Cell Cycle Genes and Related Methods

Abstract

Novel plant polysaccharide synthesis genes and polypeptides encoded by such genes are provided. These genes and polynucleotide sequences are useful regulating polysaccharide synthesis and plant phenotype. Moreover, these genes are useful for expression profiling of plant polysaccharide synthesis genes. The invention specifically provides cell cycle polynucleotide and polypeptide sequences isolated from Eucalyptus and Pinus.

1 . An isolated polynucleotide comprising a nucleic acid sequence that (i) is selected from the group consisting of SEQ ID NOs: 1-260 and variants thereof, (ii) is selected from the group consisting of SEQ ID NOs: 521-772 and variants thereof, or (iii) encodes the catalytic or substrate-binding domain of a polypeptide selected from of any one of SEQ ID NOs: 261-520, wherein the polynucleotide encodes a polypeptide having the activity of said polypeptide selected from any one of SEQ ID NOs: 261-520. 
     
     
         2 .- 5 . (canceled) 
     
     
         6 . The isolated polynucleotide of  claim 1 , wherein the variant has a sequence identity that is greater than or equal to 80% to any one of SEQ ID NOs: 1-260 or encodes a protein with an amino acid sequence having a sequence identity that is greater than 60%, 65%, 70%, 75%, 80%, 85% or 90% to any one of SEQ ID NOs: 261-520, and wherein the protein encoded by the polynucleotide possesses the activity of the protein encoded by said any one of SEQ ID NOs: 1-260. 
     
     
         7 .- 8 . (canceled) 
     
     
         9 . A DNA construct comprising at least one polynucleotide of  claim 1 , operably linked in sense or antisense orientation to a promoter, wherein the promoter is selected from the group consisting of a constitutive promoter, a strong promoter, an inducible promoter, a regulatable promoter, a temporally regulated promoter, and a tissue-preferred promoter. 
     
     
         10 .- 13 . (canceled) 
     
     
         14 . The DNA construct of  claim 9 , wherein an RNA transcript of the polynucleotide is complementary to a nucleic acid sequence selected from the group consisting of 1-260. 
     
     
         15 . A plant cell, comprising the DNA construct of  claim 9 . 
     
     
         16 . The plant cell of  claim 15 , wherein the plant cell is in a transgenic plant, and wherein the phenotype of the plant is different from a plant of the same species which does not comprise the plant cell, wherein the difference in phenotype is in lignin quality, lignin structure, wood composition, wood appearance, wood density, wood strength, wood stiffness, cellulose polymerization, fiber dimensions, lumen size, other plant components, plant cell division, plant cell development, number of cells per unit area, cell size, cell shape, cell wall composition, rate of wood formation, aesthetic appearance of wood, formation of stem defects, average microfibril angle, width of the S2 cell wall layer, rate of growth, rate of root formation, ratio of root to branch vegetative development, leaf area index, and leaf shape. 
     
     
         17 .- 20 . (canceled) 
     
     
         21 . The transgenic plant of  claim 16 , wherein the plant is of a species of  Eucalyptus  or  Pinus.    
     
     
         22 . The transgenic plant of  claim 16 , wherein the plant exhibits one or more traits selected from the group consisting of increased drought tolerance, herbicide resistance, reduced or increased height, reduced or increased branching, enhanced cold and frost tolerance, improved vigor, enhanced color, enhanced health and nutritional characteristics, improved storage, enhanced yield, enhanced salt tolerance, enhanced resistance of the wood to decay, enhanced resistance to fungal diseases, altered attractiveness to insect pests, enhanced heavy metal tolerance, increased disease tolerance, increased insect tolerance, increased water-stress tolerance, enhanced sweetness, improved texture, decreased phosphate content, increased germination, increased micronutrient uptake, improved starch composition, improved flower longevity, production of novel resins, and production of novel proteins or peptides, reduced period of juvenility, an increased period of juvenility, propensity to form reaction wood, self-abscising branches, accelerated reproductive development or delayed reproductive development as compared to a plant of the same species that has not been transformed with the DNA construct. 
     
     
         23 .- 31 . (canceled) 
     
     
         32 . A wood obtained from a transgenic tree which has been transformed with the DNA construct of  claim 9 . 
     
     
         33 . A wood pulp obtained from a transgenic tree which has been transformed with the DNA construct of  claim 9 . 
     
     
         34 .- 36 . (canceled) 
     
     
         37 . An isolated polypeptide comprising an amino acid sequence encoded by the isolated polynucleotide of  claim 1 . 
     
     
         38 .- 43 . (canceled) 
     
     
         44 . The isolated polynucleotide of  claim 1 , wherein the polynucleotide comprises fewer than about 100 nucleotide bases. 
     
     
         45 . A method of correlating gene expression in two different samples, comprising: detecting a level of expression of one or more genes encoding a product encoded by a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-260 and conservative variants thereof in a first sample; detecting a level of expression of the one or more genes in a second sample; comparing the level of expression of the one or more genes in the first sample to the level of expression of the one or more genes in the second sample; and correlating a difference in expression level of the one or more genes between the first and second samples. 
     
     
         46 . The method of  claim 45 , wherein the first sample and the second sample are plant tissues that are from the same or different plant. 
     
     
         47 . The method of claim  4 , wherein the first sample and the second sample are (i) from the same plant tissue, (ii) harvested during a different season of the year, and/or (iii) obtained from plants in different stages of development. 
     
     
         48 .- 50 . (canceled) 
     
     
         51 . The method of  claim 46  wherein the plant tissue is selected from the group consisting of vascular tissue, apical meristem, vascular cambium, xylem, phloem, root, flower, cone, fruit, and seed. 
     
     
         52 . The method of  claim 51 , wherein the plant tissues are obtained from at least one of (i) a different type of tissue, (ii) a different stage of development, or (iii) different stages of the cell cycle. 
     
     
         53 .- 54 . (canceled) 
     
     
         55 . The method of  claim 51 , wherein the plant tissues are from one or more species of  Eucalyptus  or  Pinus.    
     
     
         56 . (canceled) 
     
     
         57 . The method of  claim 45 , wherein the step of detecting is effected using one or more polynucleotides capable of hybridizing to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-260 under standard hybridization conditions. 
     
     
         58 . (canceled) 
     
     
         59 . The method of  claim 57 , wherein the step of detecting is accomplished by hybridization to a labeled nucleic acid. 
     
     
         60 . (canceled) 
     
     
         61 . The method of  claim 57 , wherein at least one of polynucleotides hybridizes to a 3′ untranslated region of the nucleic acid sequence. 
     
     
         62 . (canceled) 
     
     
         63 . The method of  claim 57 , wherein the one or more polynucleotides comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 521-772. 
     
     
         64 .- 66 . (canceled) 
     
     
         67 . The method of  claim 45 , further comprising, prior to the detecting steps, the step of amplifying at least one of the genes. 
     
     
         68 . The method of  claim 45 , further comprising, prior to the detecting steps, the step of labeling at least one of the genes with a detectable label. 
     
     
         69 . A combination for detecting expression of one or more genes, comprising two or more oligonucleotides, wherein each oligonucleotide is capable of hybridizing to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-260 or to an RNA transcript of a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-260. 
     
     
         70 . (canceled) 
     
     
         71 . The combination of  claim 69 , wherein the oligonucleotides each hybridize to different nucleic acid sequences or to different RNA transcripts. 
     
     
         72 . (canceled) 
     
     
         73 . The combination of  claim 69 , wherein at least one of the oligonucleotides hybridizes to a 3′ untranslated region of a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-260. 
     
     
         74 .- 75 . (canceled) 
     
     
         76 . The combination of  claim 69 , wherein at least one of the oligonucleotides comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 521-772. 
     
     
         77 .- 83 . (canceled) 
     
     
         84 . The combination of  claim 69 , comprising from about 2 to about 5000 oligonucleotides. 
     
     
         85 . The combination of  claim 84 , wherein each of the oligonucleotides is labeled with a detectable label. 
     
     
         86 . A microarray comprising the combination of  claim 69  provided on a solid support, wherein each of the oligonucleotides occupies a unique location on said solid support. 
     
     
         87 . (canceled) 
     
     
         88 . A method for detecting one or more nucleic acid sequences in a sample, comprising contacting the sample with the combination of  claim 69 . 
     
     
         89 .- 91 . (canceled) 
     
     
         92 . The method of  claim 88 , wherein at least one of the oligonucleotides hybridizes to a 3′ untranslated region of a gene that comprises the nucleic acid sequence of at least any one of SEQ ID NOs 1-260. 
     
     
         93 .- 103 . (canceled) 
     
     
         104 . A kit for detecting gene expression comprising the microarray of  claim 86  and one or more buffers or reagents for a nucleotide hybridization reaction.