Lineage-Specific Methyltransferases Define the Methylome of the Globally Disseminated Escherichia coli ST131 Clone.

Brian M Forde,Scott A Beatson,Wai-Fong Yin,Mark A Schembri,Mathew Upton,Teik Min Chong,Melinda M Ashcroft,Kok-Gan Chan,Minh-Duy Phan,Kate M Peters,Mitchell Stanton-Cook,Jayde A Gawthorne,Sohinee Sarkar,Vanessa Sperandio

doi:10.1128/mbio.01602-15

Brian M Forde, Scott A Beatson + Show 12 more

Open Access

https://doi.org/10.1128/mbio.01602-15

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Abstract

ABSTRACTEscherichia coli sequence type 131 (ST131) is a clone of uropathogenic E. coli that has emerged rapidly and disseminated globally in both clinical and community settings. Members of the ST131 lineage from across the globe have been comprehensively characterized in terms of antibiotic resistance, virulence potential, and pathogenicity, but to date nothing is known about the methylome of these important human pathogens. Here we used single-molecule real-time (SMRT) PacBio sequencing to determine the methylome of E. coli EC958, the most-well-characterized completely sequenced ST131 strain. Our analysis of 52,081 methylated adenines in the genome of EC958 discovered three m6A methylation motifs that have not been described previously. Subsequent SMRT sequencing of isogenic knockout mutants identified the two type I methyltransferases (MTases) and one type IIG MTase responsible for m6A methylation of novel recognition sites. Although both type I sites were rare, the type IIG sites accounted for more than 12% of all methylated adenines in EC958. Analysis of the distribution of MTase genes across 95 ST131 genomes revealed their prevalence is highly conserved within the ST131 lineage, with most variation due to the presence or absence of mobile genetic elements on which individual MTase genes are located.

Highlights

Escherichia coli sequence type 131 (ST131) is a clone of uropathogenic E. coli that has emerged rapidly and disseminated globally in both clinical and community settings
Clinical evidence suggests that some ST131 pathogens are highly virulent [7], and the EC958 genome contains a number of genes that are associated with pathogenicity, including those coding for adhesins, autotransporter proteins, and siderophore receptors [1, 8]
Subsequent single-molecule real-time (SMRT) sequencing of three EC958 knockout mutants allowed us to unequivocally assign three novel m6A modification recognition motifs to their cognate MTases: AACN4CTTT, RTACN4GTG, and CANCATC were matched to M.EcoMII, M.EcoMIII, and M.EcoMVII, respectively

Summary

Introduction

Escherichia coli sequence type 131 (ST131) is a clone of uropathogenic E. coli that has emerged rapidly and disseminated globally in both clinical and community settings. Methylation of specific bases may impart additional epigenetic information that has the potential to act as a signal for genome defense, initiation of chromosome replication and repair, nucleoid segregation, regulation of gene expression, and transposition control [12]. In their simplest form, R-M systems are comprised of an MTase that catalyzes the transfer of a methyl group from an S-adenosylmethionine (SAM) donor and its cognate REase that cleaves unmethylated DNA at internal phosphodiester bonds in the DNA backbone [16]

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