Protein structure, amino acid composition and sequence determine proteome vulnerability to oxidation-induced damage.
Aging
/ metabolism
Bacterial Proteins
/ chemistry
Computational Biology
Deinococcus
/ metabolism
Escherichia coli
Humans
Machine Learning
Neurodegenerative Diseases
/ metabolism
Oxidation-Reduction
Oxidative Stress
/ physiology
Protein Conformation
Protein Processing, Post-Translational
Proteome
/ metabolism
Proteomics
/ methods
Reactive Oxygen Species
/ metabolism
Sequence Analysis, Protein
Deinococcus radiodurans
oxidative stress
protein carbonyl
radioresistance
structural systems biology
Journal
The EMBO journal
ISSN: 1460-2075
Titre abrégé: EMBO J
Pays: England
ID NLM: 8208664
Informations de publication
Date de publication:
01 12 2020
01 12 2020
Historique:
received:
09
03
2020
revised:
16
09
2020
accepted:
22
09
2020
pubmed:
20
10
2020
medline:
13
4
2021
entrez:
19
10
2020
Statut:
ppublish
Résumé
Oxidative stress alters cell viability, from microorganism irradiation sensitivity to human aging and neurodegeneration. Deleterious effects of protein carbonylation by reactive oxygen species (ROS) make understanding molecular properties determining ROS susceptibility essential. The radiation-resistant bacterium Deinococcus radiodurans accumulates less carbonylation than sensitive organisms, making it a key model for deciphering properties governing oxidative stress resistance. We integrated shotgun redox proteomics, structural systems biology, and machine learning to resolve properties determining protein damage by γ-irradiation in Escherichia coli and D. radiodurans at multiple scales. Local accessibility, charge, and lysine enrichment accurately predict ROS susceptibility. Lysine, methionine, and cysteine usage also contribute to ROS resistance of the D. radiodurans proteome. Our model predicts proteome maintenance machinery, and proteins protecting against ROS are more resistant in D. radiodurans. Our findings substantiate that protein-intrinsic protection impacts oxidative stress resistance, identifying causal molecular properties.
Identifiants
pubmed: 33073387
doi: 10.15252/embj.2020104523
pmc: PMC7705453
doi:
Substances chimiques
Bacterial Proteins
0
Proteome
0
Reactive Oxygen Species
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e104523Subventions
Organisme : Life Sciences Research Foundation (LSRF)
ID : GBMF 2550.04
Organisme : Fonds De La Recherche Scientifique - FNRS (FNRS)
Informations de copyright
© 2020 The Authors. Published under the terms of the CC BY NC ND 4.0 license.
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