Cytoskeletons
From Purdue Genomics Database Facility
Takashi Murata (tkmurata@nibb.ac.jp), Tomomichi Fujita, Yuji Hiwatashi, Tomoaki Nishiyama (tomoakin@kenroku.kanazawa-u.ac.jp), and Mitsuyasu Hasebe
Assembly and subsequent organization of cytoskeletons are essential for plant development.
Contents |
Actin
Actin microfilaments (F-actin) are assembled from monomeric actin (G-actin) via nucleator proteins. Formin nucleates linear microfilaments de novo (Evangelista, 2003). The common ancestor of land plants had a few formin genes, and the formin gene family was expanded in angiosperm lineage. In case of group I formin, which has a transmembrane domain in N-terminous, only one gene was found in S. moellendorffii gemome. Six genes in P. patens, nine genes in O. sativa, and 11 genes in A. thaliana were found. No ortholog of group I formin was detected in a C. reinhardtii genome. Phylogenetic tree analyses revealed that group I formin genes were duplicated in P. patens and angiosperms independently. The fact suggests that functional divergence of formin genes in angiosperms occurred after the divergence of angiosperm from S. moellendorffii. Another F-actin nucleator an Arp2/3 complex nucleates F-actin on a pre-existing F-actin as a branch in metazoan cells (Pollard, 2000). Genes for the complexes are well conserved in all of the land plant genomes. The complexes are involved in cellular morphogenesis of trichomes and leaf pavement cells via formation of a fine F-actin meshwork in A. thaliana (Deeks and Hussey 2005). In contrast to formins, the numbers of genes involved in the Arp2/3 complexes are similar among the land plant genomes. The numbers of genes of a scar complex, an activator of Arp2/3 complex, are similar among each lineage except for WAVE potential orthologs, whose numbers are increased in both P. patens and angiosperms. No potential ortholog of WAVE complex genes were found in the C. reinhardtii genome. Villin and fimbrin are F-actin bundling factors, and the number of genes are similar in all land plants examined. In contrast, number of genes of F-actin depolymerizing factor, ADF, are expanded in angiosperms.
Microtubules
Microtubules are assembled on seeds of gamma-tubulin complexes (Job 2003). A metazoan gamma-tubulin complex contains five proteins of Spc98 superfamily, gamma-tubulin, and the putative targeting factor NEDD1. All of the genes were found in all land plant genomes examined. After nucleation by gamma-tubulin complexes, the nascent microtubules are reorganized by severing, bundling and stabilization (Wasteneys 2002, Sedbrook 2004). The number of the severing factor katanin gene was mostly stable in all lineages, while the members of the putative stabilizing factors, MAP215 family and EB1 family, orthologs of SPR1 and SPR2, which is involved in organization of the cortical arrays, and the microtubule bundling factor MAP65 family were expanded in each land plant lineage. A preprophase band determines the site of cytokinesis before the onset of mitosis in land plants. FASS gene in A. thaliana, which codes phosphatase 2A, is essential for preprophase band formation. FASS gene was conserved in S. moellendorffii and P. patens.
Rop GTPases
Small G proteins regulate cytoskeletal formation in many organisms. Flowering plants have their specific small G proteins, Rop GTPases. Rop potential orthologs were found in all the land plants and C. merolae, but not found in C. reinhardtii. Flowering plans have conspicuously more Rop homologs than other land plants have, suggesting their functional divergence in flowering plants.
References
M. J. Deeks, P. J. Hussey, Nature Reviews Molecular Cell Biology 6, 954 (2005)
M. Evangelista, S. Zigmond, C. Boone, Journal of Cell Science 116, 2603 (2003)
D. Job, O. Valiron, B. Oakley, Current Opinion in Cell Biology 15, 111 (2003)
T. D. Pollard, L. Blanchoin, R. D. Mullins, Annual Revew of Biophysics and Biomolecular Structure 29, 545 (2000)
J. C. Sedbrook, Current Opinion in Plant Biology 7, 632 (2004)
G. O. Wasteneys, Journal of Cell Science 115, 1345 (2002)
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 | |||
| Cytoskeleton | ATFH1 to 11 | ATFH8 | 11 | 9 | 1 (1) | 6 |
| Cytoskeleton | ATFH13 to 19, and 21 | AT2G25050 | 8 | 5 | 2 (3) | 2 |
| Cytoskeleton | ARP2/WRM | WRM | 1 | 1 | 1 (2) | 1 |
| Cytoskeleton | ARP3/DIS1 | DIS1 | 1 | 1 | 1 (2) | 2 |
| Cytoskeleton | ARPC1a and b | ARPC1b | 2 | 1 | 1 (2) | 2 |
| Cytoskeleton | ARPC2A/DIS2 and ARPC2B | DIS2 | 2 | 2 | 1 (2) | 2 |
| Cytoskeleton | ARPC3 | ARPC3 | 1 | 1 | 1 (2) | 2 |
| Cytoskeleton | ARPC4 | ARPC4 | 1 | 1 | 1 (2) | 1 |
| Cytoskeleton | ARPC5/CRK | CRK | 1 | 1 | 1 (2) | 1 |
| Cytoskeleton | WAVE1 to 5/SCAR1 to 5 | WAVE5 | 5 | 3 | 2 (3) | 7 |
| Cytoskeleton | ABI1L1 | ABI1L1 | 4 | 6 | 1 (2) | 2 |
| Cytoskeleton | PIR121/KLK/SRA1 | KLK | 1 | 1 | 1 (2) | 2 |
| Cytoskeleton | NAP125/GRL | GRL | 1 | 1 | 1 (2) | 2 |
| Cytoskeleton | HSPC300/BRK1 | BRK1 | 1 | 1 | 1 (2) | 1 |
| Cytoskeleton | ADF1 | ADF1 | 12 | 10 | 3 (6) | 1 |
| Cytoskeleton | VLN1 to 4 | VLN3 | 5 | 5 | 1 (2) | 3 |
| Cytoskeleton | ATFIM1 | ATFIM1 | 5 | 3 | 2 (4) | 2 |
| Cytoskeleton | PRF1 | PRF1 | 5 | 3 | 1 (2) | 3 |
| Cytoskeleton | TUBG1 and 2 | TUBG1 | 2 | 1 | 1 (2) | 2 |
| Cytoskeleton | ATSPC97 | AT5G17410 | 1 | 1 | 1 (2) | 3 |
| Cytoskeleton | ATSPC98 | ATSPC98 | 1 | 1 | 1 (2) | 3 |
| Cytoskeleton | ATGCP4 | AT3G53760 | 1 | 1 | 1 (2) | 1 |
| Cytoskeleton | ATGCP5/EMB1427 | AT1G80260 | 2 | 2 | 1 (2) | 1 |
| Cytoskeleton | ATGCP6 | OSJNBa0005N02.6 | 1 | 1 | 1 (2) | 1 |
| Cytoskeleton | ATNEDD1 | AT5G05970 | 1 | 1 | 2 (3) | 4 |
| Cytoskeleton | ERH3/FRA2 | ERH3 | 1 | 2 | 1 (2) | 2 |
| Cytoskeleton | MOR1/GEM1 | MOR1 | 1 | 1 | 1 (2) | 2 |
| Cytoskeleton | ATEB1A | ATEB1A | 3 | 2 | 3 (6) | 3 |
| Cytoskeleton | SPR1/SKU6 | SPR1 | 5 | 4 | 2 (4) | 4 |
| Cytoskeleton | SPR2/TOR1 | SPR2 | 6 | 4 | 2 (4) | 4 |
| Cytoskeleton | ATMAP65-1 to 9 | ATMAP65-1 | 9 | 11 | 5 (8) | 5 |
| Cytoskeleton | ROP1 to 11 | ROP2 | 11 | 7 | 2 (4) | 4 |
| Cytoskeleton | FASS/TON2 | FASS | 1 | 1 | 1 (2) | 1 |
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. See http://wiki.genomics.purdue.edu/index.php/Evolution_of_developmental_genes#Methods for brief methods.
