Light signalling
From Purdue Genomics Database Facility
Yoshikatsu Sato, Tadayoshi Hirai, Nagisa Sugimoto, and Tomoaki Nishiyama
(yoshi@nibb.ac.jp, tomoakin@kenroku.kanazawa-u.ac.jp)
Plants are sessile organisms and have established unique signalling pathway in response to light for their development during their life cycle (Chen, Chory, and Fankhauser 2004). Based on the phylogenetic trees, land plant orthologues were identified in all lineages for 43 of the 53 land plant orthologous group examined, which include 90 A. thaliana light signalling genes. It provides insights into the conservation of basic molecular mechanisms of the light signalling in land plants. Representative examples are COP10, DET1, DDB1A protein complex (CDD complex) and COP/DET/FUS genes which encode COP9 signalosome (CSN) subunits. The constant number of these genes during evolution may be due to exhibit multiple pairwise interactions between CSN subunits and form large complex. These two complexes function collaboratively with a COP1 E3 ubiquitin ligase in facilitating protein degradation. The system of the protein degradation mediated by COP/DET/FUS proteins was conserved in human. The blue light receptor, cryptochrome, directly interact with COP1 and inhibit degradation activity of COP1 against downstream transcription factors such as HY5, HYH, HFR1 and LAF1 in A. thaliana. A similar mechanism is proposed in the case of phytochrome A signalling. It is possible that plants innovate a way to de-etiolation by which photoreceptors have evolved to interact with COP1, because photoreceptor binding to COP1 seems to be plant specific. On the other hand, photoreceptors (phytochromes, cryptochromes, and phototropins) duplicated in each lineage in parallel as mentioned earlier studies (Lariguet and Dunand 2005, Mathews 2006). Early diverging of photoreceptors may be contributed to the functional divergence of each lineage in response to light environment. Actually, among PHYA specific signalling factors in A. thaliana, FAR1 and FHY3 genes, which encode transposase-related proteins and 12 additional FAR1-related genes designated as FRS1 to FRS12 were conserved only in angiosperm. These genes may be arisen by molecular co-evolution with PHYA signalling, because PHYA gene newly evolved in angiosperm. That may be also certainly the case with MYB trancription activator. The genes for both light perception and signal transduction were expanded in each lineage, suggesting that a range of modifications were made to the basic light signalling network in each lineage.
Contents |
Photoreceptors
Phytocrome, cryptochrome, and phototropin
Phytochromes have small, multigene families with ancient evolutionary origins as mentioned earlier studies. With a notable exceptions, there is only one phytochrome gene but cryptocromes and phototropins extensively diverged in S. moellendorffii.
A list of A. thaliana genes whose potential orthologs were not found in other lineage
Found only in dicots UV-B LIGHT INSENSITIVE 3 (ULI3) encodes a protein that has potential domains for heme- and diacylglycerol-binding and function in UV-B light-mediated responses. We can not find potential orthologs of this gene in any lineage except A. thaliana, suggesting that ULI3 newly evolved in dicots.
COP1-INTERACTIVE PROTEIN 1 (CIP1) encodes a potentially coiled-coil structure protein that associates with the coiled-coil region of COP1. We can not find potential orthologs of this gene in any lineage except A.thaliana.
COP1-INTERACTIVE PROTEIN 4 (CIP4) encodes a nuclear protein and functions as a positive regulator of photomorphogenesis. We can not find potential orthologs of this gene in any lineage except A.thaliana.
Found only in flowering plants
PHYTOCHROME KINASE SUBSTRATE 1 (PKS1) encodes a basic soluble protein that can associate with PHYA or PHYB and is proposed to be a negative regulator of phyB signalling. We can not find PKS1 potential orthologs in S. moellendorffii and P. patens, suggesting that PKS1 newly evolved in angiosperm lineages.
MINI ZINC FINGER 1 (MIF1) was suggested to be involved in integrating signals from multiple hormones, such as abscisic acid, auxin, brassinosteroid, cytokinin, and gibberellic acid. Potential orthologs of this gene was found in angiosperm, but not in other land plant lineages, suggesting that MIF1 newly evolved in angiosperm and may function in mediating regulation of the plant development by multiple hormones.
Found only vascular plants
ZINC FINGER PROTEIN 1 (ZFP1) encodes a C2H2 zinc-finger protein and show light regulated expression in the shoot apex including the apical meristem, developing leaves and the developing vascular system. This gene was conserved in A. thaliana, O. sativa, and S. moellendorffii, but not P. patens, suggesting that this gene newly evolved in vascular plant lineage and may function in vascular development.
COP1-INTERACTING PROTEIN 8 (CIP8) encodes a RING-H2 protein that associates with the RING finger domain of COP1. CIP8 facilitate degradation of HY5, positive regulater of photomorphogenesis. This gene was conserved in A. thaliana, O. sativa, and S. moellendorffii, but not P. patens, suggesting that this gene newly evolved in vascular plant lineage.
Not found in monocots
SHORT HYPOCOTYL UNDER BLUE 1 (SHB1) encodes a protein that has SYG1 protein conserved motifs and acts in cryptochrome signalling. and phyA-mediated far-red responses. SHB1 gene more extensively diverged in dicots than in other lineages. We found SHB1 potential orthologs in S. moellendorffii and P. patens, but not in O. sativa
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 | |||
| Light signalling | PHYA to E | PHYA | 5 | 3 | 1 (1) | 8 |
| Light signalling | CRY1, 2 | CRY1 | 2 | 3 | 3 (6) | 2 |
| Light signalling | CRY3 | CRY3 | 1 | 1 | 1 (2) | 1 |
| Light signalling | PHOT1 and 2 | PHOT1 | 2 | 2 | 2 (4) | 6 |
| Light signalling | HO1 to 4 | HO3 | 4 | 2 | 1 (1) | 5 |
| Light signalling | HY2 | HY2 | 1 | 1 | 1 (2) | 1 |
| Light signalling | PAT1 | PAT1 | 6 | 6 | 1 (1) | 2 |
| Light signalling | EID1 | EID1 | 1 | 1 | 1 (2) | 3 |
| Light signalling | LAF3 | LAF3 | 1 | 1 | 2 (4) | 1 |
| Light signalling | FAR1, FRS1 to 12, and FHY3 3) | FAR1 | 14 | 56 | 0 | 0 |
| Light signalling | FHY1 | FHY1 | 1 | 2 | 1 (2) | 1 |
| Light signalling | PIF1/PIL5, PIF3 and 4, PIL1 to 4, and HFR/PIL6 | PIL6 | 14 | 10 | 3 (6) | 3 |
| Light signalling | NDPK1 | NDPK2 | 1 | 2 | 1 (2) | 2 |
| Light signalling | NDPK2 | NDPK2 | 1 | 1 | 1 (2) | 2 |
| Light signalling | PP5 | PP5 | 1 | 1 | 1 (1) | 2 |
| Light signalling | PP7 | PP7 | 3 | 1 | 3 (5) | 3 |
| Light signalling | ATFYPP3 | ATFYPP3 | 2 | 1 | 1 (2) | 2 |
| Light signalling | HRB1 | HRB1 | 7 | 7 | 4 (7) | 4 |
| Light signalling | SHL1 | SHL1 | 3 | 4 | 2 (3) | 6 |
| Light signalling | SUB1 | SUB1 | 3 | 3 | 2 (3) | 1 |
| Light signalling | NPH3 | NPH3 | 2 | 1 | 3 (6) | 15 |
| Light signalling | RPT2 | RPT2 | 8 | 5 | 4 (8) | 4 |
| Light signalling | JAC1 | JAC1 | 7 | 5 | 4 (8) | 4 |
| Light signalling | PKS1 | PKS1 | 4 | 1 | 0 | 0 |
| Light signalling | CDF1 | CDF1 | 7 | 6 | 3 (4) | 4 |
| Light signalling | SHB1 | SHB1 | 9 | 0 | 3(6) | 2 |
| Light signalling | COP1 | SPA1 | 1 | 1 | 1 (2) | 9 |
| Light signalling | COP10/FUS9 | COP10 | 1 | 1 | 1 (1) | 2 |
| Light signalling | CIP8 | CIP8 | 6 | 3 | 2 (4) | 0 |
| Light signalling | SPA1 to 4 | SPA1 | 4 | 2 | 1 (2) | 2 |
| Light signalling | CIP1 | CIP1 | 1 | 0 | 0 | 0 |
| Light signalling | CIP4 | CIP4 | 2 | 0 | 0 | 0 |
| Light signalling | CIP7 | CIP7 | 6 | 3 | 5 (9) | 2 |
| Light signalling | HY5 and HYH | HY5 | 2 | 3 | 2 (4) | 2 |
| Light signalling | LAF1 | LAF1 | 3 | 3 | 0 | 0 |
| Light signalling | DET1/FUS2 | DET1 | 1 | 1 | 1 (2) | 3 |
| Light signalling | DDB1A | DDB1A | 2 | 1 | 1 (1) | 2 |
| Light signalling | COP11/FUS6 | COP11 | 1 | 1 | 1 (2) | 2 |
| Light signalling | COP12/FUS12 | FUS12 | 1 | 1 | 1 (2) | 3 |
| Light signalling | COP13/FUS11 | FUS11 | 1 | 1 | 1 (2) | 1 |
| Light signalling | COP8/FUS4/FUS8 | COP8 | 1 | 1 | 1 (2) | 1 |
| Light signalling | AJH1 and 2 | AJH2 | 2 | 1 | 1 (2) | 2 |
| Light signalling | CSN6A and B | CSN6A | 2 | 4 | 1 (2) | 2 |
| Light signalling | COP15/FUS5 | FUS5 | 1 | 1 | 1 (2) | 2 |
| Light signalling | COP9/FUS7 | COP9 | 1 | 2 | 1 (2) | 1 |
| Light signalling | AMP1 | AMP1 | 2 | 4 | 4 (7) | 2 |
| Light signalling | PFT1 | PFT1 | 1 | 1 | 2 (3) | 2 |
| Light signalling | TED3 | TED3 | 1 | 1 | 1 (2) | 1 |
| Light signalling | OBP3 | OBP3 | 13 | 4 | 0 | 0 |
| Light signalling | HLS1 | HLS1 | 4 | 4 | 1 (2) | 2 |
| Light signalling | CR88 | CR88 | 2 | 2 | 1 (1) | 2 |
| Light signalling | MIF1 | MIF1 | 3 | 3 | 0 | 0 |
| Light signalling | ZFP1 | ZFP1 | 27 | 27 | 6 (11) | 10 |
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.
Table of gene models in the assembly
| protein id | gene name | annotated by |
| PHYTOCHROMES | ||
|---|---|---|
| 161430 | PHYTOCHROME-1 | |
| 161807 | PHYTOCHROME-2 | |
| Cryptochrome related genes | ||
| 75166 | CRY1-1 | |
| 91442 | CRY1-2 | |
| 142524 | CRY2-1 | |
| 967 | CRY2-2 | |
| 92414 | CRY3-1 | |
| 114313 | CRY3-2 | |
| 106065 | CryD-1 | |
| 268379 | CryD-2 | |
| Phototropins | ||
| 230655 | PHOT1-1 | |
| 10296 | PHOT1-2 | |
| 172224 | PHOT2-1 | |
| 186203 | PHOT2-2 | |
| 97989 | HO-1 | |
| 83654 | HY2-1 | Yoshikatsu Sato |
| 151708 | HY2-2 | Yoshikatsu Sato |
| 449932 | PAT1-1 | |
| 95139 | PAT1-2 | |
| 127090 | EID1-1 | Tadayoshi Hirai |
| 133264 | EID1-2 | Tadayoshi Hirai |
| 164034 | LAF3A-1 | |
| 451266 | LAF3A-2 | |
| 166701 | FHY1-1 | Tadayoshi Hirai |
| 186552 | FHY1-2 | Tadayoshi Hirai |
| 171292 | NDPK1-1 | |
| 109077 | NDPK1-2 | |
| 174713 | NDPK2-1 | Yoshikatsu Sato |
| 443584 | NDPK2-2 | Yoshikatsu Sato |
| 270355 | NDPK3-1 | |
| 228272 | NDPK3-2 | |
| 182535 | PP5-1 | |
| 185525 | PP5-2 | Tadayoshi Hirai |
| 426688 | PP7A-1 | |
| 185987 | PP7A-2 | |
| 12808 | PP7B-1 | |
| 429646 | PP7B-2 | |
| 451287 | PP7C-1 | |
| 232099 | FYPP3-1 | |
| 270060 | FYPP3-2 | |
| 100159 | PPX-1 | |
| 118556 | PPX-2 | |
| 405842 | HRB1A-1 | |
| 451294 | HRB1A-2 | |
| 447111 | HRB1B-1 | |
| 451288 | HRB1B-2 | |
| 451290 | HRB1C1-1 | |
| 16505 | HRB1C2-1 | |
| 451293 | HRB1C1-2 | |
| 412601 | SHL1A-1 | |
| 431611 | SHL1A-2 | |
| 420725 | SHL1B-1 | |
| 445241 | SHL1B-2 | |
| 81611 | SUB1A-1 | |
| 128681 | SUB1A-2 | |
| 84756 | SUB1B-1 | |
| 104607 | SUB1B-2 | |
| 166345 | NPH3A-1 | |
| 183709 | NPH3A-2 | |
| 93693 | NPH3B-1 | |
| 108722 | NPH3B-2 | |
| 90150 | NPH3C-1 | |
| 51551 | NPH3C-2 | |
| 171333 | COP1-1 | |
| 176960 | COP1-2 | |
| 141846 | COP1L1-1 | |
| 101639 | COP1L1-2 | |
| 451298 | COP1L2-1 | |
| 451299 | COP1L2-2 | |
| 98534 | SPA1-1 | |
| 181056 | SPA1-2 | |
| 231529 | RPT2A-1 | |
| 443843 | RPT2A-2 | |
| 74933 | RPT2B-1 | |
| 118052 | RPT2B-2 | |
| 141980 | RPT2C-1 | |
| 447227 | RPT2C-2 | |
| 228979 | RPT2D-1 | |
| 272040 | RPT2D-2 | |
| 451301 | JAC1L1-1 | |
| 451303 | JAC1L1-2 | |
| 447002 | JAC1L2-1 | |
| 448911 | JAC1L2-2 | |
| 445035 | JAC1L3-1 | |
| 432122 | JAC1L3-2 | |
| 451314 | JAC1L4-1 | |
| 451308 | JAC1L4-2 | |
| 440428 | CDF1A-1 | |
| 443038 | CDF1A-2 | |
| 437759 | CDF1B-1 | |
| 444655 | CDF1B-2 | |
| 448037 | CDF1C-1 | |
| 61168 | SHB1A-1 | |
| 134638 | SHB1A-2 | |
| 405792 | SHB1B-1 | |
| 134575 | SHB1B-2 | |
| 430278 | SHB1C-2 | |
| 449731 | COP10-1 | Michael Gribskov |
| 449734 | COP10-2 | Michael Gribskov |
| 451319 | CIP8A-1 | |
| 429694 | CIP8A-2 | |
| 451322 | CIP8B-1 | |
| 451325 | CIP8B-2 | |
| 440988 | HY5A-1 | |
| 451326 | HY5A-2 | |
| 173274 | HY5B-1 | |
| 451330 | HY5B-2 | |
| 167525 | DET1-1 | Yoshikatsu Sato |
| 104399 | DET1-2 | Yoshikatsu Sato |
| 145521 | DDB1-1 | Yoshikatsu Sato |
| 151061 | DDB1-2 | Yoshikatsu Sato |
| 235966 | FUS6-1 | |
| 135331 | FUS6-2 | |
| 146093 | PSD6-1 | |
| 267709 | PSD6-2 | |
| 170816 | FUS12-1 | Nagisa Sugimoto |
| 147370 | FUS12-2 | Nagisa Sugimoto |
| 439255 | COP13-1 | Nagisa Sugimoto |
| 162886 | COP13-2 | Nagisa Sugimoto |
| 165253 | COP8-1 | Nagisa Sugimoto |
| 82579 | COP8-2 | Nagisa Sugimoto |
| 73440 | JAB1-1 | |
| 168868 | JAB1-2 | |
| 74712 | CSN6-1 | Yoshikatsu Sato |
| 230963 | CSN6-2 | Yoshikatsu Sato |
| 179250 | FUS5-1 | Yoshikatsu Sato |
| 123333 | FUS5-2 | Yoshikatsu Sato |
| 143083 | COP9-1 | |
| 182492 | COP9-2 | |
| 421595 | AMP1A-1 | |
| 134963 | AMP1A-2 | |
| 81471 | AMP1B-1 | |
| 88219 | AMP1B-2 | |
| 73556 | AMP1C-1 | |
| 119241 | AMP1C-2 | |
| 86742 | AMP1D1-2 | |
| 87649 | AMP1D2-2 | |
| 61588 | AMP1D3-1 | |
| 61589 | AMP1D1-1 | |
| 402884 | AMP1D2-1 | |
| 440592 | PFT1A-1 | |
| 442372 | PFT1A-2 | |
| 405603 | PFT1B-1 | |
| 408814 | PFT1B-2 | |
| 413661 | TED3-1 | |
| 416594 | TED3-2 | |
| 231183 | HLS1-1 | |
| 104443 | HLS1-2 | |
| 88538 | CR88-1 | |
| 448838 | CR88-2 | |
| 451343 | SHD-1 | |
| 444847 | SHD-2 | |
| 405785 | ZFP1a-1 | |
| 450816 | ZFP1b-1 | |
| 450814 | ZFP1b-2 | |
| 409409 | ZFP1c-1 | |
| 416162 | ZFP1c-2 | |
| 450832 | ZFP1d-1 | |
| 450839 | ZFP1d-2 | |
