Diversity within the Campylobacter jejuni type I restriction–modification loci

Abstract

The type I restriction–modification (hsd) systems of 73 Campylobacter jejuni strains were characterized according to their DNA and amino acid sequences, and/or gene organization. A number of new genes were identified which are not present in the sequenced strain NCTC 11168. The closely related organism Helicobacter pylori has three type I systems; however, no evidence was found that C. jejuni strains contain multiple type I systems, although hsd loci are present in at least two different chromosomal locations. Also, unlike H. pylori, intervening ORFs are present, in some strains, between hsdR and hsdS and between hsdS and hsdM. No definitive function can be ascribed to these ORFs, designated here as rloA–H (R-linked ORF) and mloA–B (M-linked ORF). Based on parsimony analysis of amino acid sequences to assess character relatedness, the C. jejuni type I R–M systems are assigned to one of three families: ‘IAB’, ‘IC’ or ‘IF’. This study confirms that HsdM proteins within a family are highly conserved but share little homology with HsdM proteins from other families. The ‘IC’ hsd loci are >99 % identical at the nucleotide level, as are the ‘IF’ hsd loci. Additionally, whereas the nucleotide sequences of the ‘IAB’ hsdR and hsdM genes show a high degree of similarity, the nucleotide sequences of the ‘IAB’ hsdS and rlo genes vary considerably. This diversity suggests that recombination between ‘IAB’ hsd loci would lead not only to new hsdS alleles but also to the exchange of rlo genes; five C. jejuni hsd loci are presumably the result of such recombination. The importance of these findings with regard to the evolution of C. jejuni type I R–M systems is discussed.

Inconsistency of Phenotypic and Genomic Characteristics of Campylobacter fetus Subspecies Requires Reevaluation of Current Diagnostics

“…Three of the closed C. fetus genomes, of strains 84-112, 97/608, and 03/293, contained a type I restriction modification (RM) system. This type I RM system consists of hsd genes with intervening ORFs, similar to the type I RM systems described for C. jejuni (14). The complete type I RM system is found only in C. fetus strains belonging to core genome cluster A ( Table 2).…”

Identification of host-associated alleles by multilocus sequence typing of Campylobacter coli strains from food animals

“…Genomic DNA from NCSU strains was prepared using the Qiagen DNeasy tissue kit using the protocol recommended by the manufacturer. Genomic DNA from NADC strains was prepared as described previously (Miller et al, 2005b).…”

Role of the Campylobacter jejuni Cj1461 DNA Methyltransferase in Regulating Virulence Characteristics

“…Cj1461 has the conserved domain FGG (S-adenosyl methionine [SAM] binding site) and the DNA MTase active-site motif LYLDPPF (Prosite motif PS00092), which are signatures of N 6 -adenine-specific DNA methylases. No endonuclease-encoding gene is found adjacent to the cj1461 gene, suggesting that it is not part of an R-M system (24).…”