Investigating Circadian Gating of Temperature Responsive Genes

Overview

Journal Methods Mol Biol

Specialty Molecular Biology

Date 2024 Apr 9

PMID 38594541

Authors

Rachel I Strout

Calum A Graham

Antony N Dodd

Dawn H Nagel

Affiliations

Soon will be listed here.

Abstract

Understanding gene expression dynamics in the context of the time of day and temperature response is an important part of understanding plant thermotolerance in a changing climate. Performing "gating" experiments under constant conditions and light-dark cycles allows users to identify and dissect the contribution of the time of day and circadian clock to the dynamic nature of stress-responsive genes. Here, we describe the design of specific laboratory experiments in plants (Arabidopsis thaliana and bread wheat, Triticum aestivum) to investigate temporal responses to heat (1 h at 37 °C) or cold (3 h at 4 °C), and we include known marker genes that have circadian-gated responses to temperature changes.

References

Paajanen P, de Barros Dantas L, Dodd A . Layers of crosstalk between circadian regulation and environmental signalling in plants. Curr Biol. 2021; 31(8):R399-R413. DOI: 10.1016/j.cub.2021.03.046. View

Harmer S, Hogenesch J, Straume M, Chang H, Han B, Zhu T . Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science. 2000; 290(5499):2110-3. DOI: 10.1126/science.290.5499.2110. View

PITTENDRIGH C, Skopik S . Circadian systems. V. The driving oscillation and the temporal sequence of development. Proc Natl Acad Sci U S A. 1970; 65(3):500-7. PMC: 282935. DOI: 10.1073/pnas.65.3.500. View

McWatters H, Bastow R, Hall A, Millar A . The ELF3 zeitnehmer regulates light signalling to the circadian clock. Nature. 2000; 408(6813):716-20. DOI: 10.1038/35047079. View

Covington M, Panda S, Liu X, Strayer C, Wagner D, Kay S . ELF3 modulates resetting of the circadian clock in Arabidopsis. Plant Cell. 2001; 13(6):1305-15. PMC: 135573. DOI: 10.1105/tpc.13.6.1305. View

Thines B, Harmon F . Ambient temperature response establishes ELF3 as a required component of the core Arabidopsis circadian clock. Proc Natl Acad Sci U S A. 2010; 107(7):3257-62. PMC: 2840299. DOI: 10.1073/pnas.0911006107. View

Masuda K, Tokuda I, Nakamichi N, Fukuda H . The singularity response reveals entrainment properties of the plant circadian clock. Nat Commun. 2021; 12(1):864. PMC: 7870946. DOI: 10.1038/s41467-021-21167-7. View

Millar A, Kay S . Integration of circadian and phototransduction pathways in the network controlling CAB gene transcription in Arabidopsis. Proc Natl Acad Sci U S A. 1996; 93(26):15491-6. PMC: 26432. DOI: 10.1073/pnas.93.26.15491. View

Salter M, Franklin K, Whitelam G . Gating of the rapid shade-avoidance response by the circadian clock in plants. Nature. 2003; 426(6967):680-3. DOI: 10.1038/nature02174. View

10.

Fowler S, Cook D, Thomashow M . Low temperature induction of Arabidopsis CBF1, 2, and 3 is gated by the circadian clock. Plant Physiol. 2005; 137(3):961-8. PMC: 1065397. DOI: 10.1104/pp.104.058354. View

11.

Legnaioli T, Cuevas J, Mas P . TOC1 functions as a molecular switch connecting the circadian clock with plant responses to drought. EMBO J. 2009; 28(23):3745-57. PMC: 2790485. DOI: 10.1038/emboj.2009.297. View

12.

Wilkins O, Waldron L, Nahal H, Provart N, Campbell M . Genotype and time of day shape the Populus drought response. Plant J. 2009; 60(4):703-15. DOI: 10.1111/j.1365-313X.2009.03993.x. View

13.

Wilkins O, Brautigam K, Campbell M . Time of day shapes Arabidopsis drought transcriptomes. Plant J. 2010; 63(5):715-27. DOI: 10.1111/j.1365-313X.2010.04274.x. View

14.

Greenham K, Guadagno C, Gehan M, Mockler T, Weinig C, Ewers B . Temporal network analysis identifies early physiological and transcriptomic indicators of mild drought in . Elife. 2017; 6. PMC: 5628015. DOI: 10.7554/eLife.29655. View

15.

Blair E, Bonnot T, Hummel M, Hay E, Marzolino J, Quijada I . Contribution of time of day and the circadian clock to the heat stress responsive transcriptome in Arabidopsis. Sci Rep. 2019; 9(1):4814. PMC: 6423321. DOI: 10.1038/s41598-019-41234-w. View

16.

Grinevich D, Desai J, Stroup K, Duan J, Slabaugh E, Doherty C . Novel transcriptional responses to heat revealed by turning up the heat at night. Plant Mol Biol. 2019; 101(1-2):1-19. PMC: 6695350. DOI: 10.1007/s11103-019-00873-3. View

17.

Bonnot T, Nagel D . Time of the day prioritizes the pool of translating mRNAs in response to heat stress. Plant Cell. 2021; 33(7):2164-2182. PMC: 8364243. DOI: 10.1093/plcell/koab113. View

18.

Bonnot T, Somayanda I, Jagadish S, Nagel D . Time of day and genotype sensitivity adjust molecular responses to temperature stress in sorghum. Plant J. 2023; 116(4):1081-1096. DOI: 10.1111/tpj.16467. View

19.

Medina-Chavez L, Camacho C, Martinez-Rodriguez J, Barrera-Figueroa B, Nagel D, Juntawong P . Submergence Stress Alters the Expression of Clock Genes and Configures New Zeniths and Expression of Outputs in . Int J Mol Sci. 2023; 24(10). PMC: 10218231. DOI: 10.3390/ijms24108555. View

20.

Mizoguchi T, Wright L, Fujiwara S, Cremer F, Lee K, Onouchi H . Distinct roles of GIGANTEA in promoting flowering and regulating circadian rhythms in Arabidopsis. Plant Cell. 2005; 17(8):2255-70. PMC: 1182487. DOI: 10.1105/tpc.105.033464. View