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Cited by 10Evolution and Genetic DynamicsGenomics and Phylogenetic StudiesGenetic diversity and population structure

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Intermolecular Interactions Drive Protein Adaptive and Coadaptive Evolution at Both Species and Population Levels

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Peng, Junhui, Svetec, Nicolas, Zhao, Li·2022·Molecular Biology and Evolution
DOI 10.1093/molbev/msab350PMC PMC8789070

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Abstract

Proteins are the building blocks for almost all the functions in cells. Understanding the molecular evolution of proteins and the forces that shape protein evolution is essential in understanding the basis of function and evolution. Previous studies have shown that adaptation frequently occurs at the protein surface, such as in genes involved in host–pathogen interactions. However, it remains unclear whether adaptive sites are distributed randomly or at regions associated with particular structural or functional characteristics across the genome, since many proteins lack structural or functional annotations. Here, we seek to tackle this question by combining large-scale bioinformatic prediction, structural analysis, phylogenetic inference, and population genomic analysis of Drosophila protein-coding genes. We found that protein sequence adaptation is more relevant to function-related rather than structure-related properties. Interestingly, intermolecular interactions contribute significantly to protein adaptation. We further showed that intermolecular interactions, such as physical interactions, may play a role in the coadaptation of fast-adaptive proteins. We found that strongly differentiated amino acids across geographic regions in protein-coding genes are mostly adaptive, which may contribute to the long-term adaptive evolution. This strongly indicates that a number of adaptive sites tend to be repeatedly mutated and selected throughout evolution in the past, present, and maybe future. Our results highlight the important roles of intermolecular interactions and coadaptation in the adaptive evolution of proteins both at the species and population levels.

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Metadata

Authors
Peng, J., Svetec, N., & Zhao, L.
Affiliations
Rockefeller University (US)
Corresponding author
Zhao, Li
ORCID
Venue
Molecular Biology and Evolution
Publisher
Oxford University Press (OUP)
Published
2021-12-08
Volume
39
Issue
1
ISSN
  • 0737-4038 (ISSN-L)
  • 1537-1719
DOI
10.1093/molbev/msab350
PMC
PMC8789070
OpenAlex
W4206512201
Cited by
10
References
7
Citations by year
2026: 3 · 2025: 3 · 2024: 2 · 2023: 1 · 2022: 1
FWCI
0.56
Type
journal article
Language
en
Open access
Licence
Locations
  • Molecular Biology and Evolution (publishedVersion, cc-by-nc)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
Funders
  • Robertson Foundation
  • National Institutes of Health
  • National Institute of General Medical Sciences (R35GM133780)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
Keywords
co-adaptation, intermolecular interactions, Drosophila, genetic differentiation, protein function, protein structure, host-pathogen interaction, protein-coding genes
MeSH terms
Animals, Drosophila, Phylogeny, Proteins, Genome, Evolution, Molecular

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