Features of phylogenetic distribution of ribosomal S1 proteins
As mentioned above, automated extended exhaustive analysis of 1453 S1
sequences allowed us to demonstrate that the number of structural
domains in S1 is a hallmark for the phylogenetic grouping of bacteria in
main phyla 9. Considering 1453 S1 sequences, we
obtained that about 62% of all records were identified as six-domain S1
proteins, which belong to the Proteobacteria phylum. Records with four
S1 domains were found in 33% of cases. Almost all analyzed bacteria in
this group belong to the Actinobacteria phylum (50% of all four-domain
proteins S1) and Firmicutes (47% of all four-domain S1 proteins).
Records belonging to these phyla make up 33% of all records. The least
represented two-domain proteins S1 make up about 0.6% of all records.
S1 proteins, containing one domain, account for only 0.8% of all
studied ribosomal S1 proteins. The most represented in this group is the
Tenericutes phylum. Cyanobacteria have three S1 domains9.
For this study, we used a dataset containing 1333 records identified in
24 different bacterial phyla. Phylum is the highest-level group in
bacterial domains 26 and is therefore a useful rank
for reviewing prokaryotic diversity. Features of the phylogenetic
distribution of ribosomal S1 proteins (the number of structural domains,
phylum and superphyla) in the studied dataset are shown in Table 1.
The distribution of the number of S1 structural domains in ribosomal S1
proteins and the percentage of representation of various phyla differ
little from previous results 9. 55% of all studied
sequences belong to Proteobacteria, 16% and 17% of sequences belong to
Firmicutes and Actinobacteria, respectively, and 6% to Bacteroidetes.
Here, for further analysis, we have added the existing in the literature
classifications of the studied phyla into supergroups and their division
by the Gram staining method (Table 1, File S2). For some phyla,
taxonomic classes have been added to Table 1. So, the Bacteroidetes
phylum is combined with the
Chlorobi phyla, and Fibrobacteres
into the FCB group27.
Our data (Table 1) demonstrate that the ribosomal S1 protein of this
group almost always contains six S1 domains (Chlorobi, Fibrobacteres,
Gemmatimonadates and Ignavibacteriae). An exception is the Bacteroidetes
phylum, which has one, four, or six structural S1domains. However,
proteins containing six domains cover 98% of the sequences belonging to
this phylum.
Analysis of 16S rRNA and characteristic conserved indels in some
proteins is used to group the phyla Planctomycetes, Verrucomicrobia,
Chlamydiae into the PVC clan 28. As our data show
(Table 1), bacteria of the phyla Chlamydiae and Verrucomicrobia
basically contain six S1 domains, while Planctomycetes can have four,
five, and six S1 domains. The proposed superphylum
Terrabacteria includes Actinobacteria, Cyanobacteria,
Deinococcus-Thermus, and Firmicutes 29,30. This
supergroup unites the two most representative phyla Actinobacteria and
Firmicutes, which can contain a different number of structural S1
domains ranging from one to four. In addition, these two phyla are
Gram-positive bacteria (G+). Cyanobacteria always have three S1 domains,
the Chloroflexi phylum has four S1 domains, and the Deinococcus-Thermus
phylum has five S1 domains. It has been suggested that some classes of
the phylum Proteobacteria may be a phylum in themselves, which would
make Proteobacteria a superphylum 31. For example, the
Deltaproteobacteria group does not always form a monophyletic lineage
with other Proteobacteria classes 32. According to our
data, bacterial ribosomal proteins S1 of this phylum can contain a
different number of structural S1 domains (from one to six). However,
the predominant number of sequences in this group contains six S1
domains (98%).