Abstract
Campylobacter jejuni is a major cause of foodborne gastroenteritis worldwide inflicting palpable socioeconomic costs. The ability of this pathogen to successfully infect its hosts is determined not only by the presence of specific virulence genes but also by the pathogen’s capacity to appropriately regulate those virulence genes. Therefore, DNA methylation can play a critical role in both aspects of this process because it serves as both a means to protect the integrity of the cellular DNA from invasion and as a mechanism to control transcriptional regulation within the cell. In the present study we report the comparative methylome data of C. jejuni YH002, a multidrug resistant strain isolated from retail beef liver. Investigation into the methylome identified a putative novel motif (CGCGA) of a type II restriction-modification (RM) system. Comparison of methylomes of the strain to well-studied C. jejuni strains highlighted non-uniform methylation patterns among the strains though the existence of the typical type I and type IV RM systems were also observed. Additional investigations into the existence of DNA methylation sites within gene promoters, which may ultimately result in altered levels of transcription, revealed several virulence genes putatively regulated using this mode of action. Of those identified, a flagella gene (flhB), a RNA polymerase sigma factor (rpoN), a capsular polysaccharide export protein (kpsD), and a multidrug efflux pump were highly notable.
Highlights
Campylobacteriosis is one of the most frequently acquired bacterial infections associated with the consumption of contaminated foods
DNA methylation is a base modification system that is catalyzed by methyltransferases and results in the formation of the following: C5-Methyl-cytosine (m5C), N6-methyl-adenine (m6A), and N4methyl-cytosine (m4C) (Sanchez-Romero et al, 2015)
Because generating motifs using the default settings in the modification analysis of the Single Molecule Real Time (SMRT) sequencing platform might not be ideal in all cases for motif identification (Methylome-Analysis-Technical-Note)5, we undertook a comparative analysis with various modification QV cut-off values ranging from 30 to 200
Summary
Campylobacteriosis is one of the most frequently acquired bacterial infections associated with the consumption of contaminated foods. Sequence-based methods are commonly used to identify bacterial virulence factors and as bioinformatic approaches advance, the frequency of utilizing comparative genomic analyses to identify genes involved with virulence continues to rise. Such analyses have already led to the identification of the pVir plasmid in Campylobacter jejuni (Bacon et al, 2002). DNA methylation is a base modification system that is catalyzed by methyltransferases and results in the formation of the following: C5-Methyl-cytosine (m5C), N6-methyl-adenine (m6A), and N4methyl-cytosine (m4C) (Sanchez-Romero et al, 2015) These modified bases enable the cell to identify and eliminate foreign DNA via the bacterial restriction-modification (RM) system, which has been shown to cleave double stranded DNA fragments. RM systems are common amongst bacteria with all four classes of RM systems (types I–IV) having been identified in C. jejuni
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