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PLoS One. 2015 Apr 10;10(4):e0123639. doi: 10.1371/journal.pone.0123639. eCollection 2015.

Genome-wide methylation patterns in Salmonella enterica Subsp. enterica Serovars.

Author information

1
Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America.
2
New England Biolabs, Ipswich, Massachusetts, United States of America.
3
Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America.
4
Pacific Biosciences, Menlo Park, California, United States of America.

Abstract

The methylation of DNA bases plays an important role in numerous biological processes including development, gene expression, and DNA replication. Salmonella is an important foodborne pathogen, and methylation in Salmonella is implicated in virulence. Using single molecule real-time (SMRT) DNA-sequencing, we sequenced and assembled the complete genomes of eleven Salmonella enterica isolates from nine different serovars, and analysed the whole-genome methylation patterns of each genome. We describe 16 distinct N6-methyladenine (m6A) methylated motifs, one N4-methylcytosine (m4C) motif, and one combined m6A-m4C motif. Eight of these motifs are novel, i.e., they have not been previously described. We also identified the methyltransferases (MTases) associated with 13 of the motifs. Some motifs are conserved across all Salmonella serovars tested, while others were found only in a subset of serovars. Eight of the nine serovars contained a unique methylated motif that was not found in any other serovar (most of these motifs were part of Type I restriction modification systems), indicating the high diversity of methylation patterns present in Salmonella.

PMID:
25860355
PMCID:
PMC4393132
DOI:
10.1371/journal.pone.0123639
[Indexed for MEDLINE]
Free PMC Article
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