A comparative analysis of methylome profiles of Campylobacter jejuni sheep abortion isolate and gastroenteric strains using PacBio data

Abstract

Campylobacter jejuni is a leading cause of human gastrointestinal disease and small ruminant abortions in the United States. The recent emergence of a highly virulent, tetracycline-resistant C. jejuni subsp. jejuni sheep abortion clone (clone SA) in the United States, and that strain's association with human disease, has resulted in a heightened awareness of the zoonotic potential of this organism. Pacific Biosciences' Single Molecule, Real-Time sequencing technology was used to explore the variation in the genome-wide methylation patterns of the abortifacient clone SA (IA3902) and phenotypically distinct gastrointestinal-specific C. jejuni strains (NCTC 11168 and 81-176). Several notable differences were discovered that distinguished the methylome of IA3902 from that of 11168 and 81-176: identification of motifs novel to IA3902, genome-specific hypo- and hypermethylated regions, strain level variability in genes methylated, and differences in the types of methylation motifs present in each strain. These observations suggest a possible role of methylation in the contrasting disease presentations of these three C. jejuni strains. In addition, the methylation profiles between IA3902 and a luxS mutant were explored to determine if variations in methylation patterns could be identified that might explain the role of LuxS-dependent methyl recycling in IA3902 abortifacient potential.

Keywords: Campylobacter jejuni; LuxS; methylation; methylome; quorum sensing.

Figure 1

Distinct areas of hyper- and hypomethylation in the whole-genome methylome plot of IA3902. Distribution plots of all motifs are combined per 1 kb across the genome. Gray arrows indicate hypermethylated areas, which have methylation frequencies of at least 45 and higher. Asterisks indicate major hypomethylated regions, which contain several adjacent bins with methylation frequencies of 4 or less. Black arrows indicate origin of replication (oriC) sites.

Figure 2

Circos plot displaying the distributions of each motif across the genome of IA3902.

Figure 3

Distinct areas of hyper- and hypomethylation in the whole-genome methylome plot of 11168. Distribution plots of all motifs are combined per 1 kb across the genome. Gray arrows indicate hypermethylated areas, which have methylation frequencies of at least 41 and higher. Asterisks indicate major hypomethylated regions, which contain several adjacent bins with methylation frequencies of 4 or less. Black arrows indicate origin of replication (oriC) sites.

Figure 4

Distinct areas of hyper- and hypomethylation in the whole-genome methylome plot of 81-176. Distribution plots of all motifs are combined per 1 kb across the genome. Gray arrows indicate hypermethylated areas, which have methylation frequencies of at least 41 and higher. Asterisks indicate major hypomethylated regions, which contain several adjacent bins with methylation frequencies of 4 or less. Black arrows indicate origin of replication (oriC) sites.

Figure 5

Detection of N6-methyladenine (m6A) base modification in both IA3902 strains. The following kinetic score distributions show significantly higher numbers of adenine residues above the background in IA3902 wildtype (A) and luxS mutant (B). This indicates that the only type of base modification in the wildtype and luxS mutant is m6A.