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The Plant Cell, Vol. 14, 903-916, April 2002, Copyright © 2002,
American Society of Plant Biologists

Genome-Wide Analysis of Core Cell Cycle Genes in Arabidopsis

Klaas Vandepoelea, Jeroen Raesa,b, Lieven De Veyldera, Pierre Rouzéb, Stephane Rombautsa and Dirk Inzé1,a

a Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
b Laboratoire Associé de l'Institut National de la Recherche Agronomique (France), Universiteit Gent, B-9000 Gent, Belgium

1 To whom correspondence should be addressed. E-mail diinz{at}gengenp.rug.ac.be; fax 32-9-2645349

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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 Plant CellHome page
J. T. Leiva-Neto, G. Grafi, P. A. Sabelli, R. A. Dante, Y.-m. Woo, S. Maddock, W. J. Gordon-Kamm, and B. A. Larkins
A Dominant Negative Mutant of Cyclin-Dependent Kinase A Reduces Endoreduplication but Not Cell Size or Gene Expression in Maize Endosperm
PLANT CELL, July 1, 2004; 16(7): 1854 - 1869.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
L. Hennig, W. Gruissem, U. Grossniklaus, and C. Kohler
Transcriptional Programs of Early Reproductive Stages in Arabidopsis
Plant Physiology, July 1, 2004; 135(3): 1765 - 1775.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
D. L. Remington, T. J. Vision, T. J. Guilfoyle, and J. W. Reed
Contrasting Modes of Diversification in the Aux/IAA and ARF Gene Families
Plant Physiology, July 1, 2004; 135(3): 1738 - 1752.
[Abstract] [Full Text] [PDF]

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 Plant Cell PhysiolHome page
S. Matsunaga, W. Uchida, and S. Kawano
Sex-Specific Cell Division during Development of Unisexual Flowers in the Dioecious Plant Silene latifolia
Plant Cell Physiol., June 15, 2004; 45(6): 795 - 802.
[Abstract] [Full Text] [PDF]

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 Genome ResHome page
V. Veeramachaneni and W. Makalowski
Visualizing Sequence Similarity of Protein Families
Genome Res., June 1, 2004; 14(6): 1160 - 1169.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
G. Wang, H. Kong, Y. Sun, X. Zhang, W. Zhang, N. Altman, C. W. dePamphilis, and H. Ma
Genome-Wide Analysis of the Cyclin Family in Arabidopsis and Comparative Phylogenetic Analysis of Plant Cyclin-Like Proteins
Plant Physiology, June 1, 2004; 135(2): 1084 - 1099.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
G. West, D. Inze, and G. T.S. Beemster
Cell Cycle Modulation in the Response of the Primary Root of Arabidopsis to Salt Stress
Plant Physiology, June 1, 2004; 135(2): 1050 - 1058.
[Abstract] [Full Text] [PDF]

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 ANN BOT (LOND)Home page
S. ORMENESE, J. DE ALMEIDA ENGLER, R. DE GROODT, L. DE VEYLDER, D. INZE, and A. JACQMARD
Analysis of the Spatial Expression Pattern of Seven Kip Related Proteins (KRPs) in the Shoot Apex of Arabidopsis thaliana
Ann. Bot., May 1, 2004; 93(5): 575 - 580.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
V. Boudolf, R. Barroco, J. d. A. Engler, A. Verkest, T. Beeckman, M. Naudts, D. Inze, and L. De Veylder
B1-Type Cyclin-Dependent Kinases Are Essential for the Formation of Stomatal Complexes in Arabidopsis thaliana
PLANT CELL, April 1, 2004; 16(4): 945 - 955.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
M. Weingartner, M.-C. Criqui, T. Meszaros, P. Binarova, A.-C. Schmit, A. Helfer, A. Derevier, M. Erhardt, L. Bogre, and P. Genschik
Expression of a Nondegradable Cyclin B1 Affects Plant Development and Leads to Endomitosis by Inhibiting the Formation of a Phragmoplast
PLANT CELL, March 1, 2004; 16(3): 643 - 657.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
F. Lincker, G. Philipps, and M.-E. Chaboute
UV-C response of the ribonucleotide reductase large subunit involves both E2F-mediated gene transcriptional regulation and protein subcellular relocalization in tobacco cells
Nucleic Acids Res., February 27, 2004; 32(4): 1430 - 1438.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
R. Stevens, M. Grelon, D. Vezon, J. Oh, P. Meyer, C. Perennes, S. Domenichini, and C. Bergounioux
A CDC45 Homolog in Arabidopsis Is Essential for Meiosis, as Shown by RNA Interference-Induced Gene Silencing
PLANT CELL, January 1, 2004; 16(1): 99 - 113.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
K. Himanen, C. Reuzeau, T. Beeckman, S. Melzer, O. Grandjean, L. Corben, and D. Inze
The Arabidopsis Locus RCB Mediates Upstream Regulation of Mitotic Gene Expression
Plant Physiology, December 1, 2003; 133(4): 1862 - 1872.
[Abstract] [Full Text]

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 Plant CellHome page
Y. Yu, A. Steinmetz, D. Meyer, S. Brown, and W.-H. Shen
The Tobacco A-Type Cyclin, Nicta;CYCA3;2, at the Nexus of Cell Division and Differentiation
PLANT CELL, December 1, 2003; 15(12): 2763 - 2777.
[Abstract] [Full Text] [PDF]

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 J. Biol. Chem.Home page
B. Boisson, C. Giglione, and T. Meinnel
Unexpected Protein Families Including Cell Defense Components Feature in the N-Myristoylome of a Higher Eukaryote
J. Biol. Chem., October 31, 2003; 278(44): 43418 - 43429.
[Abstract] [Full Text] [PDF]

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 J. Cell Sci.Home page
K. Vlieghe, M. Vuylsteke, K. Florquin, S. Rombauts, S. Maes, S. Ormenese, P. Van Hummelen, Y. Van de Peer, D. Inze, and L. De Veylder
Microarray analysis of E2Fa-DPa-overexpressing plants uncovers a cross-talking genetic network between DNA replication and nitrogen assimilation
J. Cell Sci., October 15, 2003; 116(20): 4249 - 4259.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
J. M. Vinardell, E. Fedorova, A. Cebolla, Z. Kevei, G. Horvath, Z. Kelemen, S. Tarayre, F. Roudier, P. Mergaert, A. Kondorosi, et al.
Endoreduplication Mediated by the Anaphase-Promoting Complex Activator CCS52A Is Required for Symbiotic Cell Differentiation in Medicago truncatula Nodules
PLANT CELL, September 1, 2003; 15(9): 2093 - 2105.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
S. Kosugi and Y. Ohashi
Constitutive E2F Expression in Tobacco Plants Exhibits Altered Cell Cycle Control and Morphological Change in a Cell Type-Specific Manner
Plant Physiology, August 1, 2003; 132(4): 2012 - 2022.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
M. Ogawa, A. Hanada, Y. Yamauchi, A. Kuwahara, Y. Kamiya, and S. Yamaguchi
Gibberellin Biosynthesis and Response during Arabidopsis Seed Germination
PLANT CELL, July 1, 2003; 15(7): 1591 - 1604.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
A. Kono, C. Umeda-Hara, J. Lee, M. Ito, H. Uchimiya, and M. Umeda
Arabidopsis D-Type Cyclin CYCD4;1 Is a Novel Cyclin Partner of B2-Type Cyclin-Dependent Kinase
Plant Physiology, July 1, 2003; 132(3): 1315 - 1321.
[Abstract] [Full Text] [PDF]

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 J Exp BotHome page
D. Inze
Why should we study the plant cell cycle?
J. Exp. Bot., April 1, 2003; 54(385): 1125 - 1126.
[Abstract] [Full Text] [PDF]

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 J Exp BotHome page
Y. Li, J.-Q. Yu, Q.-J. Ye, Z.-J. Zhu, and Z.-J. Guo
Expression of CycD3 is transiently increased by pollination and N-(2-chloro-4-pyridyl)-N'-phenylurea in ovaries of Lagenaria leucantha
J. Exp. Bot., April 1, 2003; 54(385): 1245 - 1251.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
J. Smalle, J. Kurepa, P. Yang, T. J. Emborg, E. Babiychuk, S. Kushnir, and R. D. Vierstra
The Pleiotropic Role of the 26S Proteasome Subunit RPN10 in Arabidopsis Growth and Development Supports a Substrate-Specific Function in Abscisic Acid Signaling
PLANT CELL, April 1, 2003; 15(4): 965 - 980.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
F. Roudier, E. Fedorova, M. Lebris, P. Lecomte, J. Gyorgyey, D. Vaubert, G. Horvath, P. Abad, A. Kondorosi, and E. Kondorosi
The Medicago Species A2-Type Cyclin Is Auxin Regulated and Involved in Meristem Formation But Dispensable for Endoreduplication-Associated Developmental Programs
Plant Physiology, March 1, 2003; 131(3): 1091 - 1103.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
A. Schnittger, C. Weinl, D. Bouyer, U. Schobinger, and M. Hulskamp
Misexpression of the Cyclin-Dependent Kinase Inhibitor ICK1/KRP1 in Single-Celled Arabidopsis Trichomes Reduces Endoreduplication and Cell Size and Induces Cell Death
PLANT CELL, February 1, 2003; 15(2): 303 - 315.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
W. Dewitte, C. Riou-Khamlichi, S. Scofield, J. M. S. Healy, A. Jacqmard, N. J. Kilby, and J. A. H. Murray
Altered Cell Cycle Distribution, Hyperplasia, and Inhibited Differentiation in Arabidopsis Caused by the D-Type Cyclin CYCD3
PLANT CELL, January 1, 2003; 15(1): 79 - 92.
[Abstract] [Full Text] [PDF]

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 J. Biol. Chem.Home page
E. Lechner, D. Xie, S. Grava, E. Pigaglio, S. Planchais, J. A. H. Murray, Y. Parmentier, J. Mutterer, B. Dubreucq, W.-H. Shen, et al.
The AtRbx1 Protein Is Part of Plant SCF Complexes, and Its Down-regulation Causes Severe Growth and Developmental Defects
J. Biol. Chem., December 13, 2002; 277(51): 50069 - 50080.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
N. A. Eckardt
Ins and Outs of E2Fs
PLANT CELL, December 1, 2002; 14(12): 2977 - 2980.
[Full Text] [PDF]

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 Plant CellHome page
J. C. del Pozo, M. B. Boniotti, and C. Gutierrez
Arabidopsis E2Fc Functions in Cell Division and Is Degraded by the Ubiquitin-SCFAtSKP2 Pathway in Response to Light
PLANT CELL, December 1, 2002; 14(12): 3057 - 3071.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
E. M. Egelkrout, L. Mariconti, S. B. Settlage, R. Cella, D. Robertson, and L. Hanley-Bowdoin
Two E2F Elements Regulate the Proliferating Cell Nuclear Antigen Promoter Differently during Leaf Development
PLANT CELL, December 1, 2002; 14(12): 3225 - 3236.
[Abstract] [Full Text] [PDF]


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