Role of circadian rhythm in plant system: An update from development to stress response

Srivastava, Deepti; Shamim, Md.; Kumar, Mahesh; Mishra, Anurag; Maurya, Rashmi; Sharma, Divakar; Pandey, Pramila; Singh, Karamjit

doi:10.1016/j.envexpbot.2019.02.025

Cited by 62 publications

(34 citation statements)

References 218 publications

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“…Transcription factors, such as circadian clock associated 1 (CCA1), late elongated hypocotyl (LHY), timing of CAB expression 1/ pseudo-response regulator 1 (TOC1/PRR1), pseudo-response regulator 3/5/7/9 (PRR3/5/7/9), REVEILLE 4/6/8 (RVE4/6/8), and night-light-inducible and clock-regulated 1/2 (LNK1/2), coordinately regulate the plant circadian clock (Srivastava et al, 2019). These transcription factors also regulate specialized metabolism (Nguyen & Lee, 2016).…”

Section: Introductionmentioning

confidence: 99%

Diurnal metabolic regulation of isoflavones and soyasaponins in soybean roots

et al. 2020

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Section: Introductionmentioning

confidence: 99%

Diurnal metabolic regulation of isoflavones and soyasaponins in soybean roots

et al. 2020

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“…New Phytologist length has been measured in a number of other species, and in many cases mutations conferring clock-related phenotypes in crop plants have been identified (Michael et al, 2003;Dodd et al, 2005;Bendix et al, 2015;Greenham et al, 2017;Srivastava et al, 2019). Also, light intensity is known to influence period length, and it has been shown to result in changes at very low fluences (Somers et al, 1998;Oakenfull & Davis, 2017).…”

Section: Researchmentioning

confidence: 99%

Changes in ambient temperature are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation

MacKinnon

Cole

et al. 2020

New Phytologist

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Summary Plants are continuously exposed to diurnal fluctuations in light and temperature, and spontaneous changes in their physical or biotic environment. The circadian clock coordinates regulation of gene expression with a 24 h period, enabling the anticipation of these events. We used RNA sequencing to characterize the Brachypodium distachyon transcriptome under light and temperature cycles, as well as under constant conditions. Approximately 3% of the transcriptome was regulated by the circadian clock, a smaller proportion than reported in most other species. For most transcripts that were rhythmic under all conditions, including many known clock genes, the period of gene expression lengthened from 24 to 27 h in the absence of external cues. To functionally characterize the cyclic transcriptome in B. distachyon, we used Gene Ontology enrichment analysis, and found several terms significantly associated with peak expression at particular times of the day. Furthermore, we identified sequence motifs enriched in the promoters of similarly phased genes, some potentially associated with transcription factors. When considering the overlap in rhythmic gene expression and specific pathway behavior, thermocycles was the prevailing cue that controlled diurnal gene regulation. Taken together, our characterization of the rhythmic B. distachyon transcriptome represents a foundational resource with implications in other grass species.

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“…Similarly, S. viridis genes that were rhythmic under constant conditions exhibited an approximate 24 h period. In contrast, variation in period length has been measured in a number of other species, and in many cases mutations conferring clock-related phenotypes in crop plants have been identified (Bendix et al , 2015;Greenham et al , 2017) (Michael et al , 2003;Dodd et al , 2005;Srivastava et al , 2019 ). Also, light intensity is known to influence period length, and has been shown to result in changes at very low fluences (Somers et al , 1998;Oakenfull & Davis, 2017) .…”

Section: Discussionmentioning

confidence: 99%

Changes in ambient temperature are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation

MacKinnon

Cole

et al. 2019

Preprint

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1 SUMMARY• Plants are continuously exposed diurnal fluctuations in light and temperature, and spontaneous changes in their physical or biotic environment. The circadian clock coordinates regulation of gene expression with a 24-hour period, enabling the anticipation of these events. • We used RNA sequencing to characterize the Brachypodium distachyon transcriptome under light and temperature cycles, as well as under constant conditions. • Approximately 3% of the transcriptome was regulated by the circadian clock, a smaller proportion reported in other species. For most transcripts that were rhythmic under all conditions, including many known clock genes, the period of gene expression lengthened from 24 h to 27 h in the absence of external cues. To functionally characterize the cyclic transcriptome in B. distachyon , we used Gene Ontology enrichment analysis, and found several terms significantly associated with peak expression at particular times of the day. Furthermore we identified sequence motifs enriched in the promoters of similarly-phased genes, some potentially associated with transcription factors. • When considering the overlap in rhythmic gene expression and specific pathway behavior, thermocycles controlled diurnal gene regulation. Taken together, our characterization of the rhythmic B. distachyon transcriptome represents a foundational resource with implications in other grass species. REFERENCESAdams S, Grundy J, Veflingstad SR, Dyer NP, Hannah MA, Ott S, Carré IA . 2018 . Circadian control of abscisic acid biosynthesis and signalling pathways revealed by genome-wide analysis of LHY binding targets. New Phytologist 220 : 893-907. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ . 1990 . Basic local alignment search tool. Journal of Molecular Biology 215 : 403-410. Arsovski AA, Pradinuk J, Guo XQ, Wang S, Adams KL . 2015 . Evolution of cis-regulatory elements and regulatory networks in duplicated genes of Arabidopsis. Plant Physiology 169 : 2982. AAR, et al. 2015 . ELF3 controls thermoresponsive growth in Arabidopsis. Current Biology: CB 25 : 194-199. Calixto CPG, Waugh R, Brown JWS . 2015 . Evolutionary relationships among barley and Arabidopsis core circadian clock and clock-associated genes. Journal of Molecular Evolution 80 : 108-119. Campoli C, Shtaya M, Davis S, von Korff M . 2012 . Expression conservation within the circadian clock of a monocot: natural variation at barley Ppd-H1 affects circadian expression of flowering time genes, but 17 not clock orthologs. BMC Plant Biology 12 : 97. Casal JJ, Qüesta JI . 2018 . Light and temperature cues: multitasking receptors and transcriptional integrators. The New Phytologist Dowson-Day MJ, Millar AJ . 1999 . Circadian dysfunction causes aberrant hypocotyl elongation patterns in Arabidopsis. The Plant Journal: for cell and molecular biology 17 : 63-71. Edwards KD, Anderson PE, Hall A, Salathia NS, Locke JC, Lynn JR, Straume M, Smith JQ, Millar AJ . 2006 . FLOWERING LOCUS C mediates natural variation in the high-temperature response of the Arabidopsis c...

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Role of circadian rhythm in plant system: An update from development to stress response

Cited by 62 publications

References 218 publications

Diurnal metabolic regulation of isoflavones and soyasaponins in soybean roots

Diurnal metabolic regulation of isoflavones and soyasaponins in soybean roots

Changes in ambient temperature are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation

Changes in ambient temperature are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation

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