol oxidase form, and proteases are also believed to be involved in the activation of the propolyphenol oxidase form. These proteases are thought to be induced by microbial activity, and also suggests that these enzymes can be activated by a host protease following an infection or invasion event. Secondary metabolites, such as glucans, glycoproteins, laminarins, lipopolysaccharides, etc., produced by organisms may also induce the activation of propolyphenol oxidase by proteases. These metabolites are also capable of activating the propolyphenol oxidase even in the absence of proteolytic activity.
In various plant species, polyphenol oxidase genes are encoded within the nucleus and undergo translation within the cytoplasm. Once formed, propolyphenol oxidase is transported to the chloroplast where it undergoes proteolytic cleavage, to produce the active polyphenol oxidase form (Vaughn et al., 1988, Physiol. Plant., 72: 659-665).
Monophenol Monooxygenases
Monophenol monooxygenase (EC 1.14.18.1; CAS number: 9002-10-2) catalyses the hydroxylation of monophenols to o-diphenols. The enzyme is referred to as tyrosinase in animals, since L-tyrosine is the major monophenolic substrate. Tyrosine, on the other hand, which is a monohydroxy phenol, is an important amino acid. Hydroxylation of tyrosine leads to the formation of dihydroxyphenylalanine (DOPA).
In plants, the enzyme is sometimes referred to as cresolase owing to the ability of the enzyme to utilize the monophenolic substrate, cresol. Monophenol monooxygenase is also known as monophenol monooxidase, dopa oxidase, phenol oxidase, phenoloxidase, phenoloxidase A, phenoloxidase B, and tyrosinase.
Crystallographic structure of a Streptomyces derived tyrosinase in complex with a so called “caddie protein” is described in Matoba et al (2006) J. Biol. Chem. 281(13):8981-8990, which is herein incorporated by reference in its entirety.
Diphenol Oxidases
Diphenol oxidase (EC 1.10.3.1; CAS number: 9002-10-2) is an enzyme that catalyses the oxidation of phenols such as catechol. Diphenol oxidases are also known as catechol oxidase, polyphenol oxidase, and polyphenoloxidase. Diphenol oxidase carries out the oxidation of phenols such as catechol, using dioxygen (O2). In the presence of catechol, benzoquinone is formed. Hydrogens removed from catechol combine with oxygen to form water.
Catechol oxidase is a copper-containing enzyme whose activity is similar to that of tyrosinase, a related class of copper oxidases.
Laccase (p-diphenol oxidase, E.C. 1.10.3.2) (DPO) is a type of copper-containing polyphenol oxidase. It has the unique ability of oxidizing p-diphenols, thus allowing it to be distinguished from o-diphenol oxidases such as catechol oxidase. Several phenolic substrates, including polyphenols, methoxy-substituted phenols, diamines and a considerable range of other compounds serve as substrates for laccase (Thurston, 1994, Microbiology, 140: 19-26). Laccases occur in many phytopathogenic fungi and in certain higher plants (Mayer and Harel, 1991, Phenoloxidase and their significance in fruit and vegetables. In P. F. Fx, ed. Food Enzymology, p. 373. London, Elsevier).
Isolated Nucleic Acid Molecules, and Variants and Fragments Thereof
One aspect of the invention pertains to isolated or recombinant nucleic acid molecules comprising nucleotide sequences encoding nematicidal proteins and polypeptides or biologically active portions thereof, as well as nucleic acid molecules sufficient for use as hybridization probes to identify nucleic acid molecules encoding proteins with regions of sequence homology. As used herein, the term “nucleic acid molecule” is intended to include DNA molecules (e.g., recombinant DNA, cDNA or genomic DNA) and RNA molecules (e.g., mRNA) and analogs of the DNA or RNA generated using nucleotide analogs. The nucleic acid molecule can be single-stranded or double-stranded, but preferably is double-stranded DNA.
An “isolated” or “purified” nucleic acid molecule or protein, or biologically active portion thereof, is substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized. Preferably, an “isolated” nucleic acid is free of sequences (preferably protein encoding sequences) that naturally flank the nucleic acid (i.e., sequences located at the 5′ and 3′ ends of the nucleic acid) in the genomic DNA of the organism from which the nucleic acid is derived. For purposes of the invention, “isolated” when used to refer to nucleic acid molecules excludes isolated chromosomes. For example, in various embodiments, the isolated nucleic acid molecule encoding a nematicidal protein can contain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb, or 0.1 kb of nucleotide sequences that naturally flank the nucleic acid molecule in genomic DNA of the cell from which the nucleic acid is derived. A nematicidal protein that is substantially free of cellular material includes preparations of protein having less than about 30%, 20%, 10%, or 5% (by dry weight) of non-nematicidal protein (also referred to herein as a “contaminating protein”).
Nucleotide sequences encoding the proteins of the present invention include the sequence set forth in SEQ ID NO:1, 2, 3, 6, 7, 10, 11, 12, 15, 16, 17, 19, 21, 45, or 46, and variants, fragments, and complements thereof. By “complement” is intended a nucleotide sequence that is sufficiently complementary to a given nucleotide sequence such that it can hybridize to the given nucleotide sequence to thereby form a stable duplex. The corresponding amino acid sequence for the nematicidal protein encoded by this nucleotide sequence are set forth in SEQ ID NO:4, 5, 8, 9, 13, 14, 18, 20, 22, 47, 48, or 49.
Nucleic acid molecules that are fragments of these nucleotide sequences encoding nematicidal proteins are also encompassed by the present invention. By “fragment” is intended a portion of the nucleotide sequence encoding a nematicidal protein. A fragment of a nucleotide sequence may encode a biologically active portion of a nematicidal protein, or it may be a fragment that can be used as a hybridization probe or PCR primer using methods disclosed below. Nucleic acid molecules that are fragments of a nucleotide sequence encoding a nematicidal protein comprise at least about 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1350, 1400 contiguous nucleotides, or up to the number of nucleotides present in a full-length nucleotide sequence encoding a nematicidal protein disclosed herein, depending upon the intended use. By “contiguous” nucleotides is intended nucleotide residues that are immediately adjacent to one another. Fragments of the nucleotide sequences of the present invention will encode protein fragments that retain the biological activity of the nematicidal protein and, hence, retain nematicidal and polyphenol oxidase activity. By “retains activity” is intended that the fragment will have at least about 30%, at least about 50%, at least about 70%, 80%, 90%, 95% or higher of the nematicidal and/or polyphenol oxidase activity of the reference protein protein.
Methods for measuring nematode resistance or nematicidal activity are described in, for example, U.S. Patent Publication Nos. 20050191714 and 20080153102, as well as in the Experimental Examples provided herein. Methods for measuring polyphenol oxidase activity include, for example, detecting the presence of o-quinone produced in an enzymatic reaction of the polyphenol oxidase on tyrosine. Polyphenol oxidase oxidizes tyrosine which, in turn, is oxidized to o-quinone. The latter is accompanied by an increase in absorbance at 280 nm. The rate of increase is proportional to enzyme concentration and is linear during a period of 5-10 minutes after an initial lag. One unit causes a change in absorbance at 280 nm of 0.001 per minute at 25° C., pH 6.5 under the specified conditions.
A fragment of a nucleotide sequence encoding a nematicidal protein that encodes a biologically active portion of a protein of the invention will encode at least about 15, 25, 30, 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, 450 contiguous amino acids, or up to the total number of amino acids present in a full-length nematicidal protein of the invention.
Preferred nematicidal proteins of the present invention are encoded by a nucleotide sequence sufficiently identical to the nucleotide sequence of SEQ ID NO:1, 2, 3, 6, 7, 10, 11, 12, 15, 16, 17, 19, 21, 45, or 46, or a nucleotide sequence encoding an amino acid sufficiently identical to SEQ ID NO:4, 5, 8, 9, 13, 14, 18, 20, 22, 47, 48, or 49. By “sufficiently identical” is intended an amino acid or nucleotide sequence that has at least about 60% or 65% sequence identity, about 70% or 75% sequence identity, about 80% or 85% sequence identity, about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or greater sequence identity compared to a reference sequence using one of the alignment programs described herein using standard parameters. One of skill in the art will recognize that these values can be appropriately adjusted to determine corresponding identity of proteins encoded by two nucleotide sequences by taking into account codon degeneracy, amino acid similarity, reading frame positioning, and the like.
To determine the percent identity of two amino acid sequences or of two nucleic acids, the sequences are aligned for optimal comparison purposes. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences (i.e., percent identity=number of identical positions/total number of positions (e.g., overlapping positions)×100). In one embodiment, the two sequences are the same length. In another embodiment, the percent identity is calculated across the entirety of the reference sequence (i.e., the sequence disclosed herein as any of SEQ ID NO:1-22, and 45-49). The percent identity between two sequences can be determined using techniques similar to those described below, with or without allowing gaps. In calculating percent identity, typically exact matches are counted.
The determination of percent identity between two sequences can be accomplished using a mathematical algorithm. A nonlimiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin and Altschul (1990) Proc. Natl. Acad. Sci. USA 87:2264, modified as in Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-5877. Such an algorithm is incorporated into the BLASTN and BLASTX programs of Altschul et al. (1990) J. Mol. Biol. 215:403. BLAST nucleotide searches can be performed with the BLASTN program, score=100, wordlength=12, to obtain nucleotide sequences homologous to the nucleic acid molecules of the invention. BLAST protein searches can be performed with the BLASTX program, score=50, wordlength=3, to obtain amino acid sequences homologous to protein molecules of the invention. To obtain gapped alignments for comparison purposes, Gapped BLAST (in BLAST 2.0) can be utilized as described in Altschul et al. (1997) Nucleic Acids Res. 25:3389. Alternatively, PSI-Blast can be used to perform an iterated search that detects distant relationships between molecules. See Altschul et al. (1997) supra. When utilizing BLAST, Gapped BLAST, and PSI-Blast programs, the default parameters of the respective programs (e.g., BLASTX and BLASTN) can be used. Alignment may also be performed manually by inspection.
Another non-limiting example of a mathematical algorithm utilized for the comparison of sequences is the ClustalW algorithm (Higgins et al. (1994) Nucleic Acids Res. 22:4673-4680). ClustalW compares sequences and aligns the entirety of the amino acid or DNA sequence, and thus can provide data about the sequence conservation of the entire amino acid sequence. The ClustalW algorithm is used in several commercially available DNA/amino acid analysis software packages, such as the ALIGNX module of the Vector NTI Program Suite (Invitrogen Corporation, Carlsbad, Calif.). After alignment of amino acid sequences with ClustalW, the percent amino acid identity can be assessed. A non-limiting example of a software program useful for analysis of ClustalW alignments is GENEDOCTM. GENEDOCTM (Karl Nicholas) allows assessment of amino acid (or DNA) similarity and identity between multiple proteins. Another non-limiting example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller (1988) CABIOS 4:11-17. Such an algorithm is incorporated into the ALIGN program (version 2.0), which is part of the GCG Wisconsin Genetics Software Package, Version 10 (available from Accelrys, Inc., 9685 Scranton Rd., San Diego, Calif., USA). When utilizing the ALIGN program for comparing amino acid sequences, a PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used.
Unless otherwise stated, GAP Version 10, which uses the algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48(3):443-453, will be used to determine sequence identity or similarity using the following parameters: % identity and % similarity for a nucleotide sequence using GAP Weight of 50 and Length Weight of 3, and the nwsgapdna.cmp scoring matrix; % identity or % similarity for an amino acid sequence using GAP weight of 8 and length weight of 2, and the BLOSUM62 scoring program. Equivalent programs may also be used. By “equivalent program” is intended any sequence comparison program that, for any two sequences in question, generates an alignment having identical nucleotide residue matches and an identical percent sequence identity when compared to the corresponding alignment generated by GAP Version 10.
The invention also encompasses variant nucleic acid molecules. “Variants” of the nematicidal protein encoding nucleotide sequences include those sequences that encode the nematicidal proteins disclosed herein but that differ conservatively because of the degeneracy of the genetic code as well as those that are sufficiently identical as discussed above. Naturally occurring allelic variants can be identified with the use of well-known molecular biology techniques, such as polymerase chain reaction (PCR) and hybridization techniques as outlined below. Variant nucleotide sequences also include synthetically derived nucleotide sequences that have been generated, for example, by using site-directed mutagenesis but which still encode the nematicidal proteins disclosed in the present invention as discussed below. Variant proteins encompassed by the present invention are biologically active, that is they continue to possess the desired biological activity of the native protein, that is, polyphenol oxidase and/or nematicidal activity. By “retains activity” is intended that the variant will have at least about 30%, at least about 50%, at least about 70%, or at least about 80% of the nematicidal activity and/or the polyphenol oxidase activity of the reference protein. One of skill in the art will recognize that variants may have an increase or decrease in one activity (e.g., nematicidal or polyphenol oxidase) without affecting, or only minimally affecting, the other activity. For example, variants proteins may show improved nematicidal activity relative to the native protein without concomitant improvements in polyphenol oxidase activity and vice versa. Unless otherwise specified, variants proteins will have at least 30% of each activity relative to the native protein. Methods for measuring these activities are described elsewhere herein.
The skilled artisan will further appreciate that changes can be introduced by mutation of the nucleotide sequences of the invention thereby leading to changes in the amino acid sequence of the encoded nematicidal proteins, without altering the biological activity of the proteins. Thus, variant isolated nucleic acid molecules can be created by introducing one or more nucleotide substitutions, additions, or deletions into the corresponding nucleotide sequence disclosed herein, such that one or more amino acid substitutions, additions or deletions are introduced into the encoded protein. Mutations can be introduced by standard techniques, such as site-directed mutagenesis and PCR-mediated mutagenesis. Such variant nucleotide sequences are also encompassed by the present invention.
For example, conservative amino acid substitutions may be made at one or more, predicted, nonessential amino acid residues. A “nonessential” amino acid residue is a residue that can be altered from the wild-type sequence of a nematicidal protein without altering the biological activity, whereas an “essential” amino acid residue is required for biological activity. A “conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined in the art. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine).
Amino acid substitutions may be made in nonconserved regions that retain function. In general, such substitutions would not be made for conserved amino acid residues, or for amino acid residues residing within a conserved motif, where such residues are essential for protein activity. Examples of residues that are conserved and that may be essential for protein activity include, for example, residues that are identical between all proteins contained in an alignment of similar or related toxins to the sequences of the invention (e.g., residues that are identical between all proteins contained in the alignment in FIGS. 3 and 4). Examples of residues that are conserved but that may allow conservative amino acid substitutions and still retain activity include, for example, residues that have only conservative substitutions between all proteins contained in an alignment of similar or related toxins to the sequences of the invention (e.g., residues that have only conservative substitutions between all proteins contained in the alignment in FIGS. 3, 4, and 5). However, one of skill in the art would understand that functional variants may have minor conserved or nonconserved alterations in the conserved residues.
Alternatively, variant nucleotide sequences can be made by introducing mutations randomly along all or part of the coding sequence, such as by saturation mutagenesis, and the resultant mutants can be screened for ability to confer nematicidal activity to identify mutants that retain activity. Following mutagenesis, the encoded protein can be expressed recombinantly, and the activity of the protein can be determined using standard assay techniques.
Using methods such as PCR, hybridization, and the like corresponding nematicidal sequences can be identified, such sequences having substantial identity to the sequences of the invention. See, for example, Sambrook and Russell (2001) Molecular Cloning: A Laboratory Manual. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.) and Innis, et al. (1990) PCR Protocols: A Guide to Methods and Applications (Academic Press, NY). Alternatively, polyphenol oxidase sequences can be identified using any number of polyphenol oxidase sequences known in the art.
In a hybridization method, all or part of the nematicidal nucleotide sequence can be used to screen cDNA or genomic libraries. Methods for construction of such cDNA and genomic libraries are generally known in the art and are disclosed in Sambrook and Russell, 2001, supra. The so-called hybridization probes may be genomic DNA fragments, cDNA fragments, RNA fragments, or other oligonucleotides, and may be labeled with a detectable group such as 32P, or any other detectable marker, such as other radioisotopes, a fluorescent compound, an enzyme, or an enzyme co-factor. Probes for hybridization can be made by labeling synthetic oligonucleotides based on the known nematicidal protein-encoding nucleotide sequence disclosed herein. Degenerate primers designed on the basis of conserved nucleotides or amino acid residues in the nucleotide sequence or encoded amino acid sequence can additionally be used. The probe typically comprises a region of nucleotide sequence that hybridizes under stringent conditions to at least about 12, at least about 25, at least about 50, 75, 100, 125, 150, 175, or 200 consecutive nucleotides of nucleotide sequence encoding a nematicidal protein of the invention or a fragment or variant thereof. Methods for the preparation of probes for hybridization are generally known in the art and are disclosed in Sambrook and Russell, 2001, supra herein incorporated by reference.
For example, an entire nematicidal protein sequence disclosed herein, or one or more portions thereof, may be used as a probe capable of specifically hybridizing to corresponding nematicidal protein-like sequences and messenger RNAs. To achieve specific hybridization under a variety of conditions, such probes include sequences that are unique and are preferably at least about 10 nucleotides in length, or at least about 20 nucleotides in length. Such probes may be used to amplify corresponding nematicidal sequences from a chosen organism by PCR. This technique may be used to isolate additional coding sequences from a desired organism or as a diagnostic assay to determine the presence of coding sequences in an organism. Hybridization techniques include hybridization screening of plated DNA libraries (either plaques or colonies; see, for example, Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.).
Hybridization of such sequences may be carried out under stringent conditions. By “stringent conditions” or “stringent hybridization conditions” is intended conditions under which a probe will hybridize to its target sequence to a detectably greater degree than to other sequences (e.g., at least 2-fold over background). Stringent conditions are sequence-dependent and will be different in different circumstances. By controlling the stringency of the hybridization and/or washing conditions, target sequences that are 100% complementary to the probe can be identified (homologous probing). Alternatively, stringency conditions can be adjusted to allow some mismatching in sequences so that lower degrees of similarity are detected (heterologous probing). Generally, a probe is less than about 1000 nucleotides in length, preferably less than 500 nucleotides in length.
Typically, stringent conditions will be those in which the salt concentration is less than about 1.5 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C. for long probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. Exemplary low stringency conditions include hybridization with a buffer solution of 30 to 35% formamide, 1 M NaCl, 1% SDS (sodium dodecyl sulphate) at 37° C., and a wash in 1× to 2×SSC (20×SSC=3.0 M NaCl/0.3 M trisodium citrate) at 50 to 55° C. Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37° C., and a wash in 0.5× to 1×SSC at 55 to 60° C. Exemplary high stringency conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 0.1×SSC at 60 to 65° C. Optionally, wash buffers may comprise about 0.1% to about 1% SDS. Duration of hybridization is generally less than about 24 hours, usually about 4 to about 12 hours.
Specificity is typically the function of post-hybridization washes, the critical factors being the ionic strength and temperature of the final wash solution. For DNA-DNA hybrids, the Tm can be approximated from the equation of Meinkoth and Wahl (1984) Anal. Biochem. 138:267-284: Tm=81.5° C.+16.6 (log M)+0.41 (% GC)−0.61 (% form)−500/L; where M is the molarity of monovalent cations, % GC is the percentage of guanosine and cytosine nucleotides in the DNA, % form is the percentage of formamide in the hybridization solution, and L is the length of the hybrid in base pairs. The Tm is the temperature (under defined ionic strength and pH) at which 50% of a complementary target sequence hybridizes to a perfectly matched probe. Tm is reduced by about 1° C. for each 1% of mismatching; thus, Tm, hybridization, and/or wash conditions can be adjusted to hybridize to sequences of the desired identity. For example, if sequences with >90% identity are sought, the Tm can be decreased 10° C. Generally, stringent conditions are selected to be about 5° C. lower than the thermal melting point (Tm) for the specific sequence and its complement at a defined ionic strength and pH. However, severely stringent conditions can utilize a hybridization and/or wash at 1, 2, 3, or 4° C. lower than the thermal melting point (Tm); moderately stringent conditions can utilize a hybridization and/or wash at 6, 7, 8, 9, or 10° C. lower than the thermal melting point (Tm); low stringency conditions can utilize a hybridization and/or wash at 11, 12, 13, 14, 15, or 20° C. lower than the thermal melting point (Tm). Using the equation, hybridization and wash compositions, and desired Tm, those of ordinary skill will understand that variations in the stringency of hybridization and/or wash solutions are inherently described. If the desired degree of mismatching results in a Tm of less than 45° C. (aqueous solution) or 32° C. (formamide solution), it is preferred to increase the SSC concentration so that a higher temperature can be used. An extensive guide to the hybridization of nucleic acids is found in Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biology-Hybridization with Nucleic Acid Probes, Part I, Chapter 2 (Elsevier, New York); and Ausubel et al., eds. (1995) Current Protocols in Molecular Biology, Chapter 2 (Greene Publishing and Wiley-Interscience, New York). See Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.).
Isolated Proteins and Variants and Fragments Thereof
Nematicidal proteins are also encompassed within the present invention. By “nematicidal protein” is intended a protein having the amino acid sequence set forth in SEQ ID NO:5, 8, 14, 18, 20, 22, or 48. Fragments, biologically active portions, and variants thereof are also provided, and may be used to practice the methods of the present invention.
“Fragments” or “biologically active portions” include polypeptide fragments comprising amino acid sequences sufficiently identical to the amino acid sequence set forth in SEQ ID NO:4, 5, 8, 13, 14, 18, 20, 22, 47, 48, or 49, and that exhibit polyphenol oxidase and/or nematicidal activity. In some embodiments, the biologically active fragments exhibit both polyphenol oxidase and nematicidal activity. A biologically active portion of a nematicidal protein can be a polypeptide that is, for example, 10, 25, 50, 100, 150, 200, 250 or more amino acids in length. Such biologically active portions can be prepared by recombinant techniques and evaluated for nematicidal and/or polyphenol oxidase activity. Methods for measuring nematicidal activity and polyphenol oxidase activity are described elsewhere herein. As used herein, a fragment comprises at least 8 contiguous amino acids of SEQ ID NO:4, 5, 8, 13, 14, 18, 20, 22, 47, 48, or 49. The invention encompasses other fragments, however, such as any fragment in the protein greater than about 10, 20, 30, 50, 100, 150, 200, 250, or 300 contiguous amino acids.
By “variants” is intended proteins or polypeptides having an amino acid sequence that is at least about 60%, 65%, about 70%, 75%, about 80%, 85%, about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to the amino acid sequence of SEQ ID NO: 4, 5, 8, 13, 14, 18, 20, 22, 47, 48, or 49. Variants also include polypeptides encoded by a nucleic acid molecule that hybridizes to the nucleic acid molecule of SEQ ID NO:1, 2, 3, 6, 7, 10, 12, 15, 16, 17, 19, 21, 45, or 46, or a complement thereof, under stringent conditions. Variants include polypeptides that differ in amino acid sequence due to mutagenesis. Variant proteins encompassed by the present invention are biologically active, that is they continue to possess the desired biological activity of the native protein, that is, retaining nematicidal activity and/or polyphenol oxidase activity. In some embodiments, the variants exhibit both polyphenol oxidase and nematicidal activity.
Bacterial genes, such as the some of the novel genes disclosed herein, quite often possess multiple methionine initiation codons in proximity to the start of the open reading frame. Often, translation initiation at one or more of these start codons will lead to generation of a functional protein. These start codons can include ATG codons. However, some bacteria also recognize the codon GTG as a start codon, and proteins that initiate translation at GTG codons contain a methionine at the first amino acid. Furthermore, it is not often determined a priori which of these codons are used naturally in the bacterium. Thus, it is understood that use of one of the alternate methionine codons may also lead to generation of nematicidal proteins. These nematicidal proteins are encompassed in the present invention and may be used in the methods of the present invention.
Antibodies to the polypeptides of the present invention, or to variants or fragments thereof, are also encompassed. Methods for producing antibodies are well known in the art (see, for example, Harlow and Lane (1988) Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.; U.S. Pat. No. 4,196,265).
Altered or Improved Variants
It is recognized that DNA sequences of a nematicidal protein may be altered by various methods, and that these alterations may result in DNA sequences encoding proteins with amino acid sequences different than that encoded by a nematicidal protein of the present invention. This protein may be altered in various ways including amino acid substitutions, deletions, truncations, and insertions of one or more amino acids of SEQ ID NO:4, 5, 8, 9, 13, 14, 18, 20, 22, 47, 48, or 49, including up to about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 15, about 20, about 25, about 30, about 35, about 40, about 45, about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 85, about 90, about 100, about 105, about 110, about 115, about 120, about 125, about 130, about 135, about 140, about 145, about 150, about 155, or more amino acid substitutions, deletions or insertions. Methods for such manipulations are generally known in the art. For example, amino acid sequence variants of a nematicidal protein can be prepared by mutations in the DNA. This may also be accomplished by one of several forms of mutagenesis and/or in directed evolution. In some aspects, the changes encoded in the amino acid sequence will not substantially affect the function of the protein. Such variants will possess the desired nematicidal activity. However, it is understood that the ability of a nematicidal protein to confer nematicidal activity may be improved by the use of such techniques upon the compositions of this invention. For example, one may express a nematicidal protein in host cells that exhibit high rates of base misincorporation during DNA replication, such as XL-1 Red (Stratagene, La Jolla, Calif.). After propagation in such strains, one can isolate the DNA (for example by preparing plasmid DNA, or by amplifying by PCR and cloning the resulting PCR fragment into a vector), culture the nematicidal protein mutations in a non-mutagenic strain, and identify mutated genes with nematicidal activity, for example by performing an assay to test for nematicidal activity. Generally, the protein is mixed and used in feeding assays. See, for example Marrone et al. (1985) J. of Economic Entomology 78:290-293. Such assays can include contacting plants with one or more pests and determining the plant's ability to survive and/or cause the death of the pests.
Alternatively, alterations may be made to the protein sequence of many proteins at the amino or carboxy terminus without substantially affecting activity. This can include insertions, deletions, or alterations introduced by modern molecular methods, such as PCR, including PCR amplifications that alter or extend the protein coding sequence by virtue of inclusion of amino acid encoding sequences in the oligonucleotides utilized in the PCR amplification. Alternatively, the protein sequences added can include entire protein-coding sequences, such as those used commonly in the art to generate protein fusions. Such fusion proteins are often used to (1) increase expression of a protein of interest (2) introduce a binding domain, enzymatic activity, or epitope to facilitate either protein purification, protein detection, or other experimental uses known in the art (3) target secretion or translation of a protein to a subcellular organelle, such as the periplasmic space of Gram-negative bacteria, or the endoplasmic reticulum of eukaryotic cells, the latter of which often results in glycosylation of the protein.
Variant nucleotide and amino acid sequences of the present invention also encompass sequences derived from mutagenic and recombinogenic procedures such as DNA shuffling. With such a procedure, one or more different nematicidal protein coding regions can be used to create a new nematicidal protein possessing the desired properties. In this manner, libraries of recombinant polynucleotides are generated from a population of related sequence polynucleotides comprising sequence regions that have substantial sequence identity and can be homologously recombined in vitro or in vivo. For example, using this approach, sequence motifs encoding a domain of interest may be shuffled between a nematicidal gene of the invention and other known nematicidal genes to obtain a new gene coding for a protein with an improved property of interest, such as an increased insecticidal activity. Strategies for such DNA shuffling are known in the art. See, for example, Stemmer (1994) Proc. Natl. Acad. Sci. USA 91:10747-10751; Stemmer (1994) Nature 370:389-391; Crameri et al. (1997) Nature Biotech. 15:436-438; Moore et al. (1997) J. Mol. Biol. 272:336-347; Zhang et al. (1997) Proc. Natl. Acad. Sci. USA 94:4504-4509; Crameri et al. (1998) Nature 391:288-291; and U.S. Pat. Nos. 5,605,793 and 5,837,458.
Domain swapping or shuffling is another mechanism for generating altered nematicidal proteins. Domains may be swapped between nematicidal proteins, resulting in hybrid or chimeric toxins with improved nematicidal activity or target spectrum. Methods for generating recombinant proteins and testing them for nematicidal activity are well known in the art (see, for example, Naimov et al. (2001) Appl. Environ. Microbiol. 67:5328-5330; de Maagd et al. (1996) Appl. Environ. Microbiol. 62:1537-1543; Ge et al. (1991) J. Biol. Chem. 266:17954-17958; Schnepf et al. (1990) J. Biol. Chem. 265:20923-20930; Rang et al. 91999) Appl. Environ. Microbiol. 65:2918-2925).
Protease Cleavage Site Manipulation
In various embodiments of the present invention, a nucleotide sequence encoding a cleavage fragment of the full-length polyphenol oxidase is expressed in the host cell of interest. In other embodiments, the nucleotide sequences encoding the polyphenol oxidase sequences are modified to add or remove sequences encoding proteolytic cleavage sites. For example, some full-length polyphenol oxidases, such as AXN-1 and AXN-8, are inactive precursors, which require proteolytic truncation to yield a toxin that is activate against SCN. For instance, full-length AXN-8 expressed in E. coli is not active against SCN, but when it is treated with trypsin, a C-terminal portion of the protein is removed, yielding an active truncated protein. When AXN-8 was expressed in E. coli in the truncated form, SCN activity was not seen, suggesting that the entire sequence may be needed in order for the protein to fold properly when it is synthesized. Furthermore, while not being bound by any particular theory or mechanism, it is also possible that an active polyphenol oxidase may catalyze the production of compounds that could be toxic to the plant or to animals (other than the pest of interest, e.g., nematodes) that feed on the plant. Expression of a full-length inactive protein would prevent this from occurring until the enzyme is activated by proteolytic truncation. This activation would only occur when a nematode infects the plant, and only in the area where the nematode is located. Once the nematode is killed by the toxin, no further active polyphenol oxidase will be produced because no more proteases are being produced by the nematode.
If an inactive full-length protein is expressed in a plant for either of the reasons described above, then it must be proteolytically truncated in order to show toxicity against SCN or other plant-parasitic nematodes. It is possible that plant proteases will carry out the activation to at least some extent, but more complete activation could be achieved if proteases produced by the nematode are capable of truncating the protein. If it is desirable to have the polyphenol oxidase remain inactive until a nematode infects the plant (for example, as a way of preventing the catalysis of chemical reactions that might produce compounds toxic to the plant or to non-target organisms), then any truncation site naturally occurring in the protein that is capable of being cleaved by plant proteases can be mutated so that it will no longer be cleaved. In either case, the sequence of the polyphenol oxidase can be modified (or further modified) such that it contains a recognition site for nematode proteases at the appropriate truncation location. This location can be determined by sequence analysis of active toxin isolated from its natural source, or by sequence analysis of active toxin produced by treating the full-length protein with proteases capable of carrying out the truncation, such as trypsin in the case of AXN-8. The choice of the protease recognition site will depend on the proteases that are secreted by the nematode into the plant, or that are present within the nematode digestive system. This site can be determined by isolating proteases and determining their substrate specificity, or by sequencing genes from the nematode or from a cDNA library prepared from mRNA extracted from the nematode, and determining to which protease families the genes belong. A secreted protease will activate the toxin in the plant, while a protease in the nematode's digestive system would activate the toxin after it is ingested.
Esophageal gland cells from soybean cyst nematode have been shown to express a putative cysteine proteinase (Genbank accession AF345792). This proteinase falls into the Peptidase C13 family, which consists of asparaginyl cysteine endopeptidases (proteases that cleave specifically after asparagines residues). In one example of this invention, a polyphenol oxidase expressed in a transgenic plant could be rendered activatable by SCN by altering the sequence of the polyphenol oxidase such that it contains an asparagine residue at the truncation site that results in an active enzyme. While not bound by any particular theory or mechanism, this version of the polyphenol oxidase might give greater activity than the wild-type enzyme because it would be fully activated in the presence of SCN. Furthermore, it might remain inactive in the absence of SCN, thereby avoiding the accumulation of chemical products of reactions catalyzed by the enzyme. If a recognition site for plant proteases is present in the protein, it can be mutated so that only the nematode proteases are capable of carrying out the truncation. A similar approach can be taken for any target pest. The truncation site of the polyphenol oxidase can be modified so that it will be susceptible to truncation by proteases produced by the target pest.
Vectors
A polyphenol oxidase sequence of the invention (or any other polyphenol oxidase sequences known in the art) may be provided in an expression cassette for expression in a plant of interest. In various embodiments, the polyphenol oxidase sequence is selected from any polyphenol oxidase known in the art. In another embodiment, the polyphenol oxidase is selected from the polyphenol oxidase derived from Trichoderma reesei, Bacillus thuringiensis, Glycine Max, Zea maize, Streptomyces castaneoglobisporus, Neurospora crassa species.
By “plant expression cassette” is intended a DNA construct that is capable of resulting in the expression of a protein from an open reading frame in a plant cell. Typically these contain a promoter and a coding sequence. Often, such constructs will also contain a 3′ untranslated region. Such constructs may contain a “signal sequence” or “leader sequence” to facilitate co-translational or post-translational transport of the peptide to certain intracellular structures such as the chloroplast (or other plastid), endoplasmic reticulum, or Golgi apparatus.
By “signal sequence” is intended a sequence that is known or suspected to result in cotranslational or post-translational peptide transport across the cell membrane. In eukaryotes, this typically involves secretion into the Golgi apparatus, with some resulting glycosylation. Pesticidal toxins of bacteria are often synthesized as protoxins, which are protolytically activated in the gut of the target pest (Chang (1987) Methods Enzymol. 153:507-516). In some embodiments of the present invention, the signal sequence is located in the native sequence, or may be derived from a sequence of the invention. By “leader sequence” is intended any sequence that when translated, results in an amino acid sequence sufficient to trigger co-translational transport of the peptide chain to a subcellular organelle. Thus, this includes leader sequences targeting transport and/or glycosylation by passage into the endoplasmic reticulum, passage to vacuoles, plastids including chloroplasts, mitochondria, and the like.
By “plant transformation vector” is intended a DNA molecule that is necessary for efficient transformation of a plant cell. Such a molecule may consist of one or more plant expression cassettes, and may be organized into more than one “vector” DNA molecule. For example, binary vectors are plant transformation vectors that utilize two non-contiguous DNA vectors to encode all requisite cis- and trans-acting functions for transformation of plant cells (Hellens and Mullineaux (2000) Trends in Plant Science 5:446-451). “Vector” refers to a nucleic acid construct designed for transfer between different host cells. “Expression vector” refers to a vector that has the ability to incorporate, integrate and express heterologous DNA sequences or fragments in a foreign cell. The cassette will include 5′ and 3′ regulatory sequences operably linked to a sequence of the invention. By “operably linked” is intended a functional linkage between a promoter and a second sequence, wherein the promoter sequence initiates and mediates transcription of the DNA sequence corresponding to the second sequence. Generally, operably linked means that the nucleic acid sequences being linked are contiguous and, where necessary to join two protein coding regions, contiguous and in the same reading frame. The cassette may additionally contain at least one additional gene to be cotransformed into the organism. Alternatively, the additional gene(s) can be provided on multiple expression cassettes. In various embodiments, the invention encompasses host cells comprising the insert of the vectors. By “insert of the vectors” is intended the DNA sequence comprising the gene(s) of the invention that is integrated into the host cell genome.
“Promoter” refers to a nucleic acid sequence that functions to direct transcription of a downstream coding sequence. The promoter together with other transcriptional and translational regulatory nucleic acid sequences (also termed “control sequences”) are necessary for the expression of a DNA sequence of interest. The promoters may be constitutive or inducible, or may be functional only in certain plant parts. In various embodiments, the promoter is a root-specific promoter (e.g., FaRB7, Vaughan (2006) J. Exp. Bot. 57:3901-3910). In some embodiments, the promoter is a feeding site specific promoter (e.g., TobRB7, Opperman (1994) Science 263(5144) 221-223).
Such an expression cassette is provided with a plurality of restriction sites for insertion of the nematicidal sequence to be under the transcriptional regulation of the regulatory regions.
The expression cassette will include in the 5′-3′ direction of transcription, a transcriptional and translational initiation region (i.e., a promoter), a DNA sequence of the invention, and a translational and transcriptional termination region (i.e., termination region) functional in plants. The promoter may be native or analogous, or foreign or heterologous, to the plant host and/or to the DNA sequence of the invention. Additionally, the promoter may be the natural sequence or alternatively a synthetic sequence. Where the promoter is “native” or “homologous” to the plant host, it is intended that the promoter is found in the native plant into which the promoter is introduced. Where the promoter is “foreign” or “heterologous” to the DNA sequence of the invention, it is intended that the promoter is not the native or naturally occurring promoter for the operably linked DNA sequence of the invention.
The termination region may be native with the transcriptional initiation region, may be native with the operably linked DNA sequence of interest, may be native with the plant host, or may be derived from another source (i.e., foreign or heterologous to the promoter, the DNA sequence of interest, the plant host, or any combination thereof). Convenient termination regions are available from the Ti-plasmid of A. tumefaciens, such as the octopine synthase and nopaline synthase termination regions. See also Guerineau et al. (1991) Mol. Gen. Genet. 262:141-144; Proudfoot (1991) Cell 64:671-674; Sanfacon et al. (1991) Genes Dev. 5:141-149; Mogen et al. (1990) Plant Cell 2:1261-1272; Munroe et al. (1990) Gene 91:151-158; Ballas et al. (1989) Nucleic Acids Res. 17:7891-7903; and Joshi et al. (1987) Nucleic Acid Res. 15:9627-9639.
Where appropriate, the gene(s) may be optimized for increased expression in the transformed host cell. That is, the genes can be synthesized using host cell-preferred codons for improved expression, or may be synthesized using codons at a host-preferred codon usage frequency. Generally, the GC content of the gene will be increased. See, for example, Campbell and Gowri (1990) Plant Physiol. 92:1-11 for a discussion of host-preferred codon usage. Methods are available in the art for synthesizing plant-preferred genes. See, for example, U.S. Pat. Nos. 5,380,831, and 5,436,391, and Murray et al. (1989) Nucleic Acids Res. 17:477-498, herein incorporated by reference.
In one embodiment, the protein is targeted to the chloroplast for expression. In this manner, where the protein is not directly inserted into the chloroplast, the expression cassette will additionally contain a nucleic acid encoding a transit peptide to direct the protein to the chloroplasts. Such transit peptides are known in the art. See, for example, Von Heijne et al. (1991) Plant Mol. Biol. Rep. 9:104-126; Clark et al. (1989) J. Biol. Chem. 264:17544-17550; Della-Cioppa et al. (1987) Plant Physiol. 84:965-968; Romer et al. (1993) Biochem. Biophys. Res. Commun. 196:1414-1421; and Shah et al. (1986) Science 233:478-481.
The gene to be targeted to the chloroplast may be optimized for expression in the chloroplast to account for differences in codon usage between the plant nucleus and this organelle. In this manner, the nucleic acids of interest may be synthesized using chloroplast-preferred codons. See, for example, U.S. Pat. No. 5,380,831, herein incorporated by reference.
Plant Transformation
Methods of the invention involve introducing a nucleotide construct into a plant. The methods comprise introducing at least one nucleotide sequence encoding a heterologous polyphenol oxidase enzyme into at least one plant cell. In various embodiments, the polyphenol oxidase is derived from a plant. In other embodiments, the polyphenol oxidase is derived from a non-plant organism (e.g., fungal, algal, bacterial, or other non-plant microorganism). The polyphenol oxidase may be a monophenol oxidase or a diphenol oxidase. In various embodiments, the polyphenol oxidase is selected from any of SEQ ID NO:1-22 or 45-49, or any of the polyphenol oxidases referenced in Table 13.
By “introducing” is intended to present to the plant the nucleotide construct in such a manner that the construct gains access to the interior of a cell of the plant. The methods of the invention do not require that a particular method for introducing a nucleotide construct to a plant is used, only that the nucleotide construct gains access to the interior of at least one cell of the plant. Methods for introducing nucleotide constructs into plants are known in the art including, but not limited to, stable transformation methods, transient transformation methods, and virus-mediated methods.
By “plant” is intended whole plants, plant organs (e.g., leaves, stems, roots, etc.), seeds, plant cells, propagules, embryos and progeny of the same. Plant cells can be differentiated or undifferentiated (e.g. callus, suspension culture cells, protoplasts, leaf cells, root cells, phloem cells, pollen).
“Transgenic plants” or “transformed plants” or “stably transformed” plants or cells or tissues refers to plants that have incorporated or integrated exogenous nucleic acid sequences or DNA fragments into the plant cell. These nucleic acid sequences include those that are exogenous, or not present in the untransformed plant cell. “Heterologous” refers to the nucleic acid sequences that are not endogenous to the cell or part of the native genome in which they are present, and have been added to the cell by infection, transfection, microinjection, electroporation, microprojection, or the like.
Transformation of plant cells can be accomplished by one of several techniques known in the art. The polyphenol oxidase genes described herein may be modified to obtain or enhance expression in plant cells. Typically a construct that expresses such a protein would contain a promoter to drive transcription of the gene, as well as a 3′ untranslated region to allow transcription termination and polyadenylation. The organization of such constructs is well known in the art. In some instances, it may be useful to engineer the gene such that the resulting peptide is secreted, or otherwise targeted within the plant cell. For example, the gene can be engineered to contain a signal peptide to facilitate transfer of the peptide to the endoplasmic reticulum. It may also be preferable to engineer the plant expression cassette to contain an intron, such that mRNA processing of the intron is required for expression.
Typically this “plant expression cassette” will be inserted into a “plant transformation vector”. This plant transformation vector may be comprised of one or more DNA vectors needed for achieving plant transformation. For example, it is a common practice in the art to utilize plant transformation vectors that are comprised of more than one contiguous DNA segment. These vectors are often referred to in the art as “binary vectors”. Binary vectors as well as vectors with helper plasmids are most often used for Agrobacterium-mediated transformation, where the size and complexity of DNA segments needed to achieve efficient transformation is quite large, and it is advantageous to separate functions onto separate DNA molecules. Binary vectors typically contain a plasmid vector that contains the cis-acting sequences required for T-DNA transfer (such as left border and right border), a selectable marker that is engineered to be capable of expression in a plant cell, and a “gene of interest” (a gene engineered to be capable of expression in a plant cell for which generation of transgenic plants is desired). Also present on this plasmid vector are sequences required for bacterial replication. The cis-acting sequences are arranged in a fashion to allow efficient transfer into plant cells and expression therein. For example, the selectable marker gene and the nematicidal gene are located between the left and right borders. Often a second plasmid vector contains the trans-acting factors that mediate T-DNA transfer from Agrobacterium to plant cells. This plasmid often contains the virulence functions (Vir genes) that allow infection of plant cells by Agrobacterium, and transfer of DNA by cleavage at border sequences and vir-mediated DNA transfer, as is understood in the art (Hellens and Mullineaux (2000) Trends in Plant Science 5:446-451). Several types of Agrobacterium strains (e.g. LBA4404, GV3101, EHA101, EHA105, etc.) can be used for plant transformation. The second plasmid vector is not necessary for transforming the plants by other methods such as microprojection, microinjection, electroporation, polyethylene glycol, etc.
In general, plant transformation methods involve transferring heterologous DNA into target plant cells (e.g. immature or mature embryos, suspension cultures, undifferentiated callus, protoplasts, etc.), followed by applying a maximum threshold level of appropriate selection (depending on the selectable marker gene) to recover the transformed plant cells from a group of untransformed cell mass. Explants are typically transferred to a fresh supply of the same medium and cultured routinely. Subsequently, the transformed cells are differentiated into shoots after placing on regeneration medium supplemented with a maximum threshold level of selecting agent. The shoots are then transferred to a selective rooting medium for recovering rooted shoot or plantlet. The transgenic plantlet then grows into a mature plant and produces fertile seeds (e.g. Hiei et al. (1994) The Plant Journal 6:271-282; Ishida et al. (1996) Nature Biotechnology 14:745-750). Explants are typically transferred to a fresh supply of the same medium and cultured routinely. A general description of the techniques and methods for generating transgenic plants are found in Ayres and Park (1994) Critical Reviews in Plant Science 13:219-239 and Bommineni and Jauhar (1997) Maydica 42:107-120. Since the transformed material contains many cells; both transformed and non-transformed cells are present in any piece of subjected target callus or tissue or group of cells. The ability to kill non-transformed cells and allow transformed cells to proliferate results in transformed plant cultures. Often, the ability to remove non-transformed cells is a limitation to rapid recovery of transformed plant cells and successful generation of transgenic plants.
Transformation protocols as well as protocols for introducing nucleotide sequences into plants may vary depending on the type of plant or plant cell, i.e., monocot or dicot, targeted for transformation. Generation of transgenic plants may be performed by one of several methods, including, but not limited to, microinjection, electroporation, direct gene transfer, introduction of heterologous DNA by Agrobacterium into plant cells (Agrobacterium-mediated transformation), bombardment of plant cells with heterologous foreign DNA adhered to particles, ballistic particle acceleration, aerosol beam transformation (U.S. Published Application No. 20010026941; U.S. Pat. No. 4,945,050; International Publication No. WO 91/00915; U.S. Published Application No. 2002015066), Lec1 transformation, and various other non-particle direct-mediated methods to transfer DNA.
Methods for transformation of chloroplasts are known in the art. See, for example, Svab et al. (1990) Proc. Natl. Acad. Sci. USA 87:8526-8530; Svab and Maliga (1993) Proc. Natl. Acad. Sci. USA 90:913-917; Svab and Maliga (1993) EMBO J. 12:601-606. The method relies on particle gun delivery of DNA containing a selectable marker and targeting of the DNA to the plastid genome through homologous recombination. Additionally, plastid transformation can be accomplished by transactivation of a silent plastid-borne transgene by tissue-preferred expression of a nuclear-encoded and plastid-directed RNA polymerase. Such a system has been reported in McBride et al. (1994) Proc. Natl. Acad. Sci. USA 91:7301-7305.
Following integration of heterologous foreign DNA into plant cells, one then applies a maximum threshold level of appropriate selection in the medium to kill the untransformed cells and separate and proliferate the putatively transformed cells that survive from this selection treatment by transferring regularly to a fresh medium. By continuous passage and challenge with appropriate selection, one identifies and proliferates the cells that are transformed with the plasmid vector.
A number of markers have been developed for use with plant cells, such as resistance to chloramphenicol, the aminoglycoside G418, hygromycin, or the like. Other genes that encode a product involved in chloroplast metabolism may also be used as selectable markers. For example, genes that provide resistance to plant herbicides such as glyphosate, bromoxynil, or imidazolinone may find particular use. Such genes have been reported (Stalker et al. (1985) J. Biol. Chem. 263:6310-6314 (bromoxynil resistance nitrilase gene); and Sathasivan et al. (1990) Nucl. Acids Res. 18:2188 (AHAS imidazolinone resistance gene). Additionally, the genes disclosed herein are useful as markers to assess transformation of bacterial or plant cells. Molecular and biochemical methods can then be used to confirm the presence of the integrated heterologous gene of interest into the genome of the transgenic plant. Methods for detecting the presence of a transgene in a plant, plant organ (e.g., leaves, stems, roots, etc.), seed, plant cell, propagule, embryo or progeny of the same are well known in the art. In one embodiment, the presence of the transgene is detected by testing for nematicidal activity. In another embodiment, the presence of the transgene is detected by testing for polyphenol oxidase activity.
The cells that have been transformed may be grown into plants in accordance with conventional ways. See, for example, McCormick et al. (1986) Plant Cell Reports 5:81-84. These plants may then be grown, and either pollinated with the same transformed strain or different strains, and the resulting hybrid having constitutive expression of the desired phenotypic characteristic identified. Two or more generations may be grown to ensure that expression of the desired phenotypic characteristic is stably maintained and inherited and then seeds harvested to ensure expression of the desired phenotypic characteristic has been achieved. In this manner, the present invention provides transformed seed (also referred to as “transgenic seed”) having a nucleotide construct of the invention, for example, an expression cassette of the invention, stably incorporated into their genome.
The present invention may be used for transformation of any plant species, including, but not limited to, monocots and dicots. Examples of plants of interest include, but are not limited to, corn (maize), sorghum, wheat, sunflower, tomato, crucifers, peppers, potato, cotton, rice, soybean, sugarbeet, sugarcane, tobacco, barley, and oilseed rape, Brassica sp., alfalfa, rye, millet, safflower, peanuts, sweet potato, cassava, coffee, coconut, pineapple, citrus trees, cocoa, tea, banana, avocado, fig, guava, mango, olive, papaya, cashew, macadamia, almond, oats, vegetables, ornamentals, and conifers.
Vegetables include, but are not limited to, tomatoes, lettuce, green beans, lima beans, peas, and members of the genus Curcumis such as cucumber, cantaloupe, and musk melon. Ornamentals include, but are not limited to, azalea, hydrangea, hibiscus, roses, tulips, daffodils, petunias, carnation, poinsettia, and chrysanthemum. Preferably, plants of the present invention are crop plants (for example, maize, sorghum, wheat, sunflower, tomato, crucifers, peppers, potato, cotton, rice, soybean, sugarbeet, sugarcane, tobacco, barley, oilseed rape, etc.).
Evaluation of Plant Transformation
Following introduction of heterologous foreign DNA into plant cells, the transformation or integration of heterologous gene in the plant genome is confirmed by various methods such as analysis of nucleic acids, proteins and metabolites associated with the integrated gene.
PCR analysis is a rapid method to screen transformed cells, tissue or shoots for the presence of incorporated gene at the earlier stage before transplanting into the soil (Sambrook and Russell (2001) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.). PCR is carried out using oligonucleotide primers specific to the gene of interest or Agrobacterium vector background, etc.
Plant transformation may be confirmed by Southern blot analysis of genomic DNA (Sambrook and Russell, 2001, supra). In general, total DNA is extracted from the transformant, digested with appropriate restriction enzymes, fractionated in an agarose gel and transferred to a nitrocellulose or nylon membrane. The membrane or “blot” is then probed with, for example, radiolabeled 32P target DNA fragment to confirm the integration of introduced gene into the plant genome according to standard techniques (Sambrook and Russell, 2001, supra).
In Northern blot analysis, RNA is isolated from specific tissues of transformant, fractionated in a formaldehyde agarose gel, and blotted onto a nylon filter according to standard procedures that are routinely used in the art (Sambrook and Russell, 2001, supra). Expression of RNA encoded by the nematicidal gene is then tested by hybridizing the filter to a radioactive probe derived from a nematicidal gene, by methods known in the art (Sambrook and Russell, 2001, supra).
Western blot, biochemical assays and the like may be carried out on the transgenic plants to confirm the presence of protein encoded by the nematicidal gene by standard procedures (Sambrook and Russell, 2001, supra) using antibodies that bind to one or more epitopes present on the nematicidal protein.
Methods for Screening for and Developing Plants with Polyphenol Oxidase Activity
Various plant species are known to express polyphenol oxidase. In some instances, expression of polyphenol oxidase has been shown to be associated with improved agronomic performance. For example, plants which exhibit comparably high resistance to climatic stress have been shown to posses relatively higher polyphenol oxidase levels than susceptible varieties (Thipyapong et al. (2007) Molecules 12(8):1569-95). However, prior to the present invention, resistance to nematode infestation has not been demonstrated in plants having polyphenol oxidase activity. Identification of plants having optimal polyphenol oxidase levels provides a hitherto unrecognized opportunity for developing plants suitable for cultivation in an area susceptible to nematode infestation. By “optimal polyphenol oxidase activity” is intended a level of activity sufficient to bring about death to at least one pest, or to noticeably reduce pest growth, feeding, or normal physiological development when the plant expressing the polyphenol oxidase is exposed to a nematode pest.
Thus, provided herein are methods for screening a plant or plant variety for polyphenol oxidase activity. For example, root extracts from different plants (for example, different inbred lines, or different progeny of a cross) can be tested for polyphenol oxidase activity using assays known in the art and described elsewhere herein. Plants expressing polyphenol oxidase may be tested for nematicidal activity, and the plants showing optimal activity selected for use in a field susceptible to nematode infestation, or used for further breeding for introgression of the nematode-resistance trait into a plant population. Identification of a polyphenol oxidase having optimal activity may be associated with the presence of a polyphenol oxidase, the relative level of expression or activity of a polyphenol oxidase, or the presence of a particular polymorphism associated with improved polyphenol oxidase activity and/or nematode resistance. The polymorphism may be within the polyphenol oxidase gene itself, or may be within a genetic marker identified as being associated with or linked to polyphenol oxidase expression (i.e., within a Quantitative Trait Loci (QTL) associated with polyphenol oxidase expression).
The methods of the invention further contemplate screening of existing QTLs for nematode resistance for the presence of a polyphenol oxidase gene or polymorphism. Previous studies have identified large genetic regions linked as QTLs involved in nematode resistance, and these regions may contain certain polyphenol oxidases or tyrosinases. QTLs typically contain many hundreds if not thousands of genes, yet identification of the causal gene for the associated trait often remains elusive. Thus, the invention anticipates screening for polyphenol oxidase genes (or particular polymorphisms thereof) from such regions. These genetic elements, or genetic markers closely linked to these polyphenol oxidase genetic elements, can be used in marker-assisted breeding protocols to develop plants more resistant to nematode infestation. Methods for screening a genetic region for a gene of interest are routine in the art, as are methods for marker-assisted breeding.
Germplasm Mutagenesis
Further provided are methods for developing plants with nematode resistance using germplasm mutagenesis. Mutagenesis is means of creating genetic diversity that does not exist or has not been found in existing germplasm. Treating somatic embryos, embryos derived from culturing portions of immature seeds, with mutagenic agents can be an efficient method of creating mutations because they are easier to regenerate into whole plants than cell cultures and easier to handle in large numbers than seeds. Thus, the methods encompassed herein comprise mutagenizing a plant germplasm and screening a component of the plant derived therefrom (for example, root extracts) for polyphenol oxidase activity. Isolates having optimal polyphenol oxidase activity can be used to develop a plant population suitable for cultivation in an area susceptible to nematode infestation.
Methods for germplasm mutagenesis are generally known in the art. Gamma rays are the most frequently used mutagen, but new agents including ion beams and space condition have also been used in mutation induction and breeding (Chen et al. (2006) Plant Mutation Reports Volume 1 Number 1 at www-naweb.iaea.org/nafa/pbg/public/pmr-01-01.pdf). Use of in vitro cultures for mutation induction, or use of another culture to rapidly produce homozygous lines from irradiated progenies, has proven to be very useful in several laboratories.
Methods for Controlling Nematodes in a Field
Provided herein are methods for controlling nematodes in a field susceptible to infestation by one or more plant-parasitic nematode pests. The methods comprise cultivating a plant in an area susceptible to plant-parasitic nematode infestation, wherein the plant expresses a heterologous polyphenol oxidase. An “area” or a “field” susceptible to infestation includes a geographic region or planting area that has a detectable level of one or more species of plant-parasitic nematodes. A “detectable level” includes any level of plant-parasitic nematodes sufficiently high enough to cause damage in a susceptible plant. Signs of nematode damage include stunting and yellowing of leaves, and wilting of the plants during hot periods. However, some nematodes, including soybean cyst nematode (SCN), can cause significant yield loss without obvious above-ground symptoms. In this instance, roots infected with plant-parasitic nematodes will be dwarfed or stunted compared to the roots of a plant not infected with nematodes. Various other macroscopic and microscopic detection methods of different types of nematodes are known in the art, and are typically available via local agricultural extension services. An area susceptible to nematode infestation may also include an area that has a detectable level of plant-parasitic nematodes in the soil.
Use in Pesticidal Control
General methods for employing strains comprising a nucleotide sequence of the present invention, or a variant thereof, in pest control or in engineering other organisms as pesticidal agents are known in the art. See, for example U.S. Pat. No. 5,039,523 and EP 0480762A2.
The bacterial or fungal strains containing the nucleotide sequence(s) of the present invention, or a variant thereof, or the microorganisms that have been genetically altered to contain a nematicidal gene and protein may be used for protecting agricultural crops and products from pests. In one aspect of the invention, whole, i.e., unlysed, cells of a toxin-producing organism are treated with reagents that prolong the activity of the toxin produced in the cell when the cell is applied to the environment of target pest(s).
Alternatively, the pesticide is produced by introducing a nematicidal gene into a cellular host. Expression of the nematicidal gene results, directly or indirectly, in the intracellular production and maintenance of the nematode toxin. In one aspect of this invention, these cells are then treated under conditions that prolong the activity of the toxin produced in the cell when the cell is applied to the environment of target pest(s). The resulting product retains the toxicity of the toxin. These naturally encapsulated pesticides may then be formulated in accordance with conventional techniques for application to the environment hosting a target pest, e.g., soil, water, root, seed and/or foliage of plants. See, for example EPA 0192319, and the references cited therein. In various embodiments, the polyphenol oxidase may be expressed in a bacterial cell and used as a probiotic to treat the seed of the plant. Alternatively, one may formulate the cells expressing a gene of this invention such as to allow application of the resulting material as a pesticide.
The active ingredients of the present invention are normally applied in the form of compositions and can be applied to the crop area or plant to be treated, simultaneously or in succession, with other compounds. These compounds can be fertilizers, weed killers, cryoprotectants, surfactants, detergents, pesticidal soaps, dormant oils, polymers, and/or time-release or biodegradable carrier formulations that permit long-term dosing of a target area following a single application of the formulation. The compounds can be cofactors or other molecules that enhance the activity of the polyphenol oxidase enzyme. For example, the compound can be methyl jasmonate, which has been shown to increase the expression of polyphenol oxidase genes (see, for example, Constable and Ryan (1998) Plant Mol. Biol. 36(1):55-62), a phenol such as L-DOPA or tyrosine, or a substrate capable of participating in polyphenol oxidase-mediated crosslinking (e.g., tyrosine). These compounds can be provided to the plants before, during, or after (or any combination thereof) application of the pesticidal composition. Where the compound is a polypeptide capable of expression in a plant, the susceptible plant may be transgenic for this polypeptide.
These compounds can also be selective herbicides, chemical insecticides, virucides, microbicides, amoebicides, pesticides, fungicides, bacteriocides, nematocides, molluscicides or mixtures of several of these preparations, if desired, together with further agriculturally acceptable carriers, surfactants or application-promoting adjuvants customarily employed in the art of formulation. Suitable carriers and adjuvants can be solid or liquid and correspond to the substances ordinarily employed in formulation technology, e.g. natural or regenerated mineral substances, solvents, dispersants, wetting agents, tackifiers, binders or fertilizers. Likewise the formulations may be prepared into edible “baits” or fashioned into pest “traps” to permit feeding or ingestion by a target pest of the nematicidal formulation.
Methods of applying an active ingredient of the present invention or an agrochemical composition of the present invention that contains at least one of the nematicidal proteins of the present invention include leaf application, seed coating and soil application. The number of applications and the rate of application depend on the intensity of infestation by the corresponding pest.
The composition may be formulated as a powder, dust, pellet, granule, spray, emulsion, colloid, solution, or such like, and may be prepared by such conventional means as desiccation, lyophilization, homogenation, extraction, filtration, centrifugation, sedimentation, or concentration of a culture of cells comprising the polypeptide. In all such compositions that contain at least one such nematicidal polypeptide, the polypeptide may be present in a concentration of from about 1% to about 99% by weight.
Nematode pests may be killed or reduced in numbers in a given area by the methods of the invention, or may be prophylactically applied to an environmental area to prevent infestation by a susceptible pest (i.e., nematode). Preferably the pest ingests, or is contacted with, a nematicidally-effective amount of the polypeptide. By “nematicidally-effective amount” is intended an amount of the pesticide that is able to bring about death to at least one pest, or to noticeably reduce pest growth, feeding, or normal physiological development. This amount will vary depending on such factors as, for example, the specific nematode species to be controlled, the specific environment, location, plant, crop, or agricultural site to be treated, the environmental conditions, and the method, rate, concentration, stability, and quantity of application of the nematicidally-effective polypeptide composition. The formulations may also vary with respect to climatic conditions, environmental considerations, and/or frequency of application and/or severity of pest infestation.
The nematicidal compositions described may be made by formulating either the microbial cell (or extract thereof) expressing the nematicidal gene of the invention, or isolated protein component with the desired agriculturally-acceptable carrier. The compositions may be formulated prior to administration in an appropriate means such as lyophilized, freeze-dried, desiccated, or in an aqueous carrier, medium or suitable diluent, such as saline or other buffer. The formulated compositions may be in the form of a dust or granular material, or a suspension in oil (vegetable or mineral), or water or oil/water emulsions, or as a wettable powder, or in combination with any other carrier material suitable for agricultural application. Suitable agricultural carriers can be solid or liquid and are well known in the art. The term “agriculturally-acceptable carrier” covers all adjuvants, inert components, dispersants, surfactants, tackifiers, binders, etc. that are ordinarily used in pesticide formulation technology; these are well known to those skilled in pesticide formulation. The formulations may be mixed with one or more solid or liquid adjuvants and prepared by various means, e.g., by homogeneously mixing, blending and/or grinding the nematicidal composition with suitable adjuvants using conventional formulation techniques. Suitable formulations and application methods are described in U.S. Pat. No. 6,468,523, herein incorporated by reference.
In various embodiments, the polyphenol oxidase can be used to treat or prevent the infestation of plants with insects, fungi, bacteria, mites, ticks, and the like. Insect pests include insects selected from the orders Coleoptera, Diptera, Hymenoptera, Lepidoptera, Mallophaga, Homoptera, Hemiptera, Orthroptera, Thysanoptera, Dermaptera, Isoptera, Anoplura, Siphonaptera, Trichoptera, etc., particularly Coleoptera, Lepidoptera, and Diptera.
The order Coleoptera includes the suborders Adephaga and Polyphaga. Suborder Adephaga includes the superfamilies Caraboidea and Gyrinoidea, while suborder Polyphaga includes the superfamilies Hydrophiloidea, Staphylinoidea, Cantharoidea, Cleroidea, Elateroidea, Dascilloidea, Dryopoidea, Byrrhoidea, Cucujoidea, Meloidea, Mordelloidea, Tenebrionoidea, Bostrichoidea, Scarabaeoidea, Cerambycoidea, Chrysomeloidea, and Curculionoidea. Superfamily Caraboidea includes the families Cicindelidae, Carabidae, and Dytiscidae. Superfamily Gyrinoidea includes the family Gyrimidae. Superfamily Hydrophiloidea includes the family Hydrophilidae. Superfamily Staphylinoidea includes the families Silphidae and Staphylimidae. Superfamily Cantharoidea includes the families Cantharidae and Lampyridae. Superfamily Cleroidea includes the families Cleridae and Dermestidae. Superfamily Elateroidea includes the families Elateridae and Buprestidae. Superfamily Cucujoidea includes the family Coccinellidae. Superfamily Meloidea includes the family Meloidae. Superfamily Tenebrionoidea includes the family Tenebrionidae. Superfamily Scarabaeoidea includes the families Passalidae and Scarabaeidae. Superfamily Cerambycoidea includes the family Cerambycidae. Superfamily Chrysomeloidea includes the family Chrysomelidae. Superfamily Curculionoidea includes the families Curculionidae and Scolytidae.
The order Diptera includes the Suborders Nematocera, Brachycera, and Cyclorrhapha. Suborder Nematocera includes the families Tipulidae, Psychodidae, Culicidae, Ceratopogonidae, Chironomidae, Simuliidae, Bibionidae, and Cecidomyiidae. Suborder Brachycera includes the families Stratiomyidae, Tabanidae, Therevidae, Asilidae, Mydidae, Bombyliidae, and Dolichopodidae. Suborder Cyclorrhapha includes the Divisions Aschiza and Aschiza. Division Aschiza includes the families Phoridae, Syrphidae, and Conopidae. Division Aschiza includes the Sections Acalyptratae and Calyptratae. Section Acalyptratae includes the families Otitidae, Tephritidae, Agromyzidae, and Drosophilidae. Section Calyptratae includes the families Hippoboscidae, Oestridae, Tachimidae, Anthomyiidae, Muscidae, Calliphoridae, and Sarcophagidae.
The order Lepidoptera includes the families Papilionidae, Pieridae, Lycaenidae, Nymphalidae, Danaidae, Satyridae, Hesperiidae, Sphingidae, Saturniidae, Geometridae, Arctiidae, Noctuidae, Lymantriidae, Sesiidae, and Tineidae.
Insect pests of the invention for the major crops include: Maize: Ostrinia nubilalis, European corn borer; Agrotis ipsilon, black cutworm; Helicoverpa zea, corn earworm; Spodoptera frugiperda, fall armyworm; Diatraea grandiosella, southwestern corn borer; Elasmopalpus lignosellus, lesser cornstalk borer; Diatraea saccharalis, surgarcane borer; Diabrotica virgifera, western corn rootworm; Diabrotica longicornis barberi, northern corn rootworm; Diabrotica undecimpunctata howardi, southern corn rootworm; Melanotus spp., wireworms; Cyclocephala borealis, northern masked chafer (white grub); Cyclocephala immaculata, southern masked chafer (white grub); Popillia japonica, Japanese beetle; Chaetocnema pulicaria, corn flea beetle; Sphenophorus maidis, maize billbug; Rhopalosiphum maidis, corn leaf aphid; Anuraphis maidiradicis, corn root aphid; Blissus leucopterus leucopterus, chinch bug; Melanoplus femurrubrum, redlegged grasshopper; Melanoplus sanguinipes, migratory grasshopper; Hylemya platura, seedcorn maggot; Agromyza parvicornis, corn blot leafminer; Anaphothrips obscrurus, grass thrips; Solenopsis milesta, thief ant; Tetranychus urticae, twospotted spider mite; Sorghum: Chilo partellus, sorghum borer; Spodoptera frugiperda, fall armyworm; Helicoverpa zea, corn earworm; Elasmopalpus lignosellus, lesser cornstalk borer; Feltia subterranea, granulate cutworm; Phyllophaga crinita, white grub; Eleodes, Conoderus, and Aeolus spp., wireworms; Oulema melanopus, cereal leaf beetle; Chaetocnema pulicaria, corn flea beetle; Sphenophorus maidis, maize billbug; Rhopalosiphum maidis; corn leaf aphid; Sipha flava, yellow sugarcane aphid; Blissus leucopterus leucopterus, chinch bug; Contarinia sorghicola, sorghum midge; Tetranychus cinnabarinus, carmine spider mite; Tetranychus urticae, twospotted spider mite; Wheat: Pseudaletia unipunctata, army worm; Spodoptera frugiperda, fall armyworm; Elasmopalpus lignosellus, lesser cornstalk borer; Agrotis orthogonia, western cutworm; Elasmopalpus lignosellus, lesser cornstalk borer; Oulema melanopus, cereal leaf beetle; Hypera punctata, clover leaf weevil; Diabrotica undecimpunctata howardi, southern corn rootworm; Russian wheat aphid; Schizaphis graminum, greenbug; Macrosiphum avenae, English grain aphid; Melanoplus femurrubrum, redlegged grasshopper; Melanoplus differentialis, differential grasshopper; Melanoplus sanguinipes, migratory grasshopper; Mayetiola destructor, Hessian fly; Sitodiplosis mosellana, wheat midge; Meromyza americana, wheat stem maggot; Hylemya coarctata, wheat bulb fly; Frankliniella fusca, tobacco thrips; Cephus cinctus, wheat stem sawfly; Aceria tulipae, wheat curl mite; Sunflower: Suleima helianthana, sunflower bud moth; Homoeosoma electellum, sunflower moth; zygogramma exclamationis, sunflower beetle; Bothyrus gibbosus, carrot beetle; Neolasioptera murtfeldtiana, sunflower seed midge; Cotton: Heliothis virescens, cotton budworm; Helicoverpa zea, cotton bollworm; Spodoptera exigua, beet armyworm; Pectinophora gossypiella, pink bollworm; Anthonomus grandis, boll weevil; Aphis gossypii, cotton aphid; Pseudatomoscelis seriatus, cotton fleahopper; Trialeurodes abutilonea, bandedwinged whitefly; Lygus lineolaris, tarnished plant bug; Melanoplus femurrubrum, redlegged grasshopper; Melanoplus differentialis, differential grasshopper; Thrips tabaci, onion thrips; Franklinkiella fusca, tobacco thrips; Tetranychus cinnabarinus, carmine spider mite; Tetranychus urticae, twospotted spider mite; Rice: Diatraea saccharalis, sugarcane borer; Spodoptera frugiperda, fall armyworm; Helicoverpa zea, corn earworm; Colaspis brunnea, grape colaspis; Lissorhoptrus oryzophilus, rice water weevil; Sitophilus oryzae, rice weevil; Nephotettix nigropictus, rice leafhopper; Blissus leucopterus leucopterus, chinch bug; Acrosternum hilare, green stink bug; Soybean: Pseudoplusia includens, soybean looper; Anticarsia gemmatalis, velvetbean caterpillar; Plathypena scabra, green cloverworm; Ostrinia nubilalis, European corn borer; Agrotis ipsilon, black cutworm; Spodoptera exigua, beet armyworm; Heliothis virescens, cotton budworm; Helicoverpa zea, cotton bollworm; Epilachna varivestis, Mexican bean beetle; Myzus persicae, green peach aphid; Empoasca fabae, potato leafhopper; Acrosternum hilare, green stink bug; Melanoplus femurrubrum, redlegged grasshopper; Melanoplus differentialis, differential grasshopper; Hylemya platura, seedcorn maggot; Sericothrips variabilis, soybean thrips; Thrips tabaci, onion thrips; Tetranychus turkestani, strawberry spider mite; Tetranychus urticae, twospotted spider mite; Barley: Ostrinia nubilalis, European corn borer; Agrotis ipsilon, black cutworm; Schizaphis graminum, greenbug; Blissus leucopterus leucopterus, chinch bug; Acrosternum hilare, green stink bug; Euschistus servus, brown stink bug; Delia platura, seedcorn maggot; Mayetiola destructor, Hessian fly; Petrobia latens, brown wheat mite; Oil Seed Rape: Brevicoryne brassicae, cabbage aphid; Phyllotreta cruciferae, Flea beetle; Mamestra configurata, Bertha armyworm; Plutella xylostella, Diamond-back moth; Delia ssp., Root maggots.
Methods for Increasing Plant Yield
Methods for increasing plant yield are provided. The methods comprise introducing into a plant or plant cell a polynucleotide comprising a nematicidal sequence disclosed herein. Expression of the nematicidal sequence results in improved resistance to nematode infestation which, in turn, increases the yield of a transgenic plant compared to the yield of a plant not expressing a polyphenol oxidase (when exposed to plant-parasitic nematodes). As defined herein, the “yield” of the plant refers to the quality and/or quantity of biomass produced by the plant. By “biomass” is intended any measured plant product. An increase in biomass production is any improvement in the yield of the measured plant product. Increasing plant yield has several commercial applications. For example, increasing plant leaf biomass may increase the yield of leafy vegetables for human or animal consumption. Additionally, increasing leaf biomass can be used to increase production of plant-derived pharmaceutical or industrial products. An increase in yield can comprise any statistically significant increase including, but not limited to, at least a 1% increase, at least a 3% increase, at least a 5% increase, at least a 10% increase, at least a 20% increase, at least a 30%, at least a 50%, at least a 70%, at least a 100% or a greater increase in yield compared to a plant not expressing the nematicidal sequence.
Methods for Identifying Quantitative Trait Loci Associated with Nematode Resistance
Also provided herein are methods for identifying or validating markers associated with a quantitative trait loci (QTL) for nematode resistance or tolerance. The methods comprise evaluating genetic markers within the genomic region surrounding one or more polyphenol oxidase genes in a population of plants showing resistance or tolerance to nematode infestation, and detecting an association between one or more genetic marker(s) and the nematode resistance trait. High density genetic maps have been developed for many species of plants susceptible to nematode infestation, including maize and soybean plants. Markers from these maps can be evaluated for the association, and positively-associated markers can be used in downstream applications such as marker-assisted breeding. Methods for evaluating marker:trait associations are known in the art and can be applied to genomic regions encoding genes having homology to polyphenol oxidase genes.
In another embodiment, QTLs that are known or suspected to be associated with nematode resistance can be evaluated to determine whether a polyphenol oxidase gene is within or near the QTL. In this embodiment, regions within or surrounding the QTL can be sequenced and searched for polyphenol oxidase homologs.
The following examples are offered by way of illustration and not by way of limitation.
EXPERIMENTAL
Example 1
Assay for Nematicidal Activity
Use of biogenic amines to induce feeding and/or movement from parasitic nematodes has been demonstrated previously for RNAi uptake experiments (for example, see P. E. Urwin, Catherine J. Lilley, and Howard J. Atkinson, “Ingestion of Double-Stranded RNA by Preparasitic Juvenile Cyst Nematodes Leads to RNA Interference” Molecular Plant Microbe Interaction Vol. 15, No. 8, 2002, pp. 747-752. Also see M J Kimber, S McKinney, S. McMaster T A Day, C C Flemming and A G Maule (2007) “Flp gene disruption in a parasitic nematode reveals motor dysfunction and unusual neuronal sensitivity to RNA interference” The FASEB Journal vol 21 pp 1233-1242)
Assays of SCN activity provided herein are based on use of an SCN bioassay that typically contains  ̃200 J2 nematodes (hatched within 2 days of assay) per well in a 96-well half-area plate. The nematodes are incubated in 20 mM Tris buffer (pH 8.0) containing 50 mM octopamine, and the following antibiotic and antifungal components: gentamycin (1.5 ug/ul), nystatin (0.05 ug/ul), Sigma antibiotic-antimycotic (cat #A5955) at 1×, Infuse antimycotic (1/1500 dilution from stock) all in 30 ul final volume, including the test strain or protein. The assay plate is incubated at 28 C in a humidified chamber. Scoring of the assay is facilitated by addition of sodium carbonate, which causes living nematodes to curl, while dead nematodes remain straight and rigid. Scoring must be done within  ̃10 minutes of the carbonate addition. Activity on nematodes is scored on the following scale, and compared with negative control, and positive control samples.







TABLE 1







Scoring Convention for SCN Assays


SCN Scoring Convention










Score assigned
Mortality on SCN (%)














0
 0-10%



1
11-20%



2
21-50%



3
51-75%



4
76-95%



5
96-100% 










Example 2
Enhancement of Steady-State Levels of Nematode Protein Toxins in Microbial Strains
A microbial strain of interest (e.g., a bacteria or fungal strain) is grown under media conditions that can partially limit the availability of nutrients to the microbe. For instance, the availability of carbon or nitrogen can be reduced in the minimal growth medium.
The medium is supplemented with components that are useful to stimulate microbial production of nematode toxins. As one example, the addition of gelatin to a growth medium can mimic the gelatinous cuticle found on some nematodes, and thus stimulate the microbial production of nematode protein toxins. As another example, the addition of nematodes to the growth medium (such as C. elegans or soybean cyst nematode) can stimulate the microbial production of protein toxins. As another example, a nematode extract can be prepared and added to a microbial growth medium to stimulate the production of microbial protein toxins. The various components can also be combined.
The growth medium (supplemented with a component to stimulate toxin production) is inoculated with a microbial strain or strains, and then grown under conditions appropriate for strain growth. Whole culture or some fraction of the culture (for example: culture supernatants, protein extracts, solubilized protein extracts, pellet extracts, etc) are then tested to determine if a nematode toxin has been produced by the microbial strain under the growth medium and growth conditions tested.
Example 3
Identification of Nematode Protein Toxin from Arthrobotrys oligospora 
It is known in the art that nematicidal fungi can be isolated from soil, in particular from suppressive soils. Several such fungi were obtained and tested for SCN activity, under a variety of growth conditions.
Arthrobotrys oligospora is a nematophagous fungus, and has been observed previously to have nematicidal activity in soil. This activity has been associated with nematophagous trapping in the literature (for example, see Nansen et al., 1988. Vet Parasitol., 26:329-37). There is no description of nematode protein toxins production by Arthrobotrys oligospora or related strains.
To test the ability of an Arthrobotrys oligospora strain to produce protein toxins, an Arthrobotrys oligospora strain (ATX21995) was inoculated into Arthrobotrys medium supplemented as shown below, and incubated at 30° C. with gentle shaking for 7 days. The resulting extracts were tested for ability to kill SCN.

    
    
        Arthrobotrys medium (per liter):
        
            1 g glucose
            0.5 g (NH4)2SO4 
            0.5 g MgSO4 
            2 g KH2PO4 
            0.005 g FeSO4 
            Adjust to pH 6.0 with KOH
        
        
        Optional:
        
            0.5 g gelatin
            Add C. elegans harvested from 1 MYOB plate (100 mm plate, first inoculated with E. coli to generate a lawn as diet for C. elegans) per 50 mL of medium
        
        
    
    









TABLE 2







Activity of ATX 21995 grown in various media











Activity of ATX 21995


Media
Description
extract





Media 1
Potato dextrose broth
No/Low activity


Media 2
Arthrobotrys medium
No/Low Activity


Media 3
Arthrobotrys medium + gelatin
Inconsistent Activity


Media 4
Arthrobotrys medium + gelatin +
Consistent, Strong Activity



nematodes









From each culture medium, a soluble protein extract was prepared following seven days of growth. At that time, the fungal biomass was separated from the growth medium using a disposable 0.4 micron filter unit, and this biomass was then ground in a mortar and pestle in the presence of liquid nitrogen to lyse the cells. This material was then resuspended in buffer A (50 mM Tris (pH 8.0), 1 mM DTT) and submitted for soybean cyst nematode (SCN) bioassays.
Protein extracts were prepared from Arthrobotrys oligospora (ATX21995) cultures grown in Arthrobotrys medium (+gelatin, +C. elegans) for seven days. Extracts were prepared by grinding the fungal biomass in the presence of liquid nitrogen (as described above) and resuspending the lysed cell material in buffer at pH 6.0 (50 mM MES, 1 mM DTT), pH 8.0 (50 mM Tris, 1 mM DTT) or pH 10.4 (50 mM CAPS, 1 mM DTT). Extracts prepared in this manner assayed for SCN activity all showed strong activity on SCN.
Example 4
Purification of AXN-1 from ATX21995
Purifications were carried out using extracts prepared from ATX 21995 grown in Arthrobotrys Medium contain gelatin and nematodes. Typically, purifications were carried out at large scale by growing several 250 mL flasks (approximately 30-60 flasks) with 50 mL of medium in each flask to allow sufficient quantities of protein to enter the purifications.
Two different protein purifications were carried out from cultures of strain ATX21995. The total fungal biomass from these cultures was lysed (mortar and pestle with liquid nitrogen), and the protein was fractionated by FPLC using standard purification methods. These purifications resulted in identification of an  ̃50 kDa protein that correlated with the elution of the SCN activity.
Example 5
Protein Characterization of 50 kDa Protein from ATX21995
To clone the gene encoding the  ̃50 kDa protein, approximately 10-15 micrograms of this protein was isolated, and a small quantity of the sample was electroblotted to a PVDF membrane by standard methods, stained the membrane with Coomassie dye, and the band corresponding to the 50 kDa protein excised and subjected to N-terminal sequencing as known in the art. This protein was found to yield very small amounts of free amino acids during the sequencing reactions, which suggested that the N-terminus of the protein might be chemically modified.
A gel slice containing the 50 kDa protein was digested in-gel with trypsin, and the fragments were then separated by HPLC. Individual peaks were then analyzed by MALDI to identify fragments suitable for protein sequencing. A total of 5 tryptic fragments were selected, and subjected to Edman degradation for protein sequencing (Table 3). Edman degradation sequencing reactions yielded the following sequences for each of these peaks:







TABLE 3







N-terminal sequence of tryptic fragments









Peak
Primary Sequence Identified by



Name
Edman Degradation
SEQ ID NO:





20
G-T-W-S-I A A G S R
23


 


24
D-S-T-G-E-F-N-A-T-L-Y-R
24


 


29
S-A-P-Y-A-I-T-G-I
25


 


36
Y-P-D-A-W-F-N-A-Q-S-A-Q-L-R
26


 


42
F-G-S-S-Y-P-E-L-Q-P
27









Example 6
Cloning of a cDNA that Encodes the 50 kDa Protein from ATX21995
Total RNA was isolated from ATX21995 cultures grown for 2 days, 4 days and 6 days. This RNA was reverse transcribed to generate cDNA; this cDNA was subsequently normalized to decrease the abundance of strongly expressed transcripts. Using this cDNA as a starting template, several PCR products were generated and sequenced.
Degenerate PCR Based Use of cDNA Linker Sequence.
A number of degenerate oligonucleotides based on the amino acid sequence of 24 (see Table 3) were designed and tested in combination with the oligonucleotides that represent the ends of the cDNA pool. A set of conditions was identified that resulted in amplification of an 1840 nucleotide PCR product. This PCR product, as well as several other candidate PCR products, was cloned into a TOPO vector, and the DNA sequences adjacent to the vector were determined.
Degenerate PCR Based Solely on Amino Acid Sequence.
Degenerate PCR primers were designed based on the amino acid sequences of fragments 20, 24, and 29, 36, and 42 from Table 3. This set of degenerate oligonucleotides utilized inosine in several positions to reduce the degeneracy of the resulting oligonucleotides. Also, when possible, a set of nested degenerate PCR primers was designed for each amino acid sequence in Table 3. This strategy allows use of the “outside” primers (those based on the more N-terminal amino acids of a sequence in Table 3) in the first round of PCR, and a second “nested” set of primers (based on amino acids slightly C-terminal, but overlapping the amino acids utilized for the “outside” primers).
A matrix of PCR reactions using these degenerate oligonucleotides lead to the cloning and sequencing of several amplification products, which showed DNA homology and overlap with the 1840 nucleotide clone isolated previously, and together comprised a complete cDNA open reading frame; suggesting that all of these partial cDNAs originated from a single gene.
Cloning of axn-1 cDNA, and Determination of the Genomic Sequence.
Based on the DNA sequences of several partial cDNA sequences, PCR primers were designed to repeatedly amplify and sequence the cDNA coding region. Several independent cDNAs were cloned and completely sequenced. In some cases, individual cDNA clones contained small unspliced introns, consistent with alternate splicing of the hRNA produced from this gene. For example, two variants of the 5′ untranslated region (UTR) were recovered. These variants are identical for 42 nt upstream of the start site (and including the region encoding the N-terminus of the encoded protein); however they then diverge for another 60-80 nt upstream; this is likely to presence of an alternately spliced or unspliced intron in the 5′ UTR of one of the cDNAs.
PCR primers from the cDNA were used to amplify and sequence eight independent genomic clones from the region encoding the cDNA. The sequence from this genomic region matches the cDNA sequence exactly over the length of the cDNA. Thus, the DNA sequence of the multiple genomic and full cDNA clones confirms the structure of the cDNA, and its genomic organization.
This gene encoding the cDNA is designated herein as axn-1, and the encoded full length protein is designated as AXN-1. The sequence of the axn-1 cDNA is set forth in SEQ ID NO:2, and the open reading frame is provided as SEQ ID NO:3; the sequence of the AXN-1 full length protein is provided as SEQ ID NO:4. The full-length chromosomal sequence for axn-1 is set forth in SEQ ID NO:1. The truncated amino acid sequence is set forth in SEQ ID NO:5. A synthetic DNA sequence encoding the full-length AXN-1 amino acid sequence is set forth in SEQ ID NO:6.
In addition to the 5′UTR variants, it is interesting to note that many cDNAs isolated by these experiments have internal modifications relative to the sequences described herein. For example, many clones appear to be internally deleted relative to the full-length sequence, and others clearly contain unspliced introns. So, it is likely that this gene, designated herein as axn-1, is subject to alternate mRNA processing including alternate mRNA splicing. These alternate mRNAs are likely to be minor components of the steady-state axn-1 mRNA, and the cDNA normalization process utilized in the cloning of these cDNA has likely increased the relative proportion of these variants to the fully spliced full-length transcript.
Example 7
AXN-1 is Homologous to Monophenol Oxidases
An alignment of AXN-1 to other polyphenol oxidase sequences is provided in FIG. 3, and the percent sequence identity of AXN-1 to these sequences is provided in Table 4.
Another interesting observation was that a section of the protein encoded by this cDNA contained many repeated amino acids, especially glutamine (Q), and did not show homology to polyphenol oxidases or tyrosinases in databases searches.







TABLE 4







Amino Acid Identity of AXN-1 to other fungal proteins











Percent Identity



Organism/Protein
to AXN-1







Neurospora_crassa
17%



Pyrenophora_tritici
15%



Podospora_anserina
20%



Lentinula_edodes
17%



Pycnoporus_sanguineus
19%



Pholio_nameko
18%



Tuber_melanosporum
16%



Asp_fum_tyrosinase
14%










Example 8
Nematode Toxin from Strain ATX20514
Bacterial strain ATX20514 was identified from empirical screening of strains, based on strong toxicity of cultures towards soybean cyst nematode (SCN) in the standard bioassay format.
ATX 20514 was grown in C2 medium in 96-well blocks for 3 days at 30° C. Next, the cells in each well were lyzed with a bead beater, and the lysed cell extract was fed to soybean cyst nematodes (J2 stage) in the presence of a feeding stimulant (octopamine). Five days after incubation, the toxicity towards SCN was scored on the scale of 0 to 5 as shown in Table 1.
The soluble fraction prepared from ATX20514 in this manner scored as a “5” when 5 μL of this extract was incorporated into the SCN bioassay.
A protein extract was prepared from strain ATX20514 by growing the strain in 50 mL of C2 medium at 30° C. for 3 days. At that time, cells in the culture were lysed by bead beater treatment, and the crude lysate was centrifuged at 18,000×g for 15 minutes to pellet the cell debris and insoluble proteins. The soluble protein extract was recovered as the supernatant fraction, and then filtered, and this material was then subjected to multiple treatments followed by testing in an SCN bioassay.
Heat. An aliquot of the protein extract (100 μL) was heated at 100° C. for 30 minutes, and tested in an SCN bioassay. A negative control sample was mock treated alongside, and likewise tested in SCN bioassay.
Protease. An aliquot of the protein extract (95 μL) was proteolytically digested with 5 μL of Pronase (1 mg/mL final)(Roche) for 3 hours at 37° C.
Dialysis. An aliquot of the protein extract (100 μL) was dialyzed against either 20 mM Tris, pH 8.0, (“Buffer A”) or 50 mM sodium phosphate, 150 mM NaCl, pH 7.0.
Filtration. An aliquot of the protein extract (500 μL) was placed above a spin filter membrane with a 3000 molecular weight cutoff (Millipore) and centrifuged at 12,000×g until approximately 400 μL of the total volume had passed through the filter unit. Additional protein extract was then added above the spin filter membrane, and the centrifuge step was repeated until approximately 400 μL of the total volume had again passed through the filter unit.
The results of the SCN bioassays are shown in Table 5. These results support the conclusion that the SCN activity in strain ATX20514 is due to a protein active against SCN.







TABLE 5







Characterization of ATX20514 activity









SCN


Sample
Score










Heat Treatment








ATX 20514 extract
5


ATX 20514 extract heat treated
0







Protease Treatment








Protease Treatment



Protease treated
0


Control; protease only, no extract
0







Dialysis








Dialyzed vs 20 mM Tris, pH 8.0
5


20 mM Tris, pH 8.0
0


ATX20514 extract dialyzed 50 mM sodium phosphate, 150 mM
5


NaCl, pH 7.0


50 mM sodium phosphate, 150 mM NaCl, pH 7.0
0







Size exclusion filtration








ATX20514 extract retentate from spin dialysis
5


ATX20514, filtrate from spin dialysis
0









Example 9
Purification of a Nematode Protein Toxin from ATX20514
A four-column purification was carried out, leading to the identification of a 52 kDa protein band that correlated with SCN toxicity.
ATX20514 was grown in 2 liters of C2 medium at 30° C. for 3 days. The culture was centrifuged, and the pellet was resuspended in 100 mL of 50 mM Tris (pH 8.0). The cell pellet was then lysed using a French press, centrifuged at 18,000×g for 15 minutes, and the supernatant fraction (i.e., the soluble protein extract) was forwarded into ammonium sulfate precipitation, dialysis, and column chromatography purification.
After 3 steps of column chromatography, the active fractions were dialyzed against 50 mM Tris (pH 8.0), 1 mM DTT; (“Buffer A”), loaded onto a Mono Q anion exchange column (1 mL; GE Healthcare) and washed with the same buffer. Elution was carried out with a 40 column volume gradient from 0 M to 0.2 M NaCl in Buffer A. Individual fractions were submitted for SCN bioassays, and fractions 21 through 24 were found to possess the strongest SCN toxicity. A protein of approximately 52 kDa correlated well with the SCN toxicity in these fractions.
Example 10
N-Terminal Sequence of the 52 kDa Protein from ATX20514
Individual purification fractions enriched for the 52 kDa protein were separated by gel electrophoresis, transferred to PVDF, and stained with Coomassie Blue. The section of the membrane containing the 52 kDa protein was excised and subjected to N-terminal sequencing. The resulting N-terminal sequence was compiled using the amino acid corresponding to the biggest peak at each position on the chromatograms.
Example 11
Purification and N-Terminal Sequence of 31 kDa Protein from ATX20514
In addition to the activity that correlated with the 52 kDa protein, a second active peak having SCN activity was eluted from a cation exchange column. These active fractions were subsequently loaded onto an anion exchange column to further purify the activity. Thus, a 31 kDa protein was identified that correlated with this SCN activity:
To further characterize the 31 kDa protein, N-terminal sequencing was performed. This analysis allowed us to compare the N-terminal protein sequence of the 52 kDa protein to that of the 31 kDa protein. We found the two amino acid sequences to be very similar, suggesting that the 31 kDa protein is a truncation of the 52 kDa protein:







TABLE 6







N-terminal sequences of ATX 20514 toxins









Protein
Primary Sequence Identified by



Size
Edman Degradation
SEQ ID NO:





52 kDa
STSRQDVAKLGPGWNKVLLNYALAMQALDE
28


 


31 kDa
STSGQDVAKLGPQWNKVLLNYALAMQALDE
29









Example 12
Cloning of axn-8 from ATX20514
Using the N-terminal sequence data from the 52 kDa and 31 kDa toxins, the gene encoding these proteins was cloned in several steps by a degenerate PCR and Tail strategies as known in the art, leading to the amplification of an approximately 5 kb fragment from multiple rounds of TAIL PCR. This region contains an open reading frame encoding an amino acid protein. Herein we designate this gene as axn-8 and the corresponding protein as AXN-8. The N-terminus of the predicted AXN-8 protein matches well to the amino acid sequences of the 52 kDa and 31 kDa proteins. Furthermore, the DNA sequence downstream of axn-8 contains a second open reading frame that is likely to be co-expressed with axn-8 in an operon. The DNA sequence containing regulatory elements is set forth in SEQ ID NO:11. The open reading frame for axn-8 is set forth in SEQ ID NO:12, and encodes SEQ ID NO:13. The predicted truncated protein is set forth in SEQ ID NO:14. The metal binding integral membrane protein encoded by the downstream ORF is set forth in SEQ ID NO:41. It is recognized that the truncation site may be at least about 1, at least about 2, at least about 3, 4, 5, 6, 7, 8, 9, or 10 amino acids in either direction of the arginine at position 295 of SEQ ID NO:13. A synthetic DNA sequence encoding SEQ ID NO:13 is set forth in SEQ ID NO:15.
Example 13
Homology of AXN-8 to Monophenol Oxidases
A BLAST analysis of AXN-8 shows that it shares homology with known bacterial monophenol oxidases. This class of enzymes also includes tyrosinases.







TABLE 7







Closest homologs of AXN-8













GENBANK
%
E


Enzyme
Source
Accession#
Homology
Score





Tyrosinase
Delftia
YP_001562639
55%
7e−92



acidovorans


Tyrosinase
Ruegeria
YP_166646
54%
6e−86



pomeroyi


Tyrosinase
Burkholderia
ZP_02466656
52%
6e−79



thailandensis


Monophenol
Agrobacterium
YP_002549739
50%
2e−71


oxidase
vitis


Tyrosinase
Rhizobium etli
ZP_03501998
47%
2e−60


Tyrosinase
Dyadobacter
ZP_03898981
44%
1e−56



fermentans









An alignment of AXN-8 with tyrosinase enzymes (FIG. 4) reveals that it possesses sequence motifs that are consistent with these tyrosinases, including the presence of histidine residues that are likely to be necessary for binding of copper ions by the enzyme.
Example 14
Dose Response of AXN-8 Activity
A sample of AXN-8 protein was used to assess the effect of different protein amounts on SCN. This sample was diluted in nematode assay buffer, and assays were set up to establish final AXN-8 protein concentrations up to 25 μg/ml. Nematodes were incubated, and results scored after five days. Scores are the average of two to four replicates.







TABLE 8







Dose Response of AXN-8










[AXN-8] in Assay




(μg/ml)
SCN Score














25
4.7



12.5
4



6.25
2.7



3.125
1.7



1.6
0.75



0.8
1



0.4
1



0
1










Example 15
Cloning of AXN-2 from Bacillus thuringiensis Strain ATX25028
Independently of the purification of AXN-1 and AXN-8, SCN activity was observed from several Bacillus strains. The discovery that both AXN-1 and AXN-8 encode proteins with homology to oxidase/tyrosinase suggested that perhaps the activity in these Bacillus strains was also due to oxidase/tyrosinase like activity.
ATX25028 DNA was prepared as described previously, and DNA sequence of plasmid preparations was obtained.
Analysis of the partial DNA sequences obtained from ATX25028 DNA demonstrated existence of a gene encoding an oxidase/tyrosinase-like enzyme in this strain. The DNA sequence was utilized to design PCR primers, and the open reading frame of the full gene was amplified by PCR from genomic DNA or ATX 25028. This gene is referred to herein as axn-2 (SEQ ID NO:7), and its encoded protein as AXN-2 (SEQ ID NO:8). Clone pAX5530 contains axn-2 inserted into a modified pRSF-1b vector (Novagen) as a BamHI-AscI fragment to generate a his-tag containing protein (SEQ ID NO:9). pAX5531 contains axn-2 inserted into a modified pRSF-1b vector as a PstI-AscI fragment such that the expressed protein lacks a His-tag. Lysates derived from E. coli cells expressing AXN-2 protein were generated and tested for activity on SCN. Clones both containing and lacking an N-terminal His tag exhibited strong activity on SCN.
A synthetic gene encoding AXN-2 is set forth in SEQ ID NO:10.







TABLE 9







Activity of AXN-2 clones on SCN













SCN


Clone
Protein
Sample description
score





Neg control
Neg control
Unlysed culture
0


Neg control
Neg control
Lysed culture
0


Neg control
Neg control
Tris extract concentrated 4X
0


pAX5531
AXN-2
Unlysed culture
5


pAX5531
AXN-2
Lysed culture
4


pAX5531
AXN-2
Tris extract concentrated 4X
5


pAX5530
AXN-2 5′His tag
Unlysed culture
5


pAX5530
AXN-2 5′His tag
Lysed culture
5


pAX5530
AXN-2 5′His tag
Tris extract concentrated 4X
5


—
—
LB kan media control
0


—
—
Tris Buffer buffer control
0









Example 16
Cloning of a Polyphenol Oxidase from the Nematode Active Strain ATX26455
ATX26455 was identified as a strain exhibiting strong activity in a soybean cyst nematode (SCN) assay. ATX 26455 was grown in a C2 medium in 96-well blocks for 3 days at 30° C. Cells were then lysed, and the lysed cell extract was fed to soybean cyst nematodes (J2 stage) as described herein. Five days after incubation, the toxicity towards SCN was scored as described herein. Such an assay using 5 μL of lysed extract prepared from ATX26455 was assigned a score of “5,” denoting 96-100% mortality of this extract on SCN.
Preliminary Biochemical Screening of ATX26455
A protein extract was prepared from strain ATX26455 by growing the strain in C2 medium at 30° C. for 3 days. A soluble protein extract was prepared from the culture and subjected to the following biochemical characterizations, followed by assay for activity on SCN:

    
    
        Heat treatment. An aliquot of the protein extract was heat-treated to destroy protein activity, and then tested in an SCN bioassay. A negative control sample was mock treated alongside the heat treated sample, and likewise tested in an SCN bioassay.
        Protease treatment. An aliquot of the protein extract was proteolytically digested with a protease (such as Pronase) and then tested in an SCN bioassay. Negative controls without protease were also tested in an SCN bioassay.
        Dialysis treatment. An aliquot of the protein extract was dialyzed to allow small molecules to be removed from the extract, and then tested in an SCN bioassay.
        Filtration testing. An aliquot of the protein extract was placed above a spin filter membrane with a 3000 molecular weight cutoff and then centrifuged to pass the extract through the filter unit. The retentate and the filtrate were then tested in an SCN bioassay.
    
    


The results of the SCN bioassays carried out on each of the preliminary biochemical samples are shown in Table 10. These results suggest that the nematode toxin produced by ATX26455 is conferred by a protein.







TABLE 10







Activity Tests of ATX 26455 Fractions











SCN Bioassay



Sample
Score











Heat Treatment










Extract
5



Extract, heat treated
0







Protease Treatment










Extract, protease treated
0



Protease only (negative control)
0







Dialysis Treatment










Extract, dialyzed
2



Dialysis control
0







Filtration Testing










Filter, retained by filter
4



Filter, flow through
0










Purification of Nematode Protein Toxin from ATX26455

Cells were lysed using a French press, and the lysate was centrifuged, and the supernatant collected, resulting in a clarified lysate. The clarified lysate was highly active in an SCN bioassay. The activity in this clarified lysate was confirmed to be sensitive to protease digestion. The clarified lysate was further enriched by the following ammonium sulfate precipitation steps.
First, the clarified lysate was brought to 13% saturation with ammonium sulfate, centrifuged, and the pellet discarded. This procedure was repeated at 25% saturation with ammonium sulfate. Finally, the supernatant was brought to 50% saturation with ammonium sulfate, and after centrifugation, the pellet was recovered and resuspended in buffer, and subjected to dialysis to remove the residual ammonium sulfate. The resuspended pellet was then fractionated on an anion exchange column, and the fractions that showed activity in SCN bioassay were collected and pooled. The pooled active fractions were further fractionated on a hydrophobic interaction column. This resulted in the identification of a protein band migrating at location corresponding to a protein of approximately 35 kDa. This protein (referred to herein as the “35 kDa protein”) correlated well with the SCN toxicity observed during each step of the purification, and that was highly enriched during the purification process.
Characterization of the 35 kDa Protein from ATX26455
The sequence of the N-terminal amino acids of a protein of interest from ATX 26455 was determined by Edman degradation as known in the art. A protein fraction containing the protein of interest was separated by gel electrophoresis, and the proteins in the resulting gel were transferred to a PVDF membrane. The membrane was then stained with Coomassie Blue, and the section of the membrane containing the 35 kDa protein was excised, and subjected to N-terminal sequencing. The N-terminal sequence of this protein was determined by this method to be as follows:
N-Terminal Sequence of Protein from Active Fractions of ATX26455







(SEQ ID NO: 42)


M-N-T-I-R-Q-D-V-A-T-L-G-S-G-W-D-N-K-V-L-L-N-Y-A-L-


 


A-M-R-E-L-D-K-L-P-I-T-N.






Interestingly, this protein sequence revealed sequence similarities with the AXN-8 protein described herein, suggesting that the activity of ATX 26455 is in fact, also due to activity of a homologous, but novel, polyphenol oxidase.
Cloning of Nematode Active Toxin Gene from ATX26455
The N-terminal protein sequence of the putative toxin was utilized to a degenerate oligonucleotide primer corresponding to this sequence. The sequence of that primer is shown here (using the nomenclature established by the International Union of Pure and Applied Chemistry):









(SEQ ID NO: 43)



5′ CAR GAY GTI GCI ACI YTI GGI CCI GGI TGG 3′






To generate a degenerate oligonucleotide to amplify the reverse strand of the toxin gene, the DNA sequence of the axn-8 gene was utilized as a template, resulting in generation of a series of degenerate oligonucleotide primers for testing on ATX26455. One PCR primer designed by this approach is shown here:









(SEQ ID NO: 44)



5′ RTG RTG IAG CCA RAA IAT IGG RTC 3′






PCR reactions using the degenerate primers (SEQ ID NO:43 and 44) resulted in amplification and sequencing of a 711 nucleotide PCR product. This 711 nt PCR fragment was confirmed to originate from the DNA region encoding the 35 kDa protein.
The DNA sequence of the 711 nucleotide PCR product was utilized to isolate the entire region coding for the 35 kDa protein by thermal interlaced (TAIL) PCR methods known in the art. This approach allowed assembly of the sequence of the complete open reading frame encoding the 35 kDa protein. The axn-9 open reading frame was amplified by PCR from ATX 26455 and cloned into a modified prsf1b cloning vector. The insert of the resulting clone (pAX5597) was sequenced and found to be identical to the sequence obtained by TAIL.
The sequence of the DNA fragment is provided as SEQ ID NO:45. The open reading frame contained within this DNA region is designated as axn-9 (SEQ ID NO:46), and its corresponding protein as AXN-9 (SEQ ID NO:47). The predicted truncated protein corresponds to residue 314 of SEQ ID NO:47. It is recognized that the truncation site may be at least about 1, at least about 2, at least about 3, 4, 5, 6, 7, 8, 9, or 10 amino acids in either direction of the lysine at position 314 of SEQ ID NO:47.
Inspection of the DNA sequence of the axn-9 open reading frame shows that there is a GTG codon present at nucleotides 22-24 of axn-9. Given the proximity of this codon to the ATG start site, and the tendency for some bacterial open reading frames to tolerate multiple translational start sites, it is possible that translation from this GTG codon occurs in nature, and that the resulting protein has similar properties to the full length AXN-9 protein. Thus, this protein is also provided herein as SEQ ID NO:48 and designated AXN-9 (GTG).
Example 17
Homology of AXN-9 to AXN-8 and Other Polyphenol Oxidase Proteins
ANX-9 is homologous to the AXN-8 protein disclosed herein. AXN-9 is 68% identical to AXN-8. An alignment of AXN-9 with AXN-8 is provided as FIG. 5. Given that AXN-8 is known to be truncated, and also given that most polyphenol oxidases are proteolytically processed, and given the homology between AXN-8 and AXN-9, we can predict that AXN-9 is likely to be similarly truncated by proteolysis.
Example 18
Protease-Activated AXN-9 Protein is Active in SCN Bioassay
The bacterial AXN-9 expression vector described above (pAX5597) was transformed into BL21*DE3 cells (Invitrogen). Following IPTG induction, the whole cell culture was centrifuged. The resulting pellet was resuspended in 1/10th volume of buffer (50 mM Tris (pH 8.0), 10 μM CuSO4) and then lysed by sonication. The lysate was split into 2 aliquots, and 1 aliquot was treated with freshly prepared trypsin (0.1 mg/mL of lysate) for 2 hours at 37° C. AXN-9 protein treated with trypsin showed strong activity on SCN, while untreated AXN-9 protein did not show activity on SCN (Table 11).







TABLE 11







Activity of AXN-9 clones on SCN











SCN


Clone
Sample description
score





Neg control
Buffer (50 mM Tris (pH 8.0), 10 μM CuSO4)
0


Neg control
Buffer + Trypsin
0


Pos control
Buffer + Mushroom Tyrosinase
4


pAX5597
AXN-9 protein, untreated
0


pAX5597
AXN-9 protein, trypsin-treated
5









Example 19
Activity of Mushroom Tyrosinase on SCN
Given the discovery of activity of AXN-1, AXN-8, AXN-9, and AXN-2 on SCN and the homology of AXN-1, AXN-8, AXN-9, and AXN-2 to polyphenol oxidase/tyrosinase enzymes, previously identified tyrosinase enzymes were tested for this property.
Mushroom tyrosinase (Sigma T3824) was resuspended in buffer to yield a concentrated solution. Dilutions of this solution were test on SCN as described above, and the following assay results were obtained. Though not directly stated by the provider of this enzyme, the enzyme contained in this “Mushroom tyrosinase” is likely to have been derived from the white mushroom.







TABLE 12







Titration of mushroom tyrosinase activity










[protein] in
Mushroom



Assay (μg/ml)
tyrosinase














50
4



25
3.3



12.5
3



6.25
2.7



3.125
2.7



1.6
2



0.8
1



0
1










The mushroom tyrosinase preparation obtained is demonstrated to have activity on SCN; at approximately the same relative concentration of enzyme relative to the tested amounts of AXN-1 and AXN-8.
Example 20
Possibilities of Other Polyphenol Oxidases Having SCN Activity
Given the discovery of anti-SCN activity from both fungal and bacterial proteins that have homology to polyphenol oxidases, and the observation of activity from mushroom tyrosinase, it is understood that many known polyphenol oxidases/tyrosinases are likely to have such activity when tested as described herein; for example, in an SCN bioassay containing J2 juveniles, 20 mM Tris, and 50 mM octopamine for 3-7 days at about 20° C., with shaking in a rotary incubator, contained in a plate such as a 96-well plate.
For example, Selinheimo et al describe characterization of fungal and plant tyrosinases, and demonstrate substrate and activity differences between these broad classes of enzymes, including the mushroom tyrosinase (fluka) which is likely the same enzyme described in Example 19 above. Table 2 of Selinheimo et al shows that such enzymes can have different substrate specificities toward mono- and polyphenolic compounds. In general it is understood that the plant enzyme, such as the apple and potato enzymes of the Selinheimo et al. study, have less activity on monophenol substrates such as tyrosine than fungal or bacterial enzymes. Furthermore, FIG. 3 and the text of Selinheimo et al describe that certain enzymes have the ability to cross-link a representative protein (casein). In the cited study, each of the enzymes is capable of crosslinking casein, but the enzymes differ in the amount of enzyme required of crosslinking. Further, all but one of these enzymes seemed to have a strong preference and/or requirement for a monophenol or diphenol in the reaction in order to achieve crosslinking. The notable exception to this requirement is the enzyme from T. reesei. 
The T. reesei enzyme (set forth in SEQ ID NO:21 and 22 herein) exhibits substrate and activity parameters that distinguish it from the other tested enzymes. Notably, the T. reesei enzyme showed the most efficient crosslinking of casein at the lower of the two enzyme concentrations tested. Furthermore, and in contrast to the other tested enzymes, T. reesei had strong activity in the absence of a monophenol or diphenol in the reaction; although the addition of such compounds appeared to increase the amount of such crosslinking. The other enzymes tested appear to require a monophenol or diphenol for such crosslinking activity. Selinheimo et al provides further evidence for this property of the T. reesei enzyme in additional references (Selinheimo et al. (2008) J Agric Food Chem. 56(9):3118-28 and Selinheimo et al. (2007) J Agric Food Chem. 55(15):6357-65), each of which is herein incorporated by reference in its entirety.
For example, the cDNA with GENBANK accession number AK246031 from Glycine max (SEQ ID NO:16 and 17, encoding SEQ ID NO:18; Umezawa et al (2008) DNA Res. 15(6):333-46) exhibits characteristic homologies of plant phenol oxidases.
By way further of example, the cDNA with GENBANK accession number AM418385 (SEQ ID NO:19) encoding a T. reesei enzyme (SEQ ID NO:20) with homology to polyphenol oxidases, (Selinheimo et al. (2006) FEBS Lett. 273, 4322-4335) is provided as an example of a polyphenol oxidase that given the inventions herein is likely to exhibit activity upon SCN.
Other sequences (according to GENBANK accession numbers) having homology to the sequences disclosed herein are encompassed by the present invention. An exemplary (but non-limiting) list is set forth in Table 13.







TABLE 13





GENBANK Accession Numbers of Polyphenol oxidase homologs


















AB005228.1
AB188749.1
AB277357.1
AF078789.2


AB010101.1
AB188750.1
AB277358.1
AF136926.2


AB011827.1
AB188751.1
AB277359.1
AF183578.1


AB011828.1
AB188752.1
AB280948.1
AF183583.1


AB011829.1
AB188753.1
AB280949.1
AF183588.1


AB011830.1
AB188754.1
AB280950.1
AF183593.1


AB011831.1
AB188755.1
AB353113.1
AF183599.1


AB018244.1
AB188756.1
AB430855.1
AF183604.1


AB022095.1
AB188757.1
AB430856.1
AF183609.1


AB023291.1
AB188758.1
AC007607.6
AF183614.1


AB024278.1
AB188759.1
AC007861.5
AF183619.1


AB024279.1
AB188760.1
AC025271.7
AF183624.1


AB024280.1
AB188761.1
AC084064.6
AF183629.1


AB024281.1
AB188762.1
AC084197.1
AF183634.1


AB027512.1
AB188763.1
AC084321.37
AF183639.1


AB032694.1
AB188764.1
AC084628.1
AF183644.1


AB032695.1
AB188765.1
AC090416.1
AF183649.1


AB032696.1
AB188766.1
AC115007.6
AF183654.1


AB032697.1
AB188767.1
AC116734.14
AF183659.1


AB033993.1
AB188768.1
AC119816.5
AF183664.1


AB038994.1
AB188769.1
AC122194.4
AF183669.1


AB044884.1
AB207236.1
AC122517.2
AF183674.1


AB052940.1
AB207237.1
AC138173.2
AF183679.1


AB056680.1
AB214954.1
AC138230.5
AF183684.1


AB060689.1
AB215107.1
AC157507.2
AF187155.1


AB070938.1
AB215108.1
AC157710.2
AF216388.1


AB070939.1
AB223612.1
AC163891.2
AF237792.1


AB081466.1
AB224151.1
AC166548.2
AF237794.1


AB107880.1
AB225958.1
AC182653.2
AF237797.1


AB107881.1
AB238605.1
AC185364.2
AF237799.1


AB108529.1
AB254132.1
AC208369.1
AF237802.1


AB108530.1
AB254133.1
AC210555.1
AF237804.1


AB108531.1
AB259663.1
AC214595.1
AF237807.1


AB120567.1
AB275646.1
AC215650.1
AF237809.1


AB178936.1
AB275647.1
AC216911.1
AF249161.1


AB178937.1
AB277347.1
AC217034.1
AF249162.1


AB178938.1
AB277348.1
AC232778.1
AF249163.1


AB178939.1
AB277349.1
AE016825.1
AF249164.1


AB178940.1
AB277350.1
AE017195.1
AF249165.1


AB188743.1
AB277351.1
AF001295.1
AF249166.1


AB188744.1
AB277352.1
AF020548.1
AF249167.1


AB188745.1
AB277353.1
AF020786.1
AF249168.1


AB188746.1
AB277354.1
AF039165.1
AF249169.1


AB188747.1
AB277355.1
AF064803.1
AF249170.1


AB188748.1
AB277356.1
AF076781.1
AF249171.2


AF249172.1
AJ006097.1
AK191107.1
AK209365.1


AF249173.1
AJ012048.1
AK191149.1
AK209447.1


AF249174.1
AJ223816.1
AK191393.1
AK209840.1


AF249175.1
AJ245880.1
AK192283.1
AK209886.1


AF249176.1
AJ248285.1
AK192618.1
AK209941.1


AF249177.1
AJ250302.1
AK192643.1
AK210502.1


AF249178.1
AJ252741.1
AK192803.1
AK210623.1


AF249179.1
AJ293806.1
AK192857.1
AK212036.1


AF249180.1
AJ297474.1
AK193779.1
AK212309.1


AF249181.1
AJ297475.1
AK193825.1
AK212393.1


AF249182.1
AJ309175.1
AK195046.1
AK212795.1


AF249183.1
AJ309176.1
AK195075.1
AK213314.1


AF249184.1
AJ334488.1
AK195088.1
AK213631.1


AF249185.1
AJ547813.1
AK195144.1
AK213730.1


AF249186.1
AJ556169.1
AK195566.1
AK214235.1


AF249187.1
AJ564729.1
AK195805.1
AK215621.1


AF249188.1
AJ574915.1
AK196684.1
AK216615.1


AF249189.1
AJ619741.1
AK197855.1
AK216621.1


AF249190.1
AJ635323.1
AK198477.1
AK216757.1


AF249191.1
AJ697805.1
AK198785.1
AK217145.1


AF252540.1
AJ698339.1
AK199363.1
AK217194.1


AF255610.1
AJ698340.1
AK199676.1
AK217421.1


AF261957.1
AJ698341.1
AK201739.1
AK217687.1


AF261958.1
AJ698342.1
AK201880.1
AK217984.1


AF263611.1
AJ786639.1
AK201909.1
AK218840.1


AF269192.1
AJ786640.1
AK202339.1
AK219113.1


AF280808.1
AJ845083.2
AK202954.1
AK219854.1


AF338426.3
AK014619.1
AK202956.1
AK219958.1


AF343911.2
AK027025.1
AK204044.1
AK219983.1


AF350261.1
AK027863.1
AK204101.1
AK220030.1


AF359360.3
AK033040.1
AK204148.1
AK241303.1


AF359361.3
AK108237.1
AK205161.1
AK246031.1


AF363027.1
AK115853.1
AK205196.1
AK247107.1


AF368291.1
AK115906.1
AK205614.1
AK247126.1


AF380300.1
AK116290.1
AK206598.1
AK247410.1


AF391288.1
AK148172.1
AK206970.1
AK293115.1


AF395447.2
AK148332.1
AK207020.1
AK297887.1


AF397401.1
AK148341.1
AK207203.1
AL138753.8


AF397402.1
AK148357.1
AK207218.1
AL139318.9


AF400250.1
AK148370.1
AK207451.1
AL591688.1


AF401231.1
AK148432.1
AK207965.1
AL606526.10


AF445638.2
AK148441.1
AK208194.1
AL606645.2


AF473807.2
AK177534.1
AK208432.1
AL646052.1


AF507945.1
AK190354.1
AK208651.1
AL670884.7


AJ000503.1
AK191069.1
AK208819.1
AL731611.2


AL731637.2
AY149460.1
AY333979.1
AYS12904.1


AL939108.1
AY149880.1
AY333982.1
AYS15264.1


AL939113.1
AY149881.1
AY333984.1
AY822711.1


AL954747.1
AY149882.1
AY333985.1
AY837842.1


AM418385.1
AY162287.1
AY338251.1
AY842859.1


AM420293.1
AY236224.1
AY341747.1
AY844019.1


AM424232.2
AY254101.1
AY341748.1
AY844020.1


AM440949.2
AY266330.1
AY341749.1
AY844021.1


AM442013.1
AY274808.1
AY341750.1
AY844022.1


AM448108.2
AY279540.1
AY341751.1
AY844023.1


AM451548.2
AY283062.1
AY341752.1
AY844024.1


AM467012.2
AY322334.1
AY341753.1
AY844025.1


AM478512.2
AY322335.1
AY341754.1
AY844026.1


AM502246.1
AY322336.1
AY341755.1
AY844027.1


AM746676.1
AY322337.1
AY341756.1
AY844028.1


AM774403.1
AY322338.1
AY341757.1
AY844029.1


AM920430.1
AY322339.1
AY341758.1
AY844030.1


AM920435.1
AY322340.1
AY341759.1
AY844031.1


AM920436.1
AY322341.1
AY341760.1
AY844032.1


AM920437.1
AY322342.1
AY341761.1
AY844033.1


AM949571.1
AY322343.1
AY341762.1
AY844034.1


AM949572.1
AY322344.1
AY341763.1
AY844035.1


AM949573.1
AY322345.1
AY341764.1
AY844036.1


AM949574.1
AY322346.1
AY341765.1
AY844037.1


AM949575.1
AY322347.1
AY370019.1
AY844038.1


AM949576.1
AY322348.1
AY451324.1
AY844039.1


AP000720.4
AY322349.1
AY515506.1
AY844040.1


AP003280.2
AY322350.1
AY526904.1
AY844041.1


AP003290.2
AY322351.1
AY596266.1
AY844042.1


AP008207.1
AY322352.1
AY596267.1
AY844043.1


AP008210.1
AY322353.1
AY596268.1
AY844044.1


AP009294.1
AY322354.1
AY596269.1
AY844045.1


AP009493.1
AY322355.1
AY596270.1
AY844046.1


AP009632.1
AY322356.1
AY659975.1
AY844047.1


AY017302.1
AY322357.1
AY665681.1
AY844048.1


AY017303.1
AY322358.1
AY665682.1
AY844049.1


AY017304.1
AY322359.1
AY675348.1
AY844050.1


AY046527.2
AY322360.1
AY743343.1
AY844051.1


AY052751.3
AY322361.1
AY743344.1
AY844052.1


AY052787.2
AY322362.1
AY743345.1
AY844053.1


AY072037.1
AY322363.1
AY751301.1
AY844054.1


AY072038.1
AY327520.1
AY787659.1
AY844055.1


AY075039.1
AY333967.1
AY804220.1
AY844056.1


AY103683.1
AY333970.1
AY804228.1
AY844057.1


AY123973.1
AY333975.1
AY804236.1
AY844058.1


AY844059.1
AY844104.1
AY844149.1
AY849378.1


AY844060.1
AY844105.1
AY844150.1
AY865623.2


AY844061.1
AY844106.1
AY844151.1
AY865624.1


AY844062.1
AY844107.1
AY844152.1
AY866432.1


AY844063.1
AY844108.1
AY844153.1
AY874457.1


AY844064.1
AY844109.1
AY844154.1
AY874458.1


AY844065.1
AY844110.1
AY844155.1
AY874460.1


AY844066.1
AY844111.1
AY844156.1
AY874462.1


AY844067.1
AY844112.1
AY844157.1
AY874465.1


AY844068.1
AY844113.1
AY844158.1
AY874467.1


AY844069.1
AY844114.1
AY844159.1
AY904721.1


AY844070.1
AY844115.1
AY844160.1
AY959314.1


AY844071.1
AY844116.1
AY844161.1
AY959316.1


AY844072.1
AY844117.1
AY844162.1
AY965743.1


AY844073.1
AY844118.1
AY844163.1
AY965744.1


AY844074.1
AY844119.1
AY844164.1
AY965745.1


AY844075.1
AY844120.1
AY844165.1
AY965746.1


AY844076.1
AY844121.1
AY844166.1
AY971012.1


AY844077.1
AY844122.1
AY844167.1
BA000030.3


AY844078.1
AY844123.1
AY844168.1
BA000035.2


AY844079.1
AY844124.1
AY844169.1
BC021799.1


AY844080.1
AY844125.1
AY844170.1
BC027179.1


AY844081.1
AY844126.1
AY844171.1
BC028311.1


AY844082.1
AY844127.1
AY844172.1
BC052608.1


AY844083.1
AY844128.1
AY844173.1
BC067064.1


AY844084.1
AY844129.1
AY844174.1
BC073623.1


AY844085.1
AY844130.1
AY844175.1
BC076406.1


AY844086.1
AY844131.1
AY844176.1
BC079678.1


AY844087.1
AY844132.1
AY844177.1
BC082330.1


AY844088.1
AY844133.1
AY844178.1
BC097647.1


AY844089.1
AY844134.1
AY844179.1
BC106678.1


AY844090.1
AY844135.1
AY844180.1
BC118918.1


AY844091.1
AY844136.1
AY844181.1
BC118919.1


AY844092.1
AY844137.1
AY844182.1
BC129260.1


AY844093.1
AY844138.1
AY844183.1
BC135907.1


AY844094.1
AY844139.1
AY844184.1
BC155086.1


AY844095.1
AY844140.1
AY844185.1
BC160742.1


AY844096.1
AY844141.1
AY844186.1
BC164222.1


AY844097.1
AY844142.1
AY844187.1
BT009357.1


AY844098.1
AY844143.1
AY844188.1
BT013158.1


AY844099.1
AY844144.1
AY844189.1
BT027443.1


AY844100.1
AY844145.1
AY844190.1
BT031730.1


AY844101.1
AY844146.1
AY844191.1
BT031775.1


AY844102.1
AY844147.1
AY844192.1
BX295539.1


AY844103.1
AY844148.1
AY844193.1
BX571966.1


BX842680.1
CR555306.1
DQ058416.1
DQ282930.1


BX901913.8
CR788249.6
DQ060504.1
DQ282931.1


BX950229.1
CR931725.6
DQ060505.1
DQ282932.1


CP000031.1
CR931761.6
DQ060506.1
DQ282933.1


CP000085.1
CT025512.2
DQ060507.1
DQ282934.1


CP000094.1
CT573213.2
DQ060508.1
DQ282935.1


CP000103.1
CU222605.1
DQ060509.1
DQ282936.1


CP000112.1
CU223051.1
DQ060510.1
DQ282937.1


CP000115.1
CU223259.1
DQ100014.1
DQ282938.1


CP000125.1
CU231766.1
DQ100027.1
DQ282939.1


CP000150.1
CU233197.1
DQ112679.1
DQ282941.1


CP000155.1
CU329671.1
DQ123805.1
DQ282942.1


CP000249.1
CU349019.1
DQ123806.1
DQ282943.1


CP000250.1
CU354092.1
DQ217371.1
DQ282944.1


CP000282.1
CU356179.1
DQ282898.1
DQ282945.1


CP000319.1
CU357691.1
DQ282899.1
DQ282946.1


CP000325.1
CU358302.1
DQ282900.1
DQ282947.1


CP000386.1
CU359628.1
DQ282901.1
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Example 21
Additional Monophenol Oxidases
Given the demonstration of strong SCN activity by enzyme from bacteria and fungi with homology to monophenol oxidase/tyrosinases, it is now apparent that many previously identified enzymes of this class will exhibit activity on SCN.
Example 22
Assays for Nematicidal Activity
The nucleotide sequences of the invention can be tested for their ability to produce nematicidal proteins. The ability of a protein to act as a pesticide upon a nematode pest is often assessed in a number of ways. One way well known in the art is to perform a feeding assay. In such a feeding assay, one exposes the pest to a sample containing either compounds to be tested or control samples. Often this is performed by placing the material to be tested, or a suitable dilution of such material, onto a material that the pest will ingest, such as an artificial diet. The material to be tested may be composed of a liquid, solid, or slurry. The material to be tested may be placed upon the surface and then allowed to dry. Alternatively, the material to be tested may be mixed with a molten artificial diet, then dispensed into the assay chamber. The assay chamber may be, for example, a cup, a dish, or a well of a microtiter plate.
Other types of assays can include microinjection of the test material into the mouth, or gut of the pest, as well as development of transgenic plants, followed by test of the ability of the pest to feed upon the transgenic plant. Plant testing may involve isolation of the plant parts normally consumed, for example, small cages attached to a leaf, or isolation of entire plants in cages containing insects.
Other methods and approaches to assay pests are known in the art, and can be found, for example in Robertson and Preisler, eds. (1992) Pesticide bioassays with arthropods, CRC, Boca Raton, Fla. Alternatively, assays are commonly described in the journals Arthropod Management Tests and Journal of Economic Entomology or by discussion with members of the Entomological Society of America (ESA).
Example 23
Synthetic Gene Sequences
The following genes were designed that encode either the AXN-1, AXN-2, AXN-8, or AXN-9 amino acid sequences, but utilizing a different nucleotide sequence.
SEQ ID NO:6 describes a novel AXN-1 encoding nucleotide sequence
SEQ ID NO:10 describes a novel AXN-2 encoding nucleotide sequence
SEQ ID NO:15 describes a novel AXN-8 encoding nucleotide sequence
SEQ ID NO:17 describes a novel nucleotide sequence encoding the protein predicted from GENBANK accession number AK246031 from Glycine max. 
SEQ ID NO:21 describes a novel nucleotide sequence encoding the protein predicted from genbank accession number the cDNA with GENBANK accession number AM418385 encoding a T. reesei enzyme.
Example 24
Vectoring of Genes for Plant Expression
The coding regions of the invention are connected with appropriate promoter and terminator sequences for expression in plants. Such sequences are well known in the art and may include the rice actin promoter or maize ubiquitin promoter for expression in monocots, the Arabidopsis UBQ3 promoter or CaMV 35S promoter for expression in dicots, and the nos or PinII terminators. Techniques for producing and confirming promoter-gene-terminator constructs also are well known in the art.
In one aspect of the invention, synthetic DNA sequences are designed and generated. These synthetic sequences have altered nucleotide sequence relative to the parent sequence, but encode proteins that are essentially identical to the parent amino acid sequence.
In another aspect of the invention, modified versions of the synthetic genes are designed such that the resulting peptide is targeted to a plant organelle, such as the endoplasmic reticulum or the apoplast. Peptide sequences known to result in targeting of fusion proteins to plant organelles are known in the art. For example, the N-terminal region of the acid phosphatase gene from the White Lupin Lupinus albus (GENBANK®ID GI:14276838, Miller et al. (2001) Plant Physiology 127: 594-606) is known in the art to result in endoplasmic reticulum targeting of heterologous proteins. If the resulting fusion protein also contains an endoplasmic reticulum retention sequence comprising the peptide N-terminus-lysine-aspartic acid-glutamic acid-leucine (i.e., the “KDEL” motif, SEQ ID NO:30) at the C-terminus, the fusion protein will be targeted to the endoplasmic reticulum. If the fusion protein lacks an endoplasmic reticulum targeting sequence at the C-terminus, the protein will be targeted to the endoplasmic reticulum, but will ultimately be sequestered in the apoplast.
Thus, this gene encodes a fusion protein that contains the N-terminal thirty-one amino acids of the acid phosphatase gene from the White Lupin Lupinus albus (GENBANK® ID GI:14276838, Miller et al., 2001, supra) fused to the N-terminus of the sequence of the invention, as well as the KDEL sequence at the C-terminus. Thus, the resulting protein is predicted to be targeted the plant endoplasmic reticulum upon expression in a plant cell.
The plant expression cassettes described above are combined with an appropriate plant selectable marker to aid in the selection of transformed cells and tissues, and ligated into plant transformation vectors. These may include binary vectors from Agrobacterium-mediated transformation or simple plasmid vectors for aerosol or biolistic transformation.
Example 25
Vectoring genes for Plant Expression
The coding region DNA of the genes encompassed herein are operably connected with appropriate promoter and terminator sequences for expression in plants. Such sequences are well known in the art and may include the rice actin promoter or maize ubiquitin promoter for expression in monocots, the Arabidopsis UBQ3 promoter or CaMV 35S promoter for expression in dicots, and the nos or PinII terminators. Techniques for producing and confirming promoter-gene-terminator constructs also are well known in the art.
The plant expression cassettes described above are combined with an appropriate plant selectable marker to aid in the selections of transformed cells and tissues, and ligated into plant transformation vectors. These may include binary vectors from Agrobacterium-mediated transformation or simple plasmid vectors for aerosol or biolistic transformation.
Example 26
AXN-1 Protein Expression in Soybean Root Tissue
Vector Construction
Vector pAG6004 was prepared to guide overexpression of the AXN-1 protein in soybean hairy root tissues. pAG6004 contains the full-length AXN-1 gene, organized 3′ to the UBQ10 promoter (Arabidopsis thaliana) and 5′ to the 35S terminator (cauliflower mosaic virus), in a manner likely to lead to transcription of the axn-1 gene from the UBQ10 promoter, and termination of such transcription by the 35S terminator. Also present in the vector is a visual marker (yellow fluorescent protein (YFP), under control of UBQ3 promoter), a replication origin functional in Agrobacterium species, and a gentamicin resistance gene. The organization of the vector was confirmed by DNA sequencing of the entire vector, and then introduced into Agrobacterium rhizogenes strain K599 and propagated by growth on gentamicin.
Soybean Transformation
Soybean hairy root cultures were prepared as follows. Soybean seeds (cultivar Williams 82) were germinated in a growth chamber (25° C.) for 1 week, at which time the cotyledons were excised (after removing seed coats). The cotyledons were then wounded with a scalpel that had been dipped in an overnight A. rhizogenes culture transformed with pAG6004. The infected cotyledons were placed abaxial side up on the top of a Whatman filter paper, submerged in sterile water in a Petri dish and incubated in a dark growth chamber at 25° C. for 3 to 5 days. Next, individual cotyledons were transferred to and cultured abaxial side up on MB carb medium (MS salts, B5 vitamins, 3% sucrose, 500 mg/L of carbenicillin, and solidified with 3 g/L of Gelrite). Cotyledons were sub-cultured every two weeks on the same MB carb medium to regenerate hairy roots. Roots expressing yellow fluorescent protein (YFP) gene associated with AXN-1 gene derived from pAG6004 were detected under a ZEISS stereo dissecting microscope (KL 1500 LCD) with filter set (exciting filter 508 nm; emission filter 524 nm). YFP roots were sub-cultured on the same MB carb medium every two weeks or as needed.
Detection of AXN-1 Protein in Root Tissue
Western blot analysis was utilized to identify AXN-1 protein expression in hairy root tissues. One gram of transgenic and control tissues that had been grown for approximately 6 weeks were suspended 2×LDS loading dye (Invitrogen) with 2.5 mM (3-mercaptoethanol, and then homogenized using stainless beads in a bead beater instrument. The homogenized extracts were separated on a 4-20% Big-Tris gel, transferred to nitrocellulose, and then incubated with rabbit serum from rabbits immunized with purified AXN-1 protein. Following a series of wash steps and incubation with a secondary antibody (donkey anti-rabbit, conjugated with horseradish peroxidase, Pierce), the presence of AXN-1 was visualized by ECL (Pierce). Interestingly, this analysis revealed that the soybean roots generated a truncated form of the protein (approximately 50 kDa) rather than the full-length protein (103 kDa). This observation is consistent with post-translational processing of the AXN-1 protein, and matches the size of the AXN-1 protein that was purified from the host bacterial strain, ATX21995.
Detection of AXN-8 Protein in Root Tissue
Western blot analysis was utilized to identify AXN-8 protein expression in hairy root tissues. One gram of transgenic and control tissues that had been grown for approximately 6 weeks were suspended 2×LDS loading dye (Invitrogen) with 2.5 mM β-mercaptoethanol, and then homogenized using stainless beads in a bead beater instrument. The homogenized extracts were separated on a 4-20% Big-Tris gel, transferred to nitrocellulose, and then incubated with rabbit serum from rabbits immunized with purified AXN-8 protein. Following a series of wash steps and incubation with a secondary antibody (donkey anti-rabbit, conjugated with horseradish peroxidase, Pierce), the presence of AXN-8 was visualized by ECL (Pierce). This analysis revealed that the soybean roots generated a full-length AXN-8 protein (approximately 50 kDa in size) that matches the size of the AXN-8 protein that was purified from the host bacterial strain, ATX20514, as well as additional truncated forms of the protein.
Detection of Phenol Oxidase Enzymatic Activity in Root Tissue
Several phenol oxidases, including AXN-1, can utilize tyrosine as a substrate to produce melanin. To determine if the AXN-1 protein expressed in soybean hairy roots was enzymatically active, we carried out enzymatic assays with protein extracts from AXN-1 (pAG6004) and control (pAG5385) root tissues. Each tissue (approximately 1 gram) was homogenized in liquid nitrogen, and 10 mg of each was suspended in 0.4 mL of buffer (20 mM Tris, pH 8.0). Each tissue suspension was then added at 1/10th final volume to enzyme assays containing the same buffer and 1 mM tyrosine. Assay reactions were incubated overnight, and a commercial tyrosinase preparation (Sigma-Aldrich) was used as a positive control for enzymatic activity. Both the AXN-1 root tissue and commercial tyrosinase enzyme generated a brown color in the assay that is consistent with melanin, while control root tissue was negative. Color formation was dependent on the presence of the substrate tyrosine. Thus, axn-1 is effectively expressed in soybean tissue, resulting in active polyphenol oxidase activity.
Example 27
Transformation of Maize Cells with the Nematicidal Genes Described Herein
Maize ears are best collected 8-12 days after pollination. Embryos are isolated from the ears, and those embryos 0.8-1.5 mm in size are preferred for use in transformation. Embryos are plated scutellum side-up on a suitable incubation media, such as DN62A5S media (3.98 g/L N6 Salts; 1 mL/L (of 1000× Stock) N6 Vitamins; 800 mg/L L-Asparagine; 100 mg/L Myo-inositol; 1.4 g/L L-Proline; 100 mg/L Casamino acids; 50 g/L sucrose; 1 mL/L (of 1 mg/mL Stock) 2,4-D). However, media and salts other than DN62A5S are suitable and are known in the art. Embryos are incubated overnight at 25° C. in the dark. However, it is not necessary per se to incubate the embryos overnight.
The resulting explants are transferred to mesh squares (30-40 per plate), transferred onto osmotic media for about 30-45 minutes, then transferred to a beaming plate (see, for example, PCT Publication No. WO/0138514 and U.S. Pat. No. 5,240,842).
DNA constructs designed to the genes of the invention in plant cells are accelerated into plant tissue using an aerosol beam accelerator, using conditions essentially as described in PCT Publication No. WO/0138514. After beaming, embryos are incubated for about 30 min on osmotic media, and placed onto incubation media overnight at 25° C. in the dark. To avoid unduly damaging beamed explants, they are incubated for at least 24 hours prior to transfer to recovery media. Embryos are then spread onto recovery period media, for about 5 days, 25° C. in the dark, then transferred to a selection media. Explants are incubated in selection media for up to eight weeks, depending on the nature and characteristics of the particular selection utilized. After the selection period, the resulting callus is transferred to embryo maturation media, until the formation of mature somatic embryos is observed. The resulting mature somatic embryos are then placed under low light, and the process of regeneration is initiated by methods known in the art. The resulting shoots are allowed to root on rooting media, and the resulting plants are transferred to nursery pots and propagated as transgenic plants.
Materials
DN62A5S Media












Components
Per Liter
Source


















Chu's N6 Basal Salt
3.98
g/L
Phytotechnology Labs


Mixture (Prod. No. C 416)









Chu's N6 Vitamin
1 mL/L
Phytotechnology Labs


Solution (Prod. No. C 149)
(of 1000x Stock)










L-Asparagine
800
mg/L
Phytotechnology Labs


Myo-inositol
100
mg/L
Sigma


L-Proline
1.4
g/L
Phytotechnology Labs


Casamino acids
100
mg/L
Fisher Scientific


Sucrose
50
g/L
Phytotechnology Labs









2,4-D (Prod. No. D-7299)
1 mL/L
Sigma



(of 1 mg/mL Stock)









The pH of the solution is adjusted to pH 5.8 with 1N KOH/1N KCl, Gelrite (Sigma) is added at a concentration up to 3 g/L, and the media is autoclaved. After cooling to 50° C., 2 ml/L of a 5 mg/ml stock solution of silver nitrate (Phytotechnology Labs) is added.
Example 28
Transformation of the Genes of the Invention in Plant Cells by Agrobacterium-Mediated Transformation
Ears are best collected 8-12 days after pollination. Embryos are isolated from the ears, and those embryos 0.8-1.5 mm in size are preferred for use in transformation. Embryos are plated scutellum side-up on a suitable incubation media, and incubated overnight at 25° C. in the dark. However, it is not necessary per se to incubate the embryos overnight. Embryos are contacted with an Agrobacterium strain containing the appropriate vectors for Ti plasmid mediated transfer for about 5-10 min, and then plated onto co-cultivation media for about 3 days (25° C. in the dark). After co-cultivation, explants are transferred to recovery period media for about five days (at 25° C. in the dark). Explants are incubated in selection media for up to eight weeks, depending on the nature and characteristics of the particular selection utilized. After the selection period, the resulting callus is transferred to embryo maturation media, until the formation of mature somatic embryos is observed. The resulting mature somatic embryos are then placed under low light, and the process of regeneration is initiated as known in the art.
Example 29
AXN-8 Protein Expression in Maize Leaf Tissue
Vector Construction
Vector pAG4146 was prepared to guide overexpression of the AXN-8 protein in maize tissues. pAG4146 contains the full-length AXN-8 gene, organized 3′ to the sugarcane Ubi4 ubiquitin promoter (Saccharum sp.) and 5′ to the 35S terminator (cauliflower mosaic virus), in a manner likely to lead to transcription of the axn-8 gene from the Ubi promoter, and termination of such transcription by the 35S terminator. Also present in the vector is a selectable marker that confers resistance to glyphosate (GRG23ace5, under control of sugarcane Ubi4 promoter), a replication origin functional in Agrobacterium species, and a spectinomycin resistance gene. The organization of the vector was confirmed by DNA sequencing of the entire vector.
Detection of AXN-8 Protein in Maize Leaf Tissues
Western blot analysis was utilized to identify AXN-8 protein expression in both leaf and root tissues. One gram of transgenic and control tissues were suspended 2×LDS loading dye (Invitrogen) with 2.5 mM β-mercaptoethanol, and then homogenized using stainless beads in a bead beater instrument. The homogenized extracts were separated on a 4-20% Big-Tris gel, transferred to nitrocellulose, and then incubated with rabbit serum from rabbits immunized with purified AXN-8 protein. Following a series of wash steps and incubation with a secondary antibody (donkey anti-rabbit, conjugated with horseradish peroxidase, Pierce), the presence of AXN-8 was visualized by ECL (Pierce). The size of the protein detected by Western blot was very similar for the leaf and root tissue, and is similar to that expected for the full-length AXN-8 protein (approximately 50 kDa), and matches the size of the AXN-8 protein that was purified from the host bacterial strain, ATX20514.
All publications and patent applications mentioned in the specification are indicative of the level of skill of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.
Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be obvious that certain changes and modifications may be practiced within the scope of the appended claims.

## Claims

1. A construct comprising a heterologous promoter operably linked to a nucleic acid encoding an amino acid sequence having nematicidal activity, wherein said nucleic acid is selected from the group consisting of:
a) a nucleotide sequence that encodes a polypeptide comprising the amino acid sequence of SEQ ID NO:4 or 5; and
b) the nucleotide sequence set forth in SEQ ID NO: 1, 2, or 3,
wherein said heterologous promoter is capable of directing expression of said nucleic acid in a host cell.

2. The construct of claim 1, wherein said nucleic acid is a synthetic sequence that has been designed for expression in a plant.

3. The construct of claim 2, wherein said synthetic sequence comprises SEQ ID NO:6.

4. A vector comprising the construct of claim 1.

5. The vector of claim 4, further comprising a nucleic acid molecule encoding a heterologous polypeptide.

6. A bacterial host cell that contains the construct of claim 1.

7. A transgenic plant cell comprising a nucleotide sequence encoding a polypeptide selected from the group consisting of:
a) a polypeptide comprising the amino acid sequence of SEQ ID NO:4 or 5; and
b) the polypeptide that is encoded by SEQ ID NO: 1, 2, or 3.

8. A transgenic plant regenerated from the plant cell of claim 7.

9. The transgenic plant of claim 8, wherein said plant is selected from the group consisting of maize, sorghum, wheat, cabbage, sunflower, tomato, crucifers, peppers, potato, cotton, rice, soybean, sugarbeet, sugarcane, tobacco, barley, and oilseed rape.

10. An isolated polypeptide with nematicidal activity, wherein the polypeptide comprises a heterologous leader sequence or a transit peptide operably linked to a protein selected from the group consisting of:
a) a protein comprising the amino acid sequence of SEQ ID NO:4 or 5; and
b) the protein that is encoded by SEQ ID NO: 1, 2, 3, or 6.

11. A composition comprising the polypeptide of claim 10.

12. The composition of claim 11, wherein said composition is selected from the group consisting of a powder, dust, pellet, granule, spray, emulsion, colloid, and solution.

13. The composition of claim 11, wherein said composition is prepared by desiccation, lyophilization, homogenization, extraction, filtration, centrifugation, sedimentation, or concentration of a culture of bacterial cells.

14. The composition of claim 11, comprising from about 1% to about 99% by weight of said polypeptide.

15. A method for killing or controlling a nematode pest, comprising contacting said pest with, or feeding to said pest, a nematicidally-effective amount of a composition comprising the polypeptide of claim 10.

16. A method for protecting a plant from a pest, said method comprising introducing into said plant or cell thereof at least one expression vector comprising a nucleotide sequence that encodes a nematicidal polypeptide, wherein said plant is planted in an area susceptible to nematode infestation and wherein said nucleotide sequence is selected from the group consisting of:
a) a nucleotide sequence that encodes a polypeptide comprising the amino acid sequence of SEQ ID NO:4 or 5; and
b) the nucleotide sequence set forth in SEQ ID NO: 1, 2, or 3.

17. The construct of claim 1, wherein said promoter is capable of directing expression of said nucleic acid in a plant cell.