title: SMRT sequencing of the Campylobacter coli BfR-CA-9557 genome sequence reveals unique methylation motifs.
abstract: BACKGROUND
  Campylobacter species are the most prevalent bacterial pathogen causing acute enteritis worldwide. In contrast to Campylobacter jejuni, about 5 % of Campylobacter coli strains exhibit susceptibility to restriction endonuclease digestion by DpnI cutting specifically 5'-G(m)ATC-3' motifs. This indicates significant differences in DNA methylation between both microbial species. The goal of the study was to analyze the methylome of a C. coli strain susceptible to DpnI digestion, to identify its methylation motifs and restriction modification systems (RM-systems), and compare them to related organisms like C. jejuni and Helicobacter pylori.
  
  
  RESULTS
  Using one SMRT cell and the PacBio RS sequencing technology followed by PacBio Modification and Motif Analysis the complete genome of the DpnI susceptible strain C. coli BfR-CA-9557 was sequenced to 500-fold coverage and assembled into a single contig of 1.7 Mbp. The genome contains a CJIE1-like element prophage and is phylogenetically closer to C. coli clade 1 isolates than clade 3. 45,881 6-methylated adenines (ca. 2.7 % of genome positions) that are predominantly arranged in eight different methylation motifs and 1,788 4-methylated cytosines (ca. 0.1 %) have been detected. Only two of these motifs correspond to known restriction modification motifs. Characteristic for this methylome was the very high fraction of methylation of motifs with mostly above 99 %.
  
  
  CONCLUSIONS
  Only five dominant methylation motifs have been identified in C. jejuni, which have been associated with known RM-systems. C. coli BFR-CA-9557 shares one (RAATTY) of these, but four ORFs could be assigned to putative Type I RM-systems, seven ORFs to Type II RM-systems and three ORFs to Type IV RM-systems. In accordance with DpnI prescreening RM-system IIP, methylation of GATC motifs was detected in C. coli BfR-CA-9557. A homologous IIP RM-system has been described for H. pylori. The remaining methylation motifs are specific for C. coli BfR-CA-9557 and have been neither detected in C. jejuni nor in H. pylori. The results of this study give us new insights into epigenetics of Campylobacteraceae and provide the groundwork to resolve the function of RM-systems in C. coli.
authors.affiliation: Institute for Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, D-37075, Göttingen, Germany. azautne@gwdg.de.
authors.forename: Andreas E
authors.initials: AE
authors.lastname: Zautner
authors.affiliation: Institute for Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, D-37075, Göttingen, Germany.
authors.forename: Anne-Marie
authors.initials: AM
authors.lastname: Goldschmidt
authors.affiliation: Institute for Microbiology and Genetics, Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany.
authors.forename: Andrea
authors.initials: A
authors.lastname: Thürmer
authors.affiliation: Institute for Microbiology and Genetics, Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany.
authors.forename: Jörg
authors.initials: J
authors.lastname: Schuldes
authors.affiliation: Institute for Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, D-37075, Göttingen, Germany.
authors.forename: Oliver
authors.initials: O
authors.lastname: Bader
authors.affiliation: Institute for Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, D-37075, Göttingen, Germany.
authors.forename: Raimond
authors.initials: R
authors.lastname: Lugert
authors.affiliation: Institute for Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, D-37075, Göttingen, Germany.
authors.forename: Uwe
authors.initials: U
authors.lastname: Groß
authors.affiliation: Federal Institute for Risk Assessment (BfR), Department of Biological Safety - National Reference Laboratory for Campylobacter, D-12277, Berlin, Germany.
authors.forename: Kerstin
authors.initials: K
authors.lastname: Stingl
authors.affiliation: Microarray and Deep-Sequencing Core Facility, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, D-37077, Göttingen, Germany.
authors.forename: Gabriela
authors.initials: G
authors.lastname: Salinas
authors.affiliation: Microarray and Deep-Sequencing Core Facility, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, D-37077, Göttingen, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Lingner
mesh_terms: D017000:Campylobacter coli / Q000145:classification / Q000235:genetics*; D019175:DNA Methylation; D015252:Deoxyribonucleases, Type II Site-Specific / Q000378:metabolism; D044127:Epigenesis, Genetic; D016680:Genome, Bacterial; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: C020102:endodeoxyribonuclease DpnI; D015252:Deoxyribonucleases, Type II Site-Specific