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Gene Review

PHYA  -  phytochrome A

Arabidopsis thaliana

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Disease relevance of PHYA

  • This change stabilizes the light-labile PHYA protein in light and causes a 100-fold shift in the threshold for far-red light sensitivity [1].
  • We show here that the dwarf response is related to a reduction in active gibberellins (GAs) in tobacco (Nicotiana tabacum) overexpressing oat phytochrome A under the control of the cauliflower mosaic virus (CaMV) 35S promoter and can be suppressed by foliar applications of gibberellic acid [2].

High impact information on PHYA


Biological context of PHYA

  • This mutation carries a single amino acid substitution at residue 631, from valine to methionine (V631M), in the core region within the C-terminal half of PHYA [7].
  • The triple transcription start site arrangement is similar to that of pea PHYA but different from the single start site of oat, rice and maize PHYA genes, indicating a possible monocot-dicot difference [8].
  • It was concluded that the pef1 mutant is defective in both PHYA- and PHYB-mediated signaling pathways, and may represent a lesion in an early step of the phytochrome signal transduction pathway [9].
  • One such mutant, pef1, was selectively insensitive to both red and far-red light in the inhibition of hypocotyl elongation response; a classic phytochrome phenotype mediated by both PHYA and PHYB [9].
  • Thus, PHYA and PHYB play a key role in mediating red-light-dependent positive phototropism in roots [10].

Anatomical context of PHYA

  • Difference spectra and Western blot analysis showed normal concentrations of PHYA photoreceptor apoprotein, which appeared photochemically active [9].
  • Far-red light blocks greening of Arabidopsis seedlings via a phytochrome A-mediated change in plastid development [11].
  • The gradual swelling of protoplasts that prevails under background red light is shown to be a phytochrome-mediated response in which phytochrome A contributes more than phytochrome B [12].
  • Upon light exposure, COP1 migrates to the cytosol allowing photomorphogenesis to proceed but the residual nuclear pool down-regulates light signaling mediated by phytochrome A. Here we show that weak alleles of cop1 exhibit reverse photomorphogenic responses i.e. reduced rather than enhanced cotyledon unfolding under red light compared to darkness [13].

Associations of PHYA with chemical compounds


Physical interactions of PHYA


Regulatory relationships of PHYA


Other interactions of PHYA

  • The induction of randomization was confirmed using lines that express to different levels PHYA and PHYB cDNAs [26].
  • Expression analysis revealed that PIL5 repressed the expression of GA biosynthetic genes (GA3ox1 and GA3ox2), and activated the expression of a GA catabolic gene (GA2ox) in both PHYA- and PHYB-dependent germination assays [27].
  • FHY1: a phytochrome A-specific signal transducer [28].
  • A null mutation in PHYA impaired the membrane depolarization and prevented the early cry1-dependent phase of growth inhibition as effectively and with the same time course as mutations in CRY1 [16].
  • The PHYC gene of Arabidopsis. Absence of the third intron found in PHYA and PHYB [29].

Analytical, diagnostic and therapeutic context of PHYA


  1. Natural variation in light sensitivity of Arabidopsis. Maloof, J.N., Borevitz, J.O., Dabi, T., Lutes, J., Nehring, R.B., Redfern, J.L., Trainer, G.T., Wilson, J.M., Asami, T., Berry, C.C., Weigel, D., Chory, J. Nat. Genet. (2001) [Pubmed]
  2. Phytochrome A overexpression in transgenic tobacco. Correlation of dwarf phenotype with high concentrations of phytochrome in vascular tissue and attenuated gibberellin levels. Jordan, E.T., Hatfield, P.M., Hondred, D., Talon, M., Zeevaart, J.A., Vierstra, R.D. Plant Physiol. (1995) [Pubmed]
  3. A thermosensory pathway controlling flowering time in Arabidopsis thaliana. Blázquez, M.A., Ahn, J.H., Weigel, D. Nat. Genet. (2003) [Pubmed]
  4. SPA1, a WD-repeat protein specific to phytochrome A signal transduction. Hoecker, U., Tepperman, J.M., Quail, P.H. Science (1999) [Pubmed]
  5. Phytochromes and cryptochromes in the entrainment of the Arabidopsis circadian clock. Somers, D.E., Devlin, P.F., Kay, S.A. Science (1998) [Pubmed]
  6. Photoreceptor ubiquitination by COP1 E3 ligase desensitizes phytochrome A signaling. Seo, H.S., Watanabe, E., Tokutomi, S., Nagatani, A., Chua, N.H. Genes Dev. (2004) [Pubmed]
  7. Characterization of a strong dominant phytochrome A mutation unique to phytochrome A signal propagation. Fry, R.C., Habashi, J., Okamoto, H., Deng, X.W. Plant Physiol. (2002) [Pubmed]
  8. The Arabidopsis phytochrome A gene has multiple transcription start sites and a promoter sequence motif homologous to the repressor element of monocot phytochrome A genes. Dehesh, K., Franci, C., Sharrock, R.A., Somers, D.E., Welsch, J.A., Quail, P.H. Photochem. Photobiol. (1994) [Pubmed]
  9. The pef mutants of Arabidopsis thaliana define lesions early in the phytochrome signaling pathway. Ahmad, M., Cashmore, A.R. Plant J. (1996) [Pubmed]
  10. Phytochromes A and B mediate red-light-induced positive phototropism in roots. Kiss, J.Z., Mullen, J.L., Correll, M.J., Hangarter, R.P. Plant Physiol. (2003) [Pubmed]
  11. Far-red light blocks greening of Arabidopsis seedlings via a phytochrome A-mediated change in plastid development. Barnes, S.A., Nishizawa, N.K., Quaggio, R.B., Whitelam, G.C., Chua, N.H. Plant Cell (1996) [Pubmed]
  12. Interaction of cryptochrome 1, phytochrome, and ion fluxes in blue-light-induced shrinking of Arabidopsis hypocotyl protoplasts. Wang, X., Iino, M. Plant Physiol. (1998) [Pubmed]
  13. Promotion of photomorphogenesis by COP1. Boccalandro, H.E., Rossi, M.C., Saijo, Y., Deng, X.W., Casal, J.J. Plant Mol. Biol. (2004) [Pubmed]
  14. FIN219, an auxin-regulated gene, defines a link between phytochrome A and the downstream regulator COP1 in light control of Arabidopsis development. Hsieh, H.L., Okamoto, H., Wang, M., Ang, L.H., Matsui, M., Goodman, H., Deng, X.W. Genes Dev. (2000) [Pubmed]
  15. Arabidopsis HY8 locus encodes phytochrome A. Dehesh, K., Franci, C., Parks, B.M., Seeley, K.A., Short, T.W., Tepperman, J.M., Quail, P.H. Plant Cell (1993) [Pubmed]
  16. Opposing roles of phytochrome A and phytochrome B in early cryptochrome-mediated growth inhibition. Folta, K.M., Spalding, E.P. Plant J. (2001) [Pubmed]
  17. Overexpression of Arabidopsis phytochrome B inhibits phytochrome A function in the presence of sucrose. Short, T.W. Plant Physiol. (1999) [Pubmed]
  18. A phytochrome-associated protein phosphatase 2A modulates light signals in flowering time control in Arabidopsis. Kim, D.H., Kang, J.G., Yang, S.S., Chung, K.S., Song, P.S., Park, C.M. Plant Cell (2002) [Pubmed]
  19. Transgene-induced silencing of Arabidopsis phytochrome A gene via exonic methylation. Chawla, R., Nicholson, S.J., Folta, K.M., Srivastava, V. Plant J. (2007) [Pubmed]
  20. PIL5, a phytochrome-interacting basic helix-loop-helix protein, is a key negative regulator of seed germination in Arabidopsis thaliana. Oh, E., Kim, J., Park, E., Kim, J.I., Kang, C., Choi, G. Plant Cell (2004) [Pubmed]
  21. Arabidopsis FHY3 defines a key phytochrome A signaling component directly interacting with its homologous partner FAR1. Wang, H., Deng, X.W. EMBO J. (2002) [Pubmed]
  22. Arabidopsis FHY1 protein stability is regulated by light via phytochrome A and 26S proteasome. Shen, Y., Feng, S., Ma, L., Lin, R., Qu, L.J., Chen, Z., Wang, H., Deng, X.W. Plant Physiol. (2005) [Pubmed]
  23. Missense mutation in the PAS2 domain of phytochrome A impairs subnuclear localization and a subset of responses. Yanovsky, M.J., Luppi, J.P., Kirchbauer, D., Ogorodnikova, O.B., Sineshchekov, V.A., Adam, E., Kircher, S., Staneloni, R.J., Schäfer, E., Nagy, F., Casal, J.J. Plant Cell (2002) [Pubmed]
  24. Effects of synergistic signaling by phytochrome A and cryptochrome1 on circadian clock-regulated catalase expression. Zhong, H.H., Resnick, A.S., Straume, M., Robertson McClung, C. Plant Cell (1997) [Pubmed]
  25. Effects of gibberellins on seed germination of phytochrome-deficient mutants of Arabidopsis thaliana. Yang, Y.Y., Nagatani, A., Zhao, Y.J., Kang, B.J., Kendrick, R.E., Kamiya, Y. Plant Cell Physiol. (1995) [Pubmed]
  26. Genetic and transgenic evidence that phytochromes A and B act to modulate the gravitropic orientation of Arabidopsis thaliana hypocotyls. Robson, P.R., Smith, H. Plant Physiol. (1996) [Pubmed]
  27. Light activates the degradation of PIL5 protein to promote seed germination through gibberellin in Arabidopsis. Oh, E., Yamaguchi, S., Kamiya, Y., Bae, G., Chung, W.I., Choi, G. Plant J. (2006) [Pubmed]
  28. FHY1: a phytochrome A-specific signal transducer. Desnos, T., Puente, P., Whitelam, G.C., Harberd, N.P. Genes Dev. (2001) [Pubmed]
  29. The PHYC gene of Arabidopsis. Absence of the third intron found in PHYA and PHYB. Cowl, J.S., Hartley, N., Xie, D.X., Whitelam, G.C., Murphy, G.P., Harberd, N.P. Plant Physiol. (1994) [Pubmed]
  30. Multiple transcription-factor genes are early targets of phytochrome A signaling. Tepperman, J.M., Zhu, T., Chang, H.S., Wang, X., Quail, P.H. Proc. Natl. Acad. Sci. U.S.A. (2001) [Pubmed]
  31. Dynamic properties of endogenous phytochrome A in Arabidopsis seedlings. Hennig, L., Büche, C., Eichenberg, K., Schäfer, E. Plant Physiol. (1999) [Pubmed]
  32. Phytochrome E controls light-induced germination of Arabidopsis. Hennig, L., Stoddart, W.M., Dieterle, M., Whitelam, G.C., Schäfer, E. Plant Physiol. (2002) [Pubmed]
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