title: Parallel analysis ofArabidopsiscircadian clock mutants reveals different scales of transcriptome and proteome regulation.
abstract: 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 thelhycca1,prr7prr9,giandtoc1circadian 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.
authors.affiliation: Department of Biology, ETH Zurich, 8092 Zurich, Switzerland.|Max Planck Institute of Molecular Plant Physiology, 14476 Postdam-Golm, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Graf
authors.affiliation: Department of Biology, ETH Zurich, 8092 Zurich, Switzerland.
authors.forename: Diana
authors.initials: D
authors.lastname: Coman
authors.affiliation: Department of Biology, ETH Zurich, 8092 Zurich, Switzerland.
authors.forename: R Glen
authors.identifier: 0000-0003-2773-4381
authors.initials: RG
authors.lastname: Uhrig
authors.affiliation: Department of Biology, ETH Zurich, 8092 Zurich, Switzerland.
authors.forename: Sean
authors.initials: S
authors.lastname: Walsh
authors.affiliation: Max Planck Institute of Molecular Plant Physiology, 14476 Postdam-Golm, Germany.
authors.forename: Anna
authors.initials: A
authors.lastname: Flis
authors.affiliation: Max Planck Institute of Molecular Plant Physiology, 14476 Postdam-Golm, Germany.
authors.forename: Mark
authors.initials: M
authors.lastname: Stitt
authors.affiliation: Department of Biology, ETH Zurich, 8092 Zurich, Switzerland wgruissem@ethz.ch.
authors.forename: Wilhelm
authors.initials: W
authors.lastname: Gruissem
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism / Q000502:physiology; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D056926:CLOCK Proteins / Q000235:genetics* / Q000378:metabolism; D050260:Carbohydrate Metabolism; D057906:Circadian Clocks; D002940:Circadian Rhythm; D018506:Gene Expression Regulation, Plant; D009154:Mutation; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome; D054875:Ubiquitination
chemical_list: D029681:Arabidopsis Proteins; C114425:CCA1 protein, Arabidopsis; D014157:Transcription Factors; D056926:CLOCK Proteins
keywords: Arabidopsis thaliana; circadian clock; photoperiod; proteomics; transcriptomics