Auxin
From Purdue Genomics Database Facility
N. Shinohara (shino@nibb.ac.jp) , Y Hiwatashi, T. Aoyama, N. Aono, T. Hirai, and T. Nishiyama (tomoakin@kenroku.kanazawa-u.ac.jp)
Contents |
Auxin biosynthesis and metabolism
Auxin is involved in various aspects of plant development (Murphy 2002). CYP79B2, CYP79B3, CYP83B1/SUR2, NIT1, NIT2, NIT3, YUCCA, and AAO operate in the Trp-dependent biosynthesis pathways (Woodward and Bartel, 2005a). Potential orthologs except the last two genes were not found in S. moellendorffii and P. patens. This suggests the diversity of Trp-dependent pathways among land plant lineages. Endogenous IAA levels are also controlled by metabolisms of IAA conjugates. Seven of 19 members in A. thaliana GH3 gene family are responsible for IAA-amide formation (Staswick et al., 2005). Potential orthologs of DFL1 of this family were found in all the land plant lineages and angiosperms have more potential orthologs than S. moellendorffii and P. patens have. This is concordant with the lower levels of IAA conjugates in basal land plants than angiosperms (Sztein et al., 1995).
Auxin signaling
The wide array of auxin actions in flowering plants is mediated by three groups of proteins: TIR1/AFB F-box proteins that perceive auxin molecules, Aux/IAA transcription repressors, and ARF transcription activators (Weijers and Jurgens, 2004). We found all the three gene families in each land plant, suggesting the conservation of auxin signaling system in land plants. TIR1 functions as an auxin receptor and COI1 presumably functions as a jasmonic acid receptor (Woodward and Bartel, 2005b). Phylogenetic trees of their homologs showed that TIR1 and COI1 orthologs diverged before the divergence of P. patens from other land plants. This is concordant with the divergence time of two GH3 gene groups, the DFL homologs that function in jasmonic acid and IAA-amido synthases. The number of Aux/IAA genes was conspicuously increased in the angiosperm lineage after the branching of S. moellendorffii, and we found four and two Aux/IAA potential orthologs in S. moellendorffii and P. patens (Table). The change in the number of Aux/IAA genes likely influenced the auxin signaling systems in land plants. Twenty-three members of A. thaliana ARF genes were classified into three groups (Okushima et al., 2005), and S. moellendorffii and P. patens have potential orthologs for all the groups. The numbers of ARF homologs were increased in each angiosperm, S. moellendorffii, and P. patens lineage, and as a result, each group has similar number of ARF genes in each genome.
Auxin carriers
An auxin polar transport is necessary for a proper development in all land plants examined (Cooke et al., 2002). AUX/LAX genes are involved in auxin influx to a cell, and PIN and PGP/MDR genes are in efflux. These carriers are necessary for a proper polar auxin transport. We could find AUX/LAX, PGP/MDR, and PIN potential orthologs in S. moellendorffii and P. patens. A. thaliana PIN paralogs function in different organs. PIN5 phylogenetic tree showed that they diverged in the angiosperm lineage after the branching of S. moellendorffii, although the bootstrap supports are not high. AUX paralogs were also diverged in each angiosperm, S. moellendorffii, and P. patens lineage.
References
Murphy A (2002) Auxin: the growth hormone. In L Taiz, E Zeiger, eds, Plant Physiology, Ed 3. Sinauer Associates Inc. Publishers, Sunderland, MA, pp pp 423–460
Cooke, T.J., Poli, D., Sztein, A.E., and Cohen, J.D. (2002). Evolutionary patterns in auxin action. Plant Mol Biol 49, 319-338.
Okushima, Y., Overvoorde, P.J., Arima, K., Alonso, J.M., Chan, A., Chang, C., Ecker, J.R., Hughes, B., Lui, A., Nguyen, D., Onodera, C., Quach, H., Smith, A., Yu, G., and Theologis, A. (2005). Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19. Plant Cell 17, 444-463.
Staswick, P.E., Serban, B., Rowe, M., Tiryaki, I., Maldonado, M.T., Maldonado, M.C., and Suza, W. (2005). Characterization of an Arabidopsis enzyme family that conjugates amino acids to indole-3-acetic acid. Plant Cell 17, 616-627.
Sztein, A.E., Cohen, J.D., Slovin, J.P., and Cooke, T.J. (1995). Auxin metabolism in representative land plants. American Journal of Botany 82, 1514-1521.
Weijers, D., and Jurgens, G. (2004). Funneling auxin action: specificity in signal transduction. Curr Opin Plant Biol 7, 687-693.
Woodward, A.W., and Bartel, B. (2005a). A receptor for auxin. Plant Cell 17, 2425-2429.
Woodward, A.W., and Bartel, B. (2005b). Auxin: regulation, action, and interaction. Ann Bot (Lond) 95, 707-735.
Table of gene numbers in each species
| Gene functions | Gene | Gene used as a query | The number of putative orthologs | |||
|---|---|---|---|---|---|---|
| Arabidopsis thaliana | Oryza sativa | Selaginalla moellendorffii | Physcomitrella patens | |||
| Auxin metabolism | YUCCA | YUCCA | 9 | 8 | 3 (6) | 6 |
| Auxin metabolism | CYP79B2 and B3 1) | CYP79B2 | 2 | 0 | 0 | 0 |
| Auxin metabolism | NIT1-3 | NIT1 | 3 | 0 | 0 | 0 |
| Auxin metabolism | CYP83B1/SUR2 1) | SUR2 | 2 | 0 | 0 | 0 |
| Auxin metabolism | GH3.6/DFL1 2) | GH3.6/DFL1 | 19 | 11 | 17 (29) | 2 |
| Auxin metabolism | AAO1 | AAO1 | 4 | 6 | 3 (5) | 2 |
| Auxin metabolism | TYDC1, 2 | TYDC2 | 2 | 1 | 5 (9) | 2 |
| Auxin metabolism | CYP79F1/SPS1 | SUPERSHOOT1 | 8 | 3 | 0 | 0 |
| Auxin signalling | TIR1 | TIR1 | 6 | 6 | 2 (4) | 4 |
| Auxin signalling | ABP1 | ABP1 | 1 | 1 | 2 (4) | 1 |
| Auxin signalling | IAA1 to 20, 26 to 34 2) | IAA31 | 29 | 30 | 4 (7) | 2 |
| Auxin signalling | ARF5/MP, NPH4/BIPOSTO, ARF6, 8, 16, and 19 2) | NPH4 | 5 | 8 | 3 (5) | 6 |
| Auxin signalling | ETT/ARF3, ARF1, 2, 4, 9, 11 to 15, 18, 20, and 21 | ETT | 15 | 9 | 2 (4) | 4 |
| Auxin signalling | ARF10, ARF16 | ARF16 | 2 | 4 | 2 (4) | 2 |
| Auxin signalling | ARF17 | ARF16 | 1 | 1 | 0 | 0 |
| Auxin signalling | AXR1 2) | AXR1 | 3 | 1 | 1 (2) | 2 |
| Auxin signalling | SKP1/ASK1 | SKP1 | 17 | 12 | 1 (2) | 3 |
| Auxin signalling | AXR6/ATCUL1 | ATCUL1 | 2 | 3 | 1 (2) | 3 |
| Auxin signalling | RCE1 | RCE1 | 2 | 3 | 3 (5) | 5 |
| Auxin carriers | AUX1 | AUX1 | 4 | 4 | 2 (4) | 4 |
| Auxin carriers | PIN1 to 8 2) | PIN5 | 9 | 11 | 5 (7) | 3 |
| Auxin carriers | MDR/PGP1 | PGP1 | 1 | 1 | 0 | 0 |
| Auxin carriers | PGP19 | PGP1 | 1 | 2 | 2 (4) | 2 |
| Auxin carriers | MDR4/PGP4 | PGP1 | 8 | 8 | 5 (9) | 1 |
| Auxin carriers | PID | PID | 3 | 3 | 0 | 0 |
| Auxin carriers | BIG1 | BIG1 | 1 | 1 | 1 (2) | 2 |
Table of gene models in the assembly
| protein ID | name | named by | other name | by | location | comm |
| 23133 | YUC1-1 | |||||
| 64527 | YUC1-2 | |||||
| 102211 | YUC2-1 | YUC2 | Naoki Shinohara | |||
| 80431 | YUC2-2 | |||||
| 75206 | YUC3-1 | |||||
| 87220 | YUC3-2 | |||||
| 99818 | DFL1-1 | |||||
| 103740 | DFL1-2 | |||||
| 125904 | DFL1L1-1 | |||||
| 129356 | DFL1L1-2 | |||||
| 235392 | DFL1L2-1 | |||||
| 131591 | DFL1L2-2 | |||||
| 74871 | DFL1L3-1 | |||||
| 87623 | DFL1L3-2 | |||||
| 163668 | DFL1L4A-1 | Selmo1/scaffold_0:1498358-1500323 | ||||
| 268799 | DFL1L4A-2 | Selmo1/scaffold_60:98295-100261 | ||||
| 73348 | DFL1L4B-1 | Selmo1/scaffold_0:1492572-1494472 | ||||
| 119116 | DFL1L4B-2 | Selmo1/scaffold_60:322081-323988 | ||||
| 110439 | JAR1-1 | |||||
| 131513 | JAR1-2 | |||||
| 234778 | JAR1L1-1 | |||||
| 125443 | JAR1L1-2 | |||||
| 416246 | JAR1L2-1 | |||||
| 235186 | JAR1L2-2 | |||||
| 31681 | JAR1L3-1 | |||||
| 31683 | JAR1L3-2 | |||||
| 77060 | JAR1L4-1 | |||||
| 138788 | JAR1L4-2 | |||||
| 437924 | JAR1L5-1 | |||||
| 441348 | JAR1L5-2 | |||||
| 115497 | JAR1L6-1 | |||||
| 21596 | JAR1L6-2 | |||||
| 125145 | JAR1L7-1 | Selmo1/scaffold_77:894911-896539 | left | |||
| 128888 | JAR1L7-2 | Selmo1/scaffold_92:82755-84383 | left | |||
| 124989 | JAR1L8-1 | Selmo1/scaffold_77:885872-887788 | right | |||
| 427552 | JAR1L8-2 | Selmo1/scaffold_92:74324-76231 | right | |||
| 89728 | TYDC1-1 | Selmo1/scaffold_10:416396-418439 | ||||
| 171450 | TYDC1-2 | Selmo1/scaffold_10:425812-427870 | ||||
| 89475 | TYDC2-1 | Selmo1/scaffold_10:425812-427870 | ||||
| 121532 | TYDC3-1 | |||||
| 123605 | TYDC3-2 | |||||
| 79134 | TYDC4B | Selmo1/scaffold_2:1849208-1851382 | ||||
| 78872 | TYDC4A | Selmo1/scaffold_2:559748-561523 | suspected allelic variants, although on the same scaffold | |||
| 84876 | TYDC5-1 | Selmo1/scaffold_6:2373505-2375717 | ||||
| 169665 | TYDC5-2 | Selmo1/scaffold_10:389236-391616 | ||||
| 109785 | ABP1-1 | Naoki Shinohara | right | |||
| 133599 | ABP1-2 | Selmo1/scaffold_120:47761-48411 | ||||
| 451561 | ABP2-1 | Selmo1/scaffold_39:626483-627248 | ||||
| 451562 | ABP2-2 | Selmo1/scaffold_120:48614-49385 | ||||
| 166729 | ETT1-1 | Selmo1/scaffold_4:1852401-1856602 | ||||
| 430287 | ETT1-2 | Selmo1/scaffold_127:187674-190881 | ||||
| 437944 | ETT2-1 | Selmo1/scaffold_1:4121931-4125437 | ||||
| 438973 | ETT2-2 | Selmo1/scaffold_5:122023-123827 | ||||
| 437622 | ARF10A-1 | |||||
| 451564 | ARF10A-2 | |||||
| 443304 | ARF10B-1 | |||||
| 444549 | ARF10B-2 | |||||
| 103350 | AXR1-1 | |||||
| 126167 | AXR1-2 | |||||
| 271223 | SKP1-1 | |||||
| 154042 | SKP1-2 | |||||
| 173394 | CUL1-1 | |||||
| 158171 | CUL1-2 | |||||
| 98006 | CUL3-1 | |||||
| 136955 | CUL3-2 | |||||
| 450664 | RCE1-1 | RCE2-4 | Ying Li | |||
| 450663 | RCE1-2 | RCE2-3 | Ying Li | |||
| 450656 | RCE2-1 | Ying Li | RCE2-1 | Ying Li | ||
| 450657 | RCE2-2 | Ying Li | RCE2-2 | Ying Li | ||
| 121306 | RCE3-2 | |||||
| 141341 | BIG1-1 | |||||
| 153843 | BIG1-2 | |||||
| 439204 | AUX1A-1 | |||||
| 176094 | AUX1A-2 | |||||
| 165624 | AUX1B-1 | |||||
| 112710 | AUX1B-2 | |||||
| 170974 | TIR1A-1 | |||||
| 178850 | TIR1A-2 | |||||
| 168175 | TIR1B-1 | |||||
| 179436 | TIR1B-2 | |||||
| 234325 | PIN1-1 | |||||
| 131936 | PIN1-2 | |||||
| 102666 | PIN2-1 | |||||
| 443592 | PIN2-2 | |||||
| 98910 | PIN3-1 | |||||
| 105586 | PIN3-2 | |||||
| 422990 | PIN4-1 | |||||
| 129093 | PIN4-2 | |||||
| 88887 | PIN5-1 | |||||
| 451571 | PIN5-2 | |||||
| 410515 | PGP19A-1 | SmABCB4 | Uener Kolukisaoglu | Selmo1/scaffold_13:77332-81556 | ||
| 92485 | PGP19B-1 | SmABCB5 | Uener Kolukisaoglu | Selmo1/scaffold_13:82091-86435 | ||
| 138662 | PGP19A-2 | Selmo1/scaffold_301:7964-12402 | ||||
| 114581 | PGP19B-2 | |||||
| 169182 | PGP4A-1 | SmABCB7 | ||||
| 154740 | PGP4A-2 | |||||
| 123915 | PGP4B-1 | SmABCB8 | ||||
| 184079 | PGP4B-2 | |||||
| 123936 | PGP4C-1 | SmABCB9 | ||||
| 184091 | PGP4C-2 | |||||
| 74892 | PGP4D-1 | SmABCB10 | ||||
| 87743 | PGP4D-2 | |||||
| 176522 | PGP4E-1 | SmABCB6 | ||||
| 177681 | PGP4E-2 |
