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PLoS One. 2016 Aug 24;11(8):e0161499. doi: 10.1371/journal.pone.0161499. eCollection 2016.

Comparative Methylome Analysis of the Occasional Ruminant Respiratory Pathogen Bibersteinia trehalosi.

Author information

1
New England Biolabs, Ipswich, Massachusetts, United States of America.
2
USDA-ARS U.S. Meat Animal Research Center, Clay Center, Nebraska, United States of America.
3
Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany.

Abstract

We examined and compared both the methylomes and the modification-related gene content of four sequenced strains of Bibersteinia trehalosi isolated from the nasopharyngeal tracts of Nebraska cattle with symptoms of bovine respiratory disease complex. The methylation patterns and the encoded DNA methyltransferase (MTase) gene sets were different between each strain, with the only common pattern being that of Dam (GATC). Among the observed patterns were three novel motifs attributable to Type I restriction-modification systems. In some cases the differences in methylation patterns corresponded to the gain or loss of MTase genes, or to recombination at target recognition domains that resulted in changes of enzyme specificity. However, in other cases the differences could be attributed to differential expression of the same MTase gene across strains. The most obvious regulatory mechanism responsible for these differences was slipped strand mispairing within short sequence repeat regions. The combined action of these evolutionary forces allows for alteration of different parts of the methylome at different time scales. We hypothesize that pleiotropic transcriptional modulation resulting from the observed methylomic changes may be involved with the switch between the commensal and pathogenic states of this common member of ruminant microflora.

PMID:
27556252
PMCID:
PMC4996451
DOI:
10.1371/journal.pone.0161499
[Indexed for MEDLINE]
Free PMC Article

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