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PreprintCited by 52Advanced Proteomics Techniques and ApplicationsFungal and yeast genetics researchBioinformatics and Genomic Networks

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The regulatory landscape of the yeast phosphoproteome

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Leutert, Mario, Barente, Anthony S., Fukuda, Noelle K., Rodriguez-Mias, Ricard A., Villén, Judit·2022·Nature Structural & Molecular Biology
DOI 10.1101/2022.10.23.513432PMC PMC10841839

Preprint — published as 10.1038/s41594-023-01115-3 · Paper page

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Abstract

Summary: The cellular ability to react to environmental fluctuations depends on signaling networks that are controlled by the dynamic activities of kinases and phosphatases. To gain insight into these stress-responsive phosphorylation networks, we generated a quantitative mass spectrometry-based atlas of early phosphoproteomic responses in Saccharomyces cerevisiae exposed to 101 environmental and chemical perturbations. We report phosphosites on 59% of the yeast proteome, with 18% of the proteome harboring a phosphosite that is regulated within 5 minutes of stress exposure. We identify shared and perturbation-specific stress response programs, uncover dephosphorylation as an integral early event, and dissect the interconnected regulatory landscape of kinase-substrate networks, as we exemplify with TOR signaling. We further reveal functional organization principles of the stress-responsive phosphoproteome based on phosphorylation site motifs, kinase activities, subcellular localizations, shared functions, and pathway intersections. This information-rich map of 25,000 regulated phosphosites advances our understanding of signaling networks. Highlights: Ultra-deep reference yeast phosphoproteome covers 36,000 phosphorylation sites and reveals general principles of eukaryotic protein phosphorylation. High-dimensional quantitative atlas of early phosphoproteomic responses of yeast across 101 environmental and chemical perturbations identifies 25,000 regulated perturbation-phosphosite pairs. Identification of shared and perturbation-specific stress response phosphorylation programs reveals the importance of dephosphorylation as an early stress response. Dissection of the TOR signaling network uncovers subnetworks with differential stress responsiveness and points of pathway cross-talk Identification of functional organization of the phosphoproteome by dimensionality reduction and co-regulation analysis.

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Metadata

Authors
Leutert, M., Barente, A. S., Fukuda, N. K., Rodriguez-Mias, R. A., & Villén, J.
Affiliations
University of Washington (US)
Corresponding author
  • Leutert, Mario
  • Villén, Judit
ORCID
Venue
Nature Structural & Molecular Biology
Publisher
openRxiv
Published
2022-10-24
Volume
30
Issue
11
Pages
1761-1773
ISSN
1545-9985 (ISSN-L)
DOI
10.1101/2022.10.23.513432
PMC
PMC10841839
OpenAlex
W4387666880
Cited by
52
References
1
Citations by year
2026: 18 · 2025: 12 · 2024: 13 · 2023: 9
FWCI
4.79
Type
journal article
Language
en
Open access
Licence
cc-by-nc-nd
Locations
  • Nature Structural & Molecular Biology (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • National Science Foundation
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (211122, 181503, 194379)
  • National Institutes of Health
  • National Institute on Aging (R01AG056359)
  • National Institute of General Medical Sciences (R35GM119536)
  • U.S. National Library of Medicine (T32LM012419)
Topics
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Keywords
phosphoproteome, Saccharomyces cerevisiae, stress response, phosphorylation, environmental disturbance, signaling networks
MeSH terms
Phosphoproteins, Phosphorylation, Saccharomyces cerevisiae, Signal Transduction, Proteome, Saccharomyces cerevisiae Proteins

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