Plant Physiology 135:1084-1099 (2004)
© 2004 American Society of Plant Biologists
GENETICS, GENOMICS, AND MOLECULAR EVOLUTION
Genome-Wide Analysis of the Cyclin Family in Arabidopsis and Comparative Phylogenetic Analysis of Plant Cyclin-Like Proteins1,[w]
Guanfang Wang2,
Hongzhi Kong2,
Yujin Sun2,
Xiaohong Zhang,
Wei Zhang,
Naomi Altman,
Claude W. dePamphilis and
Hong Ma*
Department of Biology and the Huck Institutes of Life Sciences (G.W., H.K., Y.S., X.Z., W.Z., C.W.D., H.M.), Intercollege Graduate Program in Plant Physiology (G.W., H.M.), Institute of Molecular Evolutionary Genetics (H.K., C.W.D., H.M.), and Department of Statistics (N.A.), Pennsylvania State University, University Park, Pennsylvania 16802; and Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China (H.K.)
Cyclins are primary regulators of the activity of cyclin-dependent kinases, which are known to play critical roles in controlling eukaryotic cell cycle progression. While there has been extensive research on cell cycle mechanisms and cyclin function in animals and yeasts, only a small number of plant cyclins have been characterized functionally. In this paper, we describe an exhaustive search for cyclin genes in the Arabidopsis genome and among available sequences from other vascular plants. Based on phylogenetic analysis, we define 10 classes of plant cyclins, four of which are plant-specific, and a fifth is shared between plants and protists but not animals. Microarray and reverse transcriptase-polymerase chain reaction analyses further provide expression profiles of cyclin genes in different tissues of wild-type Arabidopsis plants. Comparative phylogenetic studies of 174 plant cyclins were also performed. The phylogenetic results imply that the cyclin gene family in plants has experienced more gene duplication events than in animals. Expression patterns and phylogenetic analyses of Arabidopsis cyclin genes suggest potential gene redundancy among members belonging to the same group. We discuss possible divergence and conservation of some plant cyclins. Our study provides an opportunity to rapidly assess the position of plant cyclin genes in terms of evolution and classification, serving as a guide for further functional study of plant cyclins.
1 This work was supported by the National Institutes of Health (grant no. RO1 GM63871), the National Science Foundation (grant nos. MCB-0092075, IBN-0077832, and DBI-0115684), the National Natural Science Foundation of China (grant no. 30130030 to Anmin Lu), the Intercollege Graduate Program in Plant Physiology at the Pennsylvania State University (G.W.), and by funds from the Department of Biology and the Huck Institutes of Life Sciences at the Pennsylvania State University. This is the Floral Genome Project's publication number 20.
2 These authors contributed equally to this paper.
[w] The online version of this article contains Web-only data.
Article, publication date, and citation information can be found at www.plantphysiol.org/cgi/doi/10.1104/pp.104.040436.
* Corresponding author; e-mail hxm16{at}psu.edu; fax 814–863–1357.
Received February 3, 2004;
returned for revision April 6, 2004;
accepted April 6, 2004.
This article has been cited by other articles:
|
|
|
|
 
R. C. Day, R. P. Herridge, B. A. Ambrose, and R. C. Macknight
Transcriptome Analysis of Proliferating Arabidopsis Endosperm Reveals Biological Implications for the Control of Syncytial Division, Cytokinin Signaling, and Gene Expression Regulation
Plant Physiology,
December 1, 2008;
148(4):
1964 - 1984.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
N. Riehs, S. Akimcheva, J. Puizina, P. Bulankova, R. A. Idol, J. Siroky, A. Schleiffer, D. Schweizer, D. E. Shippen, and K. Riha
Arabidopsis SMG7 protein is required for exit from meiosis
J. Cell Sci.,
July 1, 2008;
121(13):
2208 - 2216.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
M. Menges, G. Pavesi, P. Morandini, L. Bogre, and J. A.H. Murray
Genomic Organization and Evolutionary Conservation of Plant D-Type Cyclins
Plant Physiology,
December 1, 2007;
145(4):
1558 - 1576.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
A. Peres, M. L. Churchman, S. Hariharan, K. Himanen, A. Verkest, K. Vandepoele, Z. Magyar, Y. Hatzfeld, E. Van Der Schueren, G. T. S. Beemster, et al.
Novel Plant-specific Cyclin-dependent Kinase Inhibitors Induced by Biotic and Abiotic Stresses
J. Biol. Chem.,
August 31, 2007;
282(35):
25588 - 25596.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
T. Ruttink, M. Arend, K. Morreel, V. Storme, S. Rombauts, J. Fromm, R. P. Bhalerao, W. Boerjan, and A. Rohde
A Molecular Timetable for Apical Bud Formation and Dormancy Induction in Poplar
PLANT CELL,
August 1, 2007;
19(8):
2370 - 2390.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
A. Kono, C. Umeda-Hara, S. Adachi, N. Nagata, M. Konomi, T. Nakagawa, H. Uchimiya, and M. Umeda
The Arabidopsis D-Type Cyclin CYCD4 Controls Cell Division in the Stomatal Lineage of the Hypocotyl Epidermis
PLANT CELL,
April 1, 2007;
19(4):
1265 - 1277.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
X. Cui, B. Fan, J. Scholz, and Z. Chen
Roles of Arabidopsis Cyclin-Dependent Kinase C Complexes in Cauliflower Mosaic Virus Infection, Plant Growth, and Development
PLANT CELL,
April 1, 2007;
19(4):
1388 - 1402.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
N. Dissmeyer, M. K. Nowack, S. Pusch, H. Stals, D. Inze, P. E. Grini, and A. Schnittger
T-Loop Phosphorylation of Arabidopsis CDKA;1 Is Required for Its Function and Can Be Partially Substituted by an Aspartate Residue
PLANT CELL,
March 1, 2007;
19(3):
972 - 985.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
K. De Schutter, J. Joubes, T. Cools, A. Verkest, F. Corellou, E. Babiychuk, E. Van Der Schueren, T. Beeckman, S. Kushnir, D. Inze, et al.
Arabidopsis WEE1 Kinase Controls Cell Cycle Arrest in Response to Activation of the DNA Integrity Checkpoint
PLANT CELL,
January 1, 2007;
19(1):
211 - 225.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
A. J. Wijeratne, C. Chen, W. Zhang, L. Timofejeva, and H. Ma
The Arabidopsis thaliana PARTING DANCERS Gene Encoding a Novel Protein Is Required for Normal Meiotic Homologous Recombination
Mol. Biol. Cell,
March 1, 2006;
17(3):
1331 - 1343.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
A. Verkest, C. Weinl, D. Inze, L. De Veylder, and A. Schnittger
Switching the Cell Cycle. Kip-Related Proteins in Plant Cell Cycle Control
Plant Physiology,
November 1, 2005;
139(3):
1099 - 1106.
[Full Text]
[PDF]
|
|
|
|
|
|
|
N. H. Masubelele, W. Dewitte, M. Menges, S. Maughan, C. Collins, R. Huntley, J. Nieuwland, S. Scofield, and J. A. H. Murray
D-type cyclins activate division in the root apex to promote seed germination in Arabidopsis
PNAS,
October 25, 2005;
102(43):
15694 - 15699.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
G. T.S. Beemster, L. De Veylder, S. Vercruysse, G. West, D. Rombaut, P. Van Hummelen, A. Galichet, W. Gruissem, D. Inze, and M. Vuylsteke
Genome-Wide Analysis of Gene Expression Profiles Associated with Cell Cycle Transitions in Growing Organs of Arabidopsis
Plant Physiology,
June 1, 2005;
138(2):
734 - 743.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
E. Kondorosi, M. Redondo-Nieto, and A. Kondorosi
Ubiquitin-Mediated Proteolysis. To Be in the Right Place at the Right Moment during Nodule Development
Plant Physiology,
April 1, 2005;
137(4):
1197 - 1204.
[Full Text]
[PDF]
|
|
|
|
|
|
|
K. Bisova, D. M. Krylov, and J. G. Umen
Genome-Wide Annotation and Expression Profiling of Cell Cycle Regulatory Genes in Chlamydomonas reinhardtii
Plant Physiology,
February 1, 2005;
137(2):
475 - 491.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
Y. Wang, J.-L. Magnard, S. McCormick, and M. Yang
Progression through Meiosis I and Meiosis II in Arabidopsis Anthers Is Regulated by an A-Type Cyclin Predominately Expressed in Prophase I
Plant Physiology,
December 1, 2004;
136(4):
4127 - 4135.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
