PXD048219-3

PXD048219 is an original dataset announced via ProteomeXchange.

Title	The natural diversity of the yeast proteome links aneuploidy tolerance to protein turnover
Description	Accessing the natural genetic diversity of species unveils hidden genetic traits, clarifies gene functions, and allows assessment of the generalizability of laboratory findings. One notable discovery made in Saccharomyces cerevisiae natural isolates is frequent (~20%) aneuploidy – an imbalance in chromosome copy numbers – that appears to contradict the significant fitness costs and transient nature reported for lab-engineered aneuploids. Here, we generated a proteomic resource and merged it with genomic and transcriptomic data for 796 euploid and aneuploid natural isolates. We found that natural and lab-generated aneuploids differ specifically at the proteome. In lab-generated aneuploids, some proteins, especially protein complex subunits, show reduced expression, yet the overall protein levels correspond to the aneuploid gene dosage. By contrast, in natural isolates, more than 70% of proteins encoded on aneuploid chromosomes are dosage-compensated, with average protein levels being shifted towards the euploid state chromosome-wide. At the molecular level, we detect an induction of structural components of the proteasome, increased levels of ubiquitination, and reveal an interdependency of protein turnover rates and attenuation. Our study thus highlights the role of protein turnover in mediating aneuploidy tolerance, and demonstrates the utility of exploiting the natural diversity of species to reach generalizable molecular insights into complex biological processes. This resource provides the SILAC dataset from this work.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:33:16.882.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Henrik Zauber
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2024-01-03 02:13:32	ID requested
1	2024-03-13 09:50:30	announced
2	2024-06-14 07:07:07	announced	2024-06-14: Updated project metadata.
⏵ 3	2024-10-22 06:33:17	announced	2024-10-22: Updated project metadata.

10.1038/s41586-024-07442-9;

Muenzner J, Tr, é, bulle P, Agostini F, Zauber H, Messner CB, Steger M, Kilian C, Lau K, Barthel N, Lehmann A, Textoris-Taube K, Caudal E, Egger AS, Amari F, De Chiara M, Demichev V, Gossmann TI, M, ü, lleder M, Liti G, Schacherer J, Selbach M, Berman J, Ralser M, Natural proteome diversity links aneuploidy tolerance to protein turnover. Nature, 630(8015):149-157(2024) [pubmed]

submitter keyword: Aneuploidy, protein stability,Yeast, SILAC

Matthias Selbach
contact affiliation	Max Delbrück Center for Molecular Medicine in the Helmholtz Association
contact email	matthias.selbach@mdc-berlin.de
lab head
Henrik Zauber
contact affiliation	MDC Berlin-Buch
contact email	henrik.zauber@mdc-berlin.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/2024/03/PXD048219

PRIDE project URI

• PRIDE
  1. PXD048219
     1. Label: PRIDE project
     2. Name: The natural diversity of the yeast proteome links aneuploidy tolerance to protein turnover