Phase transition

From Purdue Genomics Database Facility

T. Kurata, N. Aono, T. Nishiyama

tekurata@nibb.ac.jp, tomoakin@kenroku.kanazawa-u.ac.jp

Polycomb repressive complex 2 (PRC2), which functions in developmental transitions, is composed of E(Z), ESC, Su(z)12, and p55 homologues (Guitton and Berger, 2005). All components were found in all of the lineages, and Su(z)12 homologues (EMF2, FIS2, and VERN2/VEF1) were expanded in the angiosperm and moss lineages. These three genes function in the vegetative to reproductive transition, developmental arrest of the endosperm before fertilization, and vernalization, respectively, in A. thialiana. Expansions of these genes in angiosperm lineage are likely related to the evolution of specific regulation of the angiosperm life cycle. The switch from vegetative to reproductive growth in A. thaliana is induced by the transcription factor CO (Baurle and Dean, 2006; Blazquez et al., 2006), which in turn induces the FT signal. TFL1, the sister of FT, has a repressive role in flowering. CO and its putative orthologues were found in all land plants as well as in green algae, whilst putative orthologues of FT and TFL1 were found only in angiosperms. The floral repression pathway, which regulates the competence of the shoot apical meristem, is mediated by a MIKCC-type MADS-box gene FLC, whilst another MIKCC-type MADS box gene SOC and a bZIP gene FD are involved in an inductive pathway (Baurle and Dean, 2006; Blazquez et al., 2006). The MIKCC-type MADS-box genes were extensively expanded in the angiosperms, which resulted in the evolution of FLC and SOC. We could not find a putative orthologue of FD in S. moellendorffii or P. patens. The repression of FLC is managed by vernalization and an autonomous system. Vernalization in non-seed plants has not been well characterized, but a developmental response to cold temperature has been reported (Hohe et al., 2002). In A. thaliana, epigenetic factors are involved in vernalisation, such as the polycomb group gene VRN2, the DNA-binding protein coding gene VRN1, the heterochromatin protein 1 homologue TFL2/LHP1, and the PHD finger protein coding gene VIN3 (Baurle and Dean, 2006). Putative orthologues of the latter two genes were not found in P. patens, whilst those of VRN1 were extensively expanded. These data suggest divergence of the genetic network involved vernalization, if it exists. Chromatin-associated proteins and RNA-binding/processing factors are involved in the autonomous pathway of flowering. Putative orthologues of FLD, which has been implicated in histone demethylation, and those of FCA, FY, FPA, and FLK, which have direct and/or indirect RNA-binding activities (Baurle and Dean, 2006), were found in all land plants, indicating that the networks involving these genes existed before the evolution of flowering.

References

Baurle, I., and Dean, C. (2006). The timing of developmental transitions in plants. Cell 125, 655-664.

Blazquez, M.A., Ferrandiz, C., Madueno, F., and Parcy, F. (2006). How floral meristems are built. Plant Mol. Biol. 60, 855-870.

Guitton, A.E., and Berger, F. (2005). Control of reproduction by Polycomb Group complexes in animals and plants. Int. J. Dev. Biol. 49, 707-716.

Hohe, A., Rensing, S.A., Mildner, M., Lang, D., and Reski, R. (2002). Day length and temperature strongly influence sexual reproduction and expression of a novel MADS-box gene in the moss Physcomitrella patens. Plant Biol. 4, 595-602.

Table of gene numbers

note: 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.

Gene functions	Gene	Gene used as a query	The number of putative orthologs
			Arabidopsis thaliana	Oryza sativa	Selaginalla moellendorffii (a)	Physcomitrella patens
Phase transition	CLF	MEA	1	1	1 (2)	1
Phase transition	MEA	MEA	1	0	0	0
Phase transition	SWN	MEA	1	1	0	0
Phase transition	FIE	FIE	1	2	1 (2)	1
Phase transition	EMF2, FIS2, and VRN2/VEF1	EMF2	4	2	1 (2)	3
Phase transition	MSI1	MSI1	1	1	1 (2)	1
Flowering	CO	CO	18	17	3 (5)	6
Flowering	FT and TFL1	FT	5	14	0	0
Flowering	FD	FD	2	1	0	0
Flowering	VRN1	VRN1	1	2	1 (2)	6
Flowering	VIP2	VIP2	2	3	1 (2)	3
Flowering	VIP3	VIP3	1	1	1 (2)	2
Flowering	VIP4	VIP4	1	2	1 (2)	1
Flowering	TFL2/LHP1	TFL2	1	1	1 (2)	0
Flowering	VIN3	VIN3	4	4	2 (3)	0
Flowering	FLD	FLD	3	3	1 (2)	2
Flowering	FPA	FPA	2	2	1 (2)	2
Flowering	FLK	FLK	2	5	1 (2)	2