Conserved degronome features governing quality control associated proteolysis

Bayan Mashahreh; Shir Armony; Kristoffer Enøe Johansson; Alon Chappleboim; Nir Friedman; Richard G. Gardner; Rasmus Hartmann-Petersen; Kresten Lindorff-Larsen; Tommer Ravid

doi:10.1038/s41467-022-35298-y

Conserved degronome features governing quality control associated proteolysis

Bayan Mashahreh, Shir Armony, Kristoffer Enøe Johansson, Alon Chappleboim, Nir Friedman, Richard G. Gardner, Rasmus Hartmann-Petersen, Kresten Lindorff-Larsen, Tommer Ravid^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

3 Scopus citations

Abstract

The eukaryotic proteome undergoes constant surveillance by quality control systems that either sequester, refold, or eliminate aberrant proteins by ubiquitin-dependent mechanisms. Ubiquitin-conjugation necessitates the recognition of degradation determinants, termed degrons, by their cognate E3 ubiquitin-protein ligases. To learn about the distinctive properties of quality control degrons, we performed an unbiased peptidome stability screen in yeast. The search identify a large cohort of proteome-derived degrons, some of which exhibited broad E3 ligase specificity. Consequent application of a machine-learning algorithm establishes constraints governing degron potency, including the amino acid composition and secondary structure propensities. According to the set criteria, degrons with transmembrane domain-like characteristics are the most probable sequences to act as degrons. Similar quality control degrons are present in viral and human proteins, suggesting conserved degradation mechanisms. Altogether, the emerging data indicate that transmembrane domain-like degron features have been preserved in evolution as key quality control determinants of protein half-life.

Original language	American English
Article number	7588
Journal	Nature Communications
Volume	13
Issue number	1
DOIs	https://doi.org/10.1038/s41467-022-35298-y
State	Published - Dec 2022

Bibliographical note

Funding Information:
We are grateful to Prof. Richard Kulka for his inspiration and support. We thank Dr. Yifat Geffen for her assistance with establishing the reporter system, Dr. Itay Koren for advice during the setup of yGPS-P, and Dr. Yuval Reiss for diligently reviewing the manuscript. This work was supported by NSF-BSF grant 2016722 (to R.G.G and T.R) and the Novo Nordisk Foundation centre PRISM (NNF18OC0033950; to R.H.-P. and K.L.-L.). B.M. acknowledges the support of the Neubauer doctoral fellowship fund.

Publisher Copyright:
© 2022, The Author(s).

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abstract = "The eukaryotic proteome undergoes constant surveillance by quality control systems that either sequester, refold, or eliminate aberrant proteins by ubiquitin-dependent mechanisms. Ubiquitin-conjugation necessitates the recognition of degradation determinants, termed degrons, by their cognate E3 ubiquitin-protein ligases. To learn about the distinctive properties of quality control degrons, we performed an unbiased peptidome stability screen in yeast. The search identify a large cohort of proteome-derived degrons, some of which exhibited broad E3 ligase specificity. Consequent application of a machine-learning algorithm establishes constraints governing degron potency, including the amino acid composition and secondary structure propensities. According to the set criteria, degrons with transmembrane domain-like characteristics are the most probable sequences to act as degrons. Similar quality control degrons are present in viral and human proteins, suggesting conserved degradation mechanisms. Altogether, the emerging data indicate that transmembrane domain-like degron features have been preserved in evolution as key quality control determinants of protein half-life.",

author = "Bayan Mashahreh and Shir Armony and Johansson, {Kristoffer En{\o}e} and Alon Chappleboim and Nir Friedman and Gardner, {Richard G.} and Rasmus Hartmann-Petersen and Kresten Lindorff-Larsen and Tommer Ravid",

note = "Funding Information: We are grateful to Prof. Richard Kulka for his inspiration and support. We thank Dr. Yifat Geffen for her assistance with establishing the reporter system, Dr. Itay Koren for advice during the setup of yGPS-P, and Dr. Yuval Reiss for diligently reviewing the manuscript. This work was supported by NSF-BSF grant 2016722 (to R.G.G and T.R) and the Novo Nordisk Foundation centre PRISM (NNF18OC0033950; to R.H.-P. and K.L.-L.). B.M. acknowledges the support of the Neubauer doctoral fellowship fund. Publisher Copyright: {\textcopyright} 2022, The Author(s).",

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AU - Gardner, Richard G.

AU - Hartmann-Petersen, Rasmus

AU - Lindorff-Larsen, Kresten

AU - Ravid, Tommer

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N2 - The eukaryotic proteome undergoes constant surveillance by quality control systems that either sequester, refold, or eliminate aberrant proteins by ubiquitin-dependent mechanisms. Ubiquitin-conjugation necessitates the recognition of degradation determinants, termed degrons, by their cognate E3 ubiquitin-protein ligases. To learn about the distinctive properties of quality control degrons, we performed an unbiased peptidome stability screen in yeast. The search identify a large cohort of proteome-derived degrons, some of which exhibited broad E3 ligase specificity. Consequent application of a machine-learning algorithm establishes constraints governing degron potency, including the amino acid composition and secondary structure propensities. According to the set criteria, degrons with transmembrane domain-like characteristics are the most probable sequences to act as degrons. Similar quality control degrons are present in viral and human proteins, suggesting conserved degradation mechanisms. Altogether, the emerging data indicate that transmembrane domain-like degron features have been preserved in evolution as key quality control determinants of protein half-life.

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Conserved degronome features governing quality control associated proteolysis

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