# Patent

## Title
Truncated Cry35 proteins

## Abstract

This invention provides truncated Cry35 proteins that surprisingly and unexpectedly have increased pesticidal activity as compared to full-length Cry35 proteins. The subject invention also includes polynucleotides that encode these truncated proteins, transgenic plants comprising a truncated gene of the subject invention, and transgenic plants that produce these truncated proteins. This invention further provides methods of controlling plant pests, including rootworms, with these truncated proteins. The truncated Cry35 proteins of the subject invention are preferably used in combination with Cry34 proteins, which are known in the art. Various surprising advantages of the subject invention will be apparent in light of this disclosure.

## Background
CROSS-REFERENCE TO RELATED APPLICATION
This application claims priority to provisional application Ser. No. 60/584,324, filed Jun. 29, 2004, the disclosure of which is incorporated herein by reference in its entirety.


BACKGROUND OF THE INVENTION
Coleopterans are a significant group of agricultural pests that cause extensive damage to crops each year. Examples of coleopteran pests include corn rootworm and alfalfa weevils. Additional notable examples include Colorado potato beetle, boll weevil, and Japanese beetle.
Insecticidal crystal proteins from some strains of Bacillus thuringiensis (B.t.) are well-known in the art. See, e.g., Höfte et al., Microbial Reviews, Vol. 53, No. 2, pp. 242-255 (1989). These proteins are typically produced by the bacteria as approximately 130 kDa protoxins that are then cleaved by proteases in the insect midgut, after ingestion by the insect, to yield a roughly 60 kDa core toxin. These proteins are known as crystal proteins because distinct crystalline inclusions can be observed with spores in some strains of B.t. These crystalline inclusions often comprise a mixture of distinct proteins.
An entirely new insecticidal protein system was discovered in Bacillus thuringiensis as disclosed in WO 97/40162. Unlike the 130 kDa-type protoxins, this new system comprises two proteins—one of approximately 15 kDa and the other of about 45 kDa. See also U.S. Pat. No. 6,083,499; U.S. Pat. No. 6,127,180; Moellenbeck et al., Nature Biotechnology 19:668-672 (2001); and Ellis et al., Applied and Environmental Microbiology 68:1137-1145 (2002). These proteins have now been assigned to their own classes, and accordingly received the Cry designations of Cry34 and Cry35, respectively. See Crickmore et al. website (biols.susx.ac.uk/home/Neil_Crickmore/Bt/). Many other proteins of this type of system have now been disclosed. See e.g. U.S. Pat. No. 6,372,480; WO 01/14417; and WO 00/66742. Plant-optimized genes that encode such proteins, wherein the genes are engineered to use codons for optimized expression in plants, have also been disclosed. See e.g. U.S. Pat. No. 6,218,188 and WO 00/24904.
BRIEF SUMMARY OF THE INVENTION
This invention provides truncated Cry35 proteins that surprisingly and unexpectedly have increased pesticidal activity as compared to full-length Cry35 proteins. The subject invention also includes polynucleotides that encode these truncated proteins, transgenic plants comprising a truncated gene of the subject invention, and transgenic plants that produce these truncated proteins. This invention further provides methods of controlling plant pests, including rootworms, with these truncated proteins. The truncated Cry35 proteins of the subject invention are preferably used in combination with Cry34 proteins, which are known in the art. Various surprising advantages of the subject invention will be apparent in light of this disclosure.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 shows a sequence alignment of Cry35Aa1 (80JJ1), Cry35Ab1 (149B1), Cry35Ac1 (167H2), and 201L3 ( ̃45 kDa). The truncation site is in the middle of the 4-leucine (L) run towards the C terminus. The amino acid sequence to be removed starts at and includes the third and fourth “Ls” to the C terminus.



BRIEF DESCRIPTION OF THE SEQUENCES
SEQ ID NO:1 is the amino acid sequence of the wild-type 80JJ1  ̃45 kDa (Cry 35Aa1) protein.
SEQ ID NO:2 is the amino acid sequence of a preferred, truncated 80JJ1  ̃40 kDa (Cry 35Aa1) protein that exhibits enhanced toxin activity.
SEQ ID NO:3 is the amino acid sequence of the wild-type 149B1  ̃45 kDa (Cry 35Ab1) protein.
SEQ ID NO:4 is the amino acid sequence of a preferred, truncated 149B1  ̃40 kDa (Cry 35Ab1) protein.
SEQ ID NO:5 is the 4-leucine (L) run towards the C terminus, the middle of which is the truncation site.
SEQ ID NO:6 is the amino acid sequence of Cry35Ac1 (167H2) (GenBank Accession No. AAG50117) disclosed as SEQ ID NO:38 in WO 01/14417.
SEQ ID NO:7 is the amino acid sequence of 201L3 ( ̃45 kDa) disclosed as SEQ ID NO:136 in WO 01/14417.
DETAILED DESCRIPTION
This invention provides truncated Cry35 proteins that surprisingly and unexpectedly have increased pesticidal activity as compared to full-length Cry35 proteins. Preferred proteins of the subject invention are approximately 40 kDa. Wild-type Cry35 proteins are typically about 45 kDa.
The subject invention also includes polynucleotides that encode these truncated proteins, transgenic plants comprising a truncated gene of the subject invention, and transgenic plants that produce these truncated proteins. Seeds and other materials (such as pollen and germ plasm) produced by such plants are also included within the subject invention. This invention further provides methods of controlling plant pests, including rootworms, by contacting the pests with these truncated proteins. The truncated Cry35 proteins of the subject invention are preferably used in combination with Cry34 proteins, which are known in the art. Various surprising advantages of the subject invention will be apparent in light of this disclosure.
While some B.t. proteins are known to undergo protealytic processing in vivo, there was no reason to expect the subject truncations to have better activity than the wild-type form. Thus, there was no prior motivation or suggestion to use the subject truncated genes in plants. Likewise there was no motivation or suggestion to provide (i.e., directly administer) a truncated Cry35 protein to a pest so that the pest would ingest/consume the truncated protein.
Polynucleotides of the subject invention preferably have codon usage that is optimized for expression in plants. Various techniques for doing so are well-known in the art.
The subject invention includes methods of controlling and/or inhibiting pests, preferably a rootworm pest, wherein the methods includes contacting the pest with a protein of the subject invention. Preferably, the truncated protein of the subject invention is produced by and is present in a transgenic plant comprising a gene that encodes the truncated protein. By consuming material of this transgenic plant, such as root cells of such plant, the pest thereby contacts the subject proteins, which is preferably in the plant cells consumed by the pest.
Proteins of the subject invention having “toxin activity,” as the term is used herein, include proteins that enhance or improve the activity of other toxin proteins. Cry35 proteins are known to act with Cry34 proteins to exert the toxic effects. There are some reports that Cry34 proteins can be toxic alone, but that toxicity is much improved when used with Cry35 proteins. The subject invention provides a very surprising means for still further increasing the Cry34/35 activity.
When an insect comes into contact with an effective amount of a “toxin” of the subject invention delivered via transgenic plant expression, formulated protein composition(s), sprayable protein composition(s), a bait matrix or other delivery system, the results are typically death of the insect, inhibition of the growth and/or proliferation of the insect, and/or prevention of the insects from feeding upon the source (preferably a transgenic plant) that makes the toxins available to the insects. Complete lethality to feeding insects is preferred, but is not required to achieve toxin activity. If an insect avoids the toxin or ceases feeding, that avoidance will be useful in some applications, even if the effects are sublethal or lethality is delayed or indirect. For example, if insect resistant transgenic plants are desired, the reluctance of insects to feed on the plants is as useful as lethal toxicity to the insects because the ultimate objective is avoiding insect-induced plant damage. Insects inhibited by the methods and proteins of the subject invention include those that are killed by the subject methods and proteins.
Without being bound by any specific theory of a mechanism of action, and noting that the following theory is now possible in light of the subject disclosure, the removal of the C terminus could facilitate assembly of truncated Cry35 proteins into a multimer (comprised of truncated, Cry35 monomers). There are other proteins having a motif where an activation domain is protealytically removed to allow assembly of multimers. Noting that the Cry35 protein is known to act with the Cry34 ( ̃14 kDa) protein, the Cry34 protein could bind to the multimeric form of assembled Cry35 proteins. This could facilitate entry of the 14 kDa protein, which may have a cellular target via binding, or may form pores on its own. It appears unlikely that a membrane-bound Cry35 monomer associates with the membrane and then with the 14 kDa as a binding partner.
While the 149B1 protein is specifically exemplified, any other cry35 gene or protein can be used according to the subject invention, as Cry35 proteins have similar structures and features. Thus, as one skilled in the art would know, with the benefit of this disclosure, corresponding residues and segments are now identifiable in the other Cry35 proteins. Thus, the specific examples disclosed herein can be applied to the other proteins in the Cry35 family. The exact numbering of the residues might not strictly correspond to the 149B1 protein, but the corresponding residues are readily identifiable in light of the subject disclosure. In this regard, some sequences of various Cry35 proteins and genes described in various patent references are indicated below (such sequences can be used according to some embodiments of the subject invention):












Cry designation
Source isolate
GENBANK Acc. No.







35Aa1
PS80JJ1
AAG50342


35Aa2
EG5899
AAK64561


35Ab1
PS149B1
AAG41672


35Ab2
EG9444
AAK64563


35Ac1
PS167H2
AAG50117


35Ba1
EG4851
AAK64566









35Aa1, 35Ab1, and 35Ac1 are also disclosed in WO 01/14417 as follows. The location (amino acid residue numbers) of the four leucine run (LLLL) (SEO ID NO:5) is also indicated.














SEQ ID NO:

Location of LLLL


Source isolate
IN WO 01/14417
Length
(SEQ ID NO:5)


















PS80JJ1
11
385
353-356


PS167H2
38
383
353-356


PS149B1
43
383
353-356









There are many additional Cry35 sequences disclosed in WO 01/14417 that can be used according to the subject invention. For example:
















SEQ ID NO:
Location of LLLL



Source isolate
IN WO 01/14417
(SEQ ID NO:5)




















PS131W2
54
353-356



PS158T3
58
353-356



PS185FF
64
353-356



PS185GG
68
353-356



PS187F3
78
353-356



PS187L14
86
353-356



PS187Y2
90
340-344



PS69Q
116
353-356



KR589
126
353-356



PS201L3
136
355-358



PS187G1
140
353-356



PS201HH2
144
(partial sequence)



KR1369
148
353-356










Several other source isolates are also disclosed in WO 01/14417. The PS designation of the source isolate can be dropped for ease of reference when referring to a protein obtainable from that isolate. For example, it can be noted that the full-length 201L3 Cry35 protein is 387 residues long. Polynucleotides that encode various Cry35 proteins are also disclosed in various references cited herein and are known in the art.
As shown by the above tables, the typical and preferred site for truncation is after residue 354 for most Cry35 proteins. Thus, preferred truncated Cry35 proteins consist of 354 amino acid residues. Accordingly, in preferred embodiments, approximately 29 residues are removed from the C terminus of the wild-type/full-length Cry35 protein. However, approximately 31 residues (in the case of 80JJ1, for example) or 33 residues (in the case of 201L3, for example) can be removed from the C terminus. Some preferred proteins of the subject invention can be 356 amino acid residues in length (in the case of 201L3, for example).
With that noted, truncated Cry35 proteins of the subject invention can be part of a larger fusion protein. For example, an approximately 354-residue, truncated Cry35 protein can be fused to a Cry34 protein to make a Cry35/Cry34 chimeric protein. Thus, such proteins can be said to comprise approximately 354 (or 356) Cry35 residues. A Cry35/Cry34 fusion is disclosed in WO 01/14417 as SEQ ID NO:159, with LLLL (SEQ ID NO:5) occurring at residue positions 353-356.
Fragments of full-length genes can be made using commercially available exonucleases or endonucleases according to standard procedures. For example, enzymes such as Bal31 or site-directed mutagenesis can be used to systematically cut off nucleotides from the ends of these genes. Also, genes that encode activated fragments of the subject invention can be obtained using a variety of restriction enzymes. Proteases may be used to directly obtain activated fragments of the subject invention.
The polynucleotides of the subject invention can be used to form complete “genes” to encode proteins or peptides in a desired host cell. For example, as the skilled artisan would readily recognize, the subject polynucleotides can be appropriately placed under the control of a promoter in a host of interest, as is readily known in the art.
As used herein, reference to “isolated” and/or “purified” proteins and/or polynucleotides indicates that such molecules are not in their native state. Thus, reference to “isolated” and/or “purified” signifies the involvement of the “hand of man” as described herein. For example, a bacterial toxin “gene” of the subject invention put into a plant for expression is an “isolated polynucleotide.” Likewise, a protein of the subject invention that is produced by a plant is an “isolated protein.”
Because of the degeneracy/redundancy of the genetic code, a variety of different DNA sequences can encode the amino acid sequences disclosed herein. It is well within the skill of a person trained in the art to create alternative DNA sequences that encode the same, or essentially the same, toxins. These variant DNA sequences are within the scope of the subject invention.
Certain toxins of the subject invention have been specifically exemplified herein. As these toxins are merely exemplary of the proteins of the subject invention, it should be readily apparent that the subject invention comprises variant or equivalent proteins (and nucleotide sequences coding for equivalents thereof) having the same (or similar), increased toxin activity of the exemplified proteins. Genes and toxins of the subject invention include not only the specifically exemplified sequences, but also variants, mutants, chimerics, and fusions thereof. Proteins of the subject invention can have substituted amino acids so long as they retain the approximate size and the increased toxin activity of the truncated proteins exemplified herein. As used herein, reference to a “variant” or an “equivalent” sequence refers to sequences having amino acid substitutions, deletions, additions, as compared to the wild-type sequence corresponding to a truncation of the subject invention, so long as the increased toxin activity exhibited by the truncated protein is retained. Thus, truncated proteins of the subject invention include not only those having a wild-type sequence that is truncated. Some residues can be substituted. While conservative changes are preferred, nonconservative changes can also be made in some cases. Techniques for producing and confirming the activity of proteins modified accordingly are well-known in the art.
Equivalent toxins and/or genes encoding these equivalent toxins can be obtained/derived from wild-type or recombinant bacteria and/or from other wild-type or recombinant organisms using the teachings provided herein. Other Bacillus and Paenibacillus species, for example, can be used as source isolates.
Variations of genes may be readily constructed using standard techniques for making point mutations, for example. In addition, U.S. Pat. No. 5,605,793, for example, describes methods for generating additional molecular diversity by using DNA reassembly after random fragmentation. Variant genes can be used to produce variant proteins; recombinant hosts can be used to produce the variant proteins. Using these “gene shuffling” techniques, equivalent genes and proteins can be constructed that comprise any 5, 10, or 20 contiguous residues (amino acid or nucleotide) of any sequence exemplified herein. As one skilled in the art knows, the gene shuffling techniques can be adjusted to obtain equivalents having, for example, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, or 357 contiguous residues (amino acid or nucleotide) of any of the exemplified or suggested sequences (or the complements (full complements) thereof). Full-length genes obtained by shuffling can then be truncated according to the subject invention (or truncated genes can be subjected to shuffling).
Variant/equivalent, truncated (and activated) toxins included within the scope of the subject invention will be of a length suggested herein and will have some level of amino acid identity, similarity, and/or homology with an exemplified activated toxin. This degree of amino acid identity with an exemplified, truncated toxin is preferably greater than 60%, preferably greater than 75%, more preferably greater than 80%, even more preferably greater than 90%, and can be greater than 95%. Preferred polynucleotides and proteins of the subject invention can also be defined in terms of more particular identity and/or similarity ranges. For example, this identity and/or similarity can be 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% as compared to a sequence exemplified or suggested herein.
Unless otherwise specified, as used herein, percent sequence identity and/or similarity of two sequences is determined using the algorithm of Karlin and Altschul (1990), Proc. Natl. Acad. Sci. USA 87:2264-2268, modified as in Karlin and Altschul (1993), Proc. Natl. Acad. Sci. USA 90:5873-5877. Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul et al. (1990), J. Mol. Biol. 215:402-410. BLAST nucleotide searches are performed with the NBLAST program, score=100, wordlength=12. To obtain gapped alignments for comparison purposes, Gapped BLAST is used as described in Altschul et al. (1997), Nucl. Acids Res. 25:3389-3402. When utilizing BLAST and Gapped BLAST programs, the default parameters of the respective programs (NBLAST and XBLAST) are used. See NCBI/NIH website. The scores can also be calculated using the methods and algorithms of Crickmore et al. as described in the Background section, above.
The amino acid homology/similarity/identity can be highest in critical regions of the protein that account for its toxin activity or that are involved in the determination of three-dimensional configurations that are ultimately responsible for the toxin activity. In this regard, certain amino acid substitutions are acceptable and can be tolerated. For example, these substitutions can be in regions of the protein that are not critical to activity. Analyzing the crystal structure of a protein, and software-based protein structure modeling, can be used to identify regions of a protein that can be modified (using site-directed mutagenesis, shuffling, etc.) to actually change the properties and/or increase the functionality of the protein.
In many cases, conservative amino acid substitutions can be made. Unless otherwise specified, amino acids can be placed in the following classes: non-polar, uncharged polar, basic, and acidic. Conservative substitutions whereby an amino acid of one class is replaced with another amino acid of the same type are within the scope of the subject invention so long as the substitution is not adverse to the elevated toxin activity exhibited by truncated proteins of the subject invention. Table 1 provides a listing of examples of amino acids belonging to each class.










TABLE 1







Class of Amino Acid
Examples of Amino Acids









Nonpolar
Ala, Val, Leu, Ile, Pro, Met, Phe, Trp



Uncharged Polar
Gly, Ser, Thr, Cys, Tyr, Asn, Gln



Acidic
Asp, Glu



Basic
Lys, Arg, His










In some instances, non-conservative substitutions can also be made. The critical factor is that these substitutions must not significantly detract from the functional/biological/toxin activity of the protein.
In other embodiments, polynucleotides (and the proteins they encode) of the subject invention can be defined by their ability to hybridize with exemplified and/or suggested polynucleotides. The nucleotide sequences of the subject invention are particularly advantageous, and they encode proteins that are distinct from previously described proteins. Thus, exemplified or suggested polynucleotides (and/or the complements thereof) can be used as hybridization probes.
As the skilled artisan knows, DNA typically exists in a double-stranded form. In this arrangement, one strand is complementary to the other strand and vice versa. As DNA is replicated in a plant (for example), additional complementary strands of DNA are produced. The “coding strand” is often used in the art to refer to the strand that binds with the anti-sense strand. The mRNA is transcribed from the “anti-sense” strand of DNA. The “sense” or “coding” strand has a series of codons (a codon is three nucleotides that can be read as a three-residue unit to specify a particular amino acid) that can be read as an open reading frame (ORF) to form a protein or peptide of interest. In order to produce a protein in vivo, a strand of DNA is typically transcribed into a complementary strand of mRNA which is used as the template for the protein. Thus, the subject invention includes the use of the exemplified polynucleotides shown in the attached sequence listing and/or equivalents including the complementary strands. RNA and PNA (peptide nucleic acids) that are functionally equivalent to the exemplified DNA are included in the subject invention.
Polynucleotides of the subject invention, when accordingly used as probes to define other polynucleotides (or proteins) that are within the scope of the subject invention, can be made detectable by virtue of an appropriate label or may be made inherently fluorescent as described in International Application No. WO 93/16094. The probes/polynucleotides of the subject invention may be DNA, RNA, or PNA. In addition to adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U; for RNA molecules), synthetic probes (and polynucleotides) of the subject invention can also have inosine (a neutral base capable of pairing with all four bases; sometimes used in place of a mixture of all four bases in synthetic probes). Thus, where a synthetic, degenerate oligonucleotide is referred to herein, and “N” or “n” is used generically, “N” or “n” can be G, A, T, C, or inosine. Ambiguity codes as used herein are in accordance with standard IUPAC naming conventions as of the filing of the subject application (for example, R means A or G, Y means C or T, etc.).
As is well known in the art, if a probe molecule hybridizes with a nucleic acid sample, it can be reasonably assumed that the probe and sample have substantial homology/similarity/identity. Preferably, hybridization of the polynucleotide is first conducted, followed by washes under conditions of low, moderate, or high stringency by techniques well-known in the art, as described in, for example, Keller, G. H., M. M. Manak (1987) DNA Probes, Stockton Press, New York, N.Y., pp. 169-170. For example, as stated therein, low stringency conditions can be achieved by first washing with 2×SSC (Standard Saline Citrate)/0.1% SDS (Sodium Dodecyl Sulfate) for 15 minutes at room temperature. Two washes are typically performed. Higher stringency can then be achieved by lowering the salt concentration and/or by raising the temperature. For example, the wash described above can be followed by two washings with 0.1×SSC/0.1% SDS for 15 minutes each at room temperature followed by subsequent washes with 0.1×SSC/0.1% SDS for 30 minutes each at 55° C. These temperatures can be used with other hybridization and wash protocols set forth herein and as would be known to one skilled in the art (SSPE can be used as the salt instead of SSC, for example). The 2×SSC/0.1% SDS can be prepared by adding 50 ml of 20×SSC and 5 ml of 10% SDS to 445 ml of water. 20×SSC can be prepared by combining NaCl (175.3 g/0.150 M), sodium citrate (88.2 g/0.015 M), and water, adjusting pH to 7.0 with 10 N NaOH, then adjusting the volume to 1 liter 10% SDS can be prepared by dissolving 10 g of SDS in 50 ml of autoclaved water, then diluting to 100 ml.
Detection of the probe provides a means for determining in a known manner whether hybridization has been maintained. Such a probe analysis provides a rapid method for identifying toxin-encoding genes of the subject invention. The nucleotide segments which are used as probes according to the invention can be synthesized using a DNA synthesizer and standard procedures. These nucleotide sequences can also be used as PCR primers to amplify genes of the subject invention.
Hybridization characteristics of a molecule can be used to define polynucleotides of the subject invention. Thus the subject invention includes polynucleotides (and/or their complements, preferably their full complements) that hybridize with a polynucleotide exemplified herein. That is, one way to define a truncated gene of the subject invention is by the size of the protein it encodes (i.e., the protein or polypeptide segment will be of a length disclosed or suggested herein) and by its ability to hybridize (under any of the conditions specifically disclosed herein) with an exemplified or suggested sequence, such as a polynucleotide encoding a truncated protein of SEQ ID NO:2 and/or SEQ ID NO:4, for example. The same is true for a polynucleotide encoding a truncated 158×10 Cry35 protein, for example, of the subject invention.
As used herein, “stringent” conditions for hybridization refers to conditions which achieve the same, or about the same, degree of specificity of hybridization as the conditions employed by the current applicants. Specifically, hybridization of immobilized DNA on Southern blots with 32P-labeled gene-specific probes was performed by standard methods (see, e.g., Maniatis, T., E. F. Fritsch, J. Sambrook [1982] Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.). In general, hybridization and subsequent washes were carried out under conditions that allowed for detection of target sequences. For double-stranded DNA gene probes, hybridization was carried out overnight at 20-25° C. below the melting temperature (Tm) of the DNA hybrid in 6×SSPE, 5×Denhardt's solution, 0.1% SDS, 0.1 mg/ml denatured DNA. The melting temperature is described by the following formula (Beltz, G. A., K. A. Jacobs, T. H. Eickbush, P. T. Cherbas, and F. C. Kafatos [1983] Methods of Enzymology, R. Wu, L. Grossman and K. Moldave [eds.] Academic Press, New York 100:266-285):

Tm=81.5° C.+16.6 Log [Na+]+0.41(% G+C)−0.61(% formamide)−600/length of duplex in base pairs.

Washes are typically carried out as follows:

    
    
        (1) Twice at room temperature for 15 minutes in 1×SSPE, 0.1% SDS (low stringency wash).
        (2) Once at Tm-20° C. for 15 minutes in 0.2×SSPE, 0.1% SDS (moderate stringency wash).
    
    


For oligonucleotide probes, hybridization was carried out overnight at 10-20° C. below the melting temperature (Tm) of the hybrid in 6×SSPE, 5×Denhardt's solution, 0.1% SDS, 0.1 mg/ml denatured DNA. Tm for oligonucleotide probes was determined by the following formula:

Tm(° C.)=2(number T/A base pairs)+4(number G/C base pairs)

(Suggs, S. V., T. Miyake, E. H. Kawashime, M. J. Johnson, K. Itakura, and R. B. Wallace [1981] ICN-UCLA Symp. Dev. Biol. Using Purified Genes, D. D. Brown [ed.], Academic Press, New York, 23:683-693).

Washes were typically carried out as follows:

    
    
        (1) Twice at room temperature for 15 minutes 1×SSPE, 0.1% SDS (low stringency wash).
        (2) Once at the hybridization temperature for 15 minutes in 1×SSPE, 0.1% SDS (moderate stringency wash).
    
    


In general, salt and/or temperature can be altered to change stringency. With a labeled DNA fragment >70 or so bases in length, the following conditions can be used:

    
    
        Low: 1 or 2×SSPE, room temperature
        Low: 1 or 2×SSPE, 42° C.
        Moderate: 0.2× or 1×SSPE, 65° C.
        High: 0.1×SSPE, 65° C.
    
    


Duplex formation and stability depend on substantial complementarity between the two strands of a hybrid, and, as noted above, a certain degree of mismatch can be tolerated. Therefore, the probe sequences of the subject invention include mutations (both single and multiple), deletions, insertions of the described sequences, and combinations thereof, wherein said mutations, insertions and deletions permit formation of stable hybrids with the target polynucleotide of interest. Mutations, insertions, and deletions can be produced in a given polynucleotide sequence in many ways, and these methods are known to an ordinarily skilled artisan. Other methods may become known in the future.
All patents, patent applications, provisional applications, and publications referred to or cited herein are incorporated by reference in their entirety to the extent they are not inconsistent with the explicit teachings of this specification.
Following is an example that illustrates procedures for practicing the invention. These examples should not be construed as limiting. All percentages are by weight and all solvent mixture proportions are by volume unless otherwise noted.
EXAMPLE
Improved Efficacy of Truncated Cry35Ab1
The native intact Cry35Ab1 protein from B.t. PS149B1 is approximately 44 kDa. This 44-kDa protein (intact or full-length form), when expressed in the bacteria and transgenic plants, is susceptible to cleavage by proteases producing a stable truncated form. The truncated Cry35Ab1 has a molecular weight of 40.3-kDa determined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). It was determined that both the intact and truncated forms possess the same N-terminal sequence, indicating that the truncation occurred at the C-terminal domain. The results of the molecular mass determined by MALDI-TOF MS, together with data of N-terminal sequencing, suggest that the 40.3-kDa truncated Cry35Ab1 protein contains amino acids residues of 1-354 of the intact Cry35Ab1, i.e., the cleavage site is between amino acid residue #354 and #355 (L353L354↓L355L356) (SEQ ID NO:5). This cleavage site was further confirmed by the data of C-terminal sequence obtained with PSD (post source decay) mode of MALDI-TOF MS and carboxypeptidase digestion techniques.
As displayed in FIG. 1, the sequence segment of the 4 L (leucine) is quite conserved among the Cry35 protein family. This cleavage site appears to be universal to the whole family of Cry35 proteins.
The truncated version of the Cry35Ab1 protein was found to be more efficacious than the non-truncated version in terms of synergizing the Cry34Ab1 protein. This same efficacy improvement can be effected in transgenic plants and with homologous proteins.
Ten diet-overlay assays were conducted against neonate southern corn rootworm, Diabrotica undecimpuctata howardi. Purified full-length and truncated Cry35Ab1 proteins were each applied at 0.5 μg/cm2 in combination with Cry34Ab1 at 0.5 μg/cm2. Controls consisted of Cry34Ab1 alone applied at 0.5 μg/cm2, and a buffer blank. Sixteen insects were included for each treatment for each of ten bioassays. Insect weights were collected for each group of 16 insects in each bioassay after six days of exposure to the treated diet. Statistical analysis consisted of ANOVA analysis of logarithmically transformed insect weights followed by mean comparisons using Duncan's Multiple Range Test. The logarithmic transformation was used to improve the homogeneity of variance. A second ANOVA of the raw weights was also carried out for the two Cry35Ab1 treatments alone where good homogeneity of variance was seen. Mean insect weights for the buffer control, Cry34Ab1 alone, full-length Cry35Ab1+Cry34Ab1, and truncated Cry35Ab1+Cry34Ab1 treatments were 15.7, 11.9, 8.8, and 6.9 mg/16 insects, respectively. Significant differences in insect weight were seen between all treatments. The concentrations of the mixtures were based on a model generated using a preparation of Cry35Ab1 that contained a mixture of full-length and truncated protein (Herman, R. A., Scherer, P. N., Young, D. L., Mihaliak, C. A., Meade, T., Woodsworth, A. T., Stockhoff, B. A., and Narva, K. E., 2002, “Binary Insecticidal Crystal Protein from Bacillus thuringiensis strain PS149B1: effects of individual protein components and mixtures in laboratory bioassays,” J. Econ. Entomol. 95:635-639). This model predicts 50% growth inhibition (GI) at the tested concentrations. The full-length protein mixture in the tests reported here averaged 44% GI, while the truncated protein mixture averaged 56% GI. This improvement in GI translates to a ten-fold improvement in potency based on the model described in Herman et al. (2002). This analysis thus demonstrates an improvement in the activity of the truncated Cry35Ab1 protein compared to the full-length form.

## Claims

1. A polynucleotide that encodes an isolated, truncated Cry35 protein having a truncated C terminus and improved toxin enhancing activity against an insect, as compared to a full-length Cry35 molecule, wherein
said protein enhances toxin activity of a Cry34 molecule,
said protein has 354 amino acid residues,
said protein has leucine-leucine residues as its C-terminal amino acids, and
said protein has at least 95% sequence identity with an amino acid sequence selected from the group consisting of SEQ ID NO:2 and SEQ ID NO:4.

2. The polynucleotide of claim 1, wherein said protein has a molecular weight of approximately 40 kDa and said Cry35 molecule has a molecular weight of approximately 45 kDa.

3. The polynucleotide of claim 1, wherein said protein is fused to a Cry34 polypeptide.

4. A polynucleotide that encodes a protein that consists essentially of an amino acid sequence selected from the group consisting of SEQ ID NO:2 and SEQ ID NO:4.

5. The polynucleotide of claim 1, wherein any amino acid changes are conservative substitutions.

6. The polynucleotide of claim 1, wherein said insect is a corn rootworm.

7. The polynucleotide of claim 1, wherein said polynucleotide has a codon composition that is optimized for expression in plants.

8. A plant comprising the polynucleotide of claim 1.

9. A transgenic plant cell or bacterial cell comprising the polynucleotide of claim 1.

10. A method of inhibiting a rootworm wherein said method comprises providing a Cry34 protein and a truncated Cry35 protein encoded by the polynucleotide of claim 1 to said rootworm for ingestion, wherein said Cry34 protein and said truncated Cry35 protein are produced by and are present in a plant.

11. A plant expression vector comprising the polynucleotide of claim 1.