Comparative genomics reveals the diversity of restriction-modification systems and DNA methylation sites in Listeria monocytogenes

Poyin Chen, Henk C. Den Bakker, Jonas Korlach, Nguyet Kong, Dylan B. Storey, Ellen E. Paxinos, Meredith Ashby, Tyson Clark, Khai Luong, Martin Wiedmann, Bart C Weimer

Research output: Contribution to journalArticle

9 Scopus citations

Abstract

Listeria monocytogenes is a bacterial pathogen that is found in a wide variety of anthropogenic and natural environments. Genome sequencing technologies are rapidly becoming a powerful tool in facilitating our understanding of how genotype, classification phenotypes, and virulence phenotypes interact to predict the health risks of individual bacterial isolates. Currently, 57 closed L. monocytogenes genomes are publicly available, representing three of the four phylogenetic lineages, and they suggest that L. monocytogenes has high genomic synteny. This study contributes an additional 15 closed L. monocytogenes genomes that were used to determine the associations between the genome and methylome with host invasion magnitude. In contrast to previous findings, large chromosomal inversions and rearrangements were detected in five isolates at the chromosome terminus and within rRNA genes, including a previously undescribed inversion within rRNA-encoding regions. Each isolate's epigenome contained highly diverse methyltransferase recognition sites, even within the same serotype and methylation pattern. Eleven strains contained a single chromosomally encoded methyltransferase, one strain contained two methylation systems (one system on a plasmid), and three strains exhibited no methylation, despite the occurrence of methyltransferase genes. In three isolates a new, unknown DNA modification was observed in addition to diverse methylation patterns, accompanied by a novel methylation system. Neither chromosome rearrangement nor strain-specific patterns of epigenome modification observed within virulence genes were correlated with serotype designation, clonal complex, or in vitro infectivity. These data suggest that genome diversity is larger than previously considered in L. monocytogenes and that as more genomes are sequenced, additional structure and methylation novelty will be observed in this organism.

Original languageEnglish (US)
Article numbere02091-16
JournalApplied and Environmental Microbiology
Volume83
Issue number3
DOIs
StatePublished - 2017

Keywords

  • 100K Pathogen Genome Project
  • Bacterial epigenetics
  • DNA methylation
  • Genetic epidemiology
  • Genome analysis
  • Infection
  • Inversion
  • L. monocytogenes
  • Listeria
  • Methylation
  • SMRT sequencing
  • Virulence regulation

ASJC Scopus subject areas

  • Biotechnology
  • Food Science
  • Applied Microbiology and Biotechnology
  • Ecology

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    Chen, P., Den Bakker, H. C., Korlach, J., Kong, N., Storey, D. B., Paxinos, E. E., Ashby, M., Clark, T., Luong, K., Wiedmann, M., & Weimer, B. C. (2017). Comparative genomics reveals the diversity of restriction-modification systems and DNA methylation sites in Listeria monocytogenes. Applied and Environmental Microbiology, 83(3), [e02091-16]. https://doi.org/10.1128/AEM.02091-16