Genomic Legacies of Ancient Adaptation Illuminate GC-Content Evolution in Bacteria

Abstract

GC content has been shown to be an important factor in microbial ecology and evolution, and the genomic GC of bacteria can be characterized by great intergenomic heterogeneity, high intragenomic homogeneity, and strong phylogenetic inertia, as well as being associated with the environment. Current hypotheses concerning direct selection or mutational biases cannot well explain these features simultaneously.

Hydrogenimonas cancrithermarum sp. nov., a hydrogen- and thiosulfate-oxidizing mesophilic chemolithoautotroph isolated from diffuse-flow fluids on the East Pacific Rise, and an emended description of the genus Hydrogenimonas

“…A strong bias in stop codon usage was also observed (Table S4). All described species of the genus Hydrogenimonas have a variety of genes encoding proteins which have been correlated with low G+C content in a previous study [39], such as MutS2, RecJ and PfkA, but only a few genes encoding proteins correlated with high G+C content (Table S6).…”

“…urashimensis is a unique genomic feature compared not only with H. thermophila but also with other members of the class Epsilonproteobacteria as this group was characterized as a low-GC lineage [39]. When it comes to genes (e.g., DNA repair pathway) that have shown high correlation with genomic DNA G+C content in previous studies [39, 49], ISO32 T and H.…”

“…thermophila but also with other members of the class Epsilonproteobacteria as this group was characterized as a low-GC lineage [39]. When it comes to genes (e.g., DNA repair pathway) that have shown high correlation with genomic DNA G+C content in previous studies [39, 49], ISO32 T and H. urashimensis have genetic properties characteristic of low G+C content, as does H.…”

“…The relatively high genomic DNA G+C content observed in ISO32 T and H. urashimensis is a unique genomic feature compared not only with H. thermophila but also with other members of the class Epsilonproteobacteria as this group was characterized as a low-GC lineage [39]. When it comes to genes (e.g., DNA repair pathway) that have shown high correlation with genomic DNA G+C content in previous studies [39,49], ISO32 T and H. urashimensis have genetic properties characteristic of low G+C content, as does H. thermophila. Several studies have provided indications that genomic DNA G+C content correlates with phenotypic and environmental factors (e.g., aerobiosis and environmental type) [50,51]; however, these findings are not consistent with those for species of the genus Hydrogenimonas, which were isolated from the same type of environment and utilize the same level of oxygen as an electron acceptor.…”

Evolution and diversity of nucleotide and dinucleotide composition in poxviruses

“…It is thus conceivable that loss of the viral ligase impairs the repair of specific lesions, eventually leading to biased mutation patterns, as our data suggest. On the one hand, this hypothesis is further supported by data from bacteria, which also exhibit wide variations in genomic G+C content that are largely dependent on the presence of specific DNA repair systems [134–136]. On the other hand, despite the fact that poxvirus replication occurs in the cytoplasm, cellular DNA ligases have been shown to be recruited to viral replication sites, where they may compensate or replace the activity of the viral enzymes [137, 138].…”