PXD044526-2

PXD044526 is an original dataset announced via ProteomeXchange.

Title	The natural diversity of the yeast proteome links aneuploidy tolerance to genome-wide proteome
Description	Recent advancements in genome sequencing have facilitated accessing the natural genetic diversity of species, unveiling hidden genetic traits, clarifying gene functions, and the degree to which laboratory studies can be generalized. One notable discovery is the frequent (~20%) aneuploidy - an imbalance in chromosome copy numbers - in natural Saccharomyces cerevisiae (Sc) isolates, despite the significant fitness costs and transient nature reported for lab-engineered yeast aneuploids. To examine this discrepancy, we adapted a high-throughput proteomic platform to analyze the proteome of 800 diverse yeast isolates. Matching these proteomes to the natural isolates’ genomes, transcriptomes, as well as generating ubiquitinome and protein turnover data for selected isolates, we report that natural and lab-generated aneuploids differ specifically at the proteome. While lab-generated aneuploids attenuate specific proteins – mostly protein complex subunits – and do not alter the average gene dosage provided by chromosome duplications, in natural strains, 70% of proteins encoded on aneuploid chromosomes are attenuated, and protein levels are shifted towards the euploid state chromosome-wide. Our data links chromosome-wide dosage compensation in natural strains to i) genome-wide buffering of gene expression changes manifesting in trans on euploid chromosomes, ii) increased expression of structural components of the ubiquitin proteasome system, and iii) increased global rates of protein turnover. Our results encourage the exploitation of natural diversity of species to understand complex biological processes at the molecular level. This submission contains the raw files for the disomics lab engineered strains, the library used for the analysis and the corresponding DIA-NN report and associated files.
HostingRepository	PRIDE
AnnounceDate	2024-06-14
AnnouncementXML	Submission_2024-06-14_07:06:53.416.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Anja Freiwald
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	iodoacetamide derivatized residue
Instrument	TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2023-08-12 14:59:59	ID requested
1	2024-03-11 07:20:35	announced
⏵ 2	2024-06-14 07:06:54	announced	2024-06-14: 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: large-scale, proteomics, lab-engineered strains,Yeast, diversity, wild isolates, high-throughput, aneuploidy

Markus Ralser
contact affiliation	Charité Universitätsmedizin, Department of Biochemistry, 10117 Berlin, Germany The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK Max Planck Institute for Molecular Genetics, Berlin, Germany
contact email	Markus.ralser@charite.de
lab head
Anja Freiwald
contact affiliation	Charité
contact email	anja.freiwald@charite.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/PXD044526

PRIDE project URI

• PRIDE
  1. PXD044526
     1. Label: PRIDE project
     2. Name: The natural diversity of the yeast proteome links aneuploidy tolerance to genome-wide proteome