ArticleGenome biology2002
Asymmetric directional mutation pressures in bacteria.
Article in Genome biology, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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73 citing papers in PubMed.
- Hierarchical evolution of the proteobacterial essential chaperone SecB reveals non-neutral synonymous evolution under extreme purifying selection.Molecular genetics and genomics : MGG · 2026Article
- Integrative chloroplast genomics of Polygonaceae: evolutionary dynamics, codon optimization, and phylogenetic resolution.BMC plant biology · 2026Article
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- Do Noncoding and Coding Sites in Angiosperm Chloroplast DNA Have Different Mutation Processes?Genes · 2023Article
- Mechanisms governing codon usage bias and the implications for protein expression in the chloroplast of Chlamydomonas reinhardtii.The Plant journal : for cell and molecular biology · 2022Review
- An Explanation of Exceptions from Chargaff's Second Parity Rule/Strand Symmetry of DNA Molecules.Genes · 2022Article
- Review
- The bacterial epigenome.Nature reviews. Microbiology · 2020Review
- Translation-Associated Mutational U-Pressure in the First ORF of SARS-CoV-2 and Other Coronaviruses.Frontiers in microbiology · 2020Article
- Article
- Novel metrics for quantifying bacterial genome composition skews.BMC genomics · 2018Article
- Codon usage analysis of photolyase encoding genes of cyanobacteria inhabiting diverse habitats.3 Biotech · 2017Article
- Optimization of amino acid replacement costs by mutational pressure in bacterial genomes.Scientific reports · 2017Article
- Anaerobically Grown Escherichia coli Has an Enhanced Mutation Rate and Distinct Mutational Spectra.PLoS genetics · 2017Article
- Context based computational analysis and characterization of ARS consensus sequences (ACS) of Saccharomyces cerevisiae genome.Genomics data · 2016Article
- A novel skew analysis reveals substitution asymmetries linked to genetic code GC-biases and PolIII a-subunit isoforms.DNA research : an international journal for rapid publication of reports on genes and genomes · 2016Article
- Replication Termination: Containing Fork Fusion-Mediated Pathologies in Escherichia coli.Genes · 2016Review
- Diversification of DnaA dependency for DNA replication in cyanobacterial evolution.The ISME journal · 2016Article
- Multiple Evolutionary Selections Involved in Synonymous Codon Usages in the Streptococcus agalactiae Genome.International journal of molecular sciences · 2016Article
- Multiple Factors Drive Replicating Strand Composition Bias in Bacterial Genomes.International journal of molecular sciences · 2015Article
13 more citing papers are in PubMed but not listed here.
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundWhen there are no strand-specific biases in mutation and selection rates (that is, in the substitution rates) between the two strands of DNA, the average nucleotide composition is theoretically expected to be A = T and G = C within each strand. Deviations from these equalities are therefore evidence for an asymmetry in selection and/or mutation between the two strands. By focusing on weakly selected regions that could be oriented with respect to replication in 43 out of 51 completely sequenced bacterial chromosomes, we have been able to detect asymmetric directional mutation pressures.
resultsMost of the 43 chromosomes were found to be relatively enriched in G over C and T over A, and slightly depleted in G+C, in their weakly selected positions (intergenic regions and third codon positions) in the leading strand compared with the lagging strand. Deviations from A = T and G = C were highly correlated between third codon positions and intergenic regions, with a lower degree of deviation in intergenic regions, and were not correlated with overall genomic G+C content.
conclusionsDuring the course of bacterial chromosome evolution, the effects of asymmetric directional mutation pressures are commonly observed in weakly selected positions. The degree of deviation from equality is highly variable among species, and within species is higher in third codon positions than in intergenic regions. The orientation of these effects is almost universal and is compatible in most cases with the hypothesis of an excess of cytosine deamination in the single-stranded state during DNA replication. However, the variation in G+C content between species is influenced by factors other than asymmetric mutation pressure.
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