ArticleJournal of molecular evolution2020
Evolutionary Forces and Codon Bias in Different Flavors of Intrinsic Disorder in the Human Proteome.
Article in Journal of molecular evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 40 citations in OpenAlex.
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- Synonymous Codon Variant Analysis for Autophagic Genes Dysregulated in Neurodegeneration.Molecular neurobiology · 2023Article
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- Identification of Conserved Epitopes in SARS-CoV-2 Spike and Nucleocapsid Protein.Current genomics · 2021Article
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- Estimating the Influence of Physicochemical and Biochemical Property Indexes on Selection for Amino Acids Usage in Eukaryotic Cells.Journal of molecular evolution · 2021Article
- IDPology of the living cell: intrinsic disorder in the subcellular compartments of the human cell.Cellular and molecular life sciences : CMLS · 2021Article
- Codon-based indices for modeling gene expression and transcript evolution.Computational and structural biotechnology journal · 2021Review
- Towards an understanding of the role of intrinsic protein disorder on plant adaptation to environmental challenges.Cell stress & chaperones · 2021Article
- Intrinsic Disorder in Plant Transcription Factor Systems: Functional Implications.International journal of molecular sciences · 2020Review
- Bioinformatic analysis and functional predictions of selected regeneration-associated transcripts expressed by zebrafish microglia.BMC genomics · 2020Article
- Evolutionary Study of Disorder in Protein Sequences.Biomolecules · 2020Article
- Protein-Protein Interactions Mediated by Intrinsically Disordered Protein Regions Are Enriched in Missense Mutations.Biomolecules · 2020Article
- Article
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this study, we perform a systematic analysis of evolutionary forces (i.e., mutational bias and natural selection) that shape the codon usage bias of human genes encoding proteins characterized by different flavors of intrinsic disorder. Well-structured proteins are expected to be more under control by purifying natural selection than intrinsically disordered proteins because one or few mutations (even synonymous) in the genes can result in a protein that no longer folds correctly. On the contrary, intrinsically disordered proteins are thought to evolve more rapidly than well-folded proteins, due to a relaxed purifying natural selection and an increased role of mutational bias. Using different bioinformatic tools, we find evidence that codon usage in IDPs is not only affected by a basic mutational bias, but it is also more selectively constrained than the rest of the human proteome. We speculate that intrinsically disordered proteins have not only a high tolerance to mutations but also a selective propensity to preserve their structural disorder under physiological conditions. Additionally, we confirm not only that intrinsically disordered proteins are preferentially encoded by GC-rich genes, but also that they are characterized by the highest fraction of CpG sites in the sequences, implying a higher susceptibility to methylation resulting in C-T transition mutations. Overall, our results corroborate the essential role of intrinsic disorder for the evolutionary adaptability and evolvability of proteins, offering new insight about protein evolution not only in terms of functional properties and roles in diseases but also in terms of evolutionary forces they are subjected to.
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