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Prevalence of phase variable epigenetic invertons among host-associated bacteria

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posted on 2020-11-20, 11:17 authored by Xueting Huang, Juanjuan Wang, Jing Li, Yanni Liu, Xue Liu, Zeyao Li, Kurni Kurniyati, Yijie Deng, Guilin Wang, Joseph D Ralph, Megan De Ste Croix, Sara Escobar-Gonzalez, Richard J Roberts, Jan-Willem Veening, Xun Lan, Marco R Oggioni, Chunhao Li, Jing-Ren Zhang
Type I restriction-modification (R-M) systems consist of a DNA endonuclease (HsdR, HsdM and HsdS subunits) and methyltransferase (HsdM and HsdS subunits). The hsdS sequences flanked by inverted repeats (referred to as epigenetic invertons) in certain Type I R-M systems undergo invertase-catalyzed inversions. Previous studies in Streptococcus pneumoniae have shown that hsdS inversions within clonal populations produce subpopulations with profound differences in the methylome, cellular physiology and virulence. In this study, we bioinformatically identified six major clades of the tyrosine and serine family invertases homologs from 16 bacterial phyla, which potentially catalyze hsdS inversions in the epigenetic invertons. In particular, the epigenetic invertons are highly enriched in host-associated bacteria. We further verified hsdS inversions in the Type I R-M systems of four representative host-associated bacteria and found that each of the resultant hsdS allelic variants specifies methylation of a unique DNA sequence. In addition, transcriptome analysis revealed that hsdS allelic variations in Enterococcus faecalis exert significant impact on gene expression. These findings indicate that epigenetic switches driven by invertases in the epigenetic invertons broadly operate in the host-associated bacteria, which may broadly contribute to bacterial host adaptation and virulence beyond the role of the Type I R-M systems against phage infection.

History

Citation

Nucleic Acids Research, Volume 48, Issue 20, 18 November 2020, Pages 11468–11485, https://doi.org/10.1093/nar/gkaa907

Author affiliation

Department of Genetics and Genome Biology

Version

  • VoR (Version of Record)

Published in

Nucleic Acids Research

Volume

48

Issue

20

Pagination

11468-11485

Publisher

Oxford University Press (OUP)

issn

0305-1048

eissn

1362-4962

Acceptance date

2020-10-23

Copyright date

2020

Available date

2020-10-29

Language

en

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