PXD016292

PXD016292 is an original dataset announced via ProteomeXchange.

Title	Cold Triggered Paralog Rearrangements Indicate Potential Ribosome Specialization in Arabidopsis thaliana
Description	Plant ribosomes are heterogeneous due to genome duplications that resulted in several paralog genes encoding each ribosomal protein (RP). The mainstream view suggests that heterogeneity provides sufficient ribosomes throughout the Arabidopsis lifespan without any functional implications. Nevertheless, genome duplications are known to produce sub- and neofunctionalization of initially redundant genes. Functional divergence of RP paralogs can be considered ribosome specialization if the diversified functions of these paralogs remain within the context of protein translation, especially if RP divergence should contribute to a preferential or ultimately even rigorous selection of transcripts to be translated by a RP-defined ribosome subpopulation. Here we provide evidence that cold acclimation triggers a reprogramming in structural RPs at the transcriptome and proteome level. The reprogramming alters the abundance of RPs or RP paralogs in non-translational 60S large subunits (LSUs) and translational polysome fractions, a phenomenon known as substoichiometry. Cold triggered substoichiometry of ribosomal complexes differ once Arabidopsis REIL-like mediated late maturation step for the LSU is impaired. Interestingly, remodeling of ribosomes after a cold stimulus appears to be significantly constrained to specific spatial regions of the ribosome. The regions that are significantly changed during cold acclimation as judged by transcriptome or proteome data include the polypeptide exit tunnel and the P-Stalk. Both substructures of the ribosome represent plausible targets of mechanisms that may constrain translation by controlled ribosome heterogeneity. This work represents a step forward towards understanding heterogeneity and potential specialization of plant ribosomal complexes.
HostingRepository	PRIDE
AnnounceDate	2021-06-28
AnnouncementXML	Submission_2021-06-28_04:41:44.981.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Michal Gorka
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-11-15 01:54:34	ID requested
⏵ 1	2021-06-28 04:41:45	announced

Dataset with its publication pending

curator keyword: Biological

submitter keyword: functional heterogeneity, substoichiometry, stress- specialized ribosomes , ribosomal code, remodelling, ribosome biogenesis, ribosome-associated proteins, paralog subfunctionalization

Joachim Kopka
contact affiliation	AG Joachim Kopka Max-Planck-Institut für Molekulare Pflanzenphysiologie Wissenschaftspark Golm Am Mühlenberg 1 14476 Potsdam, Germany
contact email	kopka@mpimp-golm.mpg.de
lab head
Michal Gorka
contact affiliation	Max Planck Institute for Molecular Plant Physiology
contact email	gorka@mpimp-golm.mpg.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/06/PXD016292

PRIDE project URI

• PRIDE
  1. PXD016292
     1. Label: PRIDE project
     2. Name: Cold Triggered Paralog Rearrangements Indicate Potential Ribosome Specialization in Arabidopsis thaliana