Environmental F actors coordinate circadian clock function and rhythm to regulate plant development

References

• Wijnen H, Young MW. Interplay of circadian clocks and metabolic rhythms. Annu Rev Genet. 2006;40(1):409–12. doi:10.1146/annurev.genet.40.110405.090603.
   PubMedGoogle Scholar
• Más P. Circadian clock signaling in Arabidopsis thaliana: from gene expression to physiology and development. Int J Dev Biol. 2005;49(5–6):491–500. doi:10.1387/ijdb.041968pm.
   PubMed Web of Science ®Google Scholar
• Patke A, Young MW, Axelrod S. Molecular mechanisms and physiological importance of circadian rhythms. Nat Rev Mol Cell Biol. 2020 Feb;21(2):67–84. doi:10.1038/s41580-019-0179-2. Epub 2019 Nov 25. PMID: 31768006.
   PubMed Web of Science ®Google Scholar
• Herrero E, Davis SJ. Time for a nuclear meeting: protein trafficking and chromatin dynamics intersect in the plant circadian system. Mol Plant. 2012 May;5(3):554–565. doi:10.1093/mp/sss010. Epub 2012 Feb 29. PMID: 22379122.
   PubMed Web of Science ®Google Scholar
• Schober A, Blay RM, Saboor Maleki S, Zahedi F, Winklmaier AE, Kakar MY, Baatsch IM, Zhu M, Geißler C, Fusco AE, et al. MicroRNA-21 controls circadian regulation of Apoptosis in atherosclerotic lesions. Circulation. 2021 Sep 28;144(13):1059–1073. doi:10.1161/CIRCULATIONAHA.120.051614. Epub 2021 Jul 8. PMID: 34233454.
   PubMed Web of Science ®Google Scholar
• Nakamichi N. The transcriptional network in the Arabidopsis circadian clock system. Genes (Basel). 2020 Oct 29;11(11):1284. doi:10.3390/genes11111284. PMID: 33138078; PMCID: PMC7692566.
   PubMed Web of Science ®Google Scholar
• Wang X, Jiang B, Gu L, Chen Y, Mora M, Zhu M, Noory E, Wang Q, Lin C. A photoregulatory mechanism of the circadian clock in Arabidopsis. Nat Plants. 2021 Oct;7(10):1397–1408. doi:10.1038/s41477-021-01002-z. Epub 2021 Oct 14. Erratum in: Nat Plants. 2021 Oct 22;: PMID: 34650267.
   PubMed Web of Science ®Google Scholar
• Laosuntisuk K, Doherty CJ. The intersection between circadian and heat-responsive regulatory networks controls plant responses to increasing temperatures. Biochem Soc Trans. 2022 Jun 30;50(3):1151–1165. doi:10.1042/BST20190572. PMID: 35758233; PMCID: PMC9246330.
   PubMed Web of Science ®Google Scholar
• Kamioka M, Takao S, Suzuki T, Taki K, Higashiyama T, Kinoshita T, Nakamichi N. Direct repression of evening genes by CIRCADIAN CLOCK-ASSOCIATED1 in the Arabidopsis circadian clock. Plant Cell. 2016 Mar;28(3):696–711. doi:10.1105/tpc.15.00737. Epub 2016 Mar 3. PMID: 26941090; PMCID: PMC4826007.
   PubMed Web of Science ®Google Scholar
• Nakamichi N, Kiba T, Henriques R, Mizuno T, Chua NH, Sakakibara H. PSEUDO-RESPONSE REGULATORS 9, 7, and 5 are transcriptional repressors in the Arabidopsis circadian clock. Plant Cell. 2010;22(3):594–605. doi:10.1105/tpc.109.072892.
   PubMed Web of Science ®Google Scholar
• Rawat R, Takahashi N, Hsu PY, Jones MA, Schwartz J, Salemi MR, Phinney BS, Harmer SL, Copenhaver GP. REVEILLE8 and PSEUDO-REPONSE REGULATOR5 form a negative feedback loop within the Arabidopsis circadian clock. PLoS Genet. 2011;7(3):e1001350. doi:10.1371/journal.pgen.1001350.
   PubMed Web of Science ®Google Scholar
• Pruneda-Paz JL, Breton G, Para A, Kay SA. A functional genomics approach reveals CHE as a component of the Arabidopsis circadian clock. Science. 2009;323(5920):1481–1485. doi:10.1126/science.1167206.
   PubMed Web of Science ®Google Scholar
• Lu SX, Webb CJ, Knowles SM, Kim SH, Wang Z, Tobin EM. CCA1 and ELF3 Interact in the control of hypocotyl length and flowering time in Arabidopsis. Plant Physiol. 2012;158(2):1079–1088. doi:10.1104/pp.111.189670.
   PubMed Web of Science ®Google Scholar
• Gould PD, Locke JC, Larue C, Southern MM, Davis SJ, Hanano S, Moyle R, Milich R, Putterill J, Millar AJ, et al. The molecular basis of temperature compensation in the Arabidopsis circadian clock. Plant Cell. 2006;18(5):1177–1187. doi:10.1105/tpc.105.039990.
   PubMed Web of Science ®Google Scholar
• Mizuno T, Nomoto Y, Oka H, Kitayama M, Takeuchi A, Tsubouchi M, Yamashino T. Ambient temperature signal feeds into the circadian clock transcriptional circuitry through the EC night-time repressor in Arabidopsis thaliana. Plant Cell Physiol. 2014;55(5):958–976. doi:10.1093/pcp/pcu030.
   PubMed Web of Science ®Google Scholar
• Martí Ruiz MC, Jung HJ, Webb AAR. Circadian gating of dark-induced increases in chloroplast- and cytosolic-free calcium in Arabidopsis. New Phytol. 2020 Mar;225(5):1993–2005. doi:10.1111/nph.16280. Epub 2019 Nov 22. PMID: 31644821; PMCID: PMC7028143.
   PubMed Web of Science ®Google Scholar
• Lee HG, Seo PJ. The Arabidopsis JMJ29 protein controls circadian oscillation through diurnal histone demethylation at the CCA1 and PRR9 Loci. Genes (Basel). 2021 Apr 5;12(4):529. doi:10.3390/genes12040529. PMID: 33916408; PMCID: PMC8066055.
   PubMed Web of Science ®Google Scholar
• Más P, Kim WY, Somers DE, Kay SA. Targeted degradation of TOC1 by ZTL modulates circadian function in Arabidopsis thaliana. Nature. 2003 Dec 4;426(6966):567–570. doi:10.1038/nature02163.
   PubMed Web of Science ®Google Scholar
• Kiba T, Henriques R, Sakakibara H, Chua NH. Targeted degradation of PSEUDO-RESPONSE REGULATOR5 by an SCFZTL complex regulates clock function and photomorphogenesis in Arabidopsis thaliana. Plant Cell. 2007 Aug;19(8):2516–2530. doi:10.1105/tpc.107.053033.
   PubMed Web of Science ®Google Scholar
• Sanchez SE, Rugnone ML, Kay SA. Light perception: a matter of time. Mol Plant. 2020 Mar 2;13(3):363–385. doi:10.1016/j.molp.2020.02.006. Epub 2020 Feb 14. PMID: 32068156; PMCID: PMC7056494.
   PubMed Web of Science ®Google Scholar
• Greenham K, McClung CR. Integrating circadian dynamics with physiological processes in plants. Nat Rev Genet. 2015 16(10):598–610. doi: 10.1038/nrg3976. Epub 2015 Oct 15. in: Nat Rev Genet. 2015 Nov;16(11):681. PMID: 26370901.
   PubMed Web of Science ®Google Scholar
• Jang S, Marchal V, Panigrahi KC, Wenkel S, Soppe W, Deng XW, Valverde F, Coupland G. Arabidopsis COP1 shapes the temporal pattern of CO accumulation conferring a photoperiodic flowering response. Embo J. 2008 Apr 23;27(8):1277–1288. doi:10.1038/emboj.2008.68.
   PubMed Web of Science ®Google Scholar
• Wigge PA, Kim MC, Jaeger KE, Busch W, Schmid M, Lohmann JU, Weigel D. Integration of spatial and temporal information during floral induction in Arabidopsis. Science. 2005 Aug 12;309(5737):1056–1059. doi:10.1126/science.1114358.
   PubMed Web of Science ®Google Scholar
• Yamaguchi A, Kobayashi Y, Goto K, Abe M, Araki T. TWIN SISTER of FT (TSF) acts as a floral pathway integrator redundantly with FT. Plant Cell Physiol. 2005 Aug;46(8):1175–1189. doi:10.1093/pcp/pci151.
   PubMed Web of Science ®Google Scholar
• NUSINOW DA, HELFER A, HAMILTON EE, King JJ, Imaizumi T, Schultz TF, Farré EM, Kay SA. The ELF4–ELF3–LUX complex links the circadian clock to diurnal control of hypocotyl growth. Nature. 2011;475:398–402. doi:10.1038/nature10182.
   PubMed Web of Science ®Google Scholar
• Lorrain S, Allen T, Duek PD, Whitelam GC, Fankhauser C. Phytochrome-mediated inhibition of shade avoidance involves degradation of growth-promoting bHLH transcription factors. Plant J. 2008 Jan;53(2):312–323. doi:10.1111/j.1365-313X.2007.03341.x.
   PubMed Web of Science ®Google Scholar
• Oakenfull RJ, Davis SJ. Shining a light on the Arabidopsis circadian clock. Plant, Cell & Environ. 2017;40(11):2571–2585. doi:10.1111/pce.13033.
   PubMed Web of Science ®Google Scholar
• Fankhauser C, Staiger D. Photoreceptors in Arabidopsis thaliana: light perception, signal transduction and entrainment of the endogenous clock. Planta. 2002;216(1):1–16. doi:10.1007/s00425-002-0831-4.
   PubMed Web of Science ®Google Scholar
• Ronald J, Davis SJ. Focusing on the nuclear and subnuclear dynamics of light and circadian signalling. Plant, Cell & Environ. 2019 Oct;42(10):2871–2884. doi:10.1111/pce.13634. Epub 2019 Aug 16. PMID: 31369151.
   PubMed Web of Science ®Google Scholar
• Wang L, Sun S, Wu T, Liu L, Sun X, Cai Y, Li J, Jia H, Yuan S, Chen L, et al. Natural variation and CRISPR/Cas9-mediated mutation in GmPRR37 affect photoperiodic flowering and contribute to regional adaptation of soybean. Plant Biotechnol J. 2020;18(9):1869–1881. doi:10.1111/pbi.13346.
   PubMed Web of Science ®Google Scholar
• Balcerowicz M, Mahjoub M, Nguyen D, Lan H, Stoeckle D, Conde S, Jaeger KE, Wigge PA, Ezer D. An early-morning gene network controlled by phytochromes and cryptochromes regulates photomorphogenesis pathways in Arabidopsis. Mol Plant. 2021 Jun 7;14(6):983–996. doi:10.1016/j.molp.2021.03.019. Epub 2021 Mar 23. PMID: 33766657.
   PubMed Web of Science ®Google Scholar
• Somers DE, Devlin PF, Kay SA. Phytochromes and cryptochromes in the entrainment of the Arabidopsis circadian clock. Science. 1998;282(5393):1488–1490. doi:10.1126/science.282.5393.1488.
   PubMed Web of Science ®Google Scholar
• Hu W, Franklin KA, Sharrock RA, Jones MA, Harmer SL, Lagarias JC. Unanticipated regulatory roles for Arabidopsis phytochromes revealed by null mutant analysis. Proc Natl Acad Sci USA. 2013;110(4):1542–1547. doi:10.1073/pnas.1221738110.
   PubMed Web of Science ®Google Scholar
• Strasser B, Sanchez-Lamas M, Yanovsky MJ, Casal JJ, Cerdan PD. Arabidopsis thaliana life without phytochromes. Proc Natl Acad Sci USA. 2010;107(10):4776–4781. doi:10.1073/pnas.0910446107.
   PubMed Web of Science ®Google Scholar
• Kim WY, Fujiwara S, Suh SS, Kim J, Kim Y, Han L, David K, Putterill J, Nam HG, Somers DE. ZEITLUPE is a circadian photoreceptor stabilized by GIGANTEA in blue light. Nature. 2007 Sep 20;449(7160):356–360. doi:10.1038/nature06132. Epub 2007 Aug 19. PMID: 17704763.
   PubMed Web of Science ®Google Scholar
• Dixon LE, Knox K, Kozma-Bognar L, Southern MM, Pokhilko A, Millar AJ. Temporal repression of core circadian genes is mediated through EARLY FLOWERING 3 in Arabidopsis. Curr Biol. 2011 Jan 25;21(2):120–125. doi:10.1016/j.cub.2010.12.013. Epub 2011 Jan 13. PMID: 21236675; PMCID: PMC3028277.
   PubMed Web of Science ®Google Scholar
• Sheerin DJ, Menon C, zur Oven-Krockhaus S, Enderle B, Zhu L, Johnen P, Schleifenbaum F, Stierhof YD, Huq E, Hiltbrunner A. Light-activated phytochrome a and B interact with members of the SPA family to promote photomorphogenesis in Arabidopsis by reorganizing the COP1/SPA complex. Plant Cell. 2015;27(1):189–201. doi:10.1105/tpc.114.134775.
   PubMed Web of Science ®Google Scholar
• Jones MA, Hu W, Litthauer S, Lagarias JC, Harmer SL. A constitutively active allele of phytochrome B maintains circadian robustness in the absence of light. Plant Physiol. 2015;169(1):814–825. doi:10.1104/pp.15.00782.
   PubMed Web of Science ®Google Scholar
• Soy J, Leivar P, Gonzalez-Schain N, Martin G, Diaz C, Sentandreu M, Al-Sady B, Quail PH, Monte E. Molecular convergence of clock and photosensory pathways through PIF3-TOC1 interaction and co-occupancy of target promoters. Proc Natl Acad Sci USA. 2016;113(17):4870–4875. doi:10.1073/pnas.1603745113.
   PubMed Web of Science ®Google Scholar
• Li N, Zhang Y, He Y, Wang Y, Wang L. Pseudo response regulators regulate photoperiodic hypocotyl growth by repressing PIF4/5 transcription. Plant Physiol. 2020 Jun;183(2):686–699. doi:10.1104/pp.19.01599. Epub 2020 Mar 12. PMID: 32165445; PMCID: PMC7271792.
   PubMedGoogle Scholar
• Su C, Wang Y, Yu Y, He Y, Wang L. Coordinative regulation of plants growth and development by light and circadian clock. Abiotech. 2021 Mar 27;2(2):176–189. doi:10.1007/s42994-021-00041-6. PMID: 36304756; PMCID: PMC9590570.
   PubMedGoogle Scholar
• Cox KH, Takahashi JS. Circadian clock genes and the transcriptional architecture of the clock mechanism. J Mol Endocrinol. 2019 Nov;63(4):R93–R102. doi:10.1530/JME-19-0153. PMID: 31557726; PMCID: PMC6872945.
   PubMed Web of Science ®Google Scholar
• Li B, Gao Z, Liu X, Sun D, Tang W. Transcriptional profiling reveals a time-of-day-specific role of REVEILLE 4/8 in regulating the first wave of heat shock-induced gene expression in Arabidopsis. Plant Cell. 2019 Oct;31(10):2353–2369. doi:10.1105/tpc.19.00519. Epub 2019 Jul 29. PMID: 31358650; PMCID: PMC6790097.
   PubMed Web of Science ®Google Scholar
• Para A, Farre EM, Imaizumi T, Pruneda-Paz L, Harmon FG, Kay SA. PRR3 is a vascular regulator of TOC1 stability in the Arabidopsis circadian clock. Plant Cell. 2007;19(11):3462–3473. doi:10.1105/tpc.107.054775.
   PubMed Web of Science ®Google Scholar
• Wang L, Fujiwara S, Somers DE. PRR5 regulates phosphorylation, nuclear import and subnuclear localization of TOC1 in the Arabidopsis circadian clock. Embo J. 2010;29(11):1903–1915. doi:10.1038/emboj.2010.76.
   PubMed Web of Science ®Google Scholar
• Pedmale UV, Huang SC, Zander M, Cole BJ, Hetzel J, Ljung K, Reis PAB, Sridevi P, Nito K, Nery JR, et al. Cryptochromes interact directly with PIFs to control plant growth in limiting blue light. Cell. 2016;164:233–245. doi:10.1016/j.cell.2015.12.018.
   PubMed Web of Science ®Google Scholar
• FUJIMORI T, YAMASHINO T, Kato T, Mizuno T. KATO T, et al.Circadian-controlled basic/helix-loop-helix factor, PIL6, implicated in light-signal transduction in Arabidopsis thaliana. Plant And Cell Physi. 2004;45:1078–1086. doi:10.1093/pcp/pch124.
   PubMed Web of Science ®Google Scholar
• Martín G, ROVIRA A, VECIANA N, Soy J, Toledo-Ortiz G, Gommers CMM, Boix M, Henriques R, Minguet EG, Alabadí D, et al. Circadian waves of transcriptional repression shape PIF-regulated photoperiod-responsive growth in Arabidopsis. Curr Biol. 2018;28:311–318.e315. doi:10.1016/j.cub.2017.12.021.
   PubMed Web of Science ®Google Scholar
• HUANG H, ALVAREZ S, BINDBEUTEL R, Shen Z, Naldrett MJ, Evans BS, Briggs SP, Hicks LM, Kay SA, Nusinow DA, et al. Identification of evening complex associated proteins in Arabidopsis by affinity purification and mass spectrometry. Molecular & Cellular Proteomics: MCP. 2016;15(1):201–217. doi:10.1074/mcp.M115.054064.
   PubMed Web of Science ®Google Scholar
• Liu Q, Wang Q, Deng W, Wang X, Piao M, Cai D, Li Y, Barshop WD, Yu X, Zhou T, et al. Molecular basis for blue light-dependent phosphorylation of Arabidopsis cryptochrome 2. Nat Commun. 2017 May 11;8(1):15234. doi:10.1038/ncomms15234. PMID: 28492234; PMCID: PMC5437284.
   PubMedGoogle Scholar
• MILLAR AJ, STRAUME M, CHORY J, Chua N-H, Kay SA. The regulation of circadian period by phototransduction pathways in Arabidopsis. Science. 1995;267:1163–1166. doi:10.1126/science.7855596.
   PubMed Web of Science ®Google Scholar
• YU JW, RUBIO V, LEE NY, Bai S, Lee S-Y, Kim S-S, Liu L, Zhang Y, Irigoyen ML, Sullivan JA, et al. COP1 and ELF3 control circadian function and photoperiodic flowering by regulating GI stability. Mol Cell. 2008;32:617–630. doi:10.1016/j.molcel.2008.09.026.
   PubMed Web of Science ®Google Scholar
• Leivar P, Martín G, Soy J, Dalton-Roesler J, Quail PH, Monte E. Phytochrome-imposed inhibition of PIF7 activity shapes photoperiodic growth in Arabidopsis together with PIF1, 3, 4 and 5. Physiol Plant. 2020 Jul;169(3):452–466. doi:10.1111/ppl.13123. PMID: 32412656.
   PubMed Web of Science ®Google Scholar
• Shor E, Paik I, Kangisser S, Green R, Huq E. PHYTOCHROME INTERACTING FACTORS mediate metabolic control of the circadian system in Arabidopsis. New Phytol. 2017 Jul;215(1):217–228. doi:10.1111/nph.14579. Epub 2017 Apr 25. PMID: 28440582; PMCID: PMC5458605.
   PubMed Web of Science ®Google Scholar
• Zhu JY, Oh E, Wang T, Wang ZY. TOC1-PIF4 interaction mediates the circadian gating of thermoresponsive growth in Arabidopsis. Nat Commun. 2016 Dec 14;7:13692. doi:10.1038/ncomms13692. PMID: 27966533; PMCID: PMC5171658.
   PubMed Web of Science ®Google Scholar
• Nozue K, Covington MF, Duek PD, Lorrain S, Fankhauser C, Harmer SL, Maloof JN. Rhythmic growth explained by coincidence between internal and external cues. Nature. 2007;448(7151):358–361. doi:10.1038/nature05946.
   PubMed Web of Science ®Google Scholar
• Nieto C, López-Salmerón V, Davière JM, Prat S. ELF3-PIF4 interaction regulates plant growth independently of the evening complex. Curr Biol. 2015 Jan 19;25(2):187–193. doi:10.1016/j.cub.2014.10.070. Epub 2014 Dec 31. PMID: 25557667.
   PubMed Web of Science ®Google Scholar
• Zhao H, Xu D, Tian T, Kong F, Lin K, Gan S, Zhang H, Li G. Molecular and functional dissection of EARLY-FLOWERING 3 (ELF3) and ELF4 in Arabidopsis. Plant Sci. 2021 Feb;303:110786. doi:10.1016/j.plantsci.2020.110786. Epub 2020 Dec 3. PMID: 33487361.
   PubMed Web of Science ®Google Scholar
• Song Z, Heng Y, Bian Y, Xiao Y, Liu J, Zhao X, Jiang Y, Deng XW, Xu D. BBX11 promotes red light-mediated photomorphogenic development by modulating phyB-PIF4 signaling. Abiotech. 2021 Apr 26;2(2):117–130. doi:10.1007/s42994-021-00037-2. PMID: 36304757; PMCID: PMC9590482.
   PubMedGoogle Scholar
• Li S, Wang Q, Wen B, Zhang R, Jing X, Xiao W, Chen X, Tan Q, Li L. Endodormancy release can be modulated by the GA4-GID1c-DELLA2 module in peach leaf buds. Front Plant Sci. 2021 Sep 27;12:713514. doi:10.3389/fpls.2021.713514. PMID: 34646285; PMCID: PMC8504481.
   PubMed Web of Science ®Google Scholar
• Zhai H, Xiong L, Li H, Lyu X, Yang G, Zhao T, Liu J, Liu B. Cryptochrome 1 inhibits shoot branching by repressing the self-activated transciption loop of PIF4 in Arabidopsis. Plant Commun. 2020 Mar 26;1(3):100042. doi:10.1016/j.xplc.2020.100042. PMID: 33367238; PMCID: PMC7748022.
   PubMedGoogle Scholar
• Yuan L, Hu Y, Li S, Xie Q, Xu X. PRR9 and PRR7 negatively regulate the expression of EC components under warm temperature in roots. Plant Signal Behav. 2021a Feb 1;16(2):1855384. doi:10.1080/15592324.2020.1855384.
   PubMed Web of Science ®Google Scholar
• Salome PA, Weigel D, Mc Clung CR. The role of the Arabidopsis morning loop components CCA1, LHY, PRR7, and PRR9 in temperature compensation. Plant Cell. 2010;22(11):3650–3661. doi:10.1105/tpc.110.079087.
   PubMed Web of Science ®Google Scholar
• Chow BY, Sanchez, Anchez SE G, Pruneda-Paz JL, Krogan NT, Kay SA, Sanchez S. Transcriptional regulation of LUX by CBF1 mediates cold input to the circadian clock in Arabidopsis. Curr Biol. 2014;24(13):1518–1524. doi:10.1016/j.cub.2014.05.029.
   PubMed Web of Science ®Google Scholar
• Nagel DH, Pruneda-Paz JL, Kay SA. FBH1 affects warm temperature responses in the Arabidopsis circadian clock. Proc Natl Acad Sci USA. 2014;111(40):14595–14600. doi:10.1073/pnas.1416666111.
   PubMed Web of Science ®Google Scholar
• Anwer MU, Davis A, Davis SJ, Quint M. Photoperiod sensing of the circadian clock is controlled by EARLY FLOWERING 3 and GIGANTEA. Plant J. 2020 Mar;101(6):1397–1410. doi:10.1111/tpj.14604. Epub 2019 Dec 11. PMID: 31694066.
   PubMed Web of Science ®Google Scholar
• Jung JH, Domijan M, Klose C, Biswas S, Ezer D, Gao M, Khattak AK, Box MS, Charoensawan V, Cortijo S, et al. Phytochromes function as thermosensors in Arabidopsis. Science. 2016;354(6314):886–889. doi:10.1126/science.aaf6005.
   PubMed Web of Science ®Google Scholar
• Mockler TC, Michael TP, Priest HD, Shen R, Sullivan CM, Givan SA, McEntee C, Kay SA, Chory J. The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis. Cold Spring Harb Symp Quant Biol. 2007;72:353–63. doi: 10.1101/sqb.2007.72.006. PMID: 18419293.
   PubMedGoogle Scholar
• Covington MF, Covington SL, Weigel D. The circadian clock regulates auxin signaling and responses in Arabisopsis. PLoS Biol. 2007;5:e222. doi:10.1371/journal.pbio.0050222.
   PubMed Web of Science ®Google Scholar
• Rawat R, Schwartz J, Jones MA, Sairanen I, Cheng Y, Andersson CR, Zhao Y, Ljung K, Harmer SL. REVEILLE1, a Myb-like transcription factor, integrates the circadian clock and auxin pathways. Proc Natl Acad Sci USA. 2009;106:16883–16888. doi:10.1073/pnas.0813035106.
   PubMed Web of Science ®Google Scholar
• Voß U, Wilson MH, Kenobi K, Gould PD, Robertson FC, Peer WA, Lucas M, Swarup K, Casimiro I, Holman TJ, et al. The circadian clock rephases during lateral root organ initiation in Arabidopsis thaliana. Nat Commun. 2015;6:7641. doi:10.1038/ncomms8641.
   PubMed Web of Science ®Google Scholar
• Li H, Da WY, Liu W-C, Chen H-G, Lu Y-T. TIME for COFFEE controls root meristem size by changes in auxin accumulation in Arabidopsis. Journal Of Experimental Botany. 2014;65:275–286. doi:10.1093/jxb/ert374.
   PubMed Web of Science ®Google Scholar
• Zha P, Jing YJ, Xu G, Lin R. PICKLE chromatin-remodeling factor controls thermosensory hypocotyl growth of Arabidopsis. Plant, Cell & Environment. 2017;40:2426–2436. doi:10.1111/pce.13049.
   PubMed Web of Science ®Google Scholar
• Sun JQ, Qi LL, Li Y, Zhai Q, Li C. PIF4 and PIF5 transcription factors link blue light and auxin to regulate the phototropic response in Arabidopsis. The Plant Cell. 2013;25:2102–2114. doi:10.1105/tpc.113.112417.
   PubMed Web of Science ®Google Scholar
• Nagel DH, Kay SA. Complexity in the wiring and regulation of plant circadian networks. Curr Biol. 2012;22(16):R648–R657. doi:10.1016/j.cub.2012.07.025.
   PubMed Web of Science ®Google Scholar
• Hung FY, Chen FF, Li C, Chen C, Chen JH, Cui Y, Wu K. The LDL1/2-HDA6 histone modification complex interacts with TOC1 and regulates the core circadian clock components in Arabidopsis. Front Plant Sci. 2019 Feb 26;10:233. doi:10.3389/fpls.2019.00233. PMID: 30863422; PMCID: PMC6399392.
   PubMed Web of Science ®Google Scholar
• Yan J, Li S, Kim YJ, Zeng Q, Radziejwoski A, Wang L, Nomura Y, Nakagami H, Somers DE. TOC1 clock protein phosphorylation controls complex formation with NF-YB/C to repress hypocotyl growth. Embo J. 2021 Dec 15;40(24):e108684. doi:10.15252/embj.2021108684. Epub 2021 Nov 2. PMID: 34726281; PMCID: PMC8672182.
   PubMed Web of Science ®Google Scholar
• Nakamichi N, Kita M, Niinuma K, Ito S, Yamashino T, Mizoguchi T, Mizuno T. Arabidopsis clock-associated pseudo-response regulators PRR9, PRR7 and PRR5 coordinately and positively regulate flowering time through the canonical CONSTANS-dependent photoperiodic pathway. Plant Cell Physiol. 2007;48(6):822–832. doi:10.1093/pcp/pcm056.
   PubMed Web of Science ®Google Scholar
• Helfer A, Nusinow DA, Chow BY, Gehrke AR, Bulyk ML, Kay SA. LUX ARRHYTHMO encodes a nighttime repressor of circadian gene expression in the Arabidopsis core clock. Curr Biol. 2011;21(2):126–133. doi:10.1016/j.cub.2010.12.021.
   PubMed Web of Science ®Google Scholar
• Kim WY, Hicks KA, Somers DE. Independent roles for EARLY FLOWERING 3 and ZEITLUPE in the control of circadian timing, hypocotyl length, and flowering time. Plant Physiol. 2005;139(3):1557–1569. doi:10.1104/pp.105.067173.
   PubMed Web of Science ®Google Scholar
• Liu XL, Covington MF, Fankhauser C, Chory J, Wanger DR. ELF3 encodes a circadian clock-regulated nuclear protein that functions in an Arabidopsis PHYB signal transduction pathway. Plant Cell. 2001;13(6):1293–1304. doi:10.1105/TPC.000475.
   PubMed Web of Science ®Google Scholar
• Lin K, Zhao H, Gan S, Li G. Arabidopsis ELF4-like proteins EFL1 and EFL3 influence flowering time. Gene. 2019 Jun 5;700:131–138. doi:10.1016/j.gene.2019.03.047. Epub 2019 Mar 24. PMID: 30917931.
   PubMed Web of Science ®Google Scholar
• Weller JL, Liew LC, Hecht VFG, Rajandran V, Laurie RE, Ridge S, Wenden B, Vander Schoor JK, Jaminon O, Blassiau C, et al. A conserved molecular basis for photoperiod adaptation in two temperate legumes. Proc Natl Acad Sci USA. 2012;109(51):21158–21163. doi:10.1073/pnas.1207943110.
   PubMed Web of Science ®Google Scholar
• Lu SJ, Dong LD, Fang C, Liu SL, Kong LP, Cheng Q, Chen LY, Su T, Nan HY, Zhang D, et al. Stepwise selection on homeologous PRR genes controlling flowering and maturity during soybean domestication. Nat Genet. 2020;52(4):428–436. doi:10.1038/s41588-020-0604-7.
   PubMed Web of Science ®Google Scholar
• Bu TT, Lu SJ, Wang K, Dong LD, Li SL, Xie QG, Xu XD, Cheng Q, Chen LY, Fang C, et al. A critical role of the soybean evening complex in the control of photoperiod sensitivity and adaptation. Proc Natl Acad Sci USA. 2021;118(8). doi:10.1073/pnas.2010241118
   Web of Science ®Google Scholar
• Lu SJ, Zhao XH, Hu YL, Liu SL, Nan HY, Li XM, Fang C, Cao D, Shi XY, Kong LP, et al. Natural variation at the soybean J locus improves adaptation to the tropics and enhances yield. Nat Genet. 2017;49(5):773–779. doi:10.1038/ng.3819.
   PubMed Web of Science ®Google Scholar
• Koo BH, Yoo SC, Park JW, Kwon CT, Lee BD, An G, Zhang ZY, Li JJ, Li ZC, Paek NC. Natural variation in Os PRR37 regulates heading date and contributes to rice cultivation at a wide range of latitudes. Mol Plant. 2013;6(6):1877–1888. doi:10.1093/mp/sst088.
   PubMed Web of Science ®Google Scholar
• Yang Y, Peng Q, Chen GX, Li XH, Wu CY. OsELF3 is involved in circadian clock regulation for promoting flowering under long-day conditions in rice. Mol Plant. 2013;6(1):202–215. doi:10.1093/mp/sss062.
   PubMed Web of Science ®Google Scholar
• Turner A, Beales J, Faure S, Dunford RP, Laurie DA. The pseudo-response regulator Ppd-H1 provides adaptation to photoperiod in barley. Science. 2005;310(5750):1031–1034. doi:10.1126/science.1117619.
   PubMed Web of Science ®Google Scholar
• Campoli C, Pankin A, Drosse B, Casao CM, Davis SJ, Von Korff M. Hv LUX1 is a candidate gene underlying the early maturity 10 locus in barley: phylogeny, diversity, and interactions with the circadian clock and photoperiodic pathways. New Phytol. 2013;199(4):1045–1059. doi:10.1111/nph.12346.
   PubMed Web of Science ®Google Scholar
• Faure S, Turner AS, Gruszka D, Christodoulou V, Davis SJ, Von Korff M, Laurie DA. Mutation at the circadian clock gene EARLY MATURITY 8 adapts domesticated barley (Hordeum vulgare) to short growing seasons. Proc Natl Acad Sci USA. 2012;109(21):8328–8333. doi:10.1073/pnas.1120496109.
   PubMed Web of Science ®Google Scholar
• Shaw LM, Turner AS, Laurie DA. The impact of photoperiod insensitive Ppd-1a mutations on the photoperiod pathway across the three genomes of hexaploid wheat (Triticum aestivum). The Plant Journal. 2012;71(1):71–84. doi:10.1111/j.1365-313X.2012.04971.x.
   PubMed Web of Science ®Google Scholar
• Murphy RL, Klein RR, Morishige DT, Brady JA, Rooney WL, Miller FR, Dugas DV, Klein PE, Mullet JE. Coincident light and clock regulation of pseudoresponse regulator protein 37 (PRR37) controls photoperiodic flowering in sorghum. Proc Natl Acad Sci USA. 2011;108(39):16469–16474. doi:10.1073/pnas.1106212108.
   PubMed Web of Science ®Google Scholar
• Endo M, Shimizu H, Nohales MA, Araki T, Kay SA. Tissue-specific clocks in Arabidopsis show asymmetric coupling. Nature. 2014 Nov 20;515(7527):419–422. doi:10.1038/nature13919.
   PubMed Web of Science ®Google Scholar
• Sanagi M, Aoyama S, Kubo A, Lu Y, Sato Y, Ito S, Abe M, Mitsuda N, Ohme-Takagi M, Kiba T, et al. Low nitrogen conditions accelerate flowering by modulating the phosphorylation state of FLOWERING BHLH 4 in Arabidopsis. Proc Natl Acad Sci USA. 2021 May 11;118(19):e2022942118. doi:10.1073/pnas.2022942118.
   PubMed Web of Science ®Google Scholar
• Zhang S, Zhang Y, Li K, Yan M, Zhang J, Yu M, Tang S, Wang L, Qu H, Luo L, et al. Nitrogen mediates flowering time and nitrogen use efficiency via floral regulators in rice. Curr Biol. 2021 Feb 22;31(4):671–683.e5. doi:10.1016/j.cub.2020.10.095.
   PubMed Web of Science ®Google Scholar
• Mizuno T, Yamashino T. Comparative transcriptome of diurnally oscillating genes and hormone-responsive genes in Arabidopsis thaliana: insight into circadian clock-controlled daily responses to common ambient stresses in plants. Plant Cell Physiol. 2008 Mar;49(3):481–487. doi:10.1093/pcp/pcn008. Epub 2008 Jan 16. PMID: 18202002.
   PubMed Web of Science ®Google Scholar
• Adams S, Grundy J, Veflingstad SR, Dyer NP, Hannah MA, Ott S, Carré IA. Circadian control of abscisic acid biosynthesis and signalling pathways revealed by genome-wide analysis of LHY binding targets. New Phytol. 2018 Nov;220(3):893–907. doi:10.1111/nph.15415. Epub 2018 Sep 7. PMID: 30191576.
   PubMed Web of Science ®Google Scholar
• Lee KH, Piao HL, Kim HY, Choi SM, Jiang F, Hartung W, Hwang I, Kwak JM, Lee IJ, Hwang I. Activation of glucosidase via stress-induced polymerization rapidly increases active pools of abscisic acid. Cell. 2006 Sep 22;126(6):1109–1120. doi:10.1016/j.cell.2006.07.034. PMID: 16990135.
   PubMed Web of Science ®Google Scholar
• Liu T, Carlsson J, Takeuchi T, Newton L, Farré EM. Direct regulation of abiotic responses by the Arabidopsis circadian clock component PRR7. Plant J. 2013 Oct;76(1):101–114. doi:10.1111/tpj.12276. Epub 2013 Aug 10. PMID: 23808423.
   PubMed Web of Science ®Google Scholar
• Nakamichi N, Kusano M, Fukushima A, Kita M, Ito S, Yamashino T, Saito K, Sakakibara H, Mizuno T. Transcript profiling of an Arabidopsis PSEUDO RESPONSE REGULATOR arrhythmic triple mutant reveals a role for the circadian clock in cold stress response. Plant Cell Physiol. 2009 Mar;50(3):447–462. doi:10.1093/pcp/pcp004. Epub 2009 Jan 8. PMID: 19131357.
   PubMed Web of Science ®Google Scholar
• Legnaioli T, Cuevas J, Mas P. TOC1 functions as a molecular switch connecting the circadian clock with plant responses to drought. Embo J. 2009 Dec 2;28(23):3745–3757. doi:10.1038/emboj.2009.297. Epub 2009 Oct 8. PMID: 19816401; PMCID: PMC2790485.
   PubMed Web of Science ®Google Scholar
• Lee HG, Mas P, Seo PJ. MYB96 shapes the circadian gating of ABA signaling in Arabidopsis. Sci Rep. 2016 Jan 4;6:17754. doi:10.1038/srep17754. PMID: 26725725; PMCID: PMC4698719.
   PubMed Web of Science ®Google Scholar
• Yuan L, Xie GZ, Zhang S, Li B, Wang X, Li Y, Liu T, Xu X. GmLCLs negatively regulate ABA perception and signalling genes in soybean leaf dehydration response. Plant, Cell & Environ. 2021b Feb;44(2):412–424. doi:10.1111/pce.13931. Epub 2020 Nov 13. PMID: 33125160.
   PubMed Web of Science ®Google Scholar
• Gol L, Haraldsson EB, von Korff M, Jones M. Ppd-H1 integrates drought stress signals to control spike development and flowering time in barley. J Exp Bot. 2021 Jan 20;72(1):122–136. doi:10.1093/jxb/eraa261. PMID: 32459309; PMCID: PMC7816852.
   PubMed Web of Science ®Google Scholar
• Valim HF, McGale E, Yon F, Halitschke R, Fragoso V, Schuman MC, Baldwin IT. The clock gene TOC1 in shoots, not roots, determines fitness of Nicotiana attenuata under drought. Plant Physiol. 2019 Sep;181(1):305–318. doi:10.1104/pp.19.00286. Epub 2019 Jun 10. PMID: 31182558; PMCID: PMC6716261.
   PubMed Web of Science ®Google Scholar
• Kim WY, Ali Z, Park HJ, Park SJ, Cha JY, Perez-Hormaeche J, Quintero FJ, Shin G, Kim MR, Qiang Z, et al. Release of SOS2 kinase from sequestration with GIGANTEA determines salt tolerance in Arabidopsis. Nat Commun. 2013;4:1352. doi:10.1038/ncomms2357. Erratum in: Nat Commun. 2013;4:1820. PMID: 23322040.
   PubMed Web of Science ®Google Scholar
• Sakuraba Y, Bülbül S, Piao W, Choi G, Paek NC. Arabidopsis EARLY FLOWERING3 increases salt tolerance by suppressing salt stress response pathways. Plant J. 2017 Dec;92(6):1106–1120. doi:10.1111/tpj.13747. Epub 2017 Nov 20. PMID: 29032592.
   PubMed Web of Science ®Google Scholar
• Yang Y, Guo Y. Unraveling salt stress signaling in plants. J Integr Plant Biol. 2018 Sep;60(9):796–804. doi:10.1111/jipb.12689. Epub 2018 Jul 15. PMID: 29905393.
   PubMed Web of Science ®Google Scholar
• Cheng Q, Gan Z, Wang Y, Lu S, Hou Z, Li H, Xiang H, Liu B, Kong F, Dong L. The soybean gene J contributes to salt stress tolerance by up-regulating salt-responsive genes. Front Plant Sci. 2020 Mar 17;11:272. doi:10.3389/fpls.2020.00272. PMID: 32256507; PMCID: PMC7090219.
   PubMed Web of Science ®Google Scholar
• Wei H, Wang X, He Y, Xu H, Wang L. Clock component OsPRR73 positively regulates rice salt tolerance by modulating OsHKT2;1-mediated sodium homeostasis. Embo J. 2021 Feb 1;40(3):e105086. doi:10.15252/embj.2020105086. Epub 2020 Dec 21. PMID: 33347628; PMCID: PMC7849171.
   PubMed Web of Science ®Google Scholar
• Salomé PA, Oliva M, Weigel D, Krämer U. Circadian clock adjustment to plant iron status depends on chloroplast and phytochrome function. Embo J. 2013 Feb 20;32(4):511–523. doi:10.1038/emboj.2012.330. Epub 2012 Dec 14. PMID: 23241948; PMCID: PMC3579136.
   PubMed Web of Science ®Google Scholar
• de Melo JRF, Gutsch A, Caluwé T, Leloup JC, Gonze D, Hermans C, Webb AAR, Verbruggen N, de Melo JRF. Magnesium maintains the length of the circadian period in Arabidopsis. Plant Physiol. 2021 Mar 15;185(2):519–532. doi:10.1093/plphys/kiaa042. PMID: 33721908; PMCID: PMC8133681.
   PubMed Web of Science ®Google Scholar
• Jain A, Connolly EL. Mitochondrial iron transport and homeostasis in plants. Front Plant Sci. 2013 Sep 6;4:348. doi:10.3389/fpls.2013.00348.
   PubMed Web of Science ®Google Scholar
• Xu G, Jiang Z, Wang H, Lin R. The central circadian clock proteins CCA1 and LHY regulate iron homeostasis in Arabidopsis. J Integr Plant Biol. 2019 Feb;61(2):168–181. doi:10.1111/jipb.12696. Epub 2018 Aug 31. PMID: 29989313.
   PubMed Web of Science ®Google Scholar
• Hong S, Kim SA, Guerinot ML, McClung CR. Reciprocal interaction of the circadian clock with the iron homeostasis network in Arabidopsis. Plant Physiol. 2013 Feb;161(2):893–903. doi:10.1104/pp.112.208603. Epub 2012 Dec 18. PMID: 23250624; PMCID: PMC3561027.
   PubMed Web of Science ®Google Scholar
• Feeney KA, Hansen LL, Putker M, Olivares-Yañez C, Day J, Eades LJ, Larrondo LF, Hoyle NP, O’Neill JS, van Ooijen G. Daily magnesium fluxes regulate cellular timekeeping and energy balance. Nature. 2016 Apr 21;532(7599):375–379. doi:10.1038/nature17407. Epub 2016 Apr 13. PMID: 27074515; PMCID: PMC4886825.
   PubMed Web of Science ®Google Scholar
• Johnson CH, Mori T, Xu Y. A cyanobacterial circadian clockwork. Curr Biol. 2008 Sep 9;18(17):R816–R825. doi:10.1016/j.cub.2008.07.012. PMID: 18786387; PMCID: PMC2585598.
   PubMed Web of Science ®Google Scholar
• Jeong YM, Dias C, Diekman C, Brochon H, Kim P, Kaur M, Kim YS, Jang HI, Kim YI. Magnesium regulates the circadian oscillator in cyanobacteria. J Biol Rhythms. 2019 Aug;34(4):380–390. doi:10.1177/0748730419851655.
   PubMed Web of Science ®Google Scholar
• Li J, Yokosho K, Liu S, Cao HR, Yamaji N, Zhu XG, Liao H, Ma JF, Chen ZC. Diel magnesium fluctuations in chloroplasts contribute to photosynthesis in rice. Nat Plants. 2020 Jul;6(7):848–859. doi:10.1038/s41477-020-0686-3. Epub 2020 Jun 15. PMID: 32541951.
   PubMed Web of Science ®Google Scholar
• Dong MA, Farré EM, Thomashow MF. Circadian clock-associated 1 and late elongated hypocotyl regulate expression of the C-repeat binding factor (CBF) pathway in Arabidopsis. Proc Natl Acad Sci USA. 2011 Apr 26;108(17):7241–7246. doi:10.1073/pnas.1103741108. Epub 2011 Apr 6. PMID: 21471455; PMCID: PMC3084081.
   PubMed Web of Science ®Google Scholar
• Kidokoro S, Hayashi K, Haraguchi H, Ishikawa T, Soma F, Konoura I, Toda S, Mizoi J, Suzuki T, Shinozaki K, et al. Posttranslational regulation of multiple clock-related transcription factors triggers cold-inducible gene expression in Arabidopsis. Proc Natl Acad Sci USA. 2021 Mar 9;118(10):e2021048118. doi:10.1073/pnas.2021048118. PMID: 33649234; PMCID: PMC7958436.
   PubMed Web of Science ®Google Scholar
• Sun Q, Wang S, Xu G, Kang X, Zhang M, Ni M. SHB1 and CCA1 interaction desensitizes light responses and enhances thermomorphogenesis. Nat Commun. 2019 Jul 15;10(1):3110. doi:10.1038/s41467-019-11071-6. PMID: 31308379; PMCID: PMC6629618.
   PubMedGoogle Scholar
• Box MS, Huang BE, Domijan M, Jaeger KE, Khattak AK, Yoo SJ, Sedivy EL, Jones DM, Hearn TJ, Webb AAR, et al. ELF3 controls thermoresponsive growth in Arabidopsis. Curr Biol. 2015 Jan 19;25(2):194–199. doi:10.1016/j.cub.2014.10.076. Epub 2014 Dec 31. PMID: 25557663.
   PubMed Web of Science ®Google Scholar
• Cao S, Ye M, Jiang S. Involvement of GIGANTEA gene in the regulation of the cold stress response in Arabidopsis. Plant Cell Rep. 2005 Dec;24(11):683–690. doi:10.1007/s00299-005-0061-x. Epub 2005 Oct 18. PMID: 16231185.
   PubMed Web of Science ®Google Scholar
• Chen WW, Takahashi N, Hirata Y, Ronald J, Porco S, Davis SJ, Nusinow DA, Kay SA, Mas P. A mobile ELF4 delivers circadian temperature information from shoots to roots. Nat Plants. 2020 Apr;6(4):416–426. doi:10.1038/s41477-020-0634-2.
   PubMed Web of Science ®Google Scholar
• Desai JS, Lawas LMF, Valente AM, Leman AR, Grinevich DO, Jagadish SVK, Doherty CJ. Warm nights disrupt transcriptome rhythms in field-grown rice panicles. Proc Natl Acad Sci USA. 2021 Jun 22;118(25):e2025899118. doi:10.1073/pnas.2025899118. PMID: 34155145; PMCID: PMC8237568.
   PubMed Web of Science ®Google Scholar
• Xie Q, Lou P, Hermand V, Aman R, Park HJ, Yun DJ, Kim WY, Salmela MJ, Ewers BE, Weinig C, et al. Allelic polymorphism of GIGANTEA is responsible for naturally occurring variation in circadian period in Brassica rapa. Proc Natl Acad Sci USA. 2015 Mar 24;112(12):3829–3834. doi:10.1073/pnas.1421803112. Epub 2015 Mar 9. PMID: 25775524; PMCID: PMC4378452.
   PubMed Web of Science ®Google Scholar