FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2000685504> ?p ?o ?g. }

• W2000685504 endingPage "11456" @default.
• W2000685504 startingPage "11453" @default.
• W2000685504 abstract "Because plants are photo-auxotrophic they are particularly sensitive to their light environment. To fine-tune their development according to light intensity, direction, spectral quality, and periodicity they possess a multiplicity of light sensors (1Kendrick R.E. Kronenberg G. Photomorphogenesis in Plants. Martinus Nijhoff Publishers, Dordrecht, Netherlands1994Crossref Google Scholar). InArabidopsis there are eight identified photoreceptors, but this list is still incomplete. It includes three UV-A/blue light receptors (phototropin, a photoreceptor to sense light direction, and two cryptochromes that mediate many photomorphogenic responses (2Briggs W.R. Huala E. Annu. Rev. Cell Dev. Biol. 1999; 15: 33-62Crossref PubMed Scopus (330) Google Scholar, 3Cashmore A.R. Jarillo J.A. Wu Y.J. Liu D. Science. 1999; 284: 760-765Crossref PubMed Scopus (785) Google Scholar)) and five phytochromes (phy) 1The abbreviations used are:phyphytochrome(s)BLDbilin lyase domainATEN-terminal extensionPRDPAS (PER/ARNT/SIM)-related domainHKRDhistidine kinase-related domainPYPphotoactive yellow proteinbHLHbasic helix-loop-helixnamed phyA–phyE that absorb mainly red/far-red light, with phyA also responding to broad-spectrum light (UV-A to far-red) of very low intensity (4Quail P.H. Boylan M.T. Parks B.M. Short T.W. Xu Y. Wagner D. Science. 1995; 268: 675-680Crossref PubMed Scopus (651) Google Scholar). All these photoreceptors bind to a chromophore, which for the phytochromes is a linear tetrapyrrole (phytochromobilin) (5Lagarias J.C. Rapoport H. J. Am. Chem. Soc. 1980; 102: 4821-4828Crossref Scopus (259) Google Scholar). Because many light effects are induced by the co-action of several photoreceptors and because some photoreceptors regulate multiple aspects of photomorphogenesis, a genetic approach was instrumental for dissecting the specific roles of individual photoreceptors (1Kendrick R.E. Kronenberg G. Photomorphogenesis in Plants. Martinus Nijhoff Publishers, Dordrecht, Netherlands1994Crossref Google Scholar). As a consequence, research has concentrated on a few species that are particularly well suited for molecular genetic studies, in particularArabidopsis (6Bevan M. Bancroft I. Mewes H.W. Martienssen R. McCombie R. Bioessays. 1999; 21: 110-120Crossref PubMed Scopus (28) Google Scholar). phytochrome(s) bilin lyase domain N-terminal extension PAS (PER/ARNT/SIM)-related domain histidine kinase-related domain photoactive yellow protein basic helix-loop-helix Phytochromes were originally defined as the receptors responsible for red, far-red reversible, plant responses (7Parker M.W. Hendricks S.B. Borthwick H.A. Went F.W. Am. J. Bot. 1949; 36: 194-204Crossref Google Scholar, 8Borthwick H.A. Hendricks S.B. Parker M.W. Toole E.H. Toole V.K. Proc. Natl. Acad. Sci. U. S. A. 1952; 38: 662-666Crossref PubMed Google Scholar, 9Borthwick H.A. Hendricks S.B. Parker M.W. Proc. Natl. Acad. Sci. U. S. A. 1952; 38: 929-934Crossref PubMed Google Scholar). Photobiological experiments led to the proposal that phy exists in two spectral forms: the inactive Pr form (red light absorbing) phototransforms into the active Pfr form (far-red light absorbing) upon absorption of red light. This reaction can be reversed when Pfr is converted to Pr upon absorption of far-red light. Purification of phy from plants confirmed the existence of those two spectrally interconvertible forms (10Butler W.L. Norris K.H. Siegelman H.W. Hendricks S.B. Proc. Natl. Acad. Sci. U. S. A. 1959; : 1703-1708Crossref PubMed Google Scholar). phy are classified into two groups; type I (phyA in Arabidopsis) is light-labile and type II (phyB–phyE in Arabidopsis) is light-stable (11Hirschfeld M. Tepperman J.M. Clack T. Quail P.H. Sharrock R.A. Genetics. 1998; 149: 523-535Crossref PubMed Google Scholar). Numerous recent reviews cover phy-mediated photomorphogenesis in detail (12Nagy F. Schaefer E. EMBO J. 2000; 19: 157-163Crossref PubMed Scopus (71) Google Scholar, 13Lin C. Plant Physiol. 2000; 123: 39-50Crossref PubMed Scopus (168) Google Scholar, 14Neff M.M. Fankhauser C. Chory J. Genes Dev. 2000; 14: 257-271Crossref PubMed Google Scholar, 15Deng X.W. Quail P.H. Semin. Cell Dev. Biol. 1999; 10: 121-129Crossref PubMed Scopus (169) Google Scholar, 16Osterlund M.T. Ang L.H. Deng X.W. Trends Cell Biol. 1999; 9: 113-118Abstract Full Text Full Text PDF PubMed Scopus (113) Google Scholar, 17Karniol B. Chamovitz D.A. Curr. Opin. Plant Biol. 2000; 3: 387-393Crossref PubMed Scopus (39) Google Scholar, 18Hughes J. Lamparter T. Plant Physiol. 1999; 121: 1059-1068Crossref PubMed Scopus (77) Google Scholar, 19Cashmore A.R. Proc. Natl. Acad. Sci. U. S. A. 1998; 95: 13358-13360Crossref PubMed Scopus (15) Google Scholar). Photobiological and genetic studies have revealed that this small gene family plays important roles in seed germination, seedling de-etiolation, neighbor perception and avoidance, and the transition from vegetative to reproductive growth (induction of flowering). At the molecular and cellular level phy responses include: development of the chloroplast, inhibition or promotion of cell growth (depending on the organ), ion fluxes at the plasma membrane, and gene expression responses (1Kendrick R.E. Kronenberg G. Photomorphogenesis in Plants. Martinus Nijhoff Publishers, Dordrecht, Netherlands1994Crossref Google Scholar). Genetic screens to identify loci implicated in phy responses have yielded four apoprotein mutants (phyA,phyB, phyD, and phyE), two chromophore mutants (hy1 and hy2), and numerous mutants implicated in phy-mediated signaling. The analysis of these mutants highlighted the role of phytochromes in sensing light quality, intensity, and the duration of the light cycle and revealed that type I and type II phy have distinct modes of photoperception (14Neff M.M. Fankhauser C. Chory J. Genes Dev. 2000; 14: 257-271Crossref PubMed Google Scholar, 15Deng X.W. Quail P.H. Semin. Cell Dev. Biol. 1999; 10: 121-129Crossref PubMed Scopus (169) Google Scholar). Light-stable phy are responsible for the classical red/far-red reversible phy responses. In Arabidopsis phyB plays the most prominent role; it is the major red light receptor for seedling de-etiolation, and it affects many light-regulated cell elongation responses, shade avoidance, and the regulation of flowering time by day length (20Reed J.W. Nagpal P. Poole D.S. Furuya M. Chory J. Plant Cell. 1993; 5: 147-157Crossref PubMed Scopus (762) Google Scholar). phyD and phyE mutants have more subtle phenotypes that are only revealed in double or triple mutant combinations (21Whitelam G.C. Devlin P.F. Plant Cell Environ. 1997; 20: 752-758Crossref Scopus (183) Google Scholar, 22Devlin P.F. Patel S.R. Whitelam G.C. Plant Cell. 1998; 10: 1479-1488Crossref PubMed Scopus (265) Google Scholar, 23Devlin P.F. Robson P.R. Patel S.R. Goosey L. Sharrock R.A. Whitelam G.C. Plant Physiol. 1999; 119: 909-915Crossref PubMed Scopus (215) Google Scholar). Because certain phytohormone mutants also display similar phenotypes, a subset of phy responses might be mediated by light-regulated hormonal signaling (14Neff M.M. Fankhauser C. Chory J. Genes Dev. 2000; 14: 257-271Crossref PubMed Google Scholar, 24Morelli G. Ruberti I. Plant Physiol. 2000; 122: 621-626Crossref PubMed Scopus (143) Google Scholar, 25Kamiya Y. Garcia-Martinez J.L. Curr. Opin. Plant Biol. 1999; 2: 398-403Crossref PubMed Scopus (131) Google Scholar, 26Hsieh H.L. Okamoto H. Wang M. Ang L.H. Matsui M. Goodman H. Deng X.W. Genes Dev. 2000; 14: 1958-1970PubMed Google Scholar). phyA, the only type I phy in Arabidopsis, plays a major role in gene expression and germination in response to very low fluences of broad spectrum light as well as in sensing day-length extension (27Johnson E. Bradley M. Harberd N.P. Whitelam G.C. Plant Physiol. 1994; 105: 141-149Crossref PubMed Scopus (42) Google Scholar, 28Shinomura T. Nagatani A. Hanzawa H. Kubota M. Watanabe M. Furuya M. Proc. Natl. Acad. Sci. U. S. A. 1996; 93: 8129-8133Crossref PubMed Scopus (427) Google Scholar, 29Botto J.F. Sanchez R.A. Whitelam G.C. Casal J.J. Plant Physiol. 1996; 110: 439-444Crossref PubMed Scopus (173) Google Scholar, 30Hamazato F. Shinomura T. Hanzawa H. Chory J. Furuya M. Plant Physiol. 1997; 115: 1533-1540Crossref PubMed Scopus (62) Google Scholar). phyA is also essential for de-etiolation in far-red enriched light (31Nagatani A. Reed R.W. Chory J. Plant Physiol. 1993; 102: 269-277Crossref PubMed Scopus (393) Google Scholar, 32Whitelam G.C. Johnson E. Peng J. Carol P. Anderson M.L. Cowl J.S. Harberd N.P. Plant Cell. 1993; 5: 757-768Crossref PubMed Scopus (483) Google Scholar, 33Dehesh K. Franci C. Parks B.M. Seeley K.A. Short T.W. Tepperman J.M. Quail P.H. Plant Cell. 1993; 5: 1081-1088PubMed Google Scholar). Such conditions are found when a young seedling develops under a dense canopy of plants. This is a particularly interesting phy function because, contrary to most phy responses, it is induced by far-red light and inhibited by red light (see above) (34Shinomura T. Uchida K. Furuya M. Plant Physiol. 2000; 122: 147-156Crossref PubMed Scopus (141) Google Scholar). This high irradiance response to far-red light identifies a novel form of active phy, Pr, that has been cycled through Pfr, which will be referred to as Pr*. Pr* has acquired novel properties that are distinct from Pr and Pfr, but the molecular nature of the distinction between Pr* and Pr is unknown (34Shinomura T. Uchida K. Furuya M. Plant Physiol. 2000; 122: 147-156Crossref PubMed Scopus (141) Google Scholar). As illustrated above, type I and type II phy play distinct roles; however, it must be pointed out that depending on the responses their role can be overlapping, coordinated, or even antagonistic (35Reed J.W. Nagatani A. Elich T.D. Fagan M. Chory J. Plant Physiol. 1994; 104: 1139-1149Crossref PubMed Scopus (526) Google Scholar, 36Robson P.R. McCormac A.C. Irvine A.S. Smith H. Nat. Biotechnol. 1996; 14: 995-998Crossref PubMed Scopus (137) Google Scholar, 37Smith H. Xu Y. Quail P.H. Plant Physiol. 1997; 114: 637-641Crossref PubMed Scopus (63) Google Scholar, 38Somers D.E. Devlin P.F. Kay S.A. Science. 1998; 282: 1488-1490Crossref PubMed Scopus (618) Google Scholar, 39Parks B.M. Spalding E.P. Proc. Natl. Acad. Sci. U. S. A. 1999; 96: 14142-14146Crossref PubMed Scopus (80) Google Scholar). Phytochromes bind phytochromobilin (PΦB) via a thioether linkage to a cysteine residue in the most conserved domain among phy (Fig.1). The first committed step in chromophore biosynthesis is the cleavage of the tetrapyrrole ring of heme (Fig. 1A). This reaction is catalyzed by a heme oxygenase encoded by the HY1 gene in Arabidopsis(40Davis S.J. Kurepa J. Vierstra R.D. Proc. Natl. Acad. Sci. U. S. A. 1999; 96: 6541-6546Crossref PubMed Scopus (177) Google Scholar, 41Muramoto T. Kohchi T. Yokota A. Hwang I. Goodman H.M. Plant Cell. 1999; 11: 335-348Crossref PubMed Scopus (271) Google Scholar). Hy2 mutants are most probably defective in the PΦB synthase enzyme; this step is followed by an isomerization in the C-3 double bond of PΦB (42Terry M.J. Plant Cell Environ. 1997; 20: 740-745Crossref Scopus (79) Google Scholar). The nature of the PΦB isomerase is still unclear, but phy itself is capable of catalyzing this reaction (42Terry M.J. Plant Cell Environ. 1997; 20: 740-745Crossref Scopus (79) Google Scholar). phy chromophore mutants can be mimicked by overexpression of a mammalian biliverdin reductase (43Lagarias D.M. Crepeau M.W. Maines M.D. Lagarias J.C. Plant Cell. 1997; 9: 675-688PubMed Google Scholar). phy apoprotein binds to the 3E-PΦB in the cytoplasm to yield the Pr form of the photoreceptor. This reaction requires the bilin lyase domain (BLD) of the photoreceptor. Absorption of red light triggers a “Z” to “E” isomerization in the C-15 double bond between the C and D rings of the linear tetrapyrrole, resulting in the far-red light-absorbing form Pfr (44Andel III, F. Lagarias J.C. Mathies R.A. Biochemistry. 1996; 35: 15997-16008Crossref PubMed Scopus (100) Google Scholar) (Fig. 1A). Conformational changes in the protein backbone are required to maintain this high energy state of the photoreceptor (45Song P.S. J. Biochem. Mol. Biol. 1999; 32: 215-225Google Scholar). Pfr can be converted to Pr either by a slow non-photoinduced reaction (dark reversion) or much faster upon absorption of far-red light. It is generally assumed that all phy have the same chromophore. Because of the very low levels of type II phy this has not been verified in vivo. Analysis of reconstituted recombinant phyA, phyB, phyC, and phyE reveals that they have similar but not identical spectral properties (46Remberg A. Ruddat A. Braslavsky S.E. Gartner W. Schaffner K. Biochemistry. 1998; 37: 9983-9990Crossref PubMed Scopus (28) Google Scholar, 47Elich T.D. Chory J. Plant Cell. 1997; 9: 2271-2280Crossref PubMed Scopus (69) Google Scholar, 48Eichenberg K. Baurle I. Paulo N. Sharrock R.A. Rudiger W. Schafer E. FEBS Lett. 2000; 470: 107-112Crossref PubMed Scopus (67) Google Scholar). Phytochromes are soluble homodimers composed of two functional domains: an N-terminal light-sensing domain and a C-terminal signaling domain (Fig. 1). The N-terminal portion is necessary and sufficient for photoperception and possesses the bilin lyase activity allowing attachment of the chromophore to the apoprotein (42Terry M.J. Plant Cell Environ. 1997; 20: 740-745Crossref Scopus (79) Google Scholar). The minimal BLD is actually less than 200 amino acids long (49Wu S.H. Lagarias J.C. Biochemistry. 2000; 39: 13487-13495Crossref PubMed Scopus (158) Google Scholar). The first 70 amino acids of the protein are dispensable for chromophore binding; they constitute the N-terminal extension (ATE). The ATE is poorly conserved, possibly accounting for some functional differences among phy. Structure function analysis has revealed that in phyA, the ATE is composed of two subdomains (50Stockhaus J. Nagatani A. Halfter U. Kay S. Furuya M. Chua N.H. Genes Dev. 1992; 6: 2364-2372Crossref PubMed Scopus (101) Google Scholar, 51Jordan E.T. Cherry J.R. Walker J.M. Vierstra R.D. Plant J. 1996; 9: 243-257Crossref PubMed Scopus (51) Google Scholar). The ATE might be implicated in stabilization of the Pfr form of the photoreceptor, which is particularly interesting in view of the large structural changes observed in this part of the protein upon Pr to Pfr phototransformation (45Song P.S. J. Biochem. Mol. Biol. 1999; 32: 215-225Google Scholar). The importance of the C-terminal half of plant phytochromes is highlighted by the numerous missense mutations affecting this portion of the protein (4Quail P.H. Boylan M.T. Parks B.M. Short T.W. Xu Y. Wagner D. Science. 1995; 268: 675-680Crossref PubMed Scopus (651) Google Scholar, 52Krall L. Reed J.W. Proc. Natl. Acad. Sci. U. S. A. 2000; 97: 8169-8174Crossref PubMed Scopus (80) Google Scholar). This signaling domain is composed of a PAS (Per/Arndt/Sim)-related domain (PRD) and a histidine kinase-related domain (HKRD) (Fig. 1) (53Schneider-Poetsch H.A. Braun B. Marx S. Schaumburg A. FEBS Lett. 1991; 281: 245-249Crossref PubMed Scopus (92) Google Scholar, 54Yeh K.C. Lagarias J.C. Proc. Natl. Acad. Sci. U. S. A. 1998; 95: 13976-13981Crossref PubMed Scopus (351) Google Scholar). PAS domains have diverse functions; they can be used either as protein-protein interaction platforms or as co-factor binding domains (55Taylor B.L. Zhulin I.B. Microbiol. Mol. Biol. Rev. 1999; 63: 479-506Crossref PubMed Google Scholar). Interestingly such modules are used to bind the chromophore in various blue light receptors (2Briggs W.R. Huala E. Annu. Rev. Cell Dev. Biol. 1999; 15: 33-62Crossref PubMed Scopus (330) Google Scholar). In phytochromes, the PRD domain is required for interaction with phy signaling partners but might also play a role in stabilization of the Pfr form of phyB (4Quail P.H. Boylan M.T. Parks B.M. Short T.W. Xu Y. Wagner D. Science. 1995; 268: 675-680Crossref PubMed Scopus (651) Google Scholar, 47Elich T.D. Chory J. Plant Cell. 1997; 9: 2271-2280Crossref PubMed Scopus (69) Google Scholar, 56Ni M. Tepperman J.M. Quail P.H. Cell. 1998; 95: 657-667Abstract Full Text Full Text PDF PubMed Scopus (569) Google Scholar, 57Choi G. Yi H. Lee J. Kwon Y.K. Soh M.S. Shin B. Luka Z. Hahn T.R. Song P.S. Nature. 1999; 401: 610-613Crossref PubMed Scopus (253) Google Scholar). Interestingly a mutation in the BLD domain of phyB has the opposite effect, leading to a phyB protein locked in the Pfr conformation (58Kretsch T. Poppe C. Schafer E. Plant J. 2000; 22: 177-186Crossref PubMed Google Scholar). The discovery of phytochromes in prokaryotes had two important consequences: they provided a phylogenetic origin for plant phy and suggested a biochemical mechanism for phy signaling (59Kehoe D.M. Grossman A.R. Science. 1996; 273: 1409-1412Crossref PubMed Scopus (316) Google Scholar, 60Hughes J. Lamparter T. Mittman F. Hartmann E. Gärtner W. Wilde A. Börner T. Nature. 1997; 386: 663Crossref PubMed Scopus (295) Google Scholar, 61Yeh K.C. Wu S.H. Murphy J.T. Lagarias J.C. Science. 1997; 277: 1505-1508Crossref PubMed Scopus (445) Google Scholar). Cyanobacterial phytochrome 1 (Cph1) is composed of a BLD and a histidine kinase domain (Fig. 1B). Cph1 autophosphorylates and phosphorylates the Rcp1 response regulator in a light-regulated fashion (Fig. 2A) (61Yeh K.C. Wu S.H. Murphy J.T. Lagarias J.C. Science. 1997; 277: 1505-1508Crossref PubMed Scopus (445) Google Scholar). It is noteworthy that in several cases response regulators are encoded in the same operon as the photoreceptor, suggesting that light-regulated protein phosphorylation is a common theme in bacteriophytochrome signaling. More complex structures have been found in the purple bacteria Rhodospirillum centenum where the photoreceptor has an additional photoactive yellow protein (PYP) domain, which is highly related to the PAS domains present in plant phy (62Jiang Z. Swem L.R. Rushing B.G. Devanathan S. Tollin G. Bauer C.E. Science. 1999; 285: 406-409Crossref PubMed Scopus (160) Google Scholar). Bacteriophytochromes have been discovered in non-photosynthetic organisms as well (63Davis S.J. Vener A.V. Vierstra R.D. Science. 1999; 286: 2517-2520Crossref PubMed Scopus (292) Google Scholar). Their biological function is not always understood, but they play rather diverse roles depending on the species, including chromatic adaptation, resetting of the circadian clock, and regulation of pigment biosynthesis (59Kehoe D.M. Grossman A.R. Science. 1996; 273: 1409-1412Crossref PubMed Scopus (316) Google Scholar, 62Jiang Z. Swem L.R. Rushing B.G. Devanathan S. Tollin G. Bauer C.E. Science. 1999; 285: 406-409Crossref PubMed Scopus (160) Google Scholar, 63Davis S.J. Vener A.V. Vierstra R.D. Science. 1999; 286: 2517-2520Crossref PubMed Scopus (292) Google Scholar, 64Schmitz O. Katayama M. Williams S.B. Kondo T. Golden S.S. Science. 2000; 289: 765-768Crossref PubMed Scopus (220) Google Scholar). Interestingly, some of these functions have been conserved in plant phy (38Somers D.E. Devlin P.F. Kay S.A. Science. 1998; 282: 1488-1490Crossref PubMed Scopus (618) Google Scholar, 65von Lintig J. Welsch R. Bonk M. Giuliano G. Batschauer A. Kleinig H. Plant J. 1997; 12: 625-634Crossref PubMed Scopus (200) Google Scholar). The HKRD domain of plant phytochromes is only distantly related to bacterial histidine kinases, and several residues essential for kinase activity are absent in plant phy (66Quail P.H. Bioessays. 1997; 19: 571-579Crossref PubMed Scopus (71) Google Scholar). In fact, work over the past 20 years has indicated that oat phyA might be a Ser/Thr kinase, and this has been confirmed convincingly quite recently (19Cashmore A.R. Proc. Natl. Acad. Sci. U. S. A. 1998; 95: 13358-13360Crossref PubMed Scopus (15) Google Scholar, 54Yeh K.C. Lagarias J.C. Proc. Natl. Acad. Sci. U. S. A. 1998; 95: 13976-13981Crossref PubMed Scopus (351) Google Scholar). Recombinant oat phyA is a light and chromophore-modulated protein kinase with Pfr being a more active form than Pr (Fig. 2C) (54Yeh K.C. Lagarias J.C. Proc. Natl. Acad. Sci. U. S. A. 1998; 95: 13976-13981Crossref PubMed Scopus (351) Google Scholar). Oat phyA is a phosphoprotein in vivo; two phosphorylation sites have been mapped, and interestingly they correspond to residues phosphorylated after in vitro kinase assays (67Lapko V.N. Jiang X.-Y. Smith D.L. Song P.-S. Protein Sci. 1999; 8: 1-11Crossref Scopus (66) Google Scholar). Ser-7 is constitutively phosphorylated, and mutagenesis studies suggest that phosphorylation of this residue is implicated in down-regulation of phyA signaling (50Stockhaus J. Nagatani A. Halfter U. Kay S. Furuya M. Chua N.H. Genes Dev. 1992; 6: 2364-2372Crossref PubMed Scopus (101) Google Scholar). Ser-599 phosphorylation is only observed in phyA extracted from light-treated plants (67Lapko V.N. Jiang X.-Y. Smith D.L. Song P.-S. Protein Sci. 1999; 8: 1-11Crossref Scopus (66) Google Scholar). Phosphorylation of this residue might therefore be a molecular tag distinguishing between different forms of phy. The importance of this residue has been demonstrated in vitro because a S599K mutant loses light-regulated kinase activity (68Fankhauser C. Yeh K.C. Lagarias J.C. Zhang H. Elich T.D. Chory J. Science. 1999; 284: 1539-1541Crossref PubMed Scopus (330) Google Scholar). The cryptochromes and PKS1 (phytochrome kinase substrate 1) are also substrates of phyA as a protein kinase, but the role of phosphorylation during phy-mediated light signaling remains to be determined in vivo (68Fankhauser C. Yeh K.C. Lagarias J.C. Zhang H. Elich T.D. Chory J. Science. 1999; 284: 1539-1541Crossref PubMed Scopus (330) Google Scholar, 69Ahmad M. Jarillo J.A. Smirnova O. Cashmore A.R. Mol. Cell. 1998; 1: 939-948Abstract Full Text Full Text PDF PubMed Scopus (263) Google Scholar). Based on reverse genetic studies it has been proposed that PKS1 acts as a negative regulator of phyB and phyA signaling (68Fankhauser C. Yeh K.C. Lagarias J.C. Zhang H. Elich T.D. Chory J. Science. 1999; 284: 1539-1541Crossref PubMed Scopus (330) Google Scholar). 2J. Casal, J. Chory, and C. Fankhauser, unpublished data. The phyA-cryptochrome interaction might be the molecular basis for the co-action between those photoreceptors (69Ahmad M. Jarillo J.A. Smirnova O. Cashmore A.R. Mol. Cell. 1998; 1: 939-948Abstract Full Text Full Text PDF PubMed Scopus (263) Google Scholar). These studies suggest a role for phy-mediated phosphorylation; quite surprisingly, however, deletion of the HKRD domain of phyB has a milder phenotype than certain point mutations in the HKRD (52Krall L. Reed J.W. Proc. Natl. Acad. Sci. U. S. A. 2000; 97: 8169-8174Crossref PubMed Scopus (80) Google Scholar). All five members of the phy family are widely expressed (70Somers D.E. Quail P.H. Plant Physiol. 1995; 107: 523-534Crossref PubMed Scopus (64) Google Scholar, 71Goosey L. Palecanda L. Sharrock R.A. Plant Physiol. 1997; 115: 959-969Crossref PubMed Scopus (83) Google Scholar).PHYA transcription is negatively regulated by light through a negative feedback loop dependent on both phyA and phyB (72Canton F.R. Quail P.H. Plant Physiol. 1999; 121: 1207-1216Crossref PubMed Scopus (77) Google Scholar). phyB mRNA is under circadian regulation; however, this regulated gene expression has only a minor impact on the steady state level of the protein (73Bognar L.K. Hall A. Adam E. Thain S.C. Nagy F. Millar A.J. Proc. Natl. Acad. Sci. U. S. A. 1999; 96: 14652-14657Crossref PubMed Scopus (108) Google Scholar). The stability of the phyA protein is greatly dependent on the light conditions. PfrA is selectively ubiquitinated leading to proteolytic degradation, phyA protein levels being therefore about 100-fold lower in the light than in the dark (Fig. 2C) (74Clough R.C. Jordan-Beebe E.T. Lohman K.N. Marita J.M. Walker J.M. Gatz C. Vierstra R.D. Plant J. 1999; 17: 155-167Crossref PubMed Scopus (63) Google Scholar). Interestingly PrA* (PrA which has been cycled through Pfr) has a half-life similar to the one of PfrA. Ubiquitination of PrA* might therefore be the molecular tag distinguishing it from PrA. It is noteworthy that the PrA* form of phy (just like the signal generated by PrA*) is very short lived (34Shinomura T. Uchida K. Furuya M. Plant Physiol. 2000; 122: 147-156Crossref PubMed Scopus (141) Google Scholar, 74Clough R.C. Jordan-Beebe E.T. Lohman K.N. Marita J.M. Walker J.M. Gatz C. Vierstra R.D. Plant J. 1999; 17: 155-167Crossref PubMed Scopus (63) Google Scholar, 75Hennig L. Buche C. Eichenberg K. Schafer E. Plant Physiol. 1999; 121: 571-577Crossref PubMed Scopus (55) Google Scholar). Subcellular localization is probably a major level of regulation for plant phytochrome action. Both phyA and phyB are cytoplasmic in the dark, and appropriate light treatments trigger their translocation into the nucleus (Fig. 2B) (12Nagy F. Schaefer E. EMBO J. 2000; 19: 157-163Crossref PubMed Scopus (71) Google Scholar). This relocation takes several hours for phyB in contrast with the more rapid translocation of phyA. This differential behavior correlates well with the sequential action of those phy during light-induced inhibition of hypocotyl growth (39Parks B.M. Spalding E.P. Proc. Natl. Acad. Sci. U. S. A. 1999; 96: 14142-14146Crossref PubMed Scopus (80) Google Scholar). The slow nuclear translocation of phyB implies that PfrB will be present in the cytoplasm where it could also play a role. Several rapid phy effects, such as ion fluxes at the plasma membrane, have been reported; they could be induced by the cytoplasmic pool of PfrB (76Kendrick R.E. Bossen M.E. Furuya M. Phytochrome Photoregulation in Plants. Academic Press, Tokyo1987Google Scholar). Pharmacological studies using microinjection of a tomato phy mutant have identified heterotrimeric G proteins, cGMP and Ca2+, as second messengers in phy signaling (77Mustilli A.C. Bowler C. EMBO J. 1997; 16: 5801-5806Crossref PubMed Scopus (65) Google Scholar). Genetic screens have identified two classes of signaling components, those acting downstream of a single photoreceptor and those acting downstream of multiple photoreceptors (Fig. 3). This presumably reflects the fact that light signals perceived by different photoreceptors must be integrated (14Neff M.M. Fankhauser C. Chory J. Genes Dev. 2000; 14: 257-271Crossref PubMed Google Scholar, 15Deng X.W. Quail P.H. Semin. Cell Dev. Biol. 1999; 10: 121-129Crossref PubMed Scopus (169) Google Scholar). The latter class (light signal integration, see Fig. 3) includes both positively acting factors (i.e. HY5) and a large group of negative regulators of photomorphogenesis (DET/COP/FUS) (16Osterlund M.T. Ang L.H. Deng X.W. Trends Cell Biol. 1999; 9: 113-118Abstract Full Text Full Text PDF PubMed Scopus (113) Google Scholar, 17Karniol B. Chamovitz D.A. Curr. Opin. Plant Biol. 2000; 3: 387-393Crossref PubMed Scopus (39) Google Scholar). Mutants with phenotypes under specific light conditions (i.e. only red light) are considered as acting early in the cascade. The study of such mutants and of phy interacting proteins reveal a complex signaling web (Fig. 3) (14Neff M.M. Fankhauser C. Chory J. Genes Dev. 2000; 14: 257-271Crossref PubMed Google Scholar, 15Deng X.W. Quail P.H. Semin. Cell Dev. Biol. 1999; 10: 121-129Crossref PubMed Scopus (169) Google Scholar, 26Hsieh H.L. Okamoto H. Wang M. Ang L.H. Matsui M. Goodman H. Deng X.W. Genes Dev. 2000; 14: 1958-1970PubMed Google Scholar, 78Bolle C. Koncz C. Chua N.H. Genes Dev. 2000; 14: 1269-1278PubMed Google Scholar, 79Buche C. Poppe C. Schafer E. Kretsch T. Plant Cell. 2000; 12: 547-558PubMed Google Scholar, 80Huq E. Tepperman J.M. Quail P.H. Proc. Natl. Acad. Sci. U. S. A. 2000; 97: 9789-9794Crossref PubMed Scopus (255) Google Scholar, 81Huq E. Kang Y. Halliday K.J. Qin M. Quail P.H. Plant J. 2000; 23: 461-470Crossref PubMed Google Scholar, 82Fankhauser C. Chory J. Plant Physiol. 2000; 124: 39-46Crossref PubMed Scopus (92) Google Scholar). These loci can be classified into three groups: those acting specifically downstream of phyA, downstream of phyB, or downstream of both. Interestingly both nuclear and cytoplasmic factors have been identified, and these signaling branches include positive and negative regulation (Fig. 3). Most of the cloned genes code for proteins with poorly defined biochemical functions. It is currently quite hard to propose a model that integrates all those factors, particularly because the relative position of these elements in the chain of events is still largely unknown. Paradoxically the best understood branch of phy signaling appears to be rather simple (Fig. 2B). PfrB is selectively imported into the nucleus where it interacts with PIF3, a bHLH transcription factor. This interaction occurs specifically with PfrB but not PrB and irrespective of DNA binding by PIF3 (Fig. 2B) (83Martinez-Garcia J.F. Huq E. Quail P.H. Science. 2000; 288: 859-863Crossref PubMed Scopus (523) Google Scholar). How interaction with phyB affects PIF3 activity remains to be solved. RSF1/HFR1/REP1 is another bHLH transcription factor that is quite related to PIF3 and also plays an important role in phy signaling (82Fankhauser C. Chory J. Plant Physiol. 2000; 124: 39-46Crossref PubMed Scopus (92) Google Scholar,84Spiegelman J.I. Mindrinos M.N. Fankhauser C. Richards D. Lutes J. Chory J. Oefner P.J. Plant Cell. 2000; 12: 2485-2498Crossref PubMed Scopus (50) Google Scholar, 85Fairchild C.D. Schumaker M.A. Quail P.H. Genes Dev. 2000; 14: 2377-2391PubMed Google Scholar, 86Soh M.S. Kim Y.M. Han S.J. Song P.S. Plant Cell. 2000; 12: 2061-2074Crossref PubMed Scopus (106) Google Scholar). RSF1/HFR1/REP1 is, however, implicated in phyA- and not phyB-mediated signaling (82Fankhauser C. Chory J. Plant Physiol. 2000; 124: 39-46Crossref PubMed Scopus (92) Google Scholar, 84Spiegelman J.I. Mindrinos M.N. Fankhauser C. Richards D. Lutes J. Chory J. Oefner P.J. Plant Cell. 2000; 12: 2485-2498Crossref PubMed Scopus (50) Google Scholar, 85Fairchild C.D. Schumaker M.A. Quail P.H. Genes Dev. 2000; 14: 2377-2391PubMed Google Scholar, 86Soh M.S. Kim Y.M. Han S.J. Song P.S. Plant Cell. 2000; 12: 2061-2074Crossref PubMed Scopus (106) Google Scholar). There is currently no data indicating a direct interaction between RSF1/HFR1/REP1 and phyA (85Fairchild C.D. Schumaker M.A. Quail P.H. Genes Dev. 2000; 14: 2377-2391PubMed Google Scholar). The presence of bHLH transcription factors in both phyA and phyB signaling is particularly noteworthy in view of the recently uncovered convergence of multiple phy signaling pathways on a single promoter (87Cerdan P.D. Staneloni R.J. Ortega J. Bunge M.M. Rodriguez-Batiller M.J. Sanchez R.A. Casal J.J. Plant Cell. 2000; 12: 1203-1212Crossref PubMed Scopus (29) Google Scholar). Genetic studies for both PIF3 and RSF1/HFR1/REP1 have revealed that they play important roles in phy signaling, but they also indicate that these transcription factors only account for part of the response initiated by the phy (82Fankhauser C. Chory J. Plant Physiol. 2000; 124: 39-46Crossref PubMed Scopus (92) Google Scholar, 83Martinez-Garcia J.F. Huq E. Quail P.H. Science. 2000; 288: 859-863Crossref PubMed Scopus (523) Google Scholar, 85Fairchild C.D. Schumaker M.A. Quail P.H. Genes Dev. 2000; 14: 2377-2391PubMed Google Scholar, 86Soh M.S. Kim Y.M. Han S.J. Song P.S. Plant Cell. 2000; 12: 2061-2074Crossref PubMed Scopus (106) Google Scholar). These recent studies illustrate the potentially very short signaling chain initiated by the phytochromes, but we should keep in mind that much remains to be done to have a global view of the multiple events initiated by those photoreceptors. I thank Jorge Casal, Masaki Furuya, Enamul Huq, Clark Lagarias, Pill Soon Song, Rick Vierstra, and Jim Weller for communicating results prior to publication; Miguel Blazquez, Michel Goldschmidt-Clermont, and Patricia Lariguet for helpful comments on the manuscript, and Nicolas Roggli for artwork." @default.
• W2000685504 created "2016-06-24" @default.
• W2000685504 creator A5063581755 @default.
• W2000685504 date "2001-04-01" @default.
• W2000685504 modified "2023-10-11" @default.
• W2000685504 title "The Phytochromes, a Family of Red/Far-red Absorbing Photoreceptors" @default.
• W2000685504 cites W1518221802 @default.
• W2000685504 cites W1615756149 @default.
• W2000685504 cites W1763052962 @default.
• W2000685504 cites W1929598770 @default.
• W2000685504 cites W1938369637 @default.
• W2000685504 cites W1957643367 @default.
• W2000685504 cites W1963561392 @default.
• W2000685504 cites W1964606590 @default.
• W2000685504 cites W1967551062 @default.
• W2000685504 cites W1969472583 @default.
• W2000685504 cites W1971336215 @default.
• W2000685504 cites W1973987642 @default.
• W2000685504 cites W1978900927 @default.
• W2000685504 cites W1981107273 @default.
• W2000685504 cites W1981529935 @default.
• W2000685504 cites W1982998203 @default.
• W2000685504 cites W1984974398 @default.
• W2000685504 cites W1989535139 @default.
• W2000685504 cites W1999850786 @default.
• W2000685504 cites W2000869729 @default.
• W2000685504 cites W2002627943 @default.
• W2000685504 cites W2003241415 @default.
• W2000685504 cites W2007785100 @default.
• W2000685504 cites W2009225577 @default.
• W2000685504 cites W2011832991 @default.
• W2000685504 cites W2013226960 @default.
• W2000685504 cites W2021609583 @default.
• W2000685504 cites W2025266490 @default.
• W2000685504 cites W2029350076 @default.
• W2000685504 cites W2030291587 @default.
• W2000685504 cites W2035077465 @default.
• W2000685504 cites W2035697585 @default.
• W2000685504 cites W2038741882 @default.
• W2000685504 cites W2045031735 @default.
• W2000685504 cites W2047598339 @default.
• W2000685504 cites W2054927441 @default.
• W2000685504 cites W2055182928 @default.
• W2000685504 cites W2058327635 @default.
• W2000685504 cites W2061202168 @default.
• W2000685504 cites W2067347790 @default.
• W2000685504 cites W2067375839 @default.
• W2000685504 cites W2069812226 @default.
• W2000685504 cites W2071380089 @default.
• W2000685504 cites W2071547748 @default.
• W2000685504 cites W2072365862 @default.
• W2000685504 cites W2075370328 @default.
• W2000685504 cites W2075420836 @default.
• W2000685504 cites W2077943403 @default.
• W2000685504 cites W2082707175 @default.
• W2000685504 cites W2082925435 @default.
• W2000685504 cites W2083396768 @default.
• W2000685504 cites W2084186109 @default.
• W2000685504 cites W2104587420 @default.
• W2000685504 cites W2113422262 @default.
• W2000685504 cites W2113753940 @default.
• W2000685504 cites W2115884023 @default.
• W2000685504 cites W2118642686 @default.
• W2000685504 cites W2122023734 @default.
• W2000685504 cites W2123234714 @default.
• W2000685504 cites W2124005596 @default.
• W2000685504 cites W2130471243 @default.
• W2000685504 cites W2131050379 @default.
• W2000685504 cites W2135196840 @default.
• W2000685504 cites W2139551715 @default.
• W2000685504 cites W2146484009 @default.
• W2000685504 cites W2150168384 @default.
• W2000685504 cites W2152903297 @default.
• W2000685504 cites W2154144834 @default.
• W2000685504 cites W2159110379 @default.
• W2000685504 cites W2159751408 @default.
• W2000685504 cites W2165743881 @default.
• W2000685504 cites W2167011106 @default.
• W2000685504 cites W2167671547 @default.
• W2000685504 cites W2169982116 @default.
• W2000685504 cites W2171222726 @default.
• W2000685504 cites W2171241223 @default.
• W2000685504 cites W4234242724 @default.
• W2000685504 doi "https://doi.org/10.1074/jbc.r100006200" @default.
• W2000685504 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/11279228" @default.
• W2000685504 hasPublicationYear "2001" @default.
• W2000685504 type Work @default.
• W2000685504 sameAs 2000685504 @default.
• W2000685504 citedByCount "179" @default.
• W2000685504 countsByYear W20006855042012 @default.
• W2000685504 countsByYear W20006855042013 @default.
• W2000685504 countsByYear W20006855042014 @default.
• W2000685504 countsByYear W20006855042015 @default.
• W2000685504 countsByYear W20006855042016 @default.
• W2000685504 countsByYear W20006855042017 @default.
• W2000685504 countsByYear W20006855042018 @default.
• W2000685504 countsByYear W20006855042019 @default.
• W2000685504 countsByYear W20006855042020 @default.

• next