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  • C12N15/8201—Methods for introducing genetic material into plant cells, e.g. DNA, RNA, stable or transient incorporation, tissue culture methods adapted for transformation
  • C12N15/8202—Methods for introducing genetic material into plant cells, e.g. DNA, RNA, stable or transient incorporation, tissue culture methods adapted for transformation by biological means, e.g. cell mediated or natural vector
  • C12N15/8205—Agrobacterium mediated transformation
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  • C12N15/8206—Methods for introducing genetic material into plant cells, e.g. DNA, RNA, stable or transient incorporation, tissue culture methods adapted for transformation by physical or chemical, i.e. non-biological, means, e.g. electroporation, PEG mediated
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  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
  • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
  • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
  • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
  • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
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  • C12N15/09—Recombinant DNA-technology
  • C12N15/87—Introduction of foreign genetic material using processes not otherwise provided for, e.g. co-transformation
• • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
  • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
  • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
  • Y02A40/00—Adaptation technologies in agriculture, forestry, livestock or agroalimentary production
  • Y02A40/10—Adaptation technologies in agriculture, forestry, livestock or agroalimentary production in agriculture
  • Y02A40/146—Genetically Modified [GMO] plants, e.g. transgenic plants

Definitions

• the present invention relates generally to plant molecular biology. More specifically, it relates to nucleic acids and methods for modulating their expression in plants.
• Cell division plays a crucial role during all phases of plant development. The continuation of organogenesis and growth responses to a changing environment require precise spatial, temporal and developmental regulation of cell division activity in meristems. A complex network controls growth in eukaryotes. Regulatory pathways that communicate environmental constraints, such as nutrient availability, mitogenic signals such as growth factors or hormones, or developmental cues such as the transition to flowers control the timing and position of cell divisions.
• CDK cyclin- dependent-kinase
• the basic mechanism of cell cycle control is conserved among eukaryotes.
• a catalytic protein kinase and an activating cyclin subunit control progress through the cell cycle.
• the protein kinase is generally referred to as a cyclin- dependent-kinase (CDK), whose activity is modulated by phosphorylation and dephosphorylation events and by their association with regulatory subunits called cyclins.
• CDKs are a family of serine/threonine protein kinases that regulate individual cell cycle transitions. CDKs require association with cyclins for activation, and the timing of activation is largely dependent upon cyclin expression.
• Eukaryote genomes typically encode multiple cyclin and Cdk genes. In higher eukaryotes, different members of the CDK family act in different stages of the cell cycle. Cyclin genes are classified according to the timing of their appearance during the cell cycle. In addition to cyclin and CDK subunits, CDKs are often physically associated with other proteins which alter localization, substrate specificity, or activity. A few examples of such CDK interacting proteins are the CDK inhibitors, members of the Retinoblastoma-associated protein (Rb) family, and the Constitutive Kinase Subunit (CKS).
• CDK inhibitors members of the Retinoblastoma-associated protein (Rb) family
• CKS Constitutive Kinase Subunit
• the protein kinase activity of the complex is regulated by feedback control at certain check points. At such checkpoints the kinase activity becomes limiting for further progress until the feedback control network signals the completion of the dependent reactions, which then activates the kinase for passage through to the next checkpoint.
• the changes in activity are regulated by reversible phosphorylation of the cell cycle factors, by changes in subcellular localization of the complex, and by the rates of synthesis of limiting components. P.W. Doerner, Cell Cycle Regulation in Plants, Plant Phvsiol. (1994) 106:823-827.
• Plants have unique developmental features that distinguish them from other eukaryotes. In the absence of cell migration, morphogenesis is determined only by cell division, expansion and programmed cell death. Organs are formed throughout the entire life span from specialized regions called meristems. In addition, many differentiated cells have the potential to dedifferentiate and to reenter the cell cycle. There are also numerous examples of plant cell types that undergo endoreduplication, a process involving nuclear multiplication without cytokinesis. The study of plant cell cycle control genes is expected to contribute to the understanding of these unique phenomena. O. Shaul et al., Regulation of Cell Division in Arabidopsis, Critical Reviews in Plant Sciences. 15(2):97-112 (1996).
• over-expression of key cell cycle genes can either trigger cell division in non-dividing cells, or stimulate division in previously dividing cells (i.e. the duration of the cell cycle is decreased and cell size is reduced).
• genes whose over-expression has been shown to stimulate cell division include cyclins (see, e.g. Doerner, P. et al., Nature (1996) 380:520-423; Wang, T.C., et al., Nature (1994) 369:669-671; Jo D. E., et al., Genes Dev. (1993) 7:1559- 1571, E2F transcription factors (see, e.g. Johnson D. G.
• T-DNA a species of symbiotic micro-organisms are known to transfer T-DNA into recipient cells by a mechanism similar to bacterial conjugation.
• T-DNA traverses the bacterial membranes, the cell wall and cell membranes, and the nuclear membrane before integrating into the host genome through illegitimate recombination.
• Numerous bacterial proteins are also included in these processes and have been characterized. Among these proteins are at least three gene products from Agrobacterium: VirD2, VirE2, and VirF which are transcribed from the virulence region of the Ti plasmid and transferred directly into plant cells.
• VirD2 encodes a multifunctional protein which participates in the endonucleolytic cleavage of the T-DNA border sequences, the ligation of the left border nick for replacement strand synthesis, nuclear import of the T-complex, and precise integration of the 5' end of T-DNA into the host genome.
• VirD2 establishes a covalent association with the T-DNA between a specific right-border (RB) nucleotide and Tyr-29 of the protein.
• VirE2 encodes a multifunctional protein that has single-stranded DNA binding (SSB) activity and coats the T-strand.
• SSB single-stranded DNA binding
• VirE2 is the most abundant of Vir proteins with 350 to 700 copies thought to be required to coat a 20 kb T-strand.
• the function of the VirF gene product is unknown.
• the coding sequence is present in octopine strains but not in nopaline strains. Complementation of nopaline strains or VirF mutants of octopine strains extends host range.
• Agrobacterium as a protein vector for transient expression is potentially simpler and would deliver a selected protein and a desired transgene to the same cell simultaneously.
• nucleic acids and proteins relating to the control of cell division. It is another object of the present invention to provide nucleic acids and proteins that can be used to identify other interacting proteins involved in cell cycle regulation.
• It is another object of the present invention is to provide a method for increasing the number of cells undergoing cell division.
• It is another object of the present invention is to provide a method for improving transformation frequencies comprising increasing the number of dividing cells to be transformed by modulating the expression of the nucleic acids of the present invention. It is another object of the present invention to provide a method for providing a positive growth advantage in a plant comprising modulating Cks protein expression.
• the present invention relates to an isolated nucleic acid comprising a member selected from the group consisting of (a) a first polynucleotide having at least 85% identity to a second polynucleotide, wherein the second polynucleotide encodes a polypeptide having a sequence of SEQ ID NOS: 2 or 4; (b) a polynucleotide which is complementary to the polynucleotide of (a); and (c) a polynucleotide comprising at least 25 contiguous nucleotides from a polynucleotide of (a) or (b).
• the present invention relates to recombinant expression cassettes, comprising the nucleic acid operably linked to a promoter.
• the nucleic acid is operably linked in antisense orientation to the promoter.
• the present invention is directed to a host cell transfected with the recombinant expression cassette as described, supra.
• the present invention relates to an isolated protein comprising a polypeptide of at least 10 contiguous amino acids encoded by the isolated nucleic acid.
• the polypeptide has a sequence selected from the group consisting of SEQ ID NOS: 2 and 4.
• the present invention relates to an isolated nucleic acid comprising a polynucleotide of at least 25 nucleotides in length which selectively hybridizes under stringent conditions to a nucleic acid selected from the group consisting of SEQ ID NOS: 1 and 3, or a complement thereof.
• the isolated nucleic acid is operably linked to a promoter.
• the present invention relates to an isolated nucleic acid comprising a polynucleotide, the polynucleotide having at least 80% sequence identity to an identical length of a nucleic acid selected from the group consisting of SEQ ID NOS: 1 and 3 or a complement thereof.
• the present invention relates to an isolated nucleic acid comprising a polynucleotide having a sequence of a nucleic acid amplified from a Zea mays nucleic acid library using the primers selected from the group consisting of SEQ ID NOS: 5-16 or complements thereof.
• the nucleic acid library is a cDNA library.
• the present invention relates to a recombinant expression cassette comprising a nucleic acid amplified from a library as referred to supra, wherein the nucleic acid is operably linked to a promoter.
• the invention provides a method for transiently modifying the level of protein in a cell by
• the present invention relates to a host cell transfected with this recombinant expression cassette.
• the present invention relates to a protein of the present invention which is produced from this host cell.
• the present invention is directed to an isolated nucleic acid comprising a polynucleotide encoding a polypeptide wherein: (a) the polypeptide comprises at least 10 contiguous amino acid residues from a first polypeptide selected from the group consisting of SEQ ID NOS:2 and 4; (b) the polypeptide does not bind to antisera raised against the first polypeptide which has been fully immunosorbed with the first polypeptide; and (c) the polypeptide has a molecular weight in non-glycosylated form within 10% of the first polypeptide.
• the present invention relates to a heterologous promoter operably linked to a non-isolated polynucleotide of the present invention, wherein the polypeptide is encoded by a nucleic acid amplified from a nucleic acid library.
• the present invention relates to a transgenic plant comprising a recombinant expression cassette comprising a plant promoter operably linked to any of the isolated nucleic acids of the present invention.
• the present invention also provides transgenic seed from the transgenic plant.
• the present invention relates to a method of modulating expression of the genes encoding the proteins of the present invention in a plant, comprising the steps of (a) transforming a plant cell with a recombinant expression cassette comprising a polynucleotide of the present invention operably linked to a promoter; (b) growing the plant cell under plant growing conditions; and (c) inducing expression of the polynucleotide for a time sufficient to modulate expression of the genes in the plant.
• Expression of the genes encoding the proteins of the present invention can be increased or decreased relative to a non-transformed control plant.
• nucleic acids are written left to right in 5' to 3' orientation; amino acid sequences are written left to right in amino to carboxy orientation, respectively. Numeric ranges are inclusive of the numbers defining the range. Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes. The terms defined below are more fully defined by reference to the specification as a whole.
• amplified is meant the construction of multiple copies of a nucleic acid sequence or multiple copies complementary to the nucleic acid sequence using at least one of the nucleic acid sequences as a template.
• Amplification systems include the polymerase chain reaction (PCR) system, ligase chain reaction (LCR) system, nucleic acid sequence based amplification (NASBA, Cangene, Mississauga, Ontario), Q-Beta Replicase systems, transcription-based amplification system (TAS), and strand displacement amplification (SDA). See, e.g., Diagnostic Molecular Microbiology: Principles and Applications, D. H. Persing et al., Ed., American Society for Microbiology, Washington, D.C. (1993). The product of amplification is termed an amplicon.
• antibody includes reference to antigen binding forms of antibodies (e.g., Fab, F(ab) 2 ).
• antibody frequently refers to a polypeptide substantially encoded by an immunoglobulin gene or immunoglobulin genes, or fragments thereof which specifically bind and recognize an analyte (antigen).
• analyte analyte
• antibody also includes antibody fragments such as single chain Fv, chimeric antibodies (i.e., comprising constant and variable regions from different species), humanized antibodies (i.e., comprising a complementarity determining region (CDR) from a non-human source) and heteroconjugate antibodies (e.g., bispecific antibodies).
• CDR complementarity determining region
• heteroconjugate antibodies e.g., bispecific antibodies.
• antigen includes reference to a substance to which an antibody can be generated and or to which the antibody is specifically immunoreactive. The specific immunoreactive sites within the antigen are known as epitopes or antigenic determinants.
• epitopes can be a linear array of monomers in a polymeric composition - such as amino acids in a protein - or consist of or comprise a more complex secondary or tertiary structure.
• immunogens i.e., substance capable of eliciting an immune response
• antigens such as haptens
• An antibody immunologically reactive with a particular antigen can be generated in vivo or by recombinant methods such as selection of libraries of recombinant antibodies in phage or similar vectors.
• antisense orientation includes reference to a duplex polynucleotide sequence which is operably linked to a promoter in an orientation where the antisense strand is transcribed.
• the antisense strand is sufficiently complementary to an endogenous transcription product such that translation of the endogenous transcription product is often inhibited.
• chromosomal region includes reference to a length of chromosome which may be measured by reference to the linear segment of DNA which it comprises.
• the chromosomal region can be defined by reference to two unique DNA sequences, i.e., markers.
• conservatively modified variants applies to both amino acid and nucleic acid sequences. With respect to particular nucleic acid sequences, conservatively modified variants refers to those nucleic acids which encode identical or conservatively modified variants of the amino acid sequences. Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode any given protein. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine.
• nucleic acid variations are "silent variations" and represent one species of conservatively modified variation.
• Every nucleic acid sequence herein which encodes a polypeptide also describes every possible silent variation of the nucleic acid.
• each codon in a nucleic acid except AUG, which is ordinarily the only codon for methionine
• amino acid sequences one of skill will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a "conservatively modified variant" where the alteration results in the substitution of an amino acid with a chemically similar amino acid.
• conservatively modified variants any number of amino acid residues selected from the group of integers consisting of from 1 to 15 can be so altered.
• 1, 2, 3, 4, 5, 7, or 10 alterations can be made.
• Conservatively modified variants typically provide similar biological activity as the unmodified polypeptide sequence from which they are derived.
• substrate specificity, enzyme activity, or ligand/receptor binding is generally at least 30%, 40%, 50%, 60%, 70%, 80%, or 90% of the native protein for it's native substrate.
• Conservative substitution tables providing functionally similar amino acids are well known in the art.
• the following six groups each contain amino acids that are conservative substitutions for one another: 1 ) Alanine (A), Serine (S), Threonine (T);
• I Isoleucine
• L Leucine
• M Methionine
• V Valine
• F Phenylalanine
• Y Tyrosine
• W Tryptophan
• nucleic acid encoding a protein may comprise non-translated sequences (e.g., introns) within translated regions of the nucleic acid, or may lack such intervening non-translated sequences (e.g., as in cDNA).
• the information by which a protein is encoded is specified by the use of codons.
• the amino acid sequence is encoded by the nucleic acid using the "universal" genetic code.
• variants of the universal code such as is present in some plant, animal, and fungal mitochondria, the bacterium Mycoplasma capricolum (Proc. Natl. Acad. Sci.. U.S.A. 82:2306-2309 (1985)), or the ciliate Macronucleus, may be used when the nucleic acid is expressed using these organisms.
• nucleic acid sequences of the present invention may be expressed in both monocotyledonous and dicotyledonous plant species, sequences can be modified to account for the specific codon preferences and GC content preferences of monocotyledons or dicotyledons as these preferences have been shown to differ (Murray et al., Nucl. Acids Res. 17:477-498 (1989)).
• the maize preferred codon for a particular amino acid may be derived from known gene sequences from maize. Maize codon usage for 28 genes from maize plants are listed in Table 4 of Murray et al., supra.
• full-length sequence in reference to a specified polynucleotide or its encoded protein means having the entire amino acid sequence of, a native (non-synthetic), endogenous, catalytically active form of the specified protein.
• a full-length sequence can be determined by size comparison relative to a control which is a native (non-synthetic) endogenous cellular form of the specified nucleic acid or protein. Methods to determine whether a sequence is full-length are well known in the art including such exemplary techniques as northern or western blots, primer extension, S1 protection, and ribonuclease protection.
• consensus sequences typically present at the 5' and 3' untranslated regions of mRNA aid in the identification of a polynucleotide as full-length.
• the consensus sequence ANNNNAUGG where the underlined codon represents the N-terminal methionine, aids in determining whether the polynucleotide has a complete 5' end.
• Consensus sequences at the 3' end such as polyadenylation sequences, aid in determining whether the polynucleotide has a complete 3' end.
• heterologous in reference to a nucleic acid is a nucleic acid that originates from a foreign species, or, if from the same species, is substantially modified from its native form in composition and/or genomic locus by deliberate human intervention.
• a promoter operably linked to a heterologous structural gene is from a species different from that from which the structural gene was derived, or, if from the same species, one or both are substantially modified from their original form.
• a heterologous protein may originate from a foreign species or, if from the same species, is substantially modified from its original form by deliberate human intervention.
• host cell is meant a cell which contains a vector and supports the replication and/or expression of the expression vector.
• Host cells may be prokaryotic cells such as E. coli, or eukaryotic cells such as yeast, insect, amphibian, or mammalian cells.
• host cells are monocotyledonous or dicotyledenous plant cells.
• a particularly preferred monocotyledonous host cell is a maize host cell.
• hybridization complex includes reference to a duplex nucleic acid structure formed by two single-stranded nucleic acid sequences selectively hybridized with each other.
• immunoassay conditions or “immunoreactive conditions” is meant conditions which allow an antibody, generated to a particular epitope, to bind to that epitope to a detectably greater degree (e.g., at least 2-fold over background) than the antibody binds to substantially all other epitopes in a reaction mixture comprising the particular epitope.
• Immunologically reactive conditions are dependent upon the format of the antibody binding reaction and typically are those utilized in immunoassay protocols. See Harlow and Lane, Antibodies, A Laboratory Manual, Cold Spring Harbor Publications, New York (1988), for a description of immunoassay formats and conditions.
• the term "introduced” in the context of inserting a nucleic acid into a cell means “transfection” or “transformation” or “transduction” and includes reference to the incorporation of a nucleic acid into a eukaryotic or prokaryotic cell where the nucleic acid may be incorporated into the genome of the cell (e.g., chromosome, plasmid, plastid or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (e.g., transfected mRNA).
• isolated refers to material, such as a nucleic acid or a protein, which is: (1) substantially or essentially free from components which normally accompany or interact with it as found in its naturally occurring environment.
• the isolated material optionally comprises material not found with the material in its natural environment; or (2) if the material is in its natural environment, the material has been synthetically (non-naturally) altered by deliberate human intervention to a composition and/or placed at a locus in the cell (e.g., genome or subcellular organelle) not native to a material found in that environment.
• the alteration to yield the synthetic material can be performed on the material within or removed from its natural state.
• a naturally occurring nucleic acid becomes an isolated nucleic acid if it is altered, or if it is transcribed from DNA which has been altered, by non-natural, synthetic (i.e., "man-made") methods performed within the cell from which it originates. See, e.g., Compounds and Methods for Site Directed Mutagenesis in Eukaryotic Cells, Kmiec, U.S. Patent No. 5,565,350; In Vivo Homologous Sequence Targeting in Eukaryotic Cells; Zarling ef al., PCT/US93/03868.
• nucleic acid e.g., a promoter
• a naturally occurring nucleic acid becomes isolated if it is introduced by non-natural ly occurring means to a locus of the genome not native to that nucleic acid.
• Nucleic acids which are “isolated” as defined herein are also referred to as “heterologous” nucleic acids.
• the term "cell cycle nucleic acid” means a nucleic acid comprising a polynucleotide ("cell cycle polynucleotide”) encoding a cell cycle polypeptide.
• a "cell cycle gene” refers to a non-heterologous genomic form of a full-length cell cycle polynucleotide.
• chromosomal region defined by and including with respect to particular markers includes reference to a contiguous length of a chromosome delimited by and including the stated markers.
• marker includes reference to a locus on a chromosome that serves to identify a unique position on the chromosome.
• a "polymorphic marker” includes reference to a marker which appears in multiple forms (alleles) such that different forms of the marker, when they are present in a homologous pair, allow transmission of each of the chromosomes in that pair to be followed.
• a genotype may be defined by use of one or a plurality of markers.
• nucleic acid includes reference to a deoxyribonucleotide or ribonucleotide polymer in either single- or double-stranded form, and unless otherwise limited, encompasses known analogues having the essential nature of natural nucleotides in that they hybridize to single-stranded nucleic acids in a manner similar to naturally occurring nucleotides (e.g., peptide nucleic acids).
• nucleic acid library is meant a collection of isolated DNA or RNA molecules which comprise and substantially represent the entire transcribed fraction of a genome of a specified organism. Construction of exemplary nucleic acid libraries, such as genomic and cDNA libraries, is taught in standard molecular biology references such as Berger and Kimmel, Guide to Molecular Cloning Techniques, Methods in Enzymology, Vol. 152, Academic Press, Inc., San Diego, CA (Berger); Sambrook et al., Molecular Cloning - A Laboratory Manual, 2nd ed., Vol. 1-3 (1989); and Current Protocols in Molecular Biology, F.M. Ausubel et al., Eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc.
• operably linked includes reference to a functional linkage between a promoter and a second sequence, wherein the promoter sequence initiates and mediates transcription of the DNA sequence corresponding to the second sequence.
• operably linked means that the nucleic acid sequences being linked are contiguous and, where necessary to join two protein coding regions, contiguous and in the same reading frame.
• plant includes reference to whole plants, plant organs (e.g., leaves, stems, roots, etc.), seeds and plant cells and progeny of same.
• Plant cell as used herein includes, without limitation, seeds suspension cultures, embryos, meristematic regions, callus tissue, leaves, roots, shoots, gametophytes, sporophytes, pollen, and microspores.
• the class of plants which can be used in the methods of the invention is generally as broad as the class of higher plants amenable to transformation techniques, including both monocotyledonous and dicotyledonous plants.
• a particularly preferred plant is Zea mays.
• polynucleotide includes reference to a deoxy bopolynucleotide, ribopolynucleotide, or analogs thereof, that have the essential nature of a natural ribonucleotide in that they hybridize to nucleic acids in a manner similar to naturally occurring nucleotides.
• a polynucleotide can be full-length or a subsequence of a native or heterologous structural or regulatory gene. Unless otherwise indicated, the term includes reference to the specified sequence as well as the complementary sequence thereof. Thus, DNAs or RNAs with backbones modified for stability or for other reasons are "polynucleotides" as that term is intended herein.
• DNAs or RNAs comprising unusual bases, such as inosine, or modified bases, such as tritylated bases, to name just two examples are polynucleotides as the term is used herein. It will be appreciated that a great variety of modifications have been made to DNA and RNA that serve many useful purposes known to those of skill in the art.
• polynucleotide as it is employed herein embraces such chemically, enzymatically or metabolically modified forms of polynucleotides, as well as the chemical forms of DNA and RNA characteristic of viruses and cells, including inter alia, simple and complex cells.
• polypeptide polypeptide
• peptide protein
• proteins are used interchangeably herein to refer to a polymer of amino acid residues.
• the terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical analogue of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers.
• the essential nature of such analogues of naturally occurring amino acids is that, when incorporated into a protein, that protein is specifically reactive to antibodies elicited to the same protein but consisting entirely of naturally occurring amino acids.
• polypeptide polypeptide
• peptide protein
• modifications including, but not limited to, glycosylation, lipid attachment, sulfation, gamma-carboxylation of glutamic acid residues, hydroxylation and ADP-ribosylation.
• modifications are described in most basic texts, such as . Proteins - Structure and Molecular Properties, 2nd ed., T. E. Creighton, W. H. Freeman and Company, New York (1993). Many detailed reviews are available on this subject, such as, for example, those provided by Wold, F., Posttranslational Protein Modifications: Perspectives and Prospects, pp. 1-12 in Posttranslational Covalent Modification of Proteins, B. C.
• polypeptides are not always entirely linear.
• polypeptides may be branched as a result of ubiquitination, and they may be circular, with or without branching, generally as a result of posttranslation events, including natural processing event and events brought about by human manipulation which do not occur naturally.
• Circular, branched and branched circular polypeptides may be synthesized by non-translation natural process and by entirely synthetic methods, as well. Modifications can occur anywhere in a polypeptide, including the peptide backbone, the amino acid side-chains and the amino or carboxyl termini. In fact, blockage of the amino or carboxyl group in a polypeptide, or both, by a covalent modification, is common in naturally occurring and synthetic polypeptides and such modifications may be present in polypeptides of the present invention, as well. For instance, the amino terminal residue of polypeptides made in E. coli or other cells, prior to proteolytic processing, almost invariably will be N-formylmethionine.
• polypeptide encompasses all such modifications, particularly those that are present in polypeptides synthesized by expressing a polynucleotide in a host cell.
• delivery protein refers to a protein that functions in a micro-organism to deliver, integrate or otherwise move into a host cell, a region of DNA, RNA, or protein from the micro-organism.
• the DNA, RNA, or protein may be native to the micro-organism or foreign, or native to the host cell or foreign or foreign to both the micro-organism or host cell.
• pre-selected protein refers to a deliberately chosen gene product to be expressed in a host cell.
• recipient cell refers to any host cell to be transformed in a transformation system.
• co-cultivating is used to describe the process of exposing recipient cells to a transformation vector for the purpose of introducing polynucleotides or proteins into the recipient cell. Conditions for co-cultivation will vary with the type of recipient cell and transformation vector and are known in the art.
• promoter includes reference to a region of DNA upstream from the start of transcription and involved in recognition and binding of RNA polymerase and other proteins to initiate transcription.
• a "plant promoter” is a promoter capable of initiating transcription in plant cells. Exemplary plant promoters include, but are not limited to, those that are obtained from plants, plant viruses, and bacteria which comprise genes expressed in plant cells such Agrobacterium or Rhizobium. Examples of promoters under developmental control include promoters that preferentially initiate transcription in certain tissues, such as leaves, roots, seeds, fibers, xylem vessels, tracheids, or sclerenchyma. Such promoters are referred to as "tissue preferred”.
• tissue specific Promoters which initiate transcription only in certain tissue are referred to as "tissue specific".
• a "cell type” specific promoter primarily drives expression in certain cell types in one or more organs, for example, vascular cells in roots or leaves.
• An “inducible” promoter is a promoter which is under environmental control. Examples of environmental conditions that may effect transcription by inducible promoters include anaerobic conditions or the presence of light. Tissue specific, tissue preferred, cell type specific, and inducible promoters constitute the class of "non-constitutive" promoters.
• a “constitutive” promoter is a promoter which is active under most environmental conditions.
• cell cycle polypeptide refers to one or more amino acid sequences, in glycosylated or non-glycosylated form, involved in the regulation of cell division.
• the term is also inclusive of fragments, variants, homologs, alleles or precursors (e.g., preproproteins or proproteins) thereof.
• a "cell cycle protein” comprises a cell cycle polypeptide.
• recombinant includes reference to a cell or vector, that has been modified by the introduction of a heterologous nucleic acid or that the cell is derived from a cell so modified.
• recombinant cells express genes that are not found in identical form within the native (non- recombinant) form of the cell or express native genes that are otherwise abnormally expressed, under expressed or not expressed at all as a result of deliberate human intervention.
• the term "recombinant” as used herein does not encompass the alteration of the cell or vector by naturally occurring events (e.g., spontaneous mutation, natural transformation/transduction/transposition) such as those occurring without deliberate human intervention.
• a "recombinant expression cassette” is a nucleic acid construct, generated recombinantly or synthetically, with a series of specified nucleic acid elements which permit transcription of a particular nucleic acid in a target cell.
• the recombinant expression cassette can be incorporated into a plasmid, chromosome, mitochondrial DNA, plastid DNA, virus, or nucleic acid fragment.
• the recombinant expression cassette portion of an expression vector includes, among other sequences, a nucleic acid to be transcribed, and a promoter.
• amino acid residue or “amino acid residue” or “amino acid” are used interchangeably herein to refer to an amino acid that is incorporated into a protein, polypeptide, or peptide (collectively “protein”).
• the amino acid may be a naturally occurring amino acid and, unless otherwise limited, may encompass known analogs of natural amino acids that can function in a similar manner as naturally occurring amino acids.
• sequences include reference to hybridization, under stringent hybridization conditions, of a nucleic acid sequence to a specified nucleic acid target sequence to a detectably greater degree (e.g., at least 2-fold over background) than its hybridization to non-target nucleic acid sequences and to the substantial exclusion of non-target nucleic acids.
• Selectively hybridizing sequences typically have about at least 80% sequence identity, preferably 90% sequence identity, and most preferably 100% sequence identity (i.e., complementary) with each other.
• the term "specifically reactive”, includes reference to a binding reaction between an antibody and a protein having an epitope recognized by the antigen binding site of the antibody. This binding reaction is determinative of the presence of a protein having the recognized epitope amongst the presence of a heterogeneous population of proteins and other biologies.
• the specified antibodies bind to an analyte having the recognized epitope to a substantially greater degree (e.g., at least 2- fold over background) than to substantially all other analytes lacking the epitope which are present in the sample.
• Specific binding to an antibody under such conditions may require an antibody that is selected for its specificity for a particular protein.
• antibodies raised to the polypeptides of the present invention can be selected from those antibodies that are specifically reactive with polypeptides of the present invention.
• the proteins used as immunogens can be in native conformation or denatured so as to provide a linear epitope.
• immunoassay formats may be used to select antibodies specifically reactive with a particular protein (or other analyte).
• solid-phase ELISA immunoassays are routinely used to select monoclonal antibodies specifically immunoreactive with a protein. See Harlow and Lane, Antibodies, A Laboratory Manual, Cold Spring Harbor Publications, New York (1988), for a description of immunoassay formats and conditions that can be used to determine selective reactivity.
• stringent conditions or “stringent hybridization conditions” includes reference to conditions under which a probe will hybridize to its target sequence, to a detectably greater degree than other sequences (e.g., at least 2- fold over background). Stringent conditions are sequence-dependent and will be different in different circumstances. By controlling the stringency of the hybridization and/or washing conditions, target sequences can be identified which are 100% complementary to the probe (homologous probing). Alternatively, stringency conditions can be adjusted to allow some mismatching in sequences so that lower degrees of similarity are detected (heterologous probing). Generally, a probe is less than about 1000 nucleotides in length, preferably less than 500 nucleotides in length.
• stringent conditions will be those in which the salt concentration is less than about 1.5 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30°C for short probes (e.g., 10 to 50 nucleotides) and at least about 60°C for long probes (e.g., greater than 50 nucleotides).
• Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide.
• Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1 M NaCl, 1% SDS at 37°C, and a wash in 0.5X to 1X SSC at 55 to
• Exemplary high stringency conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37°C, and a wash in 0.1X SSC at 60 to 65°C.
• T m 81.5 °C + 16.6 (log M) + 0.41 (%GC) - 0.61 (% form) - 500/L; where M is the molarity of monovalent cations, %GC is the percentage of guanosine and cytosine nucleotides in the DNA, % form is the percentage of formamide in the hybridization solution, and L is the length of the hybrid in base pairs.
• the T m is the temperature (under defined ionic strength and pH) at which 50% of a complementary target sequence hybridizes to a perfectly matched probe. T m is reduced by about 1 °C for each 1 % of mismatching; thus, T m , hybridization and/or wash conditions can be adjusted to hybridize to sequences of the desired identity. For example, if sequences with >90% identity are sought, the T m can be decreased 10 °C.
• stringent conditions are selected to be about 5 °C lower than the thermal melting point (T m ) for the specific sequence and its complement at a defined ionic strength and pH.
• transgenic plant includes reference to a plant which comprises within its genome a heterologous polynucleotide.
• the heterologous polynucleotide is stably integrated within the genome such that the polynucleotide is passed on to successive generations.
• the heterologous polynucleotide may be integrated into the genome alone or as part of a recombinant expression cassette.
• 'Transgenic is used herein to include any cell, cell line, callus, tissue, plant part or plant, the genotype of which has been altered by the presence of heterologous nucleic acid including those transgenics initially so altered as well as those created by sexual crosses or asexual propagation from the initial transgenic.
• transgenic does not encompass the alteration of the genome (chromosomal or extra-chromosomal) by conventional plant breeding methods or by naturally occurring events such as random cross-fertilization, non-recombinant viral infection, non-recombinant bacterial transformation, non-recombinant transposition, or spontaneous mutation.
• vector includes reference to a nucleic acid used in transfection of a host cell and into which can be inserted a polynucleotide. Vectors are often repl icons. Expression vectors permit transcription of a nucleic acid inserted therein.
• sequence relationships between two or more nucleic acids or polynucleotides are used to describe the sequence relationships between two or more nucleic acids or polynucleotides: (a) “reference sequence”, (b) “comparison window”, (c) “sequence identity”, (d) “percentage of sequence identity”, and (e) “substantial identity”.
• reference sequence is a defined sequence used as a basis for sequence comparison.
• a reference sequence may be a subset or the entirety of a specified sequence; for example, as a segment of a full-length cDNA or gene sequence, or the complete cDNA or gene sequence.
• comparison window means includes reference to a contiguous and specified segment of a polynucleotide sequence, wherein the polynucleotide sequence may be compared to a reference sequence and wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences.
• the comparison window is at least 20 contiguous nucleotides in length, and optionally can be 30, 40, 50, 100, or longer.
• Optimal alignment of sequences for comparison may be conducted by the local homology algorithm of Smith and Waterman, Adv. APPI. Math. 2:482 (1981); by the homology alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48:443 (1970); by the search for similarity method of Pearson and Lipman, Proc. Natl. Acad. Sci.
• the BLAST family of programs which can be used for database similarity searches includes: BLASTN for nucleotide query sequences against nucleotide database sequences; BLASTX for nucleotide query sequences against protein database sequences; BLASTP for protein query sequences against protein database sequences; TBLASTN for protein query sequences against nucleotide database sequences; and TBLASTX for nucleotide query sequences against nucleotide database sequences.
• BLAST 2.0 suite of programs using default parameters is used. Altschul et al., Nucleic Acids Res. 25:3389-3402 (1997). Software for performing BLAST analyses is publicly available, e.g. through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/).
• BLAST searches assume that proteins can be modeled as random sequences. However, many real proteins comprise regions of nonrandom sequences which may be homopolymeric tracts, short-period repeats, or regions enriched in one or more amino acids. Such low-complexity regions may be aligned between unrelated proteins even though other regions of the protein are entirely dissimilar.
• a number of low-complexity filter programs can be employed to reduce such low- complexity alignments. For example, the SEG (Wooten and Federhen, Comput. Chem., 17:149-163 (1993)) and XNU (Claverie and States, Comput. Chem., 17:191-201 (1993)) low-complexity filters can be employed alone or in combination.
• sequence identity in the context of two nucleic acid or polypeptide sequences includes reference to the residues in the two sequences which are the same when aligned for maximum correspondence over a specified comparison window.
• sequence identity When percentage of sequence identity is used in reference to proteins it is recognized that residue positions which are not identical often differ by conservative amino acid substitutions, where amino acid residues are substituted for other amino acid residues with similar chemical properties (e.g. charge or hydrophobicity) and therefore do not change the functional properties of the molecule. Where sequences differ in conservative substitutions, the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution. Sequences which differ by such conservative substitutions are said to have "sequence similarity" or “similarity”.
• Means for making this adjustment are well-known to those of skill in the art. Typically this involves scoring a conservative substitution as a partial rather than a full mismatch, thereby increasing the percentage sequence identity. Thus, for example, where an identical amino acid is given a score of 1 and a non- conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1.
• the scoring of conservative substitutions is calculated, e.g., according to the algorithm of Meyers and Miller, Computer Applic. Biol. Sci.. 4:11-17 (1988) e.g., as implemented in the program PC/GENE (Intelligenetics, Mountain View, California, USA).
• percentage of sequence identity means the value determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity.
• % identity on the nucleic acid level is determined by the BESTFIT DNA Sequence Alignment software on Genescape using a gap weight of 50 and a length weight of 3.
• % identity on the amino acid level is determined by the BESTFIT DNA Sequence Alignment software on Genescape using a gap weight of 12 and a length weight of 4.
• nucleotide sequences are substantially identical is if two molecules hybridize to each other under stringent conditions. However, nucleic acids which do not hybridize to each other under stringent conditions are still substantially identical if the polypeptides which they encode are substantially identical. This may occur, e.g., when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code.
• One indication that two nucleic acid sequences are substantially identical is that the polypeptide which the first nucleic acid encodes is immunologically cross reactive with the polypeptide encoded by the second nucleic acid.
• substantially identical in the context of a peptide indicates that a peptide comprises a sequence with at least 70% sequence identity to a reference sequence, preferably 80%, more preferably 85%, most preferably at least 90% or 95% sequence identity to the reference sequence over a specified comparison window.
• Optimal alignment can be conducted using the homology alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48:443 (1970).
• An indication that two peptide sequences are substantially identical is that one peptide is immunologically reactive with antibodies raised against the second peptide.
• a peptide is substantially identical to a second peptide, for example, where the two peptides differ only by a conservative substitution.
• two-hybrid system is meant a screening method to identify protein- protein interactions, using a known gene (and its encoded product) as a “bait” or target and screening a library of expressed genes and their corresponding encoded products for specific interactions with the "bait” molecule.
• Methods for library construction and use of visual marker genes for yeast two-hybrid screens are well known in the art, and can be found in Sambrook, ef al., 1990, Ausubel et al., 1990 and G. Hannon and P. Bartel, Identification of interacting proteins using the two-hybrid system. Methods Mol. Cellular Biol. 5:289-297 (1995).
• the proteins encoded by the Cks gene are small 13kD proteins necessary for progression through mitosis.
• the Cks gene was first isolated in yeast (Hindley ef al., 1987), and a few years later in humans (Ducommun ef al., 1987). Subsequently, it has been cloned in amphibians (Patra and Dunphy, 1996), and plants. Two Cks isoforms have been found in all vertebrates tested to date (S. Reed, Plenary Lecture at the Keystone Symposium on Cell Cycle Regulations, Mar. 28 - Apr. 2, 1998).
• Suc1+ encodes a predicted 13-kilodalton protein that is essential for cell viability and is directly involved in the division cycle of Schizosaccharomyces pombe. Mol. Cell. Biol. 7:504-511.
• the present invention provides, inter alia, compositions and methods for modulating (i.e., increasing or decreasing) the total levels of proteins of the present invention and/or altering their ratios in plants.
• the present invention provides utility in such exemplary applications as the regulation of cell division.
• the polypeptides of the present invention can be expressed at times or in quantities which are not characteristic of non-recombinant plants.
• modulating cell cycle proteins is expected to provide a positive growth advantage and increase crop yield.
• Cell cycle nucleic acids can be adducted to a second nucleic acid sequence encoding a DNA-binding domain, for use in two-hybrid systems to identify cks-interacting proteins. It is expected that modulating the level of cell cycle protein, i.e. overexpression, will increase endoreduplication which is expected to increase the size of the seed, the size of the endosperm and amount of protein in the seed.
• the cell cycle protein can be used to affinity purify active maturation promoting factor (MPF) or its components.
• the present invention also provides isolated nucleic acid comprising polynucleotides of sufficient length and complementarity to a cell cycle gene to use as probes or amplification primers in the detection, quantitation, or isolation of gene transcripts.
• isolated nucleic acids of the present invention can be used as probes in detecting deficiencies in the level of mRNA in screenings for desired transgenic plants, for detecting mutations in the gene (e.g., substitutions, deletions, or additions), for monitoring upregulation of expression or changes in enzyme activity in screening assays of compounds, for detection of any number of allelic variants (polymorphisms) of the gene, or for use as molecular markers in plant breeding programs.
• the isolated nucleic acids of the present invention can also be used for recombinant expression of cell cycle polypeptides, or for use as immunogens in the preparation and/or screening of antibodies.
• the isolated nucleic acids of the present invention can also be employed for use in sense or antisense suppression of one or more cell cycle genes in a host cell, tissue, or plant. Attachment of chemical agents which bind, intercalate, cleave and/or crosslink to the isolated nucleic acids of the present invention can also be used to modulate transcription or translation.
• nucleic acid amplification to identity insertion sequence inactivated cell cycle genes from a cDNA library prepared from insertion sequence mutagenized plants. Progeny seed from the plants comprising the desired inactivated gene can be grown to a plant to study the phenotypic changes characteristic of that inactivation. See, Tools to Determine the Function of Genes, 1995 Proceedings of the Fiftieth Annual Corn and Sorghum Industry Research Conference, American Seed Trade Association, Washington, D.C., 1995.
• non- translated 5' or 3' regions of the polynucleotides of the present invention can be used to modulate turnover of heterologous mRNAs and/or protein synthesis.
• the codon preference characteristic of the polynucleotides of the present invention can be employed in heterologous sequences, or altered in homologous or heterologous sequences, to modulate translational level and/or rates.
• the present invention also provides isolated proteins comprising polypeptides including an amino acid sequence from the cell cycle polypeptides (e.g., preproenzyme, proenzyme, or enzymes) as disclosed herein.
• the present invention also provides proteins comprising at least one epitope from a cell cycle polypeptide.
• the proteins of the present invention can be employed in assays for enzyme agonists or antagonists of enzyme function, or for use as immunogens or antigens to obtain antibodies specifically immunoreactive with a protein of the present invention. Such antibodies can be used in assays for expression levels, for identifying and/or isolating nucleic acids of the present invention from expression libraries, or for purification of cell cycle polypeptides.
• the isolated nucleic acids of the present invention can be used over a broad range of plant types, including species from the genera Cucurbita, Rosa, Vitis, Juglans, Fragaria, Lotus, Medicago, Onobrychis, Trifolium, Trigonella, Vigna, Citrus, Linum, Geranium, Manihot, Daucus, Arabidopsis, Brassica, Raphanus, Sinapis, Atropa, Capsicum, Datura, Hyoscyamus, Lycopersicon, Nicotiana, Solanum, Petunia, Digitalis, Majorana, Ciahorium, Helianthus, Lactuca, Bromus, Asparagus, Antirrhinum, Heterocallis, Nemesis, Pelargonium, Panieum, Pennisetum, Ranunculus, Senecio, Salpiglossis, Cucumis, Browaalia, Glycine, Pis ⁇ m, Phaseolus, Lolium, Oryza, Ze
• the present invention provides, inter alia, isolated nucleic acids of RNA, DNA, and analogs and/or chimeras thereof, comprising a cell cycle polynucleotide encoding such enzymes as:
• the cell cycle nucleic acids of the present invention comprise isolated cell cycle polynucleotides which, are inclusive of:
• SEQ ID NOS: 5-16 which amplify polynucleotides having substantial identity to polynucleotides from amongst those having SEQ ID NOS: 1 and 3;
• a polynucleotide which selectively hybridizes under stringent conditions to a polynucleotide of (a) or (b), wherein the conditions are a buffer solution of 30 % by volume formamide, 1 M NaCl, 1 % by weight sodium dodecyl sulfate (SDS) at 37° and a wash in 2X SSC at 50°;
• a polynucleotide encoding a protein having a specified number of contiguous amino acids from a prototype polypeptide, wherein the protein is specifically recognized by antisera elicited by presentation of the protein and wherein the protein does not detectably immunoreact to antisera which has been fully immunosorbed with the protein;
• f complementary sequences of polynucleotides of (a), (b), (c), (d), or (e);
• a polynucleotide comprising at least 15 contiguous nucleotides from a polynucleotide of (a), (b), (c), (d), (e), or (f).
• the present invention provides isolated heterologous nucleic acids comprising a cell cycle polynucleotide, wherein the polynucleotide encodes a cell cycle polypeptide, disclosed herein in SEQ ID NOS: 2 and 4, or conservatively modified or polymorphic variants thereof.
• the degeneracy of the genetic code allows for a plurality of polynucleotides to encode for the identical amino acid sequence.
• Such "silent variations" can be used, for example, to selectively hybridize and detect allelic variants of polynucleotides of the present invention.
• the present invention includes polynucleotides of SEQ ID NOS: 1 and 3, and silent variations of polynucleotides encoding a polypeptide of SEQ ID NOS: 2 and 4.
• the present invention further provides isolated nucleic acids comprising polynucleotides encoding conservatively modified variants of a polypeptide of SEQ ID NOS: 2 and 4.
• Conservatively modified variants can be used to generate or select antibodies immunoreactive to the non-variant polypeptide.
• ZmCks is coded for by the polypeptides of SEQ ID NOS: 2 and 4 which are encoded for by the nucleic acids of SEQ ID NOS: 1 and 3, respectively.
• the present invention provides isolated nucleic acids comprising cell cycle polynucleotides, wherein the polynucleotides are amplified from a Zea mays nucleic acid library.
• Zea mays lines B73, PHRE1, A632, BMS-P2#10, W23, and Mo17 are known and publicly available.
• Other publicly known and available maize lines can be obtained from the Maize Genetics Cooperation (Urbana, IL).
• the nucleic acid library may be a cDNA library, a genomic library, or a library generally constructed from nuclear transcripts at any stage of intron processing.
• a cDNA nucleic acid library will be constructed to comprise a majority of full-length cDNAs.
• cDNA libraries will be normalized to increase the representation of relatively rare cDNAs.
• Total RNA Isolation Libraries can be made from a variety of maize tissues but for optimal results one should isolate RNA's from mitotically active tissues such as shoot meristems, shoot meristem cultures, callus and suspension cultures, immature ears and tassels, and young seedlings.
• cell cycle proteins are typically expressed at specific cell cycle stages it may be possible to enrich for such rare messages using exemplary cell cycle inhibitors such as aphidicolin, hydroxyurea, mimosine, and double-phosphate starvation methods to block cells at the G1/S boundary. Cells can also be blocked at this stage using the double phosphate starvation method. Hormone treatments that stimulate cell division, for example cytokinin, would also increase expression of the cell cycle RNA.
• Full length cDNA libraries from such rapidly-dividing tissues would provide opportunities for identifying full length, cell cycle related cDNAs.
• Full length cDNA libraries can be constructed using the "Biotinylated CAP Trapper” method (Carninci, P., ef al., Genomics 37:327-336, 1996) or the "mRNA Cap Retention Procedure” (Edery, I., ef al., Molecular and Cellular Biology 15:3363-3371 , 1995).
• Full length cDNA libraries can be normalized to provide a higher probability of sampling genes that express at low levels.
• cDNA library normalization methods are summarized by Bento Soares (Bonaldo, M.F., et al., Genome Research 6:791-806, 1996).
• Functional fragments of cell cycle protein can be identified using a variety of techniques such as restriction analysis, Southern analysis, primer extension analysis, and DNA sequence analysis. Function can also be determined by complementing yeast strains known to be mutant for G1 cell cycle proteins with maize homologs.
• Primer extension analysis or S1 nuclease protection analysis for example, can be used to localize the putative start site of transcription of the cloned gene.
• polynucleotides of the present invention include those amplified using the following primer pairs:
• SEQ ID NOS: 5-11 which yield an amplicon comprising a sequence having substantial identity to SEQ ID NO: 1 and
• SEQ ID NOS: 12-16 which yield an amplicon comprising a sequence having substantial identity to SEQ ID NO: 3.
• the present invention also provides subsequences of full-length nucleic acids. Any number of subsequences can be obtained by reference to SEQ ID NOS: 1 and 3, and using primers which selectively amplify, under stringent conditions to: at least two sites to the polynucleotides of the present invention, or to two sites within the nucleic acid which flank and comprise a polynucleotide of the present invention, or to a site within a polynucleotide of the present invention and a site within the nucleic acid which comprises it.
• a variety of methods for obtaining 5' and/or 3' ends is well known in the art.
• the present invention provides cell cycle polynucleotides having the sequence of the cell cycle gene, nuclear transcript, cDNA, or complementary sequences and/or subsequences thereof.
• Primer sequences can be obtained by reference to a contiguous subsequence of a polynucleotide of the present invention.
• Primers are chosen to selectively hybridize, under PCR amplification conditions, to a polynucleotide of the present invention in an amplification mixture comprising a genomic and/or cDNA library from the same species.
• the primers are complementary to a subsequence of the amplicon they yield.
• the primers will be constructed to anneal at their 5' terminal end's to the codon encoding the carboxy or amino terminal amino acid residue (or the complements thereof) of the polynucleotides of the present invention.
• the primer length in nucleotides is selected from the group of integers consisting of from at least 15 to 50.
• the primers can be at least 15, 18, 20, 25, 30, 40, or 50 nucleotides in length.
• a non- annealing sequence at the 5'end of the primer (a "tail") can be added, for example, to introduce a cloning site at the terminal ends of the amplicon.
• the amplification primers may optionally be elongated in the 3' direction with additional contiguous nucleotides from the polynucleotide sequences, such as SEQ ID NOS: 1 and 3, from which they are derived.
• the number of nucleotides by which the primers can be elongated is selected from the group of integers consisting of from at least 1 to 25.
• the primers can be elongated with an additional 1, 5, 10, or 15 nucleotides.
• a lengthened primer sequence can be employed to increase specificity of binding (i.e., annealing) to a target sequence.
• the amplification products can be translated using expression systems well known to those of skill in the art and as discussed, infra.
• the resulting translation products can be confirmed as polypeptides of the present invention by, for example, assaying for the appropriate catalytic activity (e.g., specific activity and/or substrate specificity), or verifying the presence of one or more linear epitopes which are specific to a polypeptide of the present invention.
• the present invention provides isolated nucleic acids comprising cell cycle polynucleotides, wherein the polynucleotides selectively hybridize, under selective hybridization conditions, to a polynucleotide of paragraphs (A) or (B) as discussed, supra.
• the polynucleotides of this embodiment can be used for isolating, detecting, and/or quantifying nucleic acids comprising the polynucleotides of (A) or (B).
• polynucleotides of the present invention can be used to identify, isolate, or amplify partial or full-length clones in a deposited library.
• the polynucleotides are genomic or cDNA sequences isolated from a Zea mays nucleic acid library.
• the cDNA library comprises at least 80% full-length sequences, preferably at least 85% or 90% full-length sequences, and more preferably at least 95% full-length sequences.
• the cDNA libraries can be normalized to increase the representation of rare sequences.
• Low stringency hybridization conditions are typically, but not exclusively, employed with sequences having a reduced sequence identity relative to complementary sequences.
• Moderate and high stringency conditions can optionally be employed for sequences of greater identity.
• Low stringency conditions allow selective hybridization of sequences having about 70% sequence identity and can be employed to identify orthologous or paralogous sequences.
• the present invention provides isolated nucleic acids comprising cell cycle polynucleotides, wherein the polynucleotides have a specified identity at the nucleotide level to a polynucleotide as disclosed above in paragraphs (A), (B), or (C).
• the percentage of identity to a reference sequence is at least 60% and, rounded upwards to the nearest integer, can be expressed as an integer selected from the group of integers consisting of from 60 to 99.
• the percentage of identity to a reference sequence can be at least 70%, 75%, 80%, 85%, 90%, or 95%.
• the polynucleotides of this embodiment will share an epitope with a polypeptide encoded by the polynucleotides of (A), (B), or (C).
• these polynucleotides encode a first polypeptide which elicits production of antisera comprising antibodies which are specifically reactive to a second polypeptide encoded by a polynucleotide of (A), (B), or (C).
• the first polypeptide does not bind to antisera raised against itself when the antisera has been fully immunosorbed with the first polypeptide.
• the polynucleotides of this embodiment can be used to generate antibodies for use in, for example, the screening of expression libraries for nucleic acids comprising polynucleotides of (A), (B), or (C), or for purification of, or in immunoassays for, polypeptides encoded by the polynucleotides of (A), (B), or (C).
• the polynucleotides of this embodiment embrace nucleic acid sequences which can be employed for selective hybridization to a polynucleotide encoding a polypeptide of the present invention.
• Screening polypeptides for specific binding to antisera can be conveniently achieved using peptide display libraries.
• This method involves the screening of large collections of peptides for individual members having the desired function or structure.
• Antibody screening of peptide display libraries is well known in the art.
• the displayed peptide sequences can be from 3 to 5000 or more amino acids in length, frequently from 5-100 amino acids long, and often from about 8 to 15 amino acids long.
• several recombinant DNA methods have been described.
• One type involves the display of a peptide sequence on the surface of a bacteriophage or cell. Each bacteriophage or cell contains the nucleotide sequence encoding the particular displayed peptide sequence.
• the present invention provides isolated nucleic acids comprising cell cycle polynucleotides, wherein the polynucleotides encode a protein having a subsequence of contiguous amino acids from a prototype cell cycle polypeptide.
• Exemplary prototype cell cycle polypeptides are provided in SEQ ID NOS: 2 and 4.
• the length of contiguous amino acids from the prototype polypeptide is selected from the group of integers consisting of from at least 10 to the number of amino acids within the prototype sequence.
• the polynucleotide can encode a polypeptide having a subsequence having at least 10, 15, 20, 25, 30, 35, 40, 45, or 50, contiguous amino acids from the prototype polypeptide.
• the number of such subsequences encoded by a polynucleotide of the instant embodiment can be any integer selected from the group consisting of from 1 to 20, such as 2, 3, 4, or 5.
• the subsequences can be separated by any integer of nucleotides from 1 to the number of nucleotides in the sequence such as at least 5, 10, 15, 25, 50, 100, or 200 nucleotides.
• polypeptide encoded by polynucleotides of this embodiment when presented as an immunogen, elicit the production of polyclonal antibodies which specifically bind to a prototype polypeptide such as, but not limited to, a polypeptide encoded by the polynucleotide of (b), supra, or exemplary polypeptides of SEQ ID NOS: 2 and 4.
• a protein encoded by a polynucleotide of this embodiment does not bind to antisera raised against the prototype polypeptide when the antisera has been fully immunosorbed with the prototype polypeptide.
• Methods of making and assaying for antibody binding specificity/affinity are well known in the art.
• Exemplary immunoassay formats include ELISA, competitive immunoassays, radioimmunoassays, Western blots, indirect immunofluorescent assays and the like.
• fully immunosorbed and pooled antisera which is elicited to the prototype polypeptide can be used in a competitive binding assay to test the protein.
• concentration of the prototype polypeptide required to inhibit 50% of the binding of the antisera to the prototype polypeptide is determined. If the amount of the protein required to inhibit binding is less than twice the amount of the prototype protein, then the protein is said to specifically bind to the antisera elicited to the immunogen.
• the proteins of the present invention embrace allelic variants, conservatively modified variants, and minor recombinant modifications to a prototype polypeptide.
• a polynucleotide of the present invention optionally encodes a protein having a molecular weight as the non-glycosylated protein within 20% of the molecular weight of the full-length non-glycosylated cell cycle polypeptides as disclosed herein (e.g., SEQ ID NOS:2 and 4).
• Molecular weight can be readily determined by SDS-PAGE under reducing conditions.
• the molecular weight is within 15% of a full length cell cycle polypeptide, more preferably within 10% or 5%, and most preferably within 3%, 2%, or 1% of a full length cell cycle polypeptide of the present invention.
• Molecular weight determination of a protein can be conveniently performed by SDS-PAGE under denaturing conditions.
• the polynucleotides of this embodiment will encode a protein having a specific activity at least 20%, 30%, 40%, or 50% of the native, endogenous (i.e., non-isolated), full-length cell cycle polypeptide.
• the proteins encoded by polynucleotides of this embodiment will optionally have a substantially similar apparent dissociation constant (K m ) and/or catalytic activity (i.e., the microscopic rate constant, k d ) as the native endogenous, full-length cell cycle protein.
• K m apparent dissociation constant
• catalytic activity i.e., the microscopic rate constant, k d
• kcat/ n value determines the specificity for competing substrates and is often referred to as the specificity constant.
• Proteins of this embodiment can have a value at least 10% of the non-isolated full-length cell cycle polypeptide as determined using the substrate of that polypeptide from the cell cycle specific pathways, supra.
• the n value will be at least 20%, 30%, 40%, 50%, and most preferably at least 60%, 70%, 80%, 90%, or 95% the k ⁇ t Km value of the non- isolated, full-length cell cycle polypeptide. Determination of k ., Km , and kcat/Km can be determined by any number of means well known to those of skill in the art.
• the initial rates i.e., the first 5% or less of the reaction
• the initial rates can be determined using rapid mixing and sampling techniques (e.g., continuous-flow, stopped-flow, or rapid quenching techniques), flash photolysis, or relaxation methods (e.g., temperature jumps) in conjunction with such exemplary methods of measuring as spectrophotometry, spectrofluorimetry, nuclear magnetic resonance, or radioactive procedures.
• Kinetic values are conveniently obtained using a Lineweaver-Burk or Eadie-Hofstee plot.
• the present invention provides isolated nucleic acids comprising cell cycle polynucleotides, wherein the polynucleotides are complementary to the polynucleotides of paragraphs A-E, above.
• complementary sequences base-pair throughout the entirety of their length with the polynucleotides of (A)-(E) (i.e., have 100% sequence identity over their entire length).
• Complementary bases associate through hydrogen bonding in double stranded nucleic acids. For example, the following base pairs are complementary: guanine and cytosine; adenine and thymine; and adenine and uracil.
• the present invention provides isolated nucleic acids comprising cell cycle polynucleotides, wherein the polynucleotide comprises at least 15 contiguous bases from the polynucleotides of (A) through (F) as discussed above.
• the length of the polynucleotide is given as an integer selected from the group consisting of from at least 15 to the length of the nucleic acid sequence from which the polynucleotide is a subsequence of.
• polynucleotides of the present invention are inclusive of polynucleotides comprising at least 15, 20, 25, 30, 40, 50, 60, 75, or 100 contiguous nucleotides in length from the polynucleotides of (A)-(F).
• the number of such subsequences encoded by a polynucleotide of the instant embodiment can be any integer selected from the group consisting of from 1 to 20, such as 2, 3, 4, or
• the subsequences can be separated by any integer of nucleotides from 1 to the number of nucleotides in the sequence such as at least 5, 10, 15, 25, 50, 100, or 200 nucleotides.
• the subsequences of the present invention can comprise structural characteristics of the sequence from which it is derived.
• the subsequences can lack certain structural characteristics of the larger sequence from which it is derived.
• a subsequence from a polynucleotide encoding a polypeptide having at least one linear epitope in common with a prototype sequence, such as SEQ ID NOS: 2 and 4 may encode an epitope in common with the prototype sequence.
• the subsequence may not encode an epitope in common with the prototype sequence but can be used to isolate the larger sequence by, for example, nucleic acid hybridization with the sequence from which it's derived.
• Subsequences can be used to modulate or detect gene expression by introducing into the subsequences compounds which bind, intercalate, cleave and/or crosslink to nucleic acids.
• exemplary compounds include acridine, psoralen, phenanthroline, naphthoquinone, daunomycin or chloroethylaminoaryl conjugates.
• the isolated nucleic acids of the present invention can be made using (a) standard recombinant methods, (b) synthetic techniques, or combinations thereof.
• the polynucleotides of the present invention will be cloned, amplified, or otherwise constructed from a monocot.
• the monocot is Zea mays.
• Particularly preferred is the use of Zea mays tissue from tassel and vegetative meristem.
• the nucleic acids may conveniently comprise sequences in addition to a polynucleotide of the present invention.
• a multi-cloning site comprising one or more endonuclease restriction sites may be inserted into the nucleic acid to aid in isolation of the polynucleotide.
• translatable sequences may be inserted to aid in the isolation of the translated polynucleotide of the present invention.
• a hexa-histidine marker sequence provides a convenient means to purify the proteins of the present invention.
• the nucleic acid of the present invention - excluding the polynucleotide sequence - is generally a vector, adapter, or linker for cloning and/or expression of a polynucleotide of the present invention.
• Use of cloning vectors, expression vectors, adapters, and linkers is well known in the art.
• [Exemplary nucleic acids include such vectors as: M13, lambda ZAP Express, lambda ZAP II, lambda gt10, lambda gt11, pBK-CMV, pBK-RSV, pBluescript II, lambda DASH II, lambda EMBL 3, lambda EMBL 4, pWE15, SuperCos 1, SurfZap, Uni-ZAP, pBC, pBS+/-, pSG5, pBK, pCR-Script, pET, pSPUTK, p3 * SS, pOPRSVI CAT, pOPI3 CAT, pXT1, pSG5, pPbac, pMbac, pMCIneo, pOG44, pOG45, pFRT ⁇ GAL, pNEO ⁇ GAL, pRS403, pRS404, pRS405, pRS406, pRS413, pRS414, p
• RNA, cDNA, genomic DNA, or a hybrid thereof can be obtained from plant biological sources using any number of cloning methodologies known to those of skill in the art.
• oligonucleotide probes which selectively hybridize, under stringent conditions, to the polynucleotides of the present invention are used to identify the desired sequence in a cDNA or genomic DNA library. While isolation of RNA, and construction of cDNA and genomic libraries is well known to those of ordinary skill in the art, the following highlights some of the methods employed.
• Total RNA from plant cells comprises such nucleic acids as mitochondrial RNA, chloroplastic RNA, rRNA, tRNA, hnRNA and mRNA.
• Total RNA preparation typically involves lysis of cells and removal of proteins, followed by precipitation of nucleic acids. Extraction of total RNA from plant cells can be accomplished by a variety of means. Frequently, extraction buffers include a strong detergent such as SDS and an organic denaturant such as guanidinium isothiocyanate, guanidine hydrochloride or phenol. Following total RNA isolation, poly(A) + mRNA is typically purified from the remainder RNA using oligo(dT) cellulose.
• RNA and mRNA isolation protocols are described in Plant Molecular Biology: A Laboratory Manual, Clark, Ed., Springer-Verlag, Berlin (1997); and, Current Protocols in Molecular Biology, Ausubel, ef al., Eds., Greene Publishing and Wiley-lnterscience, New York (1995).
• Total RNA and mRNA isolation kits are commercially available from vendors such as Stratagene (La Jolla, CA), Clonetech (Palo Alto, CA), Pharmacia (Piscataway, NJ), and 5'-3' (Paoli, PA). See also, U.S. Patent Nos. 5,614,391; and, 5,459,253.
• the mRNA can be fractionated into populations with size ranges of about 0.5, 1.0, 1.5, 2.0, 2.5 or 3.0 kb.
• the cDNA synthesized for each of these fractions can be size selected to the same size range as its mRNA prior to vector insertion. This method helps eliminate truncated cDNA formed by incompletely reverse transcribed mRNA.
• Construction of a cDNA library generally entails five steps. First, first strand cDNA synthesis is initiated from a poly(A) + mRNA template using a poly(dT) primer or random hexanucleotides. Second, the resultant RNA-DNA hybrid is converted into double stranded cDNA, typically by a combination of RNAse H and DNA polymerase I (or Klenow fragment). Third, the termini of the double stranded cDNA are ligated to adaptors. Ligation of the adaptors will produce cohesive ends for cloning.
• cDNA synthesis protocols are well known to the skilled artisan and are described in such standard references as: Plant Molecular Biology: A Laboratory Manual, Clark, Ed., Springer-Verlag, Berlin (1997); and, Current Protocols in Molecular Biology, Ausubel, et al., Eds., Greene Publishing and Wiley-lnterscience, New York (1995). cDNA synthesis kits are available from a variety of commercial vendors such as: Stratagene, and Pharmacia.
• Substantially pure full-length cDNA libraries are constructed to comprise at least 90%, and more preferably at least 93% or 95% full-length inserts amongst clones containing inserts.
• the length of insert in such libraries can be from 0 to 8, 9, 10, 11, 12, 13, or more kilobase pairs.
• Vectors to accommodate inserts of these sizes are known in the art and available commercially. See, e.g., the Stratagene lambda ZAP Express (cDNA cloning vector with 0 to 12 kb cloning capacity).
• a non-normalized cDNA library represents the mRNA population of the tissue it was made from. Since unique clones are out-numbered by clones derived from highly expressed genes their isolation can be laborious. Normalization of a cDNA library is the process of creating a library in which each clone is more equally represented.
• a number of approaches to normalize cDNA libraries are known in the art.
• One approach is based on hybridization to genomic DNA. The frequency of each hybridized cDNA in the resulting normalized library would be proportional to that of each corresponding gene in the genomic DNA.
• Another approach is based on kinetics. If cDNA reannealing follows second-order kinetics, rarer species anneal less rapidly and the remaining single-stranded fraction of cDNA becomes progressively more normalized during the course of the hybridization. Specific loss of any species of cDNA, regardless of its abundance, does not occur at any Cot value. Construction of normalized libraries is described in Ko, Nucl. Acids. Res..
• Subtracted cDNA libraries are another means to increase the proportion of less abundant cDNA species.
• cDNA prepared from one pool of mRNA is depleted of sequences present in a second pool of mRNA by hybridization.
• the cDNA:mRNA hybrids are removed and the remaining un- hybridized cDNA pool is enriched for sequences unique to that pool. See, Foote et al. in, Plant Molecular Biology: A Laboratory Manual, Clark, Ed., Springer- Verlag, Berlin (1997); Kho and Zarbl, Technioue. 3(2):58-63 (1991); Sive and St. John, Nucl. Acids Res..
• cDNA subtraction kits are commercially available. See, e.g., PCR-Select (Clontech).
• genomic libraries large segments of genomic DNA are generated by random fragmentation, e.g. using restriction endonucleases, and are ligated with vector DNA to form concatemers that can be packaged into the appropriate vector. Methodologies to accomplish these ends, and sequencing methods to verify the sequence of nucleic acids are well known in the art. Examples of appropriate molecular biological techniques and instructions sufficient to direct persons of skill through many construction, cloning, and screening methodologies are found in Sambrook, ef al., Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory Vols. 1-3 (1989), Methods in Enzymology, Vol. 152: Guide to Molecular Cloning Techniques, Berger and Kimmel, Eds., San Diego: Academic Press, Inc.
• the cDNA or genomic library can be screened using a probe based upon the sequence of a polynucleotide of the present invention such as those disclosed herein. Probes may be used to hybridize with genomic DNA or cDNA sequences to isolate homologous genes in the same or different plant species.
• Probes may be used to hybridize with genomic DNA or cDNA sequences to isolate homologous genes in the same or different plant species.
• degrees of stringency of hybridization can be employed in the assay; and either the hybridization or the wash medium can be stringent. As the conditions for hybridization become more stringent, there must be a greater degree of complementarity between the probe and the target for duplex formation to occur.
• the degree of stringency can be controlled by temperature, ionic strength, pH and the presence of a partially denaturing solvent such as formamide.
• the stringency of hybridization is conveniently varied by changing the polarity of the reactant solution through manipulation of the concentration of formamide within the range of 0% to 50%.
• the degree of complementarity (sequence identity) required for detectable binding will vary in accordance with the stringency of the hybridization medium and/or wash medium.
• the degree of complementarity will optimally be 100 percent; however, it should be understood that minor sequence variations in the probes and primers may be compensated for by reducing the stringency of the hybridization and/or wash medium.
• the nucleic acids of interest can also be amplified from nucleic acid samples using amplification techniques.
• PCR polymerase chain reaction
• PCR and other in vitro amplification methods may also be useful, for example, to clone nucleic acid sequences that code for proteins to be expressed, to clone flanking genomic sequences, 5' untranslated regions and 3' sequences, to make nucleic acids to use as probes for detecting the presence of the desired mRNA in samples, for nucleic acid sequencing, or for other purposes.
• PCR-based method in which the longest cDNA is identified in the first step so that incomplete clones can be eliminated from study. BioTechnigues. 22(3): 481-486 (1997).
• a primer pair is synthesized with one primer annealing to the 5' end of the sense strand of the desired cDNA and the other primer to the vector.
• Clones are pooled to allow large-scale screening. By this procedure, the longest possible clone is identified amongst candidate clones.
• the PCR product is used solely as a diagnostic for the presence of the desired cDNA and does not utilize the PCR product itself. Such methods are particularly effective in combination with a full-length cDNA construction methodology, supra.
• the isolated nucleic acids of the present invention can also be prepared by direct chemical synthesis by methods such as the phosphotriester method of Narang ef al., Meth. Enzvmol. 68:90-99 (1979); the phosphodiester method of Brown et al., Meth. Enzvmol. 68:109-151 (1979); the diethylphosphoramidite method of Beaucage ef al., Tetra. Lett. 22:1859-1862 (1981); the solid phase phosphoramidite triester method described by Beaucage and Caruthers. Tetra. Letts.
• the present invention further provides recombinant expression cassettes comprising a nucleic acid of the present invention.
• a nucleic acid sequence coding for the desired polynucleotide of the present invention for example a cDNA or a genomic sequence encoding a full length polypeptide of the present invention, can be used to construct a recombinant expression cassette which can be introduced into the desired host cell.
• a recombinant expression cassette will typically comprise a polynucleotide of the present invention operably linked to transcriptional initiation regulatory sequences which will direct the transcription of the polynucleotide in the intended host cell, such as tissues of a transformed plant.
• plant expression vectors may include (1) a cloned plant gene under the transcriptional control of 5' and 3' regulatory sequences and (2) a dominant selectable marker.
• plant expression vectors may also contain, if desired, a promoter regulatory region (e.g., one conferring inducible or constitutive, environmentally- or developmentally-regulated, or cell- or tissue- specific/selective expression), a transcription initiation start site, a ribosome binding site, an RNA processing signal, a transcription termination site, and/or a polyadenylation signal.
• the Cauliflower Mosaic Virus 35S promoter with a duplicated enhancer region is described by Gardner ef al., Nucl. Acid Res. 9:2871-2888 (1981).
• the 79 bp Tobacco Mosaic Virus leader is described by Gallie et al., Nucl. Acid Res. 15:3257-3273 (1987) and was inserted downstream of the promoter followed by the first intron of the maize alcohol dehydrogenase gene ADH1-S. Described by Dennis ef al., Nucl. Acid Res. 12:3983-3990 (1984).
• the 3' sequence pinll is described by An ef a/., Plant Cell 1:115-122 (1989).
• a plant promoter fragment can be employed which will direct expression of a polynucleotide of the present invention in all tissues of a regenerated plant.
• Such promoters are referred to herein as "constitutive" promoters and are active under most environmental conditions and states of development or cell differentiation.
• constitutive promoters include the cauliflower mosaic virus (CaMV) 35S transcription initiation region, the 1'- or 2'- promoter derived from T-DNA of Agrobacterium tumefaciens, the ubiquitin 1 promoter, the Smas promoter, the cinnamyl alcohol dehydrogenase promoter (U.S. Patent No. 5,683,439), the Nos promoter, the pEmu promoter, the rubisco promoter, the GRP1-8 promoter, and other transcription initiation regions from various plant genes known to those of skill.
• CaMV cauliflower mosaic virus
• An inducible promoter can be operably linked to a nucleotide sequence encoding ZmCks.
• the inducible promoter is operably linked to a nucleotide sequence encoding a signal sequence which is operably linked to a nucleotide sequence encoding ZmCks. With an inducible promoter the rate of transcription increases in response to an inducing agent.
• any inducible promoter can be used in the instant invention. See Ward ef al. Plant Mol. Biol. 22:361-366 (1993).
• Exemplary inducible promoters include that from the ACE1 system which responds to copper (Mett ef al., PNAS 90:4567- 4571 (1993)); In2 gene from maize which responds to benzenesulfonamide herbicide safeners (Hershey ef al., Mol. Gen. Genetics 227:229-237 (1991) and Gatz ef al., Mol. Gen. Genetics 243:32-38 (1994)) or Tet repressor from Tn10 (Gatz ef al., Mol. Gen. Genet. 227:229-237 (1991).
• a particularly preferred inducible promoter is a promoter that responds to an inducing agent to which plants do not normally respond.
• An exemplary inducible promoter is the inducible promoter from a steroid hormone gene the transcriptional activity of which is induced by a glucocorticosteroid hormone. Schena ef al., Proc. Natl. Acad. Sci. U.S.A. 88:10421 (1991).
• the expression vector comprises an inducible promoter operably linked to a nucleotide sequence encoding ZmCks.
• the expression vector is introduced into plant cells and presumptively transformed cells are exposed to an inducer of the inducible promoter.
• the cells can be screened for the presence of ZmCks protein by northern, RPA, or RT-PCR (using transgene specific probes/oligo pairs) BrdU or cell division assays, as described above.
• a tissue-specific promoter can be operably linked to a nucleotide sequence encoding a ZmCks protein.
• the tissue-specific promoter is operably linked to a nucleotide sequence encoding a signal sequence which is operably linked to a nucleotide sequence encoding ZmCks. Plants transformed with a gene encoding ZmCks operably linked to a tissue-specific promoter produce the ZmCks protein exclusively, or preferentially, in a specific tissue.
• tissue-specific or tissue-preferred promoter can be utilized in the instant invention.
• exemplary tissue-specific or tissue-preferred promoters include a seed-preferred promoter such as that from the phaseolin gene (Murai ef al., Science 23:476-482 (1983) and Sengupta-Gopalan ef al., Proc. Natl. Acad. Sci.
• an anther-specific promoter such as that from LAT52 (Twell ef al., Mol. Gen- Genet. 217:240-245 (1989)); a pollen-specific promoter such as that from Zm13 (Guerrero et al., Mol. Gen. Genet. 224:161-168 (1993)) or a microspore-preferred promoter such as that from apg (Twell ef al., Sex. Plant Reprod. 6:217-224 (1993)).
• the expression vector comprises a tissue-specific or tissue-preferred promoter operably linked to a nucleotide sequence encoding cell cycle protein.
• the expression vector is introduced into plant cells. The cells are screened for the presence of cell cycle protein by either BrdU or cell division assays, as described above.
• a constitutive promoter can be operably linked to a nucleotide sequence encoding a cell cycle protein or the constitutive promoter is operably linked to a nucleotide sequence encoding a signal sequence which is operably linked to a nucleotide sequence encoding cell cycle protein.
• constitutive promoters include the promoters from plant viruses such as the 35S promoter from CaMV (Odell ef al., Nature 313:810-812 (1985)), Commelina yellow mottled virus (R. Torbert ef al., Plant Cell Rep. 17:284-287 (1988)) and the promoters from such genes as rice actin (McElroy ef al., Plant Cell 2:163-171 (1990)); ubiquitin (Christensen ef al., Plant Mol. Biol. 12:619-632 (1989) and Christensen ef al., Plant Mol. Biol.
• ALS3 structural gene (or a nucleotide sequence that has substantial sequence similarity to said Xbal/Ncol fragment), represents a particularly useful constitutive promoter.
• the expression vector comprises a constitutive promoter operably linked to a nucleotide sequence encoding cell cycle protein.
• the expression vector is introduced into plant cells and presumptively transformed cells are screened for the presence of cell cycle protein by either BrdU or cell division assays, as described above.
• the plant promoter can direct expression of a polynucleotide of the present invention in a specific tissue or may be otherwise under more precise environmental or developmental control. Such promoters are referred to here as "inducible" promoters.
• inducible promoters include pathogen attack, anaerobic conditions, or the presence of light.
• inducible promoters are the Adh1 promoter which is inducible by hypoxia or cold stress, the Hsp70 promoter which is inducible by heat stress, and the PPDK promoter which is inducible by light.
• promoters under developmental control include promoters that initiate transcription only, or preferentially, in certain tissues, such as leaves, roots, fruit, seeds, or flowers.
• the operation of a promoter may also vary depending on its location in the genome. Thus, an inducible promoter may become fully or partially constitutive in certain locations.
• heterologous and non-heterologous (i.e., endogenous) promoters can be employed to direct expression of the nucleic acids of the present invention. These promoters can also be used, for example, in recombinant expression cassettes to drive expression of antisense nucleic acids to reduce, increase, or alter cell cycle content and/or composition in a desired tissue.
• the nucleic acid construct will comprise a promoter functional in a plant cell, such as in Zea mays, operably linked to a polynucleotide of the present invention.
• Promoters useful in these embodiments include the endogenous promoters driving expression of a polypeptide of the present invention.
• isolated nucleic acids which serve as promoter or enhancer elements can be introduced in the appropriate position (generally upstream) of a non-heterologous form of a polynucleotide of the present invention so as to up or down regulate expression of a polynucleotide of the present invention.
• endogenous promoters can be altered in vivo by mutation, deletion, and/or substitution (see, Kmiec, U.S. Patent 5,565,350; Zarling ef al., PCT/US93/03868), or isolated promoters can be introduced into a plant cell in the proper orientation and distance from a cell cycle gene so as to control the expression of the gene. Gene expression can be modulated under conditions suitable for plant growth so as to alter cell cycle content and/or composition.
• the present invention provides compositions, and methods for making, heterologous promoters and/or enhancers operably linked to a native, endogenous (i.e., non-heterologous) form of a polynucleotide of the present invention.
• promoters with a particular expression pattern in terms of, e.g., tissue type, cell type, stage of development, and/or environmental conditions, are well known in the art. See, e.g., The Maize Handbook, Chapters 114-115, Freeling and Walbot, Eds., Springer, New York (1994); Corn and Corn Improvement, 3 rd edition, Chapter 6, Sprague and Dudley, Eds., American Society of Agronomy, Madison, Wisconsin (1988).
• a typical step in promoter isolation methods is identification of gene products that are expressed with some degree of specificity in the target tissue.
• differential hybridization to cDNA libraries are well known to those of skill in the art.
• subtractive hybridization are well known to those of skill in the art.
• differential display isolating promoters are known in the art such as the Clontech (Palo Alto, CA) Universal GenomeWalker Kit.
• the amino acid sequence for at least a portion of the identified protein it is helpful to obtain the amino acid sequence for at least a portion of the identified protein, and then to use the protein sequence as the basis for preparing a nucleic acid that can be used as a probe to identify either genomic DNA directly, or preferably, to identify a cDNA clone from a library prepared from the target tissue. Once such a cDNA clone has been identified, that sequence can be used to identify the sequence at the 5' end of the transcript of the indicated gene. For differential hybridization, subtractive hybridization and differential display, the nucleic acid sequence identified as enriched in the target tissue is used to identify the sequence at the 5' end of the transcript of the indicated gene.
• any of these sequences identified as being from the gene transcript can be used to screen a genomic library prepared from the target organism. Methods for identifying and confirming the transcriptional start site are well known in the art.
• promoter sequence elements include the TATA box consensus sequence (TATAAT), which is usually an AT-rich stretch of 5-10 bp located approximately 20 to 40 base pairs upstream of the transcription start site. Identification of the TATA box is well known in the art. For example, one way to predict the location of this element is to identify the transcription start site using standard RNA-mapping techniques such as primer extension, S1 analysis, and/or RNase protection.
• TATAAT TATA box consensus sequence
• RNA-mapping techniques such as primer extension, S1 analysis, and/or RNase protection.
• a structure- function analysis can be performed involving mutagenesis of the putative region and quantification of the mutation's effect on expression of a linked downstream reporter gene. See, e.g., The Maize Handbook, Chapter 114, Freeling and Walbot, Eds., Springer, New York, (1994).
• a region of suitable size is selected from the genomic DNA that is 5' to the transcriptional start, or the translational start site, and such sequences are then linked to a coding sequence. If the transcriptional start site is used as the point of fusion, any of a number of possible 5' untranslated regions can be used in between the transcriptional start site and the partial coding sequence. If the translational start site at the 3' end of the specific promoter is used, then it is linked directly to the methionine start codon of a coding sequence.
• polypeptide expression it is generally desirable to include a polyadenylation region at the 3'-end of a polynucleotide coding region.
• the polyadenylation region can be derived from the natural gene, from a variety of other plant genes, or from T-DNA.
• the 3' end sequence to be added can be derived from, for example, the nopaline synthase or octopine synthase genes, or alternatively from another plant gene, or less preferably from any other eukaryotic gene.
• An intron sequence can be added to the 5' untranslated region or the coding sequence of the partial coding sequence to increase the amount of the mature message that accumulates in the cytosol.
• the vector comprising the sequences from a polynucleotide of the present invention will typically comprise a marker gene which confers a selectable phenotype on plant cells.
• the selectable marker gene will encode antibiotic resistance, with suitable genes including genes coding for resistance to the antibiotic spectinomycin (e.g., the aada gene), the streptomycin phosphotransferase (SPT) gene coding for streptomycin resistance, the neomycin phosphotransferase (NPT1I) gene encoding kanamycin or geneticin resistance, the hygromycin phosphotransferase (HPT) gene coding for hygromycin resistance, genes coding for resistance to herbicides which act to inhibit the action of acetolactate synthase (ALS), in particular the sulfonylurea-type herbicides (e.g., the acetolactate synthase (ALS) gene containing mutations leading to such resistance in particular the S4 and/or H
• the bar gene encodes resistance to the herbicide basta
• the nptll gene encodes resistance to the antibiotics kanamycin and geneticin
• the ALS gene encodes resistance to the herbicide chlorsulfuron.
• Typical vectors useful for expression of genes in higher plants are well known in the art and include vectors derived from the tumor-inducing (Ti) plasmid of Agrobacterium tumefaciens described by Rogers ef al., Meth. In Enzvmol. 153:253-277 (1987). These vectors are plant integrating vectors in that on transformation, the vectors integrate a portion of vector DNA into the genome of the host plant. Exemplary A.
• tumefaciens vectors useful herein are plasmids pKYLX6 and pKYLX7 of Schardl ef al., Gene 61:1-11 (1987) and Berger et al., Proc. Natl. Acad. Sci. U.S.A. 86:8402-8406 (1989).
• Another useful vector herein is plasmid pBI101.2 that is available from Clontech Laboratories, Inc. (Palo Alto, CA).
• a polynucleotide of the present invention can be expressed in either sense or anti-sense orientation as desired. It will be appreciated that control of gene expression in either sense or anti-sense orientation can have a direct impact on the observable plant characteristics.
• Antisense technology can be conveniently used to modify gene expression in plants. To accomplish this, a nucleic acid segment from the desired gene is cloned and operably linked to a promoter such that the anti-sense strand of RNA will be transcribed. The construct is then transformed into plants and the antisense strand of RNA is produced.
• antisense RNA inhibits gene expression by preventing the accumulation of mRNA which encodes the enzyme of interest, see, e.g., Sheehy ef al., Proc. Nat'l. Acad. Sci. USA 85:8805-8809 (1988); and Hiatt ef al., U.S. Patent No. 4,801-340.
• Another method of suppression is sense suppression.
• Introduction of nucleic acid configured in the sense orientation has been shown to be an effective means by which to block the transcription of target genes.
• this method to modulate expression of endogenous genes see, Napoli ef al.. The Plant Cell 2:279-289 (1990) and U.S. Patent No. 5,034,323.
• Catalytic RNA molecules or ribozymes can also be used to inhibit expression of plant genes. It is possible to design ribozymes that specifically pair with virtually any target RNA and cleave the phosphodiester backbone at a specific location, thereby functionally inactivating the target RNA.
• the ribozyme In carrying out this cleavage, the ribozyme is not itself altered, and is thus capable of recycling and cleaving other molecules, making it a true enzyme.
• the inclusion of ribozyme sequences within antisense RNAs confers RNA-cleaving activity upon them, thereby increasing the activity of the constructs.
• the design and use of target RNA-specific ribozymes is described in Haseloff ef al., Nature 334:585-591 (1988).
• a variety of cross-linking agents, alkylating agents and radical generating species as pendant groups on polynucleotides of the present invention can be used to bind, label, detect, and/or cleave nucleic acids. For example, Vlassov, V.
• N4, N4-ethanocytosine as an alkylating agent to crosslink to single-stranded oligonucleotides has also been described by Webb and Matteucci, J. Am. Chem. Soc. (1986) 108:2764-2765; Nucleic Acids Res. (1986) 14:7661-7674; Feteritz ef al., J. Am. Chem. Soc. 113:4000 (1991).
• Various compounds to bind, detect, label, and/or cleave nucleic acids are known in the art. See, for example, U.S. Patent Nos. 5,543,507; 5,672,593; 5,484,908; 5,256,648; and, 5,681941.
• the isolated proteins of the present invention comprise a polypeptide having at least 10 amino acids encoded by any one of the polynucleotides of the present invention as discussed more fully, supra, or polypeptides which are conservatively modified variants thereof.
• Exemplary polypeptide sequences are provided in SEQ ID NOS: 2 and 4.
• the proteins of the present invention or variants thereof can comprise any number of contiguous amino acid residues from a polypeptide of the present invention, wherein that number is selected from the group of integers consisting of from 10 to the number of residues in a full-length cell cycle polypeptide.
• this subsequence of contiguous amino acids is at least 15, 20, 25, 30, 35, or 40 amino acids in length, often at least 50, 60, 70, 80, or 90 amino acids in length.
• the number of such subsequences can be any integer selected from the group consisting of from 1 to 20, such as 2, 3, 4, or 5.
• the present invention includes catalytically active polypeptides of the present invention (i.e., enzymes).
• Catalytically active polypeptides have a specific activity at least 20%, 30%, or 40%, and preferably at least 50%, 60%, or 70%, and most preferably at least 80%, 90%, or 95% that of the native (non-synthetic), endogenous polypeptide.
• the substrate specificity is optionally substantially similar to the native (non-synthetic), endogenous polypeptide.
• the Km will be at least 30%, 40%, or 50%, that of the native (non-synthetic), endogenous polypeptide; and more preferably at least 60%, 70%, 80%, or 90%.
• the proteins of the present invention will, when presented as an immunogen, elicit production of an antibody specifically reactive to a polypeptide of the present invention encoded by a polynucleotide of the present invention as described, supra.
• Exemplary polypeptides include those which are full-length, such as those disclosed in SEQ ID NOS: 2 and 4.
• the proteins of the present invention will not bind to antisera raised against a polypeptide of the present invention which has been fully immunosorbed with the same polypeptide.
• Immunoassays for determining binding are well known to those of skill in the art.
• a preferred immunoassay is a competitive immunoassay as discussed, infra.
• the proteins of the present invention can be employed as immunogens for constructing antibodies immunoreactive to a protein of the present invention for such exemplary utilities as immunoassays or protein purification techniques.
• a protein of the present invention in a recombinantly engineered cell such as bacteria, yeast, insect, mammalian, or preferably plant cells.
• the cells produce the protein in a non-natural condition (e.g., in quantity, composition, location, and/or time), because they have been genetically altered through human intervention to do so.
• a non-functional fusion protein may be desirable.
• enzymatic cleavage could be used to restore function to the purified Cks protein.
• fusions with Cks can have application for affinity matrices and affinity columns used for purifying other cell cycle genes.
• His- patch thioredoxin fusions can be expressed, and the isolate His-Cks fusion protein bound to metal chelate columns. Whole cell protein extracts can then be passed through the column to selectively trap proteins that interact with Cks. See Ausubel ef al., 1990 for general methods. Similarly, glutathione-S transferase fusions can be used to attach proteins to solid-phase matrices for this type of affinity binding. This method has been used, for example, to identify cell cycle genes whose proteins bind to GST-Rb in L. Magnaghi-Jaulin ef al., Retinoblastoma protein represses transcription by recruiting a histone deacetylase. Nature 391:601-604 (1998). It may also be advantageous to fuse additional functional genes to the Cks gene. For example it would be useful to fuse a green fluorescent gene or some other reporter gene.
• the expression of isolated nucleic acids encoding a protein of the present invention will typically be achieved by operably linking, for example, the DNA or cDNA to a promoter (which is either constitutive or inducible), followed by incorporation into an expression vector.
• the vectors can be suitable for replication and integration in either prokaryotes or eukaryotes.
• Typical expression vectors contain transcription and translation terminators, initiation sequences, and promoters useful for regulation of the expression of the DNA encoding a protein of the present invention.
• expression vectors which contain, at the minimum, a strong promoter to direct transcription, a ribosome binding site for translational initiation, and a transcription/translation terminator.
• a strong promoter to direct transcription
• a ribosome binding site for translational initiation to promote a transcription/translation terminator.
• modifications can be made to a protein of the present invention without diminishing its biological activity. Some modifications may be made to facilitate the cloning, expression, or incorporation of the targeting molecule into a fusion protein. Such modifications are well known to those of skill in the art and include, for example, a methionine added at the amino terminus to provide an initiation site, or additional amino acids (e.g., poly His) placed on either terminus to create conveniently located restriction sites or termination codons or purification sequences.
• Prokaryotic cells may be used as hosts for expression. Prokaryotes most frequently are represented by various strains of E. coli; however, other microbial strains may also be used. Commonly used prokaryotic control sequences which are defined herein to include promoters for transcription initiation, optionally with an operator, along with ribosome binding site sequences, include such commonly used promoters as the beta lactamase (penicillinase) and lactose (lac) promoter systems (Chang ef al., Nature 198:1056 (1977)), the tryptophan (trp) promoter system (Goeddel ef al., Nucleic Acids Res.
• selection markers include genes specifying resistance to ampicillin, tetracycline, or chloramphenicol.
• Bacterial vectors are typically of plasmid or phage origin. Appropriate bacterial cells are infected with phage vector particles or transfected with naked phage vector DNA. If a plasmid vector is used, the bacterial cells are transfected with the plasmid vector DNA. Expression systems for expressing a protein of the present invention are available using Bacillus sp. and Salmonella (Palva, ef al., Gene 22:229-235 (1983); Mosbach, ef al., Nature 302:543-545 (1983)).
• eukaryotic expression systems such as yeast, insect cell lines, plant and mammalian cells
• yeast eukaryotic expression systems
• a of the present invention can be expressed in these eukaryotic systems.
• transformed/transfected plant cells as discussed infra, are employed as expression systems for production of the proteins of the instant invention.
• Synthesis of heterologous proteins in yeast is well known. Sherman, F., ef al., Methods in Yeast Genetics, Cold Spring Harbor Laboratory (1982) is a well recognized work describing the various methods available to produce the protein in yeast.
• Suitable vectors usually have expression control sequences, such as promoters, including 3-phosphoglycerate kinase or other glycolytic enzymes, and an origin of replication, termination sequences and the like as desired.
• promoters including 3-phosphoglycerate kinase or other glycolytic enzymes
• origin of replication termination sequences and the like as desired.
• suitable vectors are described in the literature (Botstein, et al., Gene 8:17-24 (1979); Broach, etal., Gene 8:121-133 (1979)).
• a protein of the present invention once expressed, can be isolated from yeast by lysing the cells and applying standard protein isolation techniques to the lysates.
• the monitoring of the purification process can be accomplished by using Western blot techniques or radioimmunoassay of other standard immunoassay techniques.
• sequences encoding proteins of the present invention can also be ligated to various expression vectors for use in transfecting cell cultures of, for instance, mammalian, insect, or plant origin.
• Illustrative of cell cultures useful for the production of the peptides are mammalian cells. Mammalian cell systems often will be in the form of monolayers of cells although mammalian cell suspensions may also be used.
• a number of suitable host cell lines capable of expressing intact proteins have been developed in the art, and include the HEK293, BHK21, and CHO cell lines.
• Expression vectors for these cells can include expression control sequences, such as an origin of replication, a promoter (e.g., the CMV promoter, a HSV tk promoter or pgk (phosphoglycerate kinase) promoter), an enhancer (Queen ef al., Immunol. Rev. 89:49 (1986)), and necessary processing information sites, such as ribosome binding sites, RNA splice sites, polyadenylation sites (e.g., an SV40 large T Ag poly A addition site), and transcriptional terminator sequences.
• a promoter e.g., the CMV promoter, a HSV tk promoter or pgk (phosphoglycerate kinase) promoter
• an enhancer Queen ef al., Immunol. Rev. 89:49 (1986)
• necessary processing information sites such as ribosome binding sites, RNA splice sites, polyadenylation sites (e.g.
• Appropriate vectors for expressing proteins of the present invention in insect cells are usually derived from the SF9 baculovirus.
• suitable insect cell lines include mosquito larvae, silkworm, armyworm, moth and Drosophila cell lines such as a Schneider cell line (See Schneider, J. Embrvol. Exp. Morphol. 27:353-365 (1987)).
• polyadenlyation or transcription terminator sequences are typically incorporated into the vector.
• An example of a terminator sequence is the polyadenlyation sequence from the bovine growth hormone gene. Sequences for accurate splicing of the transcript may also be included.
• An example of a splicing sequence is the VP1 intron from SV40 (Sprague, ef al., J. Virol. 45:773-781 (1983)).
• gene sequences to control replication in the host cell may be incorporated into the vector such as those found in bovine papilloma virus type-vectors.
• Cks interacting proteins i.e. proteins that specifically interact with the Cks gene-encoded products.
• This method typically done using the yeast Saccharomyces cerevisiae, exploits the fact that a functional transcription factor can be separated into two components; a DNA-binding factor and an activation domain, which when held together non- covalently will still bind DNA and activate transcription.
• the test system is constructed as follows: a DNA-binding domain is localized 5' to a reporter gene, for example luciferase, and this cassette is transformed into a yeast strain.
• the nucleic acid sequence for the DNA-binding domain of the transcriptional factor is ligated to the gene (or partial gene sequence) being used as bait. Expression of this DNA-binding domain-bait fusion is driven, for example by the yeast adhl promoter.
• a "library" of gene-fusions is also produced, using the activation domain of the transcriptional factor fused to genes (or gene fragments) from an expression library of interest (referred to as the activation domain hybrid). Expression of the activation domain hybrids is also accomplished, for example, using the yeast adhl promoter.
• plasmids encoding the DNA-binding domain hybrid and a library of activation domain hybrids are introduced (sequentially or simultaneously) into a yeast strain already containing the inactive reporter.
• Transformed yeast in which the activation domain hybrid specifically bind to the DNA-binding domain hybrid will express luciferase. Positives are further characterized by sequence analysis, and further tests of relevance of biological interactions.
• DNA-binding domains include those from lexA protein in E.coli, and the Ga14 protein in yeast.
• activation domains include B42 (bacterial) and Ga14 (yeast). For details, see Hannon G, and Bartel P, Identification of interacting proteins using the two-hybrid system, Methods Mol. Cellular Biol. 5:289-297 (1995).
• transformation/transfection is not critical to the instant invention; various methods of transformation or transfection are currently available. As newer methods are available to transform crops or other host cells they may be directly applied. Accordingly, a wide variety of methods have been developed to insert a DNA sequence into the genome of a host cell to obtain the transcription and/or translation of the sequence to effect phenotypic changes in the organism. Thus, any method which provides for efficient transformation/transfection may be employed.
• a DNA sequence coding for the desired polynucleotide of the present invention for example a cDNA or a genomic sequence encoding a full length protein, will be used to construct a recombinant expression cassette which can be introduced into the desired plant cell.
• the methods chosen vary with the host plant, and include chemical transfection methods such as calcium phosphate, microorganism-mediated gene transfer such as Agrobacterium (Horsch, ef al., Science 227:1229-31, 1985), electroporation, micro-injection, and biolistic bombardment.
• A. tumefaciens and A. rhizogenes are plant pathogenic soil bacteria which genetically transform plant cells.
• the Ti and Ri plasmids of A. tumefaciens and A. rhizogenes respectfully, carry genes responsible for genetic transformation of plants. See, for example, Kado, 1991, Crit. Rev. Plant Sci. 10:1.
• a generally applicable method of plant transformation is microprojectile- mediated transformation, where DNA is carried on the surface of microprojectiles measuring about 1 to 4 Tm.
• the expression vector is introduced into plant tissues with a biolistic device that accelerates the microprojectiles to speeds of 300 to 600 m/s which is sufficient to penetrate the plant cell walls and membranes.
• Another method for physical delivery of DNA to plants is sonication of target cells as described in Zang etal., 1991, Bio/Technology 9:996.
• liposome or spheroplast fusions have been used to introduce expression vectors into plants. See, for example, Deshayes etal., 1985, EMBO J. 4:2731 ; and Christou etal., 1987, PNAS USA 84:3962.
• Direct uptake of DNA into protoplasts using CaCI 2 precipitation, polyvinyl alcohol or poly-L-omithine have also been reported. See, for example, Hain etal., 1985, Mol. Gen. Genet.
• Electroporation of protoplasts and whole cells and tissues has also been described. See, for example, Donn et al., 1990, In: Abstracts of the Vllth Int'l Congress on Plant Cell and ⁇ ssue Culture (IAPTC), A2-38, page 53; D'Halluin ef al., 1992 Plant Cell 4:1495-1505; and Spencer ef al., 1994, Plant Mol. Biol. 24:51- 61.
• Microinjection of DNA into whole plant cells has also been described as has microinjection into protoplasts. See, for example in whole cells, Neuhaus ef al., 1987, Theor. APPI. Genet. 75:30-36; and in protoplasts, Crossway ef al., 1986, Mol. Gen. Genet. 202:179-185; and Reich ef al., 1986, Biotechnology 4:1001- 1004.
• Another useful basic transformation protocol involves a combination of wounding by particle bombardment, followed by use of Agrobacterium for DNA delivery, as described by Bidney, ef al., Plant Mol. Biol. 18:301-313 (1992).
• Useful plasmids for plant transformation include PHP9762.
• the binary backbone for PHP9762 is bin 19. See Bevan, Nucleic Acids Research 12:8711-8721 (1984).
• the intact meristem transformation method involves imbibing seed for 24 hours in the dark, removing the cotyledons and root radical, followed by culturing of the meristem explants. Twenty-four hours later, the primary leaves are removed to expose the apical meristem. The explants are placed apical dome side up and bombarded, e.g., twice with particles, followed by co-cultivation with Agrobacterium. To start the co-cultivation for intact meristems, Agrobacterium is placed on the meristem. After about a 3-day co-cultivation period the meristems are transferred to culture medium with cefotaxime (plus kanamycin for the NPTII selection). Selection can also be done using kanamycin.
• the split meristem method involves imbibing seed, breaking of the cotyledons to produce a clean fracture at the plane of the embryonic axis, excising the root tip and then bisecting the explants longitudinally between the primordial leaves.
• the two halves are placed cut surface up on the medium then bombarded twice with particles, followed by co-cultivation with Agrobacterium.
• the meristems after bombardment, the meristems are placed in an Agrobacterium suspension for 30 minutes. They are then removed from the suspension onto solid culture medium for three day co-cultivation. After this period, the meristems are transferred to fresh medium with cefotaxime (plus kanamycin for selection).
• Isolated nucleic acid acids of the present invention can be introduced into plants according techniques known in the art. Generally, recombinant expression cassettes as described above and suitable for transformation of plant cells are prepared. Techniques for transforming a wide variety of higher plant species are well known and described in the technical, scientific, and patent literature. See, for example, Weising ef al., Ann. Rev. Genet. 22:421-477 (1988).
• the DNA construct may be introduced directly into the genomic DNA of the plant cell using techniques such as electroporation, PEG poration, particle bombardment, silicon fiber delivery, or microinjection of plant cell protoplasts or embryogenic callus.
• the DNA constructs may be combined with suitable T-DNA flanking regions and introduced into a conventional Agrobacterium tumefaciens host vector.
• the virulence functions of the Agrobacterium tumefaciens host will direct the insertion of the construct and adjacent marker into the plant cell DNA when the cell is infected by the bacteria.
• the introduction of DNA constructs using polyethylene glycol precipitation is described in Paszkowski ef al., Embo J. 3:2717-2722 (1984). Electroporation techniques are described in Fromm ef al., Proc. Natl. Acad. Sci. 82:5824 (1985). Ballistic transformation techniques are described in Klein ef al., Nature 327:70-73 (1987).
• Agrobacterium tumefaciens-meditated transformation techniques are well described in the scientific literature. See, for example Horsch ef al., Science 233:496-498 (1984), and Fraley ef al., Proc. Natl. Acad. Sci. 80:4803 (1983). Although Agrobacterium is useful primarily in dicots, certain monocots can be transformed by Agrobacterium. For instance, Agrobacterium transformation of maize is described in U.S. Patent No. 5,550,318.
• tumefaciens vectors pARC8 or pARC16 (2) liposome-mediated DNA uptake (see, e.g., Freeman ef al., Plant Cell Phvsiol. 25:1353, 1984), (3) the vortexing method (see, e.g., Kindle, Proc. Natl. Acad. Sci. USA 87:1228, (1990)).
• DNA can also be introduced into plants by direct DNA transfer into pollen as described by Zhou ef al., Methods in Enzymology 101:433 (1983); D. Hess, Intern Rev. Cvto 107:367 (1987); Luo ef al., Plane Mol. Biol. Reporter 6:165 (1988).
• polypeptide coding genes can be obtained by injection of the DNA into reproductive organs of a plant as described by Pena ef al., Nature. 325:274 (1987). DNA can also be injected directly into the cells of immature embryos and the rehydration of desiccated embryos as described by Neuhaus et al., Theor. APPI. Genet.. 75:30 (1987); and Benbrook ef al., in Proceedings Bio Expo 1986, Butterworth, Stoneham, Mass., pp. 27-54 (1986).
• plant viruses that can be employed as vectors are known in the art and include cauliflower mosaic virus (CaMV), geminivirus, brome mosaic virus, and tobacco mosaic virus.
• Animal and lower eukaryotic (e.g., yeast) host cells are competent or rendered competent for transfection by various means.
• eukaryotic (e.g., yeast) host cells are competent or rendered competent for transfection by various means.
• methods of introducing DNA into animal cells include: calcium phosphate precipitation, fusion of the recipient cells with bacterial protoplasts containing the DNA, treatment of the recipient cells with liposomes containing the DNA, DEAE dextran, electroporation, biolistics, and micro-injection of the DNA directly into the cells.
• the transfected cells are cultured by means well known in the art. Kuchler, R.J., Biochemical Methods in Cell Culture and Virology, Dowden, Hutchinson and Ross, Inc. (1977).
• the proteins of the present invention can be constructed using non-cellular synthetic methods. Solid phase synthesis of proteins of less than about 50 amino acids in length may be accomplished by attaching the C-terminal amino acid of the sequence to an insoluble support followed by sequential addition of the remaining amino acids in the sequence. Techniques for solid phase synthesis are described by Barany and Merrifield, Solid-Phase Peptide Synthesis, pp. 3-284 in The Peptides: Analysis, Synthesis, Biology. Vol. 2: Special Methods in Peptide Synthesis, Part A.; Merrifield, et al., J. Am. Chem. Soc. 85:2149-2156 (1963), and Stewart et al., Solid Phase Peptide Synthesis, 2nd ed., Pierce Chem. Co., Rockford, III.
• Proteins of greater length may be synthesized by condensation of the amino and carboxy termini of shorter fragments. Methods of forming peptide bonds by activation of a carboxy terminal end (e.g., by the use of the coupling reagent N.N'-dicycylohexylcarbodiimide) is known to those of skill.
• the proteins of the present invention may be purified by standard techniques well known to those of skill in the art. Recombinantly produced proteins of the present invention can be directly expressed or expressed as a fusion protein.
• the recombinant protein is purified by a combination of cell lysis (e.g., sonication, French press) and affinity chromatography. For fusion products, subsequent digestion of the fusion protein with an appropriate proteolytic enzyme releases the desired recombinant protein.
• the proteins of this invention may be purified to substantial purity by standard techniques well known in the art, including selective precipitation with such substances as ammonium sulfate, column chromatography, immunopurification methods, and others. See, for instance, R. Scopes, Protein Purification: Principles and Practice, Springer-Verlag: New York (1982); Deutscher, Guide to Protein Purification, Academic Press (1990). For example, antibodies may be raised to the proteins as described herein. Purification from E. coli can be achieved following procedures described in U.S. Patent No. 4,511 ,503. The protein may then be isolated from cells expressing the protein and further purified by standard protein chemistry techniques as described herein. Detection of the expressed protein is achieved by methods known in the art and include, for example, radioimmunoassays, Western blotting techniques or immunoprecipitation.
• Transformed plant cells which are derived by any of the above transformation techniques can be cultured to regenerate a whole plant which possesses the transformed genotype.
• Such regeneration techniques often rely on manipulation of certain phytohormones in a tissue culture growth medium, typically relying on a biocide and/or herbicide marker which has been introduced together with a polynucleotide of the present invention.
• Plants cells transformed with a plant expression vector can be regenerated, e.g., from single cells, callus tissue or leaf discs according to standard plant tissue culture techniques. It is well known in the art that various cells, tissues, and organs from almost any plant can be successfully cultured to regenerate an entire plant. Plant regeneration from cultured protoplasts is described in Evans ef al., Protoplasts Isolation and Culture, Handbook of Plant Cell Culture, Macmillilan Publishing Company, New York, pp. 124-176 (1983); and Binding, Regeneration of Plants, Plant Protoplasts, CRC Press, Boca Raton, pp. 21-73 (1985).
• Transformed plant cells, calli or explant can be cultured on regeneration medium in the dark for several weeks, generally about 1 to 3 weeks to allow the somatic embryos to mature.
• Preferred regeneration media include media containing MS salts, such as PHI-E and PHI-F media.
• the plant cells, calli or explant are then typically cultured on rooting medium in a light/dark cycle until shoots and roots develop.
• Methods for plant regeneration are known in the art and preferred methods are provided by Kamo ef al., (Bot. Gaz. 146(3): 324-334, 1985), West ef al. , (The Plant Cell 5: 1361 -1369, 1993), and Duncan ef al. (Planta 165:322-332, 1985).
• Small piantlets can then be transferred to tubes containing rooting medium and allowed to grow and develop more roots for approximately another week.
• the plants can then be transplanted to soil mixture in pots in the greenhouse.
• Agrobacterium from leaf explants can be achieved as described by Horsch ef al., Science. 227:1229-1231 (1985). In this procedure, transformants are grown in the presence of a selection agent and in a medium that induces the regeneration of shoots in the plant species being transformed as described by Fraley ef al., Proc. Natl. Acad. Sci. U.S.A. 80:4803 (1983). This procedure typically produces shoots within two to four weeks and these transformant shoots are then transferred to an appropriate root-inducing medium containing the selective agent and an antibiotic to prevent bacterial growth. Transgenic plants of the present invention may be fertile or sterile. Regeneration can also be obtained from plant callus, explants, organs, or parts thereof.
• the recombinant expression cassette is stably incorporated in transgenic plants and confirmed to be operable, it can be introduced into other plants by sexual crossing. Any of a number of standard breeding techniques can be used, depending upon the species to be crossed.
• mature transgenic plants can be propagated by the taking of cuttings or by tissue culture techniques to produce multiple identical plants. Selection of desirable transgenics is made and new varieties are obtained and propagated vegetatively for commercial use.
• mature transgenic plants can be self crossed to produce a homozygous inbred plant. The inbred plant produces seed containing the newly introduced heterologous nucleic acid. These seeds can be grown to produce plants that would produce the selected phenotype, (e.g., altered cell cycle content or composition).
• Parts obtained from the regenerated plant such as flowers, seeds, leaves, branches, fruit, and the like are included in the invention, provided that these parts comprise cells comprising the isolated nucleic acid of the present invention. Progeny and variants, and mutants of the regenerated plants are also included within the scope of the invention, provided that these parts comprise the introduced nucleic acid sequences.
• Transgenic plants expressing the selectable marker can be screened for transmission of the nucleic acid of the present invention by, for example, standard immunoblot and DNA detection techniques. Transgenic lines are also typically evaluated on levels of expression of the heterologous nucleic acid. Expression at the RNA level can be determined initially to identify and quantitate expression- positive plants. Standard techniques for RNA analysis can be employed and include PCR amplification assays using oligonucleotide primers designed to amplify only the heterologous RNA templates and solution hybridization assays using heterologous nucleic acid-specific probes. The RNA-positive plants can then analyzed for protein expression by Western immunoblot analysis using the specifically reactive antibodies of the present invention.
• in situ hybridization and immunocytochemistry can be done using heterologous nucleic acid specific polynucleotide probes and antibodies, respectively, to localize sites of expression within transgenic tissue.
• a number of transgenic lines are usually screened for the incorporated nucleic acid to identify and select plants with the most appropriate expression profiles.
• a preferred embodiment is a transgenic plant that is homozygous for the added heterologous nucleic acid; i.e., a transgenic plant that contains two added nucleic acid sequences, one gene at the same locus on each chromosome of a chromosome pair.
• a homozygous transgenic plant can be obtained by sexually mating (selfing) a heterozygous transgenic plant that contains a single added heterologous nucleic acid, germinating some of the seed produced and analyzing the resulting plants produced for altered cell division relative to a control plant (i.e., native, non-transgenic). Back-crossing to a parental plant and out-crossing with a non- transgenic plant are also contemplated.
• a novel and useful method developed by the inventors of transiently modulating the level of protein in plant cells is provided.
• the method can be used to enhance transformation and other processes by delivering pre-selected proteins without the potential negative effects that might result from stable expression.
• An overview of this procedure is provided here. Details of how the procedure may be used with cell-cycle proteins are provided by way of Example 7.
• the methods described represent means of using the Cks gene or its encoded product to transiently stimulate DNA replication and cell division, which in turn enhances transgene integration by providing an improved cellular/molecular environment for this event to occur.
• VirE2 is the most preferred product for use as a delivery protein fusion vector. First, it is produced in high abundance. Second, it can be transmitted separately from the T-strand to plant cells. VirD2, in contrast, is covalently associated with the T-strand. Third, VirE2 has been studied intensively and functional domains are known. Relatively little information is available for VirF. Proteins delivered from Agrobacterium plasmids into plant cells are in the form of fusions with the Agrobacterium virulence proteins. Fusions are constructed between a selected gene and genes for bacterial virulence proteins such as VirE2, VirD2, or VirF which are located outside the T-DNA borders.
• the method can be used to test the efficacy of visible selectable markers such as GFP (Haseloff, J. ef al, Trends in Genetics 11(8):328-329 (1995), GUS (beta-gluconronidase), and Luciferase, (Visser, A.J ef al., Biochemistry 24(6): 1489-1496 (1985). Or the visible markers could be used in the system to test changes in protocols that would enhance transfer of molecules to various plant cells, or cells or tissues of recalcitrant species.
• FLP/RFT US Ser No. 08,972,258
• Cre/loxP Abremski- et al, Jour. Mol. Bio. 184(2):211-220, 1985
• sequence excision could be used to remove one transgene while activating a second.
• Recombinase-mediated integration, gene replacement and genomic exchanges could also be mediated through introduction of such functional fusion proteins.
• the method can also be practiced with other strains of bacteria known to deliver protein into cells. Examples are: Rhizobium sp., Phyllobacterium sp., or any other bacterium of the Rhizobiaceae taxa that transfer proteins to recipient cells.
• the method could be extended to employ multiple delivery protein fusions on the same, or coresident, binaries. This would conceivably allow the transient activity of "protein cocktails” mediating complex functions or pathways related to transformation objectives.
• the Agrobacterium strategy is potentially simpler than methods to achieve transient-only expression using current direct delivery methods such as microinjection, bombardment, electroporation or silica fiber methods.
• the present invention further provides a method for modulating (i.e., increasing or decreasing) cell cycle protein content or composition in a plant or part thereof. Modulation can be effected by increasing or decreasing the cell cycle protein content (i.e., the total amount of cell cycle protein) and/or the cell cycle protein composition (the ratio of various cell cycle monomers in the plant) in a plant.
• the method comprises transforming a plant cell, transiently or stably, with a recombinant expression cassette comprising a polynucleotide of the present invention as described above to obtain a transformed plant cell.
• the method comprises growing the transformed plant cell under plant forming conditions, and expressing the polynucleotide of the present invention in the plant for a time sufficient to modulate cell cycle protein content and/or composition in the plant or plant part.
• plant cell division may be modulated by altering, in vivo or in vitro, the promoter of a non-isolated cell cycle gene to up- or down- regulate gene expression.
• the coding regions of native cell cycle genes can be altered via substitution, addition, insertion, or deletion to decrease activity of the encoded enzyme. See, e.g., Kmiec, U.S. Patent 5,565,350, Zarling ef al., PCT/US93/03868.
• an isolated nucleic acid e.g., a vector
• a promoter sequence is transfected into a plant cell.
• a plant cell comprising the promoter operably linked to a polynucleotide of the present invention is selected for by means known to those of skill in the art such as, but not limited to, Southern blot, DNA sequencing, or PCR analysis using primers specific to the promoter and to the gene and detecting amplicons produced therefrom.
• a plant or plant part altered or modified by the foregoing embodiments is grown under plant forming conditions for a time sufficient to modulate cell cycle protein content and/or composition in the plant. Plant forming conditions are well known in the art and discussed briefly, supra.
• content or composition is increased or decreased by at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% relative to a native control plant, plant part, or cell lacking the aforementioned recombinant expression cassette.
• Modulation in the present invention may occur during and/or subsequent to growth of the plant to the desired stage of development.
• Modulating nucleic acid expression temporally and/or in particular tissues can be controlled by employing the appropriate promoter operably linked to a polynucleotide of the present invention in, for example, sense or antisense orientation as discussed in greater detail, supra.
• Induction of expression of a polynucleotide of the present invention can also be controlled by exogenous administration of an effective amount of inducing compound. Inducible promoters and inducing compounds which activate expression from these promoters are well known in the art.
• cell division is modulated in monocots, particularly maize.
• the present invention provides a method of genotyping a plant comprising a polynucleotide of the present invention.
• Genotyping provides a means of distinguishing homologs of a chromosome pair and can be used to differentiate segregants in a plant population.
• Molecular marker methods can be used for phylogenetic studies, characterizing genetic relationships among crop varieties, identifying crosses or somatic hybrids, localizing chromosomal segments affecting monogenic traits, map based cloning, and the study of quantitative inheritance. See, e.g., Plant Molecular Biology: A Laboratory Manual, Chapter 7, Clark, Ed., Springer-Verlag, Berlin (1997).
• For molecular marker methods see generally, The DNA Revolution by Andrew H. Paterson 1996 (Chapter 2) in: Genome Mapping in Plants (ed. Andrew H. Paterson) by Academic Press/R. G. Landis Company, Austin, Texas, pp.7-21.
• RFLPs restriction fragment length polymo ⁇ hisms
• RFLPs are the product of allelic differences between DNA restriction fragments caused by nucleotide sequence variability.
• RFLPs are typically detected by extraction of genomic DNA and digestion with a restriction enzyme. Generally, the resulting fragments are separated according to size and hybridized with a probe; single copy probes are preferred. Restriction fragments from homologous chromosomes are revealed. Differences in fragment size among alleles represent an RFLP.
• the present invention further provides a means to follow segregation of a cell cycle gene or nucleic acid of the present invention as well as chromosomal sequences genetically linked to these genes or nucleic acids using such techniques as RFLP analysis.
• Linked chromosomal sequences are within 50 centiMorgans (cM), often within 40 or 30 cM, preferably within 20 or 10 cM, more preferably within 5, 3, 2, or 1 cM of a cell cycle gene.
• the nucleic acid probes employed for molecular marker mapping of plant nuclear genomes selectively hybridize, under selective hybridization conditions, to a gene encoding a polynucleotide of the present invention.
• the probes are selected from polynucleotides of the present invention.
• these probes are cDNA probes or Pst I genomic clones.
• the length of the probes is discussed in greater detail, supra, but are typically at least 15 bases in length, more preferably at least 20, 25, 30, 35, 40, or 50 bases in length. Generally, however, the probes are less than about 1 kilobase in length.
• the probes are single copy probes that hybridize to a unique locus in a haploid chromosome complement.
• Some exemplary restriction enzymes employed in RFLP mapping are EcoRI, EcoRv, and Sstl.
• restriction enzyme includes reference to a composition that recognizes and, alone or in conjunction with another composition, cleaves at a specific nucleotide sequence.
• the method of detecting an RFLP comprises the steps of (a) digesting genomic DNA of a plant with a restriction enzyme; (b) hybridizing a nucleic acid probe, under selective hybridization conditions, to a sequence of a polynucleotide of the present of said genomic DNA; (c) detecting therefrom a RFLP.
• polymo ⁇ hic (allelic) variants of polynucleotides of the present invention can be had by utilizing molecular marker techniques well known to those of skill in the art including such techniques as: 1) single stranded conformation analysis (SSCP); 2) denaturing gradient gel electrophoresis (DGGE); 3) RNase protection assays; 4) allele-specific oligonucleotides (ASOs); 5) the use of proteins which recognize nucleotide mismatches, such as the E. coli mutS protein; and 6) allele-specific PCR.
• SSCP single stranded conformation analysis
• DGGE denaturing gradient gel electrophoresis
• RNase protection assays 4) allele-specific oligonucleotides (ASOs); 5) the use of proteins which recognize nucleotide mismatches, such as the E. coli mutS protein; and 6) allele-specific PCR.
• ASOs allele-specific oligonucle
• the present invention further provides a method of genotyping comprising the steps of contacting, under stringent hybridization conditions, a sample suspected of comprising a polynucleotide of the present invention with a nucleic acid probe.
• a sample suspected of comprising a polynucleotide of the present invention with a nucleic acid probe.
• the sample is a plant sample; preferably, a sample suspected of comprising a maize polynucleotide of the present invention (e.g., gene, mRNA).
• the nucleic acid probe selectively hybridizes, under stringent conditions, to a subsequence of a polynucleotide of the present invention comprising a polymo ⁇ hic marker. Selective hybridization of the nucleic acid probe to the polymo ⁇ hic marker nucleic acid sequence yields a hybridization complex. Detection of the hybridization complex indicates the presence of that polymo ⁇ hic marker in the sample.
• the nucleic acid probe comprises a polynucleotide of the present invention.
• Positive sequence motifs include translational initiation consensus sequences (Kozak, Nucleic Acids Res.15:8125 (1987)) and the 5 ⁇ G> 7 methyl GpppG cap structure (Drummond ef al., Nucleic Acids Res. 13:7375 (1985)).
• Negative elements include stable intramolecular 5' UTR stem-loop structures (Muesing ef al., Cell 48:691 (1987)) and AUG sequences or short open reading frames preceded by an appropriate AUG in the 5' UTR (Kozak, supra, Rao ef al., Mol.
• the present invention provides 5' and/or 3' UTR regions for modulation of translation of heterologous coding sequences.
• the polypeptide-encoding segments of the polynucleotides of the present invention can be modified to alter codon usage. Altered codon usage can be employed to alter translational efficiency and/or to optimize the coding sequence for expression in a desired host or to optimize the codon usage in a heterologous sequence for expression in maize.
• Codon usage in the coding regions of the polynucleotides of the present invention can be analyzed statistically using commercially available software packages such as "Codon Preference” available from the University of Wisconsin Genetics Computer Group (see Devereaux ef al., Nucleic Acids Res. 12:387-395 (1984)) or MacVector 4.1 (Eastman Kodak Co., New Haven, Conn.).
• the present invention provides a codon usage frequency characteristic of the coding region of at least one of the polynucleotides of the present invention.
• the number of polynucleotides that can be used to determine a codon usage frequency can be any integer from 1 to the number of polynucleotides of the present invention as provided herein.
• the polynucleotides will be full-length sequences.
• An exemplary number of sequences for statistical analysis can be at least 1, 5, 10, 20, 50, or 100.
• sequence shuffling provides methods for sequence shuffling using polynucleotides of the present invention, and compositions resulting therefrom. Sequence shuffling is described in PCT publication No. 96/19256. See also, Zhang, J. H., ef al. Proc. Natl. Acad. Sci. USA 94:4504-4509 (1997). Generally, sequence shuffling provides a means for generating libraries of polynucleotides having a desired characteristic which can be selected or screened for. Libraries of recombinant polynucleotides are generated from a population of related sequence polynucleotides which comprise sequence regions which have substantial sequence identity and can be homologously recombined in vitro or in vivo.
• the population of sequence-recombined polynucleotides comprises a subpopulation of polynucleotides which possess desired or advantageous characteristics and which can be selected by a suitable selection or screening method.
• the characteristics can be any property or attribute capable of being selected for or detected in a screening system, and may include properties of: an encoded protein, a transcriptional element, a sequence controlling transcription, RNA processing, RNA stability, chromatin conformation, translation, or other expression property of a gene or transgene, a replicative element, a protein- binding element, or the like, such as any feature which confers a selectable or detectable property.
• the selected characteristic will be an increased Km and/or K «rt over the wild-type protein as provided herein.
• a protein or polynculeotide generated from sequence shuffling will have a ligand binding affinity greater than the non-shuffled wild-type polynucleotide.
• the increase in such properties can be at least 110%, 120%, 130%, 140% or at least 150% of the wild-type value.
• the present invention further provides methods for detecting a polynucleotide of the present invention in a nucleic acid sample suspected of comprising a polynucleotide of the present invention, such as a plant cell lysate, particularly a lysate of corn.
• a cell cycle gene or portion thereof can be amplified prior to the step of contacting the nucleic acid sample with a polynucleotide of the present invention.
• the nucleic acid sample is contacted with the polynucleotide to form a hybridization complex.
• the polynucleotide hybridizes under stringent conditions to a gene encoding a polypeptide of the present invention.
• Formation of the hybridization complex is used to detect a gene encoding a polypeptide of the present invention in the nucleic acid sample.
• a gene encoding a polypeptide of the present invention in the nucleic acid sample.
• an isolated nucleic acid comprising a polynucleotide of the present invention should lack cross-hybridizing sequences in common with non-cell cycle genes that would yield a false positive result.
• the nucleic acid sample, or a portion thereof may be assayed by hybridization formats including but not limited to, solution phase, solid phase, mixed phase, or in situ hybridization assays.
• solution phase hybridizations both the target nucleic acid and the probe or primer are free to interact in the reaction mixture.
• solid phase hybridization assays probes or primers are typically linked to a solid support where they are available for hybridization with target nucleic in solution.
• nucleic acid intermediates in solution hybridize to target nucleic acids in solution as well as to a nucleic acid linked to a solid support.
• in situ hybridization the target nucleic acid is liberated from its cellular surroundings in such as to be available for hybridization within the cell while preserving the cellular morphology for subsequent interpretation and analysis.
• the following articles provide an overview of the various hybridization assay formats: Singer ef al., Biotechnigues 4(3):230-250 (1986); Haase ef al., Methods in Virology, Vol. VII, pp. 189-226 (1984); Wilkinson, The theory and practice of in situ hybridization in: In situ Hybridization, D.G. Wilkinson, Ed., IRL Press, Oxford University Press, Oxford; and Nucleic Acid Hybridization: A Practical Approach, Hames, B.D. and Higgins, S.J., Eds., IRL Press (1987). Nucleic Acid Labels and Detection Methods
• nucleic acids of the present invention are labeled is not a critical aspect of the present invention and can be accomplished by any number of methods currently known or later developed.
• Detectable labels suitable for use in the present invention include any composition detectable by spectroscopic, radioisotopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means.
• Useful labels in the present invention include biotin for staining with labeled streptavidin conjugate, magnetic beads, fluorescent dyes (e.g., fluorescein, Texas red, rhodamine, green fluorescent protein, and the like), radiolabels (e.g., 3 H, 125 l, ⁇ S, 14 C, or 32 P), enzymes (e.g., horse radish peroxidase, alkaline phosphatase and others commonly used in an ELISA), and colorimetric labels such as colloidal gold or colored glass or plastic (e.g., polystyrene, polypropylene, latex, etc.) beads.
• fluorescent dyes e.g., fluorescein, Texas red, rhodamine, green fluorescent protein, and the like
• radiolabels e.g., 3 H, 125 l, ⁇ S, 14 C, or 32 P
• enzymes e.g., horse radish peroxidase, alkaline
• Nucleic acids of the present invention can be labeled by any one of several methods typically used to detect the presence of hybridized nucleic acids.
• One common method of detection is the use of autoradiography using probes labeled with 3 H, 125 l, ⁇ S, 14 C, or 32 P, or the like.
• the choice of radio-active isotope depends on research preferences due to ease of synthesis, stability, and half lives of the selected isotopes.
• Other labels include ligands which bind to antibodies labeled with fluorophores, chemiluminescent agents, and enzymes.
• probes can be conjugated directly with labels such as fluorophores, chemiluminescent agents or enzymes. The choice of label depends on sensitivity required, ease of conjugation with the probe, stability requirements, and available instrumentation. Labeling the nucleic acids of the present invention is readily achieved such as by the use of labeled PCR primers.
• the label is simultaneously incorporated during the amplification step in the preparation of the nucleic acids.
• PCR polymerase chain reaction
• labeled primers or labeled nucleotides will provide a labeled amplification product.
• transcription amplification using a labeled nucleotide inco ⁇ orates a label into the transcribed nucleic acids.
• Non-radioactive probes are often labeled by indirect means.
• a ligand molecule is covalently bound to the probe.
• the ligand then binds to an anti-ligand molecule which is either inherently detectable or covalently bound to a detectable signal system, such as an enzyme, a fluorophore, or a chemiluminescent compound.
• Enzymes of interest as labels will primarily be hydrolases, such as phosphatases, esterases and glycosidases, or oxidoreductases, particularly peroxidases.
• Fluorescent compounds include fluorescein and its derivatives, rhodamine and its derivatives, dansyl, umbelliferone, etc.
• Chemiluminescers include luciferin, and 2,3-dihydrophthalazinediones, e.g., luminol.
• Ligands and anti-iigands may be varied widely. Where a ligand has a natural anti-ligand, namely ligands such as biotin, thyroxine, and cortisol, it can be used in conjunction with its labeled, naturally occurring anti-ligands. Alternatively, any haptenic or antigenic compound can be used in combination with an antibody.
• Probes can also be labeled by direct conjugation with a label.
• cloned DNA probes have been coupled directly to horseradish peroxidase or alkaline phosphatase, (Renz. M., and Kurz, K., A Colorimetric Method for DNA Hybridization, Nucl. Acids Res. 12:3435-3444 (1984)) and synthetic oligonucleotides have been coupled directly with alkaline phosphatase (Jablonski, E., ef al., Preparation of Oligodeoxynucleotide-Alkaline Phosphatase Conjugates and Their Use as Hybridization Probes, Nuc. Acids. Res.
• radiolabels may be detected using photographic film or scintillation counters
• fluorescent markers may be detected using a photodetector to detect emitted light
• Enzymatic labels are typically detected by providing the enzyme with a substrate and detecting the reaction product produced by the action of the enzyme on the substrate, and colorimetric labels are detected by simply visualizing the colored label.
• Antibodies can be raised to a protein of the present invention, including individual, allelic, strain, or species variants, and fragments thereof, both in their naturally occurring (full-length) forms and in recombinant forms. Additionally, antibodies are raised to these proteins in either their native configurations or in non-native configurations. Anti-idiotypic antibodies can also be generated. Many methods of making antibodies are known to persons of skill. The following discussion is presented as a general overview of the techniques available; however, one of skill will recognize that many variations upon the following methods are known.
• a number of immunogens are used to produce antibodies specifically reactive with a protein of the present invention.
• the proteins of the present invention are typically denatured, and optionally reduced, prior to formation of antibodies for screening expression libraries or other assays in which a putative protein of the present invention is expressed or denatured in a non-native secondary, tertiary, or quaternary structure.
• Naturally occurring cell cycle polypeptides can be used either in pure or impure form.
• the protein of the present invention is then injected into an animal capable of producing antibodies.
• Either monoclonal or polyclonal antibodies can be generated for subsequent use in immunoassays to measure the presence and quantity of the protein of the present invention.
• Methods of producing polyclonal antibodies are known to those of skill in the art.
• an immunogen preferably a purified protein, a protein coupled to an appropriate carrier (e.g., GST, keyhole limpet hemanocyanin, etc.), or a protein incorporated into an immunization vector such as a recombinant vaccinia virus (see, U.S. Patent No.
• 4,722,848 is mixed with an adjuvant and animals are immunized with the mixture.
• the animal's immune response to the immunogen preparation is monitored by taking test bleeds and determining the titer of reactivity to the protein of interest.
• blood is collected from the animal and antisera are prepared. Further fractionation of the antisera to enrich for antibodies reactive to the protein is performed where desired (See, e.g., Coligan, Current Protocols in Immunology, Wiley/Greene, NY (1991); and Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Press, NY (1989)).
• Antibodies, including binding fragments and single chain recombinant versions thereof, against predetermined fragments of a protein of the present invention are raised by immunizing animals, e.g., with conjugates of the fragments with carrier proteins as described above.
• the immunogen of interest is a protein of at least about 5 amino acids, more typically the protein is 10 amino acids in length, preferably, 15 amino acids in length and more preferably the protein is 20 amino acids in length or greater.
• the peptides are typically coupled to a carrier protein (e.g., as a fusion protein), or are recombinantly expressed in an immunization vector.
• Antigenic determinants on peptides to which antibodies bind are typically 3 to 10 amino acids in length.
• Monoclonal antibodies are prepared from cells secreting the desired antibody. Monoclonals antibodies are screened for binding to a protein from which the immunogen was derived. Specific monoclonal and polyclonal antibodies will usually have an antibody binding site with an affinity constant for its cognate monovalent antigen at least between 10 6 -10 7 , usually at least 10 8 , preferably at least 10 9 , more preferably at least 10 10 , and most preferably at least 10 11 liters/mole.
• monoclonal antibodies from various mammalian hosts, such as mice, rodents, primates, humans, etc.
• Description of techniques for preparing such monoclonal antibodies are found in, e.g., Basic and Clinical Immunology, 4th ed., Stites ef al., Eds., Lange Medical Publications, Los Altos, CA, and references cited therein; Harlow and Lane, Supra; Goding, Monoclonal Antibodies: Principles and Practice, 2nd ed., Academic Press, New York, NY (1986); and Kohler and Milstein, Nature 256:495- 497 (1975). Summarized briefly, this method proceeds by injecting an animal with an immunogen comprising a protein of the present invention.
• the animal is then sacrificed and cells taken from its spleen, which are fused with myeloma cells.
• the result is a hybrid cell or "hybridoma" that is capable of reproducing in vitro.
• the population of hybridomas is then screened to isolate individual clones, each of which secrete a single antibody species to the immunogen. In this manner, the individual antibody species obtained are the products of immortalized and cloned single B cells from the immune animal generated in response to a specific site recognized on the immunogenic substance.
• high avidity human monoclonal antibodies can be obtained from transgenic mice comprising fragments of the unrearranged human heavy and light chain Ig loci (i.e., minilocus transgenic mice). Fishwild ef al., Nature Biotech., 14:845-851 (1996). Also, recombinant immunoglobulins may be produced. See, Cabilly, U.S. Patent No.
• the antibodies of this invention are also used for affinity chromatography in isolating proteins of the present invention.
• Columns are prepared, e.g., with the antibodies linked to a solid support, e.g., particles, such as agarose,
• the antibodies can be used to screen expression libraries for particular expression products such as normal or abnormal protein. Usually the antibodies in such a procedure are labeled with a moiety allowing easy detection of presence of antigen by antibody binding.
• Antibodies raised against a protein of the present invention can also be used to raise anti-idiotypic antibodies. These are useful for detecting or diagnosing various pathological conditions related to the presence of the respective antigens.
• the proteins and antibodies of the present invention will be labeled by joining, either covalently or non-covalently, a substance which provides for a detectable signal.
• labels and conjugation techniques are known and are reported extensively in both the scientific and patent literature. Suitable labels include radionucleotides, enzymes, substrates, cofactors, inhibitors, fluorescent moieties, chemiluminescent moieties, magnetic particles, and the like.
• Means of detecting the proteins of the present invention are not critical aspects of the present invention.
• the proteins are detected and/or quantified using any of a number of well recognized immunological binding assays (see, e.g., U.S. Patents 4,366,241; 4,376,110; 4,517,288; and 4,837,168).
• immunological binding assays see, e.g., U.S. Patents 4,366,241; 4,376,110; 4,517,288; and 4,837,168.
• the immunoassays of the present invention can be performed in any of several configurations, e.g., those reviewed in Enzyme Immunoassay, Maggio, Ed., CRC Press, Boca Raton, Florida (1980); Tijan, Practice and Theory of Enzyme Immunoassays, Laboratory Techniques in Biochemistry and Molecular Biology, Elsevier Science Publishers B.V., Amsterdam (1985); Harlow and Lane, supra; Immunoassay: A Practical Guide, Chan, Ed., Academic Press, Orlando, FL (1987); Principles and Practice of Immunoassays, Price and Newman Eds., Stockton Press, NY (1991); and Non- isotopic Immunoassays, Ngo, Ed., Plenum Press, NY (1988).
• Immunological binding assays typically utilize a "capture agent" to specifically bind to and often immobilize the analyte (in this case, a protein of the present invention).
• the capture agent is a moiety that specifically binds to the analyte.
• the capture agent is an antibody that specifically binds a protein(s) of the present invention.
• the antibody may be produced by any of a number of means known to those of skill in the art as described herein.
• Immunoassays also often utilize a labeling agent to specifically bind to and label the binding complex formed by the capture agent and the analyte.
• the labeling agent may itself be one of the moieties comprising the antibody/analyte complex.
• the labeling agent may be a labeled protein of the present invention or a labeled antibody specifically reactive to a protein of the present invention.
• the labeling agent may be a third moiety, such as another antibody, that specifically binds to the antibody/protein complex.
• the labeling agent is a second antibody bearing a label.
• the second antibody may lack a label, but it may, in turn, be bound by a labeled third antibody specific to antibodies of the species from which the second antibody is derived.
• the second can be modified with a detectable moiety, such as biotin, to which a third labeled molecule can specifically bind, such as enzyme-labeled streptavidin.
• proteins capable of specifically binding immunoglobulin constant regions such as protein A or protein G may also be used as the label agent. These proteins are normal constituents of the cell walls of streptococcal bacteria. They exhibit a strong non-immunogenic reactivity with immunoglobulin constant regions from a variety of species (See, generally Kronval, ef al., J. Immunol. 111: 401-1406 (1973), and Akerstrom, et al., J. Immunol. 135:2589-2542 (1985)).
• incubation and/or washing steps may be required after each combination of reagents. Incubation steps can vary from about 5 seconds to several hours, preferably from about 5 minutes to about 24 hours. However, the incubation time will depend upon the assay format, analyte, volume of solution, concentrations, and the like. Usually, the assays will be carried out at ambient temperature, although they can be conducted over a range of temperatures, such as 10°C to 40 ⁇ C.
• the method of detecting a protein of the present invention in a biological sample generally comprises the steps of contacting the biological sample with an antibody which specifically reacts, under immunologically reactive conditions, to a protein of the present invention.
• the antibody is allowed to bind to the protein under immunologically reactive conditions, and the presence of the bound antibody is detected directly or indirectly.
• Immunoassays for detecting proteins of the present invention include competitive and noncompetitive formats.
• Noncompetitive immunoassays are assays in which the amount of captured analyte (i.e., a protein of the present invention) is directly measured.
• the capture agent e.g., an antibody specifically reactive, under immunoreactive conditions, to a protein of the present invention
• the capture agent can be bound directly to a solid substrate where they are immobilized.
• These immobilized antibodies then capture the protein present in the test sample.
• the protein thus immobilized is then bound by a labeling agent, such as a second antibody bearing a label.
• the second antibody may lack a label, but it may, in turn, be bound by a labeled third antibody specific to antibodies of the species from which the second antibody is derived.
• the second can be modified with a detectable moiety, such as biotin, to which a third labeled molecule can specifically bind, such as enzyme-labeled streptavidin.
• the amount of analyte present in the sample is measured indirectly by measuring the amount of an added (exogenous) analyte (e.g., a protein of the present invention) displaced (or competed away) from a capture agent (e.g., an antibody specifically reactive, under immunoreactive conditions, to the protein) by the analyte present in the sample.
• a capture agent e.g., an antibody specifically reactive, under immunoreactive conditions, to the protein
• the antibody is immobilized on a solid substrate.
• the amount of protein bound to the antibody may be determined either by measuring the amount of protein present in a protein/antibody complex, or alternatively by measuring the amount of remaining uncomplexed protein.
• the amount of protein may be detected by providing a labeled protein.
• a hapten inhibition assay is another preferred competitive assay.
• a known analyte such as a protein of the present invention
• a known amount of antibody specifically reactive, under immunoreactive conditions, to the protein is added to the sample, and the sample is then contacted with the immobilized protein.
• the amount of antibody bound to the immobilized protein is inversely proportional to the amount of protein present in the sample.
• the amount of immobilized antibody may be detected by detecting either the immobilized fraction of antibody or the fraction of the antibody that remains in solution. Detection may be direct where the antibody is labeled or indirect by the subsequent addition of a labeled moiety that specifically binds to the antibody as described above.
• a protein that specifically binds to or that is specifically immunoreactive with an antibody generated against a defined immunogen, such as an immunogen consisting of the amino acid sequence of SEQ ID NOS: 2 and 4, is determined in an immunoassay.
• the immunoassay uses a polyclonal antiserum which is raised to a polypeptide of the present invention (i.e., the immunogenic polypeptide). This antiserum is selected to have low crossreactivity against other proteins and any such crossreactivity is removed by immunoabsorbtion prior to use in the immunoassay (e.g., by immunosorbtion of the antisera with a protein of different substrate specificity (e.g., a different enzyme) and/or a protein with the same substrate specificity but of a different form).
• a protein of different substrate specificity e.g., a different enzyme
• a polypeptide e.g., SEQ ID NOS: 2 and 4
• recombinant protein can be produced in a mammalian or other eukaryotic cell line.
• An inbred strain of mice is immunized with the protein of using a standard adjuvant, such as Freund's adjuvant, and a standard mouse immunization protocol (see Harlow and Lane, supra).
• a synthetic polypeptide derived from the sequences disclosed herein and conjugated to a carrier protein is used as an immunogen.
• Polyclonal sera are collected and titered against the immunogenic polypeptide in an immunoassay, for example, a solid phase immunoassay with the immunogen immobilized on a solid support.
• Polyclonal antisera with a titer of 10 4 or greater are selected and tested for their cross reactivity against polypeptides of different forms or substrate specificity, using a competitive binding immunoassay such as the one described in Harlow and Lane, supra, at pages 570-573.
• a competitive binding immunoassay such as the one described in Harlow and Lane, supra, at pages 570-573.
• two or more distinct forms of polypeptides are used in this determination. These distinct types of polypeptides are used as competitors to identify antibodies which are specifically bound by the polypeptide being assayed for.
• the competitive polypeptides can be produced as recombinant proteins and isolated using standard molecular biology and protein chemistry techniques as described herein.
• Immunoassays in the competitive binding format are used for crossreactivity determinations.
• the immunogenic polypeptide is immobilized to a solid support. Proteins added to the assay compete with the binding of the antisera to the immobilized antigen. The ability of the above proteins to compete with the binding of the antisera to the immobilized protein is compared to the immunogenic polypeptide. The percent crossreactivity for the above proteins is calculated, using standard calculations. Those antisera with less than 10% crossreactivity with a distinct form of a polypeptide are selected and pooled. The cross-reacting antibodies are then removed from the pooled antisera by immunoabsorbtion with a distinct form of a polypeptide.
• the immunoabsorbed and pooled antisera are then used in a competitive binding immunoassay as described herein to compare a second "target" polypeptide to the immunogenic polypeptide.
• the two polypeptides are each assayed at a wide range of concentrations and the amount of each polypeptide required to inhibit 50% of the binding of the antisera to the immobilized protein is determined using standard techniques. If the amount of the target polypeptide required is less than twice the amount of the immunogenic polypeptide that is required, then the target polypeptide is said to specifically bind to an antibody generated to the immunogenic protein.
• the pooled antisera is fully immunosorbed with the immunogenic polypeptide until no binding to the polypeptide used in the immunosorbtion is detectable.
• the fully immunosorbed antisera is then tested for reactivity with the test polypeptide. If no reactivity is observed, then the test polypeptide is specifically bound by the antisera elicited by the immunogenic protein.
• Western blot (immunoblot) analysis is used to detect and quantify the presence of protein of the present invention in the sample.
• the technique generally comprises separating sample proteins by gel electrophoresis on the basis of molecular weight, transferring the separated proteins to a suitable solid support, (such as a nitrocellulose filter, a nylon filter, or derivatized nylon filter), and incubating the sample with the antibodies that specifically bind a protein of the present invention.
• the antibodies specifically bind to the protein on the solid support.
• These antibodies may be directly labeled or alternatively may be subsequently detected using labeled antibodies (e.g., labeled sheep anti-mouse antibodies) that specifically bind to the antibodies.
• the proteins of the present invention may be detected and quantified by any of a number of means well known to those of skill in the art. These include analytic biochemical methods such as electrophoresis, capillary electrophoresis, high performance liquid chromatography (HPLC), thin layer chromatography (TLC), hyperdiffusion chromatography, and the like, and various immunological methods such as fluid or gel precipitin reactions, immunodiffusion (single or double), immunoelectrophoresis, radioimmunoassays (RIAs), enzyme-linked immunosorbent assays (ELISAs), immunofluorescent assays, and the like.
• analytic biochemical methods such as electrophoresis, capillary electrophoresis, high performance liquid chromatography (HPLC), thin layer chromatography (TLC), hyperdiffusion chromatography, and the like
• immunological methods such as fluid or gel precipitin reactions, immunodiffusion (single or double), immunoelectrophoresis, radioimmunoassays (
• the labeling agent can be, e.g., a monoclonal antibody, a polyclonal antibody, a binding protein or complex, or a polymer such as an affinity matrix, carbohydrate or lipid.
• Detectable labels suitable for use in the present invention include any composition detectable by spectroscopic, radioisotopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means.
• Detection may proceed by any known method, such as immunobiotting, western analysis, gel-mobility shift assays, fluorescent in situ hybridization analysis (FISH), tracking of radioactive or bioluminescent markers, nuclear magnetic resonance, electron paramagnetic resonance, stopped-flow spectroscopy, column chromatography, capillary electrophoresis, or other methods which track a molecule based upon an alteration in size and/or charge.
• FISH fluorescent in situ hybridization analysis
• the particular label or detectable group used in the assay is not a critical aspect of the invention.
• the detectable group can be any material having a detectable physical or chemical property.
• Such detectable labels have been well-developed in the field of immunoassays and, in general, any label useful in such methods can be applied to the present invention.
• a label is any composition detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means.
• Useful labels in the present invention include magnetic beads, fluorescent dyes, radiolabels, enzymes, and colorimetric labels or colored glass or plastic beads, as discussed for nucleic acid labels, supra.
• the label may be coupled directly or indirectly to the desired component of the assay according to methods well known in the art. As indicated above, a wide variety of labels may be used, with the choice of label depending on the sensitivity required, ease of conjugation of the compound, stability requirements, available instrumentation, and disposal provisions.
• Non-radioactive labels are often attached by indirect means.
• a ligand molecule e.g., biotin
• the ligand then binds to an anti-ligand (e.g., streptavidin) molecule which is either inherently detectable or covalently bound to a signal system, such as a detectable enzyme, a fluorescent compound, or a chemiluminescent compound.
• an anti-ligand e.g., streptavidin
• a number of ligands and anti-ligands can be used.
• a ligand has a natural anti-ligand, for example, biotin, thyroxine, and cortisol, it can be used in conjunction with the labeled, naturally occurring anti-ligands.
• any haptenic or antigenic compound can be used in combination with an antibody.
• the molecules can also be conjugated directly to signal generating compounds, e.g., by conjugation with an enzyme or fluorophore.
• Enzymes of interest as labels will primarily be hydrolases, particularly phosphatases, esterases and glycosidases, or oxidoreductases, particularly peroxidases.
• Fluorescent compounds include fluorescein and its derivatives, rhodamine and its derivatives, dansyl, umbelliferone, etc.
• Chemiluminescent compounds include luciferin, and 2,3-dihydrophthalazinediones, e.g., luminol.
• Means of detecting labels are well known to those of skill in the art.
• means for detection include a scintillation counter or photographic film as in autoradiography.
• the label is a fluorescent label, it may be detected by exciting the fluorochrome with the appropriate wavelength of light and detecting the resulting fluorescence, e.g., by microscopy, visual inspection, via photographic film, by the use of electronic detectors such as charge coupled devices (CCDs) or photomultipliers and the like.
• CCDs charge coupled devices
• enzymatic labels may be detected by providing appropriate substrates for the enzyme and detecting the resulting reaction product.
• simple colorimetric labels may be detected simply by observing the color associated with the label. Thus, in various dipstick assays, conjugated gold often appears pink, while various conjugated beads appear the color of the bead.
• agglutination assays can be used to detect the presence of the target antibodies.
• antigen-coated particles are agglutinated by samples comprising the target antibodies.
• none of the components need be labeled and the presence of the target antibody is detected by simple visual inspection.
• the present invention also provides means for identifying compounds that bind to (e.g., substrates), and/or increase or decrease (i.e., modulate) the enzymatic activity of, catalytically active polypeptides of the present invention.
• the method comprises contacting a polypeptide of the present invention with a compound whose ability to bind to or modulate enzyme activity is to be determined.
• the polypeptide employed will have at least 20%, preferably at least 30% or 40%, more preferably at least 50% or 60%, and most preferably at least 70% or 80% of the specific activity of the native, full-length cell cycle polypeptide (e.g., enzyme). Generally, the polypeptide will be present in a range sufficient to determine the effect of the compound, typically about 1 nM to 10 ⁇ M.
• the compound will be present in a concentration of from about 1 nM to 10 ⁇ M.
• factors as enzyme concentration, ligand concentrations (i.e., substrates, products, inhibitors, activators), pH, ionic strength, and temperature will be controlled so as to obtain useful kinetic data and determine the presence of absence of a compound that binds or modulates polypeptide activity.
• Methods of measuring enzyme kinetics is well known in the art. See, e.g., Segel, Biochemical Calculations, 2 nd ed., John Wiley and Sons, New York (1976).
• plant tissue samples were pulverized in liquid nitrogen before the addition of the TRIzol Reagent, and then were further homogenized with a mortar and pestle. Addition of chloroform followed by centrifugation was conducted for separation of an aqueous phase and an organic phase. The total RNA was recovered by precipitation with isopropyl alcohol from the aqueous phase.
• cDNA Library Construction cDNA synthesis was performed and unidirectional cDNA libraries were constructed using the Superscript Plasmid System (Life Technology Inc. Gaithersburg, MD). The first stand of cDNA was synthesized by priming an oligo(dT) primer containing a Not I site. The reaction was catalyzed by Superscript Reverse Transcriptase II at 45°C. The second strand of cDNA was labeled with alpha- 32 P-dCTP and a portion of the reaction was analyzed by agarose gel electrophoresis to determine cDNA sizes. cDNA molecules smaller than 500 base pairs and unligated adapters were removed by Sephacryl-S400 chromatography. The selected cDNA molecules were ligated into pSPORTI vector in between of Not I and Sal I sites. Zea mays tissue from tassel and vegetative meristem was employed.
• Cks also historically called Sud gene expression during the G2 ⁇ M transition and during mitosis plays a prominent role in progression through the cell cycle.
• the encoded proteins (generally referred to as P13 8 " 01 ) are a critical part of the MPF (maturation promoting factor) complex.
• the Cks genes and their encoded p13 proteins can be used to identify other cell cycle regulatory proteins. This can be done using the Cks gene as bait (the target fused to the DNA-binding domain) in a yeast two hybrid screen.
• Example 3 Cks-bound affinity columns for identifying P13 proteins and their encoding genes
• Purified recombinant Cks protein can be immobilized on a matrix via a covalent crosslinking or affinity purification as described supra. This matrix can then be used to pull-down proteins that interact with Cks proteins, inter alia, cyclin-dependent kinase.
• CDK activity can then be assessed by measuring the addition of 32P to protein-substrates and CDK protein levels determined by immunoassay. Additionally, this can be used to purify the CDK activity present in different plant tissues and protein fractions. The presence and level of other CKS interacting proteins can also be determined on the basis of immunological assay, activity quantification, SDS-PAGE analysis and other methods. These measures can then be correlated with the reproductive state, capacity for division, developmental stage, or the quality of different samples.
• a Cks nucleic acid can also be adducted to a second nucleic acid sequence encoding a DNA-binding domain in order to identify Cks interacting proteins.
• Example 4 Altering Cks expression causes cell cycle arrest
• a chemically-inducible promoter is used.
• the Cks gene is cloned into a cassette with an inducible promoter such as the estrogen- inducible promoter (for example, in a cassette containing 4xERE::ZmCks::pinll).
• Either particle-mediated DNA delivery or Agrobacterium-med ⁇ ated delivery are used to introduce the 4xERE::ZmCks::pinll-containing plasmid along with a- UBI::bar::pinll-containing plasmid into maize cells capable of growth on suitable maize culture medium.
• Such competent cells can be from maize suspension culture, callus culture on solid medium, freshly isolated immature embryos or meristem cells, immature embryos of the Hi-ll genotype are used as the target for co-delivery of these two plasmids, and within 1-7 days the embryos are moved onto culture medium containing 3 mg/1 of the selective agent bialaphos. Embryos, and later callus, are transferred to fresh selection plates every 2 weeks. After 6-8 weeks, transformed calli are recovered. Transgenic callus containing both genes can be verified using PCR and Southern analysis. Northern analysis can also be used to verify which calli are expressing the bar gene but not expressing Cks at levels above normal wild-type cells (based on hybridization of probes to freshly isolated mRNA population from the cells).
• UBI::Cks Upon exposure to estrogen (or estradiol), UBI::Cks is expressed (this can be confirmed by Northern analysis).
• This induced Cks overexpression blocks cells in mitosis.
• Conventional cytological methods such as Fuelgen staining can be used to verify this cell cycle block, as can FACS sorting of nuclei, and the used of cell cycle stage-specific probes. For example, numerous spindle-associated proteins are expressed during a fairly narrow window during mitosis, and cyclins D, E, and H can be used as positive markers for the G1/S transition.
• mitotic arrest is manifested as a high degree of chromosome condensation in the cells.
• Cks gene expression using tissue-specific or cell-specific promoters blocks cell cycle progression in the expressing tissues or cells. Using a tapetum or microspore-specific promoter effectively blocks pollen development, rendering such expressing plants male sterile. Alternatively, driving Cks expression with a strongly-expressed, early, tassel-specific promoter will inhibit development of this entire reproductive structure.
• G2 for example in endosperm cells or in certain leaf cells.
• mutant Cks genes through the ability of the encoded altered plS " 01 protein to stabilize cyclin B, enhances cell division. This increase in division rate is assessed in a number of different manners, being reflected in smaller cell size, more rapid inco ⁇ oration of radiolabeled nucleotides, and faster growth (i.e. more biomass accumulation).
• Example 7 Using Agrobacterium as a Cell-Cycle Protein Vector Cloning of VirE1E2 operon The operon was cloned by PCR amplification of Agrobacterium LBA4404 cells with primers (SEQ ID NOS. 17-20 ) designed from the Genbank sequence (Accession #X04784) of the VirE1 E2 operon from pTiA6. The operon was cloned by amplifying two fragments, each ⁇ 1.2kb. The PCR reaction was carried out by mixing 2 ul of each primer(50uM), 16 ul dH20, and 180 ul of Gibco BRL supermix (Cat. # 10572-014) with a pipet tip stab of LBA4404.
• Cycle conditions were 94° C for 1 minute, 29 cycles of 92° C for 1 minute, 60° C for 1 minute, 75° C for 1.5 minutes, followed by 75° C for 5 minutes and 4° C for infinity.
• PCR fragments were run out in a 1% agarose gel, then isolated using Qiagen's Qiaquick Gel Extraction Kit (Cat# 28706). Each fragment was the subcloned into Promega's pGEM-T easy vector (Cat# A1380) and sequenced. The sequence of the amplified operon differed by two nucleotides from the Genbank sequence. This was verified in separate clones from different PCR reactions.
• the fragments were then subcloned together to form a working operon again in pPHP14918 by subcloning the 1.2 kb Bglll/Pst fragment from the pGEM plasmid containing the 3' half of the operon into the 4.1kb Bglll/Pst fragment from the pGEM plasmid containing the 5' half of the operon. All vectors were constructed using standard molecular biology techniques
• the reporter gene included the ⁇ -glucuronidase (GUS) gene (Jefferson, R.A. ef al., 1986, Proc. Natl. Acad. Sci. (USA) 83:8447-8451) into whose coding region was inserted the second intron from the potato ST-LS1 gene (Vancanneyt etal., Mol. Gen. Genet. 220:245-250, 1990), to produce intron-GUS, in order to prevent expression of the gene in Agrobacterium (see Ohta, S.
• a Cauliflower Mosaic Virus 35S promoter with a duplicated enhancer region (2X35S; bases -421 to -90 and -421 to +2 from Gardner ef al., Nucl. Acids Res. 9:2871-2888, 1981) with a flanking 5' Notl site and a 3' Pstl site was created.
• a Pstl/Sall fragment containing the 79 bp Tobacco Mosaic Virus leader (Gallie ef al., Nucl. Acids Res.
• the plasmid was constructed by inserting the GUS expression cassette as a Hindlll/Notl fragment and the BAR expression cassette as a Notl/Sacl fragment between the right and left T-DNA borders in pSB11 at Hindlll and Sacl sites.
• the GUS cassette is inserted proximal to the right T-DNA border.
• the plasmid pSB11 was obtained from Japan Tobacco Inc. (Tokyo, Japan).
• the construction of pSB11 from pSB21 and the construction of pSB21 from starting vectors is described by Komari ef al. (1996, Plant J. 10: 165-174).
• the T-DNA of pPHP8904 was integrated into the superbinary plasmid pSB1 (Saito etal., EP 672 752 A1) by homologous recombination between the two plasmids (pSB1 x pPHP8904).
• the plasmid pSB1 was also obtained from Japan Tobacco Inc.
• E. coli strain HB101 containing pPHP8904 was mated with Agrobacterium strain LBA4404 harboring pSB1 to create the cointegrate plasmid in Agrobacterium, designated as LBA4404(pPHP10525) as shown in Fig. 1c, using the method of Ditta ef al., (Proc. Natl.
• LBA4404(pPHP10525) was selected based on resistance of transformed Agrobacterium to spectinomycin and verified as a recombinant by a Sail restriction digest of the plasmid.
• Agrobacterium was streaked out from a -80° frozen aliquot onto a plate containing PHI-L medium and cultured at 28°C in the dark for 3 days.
• PHI-L media comprised 25 ml/l Stock Solution A, 25 ml/l Stock Solution B, 450.9 ml/l Stock Solution C and spectinomycin (Sigma Chemicals) added to a concentration of 50 mg/l in sterile ddH20 (stock solution A: K2HP04 60.0 g/l, NaH2P0420.0 g/l, adjust pH to 7.0 w/KOH and autoclave; stock solution B: NH4CI 20.0 g/l, MgS04.7H206.0 g/l, KCl 3.0 g/l, CaCI2 0.20 g/l, FeS04.7H20 50.0 mg/l, autoclave; stock solution C: glucose 5.56g/l, agar 16.67 g/l (#A-70
• the plate can be stored at 4°C and is viable for about 1 month.
• a single colony was picked from the master plate and streaked onto a plate containing PHI-M medium [yeast extract (Difco) 5.0 g/l; peptone (Difco)IO.O g/l; NaCl 5.0 g/l; agar (Difco) 15.0 g/l; pH 6.8, containing 50 mg/L spectinomycin] and incubated at 28°C in the dark for 2 days.
• PHI-M medium yeast extract (Difco) 5.0 g/l; peptone (Difco)IO.O g/l; NaCl 5.0 g/l; agar (Difco) 15.0 g/l; pH 6.8, containing 50 mg/L spectinomycin
• Agrobacterium was collected from the plate and suspended in the tube, then the tube was vortexed to make an even suspension.
• One ml of the suspension was transferred to a spectrophotometer tube and the OD of the suspension was adjusted to 0.72 at 550 nm by adding either more Agrobacterium or more of the same suspension medium.
• the Agrobacterium concentration was approximately 1 x 109 cfu/ml.
• the final Agrobacterium suspension was aliquoted into 2 ml microcentrifuge tubes, each containing 1 ml of the suspension. The suspensions were then used as soon as possible.
• Any embryos left in the tube were transferred to the plate using a sterile spatula.
• the Agrobacterium suspension was drawn off and the embryos placed axis side down on the media.
• the plate was sealed with Parafilm tape or Pylon Vegetative Combine Tape (product named "E.G.CUT” and is available in 18 mm x 50 m sections; Kyowa Ltd., Japan) and incubated in the dark at 23-25°C for about 3 days of co-cultivation.
• the plates are sealed as described above and incubated in the dark at 28°C for the first two weeks of selection.
• the embryos are transferred to fresh selection medium at two week intervals.
• the tissue is subcultured by transferring to fresh selection medium for a total of about 2 months.
• the herbicide-resistant calli are then "bulked up" by growing on the same medium for another two weeks until the diameter of the calli are about 1.5-2 cm.
• the calli are then cultured on PHI-E medium [MS salts 4.3 g/l; myo-inositol 0.1 g/l; nicotinic acid 0.5 mg/l, thiamine.HCI 0.1 mg/l, Pyridoxine.HCI 0.5 mg/l, Glycine 2.0 mg/l, Zeatin 0.5 mg/l, sucrose 60.0 g/l, Agar (Sigma, A-7049) 8.0 g/l, Indoleacetic acid (IAA, Sigma) 1.0 mg/l, Abscisic acid (ABA, Sigma) 0.1 ⁇ M, Bialaphos 3 mg l, carbenicillin 100 mg/l adjusted to pH 5.6] in the dark at 28°C for 1-3 weeks to allow somatic embryos to mature.
• PHI-E medium [MS salts 4.3 g/l; myo-inositol 0.1 g/l; nicotinic acid 0.5 mg/l, thiamine.HCI 0.1 mg/
• the calli are then cultured on PHI-F medium (MS salts 4.3 g/l; myo-inositol 0.1 g/l; Thiamine.HCI 0.1 mg l, Pyridoxine.HCI 0.5 mg/l, Glycine 2.0 mg/l, nicotinic acid 0.5 mg/l; sucrose 40.0 g/l; gelrite 1.5 g/l; pH 5.6] at 25°C under a daylight schedule of 16 hrs. light (270 uE m-2sec-1) and 8 hrs. dark until shoots and roots develop.
• Each small plantlet is then transferred to a 25x150 mm tube containing PHI-F medium and grown under the same conditions for approximately another week. The plants are transplanted to pots with soil mixture in a greenhouse. GUS+ events are determined at the callus stage or regenerated plant stage.
• callus transformants are confirmed through standard methods such as PCR and Southern analysis, and enzymatic methods.
• the calli are highly embryogenic, and regenerated plants are fertile and pass the transgenes to progeny in a manner consistent with expected Mendelian inheritance.

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