Micro-evolution of three Streptococcus species: selection, antigenic variation, and horizontal gene inflow

• Published in: BMC ecology and evolution 2019-03, Vol.19 (1), p.83-83, Article 83
• Main Authors: Shelyakin, Pavel V, Bochkareva, Olga O, Karan, Anna A, Gelfand, Mikhail S
• Format: Article
• Language: English
• Subjects: Adaptability; Animals; Antibiotic resistance; Antibiotics; Antigen variation; Antigenic Variation - genetics; Antigens; Bacteria; Bacterial genetics; Bacterial infections; Binding sites; Biological Evolution; Breakpoints; Chromosomes; Conserved Sequence - genetics; Deoxyribonucleic acid; Disease transmission; DNA; DNA sequencing; DNA, Intergenic; Drug development; Environmental changes; Environmental conditions; Environmental quality; Evolution; Evolutionary biology; Gene expression; Gene Flow; Gene inflow; Gene mapping; Gene Ontology; Gene Rearrangement - genetics; Gene sequencing; Gene transfer; Gene Transfer, Horizontal; Genes; Genes, Bacterial; Genetic aspects; Genetic research; Genome Size; Genomes; Genomic analysis; Genomic rearrangements; Genomics; Gram-positive bacteria; Health; Horizontal transfer; Humans; Hydrolases - metabolism; Inflow; Information processing; Inversions; Mapping; Microbial drug resistance; Mortality; Nucleotides - genetics; Pan-genome; Pathogenic microorganisms; Pathogenicity; Pathogens; Phylogeny; Physiological aspects; Pneumonia; Proteins; Rare species; Regulatory sequences; Selection in upstream regions; Selection, Genetic; Sequence Deletion; Species Specificity; Streptococcus; Streptococcus - genetics; Streptococcus infections; Streptococcus pneumoniae; Streptococcus pneumoniae - genetics; Vaccines; Virulence; Virulence (Microbiology); Virulence - genetics; Wildlife conservation
• ISSN: 1471-2148; 1471-2148; 2730-7182
• DOI: 10.1186/s12862-019-1403-6

The genus Streptococcus comprises pathogens that strongly influence the health of humans and animals. Genome sequencing of multiple Streptococcus strains demonstrated high variability in gene content and order even in closely related strains of the same species and created a newly emerged object for genomic analysis, the pan-genome. Here we analysed the genome evolution of 25 strains of Streptococcus suis, 50 strains of Streptococcus pyogenes and 28 strains of Streptococcus pneumoniae. Fractions of the pan-genome, unique, periphery, and universal genes differ in size, functional composition, the level of nucleotide substitutions, and predisposition to horizontal gene transfer and genomic rearrangements. The density of substitutions in intergenic regions appears to be correlated with selection acting on adjacent genes, implying that more conserved genes tend to have more conserved regulatory regions. The total pan-genome of the genus is open, but only due to strain-specific genes, whereas other pan-genome fractions reach saturation. We have identified the set of genes with phylogenies inconsistent with species and non-conserved location in the chromosome; these genes are rare in at least one species and have likely experienced recent horizontal transfer between species. The strain-specific fraction is enriched with mobile elements and hypothetical proteins, but also contains a number of candidate virulence-related genes, so it may have a strong impact on adaptability and pathogenicity. Mapping the rearrangements to the phylogenetic tree revealed large parallel inversions in all species. A parallel inversion of length 15 kB with breakpoints formed by genes encoding surface antigen proteins PhtD and PhtB in S. pneumoniae leads to replacement of gene fragments that likely indicates the action of an antigen variation mechanism. Members of genus Streptococcus have a highly dynamic, open pan-genome, that potentially confers them with the ability to adapt to changing environmental conditions, i.e. antibiotic resistance or transmission between different hosts. Hence, integrated analysis of all aspects of genome evolution is important for the identification of potential pathogens and design of drugs and vaccines.