DNA sequence repeats identify numerous Type I restriction‐modification systems that are potential epigenetic regulators controlling phase‐variable regulons; phasevarions

Abstract

Over recent years several examples of randomly switching methyltransferases, associated with Type III restriction-modification (R-M) systems, have been described in pathogenic bacteria. In every case examined, changes in simple DNA sequence repeats result in variable methyltransferase expression and result in global changes in gene expression, and differentiation of the bacterial cell into distinct phenotypes.These epigenetic regulatory systems are called phasevarions, phase-variable regulons, and are widespread in bacteria, with 17.4% of Type III R-M system containing simple DNA sequence repeats. A distinct, recombination-driven random switching system has also been described in Streptococci in Type I R-M systems that also regulate gene expression. Here, we interrogate the most extensive and well-curated database of R-M systems, REBASE, by searching for all possible simple DNA sequence repeats in the hsdRMS genes that encode Type I R-M systems. We report that 7.9% of hsdS, 2% of hsdM, and of 4.3% of hsdR genes contain simple sequence repeats that are capable of mediating phase variation. Phase variation of both hsdM and hsdS genes will lead to differential methyltransferase expression or specificity, and thereby the potential to control phasevarions. These data suggest that in addition to well characterized phasevarions controlled by Type III mod genes, and the previously described Streptococcal Type I R-M systems that switch via recombination, approximately 10% of all Type I R-M systems surveyed herein have independently evolved the ability to randomly switch expression via simple DNA sequence repeats. K E Y W O R D Sbacterial pathogenesis, epigenetics, phase variation, phasevarion, R-M systems | 1039 ATACK eT Al.

Systematic Analysis of REBASE Identifies Numerous Type I Restriction-Modification Systems with Duplicated, Distinct hsdS Specificity Genes That Can Switch System Specificity by Recombination

“…Our systematic analysis of REBASE identified Type I loci containing multiple hsdS genes where we detect IRs in a range of commensal organisms, such as Bacteroides fragilis and multiple Ruminococcus species, in environmental bacterial species such as Leuconostoc mesenteroides and in a number of Lactobacillus species that are important to the biotechnology and food production industries (Data Set S3). This reflects our previous studies where we observed simple sequence repeats that mediate phase variation in multiple Type I (14) and Type III methyltransferase genes (13) present in a variety of commensal and environmental organisms.…”

“…A broad range of bacterial species encode these systems. Our previous work showed that 2% of Type I hsdM and 7.9% of Type I hsdS genes contain SSRs (14). Together with our findings in this study, this means that 13.8% of all Type I systems are capable of phase-variable expression.…”

“…Many of the veterinary pathogens that we show contain inverting Type I loci also contain separate, distinct Type III or Type I R-M systems that are capable of phase varying via changes in locus located simple sequence repeats. These species include Actinobacillus pleuropneumoniae , Mannheimia haemolytica , Streptococcus suis , Glaesserella ( Haemophilus ) parasuis , and multiple Mycoplasma species ( 13 , 14 ). This means that all of these veterinary pathogens have evolved phase variation of both Type I and Type III methyltransferases, and in the case of Type I systems, by both SSR tract length changes ( 14 ) and by recombination between variable hsdS genes containing IRs (this study).…”

“…These species include Actinobacillus pleuropneumoniae , Mannheimia haemolytica , Streptococcus suis , Glaesserella ( Haemophilus ) parasuis , and multiple Mycoplasma species ( 13 , 14 ). This means that all of these veterinary pathogens have evolved phase variation of both Type I and Type III methyltransferases, and in the case of Type I systems, by both SSR tract length changes ( 14 ) and by recombination between variable hsdS genes containing IRs (this study). For example, A. pleuropneumoniae encodes two distinct Type III methyltransferase ( mod ) genes containing simple sequence repeats ( 13 ), and a Type I system containing variable hsdS loci where IRs are present (this study; Fig.…”

“…Several bacterial pathogens also contain well-characterized cytoplasmic N 6 -adenine DNA methyltransferases, which are part of restriction-modification (R-M) systems, that exhibit phase-variable expression. We recently characterized the distribution of SSR tracts in Type III mod genes and Type I hsdS , hsdM , and hsdR genes in the REBASE database of R-M systems, and we demonstrated that 17.4% of all Type III mod genes ( 13 ) and 10% of all Type I R-M systems contain SSRs that are capable of undergoing phase-variable expression ( 14 ). Phase variation of methyltransferase expression leads to genome-wide methylation differences, which can result in differential regulation of multiple genes in systems known as phasevarions ( phase-vari able regul on ).…”