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Substrate-specific effects of natural genetic variation on proteasome activity

Protein degradation is an essential biological process that regulates protein abundance and removes misfolded and damaged proteins from cells. In eukaryotes, most protein degradation occurs through the stepwise actions of two functionally distinct entities, the ubiquitin system and the proteasome. U...

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Autores principales: Collins, Mahlon A., Avery, Randi, Albert, Frank W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10174532/
https://www.ncbi.nlm.nih.gov/pubmed/37126494
http://dx.doi.org/10.1371/journal.pgen.1010734
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author Collins, Mahlon A.
Avery, Randi
Albert, Frank W.
author_facet Collins, Mahlon A.
Avery, Randi
Albert, Frank W.
author_sort Collins, Mahlon A.
collection PubMed
description Protein degradation is an essential biological process that regulates protein abundance and removes misfolded and damaged proteins from cells. In eukaryotes, most protein degradation occurs through the stepwise actions of two functionally distinct entities, the ubiquitin system and the proteasome. Ubiquitin system enzymes attach ubiquitin to cellular proteins, targeting them for degradation. The proteasome then selectively binds and degrades ubiquitinated substrate proteins. Genetic variation in ubiquitin system genes creates heritable differences in the degradation of their substrates. However, the challenges of measuring the degradative activity of the proteasome independently of the ubiquitin system in large samples have limited our understanding of genetic influences on the proteasome. Here, using the yeast Saccharomyces cerevisiae, we built and characterized reporters that provide high-throughput, ubiquitin system-independent measurements of proteasome activity. Using single-cell measurements of proteasome activity from millions of genetically diverse yeast cells, we mapped 15 loci across the genome that influence proteasomal protein degradation. Twelve of these 15 loci exerted specific effects on the degradation of two distinct proteasome substrates, revealing a high degree of substrate-specificity in the genetics of proteasome activity. Using CRISPR-Cas9-based allelic engineering, we resolved a locus to a causal variant in the promoter of RPT6, a gene that encodes a subunit of the proteasome’s 19S regulatory particle. The variant increases RPT6 expression, which we show results in increased proteasome activity. Our results reveal the complex genetic architecture of proteasome activity and suggest that genetic influences on the proteasome may be an important source of variation in the many cellular and organismal traits shaped by protein degradation.
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spelling pubmed-101745322023-05-12 Substrate-specific effects of natural genetic variation on proteasome activity Collins, Mahlon A. Avery, Randi Albert, Frank W. PLoS Genet Research Article Protein degradation is an essential biological process that regulates protein abundance and removes misfolded and damaged proteins from cells. In eukaryotes, most protein degradation occurs through the stepwise actions of two functionally distinct entities, the ubiquitin system and the proteasome. Ubiquitin system enzymes attach ubiquitin to cellular proteins, targeting them for degradation. The proteasome then selectively binds and degrades ubiquitinated substrate proteins. Genetic variation in ubiquitin system genes creates heritable differences in the degradation of their substrates. However, the challenges of measuring the degradative activity of the proteasome independently of the ubiquitin system in large samples have limited our understanding of genetic influences on the proteasome. Here, using the yeast Saccharomyces cerevisiae, we built and characterized reporters that provide high-throughput, ubiquitin system-independent measurements of proteasome activity. Using single-cell measurements of proteasome activity from millions of genetically diverse yeast cells, we mapped 15 loci across the genome that influence proteasomal protein degradation. Twelve of these 15 loci exerted specific effects on the degradation of two distinct proteasome substrates, revealing a high degree of substrate-specificity in the genetics of proteasome activity. Using CRISPR-Cas9-based allelic engineering, we resolved a locus to a causal variant in the promoter of RPT6, a gene that encodes a subunit of the proteasome’s 19S regulatory particle. The variant increases RPT6 expression, which we show results in increased proteasome activity. Our results reveal the complex genetic architecture of proteasome activity and suggest that genetic influences on the proteasome may be an important source of variation in the many cellular and organismal traits shaped by protein degradation. Public Library of Science 2023-05-01 /pmc/articles/PMC10174532/ /pubmed/37126494 http://dx.doi.org/10.1371/journal.pgen.1010734 Text en © 2023 Collins et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Collins, Mahlon A.
Avery, Randi
Albert, Frank W.
Substrate-specific effects of natural genetic variation on proteasome activity
title Substrate-specific effects of natural genetic variation on proteasome activity
title_full Substrate-specific effects of natural genetic variation on proteasome activity
title_fullStr Substrate-specific effects of natural genetic variation on proteasome activity
title_full_unstemmed Substrate-specific effects of natural genetic variation on proteasome activity
title_short Substrate-specific effects of natural genetic variation on proteasome activity
title_sort substrate-specific effects of natural genetic variation on proteasome activity
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10174532/
https://www.ncbi.nlm.nih.gov/pubmed/37126494
http://dx.doi.org/10.1371/journal.pgen.1010734
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