ArticleGenome biology2008
Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective.
Article in Genome biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed.
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- Purifying selection enduringly acts on the sequence evolution of highly expressed proteins in Escherichia coli.G3 (Bethesda, Md.) · 2022Article
- Identification of 121 variants of honey bee Vitellogenin protein sequences with structural differences at functional sites.Protein science : a publication of the Protein Society · 2022Article
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- Complement Genome Annotation Lift Over Using a Weighted Sequence Alignment Strategy.Frontiers in genetics · 2019Article
- Hfq chaperone brings speed dating to bacterial sRNA.Wiley interdisciplinary reviews. RNA · 2018Review
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- Systematic analysis of protein identity between Zika virus and other arthropod-borne viruses.Bulletin of the World Health Organization · 2017Article
- Duplication and Diversification of Dipteran Argonaute Genes, and the Evolutionary Divergence of Piwi and Aubergine.Genome biology and evolution · 2016Article
- Evolutionary insights from de novo transcriptome assembly and SNP discovery in California white oaks.BMC genomics · 2015Article
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4 authors.
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Abstract
backgroundThe rates of molecular evolution for protein-coding genes depend on the stringency of functional or structural constraints. The Ka/Ks ratio has been commonly used as an indicator of selective constraints and is typically calculated from interspecies alignments. Recent accumulation of single nucleotide polymorphism (SNP) data has enabled the derivation of Ka/Ks ratios for polymorphism (SNP A/S ratios).
resultsUsing data from the dbSNP database, we conducted the first large-scale survey of SNP A/S ratios for different structural and functional properties. We confirmed that the SNP A/S ratio is largely correlated with Ka/Ks for divergence. We observed stronger selective constraints for proteins that have high mRNA expression levels or broad expression patterns, have no paralogs, arose earlier in evolution, have natively disordered regions, are located in cytoplasm and nucleus, or are related to human diseases. On the residue level, we found higher degrees of variation for residues that are exposed to solvent, are in a loop conformation, natively disordered regions or low complexity regions, or are in the signal peptides of secreted proteins. Our analysis also revealed that histones and protein kinases are among the protein families that are under the strongest selective constraints, whereas olfactory and taste receptors are among the most variable groups.
conclusionOur study suggests that the SNP A/S ratio is a robust measure for selective constraints. The correlations between SNP A/S ratios and other variables provide valuable insights into the natural selection of various structural or functional properties, particularly for human-specific genes and constraints within the human lineage.
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