+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

Parallel analysis of Arabidopsis circadian clock mutants reveals different scales of transcriptome and proteome regulation



Parallel analysis of Arabidopsis circadian clock mutants reveals different scales of transcriptome and proteome regulation



Open Biology 7(3)



The circadian clock regulates physiological processes central to growth and survival. To date, most plant circadian clock studies have relied on diurnal transcriptome changes to elucidate molecular connections between the circadian clock and observable phenotypes in wild-type plants. Here, we have integrated RNA-sequencing and protein mass spectrometry data to comparatively analyse the lhycca1, prr7prr9, gi and toc1 circadian clock mutant rosette at the end of day and end of night. Each mutant affects specific sets of genes and proteins, suggesting that the circadian clock regulation is modular. Furthermore, each circadian clock mutant maintains its own dynamically fluctuating transcriptome and proteome profile specific to subcellular compartments. Most of the measured protein levels do not correlate with changes in their corresponding transcripts. Transcripts and proteins that have coordinated changes in abundance are enriched for carbohydrate- and cold-responsive genes. Transcriptome changes in all four circadian clock mutants also affect genes encoding starch degradation enzymes, transcription factors and protein kinases. The comprehensive transcriptome and proteome datasets demonstrate that future system-driven research of the circadian clock requires multi-level experimental approaches. Our work also shows that further work is needed to elucidate the roles of post-translational modifications and protein degradation in the regulation of clock-related processes.

Please choose payment method:






(PDF emailed within 0-6 h: $19.90)

Accession: 060065242

Download citation: RISBibTeXText

PMID: 28250106

DOI: 10.1098/rsob.160333


Related references

Transcriptome Analysis of Four Arabidopsis thaliana Mediator Tail Mutants Reveals Overlapping and Unique Functions in Gene Regulation. G3 8(9): 3093-3108, 2018

Complementary proteome and transcriptome profiling in phosphate-deficient Arabidopsis roots reveals multiple levels of gene regulation. Molecular and Cellular Proteomics 11(11): 1156-1166, 2013

A self-regulatory circuit of CIRCADIAN CLOCK-ASSOCIATED1 underlies the circadian clock regulation of temperature responses in Arabidopsis. Plant Cell 24(6): 2427-2442, 2012

A Self-Regulatory Circuit of Circadian Clock-Associated1 Underlies the Circadian Clock Regulation of Temperature Responses in Arabidopsis. The Plant Cell 24(6): 2427-2442, 2012

Silencing the circadian clock gene Clock using RNAi reveals dissociation of the circatidal clock from the circadian clock in the mangrove cricket. Journal of Insect Physiology 68: 16-22, 2015

Quantitative Circadian Phosphoproteomic Analysis of Arabidopsis Reveals Extensive Clock Control of Key Components in Physiological, Metabolic, and Signaling Pathways. Molecular and Cellular Proteomics 14(8): 2243-2260, 2016

Genomic analysis of circadian clock-, light-, and growth-correlated genes reveals PHYTOCHROME-INTERACTING FACTOR5 as a modulator of auxin signaling in Arabidopsis. Plant Physiology 156(1): 357-372, 2015

Disruption of the Arabidopsis circadian clock is responsible for extensive variation in the cold-responsive transcriptome. Plant Physiology 147(1): 263-279, 2008

Disruption of the Arabidopsis Circadian Clock Is Responsible for Extensive Variation in the Cold-Responsive Transcriptome. Plant Physiology 147(1): 263-279, 2008

Combined transcriptome and proteome profiling reveals specific molecular brain signatures for sex, maturation and circalunar clock phase. Elife 8, 2019

Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development. Genome Biology 9(8): R130, 2008

Posttranslational regulation of CIRCADIAN CLOCK ASSOCIATED1 in the circadian oscillator of Arabidopsis. Plant Physiology 150(2): 844-857, 2009

Posttranslational Regulation of Circadian Clock Associated1 in the Circadian Oscillator of Arabidopsis. Plant Physiology 150(2): 844-857, 2009

Transcriptome-wide analysis of uncapped mRNAs in Arabidopsis reveals regulation of mRNA degradation. Plant Cell 20(10): 2571-2585, 2008

Transcriptome-Wide Analysis of Uncapped mRnas in Arabidopsis Reveals Regulation of mRna Degradation. The Plant Cell 20(10): 2571-2585, 2008