PXD025009

PXD025009 is an original dataset announced via ProteomeXchange.

Title	Differential effects of environmental and endogenous 24h rhythms within a deep-coverage spatiotemporal proteome
Description	The cellular landscape of most eukaryotic cells changes dramatically over the course of a 24h day. Whilst the proteome responds directly to daily environmental cycles, it is also regulated by a cellular circadian clock that anticipates the differing demands of day and night. To quantify the relative contribution of diurnal versus circadian regulation, we mapped spatiotemporal proteome dynamics under 12h:12h light:dark cycles compared with constant light. Using Ostreococcus tauri, a prototypical eukaryotic cell, we achieved 85% coverage of the theoretical proteome and provided an unprecedented insight into the identity of proteins that drive and facilitate rhythmic cellular functions. Surprisingly, the overlap between diurnally- and circadian-regulated proteins was quite modest (11%). These proteins exhibited different phases of oscillation between the two conditions, consistent with an interaction between intrinsic and extrinsic regulatory factors. The relative amplitude of rhythmic protein abundance was much lower than would be expected from daily variations in transcript abundance. Transcript rhythmicity was poorly predictive of daily variation in abundance of the encoded protein. We observed coordination between the rhythmic regulation of organelle-encoded proteins with the nuclear-encoded proteins that are targeted to organelles. Rhythmic transmembrane proteins showed a remarkably different phase distribution compared with rhythmic soluble proteins, indicating the existence of a novel circadian regulatory process specific to the biogenesis and/or degradation of membrane proteins. Taken together, our observations argue that the daily spatiotemporal regulation of cellular proteome composition is not dictated solely by clock-regulated gene expression. Instead, it also involves extensive rhythmic post-transcriptional, translational, and post-translational regulation that is further modulated by environmental timing cues.
HostingRepository	PRIDE
AnnounceDate	2021-10-28
AnnouncementXML	Submission_2021-10-28_01:29:14.030.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sew Peak-Chew
SpeciesList	scientific name: Ostreococcus tauri; NCBI TaxID: 70448;
ModificationList	phosphorylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-03-25 08:58:54	ID requested
1	2021-10-28 01:15:10	announced
⏵ 2	2021-10-28 01:29:14	announced	2021-10-28: Updated publication reference for PubMed record(s): 34593975.

Kay H, Gr, ü, newald E, Feord HK, Gil S, Peak-Chew SY, Stangherlin A, O'Neill JS, van Ooijen G, Deep-coverage spatiotemporal proteome of the picoeukaryote Ostreococcus tauri reveals differential effects of environmental and endogenous 24-hour rhythms. Commun Biol, 4(1):1147(2021) [pubmed]

submitter keyword: Ostreococcus tauri, circadian proteomes, arrhythmic. rhythmic

Gerben van Ooijen
contact affiliation	Reader, School of Biological Science, University of Edinburgh
contact email	Gerben.vanOoijen@ed.ac.uk
lab head
Sew Peak-Chew
contact affiliation	MRC-LMB
contact email	spc@mrc-lmb.cam.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD025009
     1. Label: PRIDE project
     2. Name: Differential effects of environmental and endogenous 24h rhythms within a deep-coverage spatiotemporal proteome