Determinants and Regulation of Protein Turnover in Yeast
Open accessAbstract
Protein turnover maintains the recycling needs of the proteome, and its malfunction has been linked to aging and age-related diseases. However, not all proteins turnover equally, and the factors that contribute to accelerate or slow down turnover are mostly unknown. We measured turnover rates for 3,160 proteins in exponentially growing yeast and analyzed their dependence on physical, functional, and genetic properties. We found that functional characteristics, including protein localization, complex membership, and connectivity, have greater effect on turnover than sequence elements. We also found that protein turnover and mRNA turnover are correlated. Analysis under nutrient perturbation and osmotic stress revealed that protein turnover highly depends on cellular state and is faster when proteins are being actively used. Finally, stress-induced changes in protein and transcript abundance correlated with changes in protein turnover. This study provides a resource of protein turnover rates and principles to understand the recycling needs of the proteome under basal conditions and perturbation.
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The nuances of fluctuation analysis (such as imperfect plating) are frequently disregarded, judging by the continuing popularity of FALCOR.
“To this day the nuances are frequently disregarded, perhaps due to a lack of knowledge, judging by the unfailing popularity of FALCOR (e.g., [67-69]).”
From Efficient, robust, and versatile fluctuation data analysis using MLE MUtation Rate calculator (mlemur) (2023) · cites this paper as [68]
The Results and STAR Methods passages discuss yeast protein turnover and differences in protein half-life calculations, not fluctuation analysis. Searches for FALCOR, imperfect plating, and plating efficiency found no passage addressing the claimed popularity of FALCOR or disregard of fluctuation-analysis nuances. (LLM, conf=0.77)
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- Authors
- Martin-Perez, M., & Villén, J.
- Affiliations
- University of Washington (US)
- Corresponding author
- Villén, Judit
- ORCID
- Villén, Judit
- Venue
- Cell Systems
- Publisher
- Elsevier BV
- Published
- 2017-09
- Volume
- 5
- Issue
- 3
- Pages
- 283-294.e5
- ISSN
- 2405-4712 (ISSN-L)
- PMC
- PMC5935796
- OpenAlex
- W2755517617
- Cited by
- 99
- References
- 14
- Citations by year
- 2026: 8 · 2025: 7 · 2024: 13 · 2023: 13 · 2022: 12 · 2021: 14 · 2020: 18 · 2019: 9 · 2018: 4 · 2017: 1
- FWCI
- 3.58
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell Systems (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Nathan Shock Center of Excellence in Basic Biology of Aging (3P30AG013280)
- Ellison Medical Foundation New Scholar (AG-NS-0953-12)
- NIH (1R35GM119536)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Aging › Genetics, Aging, and Longevity in Model Organisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Keywords
- protein turnover, protein half-life, yeast, protein localization, protein connectivity, mRNA turnover, osmotic stress, aging, proteome dynamics
- MeSH terms
- Half-Life, Osmotic Pressure, Proteins, Saccharomyces cerevisiae, Protein Biosynthesis, Proteome, RNA Stability, Saccharomyces cerevisiae Proteins, Proteomics, Protein Stability, Proteolysis
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