OxyR-dependent formation of DNA methylation patterns in OpvAB^OFFand OpvAB^ONcell lineages ofSalmonella enterica

Abstract

Phase variation of the Salmonella enterica opvAB operon generates a bacterial lineage with standard lipopolysaccharide structure (OpvABOFF) and a lineage with shorter O-antigen chains (OpvABON). 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 (OBSA-D), and four methylatable GATC motifs (GATC1–4). OpvABOFF and OpvABON cell lineages display opposite DNA methylation patterns in the opvAB regulatory region: (i) in the OpvABOFF state, GATC1 and GATC3 are non-methylated, whereas GATC2 and GATC4 are methylated; (ii) in the OpvABON state, GATC2 and GATC4 are non-methylated, whereas GATC1 and GATC3 are methylated. We provide evidence that such DNA methylation patterns are generated by OxyR binding. The higher stability of the OpvABOFF lineage may be caused by binding of OxyR to sites that are identical to the consensus (OBSA and OBSc), while the sites bound by OxyR in OpvABON cells (OBSB and OBSD) are not. In support of this view, amelioration of either OBSB or OBSD 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.

Cell Cycle Constraints and Environmental Control of Local DNA Hypomethylation in α-Proteobacteria

“…We also observed an increase (136% ± 6%) in activity of P 169* - lacZ relative to P 169 - lacZ in WT , while the activity of P 2901* - lacZ was decreased compared to P 2901 - lacZ . The mutations may alter the target sequence for other regulator(s) in addition to the methylation properties, thereby affecting transcription directly or indirectly in a positive or negative fashion [42, 43]. For example, P 2901 is bound by the master cell cycle regulator CtrA in vivo and the Δ mucR1/2 mutation is known to affect CtrA expression [17], whereas the P 169 promoter is affected by the phosphate starvation response (see below) [44, 45].…”

“…In bacteria local methylation changes may correlate with altered virulence behaviour and may underlie cell cycle-control in pathogens, endosymbionts or other microbial systems. Methylation is known to influence virulence functions in γ-proteobacteria, often by imposing bistability from phase-variable virulence promoters in subpopulations via transcriptional regulators such as Lrp, Fur or OxyR [5, 9, 42, 48, 51–55]. Phenotypic heterogeneity in antibiotic drug tolerance in vivo (a state known as persistence), which is acquired in a low fraction of bacterial cells, may also underlie epigenetic changes induced stochastically by methylation, either deterministically (during the cell cycle) or environmentally.…”

DNA Adenine Methyltransferase (Dam) Overexpression Impairs Photorhabdus luminescens Motility and Virulence

“…A differential expression of several genes encoding virulence factors such as pap, agn43, sci1 in E.coli (Blyn et al, 1990 ; Henderson and Owen, 1999 ; Brunet et al, 2011 ), but also gtr , or opvAB in Salmonella (Broadbent et al, 2010 ; Cota et al, 2016 ), is related to a differential methylation state of the GATC sites found in their respective promoters. This is caused mostly by differences in DNA affinity, depending on the DNA methylation state, of various transcriptional repressors (OxyR, Lrp, or Fur).…”

Drivers and sites of diversity in the DNA adenine methylomes of 93 Mycobacterium tuberculosis complex clinical isolates

“…When DNA methylation regulates gene expression, heterogeneous methylation creates multiple phenotypes within isogenic populations ( Casadesús and Low, 2013 ). This phenotypic plasticity aids rapid adaptation to changing environmental pressures ( Cota et al, 2016 ) and nutrient constraints ( Atack et al, 2018 ) for other bacteria. However, no study has examined heterogeneous methylation in M. tuberculosis .…”