PXD043839

PXD043839 is an original dataset announced via ProteomeXchange.

Title	Direct evaluation of metabolic rhythms from quantitative circadian proteomics revealed rampant post-transcriptional regulation by Chlamydomonas clock
Description	Temporal dynamics in an organism's behavior, physiology, metabolism, and biochemistry over the course of 24 hours are governed by an inherent cellular clock. Transcriptomic studies revealed that the clock is governed by intricate transcriptional and translational feedback loops(TTFLs) involving daily transcription and translation of the clock genes. As a result, the consensus focussed on transcription as the primary driver of this daily regulation since mRNA of the clock genes show robust oscillations. However, protein dynamics across the 24-hour cycle have not been studied in great detail. The notion of mRNA rhythms corresponding to protein rhythms needs reinvestigation. Many recent studies revealed that the pattern of mRNA rhythms does not match their encoded protein rhythms. Here, we used a high-throughput quantitative mass spectrometry technique to investigate the daily variation in protein expression in a single-cell phytoplankton C.reinhardtii. We found hundreds of proteins oscillating over 24 hours. Further, we found several known and unique physiological and metabolic pathways are controlled by the circadian clock in a time-dependent manner. In addition, to gain more insights into the complex clock regulation of these pathways, we compared the RNA abundance to protein abundance. Intriguingly, we found a significant discrepancy in the peak phase distribution of RNA and proteins unraveling the intricate mechanism shaping the daily circadian physiology and metabolism in C.reinhardtii. Altogether, our study reports the first comprehensive circadian proteome and the important role of post-transcriptional control over the C.reinhardtii circadian clock.
HostingRepository	PRIDE
AnnounceDate	2025-05-27
AnnouncementXML	Submission_2025-05-27_12:38:54.015.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Dinesh Jadhav
SpeciesList	scientific name: Chlamydomonas reinhardtii; NCBI TaxID: 3055;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2023-07-17 05:15:28	ID requested
⏵ 1	2025-05-27 12:38:55	announced

Jadhav DB, Roy S, Circadian Proteomics Reassesses the Temporal Regulation of Metabolic Rhythms by Chlamydomonas Clock. Plant Cell Environ, 48(5):3512-3528(2025) [pubmed]

10.1111/pce.15354;

submitter keyword: post-transcriptional regulations, SWATH-MS, Proteomics, C. reinhardtii,Circadian Clock

Sougata Roy
contact affiliation	Department of Biology, Ashoka University
contact email	sougata.roy@ashoka.edu.in
lab head
Dinesh Jadhav
contact affiliation	Department of Biology, Ashoka University, RGEC, Sonipat, Haryana
contact email	dinesh.jadhav_phd19@ashoka.edu.in
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD043839
     1. Label: PRIDE project
     2. Name: Direct evaluation of metabolic rhythms from quantitative circadian proteomics revealed rampant post-transcriptional regulation by Chlamydomonas clock