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

John M Atack,Patrick J Blackall,Michael P Jennings,Long Yang,Yaoqi Zhou,Chengying Guo,Thomas Litfin,Mark J Mandel

doi:10.1128/msystems.00497-20

John M Atack, Patrick J Blackall + Show 6 more

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https://doi.org/10.1128/msystems.00497-20

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Abstract

N 6-Adenine DNA methyltransferases associated with some Type I and Type III restriction-modification (R-M) systems are able to undergo phase variation, randomly switching expression ON or OFF by varying the length of locus-encoded simple sequence repeats (SSRs). This variation of methyltransferase expression results in genome-wide methylation differences and global changes in gene expression. These epigenetic regulatory systems are called phasevarions, phase-variable regulons, and are widespread in bacteria. A distinct switching system has also been described in Type I R-M systems, based on recombination-driven changes in hsdS genes, which dictate the DNA target site. In order to determine the prevalence of recombination-driven phasevarions, we generated a program called RecombinationRepeatSearch to interrogate REBASE and identify the presence and number of inverted repeats of hsdS downstream of Type I R-M loci. We report that 3.9% of Type I R-M systems have duplicated variable hsdS genes containing inverted repeats capable of phase variation. We report the presence of these systems in the major pathogens Enterococcus faecalis and Listeria monocytogenes, which could have important implications for pathogenesis and vaccine development. These data suggest that in addition to SSR-driven phasevarions, many bacteria have independently evolved phase-variable Type I R-M systems via recombination between multiple, variable hsdS genes.IMPORTANCE Many bacterial species contain DNA methyltransferases that have random on/off switching of expression. These systems, called phasevarions (phase-variable regulons), control the expression of multiple genes by global methylation changes. In every previously characterized phasevarion, genes involved in pathobiology, antibiotic resistance, and potential vaccine candidates are randomly varied in their expression, commensurate with methyltransferase switching. Our systematic study to determine the extent of phasevarions controlled by invertible Type I R-M systems will provide valuable information for understanding how bacteria regulate genes and is key to the study of physiology, virulence, and vaccine development; therefore, it is critical to identify and characterize phase-variable methyltransferases controlling phasevarions.

Highlights

IMPORTANCE Many bacterial species contain DNA methyltransferases that have random on/off switching of expression
We recently characterized the distribution of simple sequence repeats (SSRs) 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]
We have recently demonstrated that almost 10% of Type I R-M systems contain SSRs and can potentially undergo phase variation, phase-variable expression of Type I R-M systems has as yet only been demonstrated in two species: an hsdM gene switches ON-OFF via SSRs changes in nontypeable H. influenzae (NTHi) [7, 23] and an hsdS gene phase varies due to SSRs alterations in N. gonorrhoeae [24]

Summary

Introduction

IMPORTANCE Many bacterial species contain DNA methyltransferases that have random on/off switching of expression. Type I hsdS genes can undergo phase-variation by recombination between inverted repeats (IRs) encoded in multiple distinct copies of hsdS genes encoded in the Type I R-M locus (25; reviewed in reference 26) (Fig. 1). The first example of a phasevarion controlled by an inverting Type I R-M system was described in the major human pathogen Streptococcus pneumoniae strain D39 [25], and subsequent studies have been conducted in strain TIGR4 [30] This system contains multiple variable hsdS loci with inverted repeats and a locus-encoded recombinase and switches between six alternate HsdS proteins that encode six different methyltransferase specificities [25] and control six different phasevarions. We carried out a systematic study of the “gold standard” restriction enzyme database REBASE using a purpose-designed program to systematically identify IRs in hsdS genes in order to determine the prevalence of inverting Type I systems in the bacterial domain

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