KEGG   PATHWAY: ath04712
Entry
ath04712                    Pathway                                
Name
Circadian rhythm - plant - Arabidopsis thaliana (thale cress)
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
ath04712  Circadian rhythm - plant
ath04712

Other DBs
GO: 0007623
Organism
Arabidopsis thaliana (thale cress) [GN:ath]
Gene
AT2G18790  PHYB; phytochrome B [KO:K12121]
AT1G09570  PHYA; phytochrome A [KO:K12120]
AT1G09530  PIF3; phytochrome interacting factor 3 [KO:K12126]
AT2G25930  ELF3; hydroxyproline-rich glycoprotein family protein [KO:K12125]
AT2G46790  PRR9; pseudo-response regulator 9 [KO:K12128]
AT5G02810  PRR7; pseudo-response regulator 7 [KO:K12129]
AT5G24470  PRR5; two-component response regulator-like protein [KO:K12130]
AT1G01060  LHY; Homeodomain-like superfamily protein [KO:K12133]
AT2G46830  CCA1; circadian clock associated 1 [KO:K12134]
AT2G23070  Protein kinase superfamily protein [KO:K03097] [EC:2.7.11.1]
AT2G23080  CKA3; Protein kinase superfamily protein [KO:K03097] [EC:2.7.11.1]
AT3G50000  CKA2; casein kinase II, alpha chain 2 [KO:K03097] [EC:2.7.11.1]
AT5G67380  CKA1; casein kinase alpha 1 [KO:K03097] [EC:2.7.11.1]
AT3G60250  CKB3; casein kinase II beta chain 3 [KO:K03115]
AT4G17640  CKB2; casein kinase II beta chain 2 [KO:K03115]
AT2G44680  CKB4; casein kinase II beta subunit 4 [KO:K03115]
AT5G47080  CKB1; casein kinase II beta chain 1 [KO:K03115]
AT5G08330  TCP11; TCP family transcription factor [KO:K16221]
AT5G23280  TCP family transcription factor [KO:K16221]
AT5G61380  TOC1; CCT motif -containing response regulator protein [KO:K12127]
AT5G57360  ZTL; Galactose oxidase/kelch repeat superfamily protein [KO:K12115]
AT1G22770  GI; gigantea protein (GI) [KO:K12124]
AT5G60100  PRR3; pseudo-response regulator 3 [KO:K12131]
AT1G56650  PAP1; production of anthocyanin pigment 1 [KO:K16166]
AT5G13930  TT4; Chalcone and stilbene synthase family protein [KO:K00660] [EC:2.3.1.74]
AT4G08920  CRY1; cryptochrome 1 [KO:K12118]
AT1G04400  CRY2; cryptochrome 2 [KO:K12119]
AT2G32950  COP1; Transducin/WD40 repeat-like superfamily protein [KO:K10143] [EC:2.3.2.27]
AT5G52250  RUP1; Transducin/WD40 repeat-like superfamily protein [KO:K10143] [EC:2.3.2.27]
AT5G23730  RUP2; Transducin/WD40 repeat-like superfamily protein [KO:K10143] [EC:2.3.2.27]
AT1G68050  FKF1; flavin-binding, kelch repeat, f box 1 [KO:K12116]
AT5G62430  CDF1; cycling DOF factor 1 [KO:K16222]
AT5G15840  CO; B-box type zinc finger protein with CCT domain-containing protein [KO:K12135]
AT1G65480  FT; PEBP (phosphatidylethanolamine-binding protein) family protein [KO:K16223]
AT4G20370  TSF; PEBP (phosphatidylethanolamine-binding protein) family protein [KO:K16223]
AT2G46340  SPA1; SPA (suppressor of phyA-105) protein family [KO:K16240]
AT4G11110  SPA2; SPA1-related 2 [KO:K16240]
AT1G53090  SPA4; SPA1-related 4 [KO:K26557]
AT3G15354  SPA3; SPA1-related 3 [KO:K26557]
AT5G11260  HY5; Basic-leucine zipper (bZIP) transcription factor family protein [KO:K16241]
AT3G17609  HYH; HY5-homolog [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
Related
pathway
ath00196  Photosynthesis - antenna proteins
KO pathway
ko04712   
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