KEGG PATHWAY: ath04712

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

Other DBs

BSID:

95649

GO:

0007623

Organism

Arabidopsis thaliana (thale cress) [GN:ath]

Gene

AT2G18790	PHYB; phytochrome B [KO:K12121]
AT1G09570	PHYA; phytochrome A [KO:K12120]
AT1G09530	PIF3; transcription factor PIF3 [KO:K12126]
AT2G25930	ELF3; protein EARLY FLOWERING 3 [KO:K12125]
AT2G46790	PRR9; two-component response regulator-like APRR9 [KO:K12128]
AT5G02810	PRR7; two-component response regulator-like APRR7 [KO:K12129]
AT5G24470	PRR5; two-component response regulator-like APRR5 [KO:K12130]
AT1G01060	LHY; protein late elongated hypocotyl [KO:K12133]
AT2G46830	CCA1; protein CCA1 [KO:K12134]
AT2G23070	casein kinase 2; K03097 casein kinase II subunit alpha [EC:2.7.11.1] [KO:K03097] [EC:2.7.11.1]
AT2G23080	putative casein kinase II subunit alpha; K03097 casein kinase II subunit alpha [EC:2.7.11.1] [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 2 subunit beta-3 [KO:K03115]
AT4G17640	CKB2; casein kinase 2 subunit beta' [KO:K03115]
AT2G44680	CKB4; casein kinase 2, beta polypeptide [KO:K03115]
AT5G47080	CKB1; casein kinase 2 subunit beta [KO:K03115]
AT5G08330	transcription factor TCP21; K16221 transcription factor TCP21 (protein CCA1 HIKING EXPEDITION) [KO:K16221]
AT5G61380	TOC1; two-component response regulator-like APRR1 [KO:K12127]
AT5G57360	ZTL; adagio protein 1 [KO:K12115]
AT1G22770	GI; gigantea protein (GI) [KO:K12124]
AT5G60100	PRR3; two-component response regulator-like APRR3 [KO:K12131]
AT1G56650	PAP1; transcription factor MYB75 [KO:K16166]
AT5G13930	TT4; chalcone synthase [KO:K00660] [EC:2.3.1.74]
AT4G08920	CRY1; cryptochrome-1 [KO:K12118]
AT1G04400	CRY2; cryptochrome 2 [KO:K12119]
AT2G32950	COP1; E3 ubiquitin-protein ligase COP1 [KO:K10143] [EC:6.3.2.19]
AT5G52250	transducin/WD40 domain-containing protein; K10143 E3 ubiquitin-protein ligase RFWD2 [EC:6.3.2.19] [KO:K10143] [EC:6.3.2.19]
AT5G23730	transducin/WD40 domain-containing protein; K10143 E3 ubiquitin-protein ligase RFWD2 [EC:6.3.2.19] [KO:K10143] [EC:6.3.2.19]
AT1G68050	FKF1; adagio protein 3 [KO:K12116]
AT5G62430	CDF1; Dof zinc finger protein DOF5.5 [KO:K16222]
AT5G15840	CO; zinc finger protein CONSTANS [KO:K12135]
AT1G65480	FT; protein FLOWERING LOCUS T [KO:K16223]
AT2G46340	SPA1; protein SUPPRESSOR OF PHYA-105 1 [KO:K16240]
AT5G11260	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)

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)

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)

Reference

PMID:8953247

Authors

Sakamoto K, Nagatani A.

Title

Nuclear localization activity of phytochrome B.

Journal

Plant J 10:859-68 (1996)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

Reference

PMID:20809800

Authors

Doherty CJ, Kay SA

Title

Circadian control of global gene expression patterns.

Journal

Annu Rev Genet 44:419-44 (2010)

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)

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)

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)

KO pathway

ko04712

All links

Pathway (1)   
   BioSystems (1)   
Genome (1)   
   KEGG GENOME (1)   
Gene (35)   
   KEGG GENES (35)   
All databases (37)   

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