Cell cycle
From Purdue Genomics Database Facility
M. Ishikawa (ishikam@nibb.ac.jp), Y. Hiwatashi, and T. Nishiyama (tomoakin@kenroku.kanazawa-u.ac.jp)
All living organisms undergo cell division, which is especially an essential event for multicellular organisms to give rise to cells that constitute tissues and organs. The eukaryotic cell cycle progression is governed by sequential waves of different cyclin and cyclin-dependent kinase (CDK) activities (Inzé and De Veylder 2006). Phylogenetic analyses of cell cycle related genes showed that the number of potential orthologs for most of each gene was similar among the land plant lineages. Cyclin A, B, and D are commonly used in cell cycle regulation in eukaryotes and their putative orthologs were found in Selaginella moellendorffii and Physcomitrella patens. It is noteworthy that the number of each cyclin and KRP, CDK inhibitor, potential ortholog was different between each land plant lineage, and angiosperms have conspicuously more CYCB, CYCD, and KRP genes than other land plants. On the other hand, the number of CYCA genes was increased in each lineage in parallel. The cyclin subunit determines which proteins are held close to the CDK and can become its substrate, suggesting that many cyclins confer different substrate specificities. Therefore, the multiple cyclin genes may be used in different tempo and space of the multicellular body of land plants, especially in angiosperms.
References
Inzé D. & De Veylder L. Cell cycle regulation in plant development. Annu. Rev. Genet. 40, 77-105 (2006)
Table of gene numbers
| Gene functions | Gene | Gene used as a query | The number of putative orthologs | |||
|---|---|---|---|---|---|---|
| Arabidopsis thaliana | Oryza sativa | Selaginalla moellendorffii (a) | Physcomitrella patens | |||
| Cell cycle regulation | CDKA;1 | CDKA;1 | 1 | 3 | 1 (1) | 2 |
| Cell cycle regulation | CDKB1;1 and 1;2 | CDKB1;1 | 2 | 1 | 2 (3) | 7 |
| Cell cycle regulation | CDKB2;1 and 2;2 | CDKB1;1 | 2 | 1 | 0 | 0 |
| Cell cycle regulation | CDKC;1 to 2 | CDKC;1 | 2 | 2 | 1 (2) | 3 |
| Cell cycle regulation | CDKD;1 to 3 | CDKD;1 | 3 | 1 | 1 (2) | 3 |
| Cell cycle regulation | CDKE;1/HEN3 | CDKE;1 | 1 | 1 | 1 (1) | 2 |
| Cell cycle regulation | CDKF;1 | CDKF;1 | 1 | 1 | 1 (2) | 1 |
| Cell cycle regulation | CYCA1;1 to 2, A2;1 to 4, and A3;1 to 4 | CYCA1;1 | 10 | 7 | 3 (6) | 8 |
| Cell cycle regulation | CYCB1;1 to 5, B2;1 to 5, and B3;1 | CYCB1;1 | 11 | 5 | 1 (2) | 2 |
| Cell cycle regulation | CYCD1;1, D2;1, D3;1 to 3, D4;1 to 2, D5;1, D6;1, and D7;1 2) | CYCD1;1 | 10 | 12 | 3 (5) | 2 |
| Cell cycle regulation | CYCH1;1 | CYCH1;1 | 1 | 1 | 1 (2) | 2 |
| Cell cycle regulation | KRP1 to 7 | KRP4 | 7 | 6 | 3 (6) | 1 |
| Cell cycle regulation | RBR1 | RBR1 | 1 | 2 | 2 (4) | 3 |
| Cell cycle regulation | E2FA, B, and C | E2Fa | 3 | 3 | 2 (4) | 4 |
| Cell cycle regulation | DEL1, 2, and 3 | DEL1 | 3 | 2 | 1 (2) | 3 |
| Cell cycle regulation | WEE1 | WEE1 | 1 | 1 | 2 (3) | 1 |
| Cell cycle regulation | Arath;CDC25 | ARATH;CDC25 | 1 | 2 | 1 (2) | 1 |
| Cell cycle regulation | HBT | HBT | 2 | 1 | 2 (3) | 2 |
| Cell cycle regulation | ANP1 | ANP1 | 3 | 2 | 1 (2) | 2 |
footnote: The number of putative orthologs here refers to number of genes that is included in a clade that corresponds to all genes derived from a single gene in the last common ancestor of P. patens, S. moellendrffii, A. thaliana, and O. sativa based on phylogenetic analyses. The alignments and trees are available through http://moss.nibb.ac.jp/treedb/ (a) number of putative loci at first and number of putative alleles detected in parentheses. That is, 1 (2), indicates we found two sequences that likely represent two alleles of one locus.
Table of gene models in the assembly
| protein id | gene name | name given by |
| 139306 | CDKA-1 | |
| 271676 | CDKA-2 | |
| 110637 | CDKB1A-1 | |
| 135071 | CDKB1A-2 | |
| 230893 | CDKB1B-1 | |
| 108475 | CDKB1B-2 | |
| 142167 | CDKC1-1 | Masaki Ishikawa |
| 169412 | CDKC1-2 | |
| 451489 | CRK1-1 | |
| 451492 | CRK1-2 | |
| 141733 | CRK2-1 | |
| 442565 | CRK2-2 | |
| 100958 | CDKD-1 | |
| 122588 | CDKD-2 | |
| 110606 | CDKE-1 | |
| 128208 | CDKE-2 | |
| 408721 | CDKF-1 | |
| 444958 | CDKF-2 | |
| 412894 | CYCA1-1 | |
| 423455 | CYCA1-2 | |
| 412891 | CYCA2-1 | |
| 423452 | CYCA2-2 | |
| 442428 | CYCA3-1 | |
| 234858 | CYCA3-2 | |
| 230742 | CYCB1-1 | |
| 231762 | CYCB1-2 | |
| 412774 | CYCD1-1 | |
| 417325 | CYCD1-2 | |
| 420671 | CYCD2-1 | |
| 421971 | CYCD2-2 | |
| 420672 | CYCD3-1 | |
| 421972 | CYCD3-2 | |
| 163567 | CYCH-1 | |
| 445744 | CYCH-2 | |
| 414644 | KRP1-1 | |
| 424738 | KRP1-2 | |
| 451520 | KRP2-1 | |
| 451516 | KRP2-2 | |
| 412497 | KRP3-1 | |
| 451521 | KRP3-2 | |
| 97707 | RBR1-1 | |
| 180795 | RBR1-2 | |
| 451524 | RBR2-1 | |
| 451523 | RBR2-2 | |
| 445661 | E2F1-1 | Masaki Ishikawa |
| 229421 | E2F1-2 | Masaki Ishikawa |
| 137588 | E2F2-1 | Masaki Ishikawa |
| 136738 | E2F2-2 | Masaki Ishikawa |
| 421405 | DEL1-1 | |
| 425021 | DEL1-2 | |
| 451533 | WEE1-1 | |
| 451532 | WEE1-2 | |
| 451535 | CDC25-1 | |
| 100212 | CDC25-2 | |
| 409868 | HBT1-1 | |
| 431029 | HBT1-2 | |
| 451540 | CDC23-1 | |
| 268860 | CDC23-2 | |
| 230838 | NPK1-1 | |
| 108118 | NPK1-2 |
