Genome-wide analysis of core cell cycle genes in Arabidopsis
Open accessAbstract
Cyclin-dependent kinases and cyclins regulate with the help of different interacting proteins the progression through the eukaryotic cell cycle. A high-quality, homology-based annotation protocol was applied to determine the core cell cycle genes in the recently completed Arabidopsis genome sequence. In total, 61 genes were identified belonging to seven selected families of cell cycle regulators, for which 30 are new or corrections of the existing annotation. A new class of putative cell cycle regulators was found that probably are competitors of E2F/DP transcription factors, which mediate the G1-to-S progression. In addition, the existing nomenclature for cell cycle genes of Arabidopsis was updated, and the physical positions of all genes were compared with segmentally duplicated blocks in the genome, showing that 22 core cell cycle genes emerged through block duplications. This genome-wide analysis illustrates the complexity of the plant cell cycle machinery and provides a tool for elucidating the function of new family members in the future.
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Cotton CDK duplication favored segmental over tandem, consistent with previous results in Arabidopsis where 22 core cell cycle genes emerged through segmental duplications.
“The results obtained for cotton CDKs in which the segmental type of duplication was highly favored as opposed to the tandem is consistent with the previous results obtained in the analysis of cyclin dependent kinases in Arabidopsis, in which 22 core cell cycle genes were found to have emerged through segmental duplications [62].”
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Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302 · see citing works
Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.22.4673 · Cited by 64,617 · see citing works
Hall, T. A. (1999) · Nucleic Acids Symposium Series · doi:10.14601/phytopathol_mediterr-14998u1.29 · Cited by 38,373 · see citing works
PHYLIP-Phylogeny inference package (Version 3.2)
Felsenstein, J. (1989) · Cladistics · Cited by 17,848 · see citing works
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
Initiative, T. A. G. (2000) · Nature · doi:10.1038/35048692 · Cited by 9,301 · see citing works
Protein secondary structure prediction based on position-specific scoring matrices.
Jones, D. C. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3091 · Cited by 5,741 · see citing works
Eddy, S. R. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.9.755 · Cited by 5,515 · see citing works
Artemis: sequence visualization and annotation
Rutherford, K. M., Parkhill, J., Crook, J., Horsnell, T., Rice, P., Rajandream, M., & Barrell, B. (2000) · Bioinform. · doi:10.1093/bioinformatics/16.10.944 · Cited by 3,295 · see citing works
de Peer, Y. V., & Wächter, R. D. (1994) · Computer applications in the biosciences · doi:10.1093/bioinformatics/10.5.569 · Cited by 2,272 · see citing works
Grau, J. M. G., & Sáiz‐Jiménez, C. (2002) · Environmental Microbiology · doi:10.1046/j.1462-2920.2002.00362.x · Cited by 1,719 · see citing works
GeneMark.hmm: new solutions for gene finding
Lukashin, A. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.4.1107 · Cited by 1,536 · see citing works
Hidden Markov models for detecting remote protein homologies.
Karplus, K. J., Barrett, C., & Hughey, R. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.10.846 · Cited by 1,108 · see citing works
The Origins of Genomic Duplications in Arabidopsis
Vision, T., Brown, D. G., & Tanksley, S. D. (2000) · Science · doi:10.1126/science.290.5499.2114 · Cited by 1,034 · see citing works
Functional Analysis of Cyclin-Dependent Kinase Inhibitors of Arabidopsis
Veylder, L. D., Beeckman, T., Beemster, G. T. S., Krols, L., Terras, F. R. G., Landrieu, I., Schueren, E. V. D., Maes, S., Naudts, M., & Inzé, D. (2001) · The Plant Cell · doi:10.1105/tpc.010087 · Cited by 640 · see citing works
Self-citationExtensive Duplication and Reshuffling in the Arabidopsis Genome
Blanc, G., Barakat, A., Guyot, R., et al. (2000) · The Plant Cell · doi:10.1105/tpc.12.7.1093 · Cited by 514 · see citing works
Performance evaluation of amino acid substitution matrices
Henikoff, S., & Henikoff, J. G. (1993) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340170108 · Cited by 450 · see citing works
Hemerly, A. S., Engler, J. D. A., Bergounioux, C., et al. (1995) · The EMBO Journal · doi:10.1002/j.1460-2075.1995.tb00064.x · Cited by 416 · see citing works
TREECON: A software package for the construction and drawing of evolutionary trees
de Peer, Y. V., & Wächter, R. D. (1993) · Computer applications in the biosciences · doi:10.1093/bioinformatics/9.2.177 · Cited by 389 · see citing works
Soni, R., Carmichael, J. P., Shah, Z. H., & Murray, J. A. H. (1995) · The Plant Cell · doi:10.1105/tpc.7.1.85 · Cited by 385 · see citing works
Pedersen, A. G., & Nielsen, H. (1997) · PubMed · Cited by 305 · see citing works
Intrinsic errors in genome annotation
Devos, D. P., & Valencia, A. (2001) · Trends in Genetics · doi:10.1016/s0168-9525(01)02348-4 · Cited by 295 · see citing works
Structural basis of DNA recognition by the heterodimeric cell cycle transcription factor E2F-DPPreprint
Zheng, N., Fraenkel, E., Pabo, C. O., & Pavletich, N. P. (1999) · Genes & Development · doi:10.1101/gad.13.6.666 · Cited by 271 · see citing works
Zhang, K., Letham, D. S., & John, P. (1996) · Planta · doi:10.1007/bf00196642 · Cited by 268 · see citing works
CDK-related protein kinases in plants
Joubès, J., Chevalier, C., Dudits, D., Heberle‐Bors, E., Inzé, D., Umeda, M., & Renaudin, J. (2000) · Plant Molecular Biology · doi:10.1023/a:1006470301554 · Cited by 264 · see citing works
Self-citationRenaudin, J., Doonan, J. H., Freeman, D., Hashimoto, J., Heribert Hirt, A., Inzé, D., Jacobs, T., Kouchi, H., Rouz�, P., Sauter, M., et al. (1996) · Plant Molecular Biology · doi:10.1007/bf00041384 · Cited by 238 · see citing works
Self-citationWhen plant cells decide to divide
Stals, H., & Inzé, D. (2001) · Trends in Plant Science · doi:10.1016/s1360-1385(01)02016-7 · Cited by 233 · see citing works
Self-citationMagyar, Z., Mészáros, T., Miskolczi, P., Deák, M., Fehér, A., Brown, S., Kondorosi, É., Athanasiadis, A., Pongor, S., Bilgin, M., et al. (1997) · The Plant Cell · doi:10.1105/tpc.9.2.223 · Cited by 198 · see citing works
The E2F Family of Transcription Factors from Arabidopsis thaliana
Mariconti, L., Pellegrini, B., Cantoni, R., Stevens, R. G., Catherine Bergounioux, A., Cella, R., & Albani, D. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m110616200 · Cited by 185 · see citing works
Gene Duplication and the Structure of Eukaryotic GenomesPreprint
Friedman, R., & Hughes, A. L. (2001) · Genome Research · doi:10.1101/gr.155801 · Cited by 180 · see citing works
A Plant-specific Cyclin-dependent Kinase Is Involved in the Control of G2/M Progression in Plants
Porceddu, A., Stals, H., Reichheld, J., Segers, G., Veylder, L. D., Barrôco, R. D. P., Casteels, P., MONTAGU, M. V., Inzé, D., & Mironov, V. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m011060200 · Cited by 173 · see citing works
Self-citationCharacterization of maize ( Zea mays L.) Wee1 and its activity in developing endosperm
Sun, Y., Dilkes, B. P., Zhang, C., Dante, R. A., Carneiro, N. P., Lowe, K. S., Jung, R., Gordon-Kamm, W. J., & Larkins, B. A. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.7.4180 · Cited by 153 · see citing works
A new D-type cyclin of Arabidopsis thaliana expressed during lateral root primordia formation
Veylder, L. D., Engler, J. D. A., Burssens, S., et al. (1999) · Planta · doi:10.1007/s004250050582 · Cited by 142 · see citing works
Cell Cycle Regulation of Cyclin-Dependent Kinases in Tobacco Cultivar Bright Yellow-2 Cells
Sorrell, D. A., Menges, M., Healy, J. M. S., et al. (2001) · PLANT PHYSIOLOGY · doi:10.1104/pp.126.3.1214 · Cited by 131 · see citing works
Herrmann, C. H., & Mancini, M. A. (2001) · Journal of Cell Science · doi:10.1242/jcs.114.8.1491 · Cited by 124 · see citing works
E2F-induced S phase requires cyclin E.Preprint
Duronio, R. J., Brook, A., Dyson, N. J., & O’Farrell, P. H. (1996) · Genes & Development · doi:10.1101/gad.10.19.2505 · Cited by 124 · see citing works
Ramírez-Parra, E., Xie, Q., Boniotti, M. B., & Gutiérrez, C. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.17.3527 · Cited by 120 · see citing works
Pavy, N., Rombauts, S., Déhais, P., et al. (1999) · Bioinformatics · doi:10.1093/bioinformatics/15.11.887 · Cited by 108 · see citing works
Self-citationIsolation and characterization of the E2F‐like gene in plants
Sekine, M., Ito, M. A., Uemukai, K., Maeda, Y., Nakagami, H., & Shinmyō, A. (1999) · FEBS Letters · doi:10.1016/s0014-5793(99)01296-x · Cited by 106 · see citing works
Characterization of two distinct DP‐related genes from Arabidopsis thaliana1
Magyar, Z., Atanassova, A., Veylder, L. D., et al. (2000) · FEBS Letters · doi:10.1016/s0014-5793(00)02238-9 · Cited by 100 · see citing works
A distinct cyclin-dependent kinase-activating kinase of Arabidopsis thaliana
Umeda, M., Bhalerao, R. P., Schell, J., et al. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.9.5021 · Cited by 100 · see citing works
The Arabidopsis Cks1At protein binds the cyclin‐dependent kinases Cdc2aAt and Cdc2bAt
Veylder, L. D., Segers, G., Glab, N., et al. (1997) · FEBS Letters · doi:10.1016/s0014-5793(97)00822-3 · Cited by 100 · see citing works
Eugène: An Eukaryotic Gene Finder That Combines Several Sources of Evidence
Schiex, T., Moisan, A., & Rouzé, P. (2001) · Lecture notes in computer science · doi:10.1007/3-540-45727-5_10 · Cited by 95 · see citing works
Self-citationcDNA cloning of a novel cdc2+/CDC28‐related protein kinase from rice
Hata, S. (1991) · FEBS Letters · doi:10.1016/0014-5793(91)80271-4 · Cited by 75 · see citing works
Tolstrup, N. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.15.3159 · Cited by 73 · see citing works
Joubès, J., Lemaire‐Chamley, M., Delmas, F., et al. (2001) · PLANT PHYSIOLOGY · doi:10.1104/pp.126.4.1403 · Cited by 72 · see citing works
Brendel, V., & Kleffe, J. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.20.4748 · Cited by 72 · see citing works
de la Luna, S., Burden, M. J., Lee, C., et al. (1996) · Journal of Cell Science · doi:10.1242/jcs.109.10.2443 · Cited by 72 · see citing works
DcE2F, a Functional Plant E2F-like Transcriptional Activator from Daucus carota
Albani, D., Mariconti, L., Ricagno, S., Pitto, L., Moroni, C., Helin, K., & Cella, R. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m909390199 · Cited by 66 · see citing works
Yamaguchi, M., Umeda, M., & Uchimiya, H. (1998) · The Plant Journal · doi:10.1046/j.1365-313x.1998.00338.x · Cited by 65 · see citing works
de Peer, Y. V., Frickey, T., Taylor, J. S., & Meyer, A. (2002) · Gene · doi:10.1016/s0378-1119(02)00689-3 · Cited by 65 · see citing works
Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome
Gopal, S., Schroeder, M., Pieper, U., Sczyrba, A., Aytekin-Kurban, G., Bekiranov, S., Fajardo, J. E., Eswar, N., Sánchez, R., Šali, A., et al. (2001) · Nature Genetics · doi:10.1038/85922 · Cited by 59 · see citing works
Novel splice variants of cyclin E with altered substrate specificity
Porter, D. C. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.23.e101 · Cited by 57 · see citing works
Genome annotation: which tools do we have for it?
Rouzé, P., Pavy, N., & Rombauts, S. (1999) · Current Opinion in Plant Biology · doi:10.1016/s1369-5266(99)80019-3 · Cited by 55 · see citing works
Self-citationIdentification of novel cyclin-dependent kinases interacting with the CKS1 protein of Arabidopsis
Boudolf, V. (2001) · Journal of Experimental Botany · doi:10.1093/jexbot/52.359.1381 · Cited by 54 · see citing works
Alternative splicing in the regulatory region of the human phosphatases CDC25A and CDC25C
Wegener, S., Hampe, W., Herrmann, D., et al. (2000) · European Journal of Cell Biology · doi:10.1078/0171-9335-00115 · Cited by 53 · see citing works
Soni, R., Carmichael, J. P., Shah, Z. H., et al. (1995) · The Plant Cell · doi:10.2307/3869840 · Cited by 52 · see citing works
Rogers, K. T., Higgins, P., Milla, M. M., et al. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.15.7594 · Cited by 50 · see citing works
An Enhancer Trap Line Associated with a D-Class Cyclin Gene in Arabidopsis
Swaminathan, K., Yang, Y., Grotz, N., et al. (2000) · PLANT PHYSIOLOGY · doi:10.1104/pp.124.4.1658 · Cited by 45 · see citing works
Mumberg, D. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.11.2098 · Cited by 39 · see citing works
CDK-related protein kinases in plants
Joubès, J., Chevalier, C., Dudits, D., et al. (2000) · Springer eBooks · doi:10.1007/978-94-010-0936-2_6 · Cited by 39 · see citing works
ForCon : a software tool for the conversion of sequence alignments
Raes, J., & de Peer, Y. V. (1999) · Ghent University Academic Bibliography (Ghent University) · Cited by 37 · see citing works
Self-citationMagyar, Z., Mészáros, T., Miskolczi, P., et al. (1997) · The Plant Cell · doi:10.2307/3870543 · Cited by 33 · see citing works
Functional Analysis of Cyclin-Dependent Kinase Inhibitors of Arabidopsis
Veylder, L. D., Beeckman, T., Beemster, G. T. S., et al. (2001) · The Plant Cell · doi:10.2307/3871392 · Cited by 29 · see citing works
Extensive Duplication and Reshuffling in the Arabidopsis Genome
Blanc, G., Barakat, A., Guyot, R., et al. (2000) · The Plant Cell · doi:10.2307/3871257 · Cited by 29 · see citing works
Identification of cdc2cAt: a new cyclin-dependent kinase expressed in Arabidopsis thaliana flowers
Lessard, P., Bouly, J., Jouannic, S., et al. (1999) · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression · doi:10.1016/s0167-4781(99)00059-7 · Cited by 22 · see citing works
Cloning and functional expression of a degradation-resistant novel isoform of p27Kip1
Hirano, K., Hirano, M., Zeng, Y., Nishimura, J., Hara, K., Muta, K., Nawata, H., & Kanaide, H. (2000) · Biochemical Journal · doi:10.1042/bj3530051 · Cited by 19 · see citing works
Alternative splicing of cyclin transcripts in maize endosperm
Sun, Y., Flannigan, B. A., Madison, J. T., et al. (1997) · Gene · doi:10.1016/s0378-1119(97)00133-9 · Cited by 17 · see citing works
A distinct cyclin-dependent kinase-activating kinase of Arabidopsis thaliana,
(1998) · Current Opinion in Plant Biology · doi:10.1016/1369-5266(88)80042-6 · Cited by 15 · see citing works
Identification of novel cyclin‐dependent kinases interacting with the CKS1 protein of Arabidopsis1
Boudolf, V., Rombauts, S., Naudts, M., et al. (2001) · Journal of Experimental Botany · doi:10.1093/jxb/52.359.1381 · Cited by 3 · see citing works
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Veylder, L. D., Joubès, J., & Inzé, D. (2003) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2003.09.001 · Cited by 184 · see citing works
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Thomann, A., Brukhin, V., Dieterle, M., Gheyeselinck, J., Vantard, M., Grossniklaus, U., & Genschik, P. (2005) · The Plant Journal · doi:10.1111/j.1365-313x.2005.02467.x · Cited by 65 · see citing works
- Authors
- Vandepoele, K., Raes, J., De Veylder, L., Rouzé, P., Rombauts, S., & Inzé, D.
- Affiliations
- Vlaams Instituut voor Biotechnologie (BE)
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
- Ghent University (BE)
- Venue
- The Plant Cell
- Publisher
- Oxford University Press (OUP)
- Published
- 2002-04
- Volume
- 14
- Issue
- 4
- Pages
- 903-916
- ISSN
- 1040-4651 (ISSN-L)
- 1532-298X
- PMC
- PMC150691
- OpenAlex
- W2116163614
- Cited by
- 594
- References
- 69
- Citations by year
- 2026: 12 · 2025: 16 · 2024: 27 · 2023: 23 · 2022: 21 · 2021: 29 · 2020: 16 · 2019: 24 · 2018: 14 · 2017: 22 · 2016: 10 · 2015: 19 · 2014: 23 · 2013: 21 · 2012: 25
- FWCI
- 55.74
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- The Plant Cell (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Ghent University Academic Bibliography (Ghent University) (submittedVersion, other-oa)
- Funders
- European Commission
- Services Fédéraux des Affaires Scientifiques, Techniques et Culturelles
- Vlaamse regering
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Health Sciences › Medicine › Oncology › Cancer-related Molecular Pathways
- Keywords
- cell cycle genes, Arabidopsis thaliana genome, cyclin-dependent kinases, cyclins, genome annotation, G1/S transition, segmental duplication, gene family evolution, plant cell cycle
- MeSH terms
- Amino Acid Sequence, Carrier Proteins, Molecular Sequence Data, Terminology as Topic, Phylogeny, Cyclins, Arabidopsis, Sequence Homology, Amino Acid, Genome, Plant, Cell Cycle Proteins, Cyclin-Dependent Kinases
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