Note: Descriptions are shown in the official language in which they were submitted.
CA 02724158 2010-12-01
DEMANDES OU BREVETS VOLUMINEUX
LA PRESENTE PARTIE DE CETTE DEMANDE OU CE BREVETS
COMPREND PLUS D'UN TOME.
CECI EST LE TOME I DE 2
NOTE: Pour les tomes additionels, veillez contacter le Bureau Canadien des
Brevets_
JUMBO APPLICATIONS / PATENTS
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THAN ONE VOLUME..
THIS IS VOLUME 1 OF 2
NOTE: For additional volumes please contact the Canadian Patent Office.
CA 02724158 2010-12-01
75529-69D
DEFENSIN POLYNUCLEOTIDES AND METHODS OF USE
This is a divisional application of Canadian
Patent Application No. 2,451,517 filed June 21, 2002 (the
parent application).
It should be understood that the expression "the
present invention" or the like used in this specification
encompasses not only the subject matter of this divisional
application but that of the parent application also.
FIELD OF INVENTION
The invention relates to the field of the genetic
manipulation of plants, particularly the modulation of gene
activity and development in plants and increased disease
resistance.
BACKGROUND OF THE INVENTION
Disease in plants is caused by biotic and abiotic
causes. Biotic causes include fungi, viruses, bacteria, and
nematodes. An example of the importance of plant disease is
illustrated by phytopathogenic fungi, which cause
significant annual crop yield losses as well as devastating
epidemics. Plant disease outbreaks have resulted in
catastrophic crop failures that have triggered famines and
caused major social change. All of the approximately
300,000 species of flowering plants are attacked by
pathogenic fungi; however, a single plant species can be
host to only a few fungal species, and similarly, most fungi
usually have a limited host range. Generally, the best
strategy for plant disease control is to use resistant
cultivars selected or developed by plant breeders for this
purpose. However, the potential for serious crop disease
epidemics persists today, as evidenced by outbreaks of the
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Victoria blight of oats and southern corn leaf blight.
Molecular methods of crop protection have the potential to
implement novel mechanisms for disease resistance and can
also be implemented more quickly than traditional breeding
methods. Accordingly, molecular methods are needed to
supplement traditional breeding methods to protect plants
from pathogen attack.
A host of cellular processes enable plants to
defend themselves against diseases caused by pathogenic
agents. These defense mechanisms are activated by initial
pathogen infection in a process known as elicitation. In
elicitation, the host plant recognizes a pathogen-derived
compound known as an elicitor; the plant then activates
disease gene expression to limit further spread of the
invading organism. It is generally believed that to
overcome these plant defense mechanisms, plant
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pathogens must find a way to suppress elicitation as well as to overcome more
physically-based barriers to infection, such as reinforcement and/or
rearrangement of
the actin filament networks near the cell's plasma membrane.
Thus, the present invention solves needs for enhancement of the plant's
defensive elicitation response via a molecularly based mechanism which can be
quickly incorporated into commercial crops.
SUMMARY OF THE INVENTION
Compositions and methods relating to disease resistance are provided.
Particularly, isolated nucleic acid molecules having nucleotide and amino acid
sequences for defensins from plants are provided. The nucleotide sequences of
the
invention encode small cysteine-rich proteins and are variously annotated or
described
as defensins, defensin-like proteins, antimicrobial peptides, anti-pathogenic
peptides,
thionins, antifungal peptides, protease inhibitors, amylase inhibitors,
scorpion toxin-
like proteins and small cysteine-rich peptides. They are referred to herein as
defensins as they exhibit similarity in primary structure to insect defensins.
Transformed plants can be obtained having altered metabolic states with
respect to the
defense response.
The defensin genes of the present invention may find use in enhancing the
plant pathogen defense system. The compositions and methods of the invention
can
be used for enhancing resistance to plant pathogens including fungal
pathogens, plant
viruses, microorganisms, nematodes, insects, and the like. The method involves
stably transforming a plant with a nucleotide sequence capable of modulating
the
plant pathogen defense system operably linked with a promoter capable of
driving
expression of a gene in a plant cell. The defensin genes additionally find use
in
manipulating these processes in transformed plants and plant cells.
Transformed plants, plant cells, and seeds, as well as methods for making such
plants, plant cells, and seeds are additionally provided. It is recognized
that a variety
of promoters will be useful in the invention, the choice of which will depend
in part
upon the desired level of expression of the disclosed genes. It is recognized
that the
levels of expression can be controlled to modulate the levels of expression in
the plant
cell.
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CA 02724158 2011-03-30
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75529-69D
According to one aspect of the present invention, there
is provided an isolated nucleic acid molecule comprising: (a) a
nucleotide sequence set forth in SEQ ID NO:25; (b) a nucleotide
sequence that encodes a polypeptide comprising the amino acid
sequence set forth in SEQ ID NO:26 or 27; (c) a nucleotide
sequence that encodes a mature polypeptide comprising the amino
acid sequence set forth in SEQ ID NO:27; (d) a nucleotide
sequence that encodes a polypeptide comprising an amino acid
sequence having at least 70 percent identity to the amino acid
sequence set forth in SEQ ID NO:27 wherein said polypeptide
retains defensin activity; (e) a nucleotide sequence that
hybridizes under stringent conditions to the complement of a
nucleotide sequence comprising the sequence set forth in SEQ ID
NO:25, wherein said nucleotide sequence encodes a polypeptide
that retains defensin activity and wherein the stringent
conditions comprise hybridization in 50% formamide, 1 M NaCl,
1% SDS at 37 C, and a wash in 0.1 X SSC at 60 to 65 C, and
wherein the duration of hybridization is for less than 24 hours;
or (f) a nucleotide sequence consisting of a complement of any
one of the nucleotide sequence in (a), (b), (c), (d), or (e).
According to another aspect of the present invention,
there is provided a method for enhancing plant disease resistance
to a fungal pathogen, said method comprising: (a) transforming a
plant with at least one stably incorporated DNA construct as
described above, wherein said promoter is a heterologous promoter
that drives expression in a cell of said plant; and (b)
determining the level of increased resistance to said fungal
pathogen in said plant.
According to still another aspect of the present
invention, there is provided an isolated polypeptide
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comprising: (a) the amino acid sequence set forth in
SEQ ID NO:26 or 27; or (b) an amino acid sequence having at
least 70% identity with the amino acid set forth in
SEQ ID NO:26 or 27, and retaining defensin activity.
According to yet a further aspect of the present
invention, there is provided an isolated polypeptide
comprising: (a) the amino acid sequence set forth in
SEQ ID NO:26 or 27; or (b) an amino acid sequence having at
least 70% identity with the amino acid set forth in
SEQ ID NO:26 or 27, and retaining anti-fungal activity.
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BRIEF DESCRIPTION OF THE DRAWINGS
Figure 1 depicts an alignment of several defensin genes and a consensus
defensin sequence (SEQ ID NO:469). Zm-PDFI is set forth in SEQ ID NO:465; Zm-
PDF2 is set forth in SEQ ID NO:463; Zm-PDF3 is set forth in SEQ ID NO:235; Zm-
PDF4 is set forth in SEQ ID NO:1; Zm-PDF6 is set forth in SEQ ID NO:4; and Zm-
PDF 13 is set forth in SEQ ID NO:10.
DETAILED DESCRIPTION OF THE INVENTION
Overview
The present invention provides, inter alia, compositions and methods for
modulating the total level of polypeptides of the present invention and/or
altering their
ratios in a plant. By "modulation" an increase or decrease in a particular
character,
quality, substance, or response is intended.
The compositions comprise nucleotide and amino acid sequences from
numerous plant species. Particularly, the nucleotide and amino acid sequences
for 85
groups of defensins are provided. By "plant defensin genes" is intended genes
that are
structurally related to plant defensins, and include thionins, small cysteine-
rich
peptides, proteinase inhibitors, amylase inhibitors, and the like. They 'are
called
defensin genes after a structural classification of proteins (SCOP)
classification
system. Defensins play a role in defense, more specifically plant defense
against
pathogens, and they share similarity in primary and secondary structure with
insect
defensins. Defensins of the invention are classified in the superfamily of
Scorpion
toxin-like proteins and in the Plant Defensin family. While not bound by any
mechanism of action, expression of the sequences and related genes around
disease
induced lesions may control symptom development, as in a hypersensitive
response
(HR), by controlling the protease mediated cell death mechanism. The
compositions
may also function directly as antipathogenic proteins by inhibiting proteases
produced
by pathogens or by binding cell wall components of pathogens. Thirdly, they
may
also act as amphipathic proteins that perturb membrane function, leading to
cellular
toxicity of the pathogens. The defensins are generally small cysteine-rich
peptides
and demonstrate antimicrobial activity. By "antimicrobial" or "antimicrobial
activity"
antibacterial, antiviral, nematocidal, insecticidal, or and antifungal
activity is
intended. Accordingly, the polypeptides of the invention may enhance
resistance to
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insects and nematodes. Any one defensin exhibits a spectrum of antimicrobial
activity that may involve one or more antibacterial, antifungal, antiviral,
insecticidal,
nematocidal, or antipathogenic activities. They may also be useful in
regulating seed
storage protein turnover and metabolism.
Plant defensins generally comprise about 45-54 amino acids with four
disulfide bridges (Broekaert et al. (1995) Plant Physiol. (Bethesda) 108:1353-
1358).
The defensins of the invention inhibit the growth of a broad range of
pathogens,
including but not limited to fungi, nematocides, bacteria, insects, and
viruses at
micromolar concentrations. Thus, by "defensin-like activity" it is intended
that the
peptides inhibit pathogen growth or damage caused by a variety of pathogens,
including but not limited to, fungi, insects, nematodes, viruses and bacteria.
Defensins inhibit pathogen damage through a variety of mechanisms including,
but
not limited to, alteration of membrane ion permeability and induction of
hyphal
branching in fungal targets (Garcia-Olmeda et al. (1998) Biopolvrners, Peptide
Science 47:479-491).
The compositions of Luc indention can be used in a variety of methods
whereby the protein products can be expressed in crop plants to function as
antimicrobial proteins. Expression will result in alterations or modulation of
the level,
tissue, or timing of expression to achieve enhanced disease, insect, nematode,
viral,
fungal, or stress resistance. The compositions of the invention may be
expressed in
the native species including, but not limited to Arachis hypogaea, Vitis
vinifera,
Licania michauxii, Cvamopsis tetragonoloba, Parthenium argentatum, Nicotiana
benthantiana, Eucalyptus grandis, Tropaeolum majus, Ricinus coanmunis,
Vernonia
mespilifolia, Ginysobalanus icaco, Glycine max, Triticurn aestivum, Oryza
sativa,
Zea shays, Brassica napus, Tulipa gesneriana, Beta vulgaris, Allium poi-rum,
Amaranthus retroflextts, Hedera helix, Picramnia pentandra, Taraxacunt kok-
saghyz.,
Tulipafosteriana, Montordica chaiantia, or alternatively, can be
heterologously
expressed in any plant of interest. In this manner, the coding sequence for
the
defensin can be used in combination with a promoter that is introduced into a
crop
plant. In one embodiment, a high-level expressing constitutive promoter may be
utilized and would result in high levels of expression of the defensin. In
other
embodiments, the coding sequence may be operably linked to a tissue-preferred
promoter to direct the expression to a plant tissue known to be susceptible to
a
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pathogen. Likewise, manipulation of the timing of expression may be utilized.
For
example, by judicious choice of promoter, expression can be enhanced early in
plant
growth to prime the plant to be responsive to pathogen attack. Likewise,
pathogen
inducible promoters can be used wherein expression of the defensin is turned
on in the
presence of the pathogen.
If desired, a transit peptide can be utilized to direct cellular localization
of the
protein product. In this manner, the native transit peptide or a heterologous
transit
peptide can be used. However, it is recognized that both extracellular
expression and
intracellular expression are encompassed by the methods of the invention.
Sequences of the invention, as discussed in more detail below, encompass
coding sequences, antisense sequences, and fragments and variants thereof.
Expression of the sequences of the invention can be used to modulate or
regulate the
expression of corresponding defensin proteins.
The defensin genes of the present invention additionally find use in enhancing
the plant pathogen defense system. The compositions and methods of the
invention
can be used for enhancing resistance to plant pathogens including fungal
pathogens,
plant viruses, insect pathogens, bacterial pathogens, nematodes, and the like.
The
method involves stably transforming a plant with a nucleotide sequence capable
of
modulating the plant pathogen defense system operably linked with a promoter
capable of driving expression of a gene in a plant cell. By "enhancing
resistance"
increasing the tolerance of the plant to pathogens is intended. That is, the
defensin
may slow or prevent pathogen infection and/or spread.
Compositions
Compositions of the invention include nucleotide sequences that have been
identified as defensins. Defensins are involved in defense response and
development.
In particular, the present invention provides for isolated nucleic acid
molecules
comprising nucleotide sequences encoding the amino acid sequences shown in SEQ
ID NO:2, 3, 5, 6, 8, 9, 11, 12, 14, 15, 17, 18, 20, 21, 23, 24, 26, 27, 29,
30, 32, 33, 35,
36, 38, 39, 41, 42, 44, 45, 47, 48, 50, 51, 53, 54, 56, 57, 59, 60, 62, 63,
65, 66, 68, 69,
71, 72, 74, 75, 77, 78, 80, 81, 83, 84, 86, 87, 89, 90, 92, 93, 95, 96, 98,
99, 101, 102,
104, 105, 107, 108, 110, 111, 113,114, 116,117, 119, 120, 122, 123, 125, 126,
128,
129, 131, 132, 134, 135, 137, 138, 140, 141, 143, 144, 146, 147, 149, 150,
152, 153,
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155, 156, 158, 159, 161, 162, 164, 165, 167, 168, 170, 171, 173, 174, 176,
177, 179,
180, 182, 183, 185, 186, 188, 189, 191, 192, 194, 195, 197, 198, 200, 201,
203, 204,
206, 207, 209, 210, 212, 213, 215, 216, 218, 219, 221, 222, 224, 225, 227,
228, 230,
231, 233, 234, 236, 237, 239, 240, 242, 243, 245, 246, 248, 249, 251, 252,
254, 255,
257, 258, 260, 261, 263, 264, 266, 267, 269, 270, 272, 273, 275, 276, 278,
279, 281,
282, 284, 285, 287, 288, 290, 291, 293, 294, 296, 297, 299, 300, 302, 303,
305, 306,
308, 309, 311, 312, 314, 315, 317, 318, 320, 321, 323, 324, 326, 327, 329,
330, 332,
333, 335, 336, 338, 339, 341, 342, 344, 345, 347, 348, 350, 351, 353, 354,
356, 357,
359, 360, 362, 363, 365, 366, 368, 369, 371, 372, 374, 375, 377, 378, 380,
381, 383,
384, 386, 387, 389, 390, 392, 393, 395, 396, 398, 399, 401, 402, 404, 405,
407, 408,
410, 411, 413, 414, 416, 417, 419, 420, 422, 423, 425, 426, 428, 429, 431,
432, 434,
435, 437, 438, 440, 441, 443, 444, 446, 447, 449, 450, 452, 453, 455, 456,
458, 459,
461, 462, 464, 466, or 468. In particular the invention provides the mature
polypeptides having the amino acid sequences set forth in SEQ ID NO:3, 6, 9,
12, 15,
18, 21, 24, 27, 30, 33, 36, 39, 42, 45, 48, 51, 54, 57, 60, 63, 66, 69, 72,
75, 78, 81, 84,
87, 90, 93, 96, 99, 102, 105, 108, 111, 114, 117, 120, 123, 126, 129, 132,
135, 138,
141, 144, 147, 150, 153, 156, 159, 162, 165, 168, 171, 174, 177, 180, 183,
186, 189,
192, 195, 198, 201, 204,207,210,213, 216, 219, 222, 225, 228, 231, 234, 237,
240,
243, 246, 249, 252, 255, 258, 261, 264, 267, 270, 273, 276, 279, 282, 285,
288, 291,
294, 297, 300, 303, 306, 309, 312, 315, 318, 321, 324, 327, 330, 333, 336,
339, 342,
345, 348, 351, 354, 357, 360, 363, 366, 369, 372, 375, 378, 381, 384, 387,
390, 393,
396, 399, 402, 405, 408, 411, 414, 417, 420, 423, 426, 429, 432, 435, 438,
441, 444,
447, 450, 453, 456, 459,or 462. Further provided are polypeptides having an
amino
acid sequence encoded by a nucleic acid molecule described herein, for example
those
set forth in SEQ ID NO:1, 4, 7, 10, 13, 16, 19, 22, 25, 28, 31, 34, 37, 40,
43, 46, 49,
52, 55, 58, 61, 64, 67, 70, 73, 76, 79, 82, 85, 88, 91, 94, 97, 100, 103, 106,
109, 112,
115, 118, 121, 124, 127, 130, 133, 136, 139, 142, 145, 148, 151, 154, 157,
160, 163,
166, 169, 172, 175, 178, 181, 184, 187, 190, 193, 196, 199, 202, 205, 208,
211, 214,
217, 220, 223, 226, 229, 232, 235, 238, 241, 244, 247, 250, 253, 256, 259,
262, 265,
268, 271, 274, 277, 280, 283, 286, 289, 292, 295, 298, 301, 304, 307, 310,
313, 316,
319, 322, 325, 328, 331, 334, 337, 340, 343, 346, 349, 352, 355, 358, 361,
364, 367,
370, 373, 376, 379, 382, 385, 388, 391, 394, 397, 400, 403, 406, 409, 412,
415, 418,
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421, 424, 427, 430, 433, 436, 439, 442, 445, 448, 451, 454, 457, 460, 463,
465, or
467.
The nucleotide sequences of the invention are sequences comprising a protein
superfamily including defensins, thionins, protease inhibitors, amylase
inhibitors,
scorpion toxin-like proteins, and small cysteine-rich peptides. The claimed
sequences
are members of the plant defensin class of genes and polypeptides. The plant
defensins are identified herein as "CS" followed by a three-digit number. The
defensins of the invention fall into 85 groups based on sequence homology. As
indicated elsewhere herein, some of the maize plant defensins are identified
as "Zm-
PDF" for Zea mays plant defensins and designated as numbers ZmPDF or PDF (e.g.
Zm-PDFI or PDFI). The_Zm-PDF and PDF nomenclature has been described
previously.
The defensins of the invention are aligned to a diverse set of mostly plant,
conic non-plant and some animal, proteuia.se-inhibitors, thionins, especially
gtuulna-
thionins, and defensins, and antifungal proteins. A consensus sequence (SEQ ID
NO:469) for some of the maize nucleotide sequences of the invention can be
seen in
Figure 1. There are homologs to these sequences in soybeans, rice, wheat, and
other
crops. They represent a diverse and conserved supergene family in plants.
Group 1 comprises three nucleotide sequences, of which CS004 (SEQ ID
NO:1, PDF4) is the representative sequence. The CS004 polypeptide (SEQ ID
NOS:2
and 3), encoded by the nucleotide sequence set forth in SEQ ID NO:1, is
expressed in
a tassel-preferred pattern. The full-length CS004 polypeptide (SEQ ID NO:2)
appears
to include a signal peptide, which when processed yields a mature polypeptide
having
the amino acid sequence set forth in SEQ ID NO:3. CS004 is extracellular.
CS006
(SEQ ID NO:4, PDF6) appears to be preferentially expressed in the tassel. The
full
length CS006 polypeptide (SEQ ID NO:5) appears to include a signal peptide,
which
when processed yields a mature polypeptide having the amino acid sequence set
forth
in SEQ ID NO:6. CS006 is extracellular. The CSO31 nucleotide sequence (SEQ ID
NO:7) was obtained from Oryza sativa. The full length CS031 polypeptide (SEQ
ID
NO:8) appears to include a signal peptide, which when processed yields a
mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:9.
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Group 2 comprises CS013 (SEQ IDNO:10, PDF13), a maize gene. PDF13 is
widely expressed. The full length CS013 polypeptide (SEQ IDNO:11) is expected
to
have a signal peptide, thus the mature protein (SEQ ID NO:12) would be
extracellular.
Group 3 comprises two maize sequences, of which CS017 (SEQ ID NO:13,
PDF17) is the representative sequence. The CS017 sequence appears to be
preferentially expressed in kernels. The full length CS017 (SEQ ID NO:14)
appears
to include a signal peptide, which when processed yields a mature polypeptide
having
the amino acid sequence set forth in SEQ ID NO:15. Thus, the predicted CS017
polypeptide would be extracellular. CS018 (SEQ IDNO:16, PDF18) is expressed in
the kernel endosperm and may be expressed elsewhere. The full length
polypeptide
(SEQ ID NO: 17) appears to include a signal peptide, which when processed
yields a
mature polypeptide having the amino acid sequence set forth in SEQ ID NO: 18.
Group 4 comprises 13 sequences of which CS065 (SEQ ID NO:43) is the
representative sequence. CS065, having the nucleotide sequence set forth in
SEQ ID
NO:43 and encoding the polypeptides set forth in SEQ 1D NOS:44 and 45, was
isolated from Triticcan aestivum. The nucleotide sequences for CSO40 (SEQ ID
NO:25), CSO41 (SEQ ID NO:28), CS051 (SEQ ID NO:31), CS057 (SEQ ID NO:34),
CS059 (SEQ ID NO:37), CS062 (SEQ ID NO:40), CS066 (SEQ ID NO:46), CS069
(SEQ ID NO:49), CS070 (SEQ ID NO:52), and CS073 (SEQ ID NO:55) were
isolated from Triticum aestivum also. These nucleotide sequences encode full
length
polypeptides having the amino acid sequences set forth in SEQ ID NOS:26, 29,
32,
35, 38, 41, 47, 50, 53, and 56, which when processed yield mature polypeptides
having the amino acid sequences set forth in SEQ ID NOS:27, 30, 33, 36, 39,
42, 48,
51, 54, and 57, respectively. The nucleotide sequences for CS028 (SEQ ID
NO:19)
and CS029 (SEQ ID NO:22) were isolated from Oryzae sativa. These nucleotide
sequences encode full length polypeptides having the amino acid sequences set
forth
in SEQ ID NOS:20 and 23, which when processed yield mature polypeptides having
the amino acid sequences set forth in SEQ ID NOS:21 and 24, respectively.
Group 5 comprises four sequences of which CS032 (SEQ ID NO:58) is the
representative sequence. CS032, having the nucleotide sequence set forth in
SEQ ID
NO:58 and encoding the full-length and mature polypeptides set forth in SEQ ID
NOS:59 and 60, was isolated from Glycine max. The nucleotide sequences for
CS034
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(SEQ ID NO:61) and CS035 (SEQ ID NO:64) were isolated from Glycine max also.
These nucleotide sequences encode full length polypeptides having the amino
acid
sequences set forth in SEQ ID NOS:62 and 65, which when processed yield mature
polypeptides having the amino acid sequences set forth in SEQ ID NOS:63 and
66,
respectively. The nucleotide sequences for CS052 (SEQ ID NO:67) was isolated
from Triticum aestivun2. This nucleotide sequence encodes a full length
polypeptide
having the amino acid sequence set forth in SEQ ID NO:68, which when processed
yields a mature polypeptide having the amino acid sequences set forth in SEQ
ID
NO:69.
Group 6 comprises two Triticum aestivum sequences of which CS044 (SEQ
ID NO:70) is the representative sequence. CS044 (SEQ ID NO:70) and CS050 (SEQ
ID NO:73) encode full length polypeptides having the amino acid sequences set
forth
in SEQ ID NOS:71 and 74, which when processed yield mature polypeptides having
the amino acid sequences set forth in SEQ ID NOS:72 and 75, respectively.
Group 7 comprises two Triticum aestivu m sequences of which CS074 (SEQ
ID NO:79) is the representative sequence. CS063 (SEQ ID NO:76) and CS074 (SEQ
ID NO:79) encode full length polypeptides having the amino acid sequences set
forth
in SEQ ID NOS:77 and 80, which when processed yield mature polypeptides having
the amino acid sequences set forth in SEQ ID NOS:78 and 81, respectively.
Group 8 comprises two Beta vulgaris sequences of which CS078 (SEQ ID
NO:85) is the representative sequence. CS079 (SEQ ID NO:82) and CS078 (SEQ ID
NO:85) encode full length polypeptides having the amino acid sequences set
forth in
SEQ ID NOS:83 and 86, which when processed yield mature polypeptides having
the
amino acid sequences set forth in SEQ ID NOS:84 and 87, respectively.
Group 9 comprises CS084 (SEQ ID NO:88), a Hedera helix sequence. This
nucleotide sequence encodes a full length polypeptide having the amino acid
sequence set forth in SEQ ID NO:89, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:90.
Group 10 comprises two sequences of which CS091 (SEQ ID NO:91) is the
representative sequence. CS091 (SEQ ID NO:91) and CS098 (SEQ ID NO:94)
encode full length polypeptides having the amino acid sequences set forth in
SEQ ID
NOS:92 and 95, which when processed yield mature polypeptides having the amino
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acid sequences set forth in SEQ ID NOS:93 and 96, respectively. CS091 was
isolated
from Tulipafosteriana, and CS098 was isolated from Tulipa gesneriana.
Group 11 comprises four sequences of which CS092 (SEQ ID NO:100) is the
representative sequence. CS092, having the nucleotide sequence set forth in
SEQ ID
NO: 100 and encoding the full-length and mature polypeptides set forth in SEQ
ID
NOS: 101 and 102, was isolated from Tulipa fosteriana. CS094 (SEQ ID NO:97),
CS093 (SEQ ID NO:103), and CS099 (SEQ ID NO:106) encode full length
polypeptides having the amino acid sequences set forth in SEQ ID NOS:98, 104,
and
107, which when processed yield mature polypeptides having the amino acid
sequences set forth in SEQ ID NOS:99, 105, and 108, respectively.
Group 12 comprises two Tulipa gesneriana sequences of which CS097 (SEQ
ID NO:112) is the representative sequence. CS 102 (SEQ ID NO:109) and CS097
(SEQ ID NO: 112) encode full length polypeptides having the amino acid
sequences
set forth in SEQ ID NOS: 110 and 113, which when processed yield mature
polypeptides having the amino acid sequences set forth in SEQ ID NOS: 111 and
114,
respectively.
Group 13 comprises two Tulipa gesneriana sequences of which CS 101 (SEQ
ID NO: 115) is the representative sequence. CS 101 (SEQ ID NO: 115) and CS 154
(SEQ ID NO: 118) encode full length polypeptides having the amino acid
sequences
set forth in SEQ ID NOS: 116 and 119, which when processed yield mature
polypeptides having the amino acid sequences set forth in SEQ ID NOS:117 and
120,
respectively.
Group 14 comprises two Monzordica charantia sequences of which CS 104
(SEQ ID NO:121) is the representative sequence. CS 104 (SEQ ID NO:121) and
CS 105 (SEQ ID NO:124) encode full length polypeptides having the amino acid
sequences set forth in SEQ ID NOS:122 and 125, which when processed yield
mature
polypeptides having the amino acid sequences set forth in SEQ ID NOS: 123 and
126,
respectively.
Group 15 comprises two Nicotiazza benthamiana sequences of which CS 112
(SEQ ID NO:127) is the representative sequence. CS 112 (SEQ ID NO:127) and
CS 166 (SEQ ID NO: 130) encode full length polypeptides having the amino acid
sequences set forth in SEQ ID NOS: 128 and 131, which when processed yield
mature
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polypeptides having the amino acid sequences set forth in SEQ ID NOS:129 and
132,
respectively.
Group 16 comprises two sequences of which CS 128 (SEQ ID NO:133) is the
representative sequence. CS128 (SEQ IDNO:133) and CS153 (SEQ IDNO:136)
encode full length polypeptides having the amino acid sequences set forth in
SEQ ID
NOS: 134 and 137, which when processed yield mature polypeptides having the
amino
acid sequences set forth in SEQ ID NOS:135 and 138, respectively. CS128 was
isolated from Tulipa fosteriana, and CS 153 was isolated from Tulipa
gesneriana.
Group 17 comprises 24 Taraxacuin kok-saghyz sequences of which CS 130
(SEQ IDNO:142) is the representative sequence. CS 129 (SEQ IDNO:139), CS 130
(SEQ ID NO:142), CS131 (SEQ ID NO:145), CS132 (SEQ ID NO:148), CS133
(SEQ ID NO:151), CS 134 (SEQ ID NO:154), CS 135 (SEQ ID NO:157), CS 136
(SEQ ID NO:160), CS 137 (SEQ ID NO:163), CS 138 (SEQ ID NO:166), CS 139
(SEQ ID NO:169), CS 140 (SEQ ID NO: 172), CS 141 (SEQ ED NO: 175), CS 142
(SEQ ID NO:178), CS 143 (SEQ ID NO:181), CS 144 (SEQ ID NO: 184), CS 145
(SEQ ID NO:187), CS 146 (SEQ ID NO:190), CS 147 (SEQ ID NO:193), CS 148
(SEQ ID NO:196), CS 149.(SEQ ID NO:199), CS150 (SEQ ID NO:202), CS 151
(SEQ ID NO:205), and CS 152 (SEQ ID NO:208) encode full length polypeptides
having the amino acid sequences set forth in SEQ ID NOS:140, 143, 146, 149,
152,
155, 158, 161, 164, 167, 170, 173, 176, 179, 182, 185, 188, 191, 194, 197,
200, 203,
206, and 209, which when processed yield mature polypeptides having the amino
acid sequences set forth in SEQ ID NOS:141, 144, 147, 150, 153, 156, 159, 162,
165,
168, 171, 174, 177, 180, 183, 186, 189, 192, 195, 198, 201, 204, 207, and 210,
respectively.
Group 18 comprises five Picraninia pentandra sequences of which CS 161
(SEQ ID NO:21 1) is the representative sequence. CS 161 (SEQ ID NO:21 1), CS
164
(SEQ ID NO:214), CS 160 (SEQ ID NO:217), CS 162 (SEQ ID NO:220), and CS 163
(SEQ ID NO:223) encode full length polypeptides having the amino acid
sequences
set forth in SEQ ID NOS:212, 215, 218, 221, and 224, which when processed
yield
mature polypeptides having the amino acid sequences set forth in SEQ ID
NOS:213,
216, 219, 222, and 225, respectively.
Group 19 comprises three Nicotiana benthanziana sequences of which CS 165
(SEQ ID NO:226) is the representative sequence. CS 165(SEQ ID NO:226), CS 168
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(SEQ ID NO:229), and CS 169 (SEQ ID NO:232) encode full length polypeptides
having the amino acid sequences set forth in SEQ ID NOS:227, 230, and 233,
which
when processed yield mature polypeptides having the amino acid sequences set
forth
in SEQ ID NOS:228, 231, and 234, respectively.
Group 20 comprises CS003 (SEQ ID NO:235, PDF3), a maize gene. The full
length CS003 polypeptide (SEQ ID NO:236) is expected to have a signal peptide,
thus
the mature protein (SEQ ID NO:237) is likely to be secreted or extracellular.
Group 21 comprises CS007 (SEQ ID NO:238, PDF7), a maize gene. PDF7 is
likely to be expressed in a kernel-specific or kernel-preferred expression
pattern. The
full length CS007 polypeptide (SEQ ID NO:239) is expected to have a signal
peptide,
thus the mature protein (SEQ ID NO:240) would be extracellular.
Group 22 comprises CS008 (SEQ ID NO:241, PDF8), a maize gene. PDFB is
expressed in a kernel-preferred expression pattern. The full length CS008
polypeptide
(SEQ ID NO:242) is expected to have a signal peptide, thus the mature protein
(SEQ
ID NO:243) would be extracellular. PDF8 may be secreted.
Group 23 comprises CS009 (SEQ ID NO:244, PDF9), a maize gene. PDF9 is
expressed in a kernel-preferred pattern, particularly an endosperm- and
pericarp-
preferred expression pattern. The full length CS009 polypeptide (SEQ ID
NO:245)
includes a predicted transit peptide, thus the mature protein (SEQ ID NO:246)
would
be extracellular.
Group 24 comprises CSOIO (SEQ ID NO:247, PDFIO), a maize gene. The
full length CSOIO polypeptide (SEQ ID NO:248) is expected to have a signal
peptide,
thus the mature protein (SEQ ID NO:249) is likely to be secreted or
extracellular.
Expression appears to be kernel-specific or kernel-preferred.
Group 25 comprises CS014 (SEQ ID NO:250, PDF14), a maize gene. PDF14
is expressed in a tassel-preferred manner. The full length CS014 polypeptide
(SEQ
ID NO:25 1) appears to include a signal peptide, thus the mature protein (SEQ
ID
NO:252) would be secreted.
Group 26 comprises CS016 (SEQ ID NO:253, PDF16), a maize gene. The
PDF16 nucleotide sequence appears to be expressed preferentially in the
kernel,
particularly in the endosperm and scutellum. The full length CSO16 polypeptide
(SEQ ID NO:254) is predicted to have a signal peptide ending at amino acid
position
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22, thus the mature protein (SEQ ID NO:255) is likely to be an extracellular
polypeptide.
Group 27 comprises CS019 (SEQ ID NO:256, PDF19), a maize gene.
Expression of the sequence appears to be kernel-preferred. The protein is
likely
extracellular as the full length CS019 polypeptide (SEQ ID NO:257) contains a
signal
peptide, thus the mature protein (SEQ ID NO:258) appears to be secreted or
extracellular.
Group 28 comprises CS020 (SEQ ID NO:259, PDF20), a maize gene.
Expression of PDF20 appears to be kernel-preferred. The predicted protein
appears to
be extracellular as it has a predicted signal peptide. The full length CS020
polypeptide (SEQ ID NO:260) is expected to have a signal peptide, thus the
mature
protein (SEQ ID NO:261) is likely to be secreted or extracellular.
Group 29 comprises CS043 (SEQ ID NO:262), a Triticuin aestivum sequence.
This nucleotide sequence encodes a full length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:263, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:264.
Group 30 comprises CS045 (SEQ ID NO:265), a Triticumi aestivum sequence.
This nucleotide sequence encodes a full length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:266, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:267.
Group 31 comprises CS046 (SEQ ID NO:268), a Triticum aestivum sequence,
This nucleotide sequence encodes a full length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:269, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:270.
Group 32 comprises CS048 (SEQ ID NO:271), a Triticun: aestivum sequence.
This nucleotide sequence encodes a full length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:272, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:273.
Group 33 comprises CS049 (SEQ ID NO:274), a Triticum aestivum sequence.
This nucleotide sequence encodes a full length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:275, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:276.
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Group 34 comprises CS060 (SEQ ID NO:277), a Triticum aestivuna sequence.
This nucleotide sequence encodes a full length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:278, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:279.
Group 35 comprises CS061 (SEQ ID NO:280), a Triticum aestivum sequence.
This nucleotide sequence encodes a full length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:28 1, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:282.
Group 36 comprises CS068 (SEQ ID NO:283), a Triticum aestivum sequence.
This nucleotide sequence encodes a full length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:284, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:285.
Group 37 comprises CS071 (SEQ ID NO:286), a Triticum aestivuin sequence.
This nucleotide sequence encodes a full length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:287, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:288.
Group 38 comprises CS072 (SEQ ID NO:289), a Triticum aestivuna sequence.
This nucleotide sequence encodes a full length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:290, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:291.
Group 39 comprises CS076 (SEQ ID NO:292), a Beta vulgaris sequence. This
nucleotide sequence encodes a full length polypeptide having the amino acid
sequence set forth in SEQ ID NO:293, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:294.
Group 40 comprises CS085 (SEQ ID NO:295), a Hedera helix sequence. This
nucleotide sequence encodes a full length polypeptide having the amino acid
sequence set forth in SEQ ID NO:296, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:297.
Group 41 comprises CS103 (SEQ ID NO:298), a Tulipa gesneriana sequence.
This nucleotide sequence encodes a full length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:299, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:300.
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Group 42 comprises CS124 (SEQ ID NO:301), an Amaranthus retroflexus
sequence. This nucleotide sequence encodes a full length polypeptide having
the
amino acid sequence set forth in SEQ ID NO:302, which when processed yields a
mature polypeptide having the amino acid sequence set forth in SEQ ID NO:303.
Group 43 comprises CS 159 (SEQ ID NO:304), an Allium pormnin sequence.
This nucleotide sequence encodes a full length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:305, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:306.
Group 44 comprises CS 113 (SEQ ID NO:307), a Nicotiana benthanziana
sequence. This nucleotide sequence encodes a full length polypeptide having
the
amino acid sequence set forth in SEQ ID NO:308, which when processed yields a
mature polypeptide having the amino acid sequence set forth in SEQ ID NO:309.
Group 45 comprises CS095 (SEQ ID NO:310), a Tulipa gesneriana sequence.
This nucleotide sequence encodes a full length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:31 1, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:312.
Group 46 comprises CS077 (SEQ ID NO:313), a Beta vulgaris sequence. This
nucleotide sequence encodes a full length polypeptide having the amino acid
sequence set forth in SEQ ID NO:314, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:315.
Group 47 comprises three Cymnopsis tetragonoloba sequences of which
CS 108 (SEQ ID NO:316) is the representative sequence. CS 108(SEQ ID NO:316),
CS 156 (SEQ ID NO:319), and CS 157 (SEQ ID NO:322) encode full length
polypeptides having the amino acid sequences set forth in SEQ ID NOS:317, 320,
and
323, which when processed yield mature polypeptides having the amino acid
sequences set forth in SEQ ID NOS:318, 321, and 324, respectively.
Group 48 comprises three sequences of which CS005 (SEQ ID NO:325,
PDF5) is the representative sequence. CSOOS was isolated from Zea mays. The
PDFS
expression pattern suggests fairly wide-distribution of expression. However,
there is
strong representation of CSOO5 in endosperms and embryos of kernels. The
mature
peptide appears to be extracellular, as a signal peptide is included in the
sequence.
CS005 (SEQ ID NO:325), CS042 (SEQ ID NO:328) and CS067 (SEQ ID NO:33 1)
encode full length polypeptides having the amino acid sequences set forth in
SEQ ID
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NOS:326, 329, and 332, which when processed yield mature polypeptides having
the
amino acid sequences set forth in SEQ ID NOS:327, 330, and 333, respectively.
CS042 and CS067 were isolated from Triticurn aestivum.
Group 49 comprises four sequences of which CS053 (SEQ ID NO:337) is the
representative sequence. CS 100 (SEQ ID NO:334), CS053 (SEQ ID NO:337), CS064
(SEQ ID NO:340), and CS096 (SEQ ID NO:343) encode full length polypeptides
having the amino acid sequences set forth in SEQ ID NOS:335, 338, 341, and
344,
which when processed yield mature polypeptides having the amino acid sequences
set
forth in SEQ ID NOS:336, 339, 342, and 345, respectively. CS100 and CS096 were
isolated from Tulipa gesneriana. CS053 and CS064 were isolated from Triticurn
aestivum.
Group 50 comprises CS036 (SEQ ID NO:346), a Glycine max sequence. This
nucleotide sequence encodes a full length polypeptide having the amino acid
sequence set forth in SEQ ID NO:347, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:348.
Group Si comprises CS 125 (SEQ ID NO:349), a Brassica napus sequence.
This nucleotide sequence encodes a full length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:350, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:351.
Group 52 comprises CS056 (SEQ ID NO:352), a Triticurn aestivum sequence.
This nucleotide sequence encodes a full length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:353, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO,_35.
Group 53 comprises CS047 (SEQ ID NO:355), a Triticurn aestivum sequence.
This nucleotide sequence encodes a full length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:356, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:357.
Group 54 comprises CS021 (SEQ ID NO:358, PDF21), a Zea mays sequence.
PDF21 may be predominately expressed in the kernel. The sequence appears to be
extracellular as it includes a signal peptide. This nucleotide sequence
encodes a full
length polypeptide having the amino acid sequence set forth in SEQ ID NO:359,
which when processed yields a mature polypeptide having the amino acid
sequence
set forth in SEQ ID NO:360.
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Group 55 comprises CS122 (SEQ ID NO:361), a Vernonia mespilifolia
sequence. This nucleotide sequence encodes a full length polypeptide having
the
amino acid sequence set forth in SEQ ID NO:362, which when processed yields a
mature polypeptide having the amino acid sequence set forth in SEQ ID NO:363.
Group 56 comprises CS 111 (SEQ ID NO:364), a Picramnia pentandra
sequence. This nucleotide sequence encodes a full length polypeptide having
the
amino acid sequence set forth in SEQ ID NO:365, which when processed yields a
mature polypeptide having the amino acid sequence set forth in SEQ ID NO:366.
Group 57 comprises CS171 (SEQ ID NO:367), a Vernonia mespilifolia
sequence. This nucleotide sequence encodes a full length polypeptide having
the
amino acid sequence set forth in SEQ ID NO:368, which when processed yields a
mature polypeptide having the amino acid sequence set forth in SEQ ID NO:369.
Group 58 comprises CS 172 (SEQ ID NO:370), a Vernonia mespilifolia
sequence. This nucleotide sequence encodes a full length polypeptide having
the
amino acid sequence set forth in SEQ ID NO:371, which when processed yields a
mature polypeptide having the amino acid sequence set forth in SEQ ID NO:372.
Group 59 comprises CS030 (SEQ ID NO:373), an Oryza sativa sequence.
This nucleotide sequence encodes a full length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:374, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:375.
Group 60 comprises CS088 (SEQ ID NO:376), a Parthenium argentaturn
sequence. This nucleotide sequence encodes a full length polypeptide having
the
amino acid sequence set forth in SEQ ID NO:377, which when processed yields a
mature polypeptide having the amino acid sequence set forth in SEQ ID NO:378.
Group 61 comprises CS107 (SEQ ID NO:379), a Cyanzopsis tetragonoloba
sequence. This nucleotide sequence encodes a full length polypeptide having
the
amino acid sequence set forth in SEQ ID NO:380, which when processed yields a
mature polypeptide having the amino acid sequence set forth in SEQ ID NO:381.
Group 62 comprises CS058 (SEQ ID NO:382), a Triticum aestivun: sequence.
This nucleotide sequence encodes a full length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:383, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:384.
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Group 63 comprises CS037 (SEQ ID NO:385), a Glycine max sequence. This
nucleotide sequence encodes a full length polypeptide having the amino acid
sequence set forth in SEQ ID NO:386, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:387.
Group 64 comprises two sequences of which CS082 (SEQ ID NO:391) is the
representative sequence. CS086 (SEQ ID NO:388) and CS082 (SEQ ID NO:391)
encode full length polypeptides having the amino acid sequences set forth in
SEQ ID
.NOS:389 and 392, which when processed yield mature polypeptides having the
amino
acid sequences set forth in SEQ ID NOS:390 and 393, respectively. CS086 was
isolated from Licania inichauxii, and CS082 was isolated from Chiysobalanus
icaco.
Group 65 comprises CS081 (SEQ ID NO:394), a Ricinus connnunis sequence.
This nucleotide sequence encodes a full length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:395, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:396.
Group 66 comprises two Vernonia mespilifolia sequences of which CS 121
(SEQ ID NO:400) is the representative sequence. CS123 (SEQ ID NO:397) and
CS 121 (SEQ ID NO:400) encode full length polypeptides having the amino acid
sequences set forth in SEQ ID NOS:398 and 401, which when processed yield
mature
polypeptides having the amino acid sequences set forth in SEQ ID NOS:399 and
402,
respectively.
Group 67 comprises CS080 (SEQ ID NO:403), a Ricinus communis sequence.
This nucleotide sequence encodes a full length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:404, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:405.
Group 68 comprises two sequences of which CS083 (SEQ ID NO:406) is the
representative sequence. CS083 (SEQ ID NO:406) and CS087 (SEQ ID NO:409)
encode full length polypeptides having the amino acid sequences set forth in
SEQ ID
NOS:407 and 410, which when processed yield mature polypeptides having the
amino
acid sequences set forth in SEQ ID NOS:408 and 411, respectively. CS083 was
isolated from Eucalyptus grandis, and CS087 was isolated from Tropaeolum
majus.
Group 69 comprises CS 155 (SEQ ID NO:412), a Cyamopsis tetragonoloba
sequence. This nucleotide sequence encodes a full length polypeptide having
the
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amino acid sequence set forth in SEQ ID NO:413, which when processed yields a
mature polypeptide having the amino acid sequence set forth in-SEQ ID NO:414.
Group 70 comprises three Vitis vinifera sequences of which CS 117 (SEQ ID
NO:421) is the representative sequence. CS l 19 (SEQ IDNO:415), CS 116 (SEQ ID
NO:418), and CS 117 (SEQ ID NO:421) encode full length polypeptides having the
amino acid sequences set forth in SEQ ID NOS:416, 419, and 422, which when
processed yield mature polypeptides having the amino acid sequences set forth
in
SEQ ID NOS:417, 420, and 423, respectively.
Group 71 comprises CS 126 (SEQ ID NO:424), a Eucalyptus grandis
sequence. This nucleotide sequence encodes a full length polypeptide having
the
amino acid sequence set forth in SEQ ID NO:425, which when processed yields a
mature polypeptide having the amino acid sequence set forth in SEQ ID NO:426.
Group 72 comprises CS109 (SEQ ID NO:427), a Cyamopsis tetragonoloba
sequence. This nucleotide sequence encodes a full length polypeptide having
the
amino acid sequence set forth in SEQ ID NO:428, which when processed yields a
mature polypeptide having the amino acid sequence set forth in SEQ ID NO:429.
Group 73 comprises CS 115 (SEQ ID NO:430), a Nicotiana benthamiana
sequence. This nucleotide sequence encodes a full length polypeptide having
the
amino acid sequence set forth in SEQ ID NO:43 1, which when processed yields a
mature polypeptide having the amino acid sequence set forth in SEQ ID NO:432.
Group 74 comprises CS089 (SEQ ID NO:433), a Parthenium argentatuin
sequence. This nucleotide sequence encodes a full length polypeptide having
the
amino acid sequence set forth in SEQ ID NO:434, which when processed yields a
mature polypeptide having the amino acid sequence set forth in SEQ ID NO-435.
Group 75 comprises CS110 (SEQ IT) NO:436), a Cyamopsis tetragonoloba
sequence. This nucleotide sequence encodes .a full length polypeptide hay ing
the
amino acid sequence set forth in SEQ ID NO:437, which when processed yields a
mature polypeptide having the amino acid sequence set forth in SEQ_ID NO:438.
Group 76 comprises CS158 (SEQ ID NO:439), a Cyamopsis tetragonoloba
sequence. This nucleotide sequence encodes a full length polypeptide having
the
amino acid sequence set forth in SEQ ID NO:440, which when processed yields a
mature polypeptide having the amino acid sequence set forth in SEQ ID NO:44 1.
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Group 77 comprises CS 127 (SEQ ID NO:442), a Licania ,nichauaii sequence.
This nucleotide sequence encodes a full length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:443, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:444.
Group 78 comprises two Vitis vinifera. sequences of which CS 118 (SEQ ID
NO:445) is the representative sequence. CSI 18 (SEQ IDNO:445) and CS170 (SEQ
ID NO:448) encode full length polypeptides having the amino acid sequences set
forth in SEQ ID NOS:446 and 449, which when processed yield mature
polypeptides
having the amino acid sequences set forth in SEQ ID NOS:447 and 450,
respectively.
Group 79 comprises CS090 (SEQ ID NO:45 1), an Arachis hypogaea
sequence. This nucleotide sequence encodes a full length polypeptide having
the
amino acid sequence set forth in SEQ ID NO:452, which when processed yields a
mature polypeptide having the amino acid sequence set forth in SEQ ID NO:453.
Group 80 comprises CS075 (SEQ ID NO:454), aBrassica napus. sequence.
This nucleotide sequence encodes a full length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:455, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:456.
Group 81 comprises CSO11 (SEQ ID NO:457, PDF11), a Zea mays sequence.
This nucleotide sequence encodes a full length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:458, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:459. PDF11
expression seems to be tassel-preferred. The mature peptide may be secreted or
exiracellular as the sequence includes a signal peptide.
Group 82 comprises CS012 (SEQ ID NO:460, PDF12), a Zea mays sequence:
This nucleotide sequence encodes a full length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:461, which when processed yields a mature
polypeptide having the amino acid sequence set forth in SEQ ID NO:462. The
sequence maybe preferentially expressed in kernels. PDF12 encodes a signal
peptide, and thus would be secreted.
Group 83 comprises CS002 (SEQ ID NO:463, PDF2), a Zea mays sequence.
This nucleotide sequence encodes a full-length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:464. PDF2 is expressed in a kernel-preferred
pattern.
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Group 84 comprises CS015 (SEQ ID NO:465, PDFI5), a Zea mays sequence.
This nucleotide sequence encodes a full-length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:466. PDF15 is preferentially expressed in
kernels.
The Zm-PDF15 sequence differs from Zm-ES-4 (Cordts et al. (2001) Plant J.
25:103-
114) by one amino acid residue. The gene appears to encode an extracellularly
localized protein as there is a signal peptide.
Group 85 comprises CS001 (SEQ ID NO:467, PDF1), a Zea mays sequence.
This nucleotide sequence encodes a full-length polypeptide having the amino
acid
sequence set forth in SEQ ID NO:468. Zm-PDF1 is predicted to be an
extracellular
protein.
The invention encompasses isolated or substantially purified nucleic acid or
protein compositions. An "isolated" or "purified" nucleic acid molecule or
protein, or
biologically active portion thereof, is substantially or essentially free from
components that normally accompany or interact with the nucleic acid molecule
or
protein as found in its naturally occurring environment. Thus, an isolated or
purified
nucleic acid molecule or protein is substantially free of other cellular
material, or
culture medium when produced by recombinant techniques, or substantially free
of
chemical precursors or other chemicals when chemically synthesized.
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 example, in various embodiments, the isolated nucleic acid
molecule 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 protein that is substantially free
of cellular
material includes preparations of protein having less than about 30%, 20%,
10%, 5%,
or I% (by dry weight) of contaminating protein. When the protein of the
invention or
biologically active portion thereof is recombinantly produced, preferably
culture
medium represents less than about 30%, 20%, 10%, 5%, or 1% (by dry weight) of
chemical precursors or non-protein-of-interest chemicals.
Fragments and variants of the disclosed nucleotide sequences and proteins
encoded thereby are also encompassed by the present invention. By "fragment"
is
intended a portion of the nucleotide sequence or a portion of the amino acid
sequence
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and hence protein encoded thereby. Fragments of a nucleotide sequence may
encode
protein fragments that retain the biological activity of the native protein
and hence
have defensin-like activity and thereby affect development, developmental
pathways,
and defense responses. Alternatively, fragments of a nucleotide sequence that
are
useful as hybridization probes generally do not encode fragment proteins
retaining
biological activity. Thus, fragments of a nucleotide sequence may range from
at least
about 20 nucleotides, about 50 nucleotides, about 100 nucleotides, and up to
the full-
length nucleotide sequence encoding the proteins of the invention.
A fragment of a defensin nucleotide sequence that encodes a biologically
active portion of a defensin protein of the invention will encode at least 15,
25, 30, 50,
100, 150, 153, 200, 250, 300 contiguous amino acids, or up to the total number
of
amino acids present in a full-length protein of the invention. Fragments of a
defensin
nucleotide sequence that are useful as hybridization probes for PCR primers
generally
need not encode a biologically active portion of a defensin protein.
Thus, a fragment of a defensin nucleotide sequence may encode a biologically
active portion of a defensin protein, or it may be a fragment that can be used
as a
hybridization probe or PCR primer using methods disclosed below. A
biologically
active portion of a defensin protein can be prepared by isolating a portion of
one of
the defensin nucleotide sequences of the invention, expressing the encoded
portion of
the defensin protein (e.g., by recombinant expression in vitro), and assessing
the
activity of the encoded portion of the defensin protein. Nucleic acid
molecules that
are fragments of a defensin nucleotide sequence comprise at least 16, 20, 50,
75, 100,
150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 683, 700, 800, or 900
nucleotides, or up to the number of nucleotides present in a full-length
defensin
nucleotide sequence disclosed herein By "variants" substantially similar
sequences are
intended. For nucleotide sequences, conservative variants include those
sequences
that, because of the degeneracy of the genetic code, encode the amino acid
sequence
of one of the defensin polypeptides of the invention. Naturally occurring
allelic
variants such as these can be identified with the use of well-known molecular
biology
techniques, as, for example, with polymerase chain reaction (PCR) and
hybridization
techniques as outlined below. Variant nucleotide sequences also include
synthetically
derived nucleotide sequences, such as those generated, for example, by using
site-
.directed mutagenesis but which still encode a defensin protein of the
invention.
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Generally, variants of a particular nucleotide sequence of the invention will
have at
least about 50%, 60%, 65%, 70%, generally at least about 75%, 80%, 85%,
preferably
at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, and more preferably at
least about 98%, 99% or more sequence identity to that particular nucleotide
sequence
as determined by sequence alignment programs described elsewhere herein using
default parameters.
By "variant protein" a protein derived from the native protein by deletion (so-
called truncation) or addition of one or more amino acids to the N-terminal
and/or C-
terminal end of the native protein; deletion or addition of one or more amino
acids at
one or more sites in the native protein; or substitution of one or more amino
acids at
one or more sites in the native protein is intended. 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, defensin-like
activity as
described herein. Such variants may result front, for example, genetic
polymorphism
or from human manipulation. Biologically active variants of a native defcusin
protein
of the invention will have at least about 40%, 50%, 60%, 65%, 70%, generally
at least
about 75%, 80%, 85%, preferably at least about 90%, 91%, 92%, 93%, 94%, 95%,
96%, 97%, and more preferably at least about 98%, 99% or more sequence
identity to
the amino acid sequence for the native protein as determined by sequence
alignment
programs described elsewhere herein using default parameters. A biologically
active
variant of a protein of the invention may differ from that protein by as few
as 1-15
amino acid residues, as few as 1-10, such as 6-10, as few as 5, as few as 4,
3, 2, or
even 1 amino acid residue.
Biological activity of the defensin polypeptides (i.e.,.influencing the plant
defense response and various developmental pathways, including, for example,
influencing cell division) can be assayed by any method known in the art.
Biological
activity of the polypeptides of the present invention can be assayed by any
method
known in the art (see for example, U.S. Patent No. 5,614,395; Thomma et al.
(1998)
Plant Biology 95:15107-15111; Liu et al. (1994) Plant Biology 91:1888-1892; Hu
et
al. (1997) Plant Mol_ Biol. 34:949-959; Cammue et al. (1992) J. Biol. Chem.
267:2228-2233; and Thevissen et al. (1996) J. Biol. Client. 271:15018-15025).
Furthermore, assays to detect defensin-
like activity include, for example, assessing antifungal and/or antimicrobial
activity
23
CA 02724158 2010-12-01
75529-69
(Terras et at. (1992) J. Biol. Chent. 267:14301-15309; Terras et al. (1993)
Plant
Physiol (Bethesda) 103:1311-1319; Terras et al. (1995) Plant Cell 7:573-588,
Moreno
et at. (1994) Eur. J. Biochem. 223:135-139; and Osborn et al. (1995) FEBSLett.
368:257-262).
The polypeptides of the invention may be altered in various ways including
amino acid substitutions, deletions, truncations, and insertions. Novel
proteins having
properties of interest may be created by combining elements and fragments of
proteins of the present invention as well as other proteins. Methods for such
manipulations are generally known in the art. For example, amino acid sequence
variants of the defensin proteins can be prepared by mutations in the DNA.
Methods
for mutagenesis and nucleotide sequence alterations are well known in the art.
See,
for example, Kunkel (1985) Proc. Natl. Acad. Sci. USA 82:488-492; Kunkel et
al.
(1987) Methods in Enzymol. 154:367-382; U.S. Patent No. 4,873,192; Walker and
Cra.astra, eds. (1983) Teclwiques in Molecular Biology (Macmillan. Publishing
Company, New York) and the references cited therein. Guidance as to
appropriate
amino acid substitutions that do not affect biological activity of the protein
of interest
may be found in the model of Dayhoff et al. (1978) Atlas of Protein Sequence
and
Structure (Natl. Biomed. Res. Found, Washington, D.C.Y.
Conservative substitutions, such as exchanging one amino acid with
another having similar properties, may be preferred.
Thus, the genes and nucleotide sequences of the invention include both the
naturally occurring sequences as well as mutant forms. Likewise, the proteins
of the
invention encompass naturally occurring proteins as well as variations and
modified
forms thereof Such variants will continue to possess the desired developmental
activity, or defense response activity. Obviously, the mutations that will be
made in
the DNA encoding the variant must not place the sequence out of reading frame
and
preferably will not create complementary regions that could produce secondary
mRNA structure. See, EP Patent Application Publication No. 75,444.
The deletions, insertions, and substitutions of the protein sequences
encompassed herein are not expected to produce radical changes in the
characteristics
of the protein- However, when it is difficult to predict the exact effect of
the
substitution, deletion, or insertion in advance of doing so, one skilled in
the art will
appreciate that the effect will be evaluated by routine screening assays. That
is, the
24
CA 02724158 2010-12-01
.5529-69
activity can be evaluated by defensin activity assays. See, for example,
Lancaster et
a!. (1994) 1 Biol. Chem. 14:1137-1142 and Terras et al. (1995) Plant Cell
7:537-588.
Additionally, differences in the expression of
specific genes between uninfected and infected plants can be determined using
gene
expression profiling. RNA was analyzed using the gene expression profiling
process
(GeneCalling(b) as described in U.S. Patent No. 5,871,697.
Variant nucleotide sequences and proteins also encompass sequences and
proteins derived from a mutagenic and recombinogenic procedure such as DNA
shuffling. With such a procedure, one or more different defensin coding
sequences
can be manipulated to create a new defensin 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.
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) 1
Mol.
Biol. 272:336-347; Zhaug et a!. (1997) Proc. Nat!. Acad. Sci. USA 94:4504-
4509;
Crameri et al. (1998) Nature 391:288-291; and U.S. Patent Nos. 5,605,793 and
5,837,458.
The nucleotide sequences of the invention can be used to isolate
corresponding sequences from other organisms, particularly other plants. In
this
manner, methods such as PCR, hybridization, and the like can be used to
identify such
sequences based on their sequence homology to the sequences set forth herein.
Sequences isolated based on their sequence identity to the entire defensin
sequences
set forth herein or to fragments thereof are encompassed by the present
invention.
Such sequences include sequences that are orthologs of the disclosed
sequences. By
"orthologs" genes derived from a common ancestral gene and which are found in
different species as a result of speciation is intended. Genes found in
different species
are considered orthologs when their nucleotide sequences and/or their encoded
protein
sequences share substantial identity as defined elsewhere herein. Functions of
orthologs are often highly conserved among species. Thus, isolated sequences
that
encode a defensin and which hybridize under stringent conditions to the
defensin
CA 02724158 2010-12-01
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sequences disclosed herein, or to fragments thereof, are encompassed by the
present
invention.
In a PCR approach, oligonucleotide primers can be designed for use in PCR
reactions to amplify corresponding DNA sequences from eDNA or genomic DNA
extracted from any plant of interest. Methods for designing PCR primers and
PCR
cloning are generally known in the art and are disclosed in Sambrook et al.
(1989)
Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory
Press, Plainview, New York). See also Innis et al., eds. (1990) PCR Protocols:
A
Guide to Methods aid Applications (Academic Press, New York); Innis and
Gelfand,
eds. (1995) PCR Strategies (Academic Press, New York); and Innis and Gelfand,
eds.
(1999) PCR Methods Manual (Academic Press, New York). Known methods of PCR
include, but are not limited to, methods using paired primers, nested primers,
single
specific primers, degenerate primers, gene-specific primers, vector-specific
primers,
partially-mismatched primers, and the like.
In hybridization techniques, all or part of a known nucleotide sequence is
used
as a probe that` selectively hybridizes to other corresponding nucleoti de
sequences
present in a population of cloned genomic DNA fragments or cDNA fragments
(i.e.,
genomic or eDNA libraries) from a chosen organism. The hybridization probes
may
be genomic DNA fragments, eDNA fragments, RNA fragments, or other
oligonucleotides, and may be labeled with a detectable group such as 32P, or
any other
detectable marker. Thus, for example, probes for hybridization can be made by
labeling synthetic oligonucleotides based on the defensin sequences of the
invention.
Methods for preparation of probes for hybridization and for construction of
eDNA
and genomic libraries are generally known in the art and are disclosed in
Sambrook et
al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor
Laboratory Press, Plainview, New York).
For example, an entire defensin sequence disclosed herein, or one or more
portions thereof, may be used as a probe capable of specifically hybridizing
to
corresponding defensin sequences and messenger RNAs. To achieve specific
hybridization under a variety of conditions, such probes include sequences
that are
unique among defensin sequences and are preferably at least about 10
nucleotides in
length, and most preferably at least about 20 nucleotides in length. Such
probes may
be used to amplify corresponding sequences from a chosen organism by PCR. This
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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, Plainview, New York).
Hybridization of such sequences may be carried out under stringent
conditions. By "stringent conditions" or "stringent hybridization conditions"
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)
is
intended. 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 IX to 2X SSC (20X SSC =
3.0
M NaCI/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 0.5X to 1X 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 O.1X 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.
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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. Biochenz. 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. T,, 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 T,,,, 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 T. 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 1, 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, Plainview, New York).
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Thus, isolated sequences that encode a defensin polypeptide and which
hybridize under stringent conditions to the defensin sequences disclosed
herein, or to
fragments thereof, are encompassed by the present invention.
The following terms are used to describe the sequence relationships between
two or more nucleic acids or polynucleotides: (a) "reference sequence", (b)
"comparison window", (c) "sequence identity", (d) "percentage of sequence
identity",
and (e) "substantial identity".
(a) As used herein, "reference sequence" is a defined sequence used as a
basis for sequence comparison. A reference sequence may be a subset or the
entirety
of a specified sequence; for example, as a segment of a full-length,cDNA or
gene
sequence, or the complete cDNA or gene sequence.
(b) As used herein, "comparison window" makes reference to a contiguous
and specified segment of a polynucleotide sequence, wherein the polynucleotide
sequence in the comparison window may comprise additions or deletions (i.e.,
gaps)
compared to the reference sequence (which does not comprise additions or
deletions)
for optimal alignment of the two sequences. Generally, the comparison window
is at
least 20 contiguous nucleotides in length, and optionally can be 30, 40, 50,
100, or '`
longer. Those of skill in the art understand that to avoid a high similarity
to a
reference sequence due to inclusion of gaps in the polynucleotide sequence a
gap
penalty is typically introduced and is subtracted from the number of matches.
Methods of alignment of sequences for comparison are well known in the art.
Thus, the determination of percent identity between any two sequences can be
accomplished using a mathematical algorithm Non-limiting examples of such
mathematical algorithms are the algorithm of Myers and Miller (1988) CABIOS
4:11-
17; the local homology algorithm of Smith et al. (1981) Adv. Appl. Math.
2:482; the
homology alignment algorithm of Needleman and Wunsch (1970) J Mol. Biol.
48:443-453; the search-for-similarity-method of Pearson and Lipman (1988)
Proc.
Natl. Acad. Sci. 85:2444-2448; 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.
Computer implementations of these mathematical algorithms can be utilized
for comparison of sequences to determine sequence identity. Such
implementations
include, but are not limited to: CLUSTAL in the PC/Gene program (available
from
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CA 02724158 2010-12-01
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Intelligenetics, Mountain View, California); the ALIGN program (Version 2.0)
and
GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software
Package, Version 8 (available from Genetics Computer Group (GCG), 575 Science
Drive, Madison, Wisconsin, USA). Alignments using these programs can be
performed using the default parameters. The CLUSTAL program is well described
by
Higgins et al. (1988) Gene 73:237-244 (1988); Higgins et al. (1989) CABIOS
5:151-
153; Corpet et al. (1988) Nucleic Acids Res. 16:10881-90; Huang et al. (1992)
CABIOS 8:155-65; and Pearson et al. (1994) Meth. Mol. Biol. 24:307-331. The
ALIGN program is based on the algorithm of Myers and Miller (1988) supra. A
PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of
4 can
be used with the ALIGN program when comparing amino acid sequences. The
BLAST programs of Altschul et al. (1990) J. Mol. Biol. 215:403 are based on
the
algorithm of Karlin and Altschul (1990) supra. BLAST nucleotide searches can
be
performed with the BLASTN program, score - 100, wordlength ~ 12, to obtain
nucleotide sequences homologous to a nucleotide sequence encoding a protein of
the
invention. BLAST protein searches can be performed with the BLASTX program,
score = 50, wordlength = 3, to obtain amino acid sequences homologous to a
protein
or polypeptide 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 (in BLAST 2.0)
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,
PSI-BLAST, the default parameters of the respective programs (e.g., BLASTN for
nucleotide sequences, BLASTX for proteins) can be used. See
the NCBI website. Alignment may also be performed manually
by inspection.
Unless otherwise stated, sequence identity/similarity values provided herein
refer to the value obtained using GAP Version 10 using the following
parameters: %
identity using GAP Weight of 50 and Length Weight of 3; % similarity using Gap
Weight of 12 and Length Weight of 4, or any equivalent program. By "equivalent
program" is intended any sequence comparison program that, for any two
sequences
in question, generates an alignment having identical nucleotide or amino acid
residue
CA 02724158 2010-12-01
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matches and an identical percent sequence identity when compared to the
corresponding alignment generated by the preferred program.
GAP uses the algorithm of Needleman and Wunsch (1970) J. Mol. Biol.
48:443-453, to find the alignment of two complete sequences that maximizes the
number of matches and minimizes the number of gaps. GAP considers all possible
alignments and gap positions and creates the alignment with the largest number
of
matched bases and the fewest gaps. It allows for the provision of a gap
creation
penalty and a gap extension penalty in units of matched bases. GAP must make a
profit of gap creation penalty number of matches for each gap it inserts. If a
gap
extension penalty greater than zero is chosen, GAP must, in addition, make a
profit
for each gap inserted of the length of the gap times the gap extension
penalty. Default
gap creation penalty values and gap extension penalty values in Version 10 of
the
Wisconsin Genetics Software Package for protein sequences are 8 and 2,
respectively.
For nucleotide sequences the default gap creation penalty is 50 while the
default gap
extension penalty is 3. The gap creation and gap extension penalties can be
expressed
as an integer selected from the group of integers consisting of from 0 to 200.
Thus,
for example, the gap creation and gap extension penalties can be 0, 1, 2, 3,
4, 5, 6, 7,
8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65 or greater.
GAP presents one member of the family of best alignments. There may be
many members of this family, but no other member has a better quality. GAP
displays four figures of merit for alignments: Quality, Ratio, Identity, and
Similarity.
The Quality is the metric maximized in order to align the sequences. Ratio is
the
quality divided by the number of bases in the shorter segment. Percent
Identity is the
percent of the symbols that actually match. Percent Similarity is the percent
of the
symbols that are similar. Symbols that are across from gaps are ignored. A
similarity
is scored when the scoring matrix value for a pair of symbols is greater than
or equal
to 0.50, the similarity threshold. The scoring matrix used in Version 10 of
the
Wisconsin Genetics Software Package is BLOSUM62 (see Henikoff and Henikoff
(1989) Proc. Natl. Acad. Sci. USA 89:10915).
(c) As used herein, "sequence identity" or "identity" in the context of two
nucleic acid or polypeptide sequences makes reference to the residues in the
two
sequences that are the same when aligned for maximum correspondence over a
specified comparison window. When percentage of sequence identity is used in
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reference to proteins it is recognized that residue positions which are not
identical
often differ by conservative amino acid substitutions, where amino acid
residues are
substituted for other amino acid residues with similar chemical properties
(e.g., charge
or hydrophobicity) and therefore do not change the functional properties of
the
molecule. When sequences differ in conservative substitutions, the percent
sequence
identity may be adjusted upwards to correct for the conservative nature of the
substitution. Sequences that differ by such conservative substitutions are
said to have
"sequence similarity" or "similarity". Means for making this adjustment are
well
known to those of skill in the art. Typically this involves scoring a
conservative
substitution as a partial rather than a full mismatch, thereby increasing the
percentage
sequence identity. Thus, for example, where an identical amino acid is given a
score
of 1 and a non-conservative substitution is given a score of zero, a
conservative
substitution is given a score between zero and 1. The scoring of conservative
substitutions is calculated, e.g., as implemented in the program PC/GENE
(Intelligenetics, Mountain View, California).
(d) As used herein, "percentage of sequence identity" means the value
determined by comparing two optimally aligned sequences over a comparison
window, wherein the portion of the polynucleotide sequence in the comparison
window may comprise additions or deletions (i.e., gaps) as compared to the
reference
sequence (which does not comprise additions or deletions) for optimal
alignment of
the two sequences. The percentage is calculated by determining the number of
positions at which the identical nucleic acid base or amino acid residue
occurs in both
sequences to yield the number of matched positions, dividing the number of
matched
positions by the total number of positions in the window of comparison, and
multiplying the result by 100 to yield the percentage of sequence identity.
(e)(i) The term "substantial identity" of polynucleotide sequences means that
a polynucleotide comprises a sequence that has at least 70% sequence identity,
preferably at least 80%, more preferably at least 90%, and most preferably at
least
95%, compared to a reference sequence using one of the alignment programs
described 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. Substantial
identity of
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amino acid sequences for these purposes normally means sequence identity of at
least
60%, more preferably at least 70%, 80%, 90%, and most preferably at least 95%.
Another indication that nucleotide sequences are substantially identical is if
two molecules hybridize to each other under stringent conditions. Generally,
stringent conditions are selected to be about 5 C lower than the thermal
melting point
(Tm) for the specific sequence at a defined ionic strength and pH. However,
stringent
conditions encompass temperatures in the range of about 1 C to about 20 C,
depending upon the desired degree of stringency as otherwise qualified herein.
Nucleic acids that do not hybridize to each other under stringent conditions
are still
substantially identical if the polypeptides they encode are substantially
identical. This
may occur, e.g., when a copy of a nucleic acid is created using the maximum
codon
degeneracy permitted by the genetic code. One indication that two nucleic acid
sequences are substantially identical is when the polypeptide encoded by the
first
nucleic acid is immunologically cross reactive with the polypeptide encoded by
the
second nucleic acid.
(e)(ii) The term "substantial identity" in the context of a peptide indicates
that
a peptide comprises a sequence with at least 70% sequence identity to a
reference
sequence, preferably 80%, more preferably 85%, most preferably at least 90% or
95%
sequence identity to the reference sequence over a specified comparison
window.
Preferably, optimal alignment is conducted using the homology alignment
algorithm
of Needleman et al. (1970) J. Mol. Biol. 48:443. An indication that two
peptide
sequences are substantially identical is that one peptide is immunologically
reactive
with antibodies raised against the second peptide. Thus, a peptide is
substantially
identical to a second peptide, for example, where the two peptides differ only
by a
conservative substitution. Peptides that are "substantially similar" share
sequences as
noted above except that residue positions that are not identical may differ by
conservative amino acid changes.
Disease and Pests
Compositions and methods for controlling pathogenic agents are provided.
The anti-pathogenic compositions comprise plant defensin nucleotide and amino
acid
sequences. Particularly, the plant nucleic acid and amino acid sequences and
fragments and variants thereof set forth herein possess anti-pathogenic
activity.
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N
Accordingly, the compositions and methods are useful in protecting plants
against
fungal pathogens, viruses, nematodes, insects, and the like. Additionally
provided are
transformed plants, plant cells, plant tissues and seeds thereof.
By "plant pathogen" or "plant pest" any organism that can cause harm to a
plant, by inhibiting or slowing the growth of a plant, by damaging the tissues
of a
plant, by weakening the immune system of a plant, reducing the resistance of a
plant
to abiotic stresses, and/or by causing the premature death of the plant, etc.
is intended.
Plant pathogens and plant pests include insects, nematodes, and organisms such
as
fungi, viruses, and bacteria.
By "disease resistance" or "pathogen resistance" it is intended that the
organisms avoid the disease symptoms which are the outcome of organism-
pathogen
interactions. That is, pathogens are prevented from causing diseases and the
associated disease symptoms, or alternatively, the disease symptoms caused by
the
pathogen is minimized or lessened.
By "anti-pathogenic compositions" is intended that the compositions of the
invention are capable of suppressing, controlling, and/or killing the invading
pathogenic organism. An antipathogenic composition of the invention will
reduce the
disease symptoms resulting from pathogen challenge by at least about 5% to
about
50%, at least about 10% to about 60%, at least about 30% to about 70%, at
least about
40% to about 80%, or at least about 50% to about 90% or greater. Hence, the
methods of the invention can be utilized to protect plants from disease,
particularly
those diseases that are caused by plant pathogens.
An "antimicrobial agent," a "pesticidal agent," a "defensin," an "antiviral
agent," and "insecticidal agent," and/or a "fungicidal agent" will act
similarly to
suppress, control, and/or kill the invading pathogen.
A defensive agent will possess defensive activity. By "defensive activity" an
antipathogenic, antimicrobial, antiviral, insecticidal, or antifungal activity
is intended.
By "antipathogenic compositions" it is intended that the compositions of the
invention have activity against pathogens; including fungi, microorganisms,
viruses,
insects and nematodes, and thus are capable of suppressing, controlling,
and/or killing
the invading pathogenic organism. An antipathogenic composition of the
invention
will reduce the disease symptoms resulting from pathogen challenge by at least
about
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5-% to about 50%, at least about 10% to about 60%, at least about 30% to about
70%,
at least about 40% to about 80%, or at least about 50% to about 90% or
greater.
Hence, the methods of the invention can be utilized to protect organisms,
particularly
plants, from disease, particularly those diseases that are caused by invading
pathogens.
Assays that measure antipathogenic activity are commonly known in the art,
as are methods to quantitate disease resistance in plants following pathogen
infection.
See, for example, U.S. Patent No. 5,614,395,. Such
techniques include, measuring over time, the average lesion diameter, the
pathogen
biomass, and the overall percentage of decayed plant tissues. For example, a
plant
either expressing an antipathogenic polypeptide or having an antipathogenic
composition applied to its surface shows a decrease in tissue necrosis (i.e.,
lesion
diameter) or a decrease in plant death following pathogen challenge when
compared
to a control plant that was not exposed to the antipathogenic composition.
Alternatively, antipathogenic activity can be measured, by a decrease in
pathogen
biomass. For example, a plant expressing an antipathogenic polypeptide or
exposed
to an antipathogenic composition is challenged with a pathogen of interest.
Over
time, tissue samples from the pathogen-inoculated tissues are obtained and RNA
is
extracted. The percent of a specific pathogen RNA transcript relative to the
level of a
plant specific transcript allows the level of pathogen biomass to be
determined. See,
for example, Thomma et at. (1998) Plant Biology 95:15107-15111õ
Furthermore, in vitro antipathogenic assays include, for example, the addition
of varying concentrations of the antipathogenic composition to paper disks and
placing the disks on agar containing a suspension of the pathogen of interest.
Following incubation, clear inhibition zones develop around the discs that
contain an
effective concentration of the antipathogenic polypeptide (Liu et al. (1994)
Plant
Biology 91:1888-1892). Additionally,
microspectrophotometrical analysis can be used to measure the in vitro
antipathogenic
properties of a composition (Hu et al. (1997) Plant Mol. Biol. 34:949-959 and
Cammue et al. (1992) J. Biol. Chem. 267: 2228-2233).
CA 02724158 2010-12-01
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In specific embodiments, methods for increasing pathogen resistance in a plant
comprise stably transforming a plant with a DNA construct comprising an anti-
pathogenic nucleotide sequence of the invention operably linked to promoter
that
drives expression in a plant. Such methods find use in agriculture
particularly in
limiting the impact of plant pathogens on crop plants. While the choice of
promoter
will depend on the desired timing and location of expression of the anti-
pathogenic
nucleotide sequences, preferred promoters include constitutive and pathogen-
inducible promoters.
It is understood in the art that plant DNA viruses and fungal pathogens
remodel the control of the host replication and gene expression machinery to
accomplish their own replication and effective infection. The present
invention may
be useful in preventing such corruption of the cell.
The defensin sequences find use in disrupting cellular function of plant
pathogens or insect pests as well as altering the defense mechanisms of a host
plant to
enhance resistance to disease or insect pests. While the invention is not
bound by any
particular mechanism of action to enhance disease resistance, the gene
products of the
defensin sequences function to inhibit or prevent diseases in a plant.
The methods of the invention can be used with other methods available in the
art for enhancing disease resistance in plants. For example, any one of a
variety of
second nucleotide sequences may be utilized, embodiments of the invention
encompass those second nucleotide sequences that, when expressed in a plant,
help to
increase the resistance of a plant to pathogens. It is recognized that such
second
nucleotide sequences may be used in either the sense or antisense orientation
depending on the desired outcome. Other plant defense proteins include those
described in PCT patent publications WO 99/43823 and WO 99/43821.
Pathogens of the invention include, but are not limited to, viruses or
viroids,
bacteria, insects, nematodes, fungi, and the like. Viruses include any plant
virus, for
example, tobacco or cucumber mosaic virus, ringspot virus, necrosis virus,
maize
dwarf mosaic virus, etc. Specific fungal and viral pathogens for the major
crops
include: Soybeans: Phytophthora nzegaspernza Esp. glycinea, Macrophomina
phaseolina, Rhizoctonia solani, Sclerotinia sclerotiozuzn, Fusarium oxysporwn,
Diaporthe phaseolorunz var. sojae (Phoinopsis sojae), Diaporthe phaseolorum
var.
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caulivora, Sclerotium rolfsii, Cercospora kikuchii, Cercospora sojina,
Peronospora
inanshurica, Colletotrichum dematium (Colletotrichurn truncatum), Corynespora
cassiicola, Septoria glycines, Phyllosticta sojicola, Alternaria alternata,
Pseudornonas syringae p.v. glycinea, Xanthomonas carnpestris p.v. phaseoli,
Microsphaera diffusa, Fusariumt semitecturn, Phialophora gregata, Soybean
mosaic
virus, Glomerella glycines, Tobacco Ring spot virus, Tobacco Streak virus,
Phakopsora pachyrhizi, Pythium aphaniderrnaturn, Pythium ultirnum, Pythiuin
debaryanum, Tomato spotted wilt virus, Heterodera glycines, Fusarium solani;
Canola: Albugo candida, Alternaria brassicae, Leptosphaeria maculans,
Rhizoctonia
solani, Sclerotinia sclerotiorum, Mycosphaerella brassiccola, Pythium
ultirnum,
Peronospora parasitica, Fusarium roseum, Alternaria alternata; Alfalfa:
Clavibacter
Michigan's subsp. insidiosum, Pythium ultimurn, Pythium irregulare, Pythium
splendens, Pythium debary~anum, Pythium aphanidermatum, Phytophthora
inegasperrna, Peronospora trifoliorurn, Phoma inedicaginis var. medicaginis,
Cercospora medicaginis, Pseudopeziza medicaginis, Leptotrochila medicaginis,
Fusarium spp., Xanthomonas carnpestris p.v. alfalfae, Aphanomyces euteiches,
Stemphyliurn herbarurn, Stemphyliurn alfalfae; Wheat: Pseudornonas syringae
p.v.
atrofaciens, Urocystis agropyri, Xanthomonas carnpestris p.v. translucens,
Pseudornonas syringae p.v. syringae, Alternaria alternata, Cladosporiurn
herbarurn,
Fusarium graminearum, Fusarium avenaceum, Fusarium culmorurn, Ustilago
tritici,
Ascochyta tritici, Cephalosporium gramineurn, Collotetrichurn graminicola,
Eiysiphe
graminis Esp. tritici, Puccinia graminis f.sp. tritici, Puccinia recondita
f.sp. tritici,
Puccinia striiformis, Pyrenophora tritici-repentis, Septoria nodorurn,
Septoria tritici,
Septoria avenae, Pseudocercosporella heipotrichoides, Rhizoctonia solani,
Rhizoctonia cerealis, Gaeumannomyces graminis var. tritici, Pythium
aphanidermatum, Pythium arrhenomanes, Pythium ultimum, Bipolaris sorokiniana,
Barley Yellow Dwarf Virus, Brome Mosaic Virus, Soil Borne Wheat Mosaic Virus,
Wheat Streak Mosaic Virus, Wheat Spindle Streak Virus, American Wheat Striate
Virus, Claviceps purpurea, Tilletia tritici, Tilletia laevis, Tilletia indica,
Pythium
gramicola, High Plains Virus, European wheat striate virus; Sunflower:
Plasmophora
halstedii, Sclerotinia sclerotioruin, Aster Yellows, Septoria helianthi,
Phomopsis
helianthi, Alternaria helianthi, Alternaria zinniae, Botrytis cinerea, Phoma
macdonaldii, Macrophoinina phaseolina, Erysiphe cichoracearuin, Rhizopus
oiyzae,
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Rhizopus arrhizus, Rhizopus stolonifer, Puccinia helianthi, Verticilliutn
dahliae,
Erwinia carotovorum p.v. carotovora, Cephalosporiufn acrentoniurn,
Phytophthora
cryptogea, Albugo tragopogonis; Corn: Fusarium moniliforrne var. subglutlnans,
Erwinia stewartii, Fusarium moniliforrne, Gibberella zeae (Fusarium
graminearutn),
Stenocaipella maydis (Diplodia maydis), Pythium ir7regulare, Pythiuin
debaryanunn,
Pythium graminicola, Pythium splendens, Pythium ultimunt, Pythium
aphaniderntatunt, Aspergillus flavus, Bipolaris maydis 0, T (Cochliobolus
heterostrophus), Helminthosporium carbonum I, II & III (Cochliobolus
carbonunt),
Exserohihan turcicurn I, II & III, Helminthosporiunt pedicellatum, Physoderina
maydis, Phyllosticta maydis, Kabatiella inaydis, Cercospora sorghi, Ustilago
maydis,
Puccinia sorghi, Puccinia polysora, Macrophomina phaseolina, Penicillium
oxalicum, Nigrospora oiyzae, Cladosporium herbaruin, Curvularia lunata,
Curvularia inaequalis, Cunvularia pallescens, Clavibacter ntichiganense subsp.
nebraskense, Trichoderma viride, Maize Dwarf Mosaic Virus A & B, Wheat Streak
Mosaic Virus, Maize Chlorotic Dwarf Virus, Claviceps sorghi, Pseudornonas
avenae,
Erwinia chrysanthemi p.v. zea, Erwinia carotovora, Corn stuntspiroplasma,
Diplodia
ntacrospora, Sclerophthona ntacrospora, Peronosclerospora sorghi,
Peronosclerospora philippinensis, Peronosclerospora inaydis, Peronosclerospora
sacchari, Sphacelotheca reiliana, Physopella zeae, Cephalosporiunt rnaydis,
Cephalosporium acremonium, Maize Chlorotic Mottle Virus, High Plains Virus,
Maize Mosaic Virus, Maize Rayado Fino Virus, Maize Streak Virus, Maize Stripe
Virus, Maize Rough Dwarf Virus; Sorghum: Exserohilum turcicuin,
Colletotriclnsrn
graminicola (Glornerella graminicola), Cercospora sorghi, Gloeocercospora
sorghi,
Ascochyta sorghina, Pseudomonas syringae p.v. syringae, Xanthomonas campestris
p.v. holcicola, Pseudomonas andropogonis, Puccinia purpurea, Macrophomina
phaseolina, Periconia circinata, Fusarium moniliforme, Alternaria alternate,
Bipolaris sorghicola, Helininthosporium sorghicola, Curvularia lunata, Phoma
insidiosa, Pseudomonas avenae (Pseudoronas alboprecipitans), Ramulispora
sorghi,
Ramulispora sorghicola, Phyllachara sacchari, Sporisoriurn reilianum
(Sphacelotheca reiliana), Sphacelotheca cruenta, Sporisorium sorghi, Sugarcane
mosaic H, Maize Dwarf Mosaic Virus A & B, Claviceps sorghi, Rhizoctonia
solani,
Acremonium stricttun, Sclerophthona inacrospora, Peronosclerospora sorghi,
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Peronosclerospora philippinensis, Sclerospora graminicola, Fusarium
grantinearurn,
Fusariunz oxysporum, Pythium arrhenornanes, Pytlziunt grarninicola, etc.
Nematodes include parasitic nematodes such as root-knot, cyst, and lesion
nematodes, including Heterodera and Globodera spp.; particularly Globodera
rostochiensis and Globodera pailida (potato cyst nematodes); Heterodera
glvcines
(soybean cyst nematode); Heterodera schachtii (beet cyst nematode); and
Heterodera
avenae (cereal cyst nematode). Additional nematodes include: Heterodera
cajani;
Heterodera trifolii; Heterodera oryzae; Globodera tabacum; Meloidogyne
incognita;
Meloidogynejavonica; Meloidogyne hapla; Meloidogyne arenaria; Meloidogyne
naasi; Meloidogyne exigua; Xiphinema index; Xiphinenza italiae; Xiphinema
americanuin; Xiphinenta diversicaudatuin; Pratylenchus penetrans; Pratylenchus
brachyurus; Pratylenchus zeae; Pratylenchus coffeae; Pratylenchus thornei;
Pratylenchus scribneri; Pratylenchus vulnus; Pratylenchus curvitatus;
Radopholus
similis; Radopholus citrophilus; Ditylenchus dipsaci; Helicotylenchus
multicintus;
Rotylenchulus reniformis; Belonolaimus spp.; Paratrichodorus anemones;
Trichodorus spp.; Printitivus spp.; Anguina tritici; Bider avenae; Subanguina
radicicola; Tvlenchorhynchus spp.; Haplolairnus seinhorsti; Tylenchulus
sendpenetrans; Hemicycliophora arenaria; Belonolaimus langicaudatus;
Paratrichodorus xiphineina; Paratrichodorus christiei; Rhadinaphelenchus
cocophilus; Paratrichodorus minor; Hoplolainius galeatus; Hoplolaintus
columbus;
Criconemella spp.; Paratylenchus spp.; Nacoabbus aberrans; Aphelenchoides
besseyi; Ditylenchus angustus; Hirchmaniella spp.; Scutellonema spp.;
Hernicriconenzoides kanayaensis; Tylenchorynchus claytoni; and Cacopaurus
pestis.
Insect pests include insects selected from the orders Coleoptera, Diptera,
Hymenoptera, Lepidoptera, Mallophaga, Homoptera, Hemiptera, Orthoptera,
Thysanoptera, Dermaptera, Isoptera, Anoplura, Siphonaptera, Trichoptera, etc.,
particularly Coleoptera and Lepidoptera. 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 rugiperda, fall armyworm;
Diatraea grandiosella, southwestern com borer; Elasmopalpus lignosellus,
lesser
cornstalk borer; Diatraea saccharalis, sugarcane borer; Diabrotica virgifera,
western
corn rootworm; Diabrotica longicornis barberi, northern corn rootworm;
Diabrotica
undecimpunctata howardi, southern corn rootworm; Melanotus spp., wireworms;
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Cyclocephala borealis, northern masked chafer (white grub); Cyclocephala
irnrnaculata, southern masked chafer (white grub); Popillia japonica, Japanese
beetle;
Chaetocnema pulicaria, corn flea beetle; Sphenophorus maidis, maize billbug;
Rhopalosiphaan inaidis, corn leaf aphid; Anuraphis maidiradicis, corn root
aphid;
Blissus leucopterus leucopterus, chinch bug; Melanoplus femurrubrum, redlegged
grasshopper; Melanoplus sanguinipes, migratory grasshopper; Hylernya platura,
seedcom maggot; Agrornyza parvicornis, corn blotch leafrniner; Anaphothrips
obscrurus, grass thrips; Solenopsis rnilesta, thief ant; Tetranychus urticae,
twospotted
spider mite; Sorghum: Chilo partellus, sorghum borer; Spodoptera rugiperda,
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 inaidis; corn leaf aphid; Sipha jlava, 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
inelanopus, cereal leaf beetle; Hypera punctata, clover leaf weevil;
Diabrotica
undecirnpunctata howardi, southern corn rootworm; Russian wheat aphid;
Schizaphis
graminum, greenbug; Macrosiphum avenae, English grain aphid; Melanoplus
femurrubrum, redlegged grasshopper; Melanoplus di. fferentialis, differential
grasshopper; Melanoplus sanguinipes, migratory grasshopper; Mayetiola
destructor,
Hessian fly; Sitodiplosis mosellana, wheat midge; Meromyza americana, wheat
stem
maggot; Hylernya 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 electellurn, sunflower
moth;
Zygograrnrna exclarnationis, sunflower beetle; Bothyrus gibbosus, carrot
beetle;
Neolasioptera inurtfeldtiana, 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; Pseudatornoscelis seriatus, cotton
fleahopper;
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Trialeurodes abutilonea, bandedwinged whitefly; Lygus lineolaris, tarnished
plant
bug; Melanoplus femurrubrum, redlegged grasshopper; Melanoplus differentialis,
differential grasshopper; Thrips tabaci, onion thrips; Franklinkiellafusca,
tobacco
thrips; Tetranychus cinnabarinus, carmine spider mite; Tetranyclucs urticae,
twospotted spider mite; Rice: Diatraea saccharalis, sugarcane borer;
Spodoptera
fi-ugiper da, fall armyworm; Helicoverpa zea, corn earworm; Colaspis brunnea,
grape
colaspis; Lissorhoptrus oiyzophilus, rice water weevil; Sitophilus ofyzae,
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;
Helicoveipa zea, cotton bollworm; Epilachna varivestis, Mexican bean beetle;
Myzus
persicae, green peach aphid; Empoasca fabae, potato leafhopper; Acrosternuni
hilare,
green stink bug; Melanoplus femur-ubrum, redlegged grasshopper; Melanoplus
differentialis, differential grasshopper; Hylennya platura, seedcorn maggot;
Sericothrips variabilis, soybean thrips; Thrips tabaci, onion thrips;
Tetranychus
turkestani, strawberry spider mite; Tetranychus urticae, twospotted spider
mite;
Barle : 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: Brevicoiyne brassicae, cabbage aphid; Phyllotreta
cruciferae, Flea beetle; Mantestra configurata, Bertha armyworm; Plutella
xylostella,
Diamond-back moth; Delia spp., Root maggots.
Expression of Sequences
The nucleic acid sequences of the present invention can be expressed in a host
cell such as bacterial, fungal, yeast, insect, mammalian, or preferably plant
cells. It is
expected that those of skill in the art are knowledgeable in the numerous
expression
systems available for expression of a nucleic acid encoding a protein of the
present
invention. No attempt to describe in detail the various methods known for the
expression of proteins in prokaryotes or eukaryotes will be made.
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As used herein, "heterologous" in reference to a nucleic acid is a nucleic
acid
that originates from a foreign species, or, if from the same species, is
substantially
modified from its native form in composition and/or genomic locus by
deliberate
human intervention. For example, a promoter operably linked to a heterologous
nucleotide sequence can be from a species different from that from which the
nucleotide sequence was derived, or, if from the same species, the promoter is
not
naturally found operably linked to the nucleotide sequence. A heterologous
protein
may originate from a foreign species, or, if from the same species, is
substantially
modified from its original form by deliberate human intervention.
By "host cell" a cell, which comprises a heterologous nucleic acid sequence of
the invention is meant. Host cells may be prokaryotic cells such as E. coli,
or
eukaryotic cells such as yeast, insect, amphibian, or mammalian cells.
Preferably,
host cells are monocotyledonous or dicotyledonous plant cells. A particularly
preferred monocotyledonous host cell is a maize host cell.
The defensin sequences of the invention are provided in expression cassettes
or DNA constructs for expression in the plant of interest. The cassette will
include 5'
and 3' regulatory sequences operably linked to a defensin sequence of the
invention.
By "operably linked" 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 is intended. 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.
Such an expression cassette is provided with a plurality of restriction sites
for
insertion of the defensin sequence to be under the transcriptional regulation
of the
regulatory regions. The expression cassette may additionally contain
selectable
marker genes.
The expression cassette will include in the 5'-3' direction of transcription,
a
transcriptional and translational initiation region, a defensin DNA sequence
of the,
invention, and a transcriptional and translational termination region
functional in
plants. The transcriptional initiation region, the promoter, may be native or
analogous
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CA 02724158 2010-12-01
75529-69
or foreign or heterologous-to the plant host. Additionally, the promoter may
be the
natural sequence or alternatively a synthetic sequence. By "foreign" is
intended that
the transcriptional initiation region is not found in the native plant into
which the
transcriptional initiation region is introduced. As used herein, a chimeric
gene
comprises a coding sequence operably linked to a transcription initiation
region that is
heterologous to the coding sequence.
While it may be preferable to express the sequences using heterologous
promoters, the native promoter sequences may be used. Such constructs would
change expression levels of defensin in the host cell (i.e., plant or plant
cell). Thus,
the phenotype of the host cell (i.e., plant or plant cell) is altered.
The termination region may be native with the transcriptional initiation
region,
may be native with the operably linked DNA sequence of interest, or may be
derived
from another source. Convenient termination regions are available from the Ti-
plasuud of A. tumefuciens, such as the octopine synthase and nopaline synthasc
termination tegious. Sae also Gueriuesu el at. (1991) /viol. Gen. Genet.
262:141-144;
Proudfoot (1991) Cell 64:671-674; Sanfacon et at. (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 plant. That is, the genes can be synthesized using plant-
preferred
codons for improved expression. 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.
Patent Nos. 5,380,831, 5,436,391, and Murray et al. (1989) Nucleic Acids Res.
17:477-498.
Additional sequence modifications are known to enhance gene expression in a
cellular host. These include elimination of sequences encoding spurious
polyadenylation signals, exon-intron splice site signals, transposon-like
repeats, and
other such well-characterized sequences that may be deleterious to gene
expression.
The G-C content of the sequence may be adjusted to levels average for a given
cellular host, as calculated by reference to known genes expressed in the
host.cell.
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When possible, the sequence is modified to avoid predicted hairpin secondary
mRNA
structures.
The expression cassettes may additionally contain 5' leader sequences in the
expression cassette construct. Such leader sequences can act to enhance
translation.
Translation leaders are known in the art and include: picornavirus leaders,
for
example, EMCV leader (Encephalomyocarditis 5' noncoding region) (Elroy-Stein
et
al. (1989) PNAS USA 86:6126-6130); potyvirus leaders, for example, TEV leader
(Tobacco Etch Virus) (Allison et al. (1986); MDMV leader (Maize Dwarf Mosaic
Virus); Virology 154:9-20), and human immunoglobulin heavy-chain binding
protein
(BiP), (Macejak et al. (1991) Nature 353:90-94); untranslated leader from the
coat
protein mRNA of alfalfa mosaic virus (AMV RNA 4) (Jobling et al. (1987) Nature
325:622-625); tobacco mosaic virus leader (TMV) (Gallie et al. (1989) in
Molecular
Biology of RNA, ed. Cech (Liss, New York), pp. 237-256); and maize chlorotic
mottle
virus leader (MCMV) (Lommel et al. (1991) Virology 81:382-385). See also,
Della-Cioppa et al. (1987) Plant Physiol. 84:965-968. Other methods known to
enhance translation can also be utilized, for example, introns, and the like.
In preparing the expression cassette, the various DNA fragments may be-
manipulated, so as to provide for the DNA sequences in the proper orientation
and, as
appropriate, in the proper reading frame. Toward this end, adapters or linkers
may be
employed to join the DNA fragments or other manipulations may be involved to
provide for convenient restriction sites, removal of superfluous DNA, removal
of
restriction sites, or the like. For this purpose, in vitro mutagenesis, primer
repair,
restriction, annealing, resubstitutions, e.g., transitions and transversions,
may be
involved.
Generally, the expression cassette will comprise a selectable marker gene for
the selection of transformed cells. Selectable marker genes are utilized for
the
selection of transformed cells or tissues. Marker genes include genes encoding
antibiotic resistance, such as those encoding neomycin phosphotransferase 11
(NEO)
and hygromycin phosphotransferase (HPT), as well as genes conferring
resistance to
herbicidal compounds, such as glyphosate, glufosinate ammonium, bromoxynil,
imidazolinones, and 2,4-dichlorophenoxyacetate (2,4-D). See generally,
Yarranton
(1992) Curr. Opin. Biotech. 3:506-511; Christopherson et al. (1992) Proc.
Natl. Acad.
Sci. USA 89:6314-6318; Yao et al. (1992) Cell 71:63-72; Reznikoff (1992) Mol.
44
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Microbiol. 6:2419-2422; Barkley et at. (1980) in The Operon, pp. 177-220; Hu
et at.
(1987) Cell 48:555-566; Brown et al. (1987) Cell 49:603-612; Figge et al.
(1988) Cell
52:713-722; Deuschle et al. (1989) Proc. Natl. Acad. Sci. USA 86:5400-5404;
Fuerst
et al. (1989) Proc. Natl. Acad. Sci. USA 86:2549-2553; Deuschle et al. (1990)
Science
248:480-483; Gossen (1993) Ph.D. Thesis, University of Heidelberg; Reines et
al.
(1993) Proc. Natl. Acad. Sci. USA 90:1917-1921; Labow et al. (1990) Mol. Cell.
Biol.
10:3343-3356; Zambretti et al. (1992) Proc. Natl. Acad. Sci. USA 89:3952-3956;
Bairn et al. (1991) Proc. Natl. Acad. Sci. USA 88:5072-5076; Wyborski et al.
(1991)
Nucleic Acids Res. 19:4647-4653; Hillenand-Wissman (1989) Topics Mol. Str7rc.
Biol.
10:143-162; Degenkolb et al. (1991) Antinricrob. Agents Chernother. 35:1591-
1595;
Kleinschnidt et al. (1988) Biochemistry 27:1094-1104; Bonin (1993) Ph.D.
Thesis,
University of Heidelberg; Gossen et al. (1992) Proc. Natl. Acad. Sci. USA
89:5547-
5551; Oliva et al. (1992) Antimicrob. Agents Chennother. 36:913-919; Hlavka et
al.
(1985) Handbook of Experimental Pharmacology, Vol. 78 ( Springer-Verlag, Berl
n);
Gill at al. (i 98R) Nature 334:721-724.
The above list of selectable marker genes is not meant to be limiting. Any
selectable marker gene can be used in the present invention.
A number of promoters can be used in the practice of the invention. The
promoters can be selected based on the desired outcome. That is, the nucleic
acids
can be combined with constitutive, tissue-preferred, or other promoters for
expression
in the host cell of interest. Such constitutive promoters include, for
example, the core
promoter of the Rsyn7 promoter and other constitutive promoters disclosed in
WO
99/43838 and U.S. Patent No. 6,072,050; the core CaMV 35S promoter (Odell et
al.
(1985) Nature 313:810-812); rice actin (McElroy et al. (1990) Plant Cell 2:163-
171);
ubiquitin (Christensen et al. (1989) Plant Mot. Biol. 12:619-632 and
Christensen et al.
(1992) Plant Mol. Biol. 18:675-689); pEMU (Last et al. (1991) Theor. Appl.
Genet.
81:581-588); NMS (Velten et al. (1984) EMBO J. 3:2723-2730); ALS promoter
((J.S.
Patent No. 5,659,026), and the like. Other constitutive promoters include, for
example, those disclosed in U.S. Patent Nos. 5,608,149; 5,608,144; 5,604,121;
5,569,597; 5,466,785; 5,399,680; 5,268,463; 5,608,142; and 6,177,611._
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Generally, it will be beneficial to express the gene from an inducible
promoter,
particularly from a pathogen-inducible promoter. Such promoters include those
from
pathogenesis-related proteins (PR proteins), which are induced following
infection by
a pathogen; e.g., PR proteins, SAR proteins, beta-l,3-glucanase, chitinase,
etc. See,
for example, Redolfi et al. (1983) Neth. J. Plant Pathol. 89:245-254; Uknes et
al.
(1992) Plant Cell 4:645-656; and Van Loon (1985) Plant Mol. Virol. 4:111-116.
See
also WO 99/43819 published September 9, 1999.
Of interest are promoters that are expressed locally at or near the site of
pathogen infection. See, for example, Marineau et al. (1987) PlantMol. Biol.
9:335-
342; Matton et al. (1989) Molecular Plant-Microbe Interactions 2:325-331;
Somsisch
et al. (1986) Proc. Natl. Acad. Sci. USA 83:2427-2430; Somsisch et al. (1988)
Mot.
Gen. Genet. 2:93-98; and Yang (1996) Proc. Natl. Acad. Sci. USA 93:14972-
14977.
See also, Chen et al. (1996) Plant J. 10:955-966; Zhang et al. (1994) Proc.
Natl.
Acad. Sci. (.VA 91:2507-2511; Warner et al. (1993) Plant J. 3:191-201;
Siobertz et al.
(1989) Plant Cell 1:961-968; U.S. Patent No. 5,750,386 (nematode-inducible);
and
the references cited therein. Of particular interest is the inducible promoter
for the
maize PRms gene, whose expression is induced by the pathogen Fusariune
moniliforme (see, for example, Cordero et al. (1992) Physiol. Mot. Plant Path.
41:189-200).
Additionally, as pathogens find entry into plants through wounds or insect
damage, a wound-inducible promoter may be used in the constructions of the
invention. Such wound-inducible promoters include potato proteinase inhibitor
(pin
II) gene (Ryan (1990) Ann. Rev. Phytopath. 28:425-449; Duan et al. (1996)
Nature
Biotechnology 14:494-498); wunl and wun2, U.S. Patent No. 5,428,148; winl and
wing (Stanford et al. (1989) Mol. Gen. Genet. 215:200-208); systemin (McGurl
et al.
(1992) Science 225:1570-1573); WIP1 (Rohmeier et al. (1993) Plant Mol. Biol.
22:783-792; Eckelkamp et al. (1993) FEBS Letters 323:73-76); MFI gene
(Corderok
et al. (1994) Plant J. 6(2):141-150); and the like.
Chemical-regulated promoters can be used to modulate the expression of a
gene in a plant through the application of an exogenous chemical regulator.
Depending upon the objective, the promoter may be a chemical-inducible
promoter,
where application of the chemical induces gene expression, or a chemical-
repressible
promoter, where application of the chemical represses gene expression.
Chemical-
46
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inducible promoters are known in the art and include, but are not limited to,
the maize
In2-2 promoter, which is activated by benzenesulfonamide herbicide safeners,
the
maize GST promoter, which is activated by hydrophobic electrophilic compounds
that
are used as pre-emergent herbicides, and the tobacco PR-la promoter, which is
activated by salicylic acid. Other chemical-regulated promoters of interest
include
steroid-responsive promoters (see, for example, the glucocorticoid-inducible
promoter
in Schena et al. (1991) Proc. Natl. Acad. Sci. USA 88:10421-10425 and McNellis
et
al. (1998) Plant J. 14(2):247-257) and tetracycline-inducible and tetracycline-
repressible promoters (see, for example, Gatz et al. (1991) Mol. Gen. Genet.
227:229-
237, and U.S. Patent Nos. 5,814,618 and 5,789,156).
Tissue-preferred promoters can be utilized to target enhanced defensin
expression within a particular plant tissue. Tissue-preferred promoters
include
Yamamoto et al. (1997) Plant J. 12(2):255-265; Kawamata et al. (1997) Plant
Cell
Physical. 38(7):792-803; Hansen et al. (1997) Mot. Gen Genet. 254(3):337-343;
Russell et al. (1997) Transgenic Res. 6(2):157-168; Rinehart et al. (1996)
Plant
Physiol. 112(3):1331-1341; Van Camp etal. (1996) PlantPlzysiol. 112(2):525-
535;
Canevascini et al. (1996) Plant, Physiol. 112(2):513-524; Yamamoto et al.
(1994)
Plant Cell Physiol. 35(5):773-778; Lam (1994) Results Probl. Cell Differ.
20:181-
196; Orozco et al. (1993) Plant Mol Biol. 23(6):1129-1138; Matsuoka et al.
(1993)
Proc Natl. Acad. Sci. USA 90(20):9586-9590; and Guevara-Garcia et al. (1993)
Plant
J. 4(3):495-505. Such promoters can be modified, if necessary, for weak
expression.
Leaf-specific promoters are known in the art. See, for example, Yamamoto et
al. (1997) Plant J. 12(2):255-265; Kwon et al. (1994) Plant Physiol. 105:35't-
67;
Yamamoto et al. (1994) Plant Cell Physiol. 35(5):773-778; Gotor et al. (1993)
Plant
J. 3:509-18; Orozco eta[. (1993) Plant Mol. Biol. 23(6):1129-1138; and
Matsuoka et
al. (1993) Proc. Natl. Acad. Sci. USA 90(20):9586-9590.
"Seed-preferred" promoters include both "seed-specific" promoters (those
promoters active during seed development such as promoters of seed storage
proteins)
as well as "seed-germinating" promoters (those promoters active during seed
germination). See Thompson et at. (1989) BioEssays 10:10$.
Such seed-preferred promoters include, but are not limited to, Cim1
(cytokinin-induced message); cZ19B I (maize 19 kDa zein); milps (myo-inositol-
1-
47
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phosphate synthase); and celA (cellulose synthase) (see WO 00/11177).
Gama-zein is a preferred endosperm-specific promoter.
Glob-I is a preferred embryo-specific promoter. For dicots, seed-specific
promoters
include, but are not limited to, bean (3-phaseolin, napin, (3-conglycinin,
soybean lectin,
cruciferin, and the like. For monocots, seed-specific promoters include, but
are not
limited to, maize 15 kDa zein, 22 kDa zein, 27 kDa zein, g-zein, waxy,
shrunken 1,
shrunken 2, globulin 1, etc. See also WO 00/12733, where seed-preferred
promoters
from end] and end2 genes are disclosed.
The method of transformation/transfection is not critical to the instant
invention; various methods of transformation or transfection are currently
available.
As newer methods are available to transform crops or other host cells they may
be
directly applied. Accordingly, a wide variety of methods have been developed
to
insert a DNA sequence into the genome of a host cell to obtain the
transcription
and/or translation of the sequence to effect phenotypic changes in the
organism.
Thus, any method, which provides for effective transfer nation/transfection
may be
employed.
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. Suitable methods of introducing
nucleotide sequences into plant cells and subsequent insertion into the plant
genome
include microinjection (Crossway et al. (1986) Biotechniques 4:320-334),
electroporation (Riggs et al. (1986) Proc. Natl. Acad. Sci. USA 83:5602-5606,
Agrobacteriurn-mediated transformation (Townsend et al., U.S. Patent No.
5,563,055;
Zhao et al., U.S. Patent No. 5,981,840), direct gene transfer (Paszkowski et
al. (1984)
EMBO J. 3:2717-2722), and ballistic particle acceleration (see,. for example,
Sanford
et al., U.S. Patent No. 4,945,050; Tomes et al., U.S. Patent No. 5,879,918;
Tomes et
al., U.S. Patent No. 5,886,244; Bidney et al., U.S. Patent No. 5,932,782;
McCabe et
al. (1988) Biotechnology 6:923-926); and Lecl transformation (WO 00/28058).
Also
see Weissinger et at. (1988) Ann. Rev. Genet. 22:421-477; Sanford et al.
(1987)
Particulate Science and Technology 5:27-3 7 (onion); Christou et al. (1988)
Plant
Physiol. 87:671-674 (soybean); McCabe et al. (1988) Bio/Technology 6:923-926
(soybean); Finer and McMullen (1991) In Vitro Cell Dev. Biol. 27P:175-182
(soybean); Singh et al. (1998) Theor. App! Genet. 96:319-324 (soybean); Datta
et al.
48
CA 02724158 2010-12-01
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(1990) Biotechnology 8:736-740 (rice); Klein et al. (1988) Proc. Natl. Acad.
Sci. USA
85:4305-4309 (maize); Klein et al. (1988) Biotechnology 6:559-563 (maize);
Tomes,
U.S. Patent No. 5,240,855; Buising et al., U.S. Patent Nos. 5,322,783 and
5,324,646;
Tomes et al. (1995) 'Direct DNA Transfer into Intact Plant Cells via
Microprojectile
S Bombardment," in Plant Cell, Tissue, and Organ Culture: Fundamental Methods,
ed.
Gamborg (Springer-Verlag, Berlin) (maize); Klein et al. (1988) Plant Physiol.
91:440-444 (maize); Fromm et al. (1990) Biotechnology 8:833-839 (maize);
Hooykaas-Van Slogteren et al. (1984) Nature (London) 311:763-764; Bowen et
al.,
U.S. Patent No. 5,736,369 (cereals); Bytebier et al. (1987) Proc. Natl. Acad.
Sci. USA
84:5345-5349 (Litiaceae); De Wet et at. (1985) in The Experimental
Manipulation of
Ovule Tissues, ed. Chapman et al. (Longman, New York), pp. 197-209 (pollen);
Kaeppler et al. (1990) Plant Cell Reports 9:415-418 and Kaeppler et al. (1992)
Theor.
Appl. Genet. 84:560-566 (whisker-mediated transformation); D'Halluin et al.
(1992)
Plant Cell 4:1495-1505 (clectroporation); Li et al. (1993) Plant Cell Reports
12:250-
255 and Christou and Ford (1995) Annals ofDotant' 75:407-413 (rice); Osjoda et
al.
(1996) Nature Biotechnology 14:745-750 (maize via Agrobacterium tumefaciens).
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 hybr id having
constitutive expression of the desired phenotypic characteristic identified.
Two or
more generations may he grown to ensure that expression of the desired
phenotypic
characteristic is stably maintained and inherited and then seeds harvested to
ensure
that expression of the desired phenotypic characteristic has been achieved.
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 (Zea mays), Brassica sp. (e.g., B.
napus, B. rapa, B.
juncea), particularly those Brassica species useful as sources of seed oil,
alfalfa
(Medicago sativa), rice (Oiyza sativa), rye (Secale cereale), sorghum (Sorghum
bicolor,
Sorghum vulgare), millet (e.g., pearl millet (Pennisetum glaucurn), proso
millet
(Panicunn miliaceum), foxtail millet (Setaria italica), finger millet
(Eleusine coracana)),
sunflower (Helianthus annuus), safflower (Carthamus tinctorius), wheat
(Triticum
49
CA 02724158 2010-12-01
WO 03/000863 PCT/US02/211'r t
aestivum), soybean (Glycine max), tobacco (Nicotiana tabacum), potato (Solanum
tuberosum), .peanuts (Arachis hypogaea), cotton (Gossypiwn barbadense,
Gossypium
hirsutuni), sweet potato (Ipornoea batatas), cassava (Manihot esculenta),
coffee (Coffea
spp.), coconut (Cocos nucifer-a), pineapple _(Ananas coinosus), citrus trees
(Citrus spp.),
cocoa (Theobroma cacao), tea (Camellia sinensis), banana (Musa spp.), avocado
(Persea americana), fig (Ficus casica), guava (Psidium guajava), mango
(Mangifera
indica), olive (Olea europaea), papaya (Carica papaya), cashew (Anacardium
occidentale), macadamia (Macadamia integrifolia), almond (Prunus amygdalus),
sugar
beets (Beta vulgaris), sugarcane (Saccharum spp.), oats, barley, vegetables,
ornamentals,
and conifers.
Vegetables include tomatoes (Lycopersicon esculentum), lettuce (e.g., Lactuca
sativa), green beans (Phaseolus vulgar is), lima beans (Phaseolus limensis),
peas
(Lathyrus spp., Pisurn spp.), and members of the genus Cucumis such as
cucumber (C.
sativus), cantaloupe (C. cantalupensis), and musk melon (C melo). Ornamentals
include azalea (Rhododendron spp.), hydrangea (Hydrangea macrophylla),
hibiscus
(Hibiscus rosasanensis), roses (Rosa spp.), tulips (Tulipa spp.), daffodils
(Narcissus
spp.), petunias (Petunia hybrida), carnation (Dianthus caryophyllus),
poinsettia
(Euphorbia pulcherrima), and chrysanthemum. Conifers that may be employed in
practicing the present invention include, for example, pines such as loblolly
pine (Pinus
taeda), slash pine (Pines elliotii), ponderosa pine (Pinusponderosa),
lodgepole pine
(Pinus contorta), and Monterey pine (Pinus radiata); Douglas-fir (Pseudotsuga
menziesii); Western hemlock (Tsuga canadensis); Sitka spruce (Picea glauca);
redwood
(Sequoia sempervirens); true firs such as silver fir (Abies amabilis) and
balsam fir (Abies
balsamea); and cedars such as Western red cedar (Tliuja plicata) and Alaska
yellow-cedar (Chamaec) paris nootkatensis). Preferably, plants of the present
invention
are crop plants (for example, corn, alfalfa, sunflower, Brassica, soybean,
cotton,
safflower, peanut, sorghum, wheat, millet, tobacco, etc.), more preferably
corn and
soybean plants, yet more preferably corn plants.
Prokaryotic cells may be used as hosts for expression. Prokaryotes most
frequently are represented by various strains of E. coli; however, other
microbial
strains may also be used. Commonly used prokaryotic control sequences which
are
defined herein to include promoters for transcription initiation, optionally
with an
operator, along with ribosome binding sequences, include such commonly used
CA 02724158 2010-12-01
WO 03/000863 PCT/US02/21177
promoters as the beta lactamase (penicillinase) and lactose (lac) promoter
systems
(Chang et al. (1977) Nature 198:1056), the tryptophan (trp) promoter system
(Goeddel et al. (1980) Nucleic Acids Res. 8:4057) and the lambda derived PL
promoter and N-gene ribosome binding site (Simatake and Rosenberg (1981)
Nature
292:128). Examples of selection markers for E. coli include, for example,
genes
specifying resistance to ampicillin, tetracycline, or chloramphenicol.
The vector is selected to allow introduction into the appropriate host cell.
Bacterial vectors are typically of plasmid or phage origin. Appropriate
bacterial cells
are infected with phage vector particles or transfected with naked phage
vector DNA.
If a plasmid vector is used, the bacterial cells are transfected with the
plasmid vector
DNA. Expression systems for expressing a protein of the present invention are
available using Bacillus sp. and Salmonella (Palva et al. (1983) Gene 22:229-
235 and
Mosbach et al. (1983) Nature 302:543-545).
A variety of eukaryotic expression systems such as yeast, insect cell lines,
plant and mammalian cells, are known to those of skill in the art. As
explained briefly
below, a polynucleotide of the present invention can be expressed in these
eukaryotic
systems. In some embodiments, transformed/transfected plant cells, as
discussed
infra, are employed as expression systems for production of the proteins of
the instant
invention. Such antimicrobial proteins can be used for any application
including
coating surfaces to target microbes as described further infra.
Synthesis of heterologous nucleotide sequences in yeast is well known.
Sherman, F., et al. (1982) Methods in Yeast Genetics, Cold Spring Harbor
Laboratory
is a well recognized work describing the various methods available to produce
proteins in yeast. Two widely utilized yeasts for production of eukaryotic
proteins are
Saccharonryces cerevisiae and Pichia pastoris. Vectors, strains, and protocols
for
expression in Saccharonryces and Pichia are known in the art and available
from
commercial suppliers (e.g., Invitrogen). Suitable vectors usually have
expression
control sequences, such as promoters, including 3-phosphoglycerate kinase or
alcohol
oxidase, and an origin of replication, termination sequences and the like, as
desired.
A protein of the present invention, once expressed, can be isolated from yeast
by lysing the cells and applying standard protein isolation techniques to the
lysates.
The monitoring of the purification process can be accomplished by using
Western blot
techniques, radioimmunoassay, or other standard immunoassay techniques.
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WO 03/000863 PCT/US02/211
The sequences of the present invention can also be ligated to various
expression vectors for use in transfecting cell cultures of, for instance,
mammalian,
insect, or plant origin. Illustrative cell cultures useful for the production
of the
peptides are mammalian cells. A number of suitable host cell lines capable of
expressing intact proteins have been developed in the art, and include the
HEK293,
BHK21, and CHO cell lines. Expression vectors for these cells can include
expression control sequences, such as an origin of replication, a promoter
(e.g. the
CMV promoter, a HSV tk promoter or pgk (phosphoglycerate kinase) promoter), an
enhancer (Queen et al. (1986) bnmunol. Rev. 89:49), and necessary processing
information sites, such as ribosome binding sites, RNA splice sites,
polyadenylation
sites (e.g., an SV40 large T Ag poly A addition site), and transcriptional
terminator
sequences. Other animal cells useful for production of proteins of the present
invention are available, for instance, from the American Type Culture
Collection.
Appropriate vectors for expressing proteins of the present invention in insect
cells are usually derived from the SF9 baculovirus. Suitable insect cell lines
include
mosquito larvae, silkworm, armyworm, moth and Drosophila cell lines such as a
Schneider cell line (See, Schneider (1987) J. Embryol. Exp. Morphol. 27:353-
365).
As with yeast, when higher animal or plant host cells are employed,
polyadenylation or transcription terminator sequences are typically
incorporated into
the vector. An example of a terminator sequence is the polyadenylation
sequence
from the bovine growth hormone gene. Sequences for accurate splicing of the
transcript may also be included. An example of a splicing sequence is the VPI
intron
from SV40 (Sprague, et al. (1983) J. Virol. 45:773-781). Additionally, gene
sequences to control replication in the host cell may be incorporated into the
vector
such as those found in bovine papilloma virus type-vectors. Saveria-Campo, M.,
(1985) Bovine Papilloma Virus DNA a Eukaryotic Cloning Vector in DNA Cloning
Vol. II a Practical Approach, D.M. Glover, Ed., IRL Press, Arlington, Virginia
pp.-
213-238.
Animal and lower eukaryotic (e.g., yeast) host cells are competent or rendered
competent for transfection by various means. There are several well-known
methods
of introducing DNA into animal cells. These include: calcium phosphate
precipitation, fusion of the recipient cells with bacterial protoplasts
containing the
DNA, treatment of the recipient cells with liposomes containing the DNA, DEAF
52
CA 02724158 2010-12-01
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dextrin, electroporation, biolistics, and micro-injection of the DNA directly
into the
cells. The transfected cells are cultured by means well known in the art.
Kuchler,
R.J. (1997) Biochemical Methods in Cell Culture and Virology, Dowden,
Hutchinson
and Ross, Inc.
It is recognized that with these nucleotide sequences, antisense
constructions,
complementary to at least a portion of the messenger RNA (mRNA) for the
defensin
sequences can be constructed. Antisense nucleotides are constructed to
hybridize
with the corresponding mRNA. Modifications of the antisense sequences may be
made as long as the sequences hybridize to and interfere with expression of
the
corresponding mRNA. In this manner, antisense constructions having 70%,
preferably 80%, more preferably 85% sequence identity to the corresponding
antisensed sequences may be used. Furthermore, portions of the antisense
nucleotides
may be used to disrupt the expression of the target gene. Generally, sequences
of at
least 50 nucleotides, 100 nucleotides, 200 ntucleotides, or.grcoter nin.y be
used.
The nucleotide sequences of the present. invention may also be used in the
sense orientation to suppress the expression of endogenous genes in plants.
Methods
for suppressing gene expression in plants using nucleotide sequences in the
sense
orientation are known in the art. The methods generally involve transforming
plants
with a DNA construct comprising a promoter that drives expression in a plant
operably linked to at least a portion of a nucleotide sequence that
corresponds to the
transcript of the endogenous gene. Typically, such a nucleotide sequence has
substantial sequence identity to the sequence of the transcript of the
endogenous gene,
preferably greater than about 65% sequence identity, more preferably greater
than
about 85% sequence identity, most preferably greater than about 95% sequence
identity. See U.S. Patent Nos. 5,283,184 and 5,034,323.
In some embodiments, the content and/or composition of polypeptides of the
present invention in a plant may be modulated by altering, in vivo or in
vitro, the
promoter of the nucleotide sequence to up- or down-regulate expression. For
instance, an isolated nucleic acid comprising a promoter sequence operably
linked to
a polynucleotide of the present invention is transfected into a plant cell.
Subsequently, a plant cell comprising the promoter operably linked to a
polynucleotide of the present invention is selected for by means known to
those of
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CA 02724158 2010-12-01
WO 03/000863 PCT/US02t21I Ti
skill in the art such as, but not limited to, Southern blot, DNA sequencing,
or PCR
analysis using primers specific to the promoter and to the gene and detecting
amplicons produced therefrom. A plant or plant part altered or modified by the
foregoing embodiments is grown under plant forming conditions for a time
sufficient
to modulate the concentration and/or composition of polypeptides of the
present
invention in the plant. Plant forming conditions are well known in the art and
discussed briefly, supra. Detection of expression of a polypeptide of the
invention
occurs through any method known to one of skill in the art including, but not
limited
to, immunolocalization.
In general, concentration or composition of the polypeptides of the invention
is increased or decreased by at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%,
80%, or 90% relative to a native control plant, plant part, or cell lacking
the
aforementioned recombinant expression cassette. Modulation in the present
invention
may occur during and/or subsequent to growth of the plant to the desired stage
of
development. Modulating nucleic acid expression temporally and/or in
particular
tissues can be controlled by employing the appropriate promoter operably
linked to a
polynucleotide of the present invention in, for example, sense or antisense
orientation
as discussed in greater detail, supra. Induction of expression of a
polynucleotide of
the present invention can also be controlled by exogenous administration of an
effective amount of inducing compound. Inducible promoters and inducing
compounds, which activate expression from these promoters, are well known in
the
art. In various embodiments, the polypeptides of the present invention are
modulated
in crop plants, particularly maize, wheat, soybean, alfalfa, barley, oats, and
rice.
The methods of the invention can be used with other methods available in the
art for enhancing disease resistance in plants. Similarly, the antimicrobial
compositions described herein may be used alone or in combination with other
nucleotide sequences, polypeptides, or agents to protect against plant
diseases and
pathogens. Although any one of a variety of second nucleotide sequences may be
utilized, specific embodiments of the invention encompass those second
nucleotide
sequences that, when expressed in a plant, help to increase the resistance. of
a plant to
pathogens.
Proteins, peptides, and lysozymes that. naturally occur in insects (Jaynes et
al.
(1987) Bioassays 6:263-270), plants (Broekaert et at. (1997) Critical Reviews
in Plant
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Sciences 16:297-323), animals (Vunnam et al. (1997) J. Peptide Res. 49:59-66),
and
humans (Mitra and Zang (1994) Plant Physiol. 106:977-981; Nakajima et al.
(1997)
Plant Cell Reports 16:674-679) are also a potential source of plant disease
resistance.
(Ko, K. (2000) the American Phytopathological Society website).
Examples of such plant resistance-conferring sequences include those encoding
sunflower rhoGTPase-Activating Protein (rhoGAP), lipoxygenase (LOX), Alcohol
Dehydrogenase (ADH), and Sclerotinia-Inducible Protein-1 (SCIP-1) described in
U.S. Patent No. 6,709,865. These nucleotide
sequences enhance plant disease resistance through the modulation of
development,
developmental pathways, and the plant pathogen defense system. Other plant
defense
proteins include those described in WO 99/43823 and WO 99/43821õ
It is recognized that such second nucleotide
sequences may be used in either the sense or antisense orientation depending
on the
desired outcome.
In another embodiment, the defensins comprise isolated polypeptides of the
invention- The defensins of the invention find use in the decontamination of
plant
pathogens during the processing of grain for animal or human food consumption;
during the processing of feedstuffs, and during the processing of plant
material for
silage. In this embodiment, the defensins of the invention are presented to
grain, plant
material for silage, or a contaminated food crop, or during an appropriate
stage of the
processing procedure, in amounts effective for antimicrobial activity. The
compositions can be applied to the environment of a plant pathogen by, for
example,
spraying, atomizing, dusting, scattering, coating or pouring, introducing into
or on the
soil, introducing into irrigation water, by seed treatment, or dusting at a
time when the
plant pathogen has begun to appear or before the appearance ofpests as a
protective
measure. It is recognized that any means that bring the defensive agent
polypeptides
in contact with the plant pathogen can be used in the practice of the
invention.
Additionally, the compositions can be used in formulations used for their
antimicrobial activities. Methods are provided for controlling plant pathogens
comprising applying a decontaminating amount of a polypeptide or composition
of
the invention to the environment of the plant pathogen. The polypeptides of
the
invention can be formulated with an acceptable carrier into a composition(s)
that is,
for example, a suspension, a solution, an emulsion, a dusting powder, a
dispersible
CA 02724158 2010-12-01
WO 03/000863 PCT/US02/2117 ,
granule, a wettable powder, an emulsifiable concentrate, an aerosol, an
impregnated
granule, an adjuvant, a coatable paste, and also encapsulations in, for
example,
polymer substances.
Such compositions disclosed above may be obtained by the addition of a
surface-active agent, an inert carrier, a preservative, a humectant, a feeding
stimulant,
an attractant, an encapsulating agent, a binder, an emulsifier, a dye, a UV
protectant, a
buffer, a flow agent or fertilizers, micronutrient donors or other
preparations that
influence plant growth. One or more agrochemicals including, but not limited
to,
herbicides, insecticides, fungicides, bacteriocides, nematocides,
molluscicides,
acaracides, plant growth regulators, harvest aids, and fertilizers, can be
combined with
carriers, surfactants, or adjuvants customarily employed in the art of
formulation or
other components to facilitate product handling and application for particular
target
mycotoxins. Suitable carriers and adjuvants can be solid or liquid and
correspond to
the substances ordinarily employed in formulation technology, e.g., natural or
regenerated mineral substances, solvents, dispersants, wetting agents,
tackifiers,
binders, or fertilizers. The 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. In some
embodiments, methods of applying an active ingredient of the present invention
or an
agrochemical composition of the present invention (which contains at least one
of the
proteins of the present invention) are foliar application, seed coating, and
soil
application.
Suitable surface-active agents include, but are not limited to, anionic
compounds such as a carboxylate of, for example, a metal; a carboxylate of a
long
chain fatty acid; an N-acylsarcosinate; mono or di-esters of phosphoric acid
with fatty
alcohol ethoxylates or salts of such esters; fatty alcohol sulfates such as
sodium
dodecyl sulfate, sodium octadecyl sulfate, or sodium cetyl sulfate;
ethoxylated fatty
alcohol sulfates; ethoxylated alkylphenol sulfates; lignin sulfonates;
petroleum
sulfonates; alkyl aryl sulfonates such as alkyl-benzene sulfonates or lower
alkylnaphtalene sulfonates, e.g., butyl-naphthalene sulfonate; salts of
sulfonated
naphthalene-formaldehyde condensates; salts of sulfonated phenol-formaldehyde
condensates; more complex sulfonates such as the amide sulfonates, e.g., the
sulfonated condensation product of oleic acid and N -methyl taurine; or the
diallcyl
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WO 03/000863 PCT/US02/21177
sulfosuccinates, e.g., the sodium sulfonate or dioctyl succinate. Non-ionic
agents
include condensation products of fatty acid esters, fatty alcohols, fatty acid
amides or
fatty-alkyl- or alkenyl-substituted phenols with ethylene oxide, fatty esters
of
polyhydric alcohol ethers, e.g., sorbitan fatty acid esters, condensation
products of
such esters with ethylene oxide, e.g. polyoxyethylene sorbitar fatty acid
esters, block
copolymers of ethylene oxide and propylene oxide, acetylenic glycols such as
2, 4, 7,
9-tetraethyl-5-decyn-4, 7-diol, or ethoxylated acetylenic glycols. Examples of
a
cationic surface-active agent include, for instance, an aliphatic mono-, di-,
or
polyamine such as an acetate, naphthenate, or oleate; or oxygen-containing
amine
such as an amine oxide of polyoxyethylene alkylamine; an amide-linked amine
prepared by the condensation of a carboxylic acid with a di- or polyamine; or
a
quaternary ammonium salt.
Examples of inert materials include, but are not limited to, inorganic
minerals
such as kaolin, phyllosilicates, carbonates, sulfates, phosphates, or
botanical materials
such as cork, powdered corncobs, peanut hulls, rice hulls, and walnut shells.
The compositions of the present invention can be in a suitable form for direct
application or as concentrate of primary composition, which requires dilution
with a
suitable quantity of water or other diluent before application. The
decontaminating
concentration will vary depending upon the nature of the particular
formulation,
specifically, whether it is a concentrate or to be used directly.
In a further embodiment, the compositions, as well as the polypeptides of the
present invention can be treated prior to formulation to prolong the activity
when
applied to the environment of a plant pathogen as long as the pretreatment is
not
deleterious to the activity. Such treatment can be by chemical and/or physical
means
as long as the treatment does not deleteriously affect the properties of the
composition(s). Examples of chemical reagents include, but are not limited to,
halogenating agents; aldehydes such as formaldehyde and glutaraldehyde; anti-
infectives, such as zephiran chloride; alcohols, such as isopropanol and
ethanol; and
histological fixatives, such as Bouin's fixative and Helly's fixative (see,
for example,
Humason (1967) Animal Tissue Techniques (W.H. Freeman and Co.)).
In an embodiment of the invention, the compositions of the invention
comprise a microbe having stably integrated the nucleotide sequence of a
defensive
agent. The resulting microbes can be processed and used as a microbial spray.
Any
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v'O 03/000863 PCT/US02/211 ~
suitable microorganism can be used for this purpose. See, for example,
Gaertner et al.
(1993) in Advanced Engineered Pesticides, Kim (Ed.). In one embodiment, the
nucleotide sequences of the invention are introduced into microorganisms that
multiply on plants (epiphytes) to deliver the defensins to potential target
crops.
Epiphytes can be, for example, gram-positive or gram-negative bacteria.
It is further recognized that whole, i.e., unlysed, cells of the transformed
microorganism can be treated with reagents that prolong the activity of the
polypeptide produced in the microorganism when the microorganism is applied to
the
environment of a target plant. A secretion signal sequence may be used in
combination with the gene of interest such that the resulting enzyme is
secreted
outside the microorganism for presentation to the target plant.
In this manner, a gene encoding a defensive agent of the invention may be
introduced via a suitable vector into a microbial host, and said transformed
host
applied to the environment, plants, or animals. Microorganism hosts that are
known
to occupy the "phytosphere" (phylloplane, phyllosphere, rhizosphere, and/or
rhizoplane) of one or more crops of interest may be selected for
transformation.
These microorganisms are selected so as to be capable of successfully
competing in
the particular environment with the wild-type microorganisms, to provide for
stable
maintenance and expression of the gene expressing the detoxifying polypeptide,
and
for improved protection of the proteins of the invention from environmental
degradation and inactivation.
Such microorganisms include bacteria, algae, and fungi. Illustrative
prokaryotes, both Gram-negative and -positive, include Enterobacteriaceae,
such as
Escherichia, Erwinia, Shigella, Salmonella, and Proteus; Bacillaceae;
Rhizobiaceae,-
such as Rhizobium; Spirillaceae, such as photobacterium, Zynzonzonas,
Serratia,
Aeromonas, Vibrio, Desulfovibrio, Spirillum; Lactobacillaceae;
Pseudomonadaceae,
such as Pseudomonas and Acetobacter; Azotobacteraceae; and Nitrobacteraceae.
Among eukaryotes are fungi, such as Phycomycetes and Ascomycetes, which
includes
yeast, such as Saccharomyces and Sclzizosaccharoznyces; and Basidionzycetes
yeast,
such as Rhodotorula, Aureobasidium, Sporobolomyces, and the like. Of
particlular
interest are microorganisms, such as bacteria, e.g., Pseudomonas, Erwinia,
Serratia,
Klebsiella, Xanthomonas, Streptomyces, Rhizobium, Rhodopseudomonas, Methylius,
Agrobacterium, Acetobacter, Lactobacillus, Arthrobacter, Azotobacter,
Leuconostoc,
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WO 03/000863 PCT/US02/21177
and Alcaligenes; fungi, particularly yeast, e.g., Saccharomyces, Pichia,
Cryptococcus,
Kluyveromyces, Sporobolomyces, Rhodotorula, Aureobasidiuni, and Gliocladium.
Of
particular interest are such phytosphere bacterial species as Pseudomonas
syringae,
Pseudoinonasfluorescens, Serratia marcescens, Acetobacterxylinum,
Agrobacteria,
Rhodopseudomonas spheroides, Xanthomonas campestris, Rhizobium melioti,
Alcaligenes entrophus, Clavibacter.xyli, and Azotobacter vinlandii; and
phytosphere
yeast species such as Rhodotorula rubra, R. glutinis, R. marina, R.
aurantiaca,
Cryptococcus albidus, C. diffluens, C. laurentii, Saccharomyces rosei, S.
pretoriensis,
S. cerevisiae, Sporobolomyces roseus, S. odorus, Kluyveroinyces veronae, and
Aureobasidium pullulans.
In an embodiment of the invention, the defensins of the invention may be used
as a pharmaceutical compound for treatment of fungal and microbial pathogens
in
humans and other animals. Diseases and disorders caused by fungal and
microbial
pathogens include but are not limited to fungal meningoencephalitis,
superficial
fungal infections, ringworm, Athlete's foot, histoplasmosis, candidiasis,
thrush,
coccidioidoina, pulmonary cryptococcus, trichosporonosis, piedra, tinea nigra,
fungal
keratitis, onychomycosis, tinea capitis, chromomycosis, aspergillosis,
endobronchial
pulmonary aspergillosis, mucormycosis, chromoblastomycosis, dermatophytosis,
tinea, fusariosis, pityriasis, mycetoma, pseudallescheriasis, and
sporotrichosis.
In particular, the compositions of the invention may be used as pharmaceutical
compounds to provide treatment for diseases and disorders associated with, but
not
limited to, the following fungal pathogens: Histoplasma capsulatum, Candida
spp. (C
albicans, C. tropicalis, C. parapsilosis, C. guilliermondii, C.
glabrata/Torulopsis
glabrata, C. krusei, C. lusitaniae), Aspergillus fumigatus, A. flavus, A.
niger,
Rhizopus spp., Rhizomucor spp., Cunninghamella spp., Apophysomyces spp.,
Saksenaee spp., Mucor spp.., and Absidia spp. Efficacy of the compositions of
the
invention as anti-fungal treatments may be determined through anti-fungal
assays
known to one in the art.
The defensins may be administered to a patient through numerous means.
Systemic administration can also be by transmucosal or transdermal means. For
transmucosal or transdermal administration, penetrants appropriate to the
barrier to be
permeated are used in the formulation. Such penetrants are generally known in
the
art, and include, for example, for transmucosal administration, detergents,
bile salts,
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CVO 031000863 PCT/US02/21 l
and fusidic acid derivatives. Transmucosal administration can be accomplished
through the use of nasal sprays or suppositories. For transdermal
administration, the
active compounds are formulated into ointments, salves, gels, or creams as
generally
known in the art. The compounds can also be prepared in the fonn of
suppositories
(e.g., with conventional suppository bases such as cocoa butter and other
glycerides)
or retention enemas for rectal delivery.
In one embodiment, the active compounds are prepared with carriers that will
protect the compound against rapid elimination from the body, such as a
controlled
release formulation, including implants and microencapsulated delivery
systems.
Biodegradable, biocompatible polymers can be used, such as ethylene vinyl
acetate,
polyanhydrides, polyglycolic acid, collagen, pol'yorthoesters, and polylactic
acid.
Methods for preparation of such formulations will be apparent to those skilled
in the
art. The materials can also be obtained commercially from Alza Corporation and
Nova Pharmaceuticals, Inc. Liposomal suspensions (including liposomes targeted
to
infected cells with monoclonal antibodies to viral antigens) can also be used
as
pharmaceutically acceptable carriers. These can be prepared according to
methods
known to those skilled in the art, for example, as described in U.S. Patent
No.
4,522,811.
It is especially advantageous to formulate oral or parenteral compositions in
dosage unit form for ease of administration and uniformity of dosage. Dosage
unit
form as used herein refers to physically discrete units suited as unitary
dosages for the
subject to be treated with each unit containing a predetermined quantity of
active
compound calculated to produce the desired therapeutic effect in association
with the
required pharmaceutical carrier. Depending on the type and severity of the
disease,
about 1 p.g/kg to about 15 mg/kg (e.g., 0.1 to 20 mg/kg) of active compound is
an
initial candidate dosage for administration to the patient, whether, for
example, by one
or more separate administrations, or by continuous infusion. A typical daily
dosage
might range from about 1 pg/kg to about 100 mg/kg or more, depending on the
factors mentioned above. For repeated administrations over several days or
longer,
depending on the condition, the treatment is sustained until a desired
suppression of
disease symptoms occurs. However, other dosage regimens may be useful. The
progress of this therapy is easily monitored by conventional techniques and
assays.
An exemplary dosing regimen is disclosed in WO 94/04188. The specification for
the
CA 02724158 2010-12-01
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dosage unit forms of the invention are dictated by and directly dependent on
the
unique characteristics of the active compound and the particular therapeutic
effect to
be achieved, and the limitations inherent in the art of compounding such an
active
compound for the treatment of individuals.
"Treatment" is herein defined as the application or administration of a
therapeutic agent to a patient, or application or administration of a
therapeutic agent to
an isolated tissue or cell line from a patient, who has a disease, a symptom
of disease
or a predisposition toward a disease, with the purpose to cure, heal,
alleviate, relieve,
alter, remedy, ameliorate, improve or affect the disease, the symptoms of
disease or
the predisposition toward disease. A "therapeutic agent"comprises, but is not
limited
to, the small molecules, peptides, antibodies, and antisense oligonucleotides
of the
invention.
The defensins of the invention can be used for any application including
coating surfaces to target microbes. In this manner, target microbes include
human
puthogeus or microorganisms. Surfaces that blight be coated with the defensins
of the
invention include carpets and sterile medical facilities. Polymer bound
polypeptides
of the invention may be used to coat surfaces. Methods for incorporating
compositions with antimicrobial properties into polymers are known in the art.
See
U.S. Patent No. 5,847,047
An isolated polypeptide of the invention can be used as an immunogen to
generate antibodies that bind defensins using standard techniques for
polyclonal and
'monoclonal antibody preparation. The full-length defensins can be used or,
alternatively, the invention provides antigenic peptide fragments of defensins
for use
as immunogens. The antigenic peptide of a defensive agent comprises at least
8,
preferably 10, 15, 20, or 30 amino acid residues of the amino acid sequence
shown in
SEQ ID NO: 2, 3, 5, 6, 8, 9, 11, 12, 14, 15, 17, 18, 20, 21, 23, 24, 26, 27,
29, 30, 32,.
33, 35, 36, 38, 39, 41, 42, 44, 45, 47, 48, 50, 51, 53, 54, 56, 57, 59, 60,
62, 63, 65, 66,
68, 69, 71, 72, 74, 75, 77, 78, 80, 81, 83, 84, 86, 87, 89, 90, 92, 93, 95,
96, 98, 99,
101, 102, 104, 105, 107, 108, 110, 111, 113,114, 116,117, 119, 120, 122, 123,
125,
126, 128, 129, 131, 132, 134, 135, 137, 138, 140, 141, 143, 144, 146, 147,
149, 150,
152, 153, 155, 156, 158, 159, 161, 162, 164, 165, 167, 168, 170, 171, 173,
174, 176,
177, 179, 180, 182, 183, 185, 186, 188, 189, 191, 192, 194, 195, 197, 198,
200, 201,
203, 204, 206, 207, 209, 210, 212, 213, 215, 216, 218, 219, 221, 222, 224,
225, 227,
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WO 03/000863 PCT/US02/2117't
228, 230, 231, 233, 234, 236, 237, 239, 240, 242, 243, 245, 246, 248, 249,
251, 252,
254, 255, 257, 258, 260, 261, 263, 264, 266, 267, 269, 270, 272, 273, 275,
276, 278,
279, 281, 282, 284, 285, 287, 288, 290, 291, 293, 294, 296, 297, 299, 300,
302, 303,
305, 306, 308, 309, 311, 312, 314, 315, 317, 318, 320, 321, 323, 324, 326,
327, 329,
330, 332, 333, 335, 336, 338, 339, 341, 342, 344, 345, 347, 348, 350, 351,
353, 354,
356, 357, 359, 360, 362, 363, 365, 366, 368, 369, 371, 372, 374, 375, 377,
378, 380,
381, 383, 384, 386, 387, 389, 390, 392, 393, 395, 396, 398, 399, 401, 402,
404, 405,
407, 408, 410, 411, 413, 414, 416, 417, 419, 420, 422, 423, 425, 426, 428,
429, 431,
432, 434, 435, 437, 438, 440, 441, 443, 444, 446, 447, 449, 450, 452, 453,
455, 456,
458, 459, 461, 462, 464, 466, or 468 and encompasses an epitope of a defensin
such
that an antibody raised against the peptide forms a specific immune complex
with the
antimicrobial polypeptides. Epitopes encompassed by the antigenic peptide are
regions of defensins that are located on the surface of the protein, e.g.,
hydrophilic
regions, which are readily ascertainable by those of skill in the art.
Accordingly, another aspect of the invention pertains to anti-defensin
polyclonal and monoclonal antibodies that bind a defensin. Polyclonal defensin-
like,
antibodies can be prepared by immunizing a suitable subject (e.g., rabbit,
goat, mouse,
or other mammal) with an defensive agent immunogen. The anti-defensin antibody
-4
titer in the immunized subject can be monitored over time by standard
techniques, 20 such as with an enzyme linked immunosorbent assay (ELISA) using
immobilized
antimicrobial polypeptides. At an appropriate time after immunization, e.g.,
when the
anti-defensive agent antibody titers are highest, antibody-producing cells can
be
obtained from the subject and used to prepare monoclonal antibodies by
standard
techniques, such as the hybridoma technique originally described by Kohler and
Milstein (1975) Nature 256:495-497, the human B cell hybridoma technique
(Kozbor
et al. (1983) Iinmunol. Today 4:72), the EBV-hybridoma technique (Cole et al.
(1985)
in Monoclonal Antibodies and Cancer Therapy, ed. Reisfeld and Sell (Alan R.
Liss,
Inc., New York, NY), pp. 77-96) or trioma techniques. The technology for
producing
hybridomas is well known (see generally Coligan et al., eds. (1994) Current
Protocols in Immunology (John Wiley & Sons, Inc., New York, NY); Gaifre et al.
(1977) Nature 266:55052; Kenneth (1980) in Monoclonal Antibodies: A Neu
Dimension In Biological Analyses (Plenum Publishing Corp., NY; and Lerner
(1981)
Yale J. Biol. Med., 54:387-402).
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Alternative to preparing monoclonal antibody-secreting hybridomas, a
monoclonal anti-defensin-like antibody can be identified and isolated by
screening a
recombinant combinatorial inununoglobulin library (e.g., an antibody phage
display
library) with a defensin to thereby isolate immunoglobulin library members
that bind
the defensive agent. Kits for generating and screening phage display libraries
are
commercially available (e.g., the Pharmacia Recombinant Phage Antibody System,
Catalog No. 27-9400-01; and the Stratagene SurJZAPTM Phage Display Kit,
Catalog
No. 240612). Additionally, examples of methods and reagents particularly
amenable
for use in generating and screening an antibody display library can be found
in, for
example, U.S. Patent No. 5,223,409; PCT Publication Nos. WO 92/18619; WO
91/17271; WO 92/20791; WO 92/15679; 93/01288; WO 92/01047; 92/09690; and
90/02809; Fuchs et al. (1991) Bio/Technology 9:1370-1372; Hay et al. (1992)
Huhn.
Antibod Hybridomas 3:81-85; Huse et al. (1989) Science 246:1275-1281;
Griffiths et
al. (1993) EMBO J. 12:725-734. The antibodies can be used to identify homologs
of
the defensins of the invention.
The following examples are offered by way of illustration and not by way of
limitation.
EXPERIMENTAL
Example 1. Transformation and Regeneration of Transgenic Plants in Maize
Immature maize embryos from greenhouse donor plants are bombarded with a
plasmid containing a defensin nucleotide sequence of the invention operably
linked to
a ubiquitin promoter and the selectable marker gene PAT (Wohlleben et al.
(1988)
Gene 70:25-37), which confers resistance to the herbicide Bialaphos.
Alternatively,
the selectable marker gene is provided on a separate plasmid. Transformation
is
performed as follows. Media recipes follow below.
Preparation of Target Tissue
The ears are husked and surface sterilized in 30% Clorox bleach plus 0.5%
Micro detergent for 20 minutes, and rinsed two times with sterile water. The
immature embryos are excised and placed embryo axis side down (scutellum side
up),
25 embryos per plate, on 560Y medium for 4 hours and then aligned within the
2.5-
cm target zone in preparation for bombardment.
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Preparation of DNA
A plasmid vector comprising a defensin nucleotide sequence of the invention
operably linked to a ubiquitin promoter is made. This plasmid DNA plus plasmid
DNA containing a PAT selectable marker is precipitated onto 1.1 m (average
diameter) tungsten pellets using a CaC12 precipitation procedure as follows:
100 l prepared tungsten particles in water
l (1 g) DNA in Tris EDTA buffer (1 g total DNA)
100 l 2.5 M CaC12
10 10 l 0.1 M spermidine
Each reagent is added sequentially to the tungsten particle suspension, while
maintained on the multitube vortexer. The final mixture is sonicated briefly
and
allowed to incubate under constant vortexing for 10 minutes. After the
precipitation
period, the tubes are centrifuged briefly, liquid removed, washed with 500 ml
100%
ethanol, and centrifuged for 30 seconds. Again the liquid is removed, and 105
l
100% ethanol is added to the final tungsten particle pellet. For particle gun
bombardment, the tungsten/DNA particles are briefly sonicated and 10 l
spotted
onto the center of each macrocarrier and allowed to dry about 2 minutes before
bombardment.
Particle Gun Treatment
The sample plates are bombarded at level #4 in particle gun #HE34-1 or
#1 E34-2. All samples receive a single shot at 650 PSI, with a total of ten
aliquots
taken from each tube of prepared particles/DNA.
Subsequent Treatment
Following bombardment, the embryos are kept on 560Y medium for 2 days,
then transferred to 560R selection medium containing 3 mg/liter Bialaphos, and
subcultured every 2 weeks. After approximately 10 weeks of selection,
selection-
resistant callus clones are transferred to 288J medium to initiate plant
regeneration.
Following somatic embryo maturation (2-4 weeks), well-developed somatic
embryos
are transferred to medium for germination and transferred to the lighted
culture room.
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Approximately 7-10 days later, developing plantlets are transferred to 272V
hormone-
free medium in tubes for 7-10 days until plantlets are well established.
Plants are then
transferred to inserts in flats (equivalent to 2.5" pot) containing potting
soil and grown
for 1 week in a growth chamber, subsequently grown an additional 1-2 weeks in
the
greenhouse, then transferred to classic 600 pots (1.6 gallon) and grown to
maturity.
Plants are monitored and scored for altered defense response defensin
activity, insect
resistance, nematode resistance, viral resistance, or fungal resistance.
Bombardment and Culture Media
Bombardment medium (560Y) comprises 4.0 g/l N6 basal salts (SIGMA C-
1416), 1.0 ml/l Eriksson's Vitamin Mix (I000X SIGMA-1511), 0.5 mg/l thiamine
HCI, 120.0 g/l sucrose, 1.0 mg/l 2,4-D, and 2.88 g/1 L-proline (brought to
volume
with D-I H2O following adjustment to pH 5.8 with KOH); 2.0 g/I Gelrite (added
after
bringing to volume with D-I H20); and 8.5 mg/I silver nitrate (added after
sterilizing
the medium and cooling to room temperature). Selection medium (560R) comprises
4.0 g11 N6 basal salts (SIGMA C-1416), 1.0 mUl Eriksson's Vitamin Mix (I000X
SIGMA-1511), 0.5 mg/I thiamine HCI, 30.0 g/l sucrose, and 2.0 mg/l 2,4-D
(brought
to volume with D-I H2O following adjustment to pH 5.8 with KOH); 3.0 g/l
Gelrite
(added after bringing to volume with D-I H2O); and 0.85 mg/t silver nitrate
and 3.0
mg/i Bialaphos (both added after sterilizing the medium and cooling to room
temperature).
Plant regeneration medium (288J) comprises 4.3 g/l MS salts (GIBCO 11117-
074), 5.0 ml/l MS vitamins stock solution (0.100 g nicotinic acid, 0.02 g/l
thiamine
HCL, 0.10 g/l pyridoxine HCL, and 0.40 g/l glycine brought to volume with
polished
D-I H20) (Murashige and Skoog (1962) Physiol. Plant. 15:473), 100 mg/l myo-
inositol, 0.5 mg/i zeatin, 60 g/l sucrose, and 1.0 ml/l of 0.1 mM abscisic
acid (brought
to volume with polished D-I H2O after adjusting to pH 5.6); 3.0 g/l Gehite
(added
after bringing to volume with D-I H20); and 1.0 mg/I indoleacetic acid and 3.0
mg/1
Bialaphos (added after sterilizing the medium and cooling to 60 C). Hormone-
free
medium (272V) comprises 4.3 g/l MS salts (GIBCO 11117-074), 5.0 ml/1 MS
vitamins stock solution (0.100 g/l nicotinic acid, 0.02 g/l thiamine HCL, 0.10
g/l
pyridoxine HCL, and 0.40 g/l glycine brought to volume with polished D-I H20),
0.1
g/l myo-inositol; and 40.0 g/1 sucrose (brought to volume with polished D-I
H2O after
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adjusting pH to 5.6); and 6 g/l bacto-agar (added after bringing to volume
with
polished D-I H20), sterilized and cooled to 60 C.
Exan le 2. Agrobacterium-mediated Transformation in Maize
S For Agrobacterium-mediated transformation of maize with a defensin
nucleotide
sequence of the invention operably linked to a ubiquitin promoter, preferably
the method
of Zhao is employed (U.S. Patent No. 5,981,840, and PCT patent publication
WO98/32326)= Briefly,
immature embryos are isolated from maize and the embryos contacted with a
suspension of Agrobacterium, where the bacteria are capable of transferring
the DNA
construct containing the defensin nucleotide sequence to at least one cell of
at least
one of the immature embryos (step 1: the infection step). In this step the
immature
embryos are preferably immersed in an Agrobacterium suspension for the
initiation of
inoculation. The embryos are co-cultured for a time with the Agrobacterium
(step 2:
the co-cultivation step). Preferably the immature embryos are cultured on
solid
medium following the infection step. Following this co-cultivation period an
optional
"resting" step is contemplated. In this resting step, the embryos are
incubated in the
presence of at least one antibiotic known to inhibit the growth of Ab
obacternan
without the addition of a selective agent for plant transformants (step 3:
resting step).
Preferably the immature embryos are cultured on solid medium with antibiotic,
but
without a selecting agent, for elimination of Agrobacterium and for a resting
phase for
the infected cells. Next, inoculated embryos are cultured on medium containing
a
selective agent and growing transformed callus is recovered (step 4: the
selection
step). Preferably, the immature embryos are cultured on solid medium with a
selective agent resulting in the selective growth of transformed cells. The
callus is
then regenerated into plants (step 5: the regeneration step), and preferably
calli grown
on selective medium are cultured on solid medium to regenerate the plants.
Example 3. Soybean Embryo Transformation
Soybean embryos are bombarded with a plasmid containing the defensin
nucleotide sequences operably linked to a ubiquitin promoter as follows. To
induce
somatic embryos, cotyledons, 3-5 mm in length dissected from surface-
sterilized,
immature seeds of the soybean cultivar A2872, are cultured in the light or
dark at
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26 C on an appropriate agar medium for six to ten weeks. Somatic embryos
producing secondary embryos are then excised and placed into a suitable liquid
medium. After repeated selection for clusters of somatic embryos that
multiplied as
early, globular-staged embryos, the suspensions are maintained as described
below.
Soybean embryogenic suspension cultures can be maintained in 35 ml liquid
media on a rotary shaker, 150 rpm, at 26 C with florescent lights on a 16:8
hour
day/night schedule. Cultures are subcultured every two weeks by inoculating
approximately 35 mg of tissue into 35 ml of liquid medium.
Soybean embryogenic suspension cultures may then be transformed by the
method of particle gun bombardment (Klein et al. (1987) Nature (London) 327:70-
73,
U.S. Patent No. 4,945,050). A Du Pont Biolistic PDS1000/HE instrument (helium
retrofit) can be used for these transformations.
A selectable marker gene that can be used to facilitate soybean transformation
is a transgene composed of the 35S promoter from Cauliflower Mosaic Virus
(Odell
et al. (1985) Nature 313:810-812), the hygromycin phosphotransferase gene from
plasmid pJR225 (from E. coli; Gritz et al. (1983) Gene 25:179-188), and the 3'
region
of the nopaline synthase gene from the T-DNA of the Ti plasmid of
Agrobacteriunt
tunmefaciens. The expression cassette comprising the defensin nucleotide
sequence
operably linked to the ubiquitin promoter can be isolated as a restriction
fragment.
This fragment can then be inserted into a unique restriction site of the
vector carrying
the marker gene.
To 50 l of a 60 mg/ml 1 m gold particle suspension is added (in order): 5 l
DNA (1 g/ l), 20 l spermidine (0.1 M), and 50 l CaC12 (2.5 M). The particle
preparation is then agitated for three minutes, spun in a microfuge for 10
seconds and
the supernatant removed. The DNA-coated particles are then washed once in 400
l
70% ethanol and resuspended in 40 l of anhydrous ethanol. The DNA/particle
suspension can be sonicated three times for one second each. Five microliters
of the
DNA-coated gold particles are then loaded on each macro carrier disk.
Approximately 300-400 mg of a two-week-old suspension culture is placed in
an empty 60x15 mm petri dish and the residual liquid removed from the tissue
with a
pipette. For each transformation experiment, approximately 5-10 plates of
tissue are
normally bombarded. Membrane rupture pressure is set at 1100 psi, and the
chamber
is evacuated to a vacuum of 28 inches mercury. The tissue is placed
approximately
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3.5 inches away from the retaining screen and bombarded three times. Following
bombardment, the tissue can be divided in half and placed back into liquid and
cultured as described above.
Five to seven days post bombardment, the liquid media may be exchanged
with fresh media, and eleven to twelve days post-bombardment with fresh media
containing 50 mg/ml hygromycin. This selective media can be refreshed weekly.
Seven to eight weeks post-bombardment, green, transformed tissue may be
observed
growing from untransformed, necrotic embryogenic clusters. Isolated green
tissue is
removed and inoculated into individual flasks to generate new, clonally
propagated,
transformed embryogenic suspension cultures. Each new line may be treated as
an
independent transformation event. These suspensions can then be subcultured
and
maintained as clusters of immature embryos or regenerated into whole plants by
maturation and germination of individual somatic embryos.
Example 4. Sunflower Meristem Tissue Transformation
Sunflower meristem tissues are transformed with an expression cassette
containing the defensin sequence operably linked to a ubiquitin promoter as
follows
(see also European Patent Number EP 0 486233,.
and Malone-Schoneberg et al. (1994) Plant Science 103:199-207). Mature
sunflower
seed (Helianthus annuus L.) are dehulled using a single wheat-head thresher.
Seeds
are surface sterilized for 30 minutes in a 20% Clorox bleach solution with the
addition
of two drops of Tween 20 per 50 ml of solution. The seeds are rinsed twice
with
sterile distilled water.
Split embryonic axis explants are prepared by a modification of procedures
described by Schrammeijer et al. (Schranuneijer et al.(1990) Plant Cell Rep.
9: 55-
60). Seeds are imbibed in distilled water for 60 minutes following the surface
sterilization procedure. The cotyledons of each seed are then broken off,
producing a
clean fracture at the plane of the embryonic axis. Following excision of the
root tip,
the explants are bisected longitudinally between the primordial leaves. The
two
halves are placed, cut surface up, on GBA medium consisting of Murashige and
Skoog mineral elements (Murashige et at. (1962) Pliysiol. Plant., 15: 473-
497),
Shepard's vitamin additions (Shepard (1980) in Emergent Techniques for the
Genetic
Improvement of Crops University of Minnesota Press, St. Paul, Minnesota), 40
mg/I
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adenine sulfate, 30 g/l sucrose, 0.5 mg/I 6-benzyl-aminopurine (BAP), 0.25
mgtl
indole-3-acetic acid (IAA), 0.1 mg/l gibberellic acid (GA3), pH 5.6, and 8 g/l
Phytagar.
The explants are subjected to microprojectile bombardment prior to
Agrobacterium treatment (Bidney et al. (1992) Plant Mol. Biol. 18: 301-313).
Thirty
to forty explarits are placed in a circle at the center of a 60 X 20 mm plate
for this
treatment. Approximately 4.7 mg of 1.8 nun tungsten microprojectiles are
resuspended in 25 ml of sterile TE buffer (10 mM Tris HCI, 1 mM EDTA, pH 8.0)
and 1.5 ml aliquots are used per bombardment. Each plate is bombarded twice
through a 150 mm nytex screen placed 2 cm above the samples in a PDS 1000
particle acceleration device.
Disarmed Agrobacterium tumefaciens strain EHA105 is used in all
transformation'experiments. A binary plasmid vector comprising the expression
cassette that contains the defensin gene operably linked to the ubiquitin
promoter is
introduced into Agrobacterium strain EHA105 via freeze-thawing as described by
Holsters et-al. (1978) Mol. Gen. Genet. 163:181-187. This plasmid further
comprises
a kanamycin selectable marker gene (i.e., nptll). Bacteria for plant
transformation
experiments are grown overnight (28 C and 100 RPM continuous agitation) in
liquid
YEP medium (10 gm/1 yeast extract, 10 gm/l Bactopeptone, and 5 gm/l NaCl, pH
7.0)
with the appropriate antibiotics required for bacterial strain and binary
plasmid
maintenance. The suspension is used when it reaches an OD600 of about 0.4 to
0.8.
The Agrobacteriuin cells are pelleted and resuspended at a final OD600 of 0.5
in an
inoculation medium comprised of 12.5 mM MES pH 5.7, 1 gm/1 NH4CI, and 0.3 gm/1
MgSO4.
Freshly bombarded explants are placed in an Agrobacterium suspension,
mixed, and left undisturbed for 30 minutes. The explants are then transferred
to GBA
medium and co-cultivated, cut surface down, at 26 C and 18-hour days. After
three
days of co-cultivation, the explants are transferred to 374B (GBA medium
lacking
growth regulators and a reduced sucrose level of 1%) supplemented with 250
mg/I
cefotaxime and 50 mg/1 kanamycin sulfate. The explants are cultured for two to
five
weeks on selection and then transferred to fresh 374B medium lacking kanamycin
for
one to two weeks of continued development. Explants with differentiating,
antibiotic-
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resistant areas of growth that have not produced shoots suitable for excision
are
transferred to GBA medium containing 250 mg/I cefotaxime for a second 3-day
. phytohonnone treatment. Leaf samples from green, kanamycin-resistant shoots
are
assayed for the presence of NPTII by ELISA and for the presence of transgene
expression by assaying for defensin-like activity.
NPTII-positive shoots are grafted to Pioneer hybrid 6440 in vitro-grown
sunflower seedling rootstock. Surface sterilized seeds are germinated in 48-0
medium
(half-strength Murashige and Skoog salts, 0.5% sucrose, 0.3% gelrite, pH 5.6)
and
grown under conditions described for explant culture. The upper portion of the
seedling is removed, a 1 cm vertical slice is made in the hypocotyl, and the
transformed shoot inserted into the cut. The entire area is wrapped with
parafilm to
secure the shoot. Grafted plants can be transferred to soil following one week
of in
vitro culture. Grafts in soil are maintained under high humidity conditions
followed
by a slow acclimatization to the greenhouse environment. Transformed sectors
of TO
;plants (parental generation) maturing in the greenhouse are identified by
NPTH
ELISA and/or by defensin-like activity analysis of leaf extracts while
transgenic seeds
harvested from NPTII-positive TO plants are identified by defensin-like
activity
analysis of small portions of dry seed cotyledon.
An alternative sunflower transformation protocol allows the recovery of
transgenic progeny without the use of chemical selection pressure. Seeds are
dehulled
and surface-sterilized for 20 minutes in a 20% Clorox bleach solution with the
addition of two to three drops of Tweed 20 per 100 ml of solution, then rinsed
three
times with distilled water. Sterilized seeds are imbibed in the dark at 26 C
for 20
hours on filter paper moistened with water. The cotyledons and root radical
are
removed, and the meristem explants are cultured on 374E (GBA medium consisting
of MS salts, Shepard vitamins, 40 mg/l adenine sulfate, 3% sucrose, 0.5 mg/l 6-
BAP,
0.25 mg/l IAA, 0.1 mg/l GA, and 0.8% Phytagar at pH 5.6) for 24 hours under
the
dark. The primary leaves are removed to expose the apical meristem, around 40
explants are placed with the apical dome facing upward in a 2 cm circle in the
center
of 374M (GBA medium with 1.2% Phytagar), and then cultured on the medium for
24
hours in the dark-
Approximately 18.8 mg of 1.8 pm tungsten particles are resuspended in 150 gl
absolute ethanol. After sonication, 8 l of it are dropped on the center of
the surface
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of macrocarrier. Each plate is bombarded twice with 650 PSI rupture discs in
the first
shelf at 26 mm of Hg helium gun vacuum.
The plasmid of interest is introduced into Ao obacterium tunzefaciens strain
EHA105 via freeze thawing as described previously. The pellet of overnight-
grown
bacteria at 28 C in a liquid YEP medium (10 g/l yeast extract, 10 g/l
Bactopeptone,
and 5 g/l NaCl, pH 7.0) in the presence of 50 pg/l kanamycin is resuspended in
an
inoculation medium (12.5 mM 2-mM 2-(N-morpholino) ethanesulfonic acid, MES, 1
g/l NH4Cl and 0.3 g/1 MgSO4 at pH 5.7) to reach a final concentration of 4.0
at OD
600. Particle-bombarded explants are transferred to GBA medium (374E), and a
droplet of bacteria suspension is placed directly onto the top of the
meristem. The
explants are co-cultivated on the medium for 4 days, after which the explants
are
transferred to 374C medium (GBA with 1% sucrose and no BAP, IAA, GA3 and
supplemented with 250 p.g/ml cefotaxime). The plantlets are cultured on the
medium
for about two weeks under 16-hour day and 26 C incubation conditions.
Explants (around 2 cm long) from. two weeks of culture in 374C medium are
screened for defensin-like activity using assays known in the art. After
positive (i. e.,
for defensin expression) explants are identified, those shoots that fail to
exhibit
defensin-like activity are discarded, and every positive explant is subdivided
into
nodal explants. One nodal explant contains at least one potential node. The
nodal
segments are cultured on GBA medium for three to four days to promote the
formation of auxiliary buds from each node. Then they are transferred to 374C
medium and allowed to develop for an additional four weeks. Developing buds
are
separated and cultured for an additional four weeks on 374C medium. Pooled
leaf
samples from each newly recovered shoot are screened again by the appropriate
defensin-like protein activity assay. At this time, the positive shoots
recovered from a
single node will generally have been enriched in the transgenic sector
detected in the
initial assay prior to nodal culture.
Recovered shoots positive for defensin-like activity expression are grafted to
Pioneer hybrid 6440 in vitro-grown sunflower seedling rootstock. The
rootstocks are
prepared in the following manner. Seeds are dehulled and surface-sterilized
for 20
minutes in a 20% Clorox bleach solution with the addition of two to three
drops of
Tween 20 per 100 ml of solution, and are rinsed three times with distilled
water. The
sterilized seeds are germinated on the filter moistened with water for three
days, then
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they are transferred into 48 medium (half-strength MS salt, 0.5% sucrose, 0.3%
geirite pH 5.0) and grown at 26 C under the dark for three days, then
incubated at 16-
hour-day culture conditions. The upper portion of selected seedling is
removed, a
vertical slice is made in each hypocotyl, and a transformed shoot is insetted
into a V-
cut. The cut area is wrapped with parafilm. After one week of culture on the
medium,
grafted plants are transferred to soil. In the first two weeks, they are
maintained
under high humidity conditions to acclimatize to a greenhouse environment.
Example 5. Assaying Defensin-Like Activity
The polypeptides described herein may be produced using any number of
methods known to those skilled in the art. Such methods include, but are not
limited
to, expression in bacteria, eukaryotic cell cultures, in planta, and viral
expression
systems in suitably infected organisms or cell lines. The instant polypeptides
may be
expressed either asfull-length polypeptides, mature forms, or as fusion
proteins by
covalent attachment to a variety of enzymes, proteins, or affinity tags.
Common
fusion protein partners include, but are not limited to, glutathione-S-
transferree,
thioredoxin, maltose binding protein, hexahistidine polypeptides, and chitin
binding
protein. The fusion proteins may be engineered with a protease recognition
site at the
fusion point so that fusion partners can be separated by protease digestion to
yield
-intact mature peptides. Examples of such proteases include, but are not
limited to,
thrombin, enterokinase, and factor Xa. Indeed, any protease which specifically
cleaves the peptide connecting the fusion protein and polypeptide of the
invention can
be used.
Purification of the polypeptides of the invention may utilize any number of
separation technologies known to those skilled in the art of protein
purification.
Examples of such methods include, but are not limited to, homogenization,
filtration,
centrifugation, heat denaturation, ammonium sulfate precipitation, desalting,
pH
precipitation, ion exchange chromatography, hydrophobic interaction
chromatography, and affinity chromatography. When the polypeptides of the
invention are expressed as fusion proteins, the purification protocol may
include the
use of an affinity resin specific for the fusion protein partner or for the
polypeptide of
interest. Additional suitable affinity resins may be synthesized by linking
the
appropriate ligands to a suitable resin such as Sepharose 4B.
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Crude, partially purified, or purified polypeptides of the invention, either
alone
or as a fusion protein, may be utilized in assays to verify expression levels
of
functional plant defensins in host cells and transgenic plants. Assays may be
conducted under well known experimental conditions which permit optimal
S enzymatic activity. See, for example, assays for plant defensin activities
presented by
Thevissen, K et al. (1996) J. Biol. Chem. 271:15018-15025 and WO 00/68405.
Example 6. Bioassay testing the Pesticidal Activity of Polypeptides against
Southern
Corn Rootworm (SCRW) and Western Corn Rootworm (WCRW)
Bio-Serv diet (catalog number F9800B, from: BIOSERV, Entomology
Division, One 8`t' Street, Suite 1, Frenchtown, New Jersey 08825) is dispensed
in 128-
well CD International Bioassay trays (catalog number BIO-BA-128 from CD
International, Pitman, New Jersey 08071).
Protein samples are applied topically to the diet surf i uc. Euotigli sample
material is supplied to provide for replicate observations per sample. The
trays are
allowed to dry. Rootworms are dispensed into the wells of the bioassay trays.
A lid
(catalog number BIO-CV-16, CD International, Pitman, New Jersey, 08071) is
placed
on each tray, and the trays are placed in an incubator at 26 C for 4 to 7
days.
For the evaluation of pesticidal activity against SCRW and. WCRW, insects
are exposed to a solution comprising either buffer (50mM carbonate buffer (pH
10))
or a solution of protein sample at selected doses, for example, 50 or 5.0
g/cm2.
The bioassays are then scored by counting "live" versus "dead" larvae.
Mortality is calculated as a percentage of dead larvae out of the total number
of larvae
tested.
Example 7. Bioassay Testing Pesticidal Activity of Polypeptides against the
Colorado
Potato Beetle (Leptinotarsa deceinlineata)
Briefly, bioassay parameters are as follows: Bio-Serv diet (catalog number
F9800B, from: BIOSERV, Entomology Division, One 8th Street, Suite 1,
Frenchtown, New Jersey 08825) is dispensed in a 96 well microtiter plate
(catalog
number 353918, Becton Dickinson, Franklin Lakes, NJ 07417-1886) having a
surface
area of 0.33 cm2. Protein samples of the invention are applied topically to
the diet
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surface. Enough sample material is supplied to provide for 8
observations/sample.
After the samples dry, 1 Colorado potato beetle neonate is added to each well
providing for a total of 8 larvae/sample. A Mylar() lid (Clear Lam Packaging,
Inc.,
1950 Pratt Blvd., Elk Grove Village, IL 60007-5993) is affixed to each tray.
Bioassay
trays are placed in an incubator at 25 C. The test is scored for mortality on
the 7th
day following live infesting.
Example 8. Bioassay Testing Pesticidal Activity of Polypeptides against
Lepidopterans
Neonate larvae are reared according to standard protocols, such as those
published by Czapla and Lang, J Economic Entomology 83:2480-2485 (1990). Test
compounds are either applied topically to the diet or incorporated into the
larvae diet
(see Czapla and Lang, I Economic Entomology 83:2480-2485 (1990)). The larvae
diet is dispensed to bioassay trays. One larva is applied per well of the
bioassay tray.
Weight and mortality are recorded 7 days following the start of the test.
Example 9. Homopteran Membrane Feeding Bioassay for Screening Proteins
This assay can be used for a variety of homopterans. The assay involves
trapping the sample protein between two layers of maximally stretched parafilm
which act as a sachet on top of a small vessel containing the insect of
choice.
The assay is prepared as follows: 1 cm diameter polystyrene tubing is cut into
15 mm lengths. One end of the tube is then capped with a fine mesh screen.
1"ive
insects are then added to the chamber after which the first layer of parafilm
is
stretched over the remaining open end. 25 l of sample (polypeptide in a 5%
sucrose
solution containing McCormick green food coloring) is then placed on top of
the
stretched parafilm. A second layer of parafilm is then stretched by hand art,
placed
over the sample. The sample is spread between the two layers of parafilm to
make a
continuous sachet on which the insects feed. The sachet is then covered
tightly with
saran wrap to prevent evaporation and produce a slightly pressurized sample.
The
assay tubes are monitored for insect reproduction and death on a 24 hour basis
and
compared to the 5% sucrose control.
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Example 10. SCN Bioassay of Transgenic TO Events
Soybean Cyst Nematodes (SCN) are used to infest transgenic TO soybean plants
in soil. SCN egg inoculum is acquired by harvesting cysts from plants infested
4-6
weeks earlier. Briefly, the soil is rinsed from the roots and passed through
nested 20
mesh and 60 mesh screens. The material retained by the 20 mesh screen is
discarded
but the material retained by the 60 mesh screen is washed thoroughly and the
creamy
white cysts are recovered (older brown cysts are ignored). Similarly, the
plant's root
system is scrubbed against the 20 mesh screen nested over the 60 mesh screen.
Cysts
are harvested from the debris on the 60 mesh screen. Eggs are released from
the cysts
by means of a dounce homogenizer in the presence of 0.5% Clorox for 2.5
minutes.
Following this treatment the eggs are washed with sterile water from the
homogenizer
onto the surface of a 200 mesh screen. The eggs are then rinsed in water for
an
additional 5 minutes. Eggs are transferred to a 50 ml conical tube and
counted. The
eggs are diluted to 5000 eggs/ml. Plants grown in 15cm conical tubes are
inoculated
with about 5000 eggs. Plants are maintained in a 26 C growth chamber with
12:12
light:dark cycle for 1 month prior to harvest and counting of cysts.
Example 11. Bioactivity of Polypeptides Against Fingal Pathogens
The proteins of the invention are suspended in. dH2O to a final concentration
of about 4 g/ 1. 12 g of purified protein is added to 200 l of 1/2 strength
potato
dextrose broth (PDB) containing a spore suspension of the fungal pathogen to
be
tested. The spore suspension contains approximately 2500 spores/ml. This
results in a
stock solution with a starting concentration of 10 M. A 0.5X dilution series
for the
protein sample to be tested from10 M through to about 0.05 M is prepared by
removing 1001il of the 1O M stock and adding it to 100 l of spore suspension
(2500
spores/ml), mixing thoroughly to achieve a 5 M protein sample concentration,
transferring l O0 1 of the 5 M suspension to a fresh 100 l spore suspension
etc.,
until about 0.005 M is reached. Two replicates per pathogen are performed.
The
fungal assay plate is scored for inhibition of fungal growth after a 48 hour
incubation
at 28 C. Inhibition of fungal growth is defined as little to no spore
germination
without detectable hyphae growth.
All publications, patents and patent applications mentioned in the
specification
are indicative of the level of those skilled in the art to which this
invention pertains.
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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.
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