Xenogeneic Silencer MvaT Differs in its DNA Binding Mechanism from Family Members H-NS and Lsr2

Xenogeneic silencers (H-NS, Lsr2 and MvaT) facilitate bacterial evolution through the cryptic maintenance of horizontally acquired genes, binding and transcriptionally silencing DNA that is more AT-rich than the resident genome. H-NS and Lsr2 employ an AT-hook motif to recognize and bind AT-rich DNA targets. MvaT lacks this motif. Structural data suggested a KGGN motif may act as an analogous AT-hook. In vitro electrophoretic mobility shift assays found that double mutant MvaT K97A/N100A had similar DNA binding affinity and discrimination for target (AT-rich DNA) compared to wild type. Competitive gel shifts also found that while MvaT bound GC-rich and AT-rich DNA with comparable affinities, MvaT greatly prefers ATrich DNA. We present a model where, within the oligomer, individual binding domains bind tightly to AT-rich DNA and loosely to GC-rich DNA. Together these data suggest that MvaT binds DNA through a novel mechanism dissimilar to xenogeneic silencing family members HNS and Lsr2.