ENTRY       sly04712                    Pathway
NAME        Circadian rhythm - plant - Solanum lycopersicum (tomato)
DESCRIPTION The circadian system is an endogenous rhythm with the period of about 24 hours to provide temporal organization of biological activity. In Arabidopsis the circadian oscillator at the core of this system is composed of the interlocked feedback loop formed by the major transcriptional factors CCA1 (circadian clock associated), LHY (late elongated hypocotyl) and TOC1 (timing of cab), a pseudo response regulator (PRR). The morning-expressed CCA1/LHY Myb transcription factors suppress TOC1 expression by binding to its promoter. Moreover, CCA1/LHY activates the expression of PRR7/9 in the morning and then PRR7/9 repress the transcription of CCA1/LHY during the rest of the day. By contrast, the evening-expressed TOC1 activates the expression of CCA1/LHY.
CLASS       Organismal Systems; Environmental adaptation
PATHWAY_MAP sly04712  Circadian rhythm - plant
DBLINKS     GO: 0007623
ORGANISM    Solanum lycopersicum (tomato) [GN:sly]
GENE        101262847  PHYB1; phytochrome B1 [KO:K12121]
            544176  phyA; Phytochrome A [KO:K12120]
            101267355  transcription factor PIF3 isoform X1 [KO:K12126]
            101268174  protein EARLY FLOWERING 3 [KO:K12125]
            101265040  ELF3-like protein 2 isoform X1 [KO:K12125]
            101267430  protein EARLY FLOWERING 3 [KO:K12125]
            101245619  protein HEADING DATE 3B-like [KO:K12125]
            101254785  two-component response regulator-like PRR37 [KO:K12129]
            101249224  two-component response regulator-like PRR73 [KO:K12129]
            101250283  two-component response regulator-like APRR5 [KO:K12130]
            101262866  two-component response regulator-like APRR9 isoform X1 [KO:K12130]
            101261662  protein LHY isoform X2 [KO:K12133]
            101246108  casein kinase II subunit alpha [KO:K03097] [EC:2.7.11.1]
            101256338  casein kinase II subunit alpha-1 [KO:K03097] [EC:2.7.11.1]
            101244750  casein kinase II subunit alpha-2 [KO:K03097] [EC:2.7.11.1]
            101249856  putative casein kinase II subunit beta-4 isoform X1 [KO:K03115]
            101245655  putative casein kinase II subunit beta-4 isoform X1 [KO:K03115]
            101257119  putative casein kinase II subunit beta-4 [KO:K03115]
            101246833  casein kinase II subunit beta-3 isoform X1 [KO:K03115]
            100736457  TCP14; TCP transcription factor 14 [KO:K16221]
            100736520  TCP15; TCP transcription factor 15 [KO:K16221]
            101259425  two-component response regulator-like APRR1 [KO:K12127]
            101259163  two-component response regulator-like APRR1 [KO:K12127]
            101262932  adagio protein 1 [KO:K12115]
            101255788  protein GIGANTEA [KO:K12124]
            101258346  protein GIGANTEA-like isoform X4 [KO:K12124]
            778294  CHS1; chalcone synthase 1 [KO:K00660] [EC:2.3.1.74]
            101245061  chalcone synthase B [KO:K00660] [EC:2.3.1.74]
            101266107  chalcone synthase J-like [KO:K00660] [EC:2.3.1.74]
            778295  CHS2; chalcone synthase 2 [KO:K00660] [EC:2.3.1.74]
            101263032  LOW QUALITY PROTEIN: chalcone synthase J [KO:K00660] [EC:2.3.1.74]
            544219  CRY1a; cryptochrome 1 [KO:K12118]
            543688  Cry1b; cryptochrome 1b [KO:K12118]
            543596  CRY2; cryptochrome 2 [KO:K12119]
            101249698  E3 ubiquitin-protein ligase COP1-like isoform X1 [KO:K10143] [EC:2.3.2.27]
            101259391  WD repeat-containing protein RUP2 [KO:K10143] [EC:2.3.2.27]
            543547  COP1; putative E3 ubiquitin-protein ligase COP1 [KO:K10143] [EC:2.3.2.27]
            101256908  adagio protein 3 [KO:K12116]
            101246029  SFT; protein single flower truss [KO:K16223]
            101249027  protein SUPPRESSOR OF PHYA-105 1-like isoform X1 [KO:K16240]
            101263834  protein SPA1-RELATED 2 isoform X1 [KO:K16240]
            543733  HY5; transcription factor HY5 [KO:K16241]
REFERENCE   PMID:11710980
  AUTHORS   McWatters HG, Roden LC, Staiger D.
  TITLE     Picking out parallels: plant circadian clocks in context.
  JOURNAL   Philos Trans R Soc Lond B Biol Sci 356:1735-43 (2001)
            DOI:10.1098/rstb.2001.0936
REFERENCE   PMID:11597501
  AUTHORS   Yanovsky MJ, Kay SA.
  TITLE     Signaling networks in the plant circadian system.
  JOURNAL   Curr Opin Plant Biol 4:429-35 (2001)
            DOI:10.1016/S1369-5266(00)00196-5
REFERENCE   PMID:10792828
  AUTHORS   Kim L, Kircher S, Toth R, Adam E, Schafer E, Nagy F.
  TITLE     Light-induced nuclear import of phytochrome-A:GFP fusion proteins is differentially regulated in transgenic tobacco and Arabidopsis.
  JOURNAL   Plant J 22:125-33 (2000)
            DOI:10.1046/j.1365-313x.2000.00729.x
REFERENCE   PMID:8953247
  AUTHORS   Sakamoto K, Nagatani A.
  TITLE     Nuclear localization activity of phytochrome B.
  JOURNAL   Plant J 10:859-68 (1996)
            DOI:10.1046/j.1365-313X.1996.10050859.x
REFERENCE   PMID:11402161
  AUTHORS   Liu XL, Covington MF, Fankhauser C, Chory J, Wagner DR.
  TITLE     ELF3 encodes a circadian clock-regulated nuclear protein that functions in an Arabidopsis PHYB signal transduction pathway.
  JOURNAL   Plant Cell 13:1293-304 (2001)
            DOI:10.1105/TPC.000475
REFERENCE   PMID:11069292
  AUTHORS   Zhu Y, Tepperman JM, Fairchild CD, Quail PH.
  TITLE     Phytochrome B binds with greater apparent affinity than phytochrome A to the basic helix-loop-helix factor PIF3 in a reaction requiring the PAS domain of PIF3.
  JOURNAL   Proc Natl Acad Sci U S A 97:13419-24 (2000)
            DOI:10.1073/pnas.230433797
REFERENCE   PMID:9845368
  AUTHORS   Ni M, Tepperman JM, Quail PH.
  TITLE     PIF3, a phytochrome-interacting factor necessary for normal photoinduced signal transduction, is a novel basic helix-loop-helix protein.
  JOURNAL   Cell 95:657-67 (1998)
            DOI:10.1016/S0092-8674(00)81636-0
REFERENCE   PMID:11743105
  AUTHORS   Toth R, Kevei E, Hall A, Millar AJ, Nagy F, Kozma-Bognar L.
  TITLE     Circadian clock-regulated expression of phytochrome and cryptochrome genes in Arabidopsis.
  JOURNAL   Plant Physiol 127:1607-16 (2001)
            DOI:10.1104/pp.900010
REFERENCE   PMID:11752379
  AUTHORS   Schultz TF, Kiyosue T, Yanovsky M, Wada M, Kay SA.
  TITLE     A role for LKP2 in the circadian clock of Arabidopsis.
  JOURNAL   Plant Cell 13:2659-70 (2001)
            DOI:10.1105/tpc.010332
REFERENCE   PMID:11260718
  AUTHORS   Jarillo JA, Capel J, Tang RH, Yang HQ, Alonso JM, Ecker JR, Cashmore AR.
  TITLE     An Arabidopsis circadian clock component interacts with both CRY1 and phyB.
  JOURNAL   Nature 410:487-90 (2001)
            DOI:10.1038/35068589
REFERENCE   PMID:11828029
  AUTHORS   Matsushika A, Makino S, Kojima M, Yamashino T, Mizuno T.
  TITLE     The APRR1/TOC1 quintet implicated in circadian rhythms of Arabidopsis thaliana: II. Characterization with CCA1-overexpressing plants.
  JOURNAL   Plant Cell Physiol 43:118-22 (2002)
            DOI:10.1093/pcp/pcf006
REFERENCE   PMID:10535927
  AUTHORS   Sugano S, Andronis C, Ong MS, Green RM, Tobin EM.
  TITLE     The protein kinase CK2 is involved in regulation of circadian rhythms in Arabidopsis.
  JOURNAL   Proc Natl Acad Sci U S A 96:12362-6 (1999)
            DOI:10.1073/pnas.96.22.12362
REFERENCE   PMID:11089975
  AUTHORS   Mas P, Devlin PF, Panda S, Kay SA.
  TITLE     Functional interaction of phytochrome B and cryptochrome 2.
  JOURNAL   Nature 408:207-11 (2000)
            DOI:10.1038/35041583
REFERENCE   PMID:9651577
  AUTHORS   Ahmad M, Jarillo JA, Smirnova O, Cashmore AR.
  TITLE     The CRY1 blue light photoreceptor of Arabidopsis interacts with phytochrome A in vitro.
  JOURNAL   Mol Cell 1:939-48 (1998)
            DOI:10.1016/S1097-2765(00)80094-5
REFERENCE   PMID:11486091
  AUTHORS   Alabadi D, Oyama T, Yanovsky MJ, Harmon FG, Mas P, Kay SA.
  TITLE     Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock.
  JOURNAL   Science 293:880-3 (2001)
            DOI:10.1126/science.1061320
REFERENCE   PMID:11148285
  AUTHORS   Borevitz JO, Xia Y, Blount J, Dixon RA, Lamb C.
  TITLE     Activation tagging identifies a conserved MYB regulator of phenylpropanoid biosynthesis.
  JOURNAL   Plant Cell 12:2383-2394 (2000)
            DOI:10.1105/tpc.12.12.2383
REFERENCE   PMID:12091722
  AUTHORS   Murakami-Kojima M, Nakamichi N, Yamashino T, Mizuno T.
  TITLE     The APRR3 component of the clock-associated APRR1/TOC1 quintet is phosphorylated by a novel protein kinase belonging to the WNK family, the gene for which is also transcribed rhythmically in Arabidopsis thaliana.
  JOURNAL   Plant Cell Physiol 43:675-83 (2002)
            DOI:10.1093/pcp/pcf084
REFERENCE   PMID:19386812
  AUTHORS   Pan Y, Michael TP, Hudson ME, Kay SA, Chory J, Schuler MA
  TITLE     Cytochrome P450 monooxygenases as reporters for circadian-regulated pathways.
  JOURNAL   Plant Physiol 150:858-78 (2009)
            DOI:10.1104/pp.108.130757
REFERENCE   PMID:11118138
  AUTHORS   Harmer SL, Hogenesch JB, Straume M, Chang HS, Han B, Zhu T, Wang X, Kreps JA, Kay SA
  TITLE     Orchestrated transcription of key pathways in Arabidopsis by the circadian clock.
  JOURNAL   Science 290:2110-3 (2000)
            DOI:10.1126/science.290.5499.2110
REFERENCE   PMID:12045273
  AUTHORS   Mouradov A, Cremer F, Coupland G
  TITLE     Control of flowering time: interacting pathways as a basis for diversity.
  JOURNAL   Plant Cell 14 Suppl:S111-30 (2002)
            DOI:10.1105/tpc.001362
REFERENCE   PMID:15568973
  AUTHORS   Chen M, Chory J, Fankhauser C
  TITLE     Light signal transduction in higher plants.
  JOURNAL   Annu Rev Genet 38:87-117 (2004)
            DOI:10.1146/annurev.genet.38.072902.092259
REFERENCE   PMID:16096959
  AUTHORS   Mas P
  TITLE     Circadian clock signaling in Arabidopsis thaliana: from gene expression to physiology and development.
  JOURNAL   Int J Dev Biol 49:491-500 (2005)
            DOI:10.1387/ijdb.041968pm
REFERENCE   PMID:17304247
  AUTHORS   Jiao Y, Lau OS, Deng XW
  TITLE     Light-regulated transcriptional networks in higher plants.
  JOURNAL   Nat Rev Genet 8:217-30 (2007)
            DOI:10.1038/nrg2049
REFERENCE   PMID:18444908
  AUTHORS   Turck F, Fornara F, Coupland G
  TITLE     Regulation and identity of florigen: FLOWERING LOCUS T moves center stage.
  JOURNAL   Annu Rev Plant Biol 59:573-94 (2008)
            DOI:10.1146/annurev.arplant.59.032607.092755
REFERENCE   PMID:19836294
  AUTHORS   Imaizumi T
  TITLE     Arabidopsis circadian clock and photoperiodism: time to think about location.
  JOURNAL   Curr Opin Plant Biol 13:83-9 (2010)
            DOI:10.1016/j.pbi.2009.09.007
REFERENCE   PMID:20459860
  AUTHORS   McClung CR
  TITLE     A modern circadian clock in the common angiosperm ancestor of monocots and eudicots.
  JOURNAL   BMC Biol 8:55 (2010)
            DOI:10.1186/1741-7007-8-55
REFERENCE   PMID:20809800
  AUTHORS   Doherty CJ, Kay SA
  TITLE     Circadian control of global gene expression patterns.
  JOURNAL   Annu Rev Genet 44:419-44 (2010)
            DOI:10.1146/annurev-genet-102209-163432
REFERENCE   PMID:20889330
  AUTHORS   McClung CR, Gutierrez RA
  TITLE     Network news: prime time for systems biology of the plant circadian clock.
  JOURNAL   Curr Opin Genet Dev 20:588-98 (2010)
            DOI:10.1016/j.gde.2010.08.010
REFERENCE   PMID:22190341
  AUTHORS   Lu SX, Webb CJ, Knowles SM, Kim SH, Wang Z, Tobin EM
  TITLE     CCA1 and ELF3 Interact in the control of hypocotyl length and flowering time in Arabidopsis.
  JOURNAL   Plant Physiol 158:1079-88 (2012)
            DOI:10.1104/pp.111.189670
REFERENCE   PMID:22705257
  AUTHORS   Lau OS, Deng XW
  TITLE     The photomorphogenic repressors COP1 and DET1: 20 years later.
  JOURNAL   Trends Plant Sci 17:584-93 (2012)
            DOI:10.1016/j.tplants.2012.05.004
REL_PATHWAY sly00196  Photosynthesis - antenna proteins
KO_PATHWAY  ko04712
///
