Ratio of non-synonymous to synonymous substitutions
For all available sequences of bacterial ribosomal S1 proteins, we calculated the ratio of non-synonymous to synonymous substitutions (using the Goldman and Yang model) for each group (in accordance with the number of structural domains) (dN/dS analysis, http://oka.protres.ru:4200). As is known, the dN/dS ratio is used to assess the balance between neutral mutations, purifying selection and beneficial mutations acting on a set of homologous genes encoding a protein 42. This ratio measures the strength and mode of natural selection acting on protein genes, with dN/dS > 1 indicating positive (adaptive or diversifying) selection, dN/dS = 1 indicating neutral evolution, and dN/dS < 1 indicating negative (purifying or cleaning) selection. The dN/dS ratio summarizes the evolutionary rates of genes and can be an informative feature, since it can determine which genes are the most (or least) conserved, as well as identify genes that may have gone through periods of adaptive evolution 43. However, in real data, positive selection does not occur, because such selection is usually observed only in a certain region of the protein (for example: a specific domain) and/or within one branch of phylogeny (some, but not all species)44–46. For S1 single domain proteins, negative selection (dN/dS < 1) was most often observed. However, for some representatives of the phylum Actinobacteria, positive selection was revealed relative to the phylum Proteobacteria (dN/dS = 1.46) and Tenericutes (dN/dS = 1.26). Also, a relatively high dN/dS ratio (0.75) was found for the phylum Bacteroidetes relative to the phylum Tenericutes. For two-domain S1 proteins, negative selection (dN/dS < 1) also predominates. Relatively high dN/dS ratios were found for Eubacterium hallii (Actinobacteria) andActinoplanes friuliensis (Firmicutes) – 0.83 and for the pairBeggiatoa sp. (Firmicutes) and Tyzzerella nexilis(Proteobacteria). For three-domain and five-domain S1 proteins, negative selection (dN/dS < 1) is characteristic of all pairs of the nucleic acid sequence in this group. For the four-domain S1 proteins, for some representatives of the phylum Actinobacteria, a relatively positive selection was revealed (for example, dN/dS = 1.05:Rhodococcus wratislaviensis and Parascardovia denticolens ). For other representatives of the four-domain S1 proteins (within and between phyla) negative selection (dN/dS < 1) is observed. For six-domain S1 proteins (within and between phyla) only negative selection (dN/dS < 1) is observed. For individual S1 domains (within and between bacteria phyla), analysis of the dN/dS ratio, unfortunately, gives ambiguous results that are difficult to interpret.