DNA methylation from a Type I restriction modification system influences gene expression and virulence in Streptococcus pyogenes

• Published in: PLoS pathogens Vol. 15; no. 6; p. e1007841
• Main Authors: Nye, Taylor M, Jacob, Kristin M, Holley, Elena K, Nevarez, Juan M, Dawid, Suzanne, Simmons, Lyle A, Watson, Jr, Michael E
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 17.06.2019; Public Library of Science (PLoS)
• Subjects: Adhesins; Analysis; Animals; Bacteria; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Biochemistry; Bioinformatics; Biology and life sciences; Cell cycle; Cell survival; Clonal deletion; Cytokines; Cytokines - metabolism; Deoxyribonucleic acid; Developmental biology; DNA; DNA Methylation; DNA Restriction-Modification Enzymes - genetics; DNA Restriction-Modification Enzymes - metabolism; DNA sequencing; DNA, Bacterial - genetics; DNA, Bacterial - metabolism; Domains; Epithelial cells; Fasciitis, Necrotizing - genetics; Fasciitis, Necrotizing - metabolism; Fasciitis, Necrotizing - pathology; Female; Gene deletion; Gene expression; Gene Expression Regulation, Bacterial; Gene sequencing; Genes; Genetic research; Genetic transformation; Genomes; Genomics; Gram-positive bacteria; Humans; Immune response; Immune system; Infectious diseases; Inflammation; Laboratory animals; Lesions; Leukocytes (neutrophilic); Medicine and health sciences; Methylation; Methyltransferases; Mice; N6-methyladenosine; Pathogens; Pediatrics; Prokaryotes; Proteins; Research and Analysis Methods; Ribonucleic acid; RNA; Skin; Skin diseases; Software; Streptococcus infections; Streptococcus pyogenes; Streptococcus pyogenes - genetics; Streptococcus pyogenes - metabolism; Streptococcus pyogenes - pathogenicity; Supervision; Transcription; Transcription (Genetics); Transformation; Virulence; Virulence (Microbiology); Ann Arbor Michigan; United States > US
• ISSN: 1553-7374; 1553-7366; 1553-7374
• DOI: 10.1371/journal.ppat.1007841

DNA methylation is pervasive across all domains of life. In bacteria, the presence of N6-methyladenosine (m6A) has been detected among diverse species, yet the contribution of m6A to the regulation of gene expression is unclear in many organisms. Here we investigated the impact of DNA methylation on gene expression and virulence within the human pathogen Streptococcus pyogenes, or Group A Streptococcus. Single Molecule Real-Time sequencing and subsequent methylation analysis identified 412 putative m6A sites throughout the 1.8 Mb genome. Deletion of the Restriction, Specificity, and Methylation gene subunits (ΔRSM strain) of a putative Type I restriction modification system lost all detectable m6A at the recognition sites and failed to prevent transformation with foreign-methylated DNA. RNA-sequencing identified 20 genes out of 1,895 predicted coding regions with significantly different gene expression. All of the differentially expressed genes were down regulated in the ΔRSM strain relative to the parent strain. Importantly, we found that the presence of m6A DNA modifications affected expression of Mga, a master transcriptional regulator for multiple virulence genes, surface adhesins, and immune-evasion factors in S. pyogenes. Using a murine subcutaneous infection model, mice infected with the ΔRSM strain exhibited an enhanced host immune response with larger skin lesions and increased levels of pro-inflammatory cytokines compared to mice infected with the parent or complemented mutant strains, suggesting alterations in m6A methylation influence virulence. Further, we found that the ΔRSM strain showed poor survival within human neutrophils and reduced adherence to human epithelial cells. These results demonstrate that, in addition to restriction of foreign DNA, gram-positive bacteria also use restriction modification systems to regulate the expression of gene networks important for virulence.