# Patent

## Title
Methods for enhancing drought tolerance in plants and compositions thereof

## Abstract

Increased tolerance to drought in a plant is provided by introducing DNA expressing a bacterial cold shock protein.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application claims benefit under 35 USC § 119(e) of U.S. provisional application Ser. No. 60/506,717 filed Sep. 29, 2003 and Ser. No. 60/530,453, filed Dec. 17, 2003.


INCORPORATION OF SEQUENCE LISTING
Two copies of the sequence listing (Seq. Listing Copy 1 and Seq. Listing Copy 2) in a computer-readable form of the sequence listing, all on CD-ROMs, each containing the file named CSP.ST25.txt, which is approximately 98 Mbytes (measured in MS-DOS) and was created on Sep. 28, 2004, are hereby incorporated by reference.
FIELD OF THE INVENTION
This invention relates to cold, drought, salt, cold germination, heat, and other abiotic stress tolerance in plants and viral, fungal, bacterial and other abiotic stress tolerance in plants. Specifically this invention relates to a method of increasing the biotic and abiotic stress tolerance of plants by expressing a cold shock protein(s) within the cells of said plant.
BACKGROUND
Seed and fruit production are multi-billion dollar commercial industries and primary sources of income for numerous states in the United States and for many countries around the world. Commercially valuable seeds include, for example, canola, cottonseeds and sunflower seeds, which are prized for the vegetable oil that can be pressed from the seed. The seeds of leguminous plants such as peas, beans, and lentils also are commercially valuable as they are rich in proteins, with soybeans, for example, consisting of 40-45% protein and 18% fats and oils. In addition, coffee is a valuable crop made from the dried and roasted seeds of Coffea arabica plants, while chocolate is made from the cacao seed or “bean.” Similarly, many fruits and seeds are commercially valuable, including, for example, corn, rice, wheat, barley and other cereals, nuts, legumes, tomatoes, and citrus fruits. For example, corn seeds are made into many food items or items used in cooking, such as taco shells, corn oil, tortillas, corn flakes, corn meal, and many others. Corn is also used as raw material in many production processes, including but not limited to, feed and ethanol production.
Seed and fruit production are both limited inherently due to biotic and abiotic stress. Soybean (Glycine max), for instance, is a crop species that suffers from loss of seed germination during storage and fails to germinate when soil temperatures are cool (Zhang et al., Plant Soil 188: (1997)). This is also true in corn and other plants of agronomic importance. Improvement of abiotic stress tolerance in plants would be an agronomic advantage to growers allowing increasing growth and/or germination in cold, drought, flood, heat, UV stress, ozone increases, acid rain, pollution, salt stress, heavy metals, mineralized soils, and other abiotic stresses. Biotic stress, such as fungal and viral infection, also cause large crop losses world wide.
Traditional breeding (crossing specific alleles of one genotype into another) has been used for centuries to increase biotic stress tolerance, abiotic stress tolerance, and yield. Traditional breeding is limited inherently to the limited number of alleles present in the parental plants. This in turn limits the amount of genetic variability that can be added in this manner. Molecular biology has allowed the inventors of the instant invention to look far and wide for genes that will improve stress tolerance in plants. Our inventors sought to determine how other organisms react to and tolerate stressful conditions. The cold shock proteins are part of a system used by bacteria and other organisms to survive cold and stressful conditions. It was posited by the inventors that placing genes encoding the cold shock proteins, and proteins related to them, into plants and expressing them would increase the cold, drought, heat, water, and other abiotic stress tolerance of plants as well as fungal, viral, and other biotic stress tolerance of plants. They also believe that using genes that are homologous to cold shock proteins, or have sequence similarity, would also increase biotic and abiotic stress tolerance.
This invention is useful to farmers to limit their losses due to biotic and abiotic stress.
SUMMARY OF THE INVENTION
The present invention provides a plant expressing a cold shock protein (Csp) in the cells of the plant. The expression of this csp leads to greater abiotic stress tolerance within said plant. In one embodiment, a polynucleotide encoding a csp is expressed by an operably linked promoter that functions in plants, and a terminator that functions in plants.
More specifically the invention provides a recombinant DNA molecule that comprises, in the 5′ to 3′ direction, a first DNA polynucleotide that comprises a promoter that functions in plants, operably linked to a second DNA polynucleotide that encodes a cold shock protein, operably linked to a 3′ transcription termination DNA polynucleotide providing a polyadenylation site. The first DNA polynucleotide is often advantageously heterologous to the second DNA polynucleotide. The invention also provides a recombinant DNA molecule having an intron inserted between the first DNA polynucleotide and the second DNA polynucleotide. The invention also provides a recombinant DNA molecule where the second DNA polynucleotide encodes a protein comprising the motif in SEQ ID NO: 3. In specific embodiments of the recombinant DNA of this invention the second DNA polynucleotide encodes a protein selected from the group consisting of

    
    
        (a) a protein with an amino acid sequence of substantial identity to an amino acid sequence of a cold shock protein from gram positive bacteria,
        (b) a cold shock protein from Bacillus subtilis, 
        (c) a homologue of Bacillus subtilis cold shock protein B (CspB),
        (d) a protein with an amino acid sequence of substantial identity to SEQ ID NO: 2,
        (e) a protein with an amino acid sequence of substantial identity to an amino acid sequence of a cold shock protein from a gram negative bacteria,
        (f) a protein comprising a cold shock protein from Escherichia coli, 
        (g) a homologue of Escherichia coli cold shock protein A (CspA),
        (h) a protein with an amino acid sequence that has substantial identity to SEQ ID NO:1,
        (i) a cold shock protein from Agrobacterium tumefaciens, and
        (j) a protein having an amino acid sequence of substantial identity to any of SEQ ID NO: 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, or 65.

The invention also provides a recombinant DNA molecule wherein the promoter is selected from the group consisting of inducible promoters, constitutive promoters, temporal-regulated promoters, developmentally-regulated promoters, tissue-preferred promoters, cold enhanced promoters, cold-specific promoters, stress enhanced promoters, stress specific promoters, drought inducible promoters, water deficit inducible promoters, and tissue-specific promoters.

    
    


The invention also provides plant cells and plants containing in their genome recombinant DNA molecules as described and the propagules and progeny produced therefrom. Plants include, but are not limited to crop plants, monocots, and dicots. More specifically these could include soybean, corn, canola, rice, cotton, barley, oats, turf grasses, cotton, and wheat.
The invention also provides abiotic stress-tolerant, transgenic plants that have been transformed with a recombinant DNA molecule that expresses a cold shock protein. Such plants and their cells and propagules such as seeds contain in their genome recombinant DNA molecules that expresses a cold shock protein. Such plants exhibit one or more of the following enhanced properties: a higher growth rate under conditions where cold temperature would be limiting for growth for a non-transformed plant of the same species,

    
    
        (a) a higher growth rate under conditions where high temperature would be limiting for growth for a non-transformed plant of the same species,
        (b) a higher growth rate under conditions where water would be limiting for growth for a non-transformed plant of the same species,
        (c) a higher growth rate under conditions where increased salts or ions in the soil and/or water would be limiting for growth of a non-transformed plant of the same species,
        (d) has a greater percentage of plants surviving after a cold shock than a non-transformed plant of the same species,
        (e) an increased yield when compared to a non-transformed plant of the same species, or
        (f) resistance to drought compared to a non-transformed plant of the same species.
    
    


A method of the invention comprises propagating plants of this invention, e.g. for the purpose of generating seeds, by simply planting such seeds in soil and allowing them to grow, e.g. under stress conditions. More specifically, this invention provides a method of producing a plant that has enhanced trait such as abiotic stress tolerance, increased yield or increased root mass. The method comprises the steps of
a) inserting into the genome of a plant cell or cells a recombinant DNA molecule comprising DNA encoding a cold shock protein,
b) obtaining a transformed plant cell or cells,
c) regenerating plants from said transformed plant cell(s); and
d) selecting plants which exhibit the enhance trait.
In one aspect of the invention plants are selected which exhibit enhanced abiotic stress tolerance selected from the group consisting of heat tolerance, salt tolerance, drought tolerance, and survival after cold shock.
The invention also provided isolated proteins which are at least 40% identity to a protein having an amino acid sequence selected from the group consisting of SEQ ID NOS: 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, and 65. In certain aspects comparable traits can be achieved by substituting a cold shock protein with a protein having higher homology than 40% identity, e.g. with a protein that is at least 50%, 60%, 70%, 80%, 90% or at least 95% identical to a cold shock protein specifically disclosed herein. Likewise, this invention also provides an isolated nucleic acid encoding a cold shock protein motif which hybridizes to a nucleic acids with a DNA sequence selected from the group comprising SEQ ID NOs: 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 90 and 92.
The invention also specifically provides isolated nucleic acids encoding a cold shock protein which has a DNA sequence that is substantially identical to a sequence in the group consisting of SEQ ID NOs: 5, 7, 9, 29, 31, 33, 35, 37, 39, 41, 43, 53, 55, 57, 59, 61, 63, and 65.
The invention also provides propagules containing the above recombinant DNA molecules, when they are planted or otherwise caused to germinate, and a field of plants germinated from said propagules, e.g. where such propagule are seeds.
The invention also provides a method of producing seed comprising planting a seed in soil;

    
    
        b) harvesting seed from said plants; and the seed produced therefrom.
    
    


A method of producing a transgenic plant is also provided, the method comprising the steps of: (i) introducing into the genome of a plant cell a DNA molecule comprising a DNA polynucleotide at least 40% homologous to a protein having an amino acid sequence selected from the group consisting of SEQ ID NOs: 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, and 65, or fragment, or cis element thereof, wherein said DNA polynucleotide is operably linked to a promoter and operably linked to a 3′ transcription termination DNA polynucleotide; and (ii) selecting said transgenic plant cell; and (iii) regenerating said transgenic plant cell into a transgenic plant; also provided are the plants made by this method.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows a plasmid map of pMON57396.
FIG. 2 shows a plasmid map of pMON23450.
FIG. 3 shows a plasmid map of pMON57397.
FIG. 4 shows a plasmid map of pMON57398.
FIG. 5 shows a plasmid map of pMON23450.
FIG. 6 shows a plasmid map of pMON57399.
FIG. 7 shows a plasmid map of pMON48421.
FIG. 8 shows a plasmid map of pMON56609.
FIG. 9 shows a plasmid map of pMON56610.
FIG. 10 shows a plasmid map of pMON73607.
FIG. 11 shows a plasmid map of pMON61322.
FIG. 12 shows a plasmid map of pMON73608.
FIG. 13 shows a plasmid map of pMON65154.
FIG. 14 shows a plasmid map of pMON72472.
FIG. 15 shows a plasmid map of pENTR1.
FIG. 16 shows the growth pattern of plants expressing the indicated gene, and controls, showing that the genes introduced provide abiotic stress tolerance.
FIG. 17 shows a plasmid map of pMON42916.
FIG. 18 shows a plasmid map of pMON73983.
FIG. 19 shows a plasmid map of pMON73984.



DETAILED DESCRIPTION OF SPECIFIC EMBODIMENTS
The instant invention provides a plant with increased tolerance to biotic and abiotic stress. The plant provided has increased stress tolerance due to the expression of cold shock protein (csp) in the cells of said plant. The invention provides examples of several embodiments and contemplates other embodiments that are expected to function in the invention.
The following definitions and methods are provided to better define the current invention and to guide those of ordinary skill in the art in the practice of the present invention. Unless otherwise noted, terms are to be understood according to conventional usage by those of ordinary skill in the art. For example, definitions of common terms used in molecular biology and molecular genetics can be found in Lewin, Genes VII, Oxford University Press and Cell Press, New York, 2000; Buchanan, et al., Biochemistry and Molecular Biology of Plants, Courier Companies, USA, 2000; Lodish, et al., Molecular Cell Biology, W.H. Freeman and Co., New York, 2000. Common terms in genetics can be found in the prior references as well as Lynch, et al., Genetics and Analysis of Quantitative Traits, Sinauer and Associates, Sunderland, Mass., 1998; Hartwell, et al., Genetics: From Genes to Genomes, McGraw-Hill Companies, Boston, Mass., 2000; Hartl, et al., Genetics: Analysis of Genes and Genomes, Jones and Bartlett Publishers, Sudbury, Mass.; Strachan, et al., Human Molecular Genetics, John Wiley and Sons, New York, 1999.
The nomenclature for DNA bases as set forth in 37 CFR § 1.822 is used. The standard one- and three-letter nomenclature for amino acid residues is used.
Many agronomic traits can affect “yield”. For example, these could include, without limitation, plant height, pod number, pod position on the plant, number of internodes, incidence of pod shatter, grain size, efficiency of nodulation and nitrogen fixation, efficiency of nutrient assimilation, resistance to biotic and abiotic stress, carbon assimilation, plant architecture, resistance to lodging, percent seed germination, seedling vigor, and juvenile traits. For example, these could also include, without limitation, efficiency of germination (including germination in stressed conditions), growth rate of any or all plant parts (including growth rate in stressed conditions), ear number, seed number per ear, seed size, composition of seed (starch, oil, protein), characteristics of seed fill. Yield can be measured in many ways, these might include test weight, seed weight, seed number per plant, seed weight per plant, seed number or weight per unit area (i.e. seeds, or weight of seeds, per acre), bushels per acre, tonnes per acre, tons per acre, kilo per hectare. In an embodiment, a plant of the present invention exhibits an enhanced trait that is a component of yield.
“Nucleic acid (sequence)” or “polynucleotide (sequence)” refers to single- or double-stranded DNA (deoxyribonucleic acid) or RNA (ribonucleic acid) of genomic or synthetic origin, i.e., a polymer of deoxyribonucleotide or ribonucleotide bases, respectively, read from the 5′ (upstream) end to the 3′ (downstream) end. The nucleic acid can represent the sense or complementary (antisense) strand.
“Native” refers to a naturally occurring (“wild-type”) nucleic acid sequence.
“Heterologous” sequence refers to a sequence which originates from a foreign source or species or, if from the same source, is modified from its original form. For example, a native promoter could be used to cause the transcription of a heterologous gene from the same or from a different species.
“Parts” of a plant include all parts or pieces of a plant including, but not limited to, roots, shoots, leaves, stems, pollen, seeds, flowers, stamen, pistils, eggs, embryos, petal, filaments, carpels (including stigma, ovary, and style), cell(s) or any piece of the above.
“Propagule” includes all products of meiosis and mitosis, including but not limited to, seed and parts of the plant able to propogate a new plant. For example, propagule includes a shoot, root, or other plant part that is capable of growing into an entire plant. Propagule also includes grafts where one portion of a plant is grafted to another portion of a different plant (even one of a different species) to create a living organism. Propagule also includes all plants and seeds produced by cloning or by bringing together meiotic products, or allowing meiotic products to come together to form an embryo or fertilized egg (naturally or with human intervention).
An “isolated” nucleic acid sequence is substantially separated or purified away from other nucleic acid sequences with which the nucleic acid is normally associated in the cell of the organism in which the nucleic acid naturally occurs, i.e., other chromosomal or extrachromosomal DNA. The term embraces nucleic acids that are biochemically purified so as to substantially remove contaminating nucleic acids and other cellular components. The term also embraces recombinant nucleic acids and chemically synthesized nucleic acids.
“Identity” or “identical” as used herein, when referring to comparisons between protein(s) or nucleic acid(s) means 98% or greater identity.
A first nucleic acid or protein sequence displays “substantial identity” or “substantial similarity” to a reference nucleic acid sequence or protein if, when optimally aligned (with appropriate nucleotide or amino acid insertions or deletions totaling less than 20 percent of the reference sequence over the window of comparison) with the other nucleic acid (or its complementary strand) or protein, there is at least about 60% nucleotide sequence equivalence, even better would be 70%, preferably at least about 80% equivalence, more preferably at least about 85% equivalence, and most preferably at least about 90% equivalence over a comparison window of at least 20 nucleotide or amino acid positions, preferably at least 50 nucleotide or amino acid positions, more preferably at least 100 nucleotide or amino acid positions, and most preferably over the entire length of the first nucleic acid or protein. Optimal alignment of sequences for aligning a comparison window may be conducted by the local homology algorithm(s), preferably by computerized implementations of these algorithms (which can be found in, for example, Wisconsin Genetics Software Package Release 7.0, Genetics Computer Group, 575 Science Dr., Madison, Wis.). The reference nucleic acid may be a full-length molecule or a portion of a longer molecule. Alternatively, two nucleic acids have substantial identity if one hybridizes to the other under stringent conditions. Appropriate hybridization conditions can be determined empirically, or can be estimated based, for example, on the relative G+C content of the probe and the number of mismatches between the probe and target sequence, if known. Hybridization conditions can be adjusted as desired by varying, for example, the temperature of hybridizing or the salt concentration (Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Press, 1989).
A first nucleic acid sequence is “operably linked” with a second nucleic acid sequence when the sequences are so arranged that the first nucleic acid sequence affects the function of the second nucleic acid sequence. Preferably, the two sequences are part of a single contiguous nucleic acid molecule and more preferably are adjacent. For example, a promoter is operably linked to a gene if the promoter regulates or mediates transcription of the gene in a cell. For example, a transcriptional termination region (terminator) is operably linked to a gene when said terminator leads to a RNA polymerase ending a transcript containing said gene at or near the terminator. For example, an enhancer is often not adjacent to the promoter that it is exhibiting its effect on, but is generally in the same nucleic acid molecule.
A “recombinant” nucleic acid or DNA, or RNA molecule is made by an artificial combination of two otherwise separated segments of sequence, e.g., by chemical synthesis or by the manipulation of isolated segments of nucleic acids by genetic engineering techniques. Techniques for nucleic-acid manipulation are well-known (see, e.g., Sambrook et al., Molecular Cloning. A Laboratory Manual, 2nd Edition, Cold Spring Harbor Press, 1989). Methods for chemical synthesis of nucleic acids are discussed, for example, in Beaucage and Carruthers, Tetra. Letts. 22:1859-1862, 1981, and Matteucci et al., J. Am. Chem. Soc. 103:3185, 1981. Chemical synthesis of nucleic acids can be performed, for example, on commercial automated oligonucleotide synthesizers.
“Expression” of a gene refers to the transcription of a gene to produce the corresponding mRNA and translation of this mRNA to produce the corresponding gene product, i.e., a peptide, polypeptide, or protein. Gene expression is controlled or modulated by regulatory elements including 5′ regulatory elements such as promoters.
The terms “recombinant DNA construct”, “recombinant vector”, “expression vector” or “expression cassette” refer to any agent such as a plasmid, cosmid, virus, BAC (bacterial artificial chromosome), autonomously replicating sequence, phage, or linear or circular single-stranded or double-stranded DNA or RNA nucleotide sequence, derived from any source, capable of genomic integration or autonomous replication, comprising a DNA molecule in which one or more DNA sequences have been linked in a functionally operative manner.
“Complementary” refers to the natural association of nucleic acid sequences by base-pairing. Complementarity between two single-stranded molecules may be partial, if only some of the nucleic acids pair are complementary; or complete, if all bases pair are complementary. The degree of complementarity affects the efficiency and strength of hybridization and amplification reactions.
“Homology” refers to the level of similarity between nucleic acid or amino acid sequences in terms of nucleotide or amino acid identity or similarity, respectively, i.e., sequence similarity or identity. Homology, homologue, and homologous also refers to the concept of similar functional properties among different nucleic acids or proteins. Homologues include genes that are orthologous and paralogous. Homologues can be determined by using the coding sequence for a gene, disclosed herein or found in appropriate database (such as that at NCBI or others) in one or more of the following ways. For a protein sequence, the sequences should be compared using algorithms (for instance see section on “identity” and “substantial identity”). For nucleotide sequences the sequence of one DNA molecule can be compared to the sequence of a known or putative homologue in much the same way. Homologues are at least 20% identical, more preferably 30%, more preferably 40%, more preferably 50% identical, more preferably 60%, more preferably 70%, more preferably 80%, more preferably 88%, more preferably 92%, most preferably 95%, across any substantial (25 nucleotide or amino acid, more preferably 50 nucleotide or amino acid, more preferably 100 nucleotide or amino acid, or most preferably the entire length of the shorter sequence) region of the molecule (DNA, RNA, or protein molecule).
Alternatively, two sequences, or DNA or RNA molecules that encode, or can encode, amino acid sequences, are homologous, or homologues, or encode homologous sequences, if the two sequences, or the complement of one or both sequences, hybridize to each other under stringent conditions and exhibit similar function. Thus if one were to determine whether two protein sequences were homologues, one would both do the computer exercises described herein, and create degenerate coding sequences of all possible nucleic acid sequences that could encode the proteins and determine whether they could hybridize under stringent conditions. Appropriate stringency conditions which promote DNA hybridization, for example, 6.0×sodium chloride/sodium citrate (SSC) at about 45° C., followed by a wash of 2.0×SSC at 50° C., are known to those skilled in the art or can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6. For example, the salt concentration in the wash step can be selected from a low stringency of about 2.0×SSC at 50° C. to the high stringency of about 0.2×SSC at 50° C. In addition, the temperature in the wash step can be increased from low stringency conditions at room temperature, about 22° C., to high stringency conditions at about 65° C. Both temperature and salt may be varied, or either the temperature or the salt concentration may be held constant while the other variable is changed. In one preferred embodiment, a nucleic acid encoding a protein described in the present invention will specifically hybridize to one or more of the nucleic acid molecules or complements thereof or fragments of either under highly stringent conditions, for example at about 2.0×SSC and about 65° C. The hybridization of the probe to the target DNA molecule can be detected by any number of methods known to those skilled in the art, these can include, but are not limited to, fluorescent tags, radioactive tags, antibody based tags, and chemiluminescent tags.
“Cold shock protein(s)” (Csp(s) or CSP(s)) are proteins that have greater than 40% identity to Escherichia coli CspA protein (SEQ ID NO: 1) or Bacillus subtilis CspB protein (SEQ ID NO: 2), or, alternatively, cold shock proteins can be found by using the conserved domain as determined in the literature. For example, as used herein a cold shock protein is 40% identical, more preferably 50% identical, more preferably 60% identical, more preferably 70% identical, more preferably 80% identical, more preferably 90% identical, more preferably 95% identical to E. coli CspA or B. subtilis CspB across the entire length of E. coli CspA or B. subtilis CspB. Several databases are available that allow one skilled in the art to determine whether a new or existing protein contains a cold shock domain or is a cold shock protein, from Genbank to protein databases designed to allow the determination of protein relationships, and/or find related proteins. Included herein within the definition are all known cold shock proteins, including but not limited to CspA, CspB, CspC, CspD, CspE, CspF, CspG, CspH, and CspI (U.S. Pat. No. 6,610,533) from Escherichia coli. 
The conserved cold shock domain is shown in SEQ ID NO: 3 ([FY]-G-F-I-x(6,7)-[DER]-[LIVM]-F-x-H-x-[STKR]-x-[LIVMFY]) (Prosite motif PS00352; Bucher and Bairoch, (In) ISMB-94; Proceedings 2nd International Conference on Intelligent Systems for Molecular Biology, Altman R., Brutlag D., Karp P., Lathrop R., Searls D., Eds., pp 53-61, AAAIPress, Menlo Park, 1994; Hofmann et al., Nucleic Acids Res. 27:215, 1999). Alternatively, cold shock proteins can be found using the Sprint database (a relational protein fingerprint database) (Attwood et al., Nucleic Acids Res. 28(1):225, 2000; Attwood, et al., Nucleic Acids Research, 30(1), in press, 2002). Alternatively, cold shock proteins can be found using a matrix based description, or Pfam. Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains (Bateman et al., Nucleic Acids Research 28:263, 2000). At this writing (November 2001; Pfam release 6) there are 3071 families. Cold shock proteins are included as PF00313. The species tree showing the distribution of cold shock proteins as determined in the Pfam database.
“Cold shock proteins” as used herein also include, but are not limited to, any protein that is found in a search, using a Cold shock protein as a query sequence, of a database using the “Blink” (Blast Link) function that can be found at the National Center for Biotechonology Information. “Blink” is a quick search function used to find proteins with similar sequences. This definition of “cold shock protein” or “cold shock domain” is in addition to those used above, and does not replace said definition. Cold shock proteins or proteins containing cold shock domains include, but are not limited to, all currently known proteins in public and private databases as well as those that have yet to be discovered that are similar enough to the claimed proteins (for example, E. coli CspA and B. subtilis CspB) to be “hits” under the standard blast search settings currently used in Blast Link (as of Nov. 1, 2001). As of this writing Blast 2 is being run, and Blast Link (“Blink”) is running the default parameters for protein-protein blast searches. As of this writing we believe the default settings used in Blink are as follows; a BLOSUM62 matrix is being run, using the “nr” database, CD search is selected, as are composition based statistics, with the complexity selected as “low complexity”, expect is 10, with a word size of 3, the gap costs are; existence 11, and extension 1. The list in Table I shows the first 200 hits for E. coli CspA using these standard settings, but we do not limit our claim to the first 200 hits. One skilled in the art would note that under these fairly stringent criteria 167 proteins of bacterial origin are found, but also 28 Metazoan and 5 plant proteins. These proteins include a broad range of proteins that, do to their homology to CspA, would be expected by the inventors to function in the present invention. This is by no means an all inclusive list, and other proteins would be expected to function in the present invention.
Table 20. Some cold shock proteins and proteins containing a cold shock domain found by similarity to E. Coli CspA. This list was compiled using the standard Blast Link settings at the National Center for Biotechnology information. The Genbank ID and name of each protein is shown. Note: Due to the way proteins are named, some proteins and sequences will have several entries, as proteins, cDNAs, alleles, etc. Genbank ID can be considered to be specific identifiers of each entry. Entries are in the approximate order of highest to lowest identity, in comparison with the query sequence.











Genbank ID #
Gene Name
















576191
Major Cold Shock Protein 7.4 (Cspa (Cs 7.4)) Of (Escherichia Coli)


349561
DNA-binding protein [Salmonella typhimurium]


3891780
Chain A, Major Cold-Shock Protein From Escherichia Coli Solution Nm


479003
cold-shock protein [Escherichia coli]


1778828
major cold shock protein CSPA2 [Yersinia enterocolitica]


6073870
major cold shock protein CSPA1 [Yersinia enterocolitica]


1468921
cold shock potein CspG [Escherichia coli]


2275140
hypothetical protein [Yersinia pestis]


12514257
homolog of Salmonella cold shock protein [Escherichia coli O157:H7


15981565
major cold shock protein Cspa1 [Yersinia pestis]


3249024
cold shock protein CspB [Yersinia enterocolitica]


15979692
cold shock protein [Yersinia pestis]


1742550
Cold shock-like protein CspB. [Escherichia coli]


16419141
RNA chaperone, negative regulator of cspA transcription [Salmonella


10039151
cold shock-like protein cspE [Buchnera sp. APS]


9957540
cold shock protein B [Yersinia enterocolitica]


1778540
cold shock-like protein [Escherichia coli]


471099
CspE (MsmC) [Escherichia coli]


2961317
cspB [Salmonella typhimurium]


16503235
cold shock protein [Salmonella enterica subsp. enterica serovar


9658370
cold shock domain family protein [Vibrio cholerae]


460698
CspC (MsmB) [Escherichia coli]


15980582
putative cold shock protein [Yersinia pestis]


10038996
cold shock-like protein cspC [Buchnera sp. APS]


15979774
cold shock protein [Yersinia pestis]


9657556
cold shock transcriptional regulator CspA [Vibrio cholerae]


4454361
cold shock protein, CSPA [Vibrio cholerae]


2970685
cold shock protein C [Salmonella typhimurium]


1402743
major cold-shock protein [Citrobacter freundii]


5869509
CspG [Shewanella violacea]


5869504
CspA [Shewanella violacea]


9968446
cold shock protein [Lactobacillus plantarum]


1405474
CspC protein [Bacillus cereus]


3850776
cold shock protein D [Lactococcus lactis]


10176234
cold-shock protein [Bacillus halodurans]


1869948
cold shock protein [Lactobacillus plantarum]


729220
COLD SHOCK PROTEIN CSPC


7379745
putative transcriptional regulator [Neisseria meningitidis Z2491]


1620431
csp [Lactobacillus plantarum]


1405472
CspB protein [Bacillus cereus]


3892590
cold shock protein E [Lactococcus lactis]


7226073
cold-shock domain family protein [Neisseria meningitidis MC58]


2493766
COLD SHOCK-LIKE PROTEIN CSPLA (CSPL)


1001878
CspA protein [Listeria monocytogenes]


13623066
putative cold shock protein [Streptococcus pyogenes M1 GAS]


758663
cold shock protein [Arthrobacter globiformis]


4468119
cold shock protein A; CspA protein [Bordetella pertussis]


2370256
cold shock protein [Lactococcus lactis]


1405470
CspA protein [Bacillus cereus]


2226349
CspC [Staphylococcus aureus]


1405476
CspD protein [Bacillus cereus]


1513079
cold acclimation protein A [Pseudomonas fragi]


7242722
cold shock protein [Streptomyces coelicolor A3(2)]


2425105
major cold-shock protein [Micrococcus luteus]


2105046
cspA [Mycobacterium tuberculosis H37Rv]


15023696
Cold shock protein [Clostridium acetobutylicum]


12720931
MsmB [Pasteurella multocida]


8101860
major cold shock protein CspA [Staphylococcus aureus]


1513081
cold acclimation protein B [Pseudomonas fragi]


3097243
small cold-shock protein [Mycobacterium leprae]


9587215
cold-shock protein CspA [Mycobacterium smegmatis]


9107526
cold shock protein [Xylella fastidiosa 9a5c]


1256629
cold-shock protein [Bacillus subtilis]


12054789
cold shock protein (CspLB) [Listeria monocytogenes]


1864167
major cold-shock protein homolog CspB [Listeria monocytogenes]


1421212
Major Cold Shock Protein (Cspb)


297761
cold shock protein (CspB) [Bacillus subtilis]


13625473
cold acclimation protein CapB [Pseudomonas sp. 30/3]


9657576
cold shock DNA-binding domain protein [Vibrio cholerae]


11933043
cold-shock like protein [Streptomyces nodosus]


11933034
cold-shock like protein [Streptomyces hygroscopicus]


8248794
cold shock protein [Streptomyces coelicolor A3(2)]


1778825
major cold shock protein CspA [Pseudomonas aeruginosa]


740006
cold shock protein


2226347
CspB [Staphylococcus aureus]


1616777
cold shock-like protein [Stigmatella aurantiaca]


7210998
cold-shock protein [Streptomyces coelicolor A3(2)]


729217
COLD SHOCK PROTEIN CSPB


1067201
cold shock protein [Streptomyces coelicolor]


7321274
cold shock protein [Streptomyces coelicolor A3(2)]


1402789
major cold-shock protein [Yersinia enterocolitica]


1513086
temperature acclimation protein B [Pseudomonas fragi]


16411332
similar to cold shock protein [Listeria monocytogenes]


5732895
F40 [Streptomyces coelicolor A3(2)]


4193390
CspA [Myxococcus xanthus]


4193394
CspC [Myxococcus xanthus]


1405478
CspE protein [Bacillus cereus]


1402753
major cold-shock protein [Klebsiella pneumoniae]


2983729
cold shock protein [Aquifex aeolicus]


2815334
cold-shock domain protein [Streptomyces coelicolor A3(2)]


4193398
CspE [Myxococcus xanthus]


4193396
CspD [Myxococcus xanthus]


2894098
cold shock protein [Thermotoga maritima]


15074838
PUTATIVE COLD SHOCK-LIKE TRANSCRIPTION REGULATOR PROTEIN


1402731
major cold-shock protein [Aeromonas hydrophila]


46789
7 kDa cold shock like protein [Streptomyces clavuligerus]


9946316
probable cold-shock protein [Pseudomonas aeruginosa]


1402769
major cold-shock protein [Proteus vulgaris]


456240
major cold shock protein (CspB) [Sporosarcina globispora]


19743
nsGRP-2 [Nicotiana sylvestris]


15026046
Cold shock protein [Clostridium acetobutylicum]


11493820
cold shock protein C [Yersinia enterocolitica]


4982460
cold shock protein [Thermotoga maritima]


15979415
cold shock-like protein [Yersinia pestis]


16419455
similar to CspA but not cold shock induced [Salmonella typhimurium


14523127
putative cold shock protein [Sinorhizobium meliloti]


9107847
temperature acclimation protein B [Xylella fastidiosa 9a5c]


3036806
glycine-rich protein [Arabidopsis thaliana]


2182333
Y4cH [Rhizobium sp. NGR234]


1402733
major cold-shock protein [Aeromonas salmonicida]


9655615
cold shock-like protein CspD [Vibrio cholerae]


3831556
major cold shock protein [Enterococcus faecalis]


3821915
major cold shock protein [Lactococcus lactis subsp. cremoris]


15160284
AGR_L_3376p [Agrobacterium tumefaciens]


6458627
cold shock protein, CSD family [Deinococcus radiodurans]


3821923
major cold shock protein [Lactobacillus helveticus]


3821911
major cold shock protein [Lactococcus lactis subsp. lactis]


15157349
AGR_C_4003p [Agrobacterium tumefaciens]


15154976
AGR_C_161p [Agrobacterium tumefaciens]


3831558
major cold shock protein [Pediococcus pentosaceus]


456238
cold shock protein [Bacillus subtilis]


117574
COLD SHOCK-LIKE PROTEIN CSPD (CSP-D)


12620649
ID534 [Bradyrhizobium japonicum]


13424521
cold-shock domain family protein [Caulobacter crescentus]


3776223
CspA [Sinorhizobium meliloti]


15075353
PUTATIVE COLD SHOCK TRANSCRIPTION REGULATOR PROTEIN



[Sinorhizobium


15075133
PROBABLE COLD SHOCK TRANSCRIPTION REGULATOR PROTEIN



[Sinorhizobium


3821913
major cold shock protein [Lactococcus lactis subsp. lactis]


13476765
cold shock protein [Mesorhizobium loti]


3821925
major cold shock protein [Streptococcus thermophilus]


3821921
major cold shock protein [Lactobacillus acidophilus]


729222
COLD SHOCK-LIKE PROTEIN CSPJ


15162334
AGR_pAT_762p [Agrobacterium tumefaciens]


13475232
cold shock protein [Mesorhizobium loti]


9947082
probable cold-shock protein [Pseudomonas aeruginosa]


13424199
cold-shock domain family protein [Caulobacter crescentus]


9948689
cold-shock protein CspD [Pseudomonas aeruginosa]


4193392
CspB [Myxococcus xanthus]


13488430
cold shock protein [Mesorhizobium loti]


12720739
CspD [Pasteurella multocida]


3831560
major cold shock protein [Bifidobacterium animalis]


1513084
temperature acclimation protein A [Pseudomonas fragi]


1169113
COLD SHOCK-LIKE PROTEIN CSPD


5714745
cold shock protein 7.4 [Rhodococcus sp. 7/1]


1402767
major cold-shock protein [Photobacterium phosphoreum]


14523160
probable CspA5 cold shock protein transcriptional regulator


15979447
cold shock-like protein [Yersinia pestis]


13488214
cold-shock protein [Mesorhizobium loti]


5714743
cold shock protein A [Rhodococcus sp. 5/14]


3861208
COLD SHOCK-LIKE PROTEIN (cspA) [Rickettsia prowazekii]


81624
glycine-rich protein 2 - Arabidopsis thaliana


15156913
AGR_C_3315p [Agrobacterium tumefaciens]


15074652
PUTATIVE COLD SHOCK TRANSCRIPTION REGULATOR PROTEIN



[Sinorhizobium


7295442
CG17334 gene product [Drosophila melanogaster]


3850772
cold shock protein A [Lactococcus lactis]


14334920
putative glycine-rich zinc-finger DNA-binding protein [Arabidopsis


3892588
cold shock protein C [Lactococcus lactis]


2708747
putative glycine-rich, zinc-finger DNA-binding protein [Arabidopsis


2739396
Y-box protein [Drosophila melanogaster]


1402763
major cold-shock protein [Photobacterium mondopomensis]


15620137
cold shock-like protein [Rickettsia conorii]


1402755
major cold-shock protein [Lactobacillus casei]


409419
Y-Box factor [Aplysia californica]


14039811
Y-box binding protein [Schistosoma japonicum]


9946868
probable cold-shock protein [Pseudomonas aeruginosa]


1483311
Y-box protein [Dugesia japonica]


1477478
Y-box binding protein [Schistosoma mansoni]


1402759
major cold-shock protein [Listeria innocua]


15159048
AGR_L_1288p [Agrobacterium tumefaciens]


2228815
major cold-shock protein CspH [Salmonella typhimurium]


6911694
cold-shock protein A [Streptococcus thermophilus]


2970679
Y box protein [Drosophila silvestris]


14602477
Similar to cold shock domain protein A [Homo sapiens]


10727970
yps gene product [Drosophila melanogaster]


1402757
major cold-shock protein [Listeria grayi]


1402751
major cold-shock protein [Enterococcus faecalis]


1083796
RYB-a protein - rat


505133
RYB-a [Rattus norvegicus]


14523481
probable CspA6 cold shock protein transcriptional regulator


8100512
Y-box protein ZONAB-B [Canis familiaris]


8100510
Y-box protein ZONAB-A [Canis familiaris]


15306095
hypothetical protein XP_053028 [Homo sapiens]


10185725
Y-box protein 3 short isoform [Mus musculus]


10185723
Y-box protein 3 long isoform [Mus musculus]


7385223
RNA binding protein MSY4 [Mus musculus]


6166110
DNA-BINDING PROTEIN A (COLD SHOCK DOMAIN PROTEIN A)


1402783
major cold-shock protein [Streptococcus pyogenes]


1167838
DNA-binding protein [Homo sapiens]


1160331
dbpA murine homologue [Mus musculus]


1101884
YB2 [Rattus norvegicus]


950340
DNA-binding protein A [Homo sapiens]


532211
Y-box binding protein [Mus musculus]


87332
DNA-binding protein A - human (fragment)


14742409
hypothetical protein XP_046353 [Homo sapiens]


14270385
cold-shock domain protein [Takifugu rubripes]


9653686
TSH receptor suppressor element-binding protein-1; TSEP-1


8249978
cold shock protein B [Streptomyces coelicolor A3(2)]


3695368
zfY1 [Danio rerio]









Bacillus subtilis (B. subtilis) CspB is a protein that accumulates in response to cold shock (Willimsky, et al. Journal of Bacteriology 174:6326 (1992)). It has homology to CspA from E. coli see Table I) and contains a single stranded nucleic acid binding domain (Lopez, et al., The Journal of Biological Chemistry 276:15511 (2001)). Using the same basic Blast search at NCBI (Blink) the following proteins are designated as “hits”. The number of hits shown here is limited to 200, but many other proteins would be expected function in the invention.
Table 21. Some cold shock proteins and proteins containing cold shock domains found searching with B. subtilis CspB. This list was compiled using the standard Blast Link (Blink) settings at the National Center for Biotechnology Information. The Genbank ID and name of each protein is shown. Note: Due to the way proteins are named, some proteins and sequences will have several entries, as proteins, cDNAs, alleles, etc. Genbank ID can be considered to be specific identifiers of each entry. Entries are in the approximate order of highest to lowest identity to the query sequence.











GenBank ID #
Gene Name
















1421212
Major Cold Shock Protein (Cspb)


1405476
CspD protein [Bacillus cereus]


729217
COLD SHOCK PROTEIN CSPB


456240
major cold shock protein (CspB) [Sporosarcina globispora]


1256629
cold-shock protein [Bacillus subtilis]


740006
cold shock protein


456238
cold shock protein [Bacillus subtilis]


12054789
cold shock protein (CspLB) [Listeria monocytogenes]


1864167
major cold-shock protein homolog CspB [Listeria monocytogenes]


1405472
CspB protein [Bacillus cereus]


8101860
major cold shock protein CspA [Staphylococcus aureus]


16411332
similar to cold shock protein [Listeria monocytogenes]


10176234
cold-shock protein [Bacillus halodurans]


2493766
COLD SHOCK-LIKE PROTEIN CSPLA (CSPL)


1001878
CspA protein [Listeria monocytogenes]


1405470
CspA protein [Bacillus cereus]


1405474
CspC protein [Bacillus cereus]


13623066
putative cold shock protein [Streptococcus pyogenes M1 GAS]


729220
COLD SHOCK PROTEIN CSPC


2226349
CspC [Staphylococcus aureus]


9968446
cold shock protein [Lactobacillus plantarum]


1402739
major cold-shock protein [Bacillus subtilis]


3892590
cold shock protein E [Lactococcus lactis]


2226347
CspB [Staphylococcus aureus]


3850776
cold shock protein D [Lactococcus lactis]


1402741
major cold-shock protein [Bacillus subtilis]


15979774
cold shock protein [Yersinia pestis]


10039151
cold shock-like protein cspE [Buchnera sp. APS]


8248794
cold shock protein [Streptomyces coelicolor A3(2)]


460698
CspC (MsmB) [Escherichia coli]


11933043
cold-shock like protein [Streptomyces nodosus]


11933034
cold-shock like protein [Streptomyces hygroscopicus]


1620431
csp [Lactobacillus plantarum]


16419141
RNA chaperone, negative regulator of cspA transcription [Salmonella typhimurium LT2]


15979692
cold shock protein [Yersinia pestis]


2894098
cold shock protein [Thermotoga maritima]


1869948
cold shock protein [Lactobacillus plantarum]


2370256
cold shock protein [Lactococcus lactis]


2970685
cold shock protein C [Salmonella typhimurium]


1778540
cold shock-like protein [Escherichia coli]


471099
CspE (MsmC) [Escherichia coli]


10038996
cold shock-like protein cspC [Buchnera sp. APS]


7242722
cold shock protein [Streptomyces coelicolor A3(2)]


15026046
Cold shock protein [Clostridium acetobutylicum]


15980582
putative cold shock protein [Yersinia pestis]


9657576
cold shock DNA-binding domain protein [Vibrio cholerae]


349561
DNA-binding protein [Salmonella typhimurium]


4982460
cold shock protein [Thermotoga maritima]


1405478
CspE protein [Bacillus cereus]


9946316
probable cold-shock protein [Pseudomonas aeruginosa]


9658370
cold shock domain family protein [Vibrio cholerae]


5869509
CspG [Shewanella violacea]


1067201
cold shock protein [Streptomyces coelicolor]


9948689
cold-shock protein CspD [Pseudomonas aeruginosa]


3891780
Chain A, Major Cold-Shock Protein From Escherichia Coli Solution Nmr Structure


576191
Major Cold Shock Protein 7.4 (Cspa (Cs 7.4)) Of (Escherichia Coli)


72232
major cold shock protein cspA - Escherichia coli


9657556
cold shock transcriptional regulator CspA [Vibrio cholerae]


6458627
cold shock protein, CSD family [Deinococcus radiodurans]


3831556
major cold shock protein [Enterococcus faecalis]


15023696
Cold shock protein [Clostridium acetobutylicum]


2425105
major cold-shock protein [Micrococcus luteus]


1402737
major cold-shock protein [Bacillus cereus]


9587215
cold-shock protein CspA [Mycobacterium smegmatis]


7226073
cold-shock domain family protein [Neisseria meningitidis MC58]


4454361
cold shock protein, CSPA [Vibrio cholerae]


479003
cold-shock protein [Escherichia coli]


3097243
small cold-shock protein [Mycobacterium leprae]


1778828
major cold shock protein CSPA2 [Yersinia enterocolitica]


758663
cold shock protein [Arthrobacter globiformis]


2105046
cspA [Mycobacterium tuberculosis H37Rv]


7379745
putative transcriptional regulator [Neisseria meningitidis Z2491]


3249024
cold shock protein CspB [Yersinia enterocolitica]


7210998
cold-shock protein [Streptomyces coelicolor A3(2)]


1513081
cold acclimation protein B [Pseudomonas fragi]


5869504
CspA [Shewanella violacea]


1778825
major cold shock protein CspA [Pseudomonas aeruginosa]


1513086
temperature acclimation protein B [Pseudomonas fragi]


12514257
homolog of Salmonella cold shock protein [Escherichia coli O157:H7 EDL933]


5732895
F40 [Streptomyces coelicolor A3(2)]


3831558
major cold shock protein [Pediococcus pentosaceus]


1468921
cold shock potein CspG [Escherichia coli]


13625473
cold acclimation protein CapB [Pseudomonas sp. 30/3]


6073870
major cold shock protein CSPA1 [Yersinia enterocolitica]


1402771
major cold-shock protein [Staphylococcus aureus]


1402761
major cold-shock protein [Lactococcus lactis subsp. cremoris]


15981565
major cold shock protein Cspa1 [Yersinia pestis]


9107847
temperature acclimation protein B [Xylella fastidiosa 9a5c]


7321274
cold shock protein [Streptomyces coelicolor A3(2)]


2815334
cold-shock domain protein [Streptomyces coelicolor A3(2)]


2275140
hypothetical protein [Yersinia pestis]


9947082
probable cold-shock protein [Pseudomonas aeruginosa]


2983729
cold shock protein [Aquifex aeolicus]


2961317
cspB [Salmonella typhimurium]


46789
7 kDa cold shock like protein [Streptomyces clavuligerus]


9107526
cold shock protein [Xylella fastidiosa 9a5c]


1513079
cold acclimation protein A [Pseudomonas fragi]


4193394
CspC [Myxococcus xanthus]


4193392
CspB [Myxococcus xanthus]


3821911
major cold shock protein [Lactococcus lactis subsp. lactis]


16503235
cold shock protein [Salmonella enterica subsp. enterica serovar Typhi]


9957540
cold shock protein B [Yersinia enterocolitica]


3821921
major cold shock protein [Lactobacillus acidophilus]


1616777
cold shock-like protein [Stigmatella aurantiaca]


1402759
major cold-shock protein [Listeria innocua]


4468119
cold shock protein A; CspA protein [Bordetella pertussis]


1742550
Cold shock-like protein CspB. [Escherichia coli]


12720739
CspD [Pasteurella multocida]


3821915
major cold shock protein [Lactococcus lactis subsp. cremoris]


1402765
major cold-shock protein [Pediococcus pentosaceus]


1513084
temperature acclimation protein A [Pseudomonas fragi]


4193396
CspD [Myxococcus xanthus]


4193398
CspE [Myxococcus xanthus]


3831560
major cold shock protein [Bifidobacterium animalis]


4193390
CspA [Myxococcus xanthus]


3821923
major cold shock protein [Lactobacillus helveticus]


12720931
MsmB [Pasteurella multocida]


3850772
cold shock protein A [Lactococcus lactis]


9655615
cold shock-like protein CspD [Vibrio cholerae]


9946868
probable cold-shock protein [Pseudomonas aeruginosa]


1402757
major cold-shock protein [Listeria grayi]


3821913
major cold shock protein [Lactococcus lactis subsp. lactis]


1402735
major cold-shock protein [Bacillus atrophaeus]


1402751
major cold-shock protein [Enterococcus faecalis]


3892588
cold shock protein C [Lactococcus lactis]


1169113
COLD SHOCK-LIKE PROTEIN CSPD


15979415
cold shock-like protein [Yersinia pestis]


117574
COLD SHOCK-LIKE PROTEIN CSPD (CSP-D)


15075133
PROBABLE COLD SHOCK TRANSCRIPTION REGULATOR PROTEIN [Sinorhizobium



meliloti]


16419455
similar to CspA but not cold shock induced [Salmonella typhimurium LT2]


11493820
cold shock protein C [Yersinia enterocolitica]


1402783
major cold-shock protein [Streptococcus pyogenes]


3821925
major cold shock protein [Streptococcus thermophilus]


1402775
major cold-shock protein [Streptococcus dysgalactiae]


8249978
cold shock protein B [Streptomyces coelicolor A3(2)]


15160284
AGR_L_3376p [Agrobacterium tumefaciens]


81624
glycine-rich protein 2 - Arabidopsis thaliana


19743
nsGRP-2 [Nicotiana sylvestris]


2916930
cspB [Mycobacterium tuberculosis H37Rv]


13475232
cold shock protein [Mesorhizobium loti]


3861208
COLD SHOCK-LIKE PROTEIN (cspA) [Rickettsia prowazekii]


2182333
Y4cH [Rhizobium sp. NGR234]


13476765
cold shock protein [Mesorhizobium loti]


3776223
CspA [Sinorhizobium meliloti]


1402755
major cold-shock protein [Lactobacillus casei]


15620137
cold shock-like protein [Rickettsia conorii]


15154976
AGR_C_161p [Agrobacterium tumefaciens]


15074838
PUTATIVE COLD SHOCK-LIKE TRANSCRIPTION REGULATOR PROTEIN



[Sinorhizobium meliloti]


14548150
RNA-binding cold-shock protein [uncultured crenarchaeote 4B7]


2440094
small cold-shock protein [Mycobacterium leprae]


14523127
putative cold shock protein [Sinorhizobium meliloti]


12620649
ID534 [Bradyrhizobium japonicum]


1063684
AtGRP2b [Arabidopsis thaliana]


13424521
cold-shock domain family protein [Caulobacter crescentus]


3036806
glycine-rich protein [Arabidopsis thaliana]


1402731
major cold-shock protein [Aeromonas hydrophila]


214642
p54 [Xenopus laevis]


15075353
PUTATIVE COLD SHOCK TRANSCRIPTION REGULATOR PROTEIN [Sinorhizobium



meliloti]


13424199
cold-shock domain family protein [Caulobacter crescentus]


14602477
Similar to cold shock domain protein A [Homo sapiens]


1175535
CYTOPLASMIC RNA-BINDING PROTEIN P56 (Y BOX BINDING PROTEIN-2) (Y-BOX



TRANSCRIPTION FACTOR) (MRNP4)


104266
Y box-binding protein 2 - African clawed frog


15157349
AGR_C_4003p [Agrobacterium tumefaciens]


8100512
Y-box protein ZONAB-B [Canis familiaris]


8100510
Y-box protein ZONAB-A [Canis familiaris]


1483311
Y-box protein [Dugesia japonica]


1402767
major cold-shock protein [Photobacterium phosphoreum]


1402733
major cold-shock protein [Aeromonas salmonicida]


15306095
hypothetical protein XP_053028 [Homo sapiens]


14742409
hypothetical protein XP_046353 [Homo sapiens]


14270385
cold-shock domain protein [Takifugu rubripes]


10185725
Y-box protein 3 short isoform [Mus musculus]


10185723
Y-box protein 3 long isoform [Mus musculus]


9653686
TSH receptor suppressor element-binding protein-1; TSEP-1 [Rattus sp.]


7385223
RNA binding protein MSY4 [Mus musculus]


6166110
DNA-BINDING PROTEIN A (COLD SHOCK DOMAIN PROTEIN A) (SINGLE-STRAND



DNA



BINDING PROTEIN NF-GMB)


3695368
zfY1 [Danio rerio]


2745892
Y box transcription factor [Mus musculus]


2073109
Y box protein 1 [Carassius auratus]


1353778
Y-Box binding protein [Columba livia]


1167838
DNA-binding protein [Homo sapiens]


1160331
dbpA murine homologue [Mus musculus]


1101884
YB2 [Rattus norvegicus]


1083796
RYB-a protein - rat


988283
mYB-1b [Mus musculus]


988281
mYB-1a [Mus musculus]


950340
DNA-binding protein A [Homo sapiens]


608518
p50 [Oryctolagus cuniculus]


532211
Y-box binding protein [Mus musculus]


516701
similar to dbpB/YB-1 of mouse [Gallus gallus]


505133
RYB-a [Rattus norvegicus]


457262
nuclease sensitive element binding protein-1 [Homo sapiens]


423015
nuclease sensitive element-binding protein 1 - human


289797
YB-1 protein [Gallus gallus]


203398
putative [Rattus norvegicus]


199821
Y box transcription factor [Mus musculus]


189299
DNA-binding protein [Homo sapiens]


162983
transcription factor EF1(A) [Bos taurus]


115848
Y BOX BINDING PROTEIN-1 (Y-BOX TRANSCRIPTION FACTOR) (YB-1)



(CCAAT-BINDING TRANSCRIPTION FACTOR I SUBUNIT A) (CBF-A) (ENHANCER



FACTOR I SUBUNIT A)



(EFI-A) (DNA-BINDING PROTEIN B) (DBPB)


112410
Y box-binding protein 1 - rat









CSPs are a group of proteins that may or may not be increased in amount when the temperature is lowered or other stress is applied. In fact, in the best studied organism with respect to the cold shock proteins, E. coli, some cold shock proteins are constitutively expressed while others are induced by cold, still others seem to be specific for specific stresses and/or growth conditions or stages. A review of this is Yamanaka, et al., Molecular Microbiology, 27:247 (1998). In this review Yamanaka and colleagues detail how the nine cold shock proteins in E. coli (CspA through CspI) are expressed. CspA, CspB, and CspG are cold inducible. CspD is induced at the stationary phase of the cell cycle and during starvation. CspC and E have been implicated in cell division.
CspA is the major cold shock protein from Escherichia coli (E. coli) (SEQ ID NO:1). CspA is also called Major Cold Shock Protein 7.4. CspA is highly induced in response to cold shock (Goldstein, et al., Proceedings of the National Academy of Science (USA) 87:283 (1990)). In some conditions of slower growth, ribosomes are slowed due to RNA or DNA secondary structure formation, and this may act as a signal for the increased synthesis of CSPs in their native organism. CSPs bind to ssDNA and RNA under in-vitro conditions (Phadtare, et al., Molecular Microbiology 33:1004 (1999)). CSPs are thought to bind to RNA in a relatively non-specific manner during translation and prevent secondary structure formation and stabilize the RNA (this function is sometimes referred as an RNA chaperone). The ribosome can then easily displace the CSPs and initiate translation on a linear RNA template. We believe that the present invention might involve the single stranded nucleic acid binding function of these proteins, and this function can come from any cold shock protein or protein containing a cold shock domain, which includes, for example, prokaryotic cold shock proteins, eukaryotic Y-Box containing genes, some glycine rich proteins (GRP), and other proteins containing the cold shock domain. These proteins include, but are not limited to, those shown in FIG. 4, Trends in Biochemical Science, 23(8):289 (1998) (paper included, herein incorporated by reference). This figure clearly shows the evolutionary relationship between these proteins. The origin of these proteins likely precedes the divergence of modern day bacteria and eukaryotes, and it has been postulated that these proteins may have been present at the advent of single cell evolution, 3.5 billion years ago. We have selected two proteins to transform into plants as examples, as shown in the figure cited above these proteins are more greatly divergent from each other than from many of their eukaryotic counterparts. We expect that the ectopic expression of these proteins may improve tolerance to biotic and abiotic stresses which could include but are not limited to the growth, vigor, yield, and health of plants under a variety of stressful conditions that may include cold, drought, salt stress, heat, survival after cold shock, fungal infection, viral infection, microbial infection, and cold germination.
Another possible explanation for the increased growth rate of plants under stress could be the elicitation of pathogen-associated molecular patterns (PAMP) provided by the expression of CSPs. In this model a plant would develop a PAMP response that would elicit a plant response somewhat like systemic acquired resistance (SAR) (much like SAR works for biotic stresses) as the plant would be “prepared” for the stress prior to its application. For this model to work the plant must be signaled that the CSP is present, this mechanism may have recently been provided through a plant receptor that binds CSP (Felix, et al, Journal of Biological Chemistry 278(8):6201-8 (2003)). This mechanism would mean that any gene that bound a receptor which elicited a PAMP-type response would function in the invention. Elicitation of PAMP-type responses has generally been studied for biotic stresses, and has often been elicited through exogenous administration of agents. Herein we could be eliciting the PAMP-type response to the CSP produced from the CSP transgene. The transgene transformed into a plant cell as part of a recombinant DNA construct, through a particle gun or agrobacterium mediated transformation. This in turn could be creating a systemic acquired resistance type response in the plant, in turn increasing resistance to abiotic stress. This response could work in both monocots and dicots, including but not limited to corn, soybean, wheat, rice, Arabidopsis, canola, and cotton. If the above PAMP method is the mode of action for the CSPs, then the CSP might be expected to provide biotic stress protection as well as abiotic stress protection. None of these mechanisms are meant to be limiting and one or both, or myriad others, could be involved in the phenotype manifested.
MF2, a Csp-like protein from Bacillus thuringensis, has been purported to give some protection against viral infection in a plant. U.S. Pat. No. 6,528,480 shows this tolerance to biotic stress via rubbing the leaves of a plant with an extract containing the protein and infecting the plant with a virus. They contemplate, but do not create, transgenic plants therein.
“Non-transformed plant of the same species” is meant to be inclusive of all plants of the same species as a transformed plant. In one embodiment the transformed plants is of the same species and strain as the transformed plant. In another embodiment the plant is as identical as possible to the transformed plant.
The “cold shock domain” (CSD) is a protein sequence that is homologous to the cold shock proteins. For the purposes of this invention, a cold shock domain containing protein is a “cold shock protein”. Greater than 40%, 50%, 60%, 70%, 80%, 90%, 95%, or 98% amino acid identity is seen between E. coli CspA or B. subtilis CspB and the cold shock domains of cold shock domain containing proteins (Wistow, Nature 344:823 (1990); Yamanaka, et al., Mol. Micro., 27:247, specifically see FIG. 1B in the Yamanaka reference; Graumann, et al. TIBS 23:286).
As used herein “yeast” regularly refers to Saccharomyces cerevissiae but could also include Schizosacchoramyces pombe and other varieties (from the genus Pichia, for example). “Corn” refers to Zea Mays and all species and varieties that can be bred with it. “Wheat” refers to all of Triticum aestivum varieties including but not limited to spring, winter, and all facultative wheat varieties. “Wheat” includes any other wheat species, including but not limited to durum wheat (Triticum durum), spelt (Triticum spelta), emmer (Triticum dicoccum), and wild wheat (Triticum monococcum). “Wheat” also includes any species that can be bred with any of the aforementioned wheat species and offspring of said crosses (including triticale, a hybrid of wheat and rye). “Soybeans” refers to Glycine max or Glycine soja and any species or variety that can be bred with them. “Rice” refers to Oryza sativa and any species or variety that can be bred with it. “Barley” refers to Hordeum vulgare and any species or variety that can be bred with it. “Oats” refers to Avena sativa and any species or variety that can be bred with it. “Canola” is a coined name recently given to seed, oil, and meal produced by genetically modified rapeseed plants, oilseed rape (Brassica napus L.) and turnip rape (B. campestris L), herein canola includes all rapeseed plants and organisms that can be bred with them. E. coli and Escherichia coli as used herein includes organisms of the Escherichia coli species and all strains of that this organism; i.e. E. coli K12. E. coli and Escherichia coli as used herein can also includes any organism that can conjugate with any E. coli strain when one is an F+ or Hfr strain, and the other is not. B. subtilis and Bacillus subtilis refers to all organism of the genus Bacillus, species subtilis. Agrobacterium tumifaciens as used herein includes all strains and types of this species. “Turf grasses” include all species and strains of grass ever planted, or that could be planted, to produce a turf, including but not limited to; a lawn, a field for playing a game (i.e. football, baseball, or soccer), and all areas of a golf course (i.e. tee, fairway, green, rough, etc.). “Cotton” refers to all plants in the genus Gossypium and all plants that can be bred with them.
“Heat tolerance” is meant herein as a measure of a plants ability to grow under conditions where heat, or warmer temperature, would detrimentally affect the growth, vigor, yield, size, of the a plant of the same species. Heat tolerant plants grow better under conditions of heat stress than non heat tolerant plants of the same species.
“Salt tolerance” refers to the ability of some plants to grow under osmotic stress, or stress caused by salts or ions in the water and soil. For example, a plant with increased growth rate, compared to a plant of the same species and/or variety, when watered with a liquid, or planted in a media, containing a mix of water and ions that detrimentally affect the growth of another plant of the same species would be said to be salt tolerant. Some transformed plants have a greater tolerance for these types of conditions than non-transformed plants of the same species and strain.
All numbers used herein should be modified by the term “about”, about means that the number can vary, in either direction, by up to 10 percent and still retain the same meaning. For example, a 1 M solution should include all solutions of that type less than, and including, 1.1 M and more than 0.9 M. For example, a percentage can also be modified, 10% is inclusive of all percentages from 9% to 11%. Terms defined by the adjective “exactly” are not defined by the term “about”.
A “glycine rich protein” is defined as a protein in a eukaryote that is, or has substantial identity with, or is a homologue of, a protein containing a cold shock domain.
“Survival after cold shock” is defined as the ability of a plant to continue growth for a significant period of time after being placed at a temperature below that normally encountered by a plant of that species at that growth stage. It should be noted that some plants, even those of the same species, have been selected for growth under cold conditions. The inbred Wigor strain of corn can tolerate cold conditions and has a significantly higher survival rate when placed in those conditions than most commercial lines sold in the U.S. Wigor is sold commercially in Poland. Thus cold tolerance for transgenic plants must be compared within plants of the same strain at the same relative age, as well as plants of the same species, to gain meaningful scientific data. Plants would then be scored immediately, or some day(s) or week(s) later to determine their viability, growth rate, and other phenotypes after the shock.
“Drought” or “water would be limiting for growth” is defined as a period of dryness that, especially when prolonged, can cause damage to crops or prevent their successful growth. Again different plants of the same species, and those of different strains of the same species, may have different tolerance for drought, dryness, and/or lack of water. In the laboratory drought can be simulated by giving plants 95% or less water than a control plant and looking for differences in vigor, growth, size, root length, and myriad other physiologic and physical measures. Drought can also be simulated in the field by watering some plants, but not others, and comparing their growth rate, especially where water is severely limited for the growth of that plant.
Abiotic stress tolerance includes, but is not limited to, increased yield, growth, biomass, health, or other measure that indicates tolerance to a stress which includes but is not limited to heat stress, salt stress, cold stress (including cold stress during germination), water stress (including but not limited to drought stress), nitrogen stress (including high and low nitrogen).
Biotic stress tolerance includes, but is not limited to, increased yield, growth, biomass, health, or other measure that indicates tolerance to a stress which includes but is not limited to fungal infection, bacterial infection, and viral infection of a plant.
Certain of the gene sequences disclosed as part of the invention are bacterial in origin, for example, certain prokaryotic cold shock proteins. It is known to one skilled in the art that unmodified bacterial genes are sometimes poorly expressed in transgenic plant cells. Plant codon usage more closely resembles that of humans and other higher organisms than unicellular organisms, such as bacteria. Several reports have disclosed methods for improving expression of recombinant genes in plants. These reports disclose various methods for engineering coding sequences to represent sequences which are more efficiently translated based on plant codon frequency tables, improvements in codon third base position bias, using recombinant sequences which avoid suspect polyadenylation or A/T rich domains or intron splicing consensus sequences. While these methods for synthetic gene construction are notable, the inventors have contemplated creating synthetic genes for cold shock proteins or proteins containing cold shock domains according to the method of Brown et al. (U.S. Pat. No. 5,689,052 1997, which is herein incorporated in its entirety by reference) and/or by the above cited, as well as other methods. Thus, the present invention provides a method for preparing synthetic plant genes express in planta a desired protein product. Briefly, according to Brown et al., the frequency of rare and semi-rare monocotyledonous codons in a polynucleotide sequence encoding a desired protein are reduced and replaced with more preferred monocotyledonous codons. Enhanced accumulation of a desired polypeptide encoded by a modified polynucleotide sequence in a monocotyledonous plant is the result of increasing the frequency of preferred codons by analyzing the coding sequence in successive six nucleotide fragments and altering the sequence based on the frequency of appearance of the six-mers as to the frequency of appearance of the rarest 284, 484, and 664 six-mers in monocotyledonous plants. Furthermore, Brown et al. disclose the enhanced expression of a recombinant gene by applying the method for reducing the frequency of rare codons with methods for reducing the occurrence of polyadenylation signals and intron splice sites in the nucleotide sequence, removing self-complementary sequences in the nucleotide sequence and replacing such sequences with nonself-complementary nucleotides while maintaining a structural gene encoding the polypeptide, and reducing the frequency of occurrence of 5′-CG-3′ dinucleotide pairs in the nucleotide sequence. These steps are performed sequentially and have a cumulative effect resulting in a nucleotide sequence containing a preferential utilization of the more-preferred monocotyledonous codons for monocotyledonous plants for a majority of the amino acids present in the desired polypeptide. Specifically all the protein mentioned herein are contemplated to be made into synthetic genes as discussed above, or using similar methods, including but not limited to Escherichia coli CspA and Bacillus subtilis CspB.
The work described herein has identified methods of potentiating in planta expression of cold shock proteins and proteins containing cold shock domains, which may confer resistance to many plant stresses, which can include but are not limited to cold, heat, drought, salt, and other stresses, or stress related phenotypes (cold germination, survival after cold stress, and other abiotic stresses) when ectopically expressed after incorporation into the nuclear, plastid, or chloroplast genome of susceptible plants. U.S. Pat. No. 5,500,365 (specifically incorporated herein by reference) describes a method for synthesizing plant genes to optimize the expression level of the protein for which the synthesized gene encodes. This method relates to the modification of the structural gene sequences of the exogenous transgene, to make them more “plant-like” and therefore more likely to be translated and expressed by the plant, monocot or dicot. However, the method as disclosed in U.S. Pat. No. 5,689,052 provides for enhanced expression of transgenes, preferably in monocotyledonous plants.
In developing the nucleic acid constructs of this invention, the various components of the construct or fragments thereof will normally be inserted into a convenient cloning vector, e.g., a plasmid that is capable of replication in a bacterial host, e.g., E. coli. Numerous vectors exist that have been described in the literature, many of which are commercially available. After each cloning, the cloning vector with the desired insert may be isolated and subjected to further manipulation, such as restriction digestion, insertion of new fragments or nucleotides, ligation, deletion, mutation, resection, etc. so as to tailor the components of the desired sequence. Once the construct has been completed, it may then be transferred to an appropriate vector for further manipulation in accordance with the manner of transformation of the host cell.
A double-stranded DNA molecule of the present invention containing, for example, a cold shock protein in an expression cassette can be inserted into the genome of a plant by any suitable method. Suitable plant transformation vectors include those derived from a Ti plasmid of Agrobacterium tumefaciens, as well as those disclosed, e.g., by Herrera-Estrella et al. (1983), Bevan (1984), Klee et al. (1985) and EPO publication 120,516. In addition to plant transformation vectors derived from the Ti or root-inducing (Ri) plasmids of Agrobacterium, alternative methods can be used to insert the DNA constructs of this invention into plant cells. Such methods may involve, but are not limited to, for example, the use of liposomes, electroporation, chemicals that increase free DNA uptake, free DNA delivery via microprojectile bombardment, and transformation using viruses or pollen.
A plasmid expression vector suitable for the introduction of a gene coding for a cold shock protein, or protein containing a cold shock domain in monocots using electroporation could be composed of the following: a promoter that functions in plants; an intron that provides a splice site to facilitate expression of the gene, such as the Hsp70 intron (PCT Publication WO93/19189); and a 3′ polyadenylation sequence such as the nopaline synthase 3′ sequence (NOS 3′). This expression cassette may be assembled on high copy replicons suitable for the production of large quantities of DNA.
An example of a useful Ti plasmid cassette vector for plant transformation is pMON-17227. This vector is described in PCT Publication WO 92/04449 and contains a gene encoding an enzyme conferring glyphosate resistance (denominated CP4), which is an excellent selection marker gene for many plants. The gene is fused to the Arabidopsis EPSPS chloroplast transit peptide (CTP2) and expressed from the FMV promoter as described therein. When an adequate numbers of cells (or protoplasts) containing the sedoheptulose-1,7-bisphosphatase gene or cDNA are obtained, the cells (or protoplasts) are regenerated into whole plants. Choice of methodology for the regeneration step is not critical, with suitable protocols being available for hosts from Leguminosae (alfalfa, soybean, clover, etc.), Umbelliferae (carrot, celery, parsnip), Cruciferae (cabbage, radish, canola/rapeseed, etc.), Cucurbitaceae (melons and cucumber), Gramineae (wheat, barley, rice, maize, etc.), Solanaceae (potato, tobacco, tomato, peppers), various floral crops, such as sunflower, and nut-bearing trees, such as almonds, cashews, walnuts, and pecans.
Plants that can be made to express cold shock proteins by practice of the present invention include, but are not limited to, Acacia, alfalfa, aneth, apple, apricot, artichoke, arugula, asparagus, avocado, banana, barley, beans, beet, blackberry, blueberry, broccoli, brussels sprouts, cabbage, canola, cantaloupe, carrot, cassava, cauliflower, celery, cherry, cilantro, citrus, clementines, coffee, corn, cotton, cucumber, Douglas fir, eggplant, endive, escarole, eucalyptus, fennel, figs, gourd, grape, grapefruit, honey dew, jicama, kiwifruit, lettuce, leeks, lemon, lime, Loblolly pine, mango, melon, mushroom, nut, oat, okra, onion, orange, an ornamental plant, papaya, parsley, pea, peach, peanut, pear, pepper, persimmon, pine, pineapple, plantain, plum, pomegranate, poplar, potato, pumpkin, quince, radiata pine, radicchio, radish, raspberry, rice, rye, sorghum, Southern pine, soybean, spinach, squash, strawberry, sugarbeet, sugarcane, sunflower, sweet potato, sweetgum, tangerine, tea, tobacco, tomato, turf, a vine, watermelon, wheat, yams, zucchini, or any other plant.
“Promoter” refers to a DNA sequence that binds an RNA polymerase (and often other transcription factors) and promotes transcription of a downstream DNA sequence. Promoters are often provide enhanced or reduced expression in some tissues when compared to others. Promoter selection, specifically selecting promoters that increase expression when a plant is undergoing abiotic stress could be particularly useful in the instant invention.
It has been observed in the art that some stress responses have similar effects on the plant, and resistance to one may provide resistance to another. This is seen, for example, between the responses to dehydration and low temperature (Shinozaki, et al., Current Opinions in Plant Biology 3(3):217, 2000). Many other papers show the general interrelationship between different abiotic stresses, and might indicate that tolerance to one stress might lead to greater tolerance of several other abiotic stresses (Pemas, el al., FEBS Lett 467(2-3):206, 2000; Knight, Int Rev Cytol 195:269, 2000; Didierjean, et al., Planta 199: 1, 1996; Jeong, et al., Mol Cells 12:185, 2001).
Expression cassettes and regulatory elements found in the DNA segment outside of the plant expression elements contained in the T-DNA are common in many plasmid DNA backbones and function as plasmid maintenance elements, these include, but are not limited to, the aad (Spc/Str) gene for bacterial spectinomycin/streptomycin resistance, the pBR322 ori (ori322) that provides the origin of replication for maintenance in E. coli, the bom site for the conjugational transfer into the Agrobacterium tumefaciens cells, and a DNA segment is the 0.75 kb oriV containing the origin of replication from the RK2 plasmid. In addition, those plasmids intended for transformation into plants often contain the elements necessary for the endogenous DNA integration proteins of Agrobacterium to function to insert the element. These include borders (right (RB) and left (LB) borders).
The laboratory procedures in recombinant DNA technology used herein are those well known and commonly employed in the art. Standard techniques are used for cloning, DNA and RNA isolation, amplification and purification. Generally enzymatic reactions involving DNA ligase, DNA polymerase, restriction endonucleases and the like are performed according to the manufacturer's specifications. These techniques and various other techniques are generally performed according to Sambrook et al., Molecular Cloning—A Laboratory Manual, 2nd. ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1989).
All publications and published patent documents cited in this specification are incorporated herein by reference to the same extent as if each individual publication or patent application is specifically and individually indicated to be incorporated by reference.
The following examples are included to demonstrate embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples that follow represent techniques discovered by the inventors to function well in the practice of the invention. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention, therefore all matter set forth or shown in the accompanying drawings and examples is to be interpreted as illustrative and not in a limiting sense.
EXAMPLES
Example 1
pMON57396 (FIG. 1) is a binary vector for Agrobacterium-mediated transformation and constitutive expression of a protein (SEQ ID NO: 56) similar to Escherichia coli CspA in Arabidopsis. To clone the E. coli CspA gene, two gene specific primers, MF1 and MF2, were designed based on the CspA sequence information (Genbank M30139, GI:409136) from the National Center for Biotechnology Information, which is part of the National Library of Medicine, in turn part of the National Institutes of Health (NCBI). The sequence for MF1 is AGGTAATACACCATGGCCGGTAA (SEQ ID NO: 66), which anneals at the translational start site of CspA and introduces an NcoI site at the 5′ end, while the sequence of MF2 is TTAAGCAGAGAATTCAGGCTGGTT (SEQ ID NO: 67), which anneals at the last codon of CspA and introduces an EcoRI site at the end of the primer. PCR was performed to isolate E. coli CspA. Specifically, E. coli DH5α cells were lysed and a small amount of the lysate was used as a template to amplify the CspA gene using MF1 and MF2 primers, Taq polymerase and dNTPs from Roche Molecular Biochemicals (Indianapolis, Ind.). The thermal cycling conditions were as follows: 94° C., 1 min, followed by 30 cycles of 94° C., 16 seconds; 55° C., 1 min and 72° C., 1 min. The amplified CspA DNA was purified by gel-electrophoresis, digested with NcoI and EcoRI and ligated to a binary vector pMON23450 (FIG. 2) that had previously been linearized by digestion with NcoI and EcoRI. Ligation was performed using T4 ligase and following procedures recommended by the manufacturer (BRL/Life Technologies, Inc., Gaithersburg, Md.). The ligation mix was transformed into E. coli cells for plasmid propagation (Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Press, 1989). The transformed cells were plated on appropriate selective media (Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Press, 1989) and colonies were scored hours or days later. Plasmids were prepared from individual colonies and full-insert sequence was determined.
The resulting plasmid was also confirmed by restriction mapping (for example, see Griffiths, et al, An Introduction to Genetic Analysis, 6th Edition pp 449-451, ISBN 0-7167-2604-1, W.H. Freeman and Co., New York) and sequencing. As the chosen NcoI-EcoRI cloning site in the vector was flanked by a CaMV e35S promoter at the upstream (5′) and an epitope tag (Flag, which encodes the oligopeptide DYKDDDK (SEQ ID NO: 68), SIGMA, St Louis) at the downstream (3′), the E. coli CspA in this construct is thus tagged at the C-terminus by the Flag epitope tag and will be driven transcriptionally by the CaMV e35S promoter upon transformation in Arabidopsis. The above cloning results in a plasmid encoding a protein similar to SEQ ID NO: 55. The resulting plasmid is called pMON57396.
Example 2
pMON57397 (FIG. 2) is a binary vector for Agrobacterium-mediated transformation and constitutive expression of a protein (SEQ ID NO: 57), like Escherichia coli CspA protein, in Arabidopsis. To create pMON57397, the binary vector pMON57396 containing the Escherichia coli CspA gene (see example above) tagged at the C-terminus by the Flag epitope tag, was digested with restriction enzymes XhoI and SalI to cleave these sites in the vector and release the FLAG epitope tag (The FLAG tag encodes the oligopeptide DYKDDDK, SIGMA, St Louis). The linearized plasmid was then purified and religated. Ligation was performed using T4 ligase and following procedures recommended by the manufacturer (BRL/Life Technologies, Inc., Gaithersburg, Md.). The ligation mix was transformed into E. coli cells for plasmid propagation (Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Press, 1989). The transformed cells were plated on appropriate selective media (Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Press, 1989) and colonies were scored hours or days later. Plasmids were prepared from individual colonies and full-insert sequence was determined. The cloning above results in the creation of a plasmid encoding a protein similar to SEQ ID NO: 57.
The resulting plasmid was also confirmed by restriction mapping to ensure that XhoI and SalI sites were absent (for example, see Griffiths, et al, An Introduction to Genetic Analysis, 6th Edition pp 449-451, ISBN 0-7167-2604-1, W.H. Freeman and Co., New York) and sequencing. The E. coli CspA gene in this construct is untagged at the C-terminus and is driven transcriptionally by the CaMV e35S promoter.
Example 3
pMON57398 (FIG. 4) is a binary vector for Agrobacterium-mediated transformation and constitutive expression of a protein (SEQ ID NO: 59) like Bacillus subtilis CspB, in Arabidopsis. To clone the B. subtilis CspB gene, two gene-specific primers, MF3 and MF4a, were designed based on the CspB sequence information (Genbank U58859, gi:1336655) from the National Center for Biotechnology Information, which is part of the National Library of Medicine, in turn part of the National Institutes of Health (NCBI). The sequence for MF3 is AGGAGGAAATTCCATGGTAGAAG (SEQ ID NO: 69), which anneals at the translational start site of CspB and introduces an NcoI site at the 5′ end, while the sequence of MF4a is TCAATTTATGAATTCGCTTCTTTAGT (SEQ ID NO: 70), which anneals at the last codon of CspB and introduces an EcoRI site at the end of the primer. PCR was performed to isolate B. subtilis CspB. Bacills subtilis cells were obtained from Carolina Biological Supply (Burlington, N.C.), the cells were lysed and a small amount of the lysate was used as a template to amplify the CspB gene using MF3 and MF4a primers, Taq polymerase and dNTPs from Roche Molecular Biochemicals. The thermal cycling conditions were as follows: 94° C., 1 min, followed by 30 cycles of 94° C., 16 seconds; 55° C., 1 min and 72° C., 1 min. The amplified CspB DNA was purified by gel-electrophoresis, digested with NcoI and EcoRI and ligated to a binary vector pMON23450 (FIG. 5) that had previously been linearized by digestion with NcoI and EcoRI. Ligation was performed using T4 ligase and following procedures recommended by the manufacturer (BRL/Life Technologies, Inc., Gaithersburg, Md.). The ligation mix was transformed into E. coli cells for plasmid propagation. The transformed cells were plated on appropriate selective media (Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Press, 1989) and colonies were scored a day later. Plasmids were prepared from individual colonies and full-insert sequence was determined.
The resulting plasmid was also confirmed by restriction mapping (for example, see Griffiths, et al, An Introduction to Genetic Analysis, 6th Edition pp 449-451, ISBN 0-7167-2604-1, W.H. Freeman and Co., New York) and sequencing. As the chosen NcoI-EcoRI cloning site in the vector was flanked by a CaMV e35S promoter at the upstream (5′) and an epitope tag (Flag, which encodes the oligopeptide DYKDDDK (SIGMA, St Louis) at the downstream (3′), the B. subtilis CspB like gene in this construct is thus tagged at the C-terminus by the Flag epitope tag and will be driven transcriptionally by the CaMV e35S promoter upon transformation in Arabidopsis. This cloning results in a plasmid with the sequence encoding a protein similar to SEQ ID NO: 59 being inserted into said plasmid.
Example 4
pMON57399 (FIG. 6) is a binary vector for Agrobacterium-mediated transformation and constitutive expression of a protein (SEQ ID NO: 61) like Bacillus subtilis CspB in Arabidopsis. To create pMON57399, the binary vector pMON57398 containing the Bacillus subtilis CspB gene (see example above) tagged at the C-terminus by the Flag epitope tag, was digested with restriction enzymes XhoI and SalI to cleave these sites in the vector and release the FLAG epitope tag (The FLAG tag encodes the oligopeptide DYKDDDK, SIGMA, St Louis). The linearized plasmid was then purified and religated. Ligation was performed using T4 ligase and following procedures recommended by the manufacturer (BRL/Life Technologies, Inc., Gaithersburg, Md.). The ligation mix was transformed into E. coli cells for plasmid propagation (Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Press, 1989). The transformed cells were plated on appropriate selective media (Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Press, 1989) and colonies were scored hours or days later. Plasmids were prepared from individual colonies and full-insert sequence was determined. This cloning results in a plasmid with a sequence encoding a protein similar to SEQ ID NO: 61 being inserted into said plasmid.
The resulting plasmid was also confirmed by restriction mapping to ensure that XhoI and SalI sites were absent (for example, see Griffiths, et al, An Introduction to Genetic Analysis, 6th Edition pp 449-451, ISBN 0-7167-2604-1, W.H. Freeman and Co., New York) and sequencing. As the chosen NcoI-EcoRI cloning site in the vector was flanked by a CaMV e35S promoter at the upstream (5′) N-terminus, the B. subtilis CspB gene in this construct is untagged at the C-terminus and is driven transcriptionally by the CaMV e35S promoter upon transformation in Arabidopsis. Said plasmids were transformed into Agrobacterium tumefaciens. 
Example 5
Arabidopsis plants may be transformed by any one of many available methods. For example, Arabidopsis plants may be transformed using In planta transformation method by vacuum infiltration (see, Bechtold et al., In planta Agrobacterium mediated gene transfer by infiltration of adult Arabidopsis thaliana plants. CR Acad. Sci. Paris Sciences de la vie/life sciences 316: 1194-1199 (1993). This example illustrates how Arabidopsis plants may be transformed.
Stock Plant Material and Growth Conditions
Prepare 2.5 inch pots with soil and cover them with a mesh screen, making sure that the soil is not packed too tightly and the mesh is in contact with the soil surface (this ensures that the germinating seedlings will be able to grow through the mesh). Sow seeds and cover with a germination dome. Vernalize seeds for 3-4 days. Grow plants under conditions of 16 hours light/8 hours dark at 20-22° C., 70% humidity. Water twice weekly, and fertilize from below with 1⁄2× (half of the strength recommended by the manufacturer) Peters 20-20-20 fertilizer (from Hummert International, Earth City, Mo.). Add micronutrients (Hummert's Dyna-grain Soluble Trace Elements) (in full strength recommended by the manufacturer) every other week. After about 1-2 weeks, remove the dome and thin the pots to one or two plants per pot. Clip the primary bolt, when it develops, to encourage more secondary bolt formation. In 5-7 days the plants will be ready for infiltration.
Agrobacterium Preparation (Small Scale and Large Scale Cultures):
Agrobacterium strain ABI is streaked onto an LB plate containing Spectinomycin 100 mg/L, Streptomycin 100 mg/L, Chloramphenicol 25mg/L, and Kanamycin 50mg/L (denoted SSCK). Two days prior to infiltration, a loop of Agrobacterium is placed into a tube containing 10 mls LB/SSCK and put on a shaker in the dark at 28° C. to grow overnight. The following day, the Agrobacterium is diluted 1:50 in 400 mls YEP/SSCK and put on a shaker at 28° C. to grow for 16-20 hours. (Note: we have found the transformation rate is significantly better when LB is used for the first overnight growth and YEP is used for the large scale overnight culture).
Infiltration
Harvest the Agrobacterium cells by pouring into a 500 ml centrifuge bottle and spinning at 3500 rpm for 20-25 minutes. Pour off the supernatant. Dry the pellet and then resuspend in 25 ml Infiltration Medium (MS Basal Salts 0.5%, Gamborg's B-5 Vitamins 1%, Sucrose 5%, MES 0.5 g/L, pH 5.7) with 0.44 nM benzylaminopurine (BAP) (10 μl of a 1.0 mg/L stock in DMSO per liter) and 0.02% Vac-In-Stuff (Silwet L-77) from Lehle Seeds (Round Rock, Tex.). The BAP and Silwet L-77 are added fresh the day of infiltration. Add 200 μl of Silwet L-77, and 20 μl of BAP (0.5 mg/L stock). Using Infiltration Medium as your blank, take the OD600 of a 1:10 dilution of the Agrobacterium suspensions. Calculate the volume needed for 400 ml of Agrobacterium suspension/infiltration medium, OD600=0.6, for the vacuum infiltration.




  
    Equation
    :
    
      
        
          (
          
            final
            ⁢
            
              
            
            ⁢
            volume
          
          )
        
        *
        
          (
          
            final
            ⁢
            
              
            
            ⁢
            
              OD
              ⁢
              600
            
          
          )
        
      
      
        OD
        ⁢
        
          
        
        ⁢
        600
      
    
  
  =
  
    Volume needed for final 
    OD
    600 of 0.6
  




Place resuspended culture in a Rubbermaid container inside a vacuum dessicator. Invert pots containing plants to be infiltrated into the solution so that the entire plant is covered, including the rosette, but not too much of the soil is submerged. Soak the plants with water for at least 30 min. prior to infiltration. (This keeps the soil from soaking up the Agrobacterium suspension).
Draw a vacuum of  ̃23-27 in. Hg for 10 min. Quickly release the vacuum. Briefly drain the pots, place them on their sides in a diaper-lined tray, cover the tray with a dome to maintain humidity, and return to growth chamber. The following day, uncover the pots, set them upright, and remove the diaper. Do not water plants for  ̃5 days. After the 5 days are up, allow the plants to be watered and to continue to grow under the same conditions as before. (The leaves that were infiltrated may degenerate but the plant should survive until it is finished flowering).
Harvesting and Sterilizing Seed
Cone the plants, individually, by using the Lehle Aracons (Lehle Seeds, Round Rock, Tex.) approximately 2 weeks after infiltration. After all of the seed is matured and has set ( ̃4 weeks post-infitration), remove the plants from water to dry down the seeds. Approximately 2 weeks later harvest the seeds by cutting the branches below the cone. Clean the seed by using a sieve to catch the silique and branch material and allow the seed to go through. Place the seed in an envelope or in 15 ml conical tubes.
Transfer desired amount of seeds to 15 ml conical tubes prior to sterilization. Loosen the lid to the conicals and place them on their side in a vacuum dessicator with a beaker containing 400 ml of bleach Clorox (Clorox Company, Oakland, Calif.) and 4 ml of Hydrochloric Acid. (Add the HCl to the Clorox in a fume hood). Pull a vacuum just to seal the dessicator, and close the suction (i.e. so that the dessicator is still under a vacuum but the vacuum is not still being directly pulled) for  ̃16 hrs. After sterilization, release the vacuum and place tubes containing seed in a sterile hood (keep caps loose so gas can still be released).
Plate (“sprinkle”) the seed on selection plates containing MS Basal Salts 4.3 g/L, Gamborg'a B-5 (500×) 2.0 g/L, Sucrose 10 g/L, MES 0.5 g/L, and 8 g/L Phytagar (Life Technologies, Inc., Rockville, Md.) with Carbenicillin 250 mg/L, Cefotaxime 100 mg/L. Selection levels will either be kanamycin 60 mg/L, Glyphosate 60 μM, or Bialaphos 10 mg/L.
A very small amount of seed can be first plated out to check for contamination. If there is contamination, re-sterilized seeds for  ̃4 more hours and check for contamination again. The second sterilization is usually not necessary, but sometimes the seed harbors a fungal contaminant and repeat sterilizations are needed. (The sterilization duration generally is shorter than 16 hours because of significantly decreased germination rates starting at 24 hr. sterilization duration). Seal plates with parafilm and place in a cold room to vernalize for  ̃2-4 days. After seeds are vernalized, place in percival with cool white bulbs.
Transfer to Soil
After 5-10 days at  ̃26° C. and a 16/8 light cycle, the transformants will be visible as green plants. After another 1-2 weeks, plants will have at least one set of true leaves. Transfer plants to soil, cover with a germination dome, and move to a growth chamber with normal Arabidopsis growth conditions. Keep covered until new growth is apparent (usually 5-7 days).
Example 6
In order to compare the growth of wildtype non-transgenic and CspA or CspB transgenic Arabidopsis plants, verticle growth was allowed in sterile Petri dishes:
Wildtype or transgenic seeds were liquid sterilized using the following method:

    
    
        5 minute incubation in 70% ethanol following vortex mixing
        5 minute incubation in 30% Chlorox (6.15% sodium hypochlorite)+0.01% Triton X-100 following vortex mixing
        5 consecutive sterile water washes
    
    


Seeds were plated onto plastic, 100×15 mm square petri dishes (Becton Dickinson—Falcon # 35-1112), each containing 40 ml of agar media made as follows:
0.5× Murashige and Skoog media with macronutrients, micronutrients and vitamins (Sigma #M5519), adjusted to pH 5.8 with ammonium hydroxide and containing 1% Phytagel (Sigma # P8169) for solid support.
Ten wild type Arabidopsis seeds were plated across one half of a petri dish, approximately 1 cm from the edge and evenly spaced. This was done with a Gilson P-200 Pipetteman using sterile tips. Ten CspA or CspB transgenic Arabidopsis seeds were similarly plated across the other half of the petri dish, evenly spaced. The plates were labeled with a marking pen to indicate which half contained the transgenic seeds.
The petri dishes were put at 4° C. for 3 days in the dark to stratify the seeds and then placed in a Percival incubator (model AR-36L) at 8° C. for 6 weeks at 24 hour constant light of 120 microeinsteins/square meter. At the end of this incubation, the size of the CspA and CspB rosettes were compared to that of wildtype and found to be larger. This can be seen in FIG. 16. This can be seen in the first, second, and last pictured plate where the above assay was used. In FIG. 16, the third picture (CspB+Flag, pMON57399) displays a plate wherein the plants were put through a cold shock assay similar to that described below.
Cold Shock Seedling Vigor Assessment of Transgenic Arabidopsis thaliana Seeds: Horizontal Plate Assay.
Introduction:
This is a procedure for assessing the ability of transgenic Arabidopsis seeds that have germinated at normal temperatures on media agar in horizontal petri plates to continue to grow upon a shift to chilling. In short, seeds from control plants and seeds from tester transgenic plants are sterilized, stratified, and plated in 6×8 grids on either half of a petri dish. The plate is incubated at normal temperature in a horizontal position for one week and then shifted to chilling temperature for two additional weeks, maintaining the horizontal position of the plate. The canopy area of seedlings is recorded by digital photography and quantitated using imaging software. The ratio of the total canopy area of the tester seedlings to that of the control seedlings can be used as a quantitative parameter to compare the cold tolerance potential of various genes of interest in transgenic tester lines.

Materials: The Following Assumes the Normal Capital Equipment Available in a Standard Biotechnology Laboratory (Autoclave, Balance, Laminar Flow Hood, etc.)

    
    
        Arabidopsis seed: the protocols here have been used with Arabidopsis thaliana cv. Columbia, but ought to be suitable for other Arabidopsis species as well.
        Petri dishes: Falcon #35-1112 (100 mm square×15mm deep)
        Media: Sigma M5519=Murashige & Skoog Basal Media
        Phytagel (Sigma #P-8169)
        1-liter glass bottles in which to autoclave media agar and from which to pour plates. We use Coming glass bottles with the orange screw caps.
        Magnetic stirrers and magnetic stir bars
        Electric pipettor usable with 50 ml plastic pipettes.
        Small fluorescent light box with plastic magnifying lense for plating seeds.
        P1000 Gilson pipetor (or equivalent) and sterile tips
        P200 Gilson pipetor (or equivalent) and sterile tips
        70% Ethanol, sterile
        30% Chlorox bleach+0.1% Tween 20
        Sterile filtered deionized water
        Sterile microcentrifuge tubes and tube racks
        4° C. cold room, cold box or refrigerator, preferably dark
        22 degrees C. Percival plant growth chamber or equivalent with  ̃150 μE/m2/sec light source
        8 degress C. Percival plant growth chamber or equivalent with  ̃150 μE/m2/sec light source
        Semipermeable surgical tape 3M Micropore tape (3M #1530-1)
        Black (Sharpie) marker
        Vacuum aspirator with trap
        Glassine balance weighing paper (VWR #12578-165)
        Calculator
        Notebook
        IBM compatible computer
        Image-Pro Plus software, version 4.1.0.0
        Microsoft Excel software

Protocol:

        1—Aliquot seeds for storage vials or envelopes to sterile microcentrifuge tubes
        2—Label tubes with sharpie to retain identity of seeds
        3—Surface sterilize seeds in tubes by successive washing with the following solutions and waiting times listed below. Note, invert tubes during washings at least twice to ensure good surface contact of solutions on seeds. Seeds will fall down to the bottom of the tube, making a soft pellet:
        
            a. 70% Ethanol, sterile, for 3 to 5 minutes
            b. 30% Chlorox bleach+0.1% Tween 20, for 3 to 5 minutes
            c. Sterile filtered deionized water, for 30 seconds
            d. Repeat c. four more times and on the last time, leave  ̃0.5 ml of sterile water remaining over the seed pellet.
        
        
        1—Place microcentrifuge tubes in the dark at 4° C. for three days to stratify the seeds for more uniform germination upon plating.
    
    


[Alternatively, the seeds can be directly plated onto media agar petri dishes, taped sealed and the petri dish can be put at 4° C. in the dark for three days prior to the 8° C. cold incubation—see below.]

    
    
        2—Make plates by preparing 1-liter aliquots of 0.5× Murashige and Skoog media in the glass bottles, adjust pH to 5.8 with ammonium hydroxide, then add 10 grams of Phytagel. Use a magnetic stirrer when adjusting the pH and to mix in the phytagel uniformly, then autoclave on liquid setting (slow exhaust) for 45 minutes.
        3—Pour plates in the laminar flow hood using the electric pipettor with the 50 ml sterile pipette to deliver 40 ml of media to each plate, immediately covering the plate with the lid.
        4—Allow plates to cool in laminar flow hood for at least 2 hours with the blower off and store in dated plastic bags at 4° C.
        5—Label plates and plate seeds:
        1—Tape all four edges of the plate with semipermeable micropore tape, label with the date and put plates in a Percival incubator set at 22 C and 16 hour day light cycle at  ̃100 μE/m2 sec. Place the plates in a horizontal position only one layer thick and incubate for 7 days. Photograph each plate with a digital camera and store the data to a compact disk.
        2—Transfer plates to a Percival incubator set at 8° C. and 24 hour day light cycle at  ̃100 μE/m2 sec, Place the plates in a horizontal position only one layer thick and incubate for upto 3 additional weeks. Photograph each plate with a digital camera and store the data to a compact disk.
        3—Observe plates every 2 to 3 days to see how tester germplasms are proceeding compared to controls and digitally photograph at times that are representative of the general performance of the germplasms. This should take less than 2 weeks (3 weeks at the most) of incubation at 8° C. Those germplasms that take longer to show a difference need to be plated at a lower seed density to avoid overcrowding at the time the digitial photograph is taken.
        4—Measure rosette canopy area using digital camera photography and Image-Pro Plus software. Calculate the average seedling canopy for control and tester populations, eliminating seeds from the analysis that never germinated. Calculate the ratio between the average seedling canopy area post temperature shift for the control seedlings and the tester seedlings, the standard deviation and standard error for control and tester seedling sets. Ascertain if there is a statistical difference between the tester seedlings and the control seedlings. Record results in a notebook.
        5—Discard plates and seedlings in appropriate disposal containers for transgenic plant materials (gray bins with clear plastic waste bags).
    
    


Example 7
PCR products of the CspA and CspB genes were ligated to vector pCR-TOPO 2.1 according to the manufacturer's protocol (Invitrogen, Carlsbad, Calif.). The NcoI/EcoRI fragments of the pCR-TOPO 2.1 derivatives were subcloned into pMON48421 (FIG. 7), linearized by the same restriction enzymes. The NotI fragments of the pMON48421 derivatives encompassing the 35S promoter, Csp genes, and the e9 terminator were subcloned into pMON42916 (FIG. 17) at the NotI site to create pMON56609 (FIG. 8) and pMON56610 (FIG. 9) which contain the CspA and CspB genes, respectively. Said plasmids were transformed into Agrobacterium tumefaciens by known methods. pMON56609 is thought to contain a nucleotide sequence encoding a protein similar to SEQ ID NO: 7. pMON56610 is thought to contain a nucleotide sequence encoding a protein similar to SEQ ID NO: 9.
Example 8
Agrobacterium Preparation:
Agrobacterium strain EHA105 is streaked on LB plate containing Kanamycin 50 mg/L and Hygromycin 50 mg/L (denoted LB/KH). Two days prior to co-cultivation, a loop of Agrobacterium is transferred to a tube containing 10 ml LB/KH and incubated on a shaker in dark at 28 C for 24 hours. This culture is diluted to 1: 100 in 20 ml LB/KH and incubated on a shaker in dark at 28 C overnight. The following day 1 ml of 1:2 dilution of this culture is taken in a cuvette and OD600 is taken with LB/KH as blank. Calculate the volume needed for 5 ml of agrobacterium suspension of O.D 1.0 for co-cultivation.




  
    
      
        
          
            
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Take the required volume of agrobacterium culture in a 40 ml centrifuge tube and spin at 7000 rpm for 7 minutes. Discard the supernatant and dry the pellet. Resuspend the pellet in 5 ml of co-cultivation media (CC MEDIA-MS Basal salts, Sucrose 20 g/L, Glucose 10 g/L, thiamine HCl 0.5 mg/L, L-Proline 115 mg/L, 2,4-D 2mg/L) with 20 mg/L of acetosyringone.
Transformation of Rice Embryos:
Panicles were harvested from greenhouse grown Nipponbare and Taipai 309 rice varieties. The panicles were sterilized by immersing in 50% commercial bleach for 10 minutes followed by rinsing in sterile distilled water. The panicles were given a 70% alcohol treatment for 3 mins. The seeds were then removed from the panicles and dehusked individually and transferred to a falcon tube containing 0.1% tween 20 solution. The seeds were then treated with 70% alcohol in the laminar air flow chamber. Then the seeds were rinsed with sterile water. This was followed by a 50% bleach treatment for 45 minutes. The seeds were rinsed 5 times in sterile distilled water. Finally the seeds are given 0.1% mercuric chloride treatment for 5 minutes. The seeds were again washed 8 times with sterile distilled water.
The embryos were excised aseptically from the sterile seeds in the laminar flow chamber and placed on solid co-cultivation media (CC MEDIA with 2 g/L phytagel). 50 μL drops of the agrobacterium suspension were placed on a sterile petri-plate. 10 embryos were transferred to each drop. The infection was allowed for 15 minutes. The agrobacterium suspension was removed with a sterile pipette tip. The infected embryos were transferred to a fresh solid CC MEDIA plate and kept in dark for 2 days. On the third day the embryos were washed with cefotaxime 500 mg/L. The embryos were then dried on sterile filter paper and placed on Delay media (MS Basal salts, Thiamine HCl 1 mg/L, Glutamine 500 mg/L, Magnesium Chloride 750 mg/L, casein hyrolysate 100 mg/L, Sucrose 20 mg/L, 2,4D 2 mg/L, Pichloram 2.2 mg/L, Cefotaxime 250 mg/L). the embryos are kept on delay medium in dark for a period of 7 days. During this period calli are formed. The calli are transferred to selection media (Delay medium with 50 mg/L Hygromycin) and stored in dark for 10 days. The calli are sub-cultured to fresh selection media after this 10 day period. After another 10 days the calli are transferred to regeneration media (MS Basal salts, sucrose 30 mg/L, Kinetin 2 mg/L, NAA 0.2 mg/L, Cefotaxime 250 mg/L, hygromycin 25 mg/L) and kept in dark for 7 days. The calli are then transferred to fresh regeneration media and moved to a 16-hour photoperiod at 30 C. The shoots developed on this callus are transferred to rooting media (half strength MS Basal salts, sucrose 15 g/L, Cefotaxime 250 mg/L, Hygromycin 25 mg/L). The rooted shoots are transferred to test-tubes containing water and placed in a mist chamber for hardening.
Plants were selected as positive. This could be done, for example, using methods similar to those described in examples 12-14, and 26-29. Including breeding methods described to create the next generation of transgenic plants.
Example 9
Cold Stress Response at Three Leaf Stage—CspB and CspA Rice Transgenic Plants
Plant Material Preparation:
Germination: Seeds were sterilized by treating with 0.01 percent mercuric chloride for 3 minutes and washed thoroughly for ten times in milique water to remove the traces of mercuric chloride. Sterilized seeds were allowed to imbibe by soaking in milique water for 3 hours. The imbibed seeds were germinated on a sterilized moist filter paper at 30° C. temperature and 60% RH using a seed germinator (Serwell Instruments Inc.).
Establishment of three leaf stage seedlings: The three day old germinated seedlings were transferred to portrays (52.5 mm (length)×26 mm (depth)×5.2 mm (diameter)) in the greenhouse having light intensity of 800 micro mol./mt2/sec.and 60% RH. The seedlings were grown till three-leaf stage (Approximately for 12 days) in portrays containing red sandy loam soil. Fertilizer solution was applied to the seedlings once a week till the completion of the experiments (N—75 PPM, P—32 PPM, K—32 PPM, Zn—8 PPM, Mo—2 PPM, Cu—0.04 PPM, B—0.4 PPM and Fe—3.00 PPM).
CspB-R2 Plant Analysis
Protocol: Three leaf stage rice seedlings (12 day old) were subjected to a cold stress of 10° C. for 4 days in presence of 100 micro mol./mt2/sec.light and 70% RH (Percival growth chamber). After the stress treatment the plants were allowed to recover in the greenhouse for 10 days and on the 10th day the growth observations for survived plants and photographic evidences were recorded. Each treatment had 10 replications per line and they were completely randomized.
Results: Among eight different lines tested for cold stress tolerance six lines exhibited significantly higher cold tolerance compared to the wild type. The lines including R2-226-6-9-3, R2-226-29-1-1, R2-257-20-2-1, R2-238-1-1-3, R2-230-4-4-2 and R2-257-3-1-3 showed high cold tolerance by exhibiting high recovery growth and less percent reduction in growth (over non-stressed control) compared to the wild type (table-1, plate-1). The line R2-230-4-42, has performed extremely well, it exhibited 100 percent survival and maintained good growth during recovery (Table 1).







TABLE 1







Three leaf stage cold stress recovery growth observations


of CspB R2 transgenic lines.













% Reduction



% Survival

in plant



at end
Plant height (cm)
height over











Lines
of recovery
Stressed
Non-stressed
non-stressed














R2-257-17-1-1
13
21.5 ± 11 
43.44 ± 4.09
50.38


R2-230-34-1-2
53
20.78 ± 6.3 
 45.0 ± 3.51
53.82


R2-226-6-9-3
60
27.5 ± 7  
33.74 ± 4.65
18.49


R2-226-29-1-1
53
 27.6 ± 10.7
35.22 ± 4.06
21.63


R2-257-20-2-1
93
32.39 ± 5.48
 44.0 ± 2.95
27.27


R2-238-1-1-3
80
29.25 ± 8.19
40.72 ± 5.8 
25


R2-230-4-4-2
100
33.95 ± 4.10
  45 ± 3.98
24


R2-257-3-1-3
40
29.80 ± 2.66
  42 ± 4.11
28.5


WT-Taipei
26
23.93 ± 5.61
45.0 ± 3.7
46.6





(Index: WT = Wild type)






CspB-R3 Plant Analysis

Protocol: Three leaf stage seedlings were exposed to cold stress of 8 degree Celsius for 1 day in presence of 1000 micro mol./mt2/sec. of light. Later the seedlings were allowed to recover at 28 degree Celsius in the greenhouse for 15 days and at the end of recovery the plant height was recorded.
Results: Eight different lines tested for cold stress tolerance and all the eight lines showed improved tolerance compared to wild type (non-transgenic) plants. These results confirmed the R2 analysis data showing improved cold tolerance (Table 2).







TABLE 2







Three leaf stage cold stress recovery growth observations


of CspB R3 transgenic lines.











Stressed-plant
Non-stressed
Percent



height (cm)
plant height
reduction



at end of
(cm) at end
in plant height


Lines
recovery
of recovery
over non-stress













R3-226-6-9-3
 28.8 ± 2.88
29.34 ± 7.20
1.84


R3-226-29-1-3-4
30.18 ± 3.19
32.07 ± 3.79
5.89


R3-230-4-4-2-1
30.42 ± 2.16
35.09 ± 4.19
13.30


R3-230-34-1-2-1
32.14 ± 3.41
 37.4 ± 5.68
14.01


R3-238-1-1-3-4
29.54 ± 3.61
 32.2 ± 3.56
8.26


R3-257-3-1-3-1
27.12 ± 3.38
30.86 ± 3.82
12.11


R3-257-15-1-1-2
23.84 ± 2.85
26.71 ± 1.92
10.74


R3-257-20-2-1-1
 33.8 ± 3.48
38.82 ± 1.97
12.93


WT-Taipei
 23.9 ± 3.74
36.65 ± 4.01
34.78









CspA-R2 Plant Analysis

Protocol: Three leaf stage rice seedlings (12 day old) were subjected to a cold stress of 10° C. for 3 days in presence of 1000 micro mol./mt2/sec. and 70% RH in a growth chamber. After the stress treatment the plants were allowed to recover in the green house for 15 days and on the 15th day the growth observations were recorded. Each value is an average of 12 observations and the experiment was conducted by following completely randomized (CRD) experimental design.
Results: Out of seven independent CspA transgenic lines tested 6 lines showed improved cold tolerance compared to wild type. In this experiment plant height was reduced to close to 50% in cold treated control plants (WT) compared to non-stressed plants. Where as in transgenic plants with CspA gene reduction in plant height upon cold treatment varied 4.5% to 22.50% among different independent lines (except one line where reduction in growth was 47.09%). These results suggest that CspA improves the cold tolerance of rice (Table 3).







TABLE 3







Three leaf stage cold stress recovery growth observations


of CspA R2 transgenic rice lines.










Plant height at the
Percent



end of recovery (cm)
reduction in plant height










Lines
Stressed
Non-stressed
over non-stressed













R2-362-3-1-2
28.75 ± 3.11
30.08 ± 2.9 
4.5


R2-328-2-1-1
 29.5 ± 2.92
35.58 ± 3.12
17.08


R2-362-7-1-2
15.83 ± 2.92
29.92 ± 1.73
47.09


R2-365-4-5-3
26.08 ± 3.75
32.08 ± 2.27
18.7


R2-362-6-1-6
27.17 ± 2.25
32.00 ± 1.76
15.05


R2-362-3-1-10
29.58 ± 3.50
38.17 ± 2.59
22.50


R2-362-7-1-2
24.58 ± 3.42
27.25 ± 2.01
9.79


WT-
20.58 ± 1.73
37.92 ± 8.59
46.05


Nipponbare









CspA-R3 Plant Analysis

Experiment I
Protocol: Three leaf stage seedlings were exposed to cold stress of 10 degree Celsius for 3 days in presence of 1000 micro mol. of light. Later the seedlings were allowed to recover at 28 degree Celsius in the greenhouse for 30 days and at the end of recovery the plant height and percent seedling survival were recorded. (In this experiment 8 replications were used for each transgenic line and 10 replications were used for wild type.)
Results: The six transgenic lines subjected to cold stress performed better under cold stress than wild type. These results further confirmed the R2 analysis data by showing improved cold tolerance (Table 4).







TABLE 4







Three leaf stage cold stress recovery growth observations


of CspA R3 transgenic rice lines.












Stressed -
Non-stressed
Percent




plant height
plant height
reduction in



(cm) at the
(cm) at the
plant height
Percent



end of
end of
over
seedling


Lines
recovery
recovery
non-stress
Survival














R3-362-3-1-2-2
 25.5 ± 4.46
32.25 ± 5.03
20.93
100


R3-362-3-1-3-2
25.62 ± 3.36
34.43 ± 6.24
25.58
66


R3-365-10-1-2-3
27.35 ± 3.24
33.75 ± 4.58
18.96
100


R3-362-6-1-2-1
  28 ± 2.45
34.45 ± 2.29
18.72
100


R3-362-7-1-2-3
 27.5 ± 24.17
29.94 ± 5.03
8.1
100


R3-362-7-1-3-3
27.88 ± 4.22
31.92 ± 2.89
12.65
100


WT-Nipponbare
26.25 ± 3.95
36.34 ± 4.06
27.76
40





Note:


Plant height was recorded only for survived plants and their averages are given above.






Experiment II
Protocol: Three leaf stage seedlings were exposed to cold stress of 10 degree Celsius for 1 day in presence of 1000 micro mol. of light. Later the seedlings were allowed to recover at 28 degree Celsius in the green house for 30 days and at the end of recovery the plant height and percent seedling survival were recorded.
Results: The five transgenic lines subjected to cold stress performed better under cold stress than wild type. These results further confirmed the R2 analysis data by showing improved cold tolerance (Table 5).







TABLE 5







Three leaf stage cold stress recovery growth observations


of CspA R3 transgenic rice lines.











Stressed -
Non-stressed
Percent



plant height
plant height
reduction in plant



(cm) at end
(cm) at end
height over non-


Lines
of recovery
of recovery
stress





R3-362-3-1-2-2
32.76 ± 3.49
32.25 ± 5.03
Nil


R3-362-3-1-3-2
36.11 ± 2.04
34.43 ± 6.24
Nil


R3-365-10-1-2-3
35.85 ± 2.94
33.75 ± 4.58
Nil


R3-362-6-1-2-1
21.54 ± 5.84
34.45 ± 2.29
37.4 


R3-362-7-1-2-3
32.55 ± 2.73
29.94 ± 5.03
Nil


R3-362-7-1-3-3
32.17 ± 3.27
31.92 ± 2.89
Nil


WT-Nipponbare
31.92 ± 2.66
36.34 ± 4.06
12.16









Heat Stress Response at Three Leaf Stage
Plant Material Preparation:
Germination: Seeds were sterilized by treating with 0.01 percent mercuric chloride for 3 minutes and washed thoroughly ( ̃ten times in deionized water) to remove the traces of mercuric chloride. Sterilized seeds were allowed to imbibe by soaking in milique water for 3 hours. The imbibed seeds were germinated on a sterilized moist filter paper at 30° C. temperature and 60% RH using a seed germinator (Serwell Instruments Inc.).
Establishment of three leaf stage seedlings: The three day old germinated seedlings were transferred to portrays (52.5 mm (length)×26 mm (depth)×5.2 mm (diameter)) in the green house having light intensity of 800 micro mol./mt2/sec. and 60% RH. The seedlings were grown till three-leaf stage (Approximately for 12 days) in portrays containing red soil. Fertilizer solution was sprayed to the seedlings once a week till the completion of the experiments (N-75 PPM, P—32 PPM, K—32 PPM, Zn—8 PPM, Mo—2 PPM, Cu—0.04 PPM, B—0.4 PPM and Fe—3.00 PPM).
CspA-R2 Plant Analysis
Protocol: Three leaf stage rice seedlings (12 day old) were subjected to the heat stress of 50° C. for 3 hours in presence of 70% RH. After the stress treatment the plants were allowed to recover in the green house for 15 days and on the 15th day the growth observations were recorded. Each value is an average of 12 observations.
Results: Out of seven independent CspA transgenic lines tested 6 lines showed improved heat tolerance compared to wild type. In this experiment plant height was reduced by more than 50% in heat-treated control plants (WT) compared to no stressed plants. Where as in transgenic plants with CspA gene reduction in plant height upon heat treatment varied from 9.5% to 35% among different independent lines. These results suggest that CspA improves the heat tolerance of rice (Table 6).







TABLE 6







Three leaf stage plant heat stress recovery growth observations


of CspA R2 transgenic rice lines.










Plant height at the
Percent reduction



end of recovery (cm)
in plant height










Lines
Stressed
Non-stressed
over non-stressed













R2-362-3-1-2
26.67 ± 4.97
30.08 ± 2.9 
11.33


R2-328-2-1-1
26.17 ± 3.49
35.58 ± 3.12
26.41


R2-362-7-1-2
25.17 ± 1.94
29.92 ± 1.73
15.87


R2-365-4-5-3
20.83 ± 1.17
32.08 ± 2.27
35.06


R2-362-6-1-6
23.17 ± 1.83
32.00 ± 1.76
27.59


R2-362-3-1-10
29.33 ± 5.01
38.17 ± 2.59
23.15


R2-362-7-1-2
24.67 ± 2.8 
27.25 ± 2.01
9.4


WT-Nipponbare
18.5 3.51
37.92 ± 8.59
51.21









CspB-R3 Plant Analysis

Protocol: Three-leaf stage seedlings were exposed to high temperature stress of 53 degree Celsius for 2 hours and later the seedlings were allowed to recover at 28 degree Celsius in the greenhouse for 15 days and at the end of recovery the plant height was recorded.
Results: Out of eight transgenic lines tested seven lines performed better under heat stress tested compared to wild type. These results suggest that CspB improves heat tolerance of rice (Table 7).







TABLE 7







Three leaf stage plant heat stress recovery growth


observations of CspB R3 transgenic rice lines.











Stressed-plant
Non-stressed
Percent



height (cm) at
plant height
reduction in



end of
(cm) at end of
plant height


Lines
recovery
recovery
over non-stress













R3-226-6-9-3
34.53 ± 2.14
35.54 ± 2.07 
2.84


R3-226-29-1-3-4
32.38 ± 1.47
37.06 ± 2.92 
12.62


R3-230-4-4-2-1
28.78 ± 4.16
35.06 ± 2.07 
17.41


R3-230-34-1-2-1
 33.3 ± 3.94
37.6 ± 3.05
11.43


R3-238-1-1-3-4
33.96 ± 2.06
41.2 ± 3.83
17.57


R3-257-3-1-3-1
33.76 ± 3.74
35.4 ± 2.07
4.63


R3-257-15-1-1-2
25.68 ± 4.27
38.2 ± 3.11
32.77


R3-257-20-2-1-1
34.78 ± 1.7 
42.2 ± 2.97
17.5


WT-Taipei
 25.5 ± 2.97
36.65 ± 4.8 
30.42









CspA-R3 Plant Analysis

Experiment I
Protocol: Three-leaf stage seedlings were exposed to high temperature stress of 53 degree Celsius for 3 hours and later the seedlings were allowed to recover at 28 degree Celsius in the greenhouse for 30 days and at the end of recovery the plant height was recorded.
Results: These results confirmed the R2 analysis data by showing improved heat tolerance (Table 8).







TABLE 8







Three leaf stage plant heat stress recovery growth


observations of CspA R3 transgenic rice lines.











Stressed -
Non-stressed
Percent



plant height
plant height
reduction in plant



(cm) at end
(cm) at end
height over non-


Lines
of recovery
of recovery
stress













R3-362-3-1-2-2
31.07 ± 7.01
32.25 ± 5.03
3.6


R3-362-3-1-3-2
30.28 ± 4.74
34.43 ± 6.24
12.05


R3-365-10-1-2-3
24.23 ± 7.60
33.75 ± 4.58
28.20


R3-362-6-1-2-1
26.93 ± 2.97
34.45 ± 2.29
21.82


R3-362-7-1-2-3
29.52 ± 2.61
29.94 ± 5.03
1.40


R3-362-7-1-3-3
21.30 ± 6.37
31.92 ± 2.89
33.27


WT-Nipponbare
22.68 ± 2.96
36.34 ± 4.06
37.58









Experiment II
Protocol: Three leaf stage seedlings were exposed to high temperature stress of 50 degree Celsius for 1 hour in the presence of 1000 micro mol. of light and later the seedlings were allowed to recover at 28 degree Celsius in the greenhouse for 30 days and at the end of recovery the plant height was recorded.
Results: These results confirmed the R2 analysis data by showing improved heat tolerance (Table 9).







TABLE 9







Three leaf stage plant heat stress recovery growth


observations of CspA R3 transgenic rice lines.













Percent



Stressed - plant
Non-stressed
reduction in plant



height (cm) at
plant height (cm)
height over non-


Lines
end of recovery
at end of recovery
stress













R3-362-3-1-2-2
31.57 ± 2.39
32.25 ± 5.03
2.10


R3-362-3-1-3-2
34.20 ± 3.87
34.43 ± 6.24
0.6


R3-365-10-1-2-3
31.63 ± 4.32
33.75 ± 4.58
6.28


R3-362-6-1-2-1
19.72 ± 6.76
34.45 ± 2.29
42.75


R3-362-7-1-2-3
32.18 ± 3.25
29.94 ± 5.03
Nil


R3-362-7-1-3-3
32.80 ± 1.51
31.92 ± 2.89
Nil


WT-Nipponbare
28.20 ± 2.79
36.34 ± 4.06
22.39









Water Stress Response
Plant Material Preparation:
Germination: Seeds were sterilized by treating with 0.01 percent mercuric chloride for 3 min later washed thoroughly for ten times in milique water to remove the traces of mercuric chloride. Sterilized seeds were allowed to imbibe by soaking in milique water for 3 hours. The imbibed seeds were germinated on a sterilized moist filter paper at 30° C. temperature and 60% RH using a seed germinator (Serwell Instruments Inc.).
CspB-R2 Plant Analysis
Experimental Protocol
The germinated seedlings (3 day old) were transferred to two different levels of water stress, created in PVC pots containing vermiculite, which is measured in terms of field capacity (FC). The FC-100% is a saturated condition (i.e. 100 g vermiculite requires 350 ml of water) (Sharp et.al., 1988, Plant physiol. 87: 50-57). The different levels of water stress (i.e. 50% FC and 25% FC) were created in a PVC pots containing vermiculite by adding required amount of water. The water status in different stress levels was constantly maintained, by adding each day the amount of water lost due to evapotranspiration, through out the experiment. The seedlings were allowed to grow for 15 days in the water stress condition in the greenhouse in presence of 800 micro mol./mt2/sec.light intensity and 60% RH. At 15th day the growth of root and shoot were recorded and photographs were taken. Each treatment had 10 replications per line and they were completely randomized.
The percent reduction in growth was computed by adopting following formula.




  
    %
    ⁢
    
      
    
    ⁢
    reduction
    ⁢
    
      
    
    ⁢
    over
    ⁢
    
      
    
    ⁢
    absolute
    ⁢
    
      
    
    ⁢
    control
  
  =
  
    
      
        
          
            
              
                Growth
                ⁢
                
                  
                
                ⁢
                of
                ⁢
                
                  
                
                ⁢
                
                  root
                  /
                  shoot
                
                ⁢
                
                  
                
                ⁢
                of
                ⁢
                
                  
                
                ⁢
                absolute
                ⁢
                
                  
                
                ⁢
                control
              
              -
            
          
        
        
          
            
              
                Growth
                ⁢
                
                  
                
                ⁢
                of
                ⁢
                
                  
                
                ⁢
                
                  root
                  /
                  shoot
                
                ⁢
                
                  
                
                ⁢
                of
                ⁢
                
                  
                
                ⁢
                FC
              
              -
              
                25
                ⁢
                %
              
            
          
        
      
      
        Growth
        ⁢
        
          
        
        ⁢
        of
        ⁢
        
          
        
        ⁢
        
          root
          /
          shoot
        
        ⁢
        
          
        
        ⁢
        of
        ⁢
        
          
        
        ⁢
        absolute
        ⁢
        
          
        
        ⁢
        control
      
    
    ×
    100
  




Results: Four different CspB transgenic lines were analyzed for water stress tolerance. All the CspB transgenic lines tested exhibited significantly higher growth during stress compared to the wild type plants. The transgenic lines including R2-257-15-1-1, R2-238-1-1-3, R2-257-3-1-6 and R2-226-6-9-3 exhibited least percent reduction in root and shoot growth over non-stress control (FC-100%). The reduction in root and shoot growth in these lines ranged between 11 to 25%. Where as, the wild type plants exhibited maximum reduction in growth, which is close to 50%. These results suggest that CspA improves the water stress tolerance of rice (Table-10 and Table-11).







TABLE 10







Comparison of root and shoot growth at the end of water stress of cspB


transgenic lines and the wild type.














FC - 100%

FC - 50%

FC - 25%

















Lines
Root
Shoot
R:S
Root
Shoot
R:S
Root
Shoot
R:S



















R2-257-15-1-1
 9.2 ± 2.2
 24.3 ± 2
.37
  9 ± 1.27
23.7 ± 1.5
.37
 8.1 ± 1.5
18.5 ± 2.2
.43


R2-238-1-1-3
9.65 ± 2.7
 26.3 ± 13.8
.36
8.35 ± 1.56
22.9 ± 1.26
.36
7.15 ± 1.0
18.1 ± 1.6
.39


R2-257-3-1-6
7.35 ± 2.2
 26.1 ± 1.31
.28
 6.4 ± 1.15
23.0 ± 1.57
.27
 6.9 ± 1.07
19.5 ± 1.96
.35


R2-226-6-9-3
8.95 ± 1.82
25.05 ± 1.6
.35
 7.4 ± 1.2
19.0 ± 2.24
.38
7.25 ± 1.5
17.4 ± 2.15
.41


WT-Taipei
 9.2 ± 1.62
 24.6 ± 1.58
.37
 7.4 ± 1.66
22.4 ± 0.97
.33
6.58 ± 0.9
12.8 ± 3.2
.51





(Index: WT = wild type, R:S = Root to Shoot ratio)













TABLE 11







Comparison of percent reduction in growth of root


and shoot of cspB transgenic lines and the wild type.











% Reduction in
% Reduction in
% Reduction in


Lines
root growth
shoot growth
root and shoot growth













R2-257-15-1-1
11
23.8
20


R2-238-1-1-3
25
31
30


R2-257-3-1-6
6
25.2
21


R2-226-6-9-3
19
30.5
27.5


WT-Taipei
28.4
47.9
42.8









CspA-R2 Plant Analysis
a. Plant Material Preparation:
Germination: Seeds were sterilized by treating with 0.01 percent mercuric chloride for 3 minutes and washed thoroughly for ten times in milique water to remove the traces of mercuric chloride. Sterilized seeds were allowed to imbibe by soaking in milique water for 3 hours. The imbibed seeds were germinated on a sterilized moist filter paper at 30° C. temperature and 60% RH using a seed germinator (Serwell Instruments Inc.).
Establishment of three leaf stage seedlings: The three day old germinated seedlings were transferred to portrays (52.5 mm (length)×26 mm (depth)×5.2 mm (diameter)) in the green house having light intensity of 800 micro mol./mt2/sec.and 60% RH. The seedlings were grown till three-leaf stage (Approximately for 12 days) in portrays containing red sandy loam soil. Fertilizer solution was sprayed to the seedlings once a week till the completion of the experiments (N-75 PPM, P-32 PPM, K-32 PPM, Zn-8 PPM, Mo-2 PPM, Cu-0.04 PPM, B-0.4 PPM and Fe-3.00 PPM).
Protocol: One-month-old seedlings were subjected to water stress for three days in presence of 800 micro mol./mt2/sec. light and 60% RH in the greenhouse. Water stress was imposed by withholding irrigation. At the end of three days, plants started showing the wilting symptom. The stress was alleviated by irrigating the plants with water and 24 hours later the observations on percent plants showing wilting symptoms were recorded. A minimum of 12 plants was maintained per line per treatment.
Results: Out of seven independent CspA transgenic lines tested 6 lines showed improved water stress tolerance compared to wild type. Sixty six percent of control plants did not recover from wilting after irrigation where as in CspA transgenic plants percentage of plants showing wilting symptoms after irrigation varied from 5% to 43% among different independent lines (except one line where percentage of plants showing wilting was 85%). These results suggest that CspA improves the water stress tolerance in rice (Table 12).







TABLE 12







Water stress response of CspA R2 transgenic rice lines.











Percentage



Lines
plants showing wilting














R2-362-3-1-2
17



R2-328-2-1-1
43



R2-362-7-1-2
85



R2-365-4-5-3
5



R2-362-6-1-6
Nil



R2-362-3-1-10
15



R2-362-7-1-2
8



WT-
66



Nipponbare










Salt Stress Response
CspB-R3 Plant Analysis
Protocol: Germinated seedlings (48 h. old) were subjected to salinity stress by transferring them to PVC pots with vermiculite containing 200 mM of NaCl and grown for 10 days. After 10 days of stress the seedlings were allowed to recover for 15 days by transferring them to a fresh trays of vermiculite containing water. The growth observation such as plant height was recorded at the end of recovery. This experiment was conducted in the greenhouse by following Completely Randomized Design (CRD) and maintained eight replications per treatment.
Results: Seven CspB transgenic lines and wild type plants were subjected to 200 mM NaCl stress. Under this condition five transgenic lines performed better compared to wild type. These results suggest that CspB improves tolerance of rice plants to salt stress (Table 13).







TABLE 13







Salt stress recovery growth observations of CspA R2


transgenic rice lines.











Stressed-plant
Non-stressed
Percent reduction



height (cm) at
plant height (cm)
in plant height


Lines
end of recovery
at end of recovery
over non-stressed





R3-226-6-9-3
12.68 ± 2.83
23.48 ± 3.85
45.99


R3-226-29-1-3-4
19.24 ± 3.46
25.54 ± 3.64
24.66


R3-230-4-4-2-1
15.39 ± 3.05
 25.2 ± 2.14
38.92


R3-230-34-1-2-1
15.78 ± 3.31
23.26 ± 1.98
32.15


R3-238-1-1-3-4
13.41 ± 2.73
23.63 ± 4.61
43.25


R3-257-3-1-3-1
21.07 ± 3.28
28.95 ± 4.37
27.64


R3-257-20-2-1-1
19.01 ± 3.98
26.35 ± 2.84
27.85


WT-Taipei
14.71 ± 2.28
27.43 ± 2.75
46.37





R3 water stress assay






Germinated seedlings (3 day old) from four independent transgenic lines (1, 2, 3, 4) of cspA and wild type (Nipponbare—Number.5) were subjected to water stress by transferring them into a pot containing vermiculite. Three levels of water regimes were maintained, they are 100% field capacity (FC-100=3.72 ml of water/g vermiculite)
25% field capacity (FC25=0.93 ml of water/g vermiculite) 15% field capacity (FC 15=0.558 ml/g vermiculite). The seedlings were grown in different water regimes for 30 days in presence of 800 micro mol./mt2/sec.light intensity and 60% RH in the greenhouse. The water status in different stress levels was constantly maintained, by adding each day the amount of water lost due to vapotranspiration, throughout the experiment. At the end of 30th day plants were allowed to recover by adding water to bring it the level of FC100 and maintained for 15 days. During the experiment the growth observations such as plant height (pl. ht.) at the end of stress (ES) and root (R) shoot (S) length and dry weight at the end of the recovery were recorded.
Each treatment had 10 replications per line and they were completely randomized.







TABLE 14







Average shoot and root length (cm) at the end of recovery














Line code
Lines
FC100_Root
FC100_Shoot
FC25_Root
FC25_Shoot
FC15_Root
FC15_Shoot





1
R2-362-3-1-3-4
 24.5 ± 1.9
49.1 ± 3.6
17.0 ± 2.6
 34.5 ± 2.4
12.5 ± 1.4
31.2 ± 1.8


2
R2-362-6-1-2-2
 23.3 ± 1.3
45.6 ± 1.5
17.5 ± 1.8
 31.5 ± 1.5
17.6 ± 2.3
32.0 ± 0.7


3
R2-362-7-1-3-3
 24.5 ± 1.3
47.6 ± 3.3
17.8 ± 2.0
 33.5 ± 1.7
15.9 ± 1.7
31.9 ± 1.7


4
R2-365-10-1-2-1
24.03 ± 1.5
44.4 ± 2.2
13.8 ± 1.3
30.24 ± 1.1
13.9 ± 1.3
28.9 ± 0.9


5
WT-Nipponbare
23.84 ± 1.25
44.8 ± 2.0
12.9 ± 1.8
 31.6 ± 1.2
13.9 ± 1.9
31.5 ± 1.2
















TABLE 15







Average shoot and root dry weight (mg) at the end of recovery














Line code
Lines
FC100_Root
FC100_Shoot
FC25_Root
FC25_Shoot
FC15_Root
FC15_Shoot





1
R2-362-3-1-3-4
  231 ± 21.8
563.9 ± 60.7
57.6 ± 6.8
  189 ± 16.3
44.7 ± 6.3
152.9 ± 22.1


2
R2-362-6-1-2-2
  226 ± 14.2
531.8 ± 63
72.1 ± 5.1
179.8 ± 17
53.9 ± 7.9
146.3 ± 21.1


3
R2-362-7-1-3-3
229.5 ± 30.2
  533 ± 48.5
66.1 ± 11.9
  183 ± 13.9
60.6 ± 5.7
147.4 ± 14.7


4
R2-365-10-1-2-1
  219 ± 43.5
  557 ± 71.9
56.2 ± 9.3
173.9 ± 27.3
47.3 ± 3.1
133.7 ± 7.7


5
WT-Nipponbare
  226 ± 34.5
  525 ± 31.3
61.1 ± 4.2
151.1 ± 16.8
45.2 ± 7.5
132.2 ± 11.03
















TABLE 16







Average shoot length (cm) at the end of stress











Line code
Lines
FC100
FC25
FC15





1
R2-362-3-1-3-4
 42 ± 4.6
28.4 ± 1.7
27.4 ± 2.1


2
R2-362-6-1-2-2
40.4 ± 2.1 
26.1 ± 1.1
25.2 ± 2.2


3
R2-362-7-1-3-3
40.1 ± 2.7 
  27 ± 2.0
26.3 ± 1.4


4
R2-365-10-1-2-1
38.9 ± 2.3 
26.3 ± 1.6
23.3 ± 2.4


5
WT-Nipponbare
39.5 ± 1.05
24.2 ± 2.0
24.7 ± 1.9









Example 10
cspA
Construction of pMON73607 (FIG. 10)
1. Vector pMON61322 cut with NcoI and ApaI to open up backbone and drop out Csp A gene. Backbone fragment isolated by gel purification.
2. E. coli cspA gene PCR amplified from pMON56609 (FIG. 8) vector. PCR primers used left the NcoI site at the 5′ end of the gene and created a SwaI and an ApaI site at the 3′ end.
3. Ligated PCR fragment and pMON61322 (FIG. 11) backbone. Transformed into library efficiency DH5α cells. Screened colonies using ApaI and NcoI to identify clones with inserts.
4. Sequenced vector to confirm fidelity of the cspA gene and other selected regions of the plasmid.
cspB
Construction of pMON73608 (FIG. 12)
1. Vector pMON61322 cut with NcoI and ApaI to open up backbone and drop out HVA1 gene. Backbone fragment isolated by gel purification.
2. Bacillus subtilis cspB gene PCR amplified from pMON56610 vector. PCR primers used left the NcoI site at the 5′ end of the gene and created a Swal and an ApaI site at the 3′ end.
3. Ligated PCR fragment and pMON61322 backbone. Transformed into library efficiency DH5α cells. Screened colonies using ApaI and NcoI to identify clones with inserts.
4. Sequenced vector to confirm CspB gene and other selected regions of the plasmid.
Example 11
Maize Plant Transformation
Maize plants can be transformed by methods known in the art, for example, see Examples 20-25 herein.
Example 12
Analysis of transgenic plants for copy number will be done in the following manner.
Leaf tissue is collected from a young leaf, from as close to the base as possible and from one side of the leaf. Samples are placed in 96-well plates lyophilized overnight. Tissues are homogenized by placing three 3 mm metal balls in each well and shaking using a Mega Grinder at 1200 rpm for 2 minutes. DNA is extracted using standard buffers containing beta-mercaptoethanol, Tris buffered to pH8, EDTA, NaCl, and sodium dodecyl sulfate. Extraction is performed with potassium acetate followed by chloroform and precipitation is performed with isopropanol. Following centrifugation, washing with ethanol solution, and drying, DNA is resuspended in Tris-EDTA buffer prior to further analysis.
DNA is digested with multiple restriction endonucleases and fragments are separated by non-denaturing agarose gel electrophoresis. DNA is denatured by NaOH solution. The gel is neutralized in NaCl-containing Tris buffer and blotted to nylon filters by capillary action. Nylon filters are pre-hybridized in buffered solution containing salmon sperm DNA prior to addition of appropriate probes, either radioactive or DIG-labeled. Following hybridization, blots are washed and detected by exposure to autoradiography film or detection of DIG with anti-DIG antibody conjugates and appropriate substrates.
Example 13
We are using the full length open reading frame of cspA and cspB for expression in E. coli using vectors (Novagen, an affiliate of Merck KgaA, Darmstadt, Germany) that allow synthesis and purification of His-tagged antigen. Purified antigen will be used to generate polyclonal antibodies using a commercial provider, for example Strategic Biosolutions. Antibodies produced will be used to test plants for expression of CSP proteins.
Example 14
Transgenic maize line advancement. Primary transformants are generated in germplasm such as CORN OF GERMPLASM A, CORN OF GERMPLASM C, and CORN OF GERMPLASM D. Primary transformants are selfed as well as backcrossed to non-transgenic plants of the same inbred genotype. Seed from selfed plants is planted in the field and assayed by Taqman zygosity assay to identify putative homozygous selections, putative heterozygous selections, and negative selections. Putative heterozygous selections are crossed with multiple plants of appropriate testers, e.g. CORN OF GERMPLASM B and CORN OF GERMPLASM D. Hybrid seed is harvested, hand shelled, and pooled by selection. Other breeding methods may also be employed, for example, see example 29 herein.
Example 15
Seedlings will receive a treatment that limits available water to a sub-optimal level such that the treatment results in a measurable phenotypic response. For example, this treatment could take the form of restricting the amount of water over a number of days leading to a progressive water deficit, or the form of an acute deficit by osmotically stressing the seedlings hydroponically or with a salt treatment. Transgene positive plants will be screened for an improved phenotypic response to the treatment. The phenotypic responses measured may include shoot growth rate or dry weight accumulation during the treatment or following a post-treatment recovery period, wilting or wilt recovery, and root growth rates and dry weight accumulation. Those with improved response will be advanced to a field efficacy trial. Screens will require a number of transgene positive and transgene negative plants to be grown in small pots in a controlled environment such as a growth chamber or greenhouse. The number of plants screened is dictated by the variance associated with treatments applied and phenotypes measured.
Example 16
Field grown plants will receive a treatment that limits available water to a sub-optimal level such that the treatment results in a measurable phenotypic response. For example, this treatment could take the form of restricting the amount of water available to the plants over a number of days leading to a progressive water deficit either during late vegetative or early reproductive development of the plants. Transgene positive plants will be screened for an improved phenotypic response to the treatment relative to transgene negative plants. The phenotypic responses measured may include shoot growth rate during the treatment, leaf wilting, grain yield, and ear yield components such as kernel number and kernel weight. Those events with improved response will be advanced to a first year yield trial. Screens will be applied at typical planting densities at two dryland field locations with controllable irrigation. The number of plants screened is dictated by the variance associated with treatments applied and phenotypes measured.
Example 17
Several of the genes described will be cloned, transformed into plants, and be phenotyped in a manner similar to the following (Examples 17-30). For example, nucleotides and nucleotides encoding SEQ ID NOS: 4-53.
Construction of the Destination Vector.
A GATEWAYTM Destination (Invitrogen Life Technologies, Carlsbad, Calif.) plant expression vector was constructed (pMON65154, FIG. 13) using methods known to those of skill in the art. The elements of the expression vector are summarized in Table 17. The backbone of the plasmid pMON65154 comprising the bacterial replication functions and an ampicillin resistance gene expressed in E. coli were derived from the plasmid pSK-. The plant expression elements in pMON64154 are available to those of skill in the art and references are provided for each element in Table 17. All references in Table 17 to location refer to base pair coordinates for each element on the plasmid map disclosed in FIG. 13. Generally, pMON65154 comprises a selectable marker expression cassettte comprising a Cauliflower Mosaic Virus 35S promoter operablly linked to a gene encoding neomycin phosphotransferase II (nptII). The 3′ region of the selectable marker expression cassette comprises the 3′ region of the Agrobacterium tumefaciense nopaline synthase gene (nos) followed 3′ by the 3′ region of the potato proteinase inhibitor II (pinII) gene. The plasmid pMON 65154 further comprises a plant expression cassette into which a gene of interest may be inserted using GATEWAYTM cloning methods. The GATEWAYTM cloning cassette is flanked 5′ by a rice actin 1 promoter, exon and intron and flanked 3′ by the 3′ region of the potato pinII gene. Using GATEWAYTM methods, the cloning cassette was replaced by a gene of interest. The vector pMON65154 and derivaties thereof comprising a gene of interest, were particularly useful in methods of plant transformation via direct DNA delivery, such as microprjectile bombardment. One of skill in the art could construct an expression vector with similar features using methods known in the art. Furthermore, one of skill in the art would appreciate that other promoters and 3′ regions would be useful for expression of a gene of interest and other selectable markers may be used.







TABLE 17







Elements of Plasmid pMON65154











CASSETTE
FUNCTION
ELEMENT
LOCATION
REFERENCE





Plant gene of
Promoter
Rice actin 1
1796-2638
Wang et al., 1992


interest expression



Enhancer
Rice actin 1 exon
2639-3170
Wang et al., 1992




1, intron 1


GATEWAY TM
Recombination
AttR1
3188-3312
GATEWAY TM Cloning


cloning



Technology Instruction






Manual (Invitrogen Life






Technologies, Carlsbad,






CA)



Bacterial
CmR gene
3421-4080
GATEWAY TM Cloning



chloramphenical


Technology Instruction



resistance gene


Manual (Invitrogen Life






Technologies, Carlsbad,






CA)



Bacterial negative
ccdA, ccdB
4200-4727
GATEWAY TM Cloning



selectable markers
genes

Technology Instruction






Manual (Invitrogen Life






Technologies, Carlsbad,






CA)



GATEWAY TM
attR2
4768-4892
GATEWAY TM Cloning



recombination site


Technology Instruction






Manual (Invitrogen Life






Technologies, Carlsbad,






CA)


Plant gene of
3′ region
Potato pinII
4907-5846
An et al., 1989


interest expression


cassette


Plant selectable
Promoter
Cauliflower
5895-6218
U.S. Pat. No. 5352605


marker gene

Mosaic Virus


expression cassette

35S



Selectable marker
nptII
6252-7046
U.S. Pat. No. 6174724



gene



3′ region
nos
7072-7327
Bevan et al., 1983



3′ region
pinII
7339-8085
An et al., 1989


Maintenance in E. coli
Origin of replication
ColE1
 858-1267
Oka et al, 1979


Maintenance in E. coli
Origin of replication
F1
8273-3673
Ravetch et al., 1977


Maintenance in E. coli
Ampicillin resistance
bla
8909-551
Heffron et al., 1979









A separate plasmid vector (pMON72472, FIG. 14) was constructed for use in Agrobacterium mediated methods of plant transformation. The plasmid pRG76 comprises the gene of interest plant expression, GATEWAYTM cloning, and plant selectable marker expression cassettes present in pMON65154. In addition left and right T-DNA border sequences from Agrobacterium were added to the plasmid. The right border sequence is located 5′ to the rice actin 1 promoter and the left border sequence is located 3′ to the pinII 3′ sequence situated 3′ to the nptII gene. Furthermore the pSK-backbone of pMON65164 was replaced by a plasmid backbone to facilitate replication of the plasmid in both E. coli and Agrobacterium tumefaciens. The backbone comprises an oriV wide host range origin of DNA replication functional in Agrobacterium, the rop sequence, a pBR322 origin of DNA replication functional in E. coli and a spectinomycin/stretptomycin resistance gene for selection for the presence of the plasmid in both E. coli and Agrobacterium. 
The elements present in plasmid vector pRG81 are described in Table 18.







TABLE 18







Genetic Elements of Plasmid Vector pRG81











CASSETTE
FUNCTION
ELEMENT
LOCATION
REFERENCE





Plant gene of
Promoter
Rice actin 1
5610-6452
Wang et al., 1992


interest


expression



Enhancer
Rice actin 1
6453-6984
Wang et al., 1992




exon 1, intron 1


GATEWAY TM
Recombination
AttR1
7002-7126
GATEWAY TM Cloning


cloning



Technology Instruction






Manual (Invitrogen Life






Technologies, Carlsbad,






CA)



Bacterial
CmR gene
7235-7894
GATEWAY TM Cloning



chloramphenical


Technology Instruction



resistance gene


Manual (Invitrogen Life






Technologies, Carlsbad,






CA)



Bacterial negative
ccdA, ccdB
8014-8541
GATEWAY TM Cloning



selectable markers
genes

Technology Instruction






Manual (Invitrogen Life






Technologies, Carlsbad,






CA)



GATEWAY TM
attR2
8582-8706
GATEWAY TM Cloning



recombination site


Technology Instruction






Manual (Invitrogen Life






Technologies, Carlsbad,






CA)


Plant gene of
3′ region
Potato pinII
8721-9660
An et al., 1989


interest


expression


cassette


Plant selectable
Promoter
Cauliflower
  1-324
U.S. Pat. No. 5352605


marker gene

Mosaic Virus


expression

35S


cassette



Selectable marker
nptII
 358-1152
U.S. Pat. No. 6174724



gene



3′ region
nos
1178-1433
Bevan et al., 1983



3′ region
pinII
1445-2191
An et al., 1989


Agrobacterium
DNA transfer
Left border
2493-2516
Zambryski et al., 1982;


mediated



GenBank Accession


transformation



AJ237588


Maintenance of
Origin of replication
Ori-V
2755-3147
Honda et al., 1988


plasmid in E. coli or


Agrobacterium


Maintenance of
Origin of replication
ColE1
3545-4199
Oka et al., 1972


plasmid in E. coli


Maintenance of
Spectinomycin/ststreptomycin
Spc/Str
4242-5030
Fling et al., 1985


plasmid in E. coli or
resistance


Agrobacterium


Agrobacterium
DNA transfer
Right
5514-5538
Zambryski et al., 1982;


mediated

border

GenBank Accession


transformation



AJ237588









Example 18
Coding sequences were amplified by PCR prior to insertion in a GATEWAYTM Destination plant expression vector such as pMON65154 (FIG. 13). All coding sequences were available as either a cloned full length sequence or as DNA sequence information which allowed amplification of the desired sequence from a cDNA library. Primers for PCR amplification were designed at or near the start and stop codons of the coding sequence, in order to eliminate most of the 5′ and 3′ untranslated regions. PCR products were tailed with attB1 and attB2 sequences in order to allow cloning by recombination into GATEWAYTM vectors (Invitrogen Life Technologies, Carlsbad, Calif.).
Two methods were used to produce attB flanked PCR amplified sequences of interest. Both methods are described in detail in the GATEWAYTM Cloning Technology Instruction Manual (Invitrogen Life Technologies, Carlsbad, Calif.). In the first method, a single primer set comprising attB and template specific sequences was used. The primer sequences are as follows:

    
    
        attB1 forward primer:
    
    
    5′ GGG CAC TTT GTA CAA GAA AGC TGG GTN template specific sequence 3′ (SEQ ID NO: 71)
    
        attB2 reverse primer
    
    
    ′ GGGG CAC TTT GTA CAA GAA AGC TGG GTN template specific sequence 3′ (SEQ ID NO: 72)


Alternatively, attB adapter PCR was used to prepare attB flanked PCR products. attB1 adapter PCR uses two sets of primers, i.e., gene specific primers and primers to install the attB sequences. Desired DNA sequence primers were designed which included 12 base pairs of the attB1 or attB2 sequences at the 5′ end. The primers that were used were as follows:

    
    
        attB1 gene specific forward primer
    
    
    5′ CCTGCAGGACCATG forward gene specific primer 3′ (SEQ ID NO 73)
    
        attB2 gene specific reverse primer
    
    
    5′ CCTGCAGGCTCGAGCTA reverse gene specific primer 3′ (SEQ ID NO: 74)


The second set of primers were attB adapter primers with the following sequences:

    
    
        attB1 adapted forward primer
    
    
    5′ GGGGACAAGTTTGTACAAAAAAGCAGGCTCCTGCAGGACCATG 3′ (SEQ ID NO: 75)
    
        attB2 adapted reverse primer
    
    
    5′ GGGGACCACTTTGTACAAGAAAGCTGGGTCCCTGCAGGCTCGAGCTA 3′ (SEQ ID NO: 76)


attB1 and attB2 flanked sequences were amplified by PCR according to the methods described by Invitrogen Life Technologies (Carlsbad, Calif.). attB flanked PCR products were purified and recovered from a gel as described above.
In some instances, attB flanked sequences were recovered from PCR, but could not be inserted into the Donor Vector using GATEWAYTM technology. Conventional cloning methods using ligases were used to insert a DNA sequence into an Entry Vector (Invitrogen Life Technologies, Carlsbad, Calif.) when GATEWAYTM recombination into the Donor Vector failed. The choice of Entry Vector depended on the compatibility of restriction endonuclease sites in the Entry Vector and desired insert sequence. The Entry Vector was digested with a selected restriction endonuclease to remove the ccdB gene, dephosphorylated and gel purified. The selected restriction endonuclease depeneded on the Entry Vector used and the sequence of the desired insert sequence. For example, the ccdb gene was removed from pENTR11 (FIG. 15) using EcoR1 or other combinations of restriction endonucleases such as EcoRV, and XmaI or NcoI and XhoI. Other restriction nucleases could be used with other Entry Vectors for use in the GATEWAYTM process. To use restriction endonuclease digested Entry Vectors, it was necessary to be able to produce compatible sticky ends on the desired PCR product. Sticky ends could be produced by a number of methods known to those of skill in the art, such as restriction endonuclease digestion, adapter ligation or addition of restriction sites during PCR.
In some instances, it was not possible to produce compatible sticky ends on a PCR fragment and an Entry Vector. Alternatively, compatible sticky ends could be produced directed by restriction enzyme digestion of a cDNA clone. It was possible, however, to blunt end ligate PCR fragments into an Entry Vector. Using this method, the Entry Vector was cut with a restriction endonuclease to remove the ccdB gene. A gel purified linear Entry Vector was made blunt ended with T4 DNA polymerase. One of skill in the art is aware of other methods of making blunt ended DNA molecules, such as the use of Klenow DNA polymerase. The PCR product was made blunt ended and preferably dephosphorylated by incubation with T4 DNA polymerase, or another suitable polymerase, T4 polynucleotide kinase and a phosphatase enzyme. The Entry Vector and PCR product were blunt end ligated using methods known in the art. Ligation products were transformed into E. coli and plasmids from individual colonies analyzed for presence of the insert DNA and the desired orientation relative to the attL sites in the Entry Vector. Clones with the attL1 sequence next to the amino end of the open reading frame were selected.
Preferably, the TA method of cloning PCR products (Marchuk et al., 1991) was used when attB flanked PCR products could not be inserted into a plasmid using GATEWAYTM methods. The TA method takes advantage of Taq polymerase terminal transferase activity. An Entry Vector was cut with a restriction endonuclease and made blunt ended using the methods described herein. The blunt ended linear Entry Vector was incubated with dTTP and Taq polymerase resulting in the addition of a single thymidine residue at the 3′ end of each DNA strand. Since Taq polymerase has a strong preference for dATP, PCR products are most often produced with a single adenosine added to the 3′ end. Therefore,the Entry Vector and PCR product have complimentary single base 3′ overhangs. Following ligation under conditions known to those of skill in the art, plasmids were transformed into E. coli. Plasmids were isolated from individual colonies and analyzed to identify plasmids with the desired insert in the correct orientation. Alternatively, PCR products, tailed with attB sites were TA cloned into a commercial TA cloning vector, such as pGEM-T EASY (Promega Corporation, Madison, Wis.).
All PCR amplification products were sequenced prior to introduction into a plant. PCR inserts in Destination expression vectors produced by GATEWAYTM methods were sequenced to confirm that the inserted sequenced encoded the expected amino acid sequence. If Entry Vectors were produced using ligation methods, the inserted sequence was sequenced in the Entry Vector prior to production of the Destination expression vector using GATEWAYTM technology. Point mutations which did not affect the amino acid coding sequence, i.e., silent mutations, were accepted.
Example 19
Construction of Expression Vectors
GATEWAYTM cloning methods (Invitrogen Life Technologies, Carlsbad, Calif.) were used to construct expression vectors for use in maize transformation. The GATEWAYTM methods are fully described in the GATEWAYTM Cloning Technology Instruction Manual (Invitrogen Life Technologies, Carlsbad, Calif.). Use of the GATEWAYTM system facilitates high throughput cloning of coding sequences into a plant expression vector. Gene sequences flanked by attB1 and attB2 sequences were produced by PCR as described above. Depending on which recombination sequence, attB1 and attB2, was placed 5′ and 3′ to the coding sequence, sense or antisense expression vectors were produced. A plant expression vector, pMON65154 (FIG. 13), into which any coding sequence could be inserted in a sense or antisense orientation was constructed as described in Example 1 and was used as a destination vector in the GATEWAYTM cloning process.
Two alternative processes were used for inserting a PCR amplified coding sequence into a plant expression vector. In the first method, a PCR product comprising the coding sequence of interest flanked by attB1 and attB2 sequences at the 5′ and 3′ ends was incubated with the donor vector (pDONR201TM, Invitrogen Life Technologies, Carlsbad, Calif.) in the presence of BP CLONASETM. GATEWAYTM entry clones were produced from this reaction and transformed into E. coli. Plasmid DNA was isolated from entry clones. Inserted coding sequences could be sequenced from entry vectors in order to confirm the fidelity of PCR amplification. Plasmid DNA, isolated from entry clone E. coli colonies, was incubated with linearized destination vector, preferably pMON65154, in the presence of LR CLONASETM to produce plant expression vectors comprising the coding sequence of interest. DNA from the LR CLONASETM reaction was transformed into E. coli. Plasmid DNA from destination expression vectors was isolated and sequenced in order to determine correct orientation and sequence of the plant expression vector.
In the second method of generating plant expression vectors, a PCR product flanked by attB1 and attB2 sequences was incubated with a donor vector (pDONR201TM, Invitrogen Life Technologies, Carlsbad, Calif.), and BP CLONASETM as described above. Following incubation, an aliquot of the reaction mix was further incubated with linearized destination vector and LR CLONASETM. The resultant DNA was transformed into E. coli and plant expression vectors containing the coding sequence of interest selected using PCR or Southern blot analysis techniques known in the art. Both methods of producting plant expression vectors comprising a coding sequence of interest were described by Invitrogen Life Technologies (GATEWAYTM Cloning Technology Instruction Manual).
Alternatively, Entry Vectors were produced using restriction endonucleases and ligases. Entry Vectors are available from Invitrogen Life Technlogies (Carlsbad, Calif.). Each entry vector, e.g., pENTR1A, pENTR2B, pENTR3C, pENTR4, and pENTR11, has unique cloning and expression features. pENTR11 was preferably used in the practice of the present invention. Those of skill in the art will recognize the usefulness of the other Entry Vectors. Before using restriction endonucleases and ligases to insert desired sequences into one of the Entry Vectors, it was necessary to restriction digest the Entry Vector on each side of the ccdB gene. A number of different combinations of restriction endonucleases were used depending on the restriction sites present on the DNA sequence to be inserted into the Entry Vector. Preferably the Entry Vector was dephosphorylated and gel purified after restriction digestion. The desired DNA sequence was inserted into the Entry Vector using conventional methods of molecular biology known to those of skill in the art. TA cloning (U.S. Pat. No. 5,827,657) is a preferable method of cloning PCR fragments into an Entry Vector.
Vectors (designated as pMON and a 5 digit number) and coding sequences contained therein that were produced using the GATEWAYTM cloning methods are, for example, SEQ ID NOS: 4-28. It is expected that some of the coding sequences of the present invention may be cloned into a plant expression vectors using the methods described herein.
Example 20
CORN OF GERMPLASM A plants were grown in the greenhouse. Ears were harvested from plants when the embryos were 1.5 to 2.0 mm in length, usually 10 to 15 days after pollination, and most frequently 11 to 12 days after pollination. Ears were surface sterilized by spraying or soaking the ears in 80% ethanol, followed by air drying. Alternatively, ears were surface sterilized by immersion in 50% CLOROXTM containing 10% SDS for 20 minutes, followed by three rinses with sterile water.
Immature embryos were isolated from individual kernels using methods known to those of skill in the art. Immature embryos were cultured on medium 211 (N6 salts, 2% sucrose, 1 mg/L 2,4-D, 0.5 mg/L niacin, 1.0 mg/L thiamine-HCl, 0.91 g/L L-asparagine, 100 mg/L myo-inositiol, 0.5 g/L MES, 100 mg/L casein hydrolysate, 1.6 g/L MgCl2, 0.69 g/L L-proline, 2 g/L GELGROTM, pH 5.8) containing 16.9 mg/L AgNO3, (designated medium 211V) for 3-6 days, preferably 3-4 days prior to microprojectile bombardment.
Example 21
Methods of Agrobacterium mediated transformation of maize cells and other monocots are known (Hiei et al., 1997; U.S. Pat. No. 5,591,616; U.S. Pat. No. 5,981,840; published EP patent application EP 0 672 752). Although various strains of Agrobacterium may be used (see references above), strain ABI is used preferably by the present inventors. The ABI strain of Agrobacterium is derived from strain A208, a C58 nopaline type strain, from which the Ti plasmid was eliminated by culture at 37° C., and further containing the modified Ti plasmid pMP90RK (Koncz and Schell, 1986). An Agrobacterium tumefaciens binary vector system (An et al., 1998) is preferably used to transform maize. Alternative cointegrating Ti plasmid vectors have been described (Rogers et al., 1988) and could be used to transform maize. A binary vector comprising one or more genes of interest may be introduced into a disarmed Agrobacterium strain using electroporation (Wen-jun and Forde, 1989) or triparental mating (Ditta et al., 1980). A binary vector may contain a selectable marker gene, a screenable marker gene and/or one or more genes that confer a desirable phenotypic trait on the transformed plant. An exemplary binary vector, pMON30113, is shown in FIG. 4. Other binary vectors may be used and are known to those of skill in the art.
Prior to co-culture of maize cells, Agrobacterium cells may be grown at 28° C. in LB (DIFCO) liquid medium comprising appropriate antibiotics to select for maintenance of the modified Ti plasmid and binary vector. For example, ABI/pMON30113, may be grown in LB medium containing 50 ug/ml kanamycin to select for maintenance of the pMP90RK modified Ti plasmid and 100 ug/ml spectinomycin to select for maintenance of the binary vector pMON30113. It will be obvious to one of skill in the art to use appropriate selection agents to maintain plasmids in the host Agrobacterium strain. Prior to inoculation of maize cells, Agrobacterium cells are grown overnight at room temperature in AB medium (Chilton et al., 1974) comprising appropriate antibiotics for plasmid maintenance and 200 uM acetosyringone. Immediately prior to inoculation of maize cells, Agrobacterium are preferably pelleted by centrifugation, washed in 1⁄2 MSVI medium (2.2 g/L GIBCO (Carlsbad, Calif.) MS salts, 2 mg/L glycine, 0.5 g/L niacin, 0.5 g/L L-pyridoxine-HCl, 0.1 mg/L thiamine, 115 g/L L-proline, 10 g/L D-glucose, and 10 g/L sucrose, pH 5.4) containing 200 uM acetosyringone, and resuspended at 0.1 to 1.0×109 cells/ml in 1⁄2 MSPL medium (2.2 g/L GIBCO (Carlsbad, Calif.) MS salts, 2 mg/L glycine, 0.5 g/L niacin, 0.5 g/L L-pyridoxine-HCl, 0.1 mg/L thiamine, 115 g/L L-proline, 26 g/L D-glucose, 68.5 g/L sucrose, pH 5.4) containing 200 uM acetosyringone. One of skill in the art may substitute other media for 1⁄2 MSVI or 1⁄2 MSPL.
Immature maize embryos are isolated as described previously. Embryos are inoculated with Agrobacterium 0-7 days after excision, preferably immediately after excision. Alternatively, immature embryos may be cultured for more than 7 days. For example, embryogenic callus may be initiated as described above and co-cultured with Agrobacterium. Preferably, immature maize embryos are excised, immersed in an Agrobacterium suspension in 1⁄2 MSPL medium prepared as described above and incubated at room temperature with Agrobacterium for 5-20 minutes.
Following inoculation embryos are transferred to one-half strength MS medium (Murashige and Skoog, 1962) containing 3.0 mg/L 2,4-dichlorophenyoxyacetic acid (2,4-D), 1% D-glucose, 2% sucrose, 0.115 g/L L-proline, 0.5 mg/L thiamine-HCl, 200 uM acetosyringone, and 20 uM silver nitrate or silver thiosulfate. Immature embryos are co-cultured with Agrobacterium for 1 to 3 days at 23° C. in the dark. One of skill in the art may substitute other media for the described media.
Co-cultured embryos are transferred to medium 15AA (462 mg/L (NH4)SO4, 400 mg/L KH2PO4, 186 mg/L MgSO4-7H20, 166 mg/L CaCl2-2H20, 10 mg/L MnSO4-H20, 3 mg/L H3B03, 2 mg/L ZnSO4-7H20, 0.25 mg/L NaMoO4-2H20, 0.025 mg/L CuSO4-5H20, 0.025 mg/L CoCl2-6H20, 0.75 mg/L KI, 2.83 g/L KNO3, 0.2 mg/L niacin, 0.1 mg/L thiamine-HCl, 0.2 mg/L pyridoxine-HCl, 0.1 mg/L D-biotin, 0.1 mg/L choline chloride, 0.1 mg/L calcium pantothenate, 0.05 mg/L folic acid, 0.05 mg/L p-aminobenzoic acid, 0.05 mg/L riboflavin, 0.015 mg/L vitamin B12, 0.5 g/L casamino acids, 33.5 mg/L Na2EDTA, 1.38 g/L L-proline, 20 g/L sucrose, 10 g/L D-glucose), or MS medium containing 1.5 mg/L 2,4-D, 500 mg/L carbenicillin, 3% sucrose, 1.38 g/L L-proline and 20 uM silver nitrate or silver thiosulfate and cultured for 0 to 8 days in the dark at 27° C. without selection. Culture media used for selection of transformants and regeneration of plants preferably contains 500 mg/L carbenicillin. One of skill in the art may substitute other antibiotics that control growth of Agrobacterium. Other culture media that support cell culture may be used alternatively. In the absence of a delay of selection (0 day culture), selection may be initiated on 25 mg/L paromomycin. Selection medium may comprise medium 211 (described above) or a variant of medium 211 in which N6 salts are replaced by MS salts. After two weeks, embryogenic callus are transferred to culture medium containing 100 mg/L paromomycin and subcultured at about two week intervals. When selection is delayed following co-culture, embryos are initially cultured on medium containing 50 mg/L paromomycin followed by subsequent culture of embryogenic callus on medium containing 100-200 mg/L paromomycin. One of skill in the art will culture tissue on concentrations of paromomycin which inhibit growth of cells lacking the selectable marker gene, but a concentration on which transformed callus will proliferate. Alternatively, one may use other selectable markers to identify transformed cells. It is believed that initial culture on 25 to 50 mg/L paromocyin for about two weeks, followed by culture on 50-200 mg/L paromoycin will result in recovery of transformed callus. Transformants are recovered 6 to 8 weeks after initiation of selection. Plants are regenerated from transformed embryogenic callus as described above for transformants recovered following microprojectile bombardment.
Example 22
Agrobacterium Mediated Transformation of Maize Callus
This example describes methods for transformation of maize callus using Agrobacterium. The method is exemplified using an nptII selectable marker gene and paromomycin selective agent. One of skill in the art will be aware of other selectable marker and selective agent combinations that could be used alternatively.
Callus was initiated from immature embryos using methods known to those of skill in the art. For example, 1.5 mm to 2.0 mm immature embryos were excised from developing maize seed of a genotype such as CORN OF GERMPLASM A and cultured with the embryonic axis side down on medium 211 V, usually for 8-21 days after excision. Alternatively, established an established callus culture may be initiated and maintained by methods known to those of skill in the art.
Agrobacterium was prepared for inoculation of plant tissue according to the methods described in Example 21. Fifty to 100 pieces of callus was transferred to a 60 mm×20 mm petri dish containing about 15 ml of Agrobacterium suspension at 0.1 to 1.0×109 cfu/ml. A piece of callus was usually all of the callus produced by an immature embryo in up to 21 days of culture or a piece of established callus of 2 mm to 8 mm in diameter. Callus was incubated for about 30 minutes at room temperature with the Agrobacterium suspension, followed by removal of the liquid by aspiration.
About 50 μL of sterile distilled water was added to a Whatman #1 filter paper in a 60 mm×20 mm petri dish. After 1-5 minutes, 15 to 20 pieces of callus were transferred to each filter paper and the plate sealed with PARAFILM®, for example. The callus and Agrobacterium were co-cultured for about 3 days at 23° C. in the dark.
Calli were transferred from filter paper to medium 211 with 20 μM silver nitrate and 500 mg/L carbenicillin and cultured in the dark at 27° C. to 28° C. for 2-5 days, preferably 3 days. Selection was initiated by transferring callus to medium 211 containing 20 μM silver nitrate, 500 mg/L carbenicillin and 25 mg/L paromomycin. After 2 weeks culture in the dark at 27° C. to 28° C., callus was transferred to medium 211 with 20 μM silver nitrate, 500 mg/L carbenicillin and 50 mg/L paromomycin (medium 211QRG). Callus was subcultured after two weeks to fresh medium 211 QRG and further cultured for two weeks in the dark at 27° C. to 28° C. Callus was then transferred to medium 211 with 20 μM silver nitrate, 500 mg/L carbenicillin and 75 mg/L paromomycin. After 2-3 weeks culture in the dark at 27° C. to 28° C., paromomycin resistant callus was identified. One of skill in the art would recognize that times between subcultures of callus are approximate and one may be able to accelerate the selection process by transferring tissue at more frequent intervals, e.g., weekly rather than biweekly.
Plants were regenerated from transformed callus, transferred to soil and grown in the greenhouse as described. Following Agrobacterium mediated transformation, medium 217 (see Example 9) further contained 500 mg/L carbenicillin and medium 127T (see Example 9) further contained 250 mg/L carbenicillin. Transformed maize plants comprising genes of the present invention that were produced using Agrobacterium mediated transformation are summarized in table Y.
Example 23
Methods of Microprojectile Bombardment
Approximately four hours prior to microprojectile bombardment, immature embryos were transferred to medium 211SV (medium 211V with the addition of sucrose to 12%). Twenty five immature embryos were preferably placed in a 60×15 mm petri dish, arranged in a 5×5 grid with the coleoptilar end of the scutellum pressed slightly into the culture medium at a 20 degree angle. Tissue was maintained in the dark prior to bombardment.
Prior to microprojectile bombardment, a suspension of gold particles was prepared onto which the desired DNA was precipitated. Ten milligrams of 0.6 μm gold particles (BioRad) were suspended in 50 μL buffer (150 mM NaCl, 10 mM Tris-HCl, pH 8.0). Twenty five μL of a 2.4 nM solution of the desired DNA was added to the suspension of gold particles and gently vortexed for about five seconds. Seventy five μL of 0.1M spermidine was added and the solution vortexed gently for about 5 seconds. Seventy five μL of a 25% solution of polyethylene glycol (3000-4000 molecular weight, American Type Culture Collection) was added and the solution was gently vortexed for five seconds. Seventy five pL of 2.5 M CaCl2 was added and the solution vortexed for five seconds. Following the addition of CaCl2, the solution was incubated at room temperature for 10 to 15 minutes. The suspension was subsequently centrifuged for 20 seconds at 12,000 rpm (Sorval MC-12V centrifuge) and the supernatant discarded. The gold particle/DNA pellet was washed twice with 100% ethanol and resuspended in 10 mL 100% ethanol. The gold particle/DNA preparation was stored at −20° C. for up to two weeks.
DNA was introduced into maize cells using the electric discharge particle acceleration gene delivery device (U.S. Pat. No. 5,015,580). The gold particle/DNA suspension was coated on Mylar sheets (Du Pont Mylar polyester film type SMMC2, aluminum coated on one side, over coated with PVDC co-polymer on both sides, cut to 18 mm square) by dispersion of 310 to 320 μL of the gold particle/DNA suspension on a sheet. After the gold particle suspension settled for one to three minutes, excess ethanol was removed and the sheets were air dried. Microprojectile bombardment of maize tissue was conducted as described in U.S. Pat. No. 5,015,580. AC voltage may be varied in the electric discharge particle delivery device. For microprojectile bombardment of CORN OF GERMPLASM A pre-cultured immature embryos, 35% to 45% of maximum voltage was preferably used. Following microprojectile bombardment, tissue was cultured in the dark at 27° C.
Example 24
Selection of Transformed Cells
Transformants were selected on culture medium comprising paromomycin, based on expression of a transgenic neomycin phosphotransferase II (nptII) gene. Twenty four hours after DNA delivery, tissue was transferred to 211V medium containing 25 mg/L paromomycin (medium 211HV). After three weeks incubation in the dark at 27° C., tissue was transferred to medium 211 containing 50 mg/L paromomycin (medium 211G). Tissue was transferred to medium 211 containing 75 mg/L paromomycin (medium 211XX) after three weeks.
Transformants were isolated following 9 weeks of selection. Table Y dislcoses results of transformant experiments using the methods of microprojectile bombardment disclosed herein.
Example 25
Regeneration of Fertile Transgenic Plants
Fertile transgenic plants were produced from transformed maize cells. Transformed callus was transferred to medium 217 (N6 salts, 1 mg/L thiamine-HCl, 0.5 mg/L niacin, 3.52 mg/L benzylaminopurine, 0.91 mg/L L-asparagine monohydrate, 100 mg/L myo-inositol, 0.5 g/L MES, 1.6 g/L MgCl2-6H2O, 100 mg/L casein hydrolysate, 0.69 g/L L-proline, 20 g/L sucrose, 2 g/L GELGROTM, pH 5.8) for five to seven days in the dark at 27° C. Somatic embryos mature and shoot regeneration began on medium 217. Tissue was transferred to medium 127T (MS salts, 0.65 mg/L niacin, 0.125 mg/L pyridoxine-HCl, 0.125 mg/L thiamine-HCl, 0.125 mg/L Ca pantothenate, 150 mg/L L-asparagine, 100 mg/L myo-inositol, 10 g/L glucose, 20 g/L L-maltose, 100 mg/L paromomycin, 5.5 g PHYTAGARTM, pH 5.8) for shoot development. Tissue on medium 127T was cultured in the light at 400-600 lux at 26° C. Plantlets are transferred to soil, preferable 3 inch pots, about four to 6 weeks after transfer to 127T medium when the plantlets are about 3 inches tall and have roots. Plants were maintained for two weeks in a growth chamber at 26° C., followed by two weeks on a mist bench in a greenhouse before transplanting to 5 gallon pots for greenhouse growth. Plants were grown in the greenhouse to maturity and reciprocal pollinations were made with the inbred CORN OF GERMPLASM A. Seed was collected from plants and used for further breeding activities.
Example 26
Isolation of Nucleic Acids from Plants
Nucleic acids were isolated from leaf tissue of R0 plants, collected and flash frozen in a 96 well collection box, 0 to 2 weeks after plantlets were transferred to soil. Approximately 100 milligrams of tissue was collected from each plant and stored at −80° C. until analysis.
DNA and RNA were isolated from a single tissue sample using the Qiagen Rneasy 96TM kit (Qiagen Inc., Valencia, Calif.) with modifications. One hundred milligrams of frozen tissue was homogenized in 700 μL RneasyTM RTL buffer (Qiagen Inc., Valencia, Calif.) using a Bead BeaterTM (Biospec Products, Bartlesville, Okla.). Samples were centrifuged at 3200 rpm for 15 minutes and all of the supernatant transferred the wells of a Promega WIZARDTM clearing plate (Promega Corporation, Madison, Wis.). The sample solutions were clarified by vacuum filtration through the clearing plate. The cleared supernatant was used for nucleic acid extractions.
For DNA extractions, 70 μL of the cleared sample was transferred to a v-well PCR plate, covered with adhesive foil, and heated to 95° C. for 8 minutes. The samples were incubated at 0° C. for five minutes, followed by centrifugation for 3 minutes to remove insoluble materials. A Sephadex G-50 gel filtration box (Edge Biosystems, Gaithersburg, Mo.) was conditioned for 2 min at 2000 rpm. Forty μL of the heat-treated supernatant was loaded into each well and the box centrifuged for two minutes at 2500 rpm. An additional 20 μL of TE buffer was added to the column effluent and the sample plate was stored at −20° C. until analysis.
For RNA extractions, five hundred microliters of cleared solution was transfer to a clean 96 well sample box. Two hundred and fifty microliters of 100% ethanol was added to each sample and the sample was thoroughly mixed. All of the approximately seven hundred and fifty microliters of solution was then loaded into the wells of a Qiagen RneasyTM binding plate in a Promega WIZARDTM filtration unit. Five hundred microliters of RW1 buffer (Qiagen Inc., Valencia, Calif.) was added to each well and the buffer removed by vacuum filtration. Eighty microliters of RNAase free DNAase (Qiagen Inc., Valencia, Calif.) was added to each well, incubated at room temperature for 15 minutes the DNAase solution drawn through the wells by vacuum filtration. An additional five hundred microliters RW1 buffer (Qiagen Inc., Valencia, Calif.) was added to the wells and the buffer removed by vacuum filtration. The sample was further washed by vacuum filtration with 500 μL RPE buffer 2× (Qiagen, Valencia, Calif.). The extraction plate was placed on a microtiter plate and centrifuged for three minutes at 3000 rpm to remove any residual RPE buffer solution in the filter. Eighty microliters of RNA grade water (DNAse free) was added to each well, followed by incubation at room temperature for two minutes. The extraction plate and microtiter plate were centrifuged for three minutes at 3000 rpm and the RNA preparation stored frozen in the collection plate at −80° C.
Example 27
Assays for Copy Number
Copy number of transgenes in R0 plants was determined using TAQMAN® methods. The pMON65154 and pRG76 GATEWAYTM destination vectors were constructed with a sequence derived from the 3′ region of the potato pinII gene which could be used to assay copy number of transgene insertions. The pinII forward and reverse primers were as follows:

    
    
        Forward primer 5′ ccccaccctgcaatgtga 3′ (SEQ ID NO: 77)
        Reverse primer 5′ tgtgcatccttttatttcatacattaattaa 3′ (SEQ ID NO: 78)
        The pinII TAQMAN® probe sequence was 5′ cctagacttgtccatcttctggattggcca 3′ (SEQ ID NO: 79)
    
    


The probe was labelled at the 5′ end with the fluorescent dye FAM (6-carboyxfluorescein) and the quencher dye TAMRA (6-carboxy-N,N,N′,N′-tetramethylrhodamine) was attached via a linker to the 3′ end of the probe. The TAQMAN® probe was obtained from Applied Biosystems (Foster City, Calif.)._SAT, a single copy maize gene was used as an internal control in TAQMAN® copy number assays. The SAT primers were as follows

    
    
        Forward primer 5′ gcctgccgcagaccaa 3′ (SEQ ID NO: 80)
        Reverse primer 5′ atgcagagctcagcttcatc 3′ (SEQ ID NO:81)
        The SAT TAQMAN® probe sequence was 5′ tccagtacgtgcagtccctcctcc 3′ (SEQ ID NO: 82)
    
    


the probe was labelled at its 5′ end with the fluorescent dye VICTM (Applied Biosystems, Foster City, Calif.) and the quencher dye TAMRA at is 3′ end.
TAQMAN® PCR was performed according to the manufacturer's instructions (Applied Biosystems, Foster City, Calif.). Five to 100 nanograms DNA was used in each assay. PCR amplification and TAQMAN® probe detection were performed in 1× TAQMAN® Universal PCR Master Mix (Applied Biosystems, Foster City, Calif.) which contains AmpliTaq Gold® DNA polymerase, AmpErase® UNG, dNTPs with dUTP, Passive Reference 1, and optimized buffer. Eight hundred nM each forward and reverse pinII primers and 150 nM pinII TAQMAN® probe were used in the TAQMAN® assay. 200 nM each Sat forward and reverse primers and 150 nM Sat TAQMAN® probe were used in the TAQMAN® copy number assay. TAQMAN® PCR was carried out for 2 minutes at 50° C., 10 minutes at 95° C., followed by 40 cycles of 15 seconds at 95° C. and one minute at 60° C. Real time TAQMAN® probe fluorescence was measured using an ABI Prism 7700 Sequence Detection System or ABI7900HT Sequence Detection System (Applied Biosystems, Foster City, Calif.). CT values were calculated according to the TAQMAN® EZ RT-PCR kit instruction manual (Applied Biosystems, Foster City, Calif.). The ΔΔ CT value was calculated as CT (internal control gene (Sat))−CT (transgene)−CT (internal control gene (Sat) in nontransgenic plant). The copy number was assigned as follows according to the criteria in Table 19.







TABLE 19







Critera for Copy Number Determination by TAQMAN ®








Copy Number
Criteria











1
−0.5 < ΔΔCT < 0.50


2
  0.5 < ΔΔCT < 1.50


>2
ΔΔCT > 1.50









Plants comprising genes of the present invention will be anyalyzed by TAQMAN® methods for copy number. Southern blot analysis to confirm the TAQMAN® copy number determination in about 80% of the plants that were analyzed by both TAQMAN® and Southern blot hybridization.
Example 28
Assays for Gene Expression
Expression of a transgene of the present invention was assayed by TAQMAN® RT-PCR using the TAQMAN® EZ RT-PCR kit from Applied Biosystems (Foster City, Calif.). RNA expression was assyed relative to expression in a transgenic standard, a transgenic maize event designated DBT418, comprising a B. thuringiensis cryIAI gene operably linked to apinII 3′ untranslated region. The DBT418 event expresses the cryIAI gene at a level which confers commercial levels of resistance to lepdiopteran insects such as European Corn Borer and was commercially sold by DEKALB Genetics Corporation under the brand name DEKALBt®. The pMON65154 and pRG76 GATEWAYTM destination vectors were constructed with a sequence derived from the 3′ region of the potato pinII gene which could be used to assay transgene transcript levels for any coding sequence inserted into the Destination Vector. The pinII primers and probe previously described in were used for TAQMAN® RT-PCR. Ubiquitin fusion protein (UBI) RNA was used as an internal control in all TAQMAN® RT-PCR assays. The UBI primers used were as follows:

    
    
        Forward primer 5′ cgtctacaatcagaaggcgtaatc 3′ (SEQ ID NO: 83)
        Reverse primer 5′ ccaacaggtgaatgcttgatagg 3′ (SEQ ID NO: 84 )
        The sequence of the UBI TAQMAN® probe was 5′ catgcgccgctttgcttc 3′ (SEQ ID NO: 85 )
    
    


The UBI TAQMAN® probe was labeled at its 5′ end with the fluorescent dye VICTM (Applied Biosystems, Foster City, Calif.) and the quencher dye TAMRA at is 3′ end
Reverse transcription, PCR amplification and TAQMAN® probing were performed according to the one step procedure described in the TAQMAN® EZ RT-PCR kit (Applied Biosystems, Foster City, Calif.). Five to 100 nanograms total RNA was used in each assay. In vitro transcribed control RNA from the DBT418 event was included as a control on every plate and run over a concentration range from 0.01 picograms to 10 picograms. Total RNA from DBT418 leaf and from the non-transgenic inbred CORN OF GERMPLASM A were run as positive and negative controls respectively. RT-PCR was performed in TAQMAN® EZ Buffer (50 mM Bicine, 115 mM potassium acetate, 0.01 mM EDTA, 60 mM Passive Reference 1, 8% glycerol, pH 8.2, Applied Biosystems, Foster City, Calif.) containing 3 mM manganese acetate, 300 μM each dATP, dCTP, dGTP, and dUTP, 100 units rTthTM (Applied Biosystems, Foster City, Calif.) DNA polymerase, and 25 units AmpErase UNG (Applied Biosytems, Foster City, Calif.). RT-PCR was carred out as follows: 2 minutes at 50° C., 30 minutes at 60° C., 5 minutes at 95° C., followed by 40 cycles of 20 seconds at 95° C. and 1 minute at 60° C. 400 nM each forward and reverse primers were used for amplification of the pinII sequence and 200 nM TAQMAN® pinII probe used for detection. UBI RNA was amplified using 400 nM each forward and reverse primers and 200 nM UBI TAQMAN® probe was used for detection. TAQMAN® fluorescence was measured using an ABI Prism 7700 Sequence Detection System or ABI7900HT Sequence Detection System (Applied Biosystems, Foster City, Calif.). Expression of transgenes of the present invention was quantitated relative to transgene expression in DBT418 and reported as a ratio of transgene expression to DBT418 expression, i.e., 2−(ΔΔCT) (transgene)/2−(ΔΔCT) (DBT418).
Example 29
Plant Breeding
Backcrossing can be used to improve a starting plant. Backcrossing transfers a specific desirable trait from one source to an inbred or other plant that lacks that trait. This can be accomplished, for example, by first crossing a superior inbred (A) (recurrent parent) to a donor inbred (non-recurrent parent), which carries the appropriate gene(s) for the trait in question, for example, a construct prepared in accordance with the current invention. The progeny of this cross first are selected in the resultant progeny for the desired trait to be transferred from the non-recurrent parent, then the selected progeny are mated back to the superior recurrent parent (A). After five or more backcross generations with selection for the desired trait, the progeny are hemizygous for loci controlling the characteristic being transferred, but are like the superior parent for most or almost all other genes. The last backcross generation would be selfed to give progeny which are pure breeding for the gene(s) being transferred, i.e. one or more transformation events.
Therefore, through a series of a breeding manipulations, a selected transgene may be moved from one line into an entirely different line without the need for further recombinant manipulation. Transgenes are valuable in that they typically behave genetically as any other gene and can be manipulated by breeding techniques in a manner identical to any other corn gene. Therefore, one may produce inbred plants which are true breeding for one or more transgenes. By crossing different inbred plants, one may produce a large number of different hybrids with different combinations of transgenes. In this way, plants may be produced which have the desirable agronomic properties frequently associated with hybrids (“hybrid vigor”), as well as the desirable characteristics imparted by one or more transgene(s).
It is desirable to introgress the genes of the present invention into maize hybrids for characterization of the phenotype conferred by each gene in a transformed plant. The host genotype into which the transgene was introduced, preferably CORN OF GERMPLASM A, is an elite inbred and therefore only limited breeding is necessary in order to produce high yielding maize hybrids. The transformed plant, regenerated from callus is crossed, to the same genotype, e.g., CORN OF GERMPLASM A. The progeny are self pollinated twice and plants homozygous for the transgene are identified. Homozygous transgenic plants are crossed to a testcross parent in order to produce hybrids. The test cross parent is an inbred belonging to a heterotic group which is different from that of the transgenic parent and for which it is known that high yielding hybrids can be generated, for example hybrids are produced from crosses of CORN OF GERMPLASM A to either CORN OF GERMPLASM E or CORN OF GERMPLASM B.
Example 30
Methods of Evaluating Phenotype
Expression of the genes of the present invention leads to various phenotypes as disclosed herein in transformed cells and plants. Phenotypic data is collected during the transformation process in callus as well as during plant regeneration, as well as in plants and progeny. Phenotypic data is collected in transformed callus relating to the morphological appearance as well as growth of the callus, e.g., shooty, rooty, starchy, mucoid, non-embryogenic, increased growth rate, decreased growth rate, dead. It is expected that one of skill in the art may recognize other phenotypic characteristics in transformed callus.
Phenotypic data is also collected during the process of plant regeneration as well as in regenerated plants transferred to soil. Phentoypic data includes characteristics such as normal plants, bushy plants, narrow leaves, striped leaves, knotted phenotype, chlorosis, albino, anthocyanin production, buggy whipped (a phenomenon known to the art in which the most recently emerged leaves are elongated and wrap around each other), or altered tassels, ears or roots. It is expected that one of skill in the art may recognize other phenotypic characteristics in transformed plants.
A wide variety of phenotypes are monitored during the process of plant breeding and testing in both inbred and hybrid plants. For example, in R0 and R1 plants (plants directly regenerated from callus and the direct progeny of those plants), plant type (general morphological characteristics such as those described above for plantlets) and nutritional composition of grain produced by the plants are recorded. Nutritional composition analysis may include amino acid composition, amount of protein, starch and oil, characteristics of protein, starch and oil, fiber, ash, mineral content may all be measured. It is expected that one of skill in the art may include analyses of other components of the grain. In R2 and R3 plants, days to pollen shed, days to silking, and plant type are observed. Furthermore, metabolite profiling of R2 plants is conducted. Using methods available to those of skill in the art, 50 to 100 or more metabolites may be analyzed in a plant, thereby establishing a metabolic fingerprint of the plant. In addition in R3 plants, leaf extension rate is measured under field conditions. A variety of phenotypes will be assayed in hybrids comprising a transgene of the present invention. For example, yield, moisture, test weight, nutritional composition, chlorophyll content, leaf temperature, stand, seedling vigor, plant height, leaf number, tillering, brace roots, stay green, stalk lodging, root lodging, plant health, barreness/prolificacy, green snap, pest resistance (including diseases, viruses and insects) and metabolic profiles will be recorded. In addition, phenotypic characteristics of grain harvested from hybrids will be recorded, including number of kernels per row on the ear, number of rows of kernels on the ear, kernel abortion, kernel weight, kernel size, kernel density and physical grain quality. Furthermore, characteristics such as photosynthesis, leaf area, husk structure, kernel dry down rate and internode length may be measured in hybrids or inbreds. It is expected that transcriptional profiling may be performed on transgenic plants expressing genes of the present invention.
In order to determine hybrid yield in transgenic plants expressing genes of the present invention, it is recognized that hybrids must be tested at multiple locations in a geographical location where maize is conventionally grown, e.g., Iowa, Illinois or other locations in the midwestern United States. It is expected that more than one year of yield testing is desirable in order to identify transgenes which contribute to improvement of a maize hybrid. Therefore, transgenic hybrids will be evaluated in a first year at a sufficient number of locations to identify at least an approximately 10% yield difference from a non-transgenic hybrid counterpart. A second year of yield tests is conducted at sufficient locations and with sufficient repetitions to be able to identify a 4-5% yield difference between two hybrids. Furthermore, in the second year of yield tests, hybrids will be evaluated under normal field conditions as well as under stress conditions, e.g., under conditions of water or population density stress. One of skill in the art knows how to design a yield trial such that a statistically significant yield difference can be detected between two hybrids at the desired rate of precision.
Example 31
Surface Sterilization and Imbibition of Corn Seeds
For each transgenic lot, surface sterilize about 50 corn seeds by putting them in a sterile 500 ml Erlenmyer flask with 50 ml of 30% bleach (sodium hypochlorite solution=Chlorox or equivalent) solution containing 0.01% triton X-100 and rotating the flask on an orbital shaker for 5 minutes. Then pour off the bleach solution and wash with about 100 ml of sterile deionized water and pour off the water wash. Repeat the sterile water wash 4 more times, leaving the last water wash on the seeds. Incubate the seeds in this water at room temperature for 24 h for imbibition under air bubbling (pass through 0.2 μm filter).
I. Preparation of Media in Phytotrays.
Prepare water-agar media for several Phytotrays. We are using Phytotray II (or plastic box: 60×30×15 cm) in the inverted position so that the larger depth side of the vessel is on the bottom and the smaller side is used as the lid. Prepare enough water-agar media for 100 ml per Phytotray by autoclaving 0.3% BactoAgar in deionized water for 45 minutes on the liquid cycle. Cool the media to the extent it can be handled easily and pour approximately 100 ml per Phytotray while still molten.
II. Corn Cold Seedling Vigor Assay.

    
    
        When the media has solidified, bring it and the sterile seeds to a laminar flow hood.
        Using sterile forceps, select 20 healthy, most uniform seeds and place the seeds in each Phytotray used for the assay, spacing the seeds evenly so that any individuals can be easily removed later.
        Place seeds so that the embryo side is diagonally inserted downward and the seed is just under the surface of the agar. In this position, the emerging shoot and root will be able to directly elongate without cramping.
        Incubate the seeds in the media at 22° C. for one week, or until most of the seeds have extruded radicles and are beginning to emerge from the agar.
        Remove all but the 10 most uniformly grown seedlings in a laminar flow hood.
        Shift the Phytotrays to a cold plant growth chamber set at 10° C. with 16 hour day cycle and incubate there for 2 weeks.
        Shift the Phytotrays back to 22° C. for one week.
        Remove seedlings, measure root length and shoot length for every seedling, and measure fresh weight g/3 seedlings record in notebook.
    
    


Adaptation for cold germination and emergence assay.
Same as above with the following exceptions:

    
    
        After the last water wash in I., place the flasks at 10° C. during the overnight imbibition step. Also prechill the Phytotrays with solidified media at 10° C.
        After seeding the chilled Phytotrays with cold imbibed seeds, they are put directly into the 10° C. chamber.
        After about 5 days, remove all but the 10 most uniformly germinated seeds, those whose radicles are about the same length. Return Phytotrays to 10° C. chamber for 1-2 weeks. Remove seedlings, measure root length and shoot length for every seedling, and measure fresh weight from every 3 seedlings, record in notebook.
        Shift the the 2nd set Phytotrays to 22° C. for 1 week.
    
    


Remove seedlings, measure root length and shoot length for every seedling, record in notebook.
Example 32
Creation of Plasmids for Transformation of Soybean
Example (For CspA and B Constructs—pMON73983 and 73984)
pMON73983 (FIG. 18) is a binary vector for Agrobacterium-mediated transformation and constitutive expression of a protein (SEQ ID NO: 1) like Bacillus subtilis CspA in Soybean. To clone the B. subtilis CspA gene, two gene-specific primers, MSA452 and MSA453 were designed based on the CspA sequence information (Genbank # M30139) from the National Center for Biotechnology Information, which is part of the National Library of Medicine, in turn part of the National Institutes of Health (NCBI). The sequence for MSA452 is GCGCAGGCCTAGATGTACCATGTCCGGTAAAATGACTGGTATCGTAAAATGG (SEQ ID NO: 86), which anneals at the translational start site of CspA and introduces StuI and BglII sites at the 5′ end, while the sequence of MSA453 is CGCGAATTCGGATCCTTATTACAGGCTGGTTACGTTACCAGCTGCC (SEQ ID NO: 87), which anneals at the last codon of CspA and introduces BamHI and EcoRI sites at the end of the primer. The reverse primer MSA453 was designed to match the 3′ end of the Genbank gene sequence. The PCR reaction was carried out using primers MSA452 and MSA453, High Fidelity Taq Polymerase (BRL) and pMON57397 (FIG. 3) as the template. This template differs at the 3′ end of the gene CspA, from that of the GeneBank sequence. The amplified CspB DNA was purified by gel-electrophoresis and ligated to pCR-XL-TOPO vector (Invitrogen). The ligation reaction was transformed into E. coli Top10 cells (Invitrogen) as per manufacturer's protocol. Four transformant colonies were picked and miniprep DNA was prepared using Qiagen Miniprep Kit. The inserts were sequenced using M13-specific Forward and Reverse primers. Clone with the correct sequence was named pMON73981 and used for further subcloning.
PMON73881 DNA was digested with StuI and BamHI to isolate the CspA gene fragment. pMON73980 DNA was digested with StuI and BamHI sequentially, and then purified by Gene Clean II kit. The CspB fragment and this purified vector pMON73980 were ligated and the ligation reaction was electrotransformed into E. coli DH10 B cells. The transformants were selected on Spectinomycin containing media. The miniprep DNA was prepared from the trasformants and the DNA was checked for the presence of the insert by using CaMV35S-promoter-specific forward primer. The clone containing this insert was named as pMON73983. A larger DNA prep was made and a series of confirmatory digests were carried out, including BglII, EcoRI, PstI, EcoRI+BamHI, StuI+XhoI. These confirmed the correct cloning.
pMON73984 is a binary vector for Agrobacterium-mediated transformation and constitutive expression of a protein (SEQ ID NO: 2) like Bacillus subtilis CspB in Arabidopsis. To clone the B. subtilis CspB gene, two gene-specific primers, MSA454 and MSA455 were designed based on the CspB sequence information (Genbank # X59715) from the National Center for Biotechnology Information, which is part of the National Library of Medicine, in turn part of the National Institutes of Health (NCBI). The sequence for MSA454 is GCGCAGGCCTAGATGTACCATGTTAGAAGGTAAAGTAAAATGGTTCAACTCTG (SEQ ID NO: 88), which anneals at the translational start site of CspB and introduces StuI and BglII sites at the 5′ end, while the sequence of MSA455 is CGCGAATTCGGATCCTTATTACGCTTCTTTAGTAACGTTAGCAGCTTGTGG (SEQ ID NO: 89), which anneals at the last codon of CspB and introduces BamHI and EcoRI sites at the end of the primer. The reverse primer MSA455 was designed to match the 3′ end of the Genbank gene sequence. The PCR reaction was carried out using primers MSA454 and MSA455, High Fedelity Taq Polymerase (BRL) and pMON57399 as the template. This template differs at the 3′ end of the gene CspB, from that of the GeneBank sequence. The amplified CspB DNA was purified by gel-electrophoresis and ligated to pCR-XL-TOPO vector (Invitrogen). The ligation reaction was transformed into E. coli Top10 cells (Invitrogen) as per manufacturer's protocol. Four transformant colonies were picked and miniprep DNA was prepared using Qiagen Miniprep Kit. The inserts were sequenced using M13-specific Forward and Reverse primers. Clone with the correct sequence was named pMON73982 and used for further subcloning.
PMON73882 DNA was digested with StuI and BamHII to isolate the CspB gene fragment. pMON73980 DNA was digested with StuI and BamHI sequentially, and then purified by Gene Clean II kit. The CspB fragment and this purified vector pMON73980 were ligated and the ligation reaction was electrotransformed into E. coli DH10 B cells. The transformants were selected on Spectinomycin containing media. The miniprep DNA was prepared from the trasformants and the DNA was checked for the presence of the insert by using CaMV35S-promoter-specific forward primer. The clone containing this insert was named as pMON73984. A larger DNA prep was made and a series of confirmatory digests were carried out, including BglII, EcoRI, PstI, EcoRI+BamHI, StuI+XhoI. These confirmed that the cloning was correct.
Soybean plants were created, through transformation, with the pMON constructs above stably integrated in their genome.
Example 33.
Corn plant transformed with DNA contructs from examples 10 and 11, above, were studied.
Greenhouse


    
    
        Two experiments were performed, one testing 10 cspA events and one testing 10 cspB events for drought tolerance.
        24 transgene positive and 24 transgene negative hybrid seedlings from each event were tested (all seeds derived from segregating hybrid ears).
        The test was performed on benches in a greenhouse.
        The treatment consisted of withholding water and monitoring total pot weight of each pot containing a plant. Fully watered pots weigh about 1000 grams each and water was withheld until each pot's weight reached 400 grams, then pots were maintained at that weight during the remainder of the treatment.
        Throughout the treatment, plant height was determined by measuring the distance from the soil surface in the pot to the tip of the “tallest” leaf. From these measurements LER (leaf extension rates) were determined by comparing the heights at the intervals between measurements.
        LER comparisons during the drought were made between transgene negative and transgene positive plants within an event.
        For three of ten events tested, cspA transgenic plants were significantly (p<0.10) improved for LER during the treatment.
        For three of ten events tested, cspB transgenic plants were significantly (p<0.10) improved for LER during the treatment.

Field Efficacy

        Three experiments were performed using hybrid seed, one testing 16 cspB events (CA), one testing 21 cspB events (KS), and one testing 14 cspA events (HI) for drought tolerance during the late vegetative stage of growth.
        For the CA and HI trials, rows containing  ̃34 plants, segregating for presence of the transgene, were present in six and four replicates, respectively. Segregating rows were derived from segregating ears.
        For KS experimental rows contained  ̃34 plants; as transgenic and non-transgenic paired rows, with six replicates.
        The treatment consisted of withholding water for approximately ten days during the late vegetative phase of growth (giving a small amount as needed to maintain viable plants). At the end of the ten-day period plants were then well irrigated until harvest.
        Throughout the treatment a number of phenotypes were measured including LER, chlorophyll (by SPAD meter), and photosynthesis rate. Following the treatment additional phenotypes measured included: days to pollen shed and silk emergence, and ear components such as kernels/ear, ears with kernels, kernel weight, and yield.
        Phenotype comparisons were made between transgene positive and negative plants within an event and across the construct.
        In the CA trial, cspB as a construct (across all events for vegetative traits and across the “best” six events for reproductive traits) transgene positive plants were significantly (p<0.10) improved for LER, leaf temperature, and kernels/ear during or following the drought treatment.
        In the CA trial, individual events were significantly (p<0.10) improved for LER, average ear length, kernel mass/ear, stomatal conductance, and days to silking during or following the drought treatment.
        In the KS trial, cspB as a construct (across all events for vegetative traits and across the “best” six events for reproductive traits) transgene positive plants were significantly (p<0.10) improved for LER, kernel bearing ears/row, kernels/ear, kernels/plant, shell weight, and yield.
        In the KS trial, individual events were significantly (p<0.10) improved for LER, photosynthetic rate, stomatal conductance, ears/row, and kernels/plant.
        In the HI trial, three events were significantly (p<0.10) improved for LER (chlorophyll content was the only other phenotype measured in HI)
    
    


Summaries of CA and KS Results:
Summary of Field Efficacy Results for cspb-KS Site


    1. The field design, site uniformity, and execution of planting and sampling were all consistent with a high quality experiment capable of generating informative data sets.
    2. The water-limited treatment was applied in a manner that resulted in treatment impacts on all phenotypes measured, particularly LER, chlorophyll, and photosynthetic rates.
    3. The treatment impacts on vegetative and reproductive phenotypes were sufficient to be statistically real and to allow for transgene-mediated improvements to be observed at statistically significant levels.
    4. One or more events were statistically improved in transgene containing plants for LER, chlorophyll, photosynthetic rate, stomatal conductance leaf temperature, days to pollen shed, days to silking, anthesis silking interval, ears/plot, kernels/ear, kernels/plant, shell weight, and estimated yield.
    5. Construct level statistical improvement was observed at p<0.10 in the dry treatment for LER, ears/plot, kernels/ear, kernels/plant, shell weight, and estimated yield, and for LER in the wet treatment.












TABLE 20





Event
Treatment
Improved phenotype
P value







Construct
Dry
LER (T1-T0)
0.009



Dry
LER (T2-T0)
0.009



Dry
LER (T2-T1)
0.096



Dry
Stomatal conductance
0.150



Dry
Photosynthesis
0.141



Dry
Ears/plot
0.012



Dry
Kernels/ear
0.062



Dry
Kernels/plant
0.006



Dry
Shell weight
0.009



Dry
Est. Yield
0.008



Wet
LER (T2-T1)
0.025



Wet
Chlorophyll (−)
0.062



Wet
Ears/plot (−)
0.185



Wet
Kernels/ear (−)
0.121



Wet
Kernels/plant (−)
0.083



Wet
Shell weight (−)
0.132



Wet
Est. Yield (−)
0.101


ZM_M38835
Dry
LER (T1-T0)
0.008



Dry
Photosynthesis
0.066



Dry
Stomatal conductance
0.064



Dry
Transpiration
0.126



Dry
Kernels/plant
0.160



Dry
Shell weight
0.149



Dry
Yield
0.153



Wet
LER (T1-T0)
0.099



Wet
LER (T2-T1) (−)
0.026


ZM_M38737
Dry
Photosynthesis
0.108









Summary of Field Efficacy Results for cspB-CS Site

    1. The field design, site uniformity, and execution of planting and sampling were all consistent with a high quality experiment capable of generating informative data sets.
    2. The water-limited treatment was applied in a manner that resulted in treatment impacts on all vegetative phenotypes measured, particularly LER, chlorophyll, and photosynthetic rates, but not on all reproductive phenotypes.
    3. The treatment impacts on phenotypes (vegetative) of interest were sufficient to be statistically real and to allow for transgene-mediated improvements to be observed at statistically significant levels.
    4. One or more events were statistically improved in transgene containing plants for LER, chlorophyll, photosynthetic rate, stomatal conductance leaf temperature, days to pollen shed, days to silking, anthesis silking interval, kernels/ear, average ear length, and kernel mass/ear.
    5. Construct level statisitical improvement was observed in the dry treatment for LER, leaf temperature, and days to pollen shed, and for ASI in the wet treatment.












TABLE 21





Event
Treatment
Improved phenotype
P value







Construct
Dry
LER
0.009



Dry
Leaf temperature
0.027



Dry
Days to pollen shed
0.192



Dry
Kernels/ear
0.080



Dry
Kernel mass/ear
0.197



Dry
Test Wt (lb/bu) Neg
0.084



Wet
LER
0.157



Wet
Days to pollen shed
0.098



Wet
Ave ear length
0.091



Wet
Kernel mass/ear
0.010



Wet
Test Wt (lb/bu) Neg
0.188


ZM_M39583
Dry
LER
0.051



Dry
Kernels/ear
0.200



Wet
Ave ear length
0.058



Wet
Kernel mass/ear
0.070


ZM_M39872
Dry
LER
0.159



Wet
Days to silking
0.024



Wet
ASI
0.064


ZM_M40946
Dry
LER
0.201


ZM_M38238
Dry
Days to silking
0.176



Dry
Kernels/ear
0.192



Wet
LER
0.151



Wet
Kernel mass/ear
0.034


ZM_M38244
Dry
Stomatal Conductance
0.092



Dry
Photosynthesis
0.132



Dry
Leaf Temperature
0.155


ZM_M38230
Dry
Days to silking
0.176


ZM_M38721
Dry
Days to silking
0.066



Dry
ASI
0.109



Wet
Days to silking
0.117


ZM_M38714
Wet
Days to silking
0.010



Wet
ASI
0.025


ZM_M40939
Dry
ASI
0.109









Many of these events have been subsequently tested for improvements in cold germination efficincy and seedling growth under cold conditions, and have not proved efficacious. Thus, these genes driven by this promoter are unlikely to function in maize for improvement of cold germination or seedling growth under cold conditions, but different propomters driving the same genes, or different cold shock proteins may function in maize to improve these phenotypes.

## Claims

1. A drought tolerant transgenic plant selected from the group consisting of corn, and rice that has been transformed with a DNA molecule that expresses a protein having the amino acid sequence of SEQ ID NO:63 or a protein having the amino acid sequence of SEQ ID NO:65.

2. A transgenic propagule of the plant of claim 1.

3. A transgenic progeny of the plant of claim 1.

4. The plant of claim 1 that has an increased yield when compared to a non-transformed plant of the same species and when said transgenic plant and said non-transformed plant are grown under drought stress.

5. A field crop comprising transgenic plants germinated from a propagule comprising a protein having the amino acid sequence of SEQ ID NO:63 or a protein having the amino acid sequence of SEQ ID NO:65, wherein said field crop is selected from the group consisting of corn and rice.

6. A drought tolerant transgenic corn plant having a recombinant DNA expressing a protein having the amino acid sequence of SEQ ID NO:63.

7. A drought tolerant transgenic corn plant having a recombinant DNA expressing a protein having the amino acid sequence of SEQ ID NO:65.

8. Seed for growing a drought tolerant corn plant, said seed having a recombinant DNA encoding a protein having the amino acid sequence of SEQ ID NO:63.

9. Seed for growing a drought tolerant corn plant, said seed having a recombinant DNA encoding a protein having the amino acid sequence of SEQ ID NO:65.

10. A method of improving drought tolerance in a corn line comprising crossing a corn plant of said corn line with a drought tolerant transgenic corn plant having a recombinant DNA expressing a protein having the amino acid sequence of SEQ ID NO:63 to produce a corn seed having the recombinant DNA.

11. A method of improving drought tolerance in a corn line comprising crossing a corn plant of said corn line with a drought tolerant transgenic corn plant having a recombinant DNA expressing a protein having the amino acid sequence of SEQ ID NO:65 to produce a corn seed having the recombinant DNA.

12. A method for increasing yield in a corn crop subject to water deficit during its growth, said method comprising planting seeds having a recombinant DNA expressing a protein having the amino acid sequence of SEQ ID NO:63 or a protein having the amino acid sequence of SEQ ID NO:65 and allowing said seeds to grow to mature corn plants while being subjected to drought during at least one ten day period during vegetative phase of growth.

13. A transgenic propagule of a drought tolerant transgenic corn plant having a recombinant DNA expressing a protein having the amino acid sequence of SEQ ID NO:63 or a protein having the amino acid sequence of SEQ ID NO:65.

14. A transgenic progeny of a drought tolerant transgenic corn plant having a recombinant DNA expressing a protein having the amino acid sequence of SEQ ID NO:63 or a protein having the amino acid sequence of SEQ ID NO:65.

15. A drought tolerant transgenic cotton plant that has been transformed with a DNA molecule that expresses a cold shock protein having the amino acid sequence of SEQ ID NO:63.

16. Seed for growing a drought tolerant cotton plant, said seed having a recombinant DNA encoding a protein having the amino acid sequence of SEQ ID NO:63.

17. A method of improving drought tolerance in a cotton line comprising crossing a cotton plant of said cotton line with a drought tolerant transgenic cotton plant having a recombinant DNA expressing a protein having the amino acid sequence of SEQ ID NO:63 to produce a cotton seed having the recombinant DNA.

18. A transgenic propagule of a drought tolerant transgenic cotton plant having a recombinant DNA expressing a protein having the amino acid sequence of SEQ ID NO:63.

19. A transgenic progeny of a drought tolerant transgenic cotton plant having a recombinant DNA expressing a protein having the amino acid sequence of SEQ ID NO:63.