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

Abstract

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 A encodes the sequence recognition subunit of this type-I R-M DNA methyltransferase, these site-specific recombinations generate pneumococcal cells with variable HsdSA alleles and thereby diverse genome methylation patterns. Most importantly, the DNA methylation pattern specified by the HsdSA1 allele leads to the formation of opaque colonies, whereas the pneumococci lacking HsdSA1 produce transparent colonies. Furthermore, this HsdSA1-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.

Comparative analysis ofStreptococcusgenomes

“…7). As phase variation is known to be important for S. pneumoniae infection (Li et al, 2016), the observed parallel inversion might indicate the action of an antigen variation mechanisms, which is important, as PhtD is a candidate for a next-generation pneumococcal vaccine (Yun et al, 2015). As more than 80% core genes in Streptococcus spp.…”

Selective and non‐selective bottlenecks as drivers of the evolution of hypermutable bacterial loci

“…For example, sub‐components of the hsdS gene of the well‐characterised complex PV RM of Streptococcus pneumoniae , SpnIII, can exist in one of six possible orientations. Each of these unique TRD combinations is associated with a different DNA methylation pattern and some of them can impact on invasive disease potential in mice and the invasion‐associated opaque colony phenotype (Li et al, , ; Manso et al, ; Oliver, Roy, Kumar, Lefkowitz & Swords, ). The simplicity of these findings is challenged by variable experimental observations, suggesting that genetic background may influence links between methylation and colony opacity, and by the extensive hsdS allelic variation resulting in differing dominant methylation patterns among pneumococcal strains (De Ste Croix et al, ).…”

Sequence analysis allows functional annotation of tyrosine recombinases in prokaryotic genomes

“…The largest subgroup, Xer includes proteins responsible for chromosome dimer resolution in bacteria and archaea, such as XerC/D, XerH, XerS and XerA [31][32][33][34]. In addition, an integrase of the Helicobacter conjugative transposon TnPZ (XerT) [35] and a highly abundant recombinase that drives production of different methyltransferase gene alleles in Streptococcus pneumonia [5,6] (PsrA; Figure 1C). As judged by the sequence logos, Xer is the most evolutionary conserved subgroup: it has highly conserved residues also outside of the active site pocket and the hydrophobic core of the catalytic domain.…”

“…Xer is also the most widely distributed subgroup. It is present in all bacterial and archaeal classes where TRs were found, with the exception of 6 Oscillatoriophycideae, Ktedonobacteria, Rubrobacteria , Deinococci and Halobacteria ( Figure 1B, Supplementary table 2). Such broad distribution is consistent with the essential role of Xer proteins in chromosome dimer resolution in bacteria and archaea.…”