OxyR-dependent formation of DNA methylation patterns in OpvAB(OFF) and OpvAB(ON) cell lineages of Salmonella enterica

Phase variation of the Salmonella enterica opvAB operon generates a bacterial lineage with standard lipopolysaccharide structure (OpvAB(OFF)) and a lineage with shorter O-antigen chains (OpvAB(ON)). Regulation of OpvAB lineage formation is transcriptional, and is controlled by the LysR-type factor OxyR and by DNA adenine methylation. The opvAB regulatory region contains four sites for OxyR binding (OBS(A-D)), and four methylatable GATC motifs (GATC(1–4)). OpvAB(OFF) and OpvAB(ON) cell lineages display opposite DNA methylation patterns in the opvAB regulatory region: (i) in the OpvAB(OFF) state, GATC(1) and GATC(3) are non-methylated, whereas GATC(2) and GATC(4) are methylated; (ii) in the OpvAB(ON) state, GATC(2) and GATC(4) are non-methylated, whereas GATC(1) and GATC(3) are methylated. We provide evidence that such DNA methylation patterns are generated by OxyR binding. The higher stability of the OpvAB(OFF) lineage may be caused by binding of OxyR to sites that are identical to the consensus (OBS(A) and OBS(c)), while the sites bound by OxyR in OpvAB(ON) cells (OBS(B) and OBS(D)) are not. In support of this view, amelioration of either OBS(B) or OBS(D) locks the system in the ON state. We also show that the GATC-binding protein SeqA and the nucleoid protein HU are ancillary factors in opvAB control.