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.