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Gene Review

PHYB  -  phytochrome B

Arabidopsis thaliana

Synonyms: HY3, MSF3.17, MSF3_17, OOP1, OUT OF PHASE 1, ...
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High impact information on PHYB


Biological context of PHYB

  • 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 [4].
  • 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 [4].
  • To determine whether differential temporal or spatial expression patterns of the PHYA and PHYB genes contribute to this phenomenon the expression of PHYA-GUS and PHYB-GUS reporter genes has been examined in transgenic Arabidopsis [5].
  • Later in the life cycle of the plant, PHYB and GAs have opposite effects on flowering [6].
  • Based on Southern analyses of five black cottonwood genotypes representing three photoperiodic ecotypes, substantial polymorphism was detected for at least one of the PHYB loci but not for the PHYA locus [7].

Anatomical context of PHYB


Associations of PHYB with chemical compounds


Physical interactions of PHYB


Regulatory relationships of PHYB

  • Phytochrome B in the mesophyll delays flowering by suppressing FLOWERING LOCUS T expression in Arabidopsis vascular bundles [8].
  • PHYTOCHROME B (phyB) controls period length in red light as well as the phase of the clock in white light. phyB interacts with ARABIDOPSIS RESPONSE REGULATOR4 (ARR4) in a light-dependent manner [17].
  • Phytochrome A negatively or positively regulates phytochrome B signaling, depending on light conditions [18].
  • Recent work indicates that ELF3 encodes a novel nuclear protein that is expressed rhythmically and interacts with phytochrome B. How ELF3 mediates the circadian gating of light responses and regulates light input to the clock is the subject of discussion [19].

Other interactions of PHYB

  • PIL5 preferentially interacts with the Pfr forms of Phytochrome A (PhyA) and Phytochrome B (PhyB) [20].
  • Hence, the PHYB, PHYD, and PHYE genes differ in expression pattern but these patterns overlap and interaction of these receptor forms within individual cells is possible [21].
  • We demonstrate that PIF3 is polyubiquitinated rapidly and subsequently degraded in PHYA and PHYB-mediated light signaling [22].
  • Interaction with PHYB was unaffected by mutation of any ZTL domain [23].
  • Since phyB did not change the GA responsiveness of the LFY promoter and suppressed the lack of flowering of severe GA-deficient mutants under short days, we propose that PHYB modulates flowering time at least partially through a GA-independent pathway [6].

Analytical, diagnostic and therapeutic context of PHYB

  • Fragments of these two PHYB were cloned following amplification by the polymerase chain reaction of a portion of their relatively well conserved 5' coding regions [24].


  1. Functional interaction of phytochrome B and cryptochrome 2. Más, P., Devlin, P.F., Panda, S., Kay, S.A. Nature (2000) [Pubmed]
  2. Binding of phytochrome B to its nuclear signalling partner PIF3 is reversibly induced by light. Ni, M., Tepperman, J.M., Quail, P.H. Nature (1999) [Pubmed]
  3. Interaction of the response regulator ARR4 with phytochrome B in modulating red light signaling. Sweere, U., Eichenberg, K., Lohrmann, J., Mira-Rodado, V., Bäurle, I., Kudla, J., Nagy, F., Schafer, E., Harter, K. Science (2001) [Pubmed]
  4. The pef mutants of Arabidopsis thaliana define lesions early in the phytochrome signaling pathway. Ahmad, M., Cashmore, A.R. Plant J. (1996) [Pubmed]
  5. Temporal and spatial expression patterns of PHYA and PHYB genes in Arabidopsis. Somers, D.E., Quail, P.H. Plant J. (1995) [Pubmed]
  6. Independent regulation of flowering by phytochrome B and gibberellins in Arabidopsis. Blázquez, M.A., Weigel, D. Plant Physiol. (1999) [Pubmed]
  7. Evidence that the phytochrome gene family in black cottonwood has one PHYA locus and two PHYB loci but lacks members of the PHYC/F and PHYE subfamilies. Howe, G.T., Bucciaglia, P.A., Hackett, W.P., Furnier, G.R., Cordonnier-Pratt, M.M., Gardner, G. Mol. Biol. Evol. (1998) [Pubmed]
  8. Phytochrome B in the mesophyll delays flowering by suppressing FLOWERING LOCUS T expression in Arabidopsis vascular bundles. Endo, M., Nakamura, S., Araki, T., Mochizuki, N., Nagatani, A. Plant Cell (2005) [Pubmed]
  9. 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]
  10. HYPERSENSITIVE TO RED AND BLUE 1, a ZZ-type zinc finger protein, regulates phytochrome B-mediated red and cryptochrome-mediated blue light responses. Kang, X., Chong, J., Ni, M. Plant Cell (2005) [Pubmed]
  11. Regulation of hormone metabolism in Arabidopsis seeds: phytochrome regulation of abscisic acid metabolism and abscisic acid regulation of gibberellin metabolism. Seo, M., Hanada, A., Kuwahara, A., Endo, A., Okamoto, M., Yamauchi, Y., North, H., Marion-Poll, A., Sun, T.P., Koshiba, T., Kamiya, Y., Yamaguchi, S., Nambara, E. Plant J. (2006) [Pubmed]
  12. Overexpression of Arabidopsis phytochrome B inhibits phytochrome A function in the presence of sucrose. Short, T.W. Plant Physiol. (1999) [Pubmed]
  13. Mutations causing defects in the biosynthesis and response to gibberellins, abscisic acid and phytochrome B do not inhibit vernalization in Arabidopsis fca-1. Chandler, J., Martinez-Zapater, J.M., Dean, C. Planta (2000) [Pubmed]
  14. Multiple phytohormones influence distinct parameters of the plant circadian clock. Hanano, S., Domagalska, M.A., Nagy, F., Davis, S.J. Genes Cells (2006) [Pubmed]
  15. ELF3 encodes a circadian clock-regulated nuclear protein that functions in an Arabidopsis PHYB signal transduction pathway. Liu, X.L., Covington, M.F., Fankhauser, C., Chory, J., Wagner, D.R. Plant Cell (2001) [Pubmed]
  16. Identification of phytochrome-interacting protein candidates in Arabidopsis thaliana by co-immunoprecipitation coupled with MALDI-TOF MS. Phee, B.K., Shin, D.H., Cho, J.H., Kim, S.H., Kim, J.I., Lee, Y.H., Jeon, J.S., Bhoo, S.H., Hahn, T.R. Proteomics (2006) [Pubmed]
  17. Arabidopsis response regulators ARR3 and ARR4 play cytokinin-independent roles in the control of circadian period. Salomé, P.A., To, J.P., Kieber, J.J., McClung, C.R. Plant Cell (2006) [Pubmed]
  18. 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]
  19. ELF3: a circadian safeguard to buffer effects of light. Carré, I.A. Trends Plant Sci. (2002) [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. Differential patterns of expression of the Arabidopsis PHYB, PHYD, and PHYE phytochrome genes. Goosey, L., Palecanda, L., Sharrock, R.A. Plant Physiol. (1997) [Pubmed]
  22. Degradation of phytochrome interacting factor 3 in phytochrome-mediated light signaling. Park, E., Kim, J., Lee, Y., Shin, J., Oh, E., Chung, W.I., Liu, J.R., Choi, G. Plant Cell Physiol. (2004) [Pubmed]
  23. Forward genetic analysis of the circadian clock separates the multiple functions of ZEITLUPE. Kevei, E., Gyula, P., Hall, A., Kozma-Bognár, L., Kim, W.Y., Eriksson, M.E., Tóth, R., Hanano, S., Fehér, B., Southern, M.M., Bastow, R.M., Viczián, A., Hibberd, V., Davis, S.J., Somers, D.E., Nagy, F., Millar, A.J. Plant Physiol. (2006) [Pubmed]
  24. Tomato contains two differentially expressed genes encoding B-type phytochromes, neither of which can be considered an ortholog of Arabidopsis phytochrome B. Pratt, L.H., Cordonnier-Pratt, M.M., Hauser, B., Caboche, M. Planta (1995) [Pubmed]
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