PXD056947-1

PXD056947 is an original dataset announced via ProteomeXchange.

Title	Interaction of genetic variants activates latent metabolic pathways in yeast
Description	Genetic interactions are fundamental to the architecture of complex traits, yet the molecular mechanisms by which variant combinations influence cellular pathways remain poorly understood. Here, we answer the question of whether interactions between genetic variants can activate unique pathways and if such pathways can be targeted to modulate phenotypic outcomes. The model organism Saccharomyces cerevisiae was used to dissect how two causal SNPs , MKT189G and TAO34477C, interact to modulate metabolic and phenotypic outcomes during sporulation. By integrating time-resolved transcriptomics, absolute proteomics, and targeted metabolomics in isogenic allele replacement yeast strains, we show that the combined presence of these SNPs uniquely activates the arginine biosynthesis pathway and suppresses ribosome biogenesis, reflecting a metabolic trade-off that enhances sporulation efficiency. Functional validation demonstrates that the arginine pathway is essential for mitochondrial activity and efficient sporulation only in the double-SNP background. Our findings show how genetic variant interactions can rewire core metabolic networks, providing a mechanistic framework for understanding polygenic trait regulation and the emergence of additive effects in complex traits.
HostingRepository	PRIDE
AnnounceDate	2025-07-22
AnnouncementXML	Submission_2025-07-22_05:47:38.056.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Suresh Sudarsan
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-18 06:34:37	ID requested
⏵ 1	2025-07-22 05:47:38	announced

Dataset with its publication pending

submitter keyword: proteomics,Sporulation, yeast, amino acid metabolism, ribosome pathways, single nucleotide polymorphism, transcriptomics

Suresh Sudarsan
contact affiliation	The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
contact email	sursud@biosustain.dtu.dk
lab head
Suresh Sudarsan
contact affiliation	DTU-Biosustain
contact email	sursud@biosustain.dtu.dk
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/2025/07/PXD056947

PRIDE project URI

• PRIDE
  1. PXD056947
     1. Label: PRIDE project
     2. Name: Interaction of genetic variants activates latent metabolic pathways in yeast