Epigenetic Switch Driven by DNA Inversions Dictates Phase Variation in Streptococcus pneumoniae

Jing Li, Jing-Wen Li, Zhixing Feng, Juanjuan Wang, Haoran An, Yanni Liu, Yang Wang, Kailing Wang, Xuegong Zhang, Zhun Miao, Wenbo Liang, Robert Sebra (+4 others)
2016 PLoS Pathogens  
DNA methylation is an important epigenetic mechanism for phenotypic diversification in all forms of life. We previously described remarkable cell-to-cell heterogeneity in epigenetic pattern within a clonal population of Streptococcus pneumoniae, a leading human pathogen. We here report that the epigenetic diversity is caused by extensive DNA inversions among hsdS A, hsdS B, and hsdS C , three methyltransferase hsdS genes in the Spn556II type-I restriction modification (R-M) locus. Because hsdS
more » ... encodes the sequence recognition subunit of this type-I R-M DNA methyltransferase, these site-specific recombinations generate pneumococcal cells with variable HsdS A alleles and thereby diverse genome methylation patterns. Most importantly, the DNA methylation pattern specified by the HsdS A1 allele leads to the formation of opaque colonies, whereas the pneumococci lacking HsdS A1 produce transparent colonies. Furthermore, this HsdS A1 -dependent phase variation requires intact DNA methylase activity encoded by hsdM in the Spn556II (renamed colony opacity determinant or cod) locus. Thus, the DNA inversion-driven ON/OFF switch of the hsdS A1 allele in the cod locus and resulting epigenetic switch dictate the phase variation between the opaque and transparent phenotypes. Phase variation has been well documented for its importance in pneumococcal carriage and invasive infection, but its molecular basis remains unclear. Our work has discovered a novel epigenetic cause for this significant pathobiology phenomenon in S. pneumoniae. Lastly, our findings broadly represents a significant advancement in our understanding of bacterial R-M systems and their potential in shaping epigenetic and phenotypic diversity of the prokaryotic organisms because similar site-specific recombination systems widely exist in many archaeal and bacterial species. PLOS Pathogens | DNA methylation is a well-known epigenetic mechanism for phenotypic diversification in all forms of life. This study reports our discovery that the Spn556II type-I RM locus in human pathogen Streptococcus pneumoniae undergoes extensive DNA inversions among three homologous DNA methyltransferase genes. These site-specific recombinations generate subpopulations of progeny cells with dramatic epigenetic and phenotypic differences. This is exemplified by the striking differences in colony morphology among the pneumococcal variants that carried different allelic variants of the methyltransferase genes. Phase variation has been well documented for its importance in pneumococcal pathogenesis, but it is currently unknown how this phenotypic switch occurs at the molecular level. This work has thus discovered an epigenetic cause for pneumococcal phase variation. Our findings have a broad implication on the epigenetic and phenotypic diversification in prokaryotic organisms because similar DNA rearrangement systems also exist in many archaeal and bacterial species. Epigenetic Cause of Pneumococcal Phase Variation PLOS Pathogens | Results DNA rearrangements occur in the Spn556II locus Our recent study identified three DNA motifs specifically methylated by three R-M systems (two type-I: Spn556II and Spn556III; a type-II: Spn556I) in the multi-drug resistant type 19F strain ST556 of S. pneumoniae (Fig 1A) [35]. We observed remarkable heterogeneity in Epigenetic Cause of Pneumococcal Phase Variation PLOS Pathogens | 7 / 36 Fig 4. The pneumococcal genomic DNA motifs methylated by the hsdS A allelic variants. The DNA methylation sequences in the genomes of strain ST556 (WT) or its derivatives (A1-A9) each possessing one of the 9 hsdS A alleles were detected by SMRT sequencing. The methylation motifs recognized by Spn556I and Spn556III were also detected in all of the strains but are not shown here for the sake of space; methylated m6A bases are indicated with red characters. R = A or G, Y = T or C.
doi:10.1371/journal.ppat.1005762 pmid:27427949 pmcid:PMC4948785 fatcat:r3zwtbunnrffri66um5qtaysby