DNA Inversion Regulates Outer Membrane Vesicle Production in Bacteroides fragilis

Abstract

Phase changes in Bacteroides fragilis, a member of the human colonic microbiota, mediate variations in a vast array of cell surface molecules, such as capsular polysaccharides and outer membrane proteins through DNA inversion. The results of the present study show that outer membrane vesicle (OMV) formation in this anaerobe is also controlled by DNA inversions at two distantly localized promoters, IVp-I and IVp-II that are associated with extracellular polysaccharide biosynthesis and the expression of outer membrane proteins. These promoter inversions are mediated by a single tyrosine recombinase encoded by BF2766 (orthologous to tsr19 in strain NCTC9343) in B. fragilis YCH46, which is located near IVp-I. A series of BF2766 mutants were constructed in which the two promoters were locked in different configurations (IVp-I/IVp-II = ON/ON, OFF/OFF, ON/OFF or OFF/ON). ON/ON B. fragilis mutants exhibited hypervesiculating, whereas the other mutants formed only a trace amount of OMVs. The hypervesiculating ON/ON mutants showed higher resistance to treatment with bile, LL-37, and human β-defensin 2. Incubation of wild-type cells with 5% bile increased the population of cells with the ON/ON genotype. These results indicate that B. fragilis regulates the formation of OMVs through DNA inversions at two distantly related promoter regions in response to membrane stress, although the mechanism underlying the interplay between the two regions controlled by the invertible promoters remains unknown.

Long-term persistence of crAss-like phage crAss001 is associated with phase variation inBacteroides intestinalis

“…Genome plasticity, extensive regulation of gene expression and high adaptability to changes in their environment are characteristic features of this bacterial group (35). Phase variation of surface structures resulting from DNA inversions catalysed by serine and tyrosine recombinases has been implicated as an important mechanism in Bacteroides for adaptation to environmental change, improved fitness, and efficient colonisation of the mammalian gut (20,24,(36)(37)(38). Recently, phase variation of multiple surface structures including CPS, S-layer lipoproteins, TonB-dependent nutrient receptors and OmpA-like proteins, has also been implicated in dynamic switching of diverse phage resistance/sensitivity patterns in B. thetaiotaomicron (14).…”

Molecular Mechanisms of hsdS Inversions in the cod Locus of Streptococcus pneumoniae

“…In the context of the "diphasic salmonella" observation (9), Zieg et al discovered that the Hin recombinase reversibly switches the orientation of the flagellin promoter by DNA inversions and thereby the transcription of two flagellin genes, resulting in alternate switch in the biochemical and antigenic characteristics of the flagellum (8,10). DNA inversions have since been reported to drive phase variation in surface-associated polysaccharide and/or protein antigens of Bacteroides fragilis (11)(12)(13)(14)(15), Campylobacter fetus (16), Clostridium difficile (17), Dichelobacter nodosus (18), Escherichia coli (19)(20)(21), Proteus mirabilis (22,23), and Mycoplasma species (24)(25)(26)(27)(28). Promoter inversion is also a common strategy for alternate expression of tail fiber proteins by bacterial phages, which enables the phages to adsorb to multiple bacterial hosts, and thereby broadens the phage host range (10).…”

Shining Light on Human Gut Bacteriophages

“…It occurs by variable expression of gene loci due to hypermutation or methylation resulting in genes being reversibly switched “on or off” (Bayliss, 2009 ). This is mediated by recombinases, integrases or invertases that act on invertible regions containing promotors of gene loci often associated with expression of surface features such as Sus-like systems, capsule polysaccharides, S-layer and Ton-dependent transporters which can act as phage receptors, outer membrane vesicles, flagella or restriction modification systems (Zaleski et al, 2005 ; Coward et al, 2006 ; Nakayama-Imaohji et al, 2009 , 2016 ; Zitomersky et al, 2011 ; Porter et al, 2020 ). These phenotypic switches allow the host to adapt to environmental stresses, which are abundant in the human gut, while minimizing the fitness impact on the total population (Moxon et al, 1994 ).…”