KEGG   PATHWAY: osa04712
Entry
osa04712                    Pathway                                
Name
Circadian rhythm - plant - Oryza sativa japonica (Japanese rice) (RefSeq)
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
osa04712  Circadian rhythm - plant
osa04712

Other DBs
GO: 0007623
Organism
Oryza sativa japonica (Japanese rice) (RefSeq) [GN:osa]
Gene
4332623  phytochrome B isoform X2 [KO:K12121]
4333930  phytochrome A [KO:K12120]
4327916  transcription factor APG-like isoform X1 [KO:K12126]
4327931  protein EARLY FLOWERING 3 [KO:K12125]
4340087  protein EARLY FLOWERING 3 [KO:K12125]
4332464  two-component response regulator-like PRR73 [KO:K12129]
4344399  two-component response regulator-like PRR37 isoform X1 [KO:K12129]
4347674  two-component response regulator-like PRR95 [KO:K12130]
4349831  two-component response regulator-like APRR3 [KO:K12130]
4344703  protein LHY isoform X1 [KO:K12133]
4342248  casein kinase II subunit alpha [KO:K03097] [EC:2.7.11.1]
4334206  casein kinase II subunit alpha [KO:K03097] [EC:2.7.11.1]
4332003  casein kinase II subunit alpha [KO:K03097] [EC:2.7.11.1]
4343287  putative casein kinase II subunit beta-4 isoform X1 [KO:K03115]
4349414  putative casein kinase II subunit beta-4 isoform X1 [KO:K03115]
107277483  transcription factor TCP21-like [KO:K16221]
9272106  transcription factor TCP7 [KO:K16221]
4330080  transcription factor TCP7 [KO:K16221]
4330000  two-component response regulator-like PRR1 [KO:K12127]
4341923  adagio-like protein 1 [KO:K12115]
4328313  putative adagio-like protein 2 [KO:K12115]
4325329  protein GIGANTEA [KO:K12124]
4350636  chalcone synthase 1 [KO:K00660] [EC:2.3.1.74]
4342725  chalcone synthase 2 [KO:K00660] [EC:2.3.1.74]
4329738  cryptochrome-1 isoform X1 [KO:K12118]
4336008  cryptochrome-1 isoform X1 [KO:K12118]
9270575  cryptochrome-1 isoform X1 [KO:K12119]
4330868  E3 ubiquitin-protein ligase COP1 [KO:K10143] [EC:2.3.2.27]
107279948  WD repeat-containing protein RUP2-like [KO:K10143] [EC:2.3.2.27]
4350698  adagio-like protein 3 isoform X1 [KO:K12116]
4340185  protein HEADING DATE 3A [KO:K16223]
4324585  protein HEADING DATE 3B-like [KO:K16223]
107276210  protein TWIN SISTER of FT-like [KO:K16223]
107280190  protein FLOWERING LOCUS T-like [KO:K16223]
4336228  protein FLOWERING LOCUS T [KO:K16223]
4341272  protein FLOWERING LOCUS T isoform X1 [KO:K16223]
9268282  protein FLOWERING LOCUS T [KO:K16223]
9271430  protein FLOWERING LOCUS T isoform X1 [KO:K16223]
4339663  protein SUPPRESSOR OF PHYA-105 1 [KO:K16240]
4328662  transcription factor HY5 [KO:K16241]
9268301  transcription factor HY5 isoform X1 [KO:K16241]
Reference
  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
  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
  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
  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
  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
  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
  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
  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
  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
  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
  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
  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
  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
  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
  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
  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
  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
  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
  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
  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
  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
  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
  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
  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
  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
  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
  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
Related
pathway
osa00196  Photosynthesis - antenna proteins
KO pathway
ko04712   
LinkDB

DBGET integrated database retrieval system