The number of domains in the ribosomal protein S1 as a hallmark of the phylogenetic grouping of bacteria

PLoS One. 2019 Aug 22;14(8):e0221370. doi: 10.1371/journal.pone.0221370. eCollection 2019.

Abstract

The family of ribosomal proteins S1 contains about 20% of all bacterial proteins including the S1 domain. An important feature of this family is multiple copies of structural domains in bacteria, the number of which changes in a strictly limited range from one to six. In this study, the automated exhaustive analysis of 1453 sequences of S1 allowed us to demonstrate that the number of domains in S1 is a distinctive characteristic for phylogenetic bacterial grouping in main phyla. 1453 sequences of S1 were identified in 25 out of 30 different phyla according to the List of Prokaryotic Names with Standing in Nomenclature. About 62% of all records are identified as six-domain S1 proteins, which belong to phylum Proteobacteria. Four-domain S1 are identified mainly in proteins from phylum Firmicutes and Actinobacteria. Records belonging to these phyla are 33% of all records. The least represented two-domain S1 are about 0.6% of all records. The third and fourth domains for the most representative four- and six-domain S1 have the highest percentage of identity with the S1 domain from polynucleotide phosphorylase and S1 domains from one-domain S1. In addition, for these groups, the central part of S1 (the third domain) is more conserved than the terminal domains.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Actinobacteria / classification*
  • Actinobacteria / genetics
  • Amino Acid Sequence
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Conserved Sequence
  • Firmicutes / classification*
  • Firmicutes / genetics
  • Gene Expression
  • Phylogeny*
  • Polyribonucleotide Nucleotidyltransferase / chemistry
  • Polyribonucleotide Nucleotidyltransferase / genetics
  • Protein Conformation, alpha-Helical
  • Protein Conformation, beta-Strand
  • Protein Domains
  • Proteobacteria / classification*
  • Proteobacteria / genetics
  • Ribosomal Proteins / chemistry*
  • Ribosomal Proteins / genetics
  • Sequence Alignment
  • Sequence Homology, Amino Acid

Substances

  • Bacterial Proteins
  • Ribosomal Proteins
  • ribosomal protein S1
  • Polyribonucleotide Nucleotidyltransferase

Grant support

Funded by Russian Science Foundation, grant number 18-14-00321 for all authors. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.