Analyses of phylogeny, evolution, conserved sequences and genome-wide expression of the ICK/KRP family of plant CDK inhibitors.
Identifieur interne : 002E92 ( Main/Corpus ); précédent : 002E91; suivant : 002E93Analyses of phylogeny, evolution, conserved sequences and genome-wide expression of the ICK/KRP family of plant CDK inhibitors.
Auteurs : Juan Antonio Torres Acosta ; Larry C. Fowke ; Hong WangSource :
- Annals of botany [ 1095-8290 ] ; 2011.
English descriptors
- KwdEn :
- Amino Acid Motifs (MeSH), Amino Acid Sequence (MeSH), Arabidopsis (genetics), Conserved Sequence (genetics), Cyclin-Dependent Kinase Inhibitor Proteins (chemistry), Cyclin-Dependent Kinase Inhibitor Proteins (genetics), Cyclin-Dependent Kinase Inhibitor Proteins (metabolism), Evolution, Molecular (MeSH), Exons (genetics), Gene Duplication (genetics), Gene Expression Regulation, Plant (MeSH), Genes, Plant (genetics), Genome, Plant (genetics), Introns (genetics), Molecular Sequence Data (MeSH), Multigene Family (genetics), Oryza (genetics), Phylogeny (MeSH), Plants (genetics), Populus (genetics), Protein Structure, Tertiary (MeSH), Species Specificity (MeSH).
- MESH :
- chemical , chemistry : Cyclin-Dependent Kinase Inhibitor Proteins.
- genetics : Arabidopsis, Conserved Sequence, Cyclin-Dependent Kinase Inhibitor Proteins, Exons, Gene Duplication, Genes, Plant, Genome, Plant, Introns, Multigene Family, Oryza, Plants, Populus.
- chemical , metabolism : Cyclin-Dependent Kinase Inhibitor Proteins.
- Amino Acid Motifs, Amino Acid Sequence, Evolution, Molecular, Gene Expression Regulation, Plant, Molecular Sequence Data, Phylogeny, Protein Structure, Tertiary, Species Specificity.
Abstract
BACKGROUND AND AIMS
The cell cycle is controlled by cyclin-dependent kinases (CDKs), and CDK inhibitors are major regulators of their activities. The ICK/KRP family of CDK inhibitors has been reported in several plants, with seven members in arabidopsis; however, the phylogenetic relationship among members in different species is unknown. Also, there is a need to understand how these genes and proteins are regulated. Furthermore, little information is available on the functional differences among ICK/KRP family members.
METHODS
We searched publicly available databases and identified over 120 unique ICK/KRP protein sequences from more than 60 plant species. Phylogenetic analysis was performed using 101 full-length sequences from 40 species and intron-exon organization of ICK/KRP genes in model species. Conserved sequences and motifs were analysed using ICK/KRP protein sequences from arabidopsis (Arabidopsis thaliana), rice (Oryza sativa) and poplar (Populus trichocarpa). In addition, gene expression was examined using microarray data from arabidopsis, rice and poplar, and further analysed by RT-PCR for arabidopsis.
KEY RESULTS AND CONCLUSIONS
Phylogenetic analysis showed that plant ICK/KRP proteins can be grouped into three major classes. Whereas the C-class contains sequences from dicotyledons, monocotyledons and gymnosperms, the A- and B-classes contain only sequences from dicotyledons or monocotyledons, respectively, suggesting that the A- and B-classes might have evolved from the C-class. This classification is also supported by exon-intron organization. Genes in the A- and B- classes have four exons, whereas genes in the C-class have only three exons. Analysis of sequences from arabidopsis, rice and poplar identified conserved sequence motifs, some of which had not been described previously, and putative functional sites. The presence of conserved motifs in different family members is consistent with the classification. In addition, gene expression analysis showed preferential expression of ICK/KRP genes in certain tissues. A model has been proposed for the evolution of this gene family in plants.
DOI: 10.1093/aob/mcr034
PubMed: 21385782
PubMed Central: PMC3091803
Links to Exploration step
pubmed:21385782Le document en format XML
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Fowke</name></author><author><name sortKey="Wang, Hong" sort="Wang, Hong" uniqKey="Wang H" first="Hong" last="Wang">Hong Wang</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2011">2011</date><idno type="RBID">pubmed:21385782</idno><idno type="pmid">21385782</idno><idno type="doi">10.1093/aob/mcr034</idno><idno type="pmc">PMC3091803</idno><idno type="wicri:Area/Main/Corpus">002E92</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">002E92</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Analyses of phylogeny, evolution, conserved sequences and genome-wide expression of the ICK/KRP family of plant CDK inhibitors.</title><author><name sortKey="Torres Acosta, Juan Antonio" sort="Torres Acosta, Juan Antonio" uniqKey="Torres Acosta J" first="Juan Antonio" last="Torres Acosta">Juan Antonio Torres Acosta</name><affiliation><nlm:affiliation>Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Fowke, Larry C" sort="Fowke, Larry C" uniqKey="Fowke L" first="Larry C" last="Fowke">Larry C. Fowke</name></author><author><name sortKey="Wang, Hong" sort="Wang, Hong" uniqKey="Wang H" first="Hong" last="Wang">Hong Wang</name></author></analytic><series><title level="j">Annals of botany</title><idno type="eISSN">1095-8290</idno><imprint><date when="2011" type="published">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Motifs (MeSH)</term><term>Amino Acid Sequence (MeSH)</term><term>Arabidopsis (genetics)</term><term>Conserved Sequence (genetics)</term><term>Cyclin-Dependent Kinase Inhibitor Proteins (chemistry)</term><term>Cyclin-Dependent Kinase Inhibitor Proteins (genetics)</term><term>Cyclin-Dependent Kinase Inhibitor Proteins (metabolism)</term><term>Evolution, Molecular (MeSH)</term><term>Exons (genetics)</term><term>Gene Duplication (genetics)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Genes, Plant (genetics)</term><term>Genome, Plant (genetics)</term><term>Introns (genetics)</term><term>Molecular Sequence Data (MeSH)</term><term>Multigene Family (genetics)</term><term>Oryza (genetics)</term><term>Phylogeny (MeSH)</term><term>Plants (genetics)</term><term>Populus (genetics)</term><term>Protein Structure, Tertiary (MeSH)</term><term>Species Specificity (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Cyclin-Dependent Kinase Inhibitor Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Conserved Sequence</term><term>Cyclin-Dependent Kinase Inhibitor Proteins</term><term>Exons</term><term>Gene Duplication</term><term>Genes, Plant</term><term>Genome, Plant</term><term>Introns</term><term>Multigene Family</term><term>Oryza</term><term>Plants</term><term>Populus</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Cyclin-Dependent Kinase Inhibitor Proteins</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Motifs</term><term>Amino Acid Sequence</term><term>Evolution, Molecular</term><term>Gene Expression Regulation, Plant</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Protein Structure, Tertiary</term><term>Species Specificity</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND AND AIMS</b></p><p>The cell cycle is controlled by cyclin-dependent kinases (CDKs), and CDK inhibitors are major regulators of their activities. The ICK/KRP family of CDK inhibitors has been reported in several plants, with seven members in arabidopsis; however, the phylogenetic relationship among members in different species is unknown. Also, there is a need to understand how these genes and proteins are regulated. Furthermore, little information is available on the functional differences among ICK/KRP family members.</p></div><div type="abstract" xml:lang="en"><p><b>METHODS</b></p><p>We searched publicly available databases and identified over 120 unique ICK/KRP protein sequences from more than 60 plant species. Phylogenetic analysis was performed using 101 full-length sequences from 40 species and intron-exon organization of ICK/KRP genes in model species. Conserved sequences and motifs were analysed using ICK/KRP protein sequences from arabidopsis (Arabidopsis thaliana), rice (Oryza sativa) and poplar (Populus trichocarpa). In addition, gene expression was examined using microarray data from arabidopsis, rice and poplar, and further analysed by RT-PCR for arabidopsis.</p></div><div type="abstract" xml:lang="en"><p><b>KEY RESULTS AND CONCLUSIONS</b></p><p>Phylogenetic analysis showed that plant ICK/KRP proteins can be grouped into three major classes. Whereas the C-class contains sequences from dicotyledons, monocotyledons and gymnosperms, the A- and B-classes contain only sequences from dicotyledons or monocotyledons, respectively, suggesting that the A- and B-classes might have evolved from the C-class. This classification is also supported by exon-intron organization. Genes in the A- and B- classes have four exons, whereas genes in the C-class have only three exons. Analysis of sequences from arabidopsis, rice and poplar identified conserved sequence motifs, some of which had not been described previously, and putative functional sites. The presence of conserved motifs in different family members is consistent with the classification. In addition, gene expression analysis showed preferential expression of ICK/KRP genes in certain tissues. A model has been proposed for the evolution of this gene family in plants.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">21385782</PMID><DateCompleted><Year>2011</Year><Month>08</Month><Day>30</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1095-8290</ISSN><JournalIssue CitedMedium="Internet"><Volume>107</Volume><Issue>7</Issue><PubDate><Year>2011</Year><Month>May</Month></PubDate></JournalIssue><Title>Annals of botany</Title><ISOAbbreviation>Ann Bot</ISOAbbreviation></Journal><ArticleTitle>Analyses of phylogeny, evolution, conserved sequences and genome-wide expression of the ICK/KRP family of plant CDK inhibitors.</ArticleTitle><Pagination><MedlinePgn>1141-57</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/aob/mcr034</ELocationID><Abstract><AbstractText Label="BACKGROUND AND AIMS" NlmCategory="OBJECTIVE">The cell cycle is controlled by cyclin-dependent kinases (CDKs), and CDK inhibitors are major regulators of their activities. The ICK/KRP family of CDK inhibitors has been reported in several plants, with seven members in arabidopsis; however, the phylogenetic relationship among members in different species is unknown. Also, there is a need to understand how these genes and proteins are regulated. Furthermore, little information is available on the functional differences among ICK/KRP family members.</AbstractText><AbstractText Label="METHODS" NlmCategory="METHODS">We searched publicly available databases and identified over 120 unique ICK/KRP protein sequences from more than 60 plant species. Phylogenetic analysis was performed using 101 full-length sequences from 40 species and intron-exon organization of ICK/KRP genes in model species. Conserved sequences and motifs were analysed using ICK/KRP protein sequences from arabidopsis (Arabidopsis thaliana), rice (Oryza sativa) and poplar (Populus trichocarpa). In addition, gene expression was examined using microarray data from arabidopsis, rice and poplar, and further analysed by RT-PCR for arabidopsis.</AbstractText><AbstractText Label="KEY RESULTS AND CONCLUSIONS" NlmCategory="CONCLUSIONS">Phylogenetic analysis showed that plant ICK/KRP proteins can be grouped into three major classes. Whereas the C-class contains sequences from dicotyledons, monocotyledons and gymnosperms, the A- and B-classes contain only sequences from dicotyledons or monocotyledons, respectively, suggesting that the A- and B-classes might have evolved from the C-class. This classification is also supported by exon-intron organization. Genes in the A- and B- classes have four exons, whereas genes in the C-class have only three exons. Analysis of sequences from arabidopsis, rice and poplar identified conserved sequence motifs, some of which had not been described previously, and putative functional sites. The presence of conserved motifs in different family members is consistent with the classification. In addition, gene expression analysis showed preferential expression of ICK/KRP genes in certain tissues. 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