Analysis of the Campylobacter jejuni Genome by SMRT DNA Sequencing Identifies Restriction-Modification Motifs

Campylobacter jejuni is a leading bacterial cause of human gastroenteritis. The goal of this study was to analyze the C. jejuni F38011 strain, recovered from an individual with severe enteritis, at a genomic and proteomic level to gain insight into microbial processes. The C. jejuni F38011 genome is comprised of 1,691,939 bp, with a mol.% (G+C) content of 30.5%. PacBio sequencing coupled with REBASE analysis was used to predict C. jejuni F38011 genomic sites and enzymes that may be involved in DNA restriction-modification. A total of five putative methylation motifs were identified as well as the C. jejuni enzymes that could be responsible for the modifications. Peptides corresponding to the deduced amino acid sequence of the C. jejuni enzymes were identified using proteomics. This work sets the stage for studies to dissect the precise functions of the C. jejuni putative restriction-modification enzymes. Taken together, the data generated in this study contributes to our knowledge of the genomic content, methylation profile, and encoding capacity of C. jejuni.


Introduction
Campylobacter jejuni is an important pathogen causing significant morbidity and mortality. C. jejuni is a Gram-negative, comma-shaped, microaerophilic bacterium, and is motile by means of unipolar or bipolar flagella. The genus Campylobacter was proposed in 1963, separating these bacteria from Vibrio-like organisms based on morphology, DNA composition, microaerobic growth requirement, and non-fermentive metabolism [1]. C. jejuni was first isolated from human feces in 1972 [2]. Human infection, also called campylobacteriosis, often occurs after handling or ingesting food contaminated by raw poultry products. Clinical infection with C. jejuni presents as diarrhea with blood and leukocytes, fever, nausea, and severe abdominal cramps that occur 2-5 days following ingestion [3,4]. In recent years, infection rates with Campylobacter spp. has been comparable to or has exceeded that of other enteric pathogens, including Salmonella spp. and Shigella spp. The highest prevalence of Campylobacter-mediated disease is among children less than The C. jejuni F38011 strain was isolated from an individual with bloody diarrhea. C. jejuni F38011 strain has been shown to efficiently colonize chickens and cause disease in piglets and mice [17][18][19]. To better understand the genomic content and proteomic capacity of this strain compared to other C. jejuni strains, we have sequenced the genome and determined the proteome of the C. jejuni F38011 strain using Pacific Biosciences (PacBio) Single-Molecule Real-Time (SMRT) sequencing technology and LC-MS/MS, respectively. The results of this study demonstrate that the use of new technologies can illuminate differences between genomes and possibly uncover unique features.

Bacterial strains and growth conditions
The C. jejuni F38011 clinical strain was used throughout this study. The strain was cultured under microaerobic conditions (85% N 2 , 10% CO 2 , 5% O 2 ) on Mueller-Hinton (MH) agar plates supplemented with 5% citrated bovine blood (MHB) at 37°C and passaged to a fresh plate at least once every 48 h. These conditions are optimal for C. jejuni growth. Assays were performed with C. jejuni grown on MH agar plates for 48 h and diluted in PBS.
The C. jejuni F38011 CJH00185 deletion mutant (annotated Cj0031 in NCTC 11168) was generated by double-crossover recombination. The C. jejuni NCTC 11168 Cj0031 ORF was previously annotated as two genes; however, it has been re-annotated as a single ORF at the time of this study. The PCR primers used for amplifying CJH00185 are 5'-GGGAA-CAAAAGCTGGAGCTCGTTTGAGTGATATAAATATATTTGATGC-3' and 5'-AAGGAA-CACCCGCGGTCTTTTTCATTTAGCAAAGTGAAATGC-3' to amplify the upstream fragment and 5'-CGGGCCCCCCCTCGAGGACATAAAGCAAATCCAACTAAACC-3' and 5'-CGGGCCCCCCCTCGAGGACATAAAGCAAATCCAACTAAACC-3' to amplify the downstream fragment. The chloramphenicol resistance cassette was PCR amplified using primers 5'-AAGGAACACCCGCGG-3' and 5'-GCGCAGATCCCGCGG-3' from a previously constructed pBSK vector template. The CJH00185 upstream, CJH00185 downstream, and the amplified chloramphenicol resistance cassette fragments were ligated into the pBSK-kan2 vector, which was linearized with SacI and XhoI, in a 4-way infusion reaction (Clontech Laboratories, Inc., Mountain View, CA). The upstream and downstream fragment primers contain the overlapping sequences for the cloning reaction. The resulting pBSK-kan vector, which harbors the chloramphenicol resistance cassette flanked by 5' and 3' fragments for the deletion of CJH00185, was transformed into the C. jejuni wild-type strain and chloramphenicol resistant colonies were isolated. Deletion of the CJH00185 gene in the C. jejuni CJH00185 mutant was confirmed by PCR and genomic sequence analysis.

Genome Sequencing, Methylation and Bioinformatics
DNA was isolated from the C. jejuni F38011 wild-type strain and the CJH00185 mutant following standard laboratory procedures for phenol/chloroform extraction. The DNA libraries were prepared following PacBio guidelines and sequenced on SMRT cells using Pacific Biosciences RS sequencing technology (Pacific Biosciences, Menlo Park, CA) at Washington State University. Two separate libraries were constructed for sequencing: a small fragment library used to target high quality circular consensus reads generated during polymerase strand displacement mode and a large fragment library targeting continuous long reads. Small fragments were obtained by shearing 5 μg of genomic DNA through the small orifice ruby of a Hydroshear Plus (Digilabs) for 20 cycles at speed code seven. Small fragment library preparation was performed using the Pacific Biosciences DNA Template Prep Kit 2.0 (250 bp to < 3 kb range). Size selection and library purification was performed with 0.6X AMPure beads (Beckmann-Coulter Genomics). The resulting library had a peak size of 2.7 kb and ranged from 900 bp to 9 kb. This library was bound to C2 DNA polymerase, loaded into four SMRT cells, and polymerization was observed using two 45 min movies for each cell. Large fragment library preparation was performed by shearing 5 μg of genomic DNA using a Hydroshear large orifice ruby for 20 cycles at speed code 20. The large fragment library preparation was performed using the Pacific Biosciences DNA Template Prep Kit 2.0 (3 to 10 kb range). Size selection and library purification was performed using 0.45X AMPure beads (Beckmann-Coulter Genomics). The resulting library had a peak size of 16.5 kb and ranged from 4 to 35 kb. The large fragment library was bound to C2 DNA polymerase, mag-bead loaded into five SMRT cells, stage started, and observed using a single 2 h movie for each cell. The 13 movies generated 232k reads with an average length of 3743 bp.
Assembly was performed using the RS_ Hierarchical Genome Assembly Process (HGAP) _Assembly.1 protocol incorporated into SMRT Analysis v2.0. A preassembled correction contained 48 Mb of long and 628 Mb of short reads using a software calculated minimum seed read length of 9624 bp generating 4272 reads with an N50 length of 10,548 bp. The preassembled reads were assembled using Celera2.0 and polished with Quiver into two contigs with perfect circularizing overlap (1,691,939 bp and 19,277 bp). Mapping concordance of the final assembly was 99.9999. The RS_Modification_and_Motif_Analysis.1 protocol of the SMRT analysis v2.0 was used to identify methylation and the corresponding motifs of the responsible DNA methylases.
Genome annotation was performed by the National Center for Biotechnology Information (NCBI) Prokaryotic Genomes Automatic Annotation Pipeline and is published as Campylobacter jejuni F38011 with 'CJH' locus tags (BioSubmission: SUB358967; BioProject ID: PRJNA222831). The C. jejuni F38011 genome was visualized using CGView [20]. C. jejuni F38011 and NCTC 11168 genomic DNA sequences (accession number 700819) were compared using Artemis Comparison Tool (ACT), as described elsewhere [21]. Consensus sequence logos were created as described elsewhere [22].

Proteomic Analysis
A C. jejuni whole cell lysate was digested with trypsin. The resulting peptides were analyzed by LC-MS/MS, using a Waters nanoAcquity UPLC coupled to a Thermo Velos-FTICR mass spectrometer [23]. Peptides were loaded onto a 3 cm x 100 μm inner diameter fused silica trap column packed with a stationary phase consisting of MichromMagic C18, 5 μm diameter, 200 A pore size particles (Bruker) with a flow rate of 2 μL/min of mobile phase consisting of 98% solvent A (H 2 O containing 0.1% formic acid) and 2% solvent B (ACN containing 0.1% formic acid) for 10 minutes. Peptides were then fractionated over a 60 cm x 75 μm inner diameter fused silica analytical column packed with Michrom Magic C18, 5 μm diameter, 100 A pore size particles by applying a linear gradient from 95% solvent A, 5% solvent B to 65% solvent A, 35% solvent B over 120 minutes at a flow rate of 300 nL/min. Eluting peptide ions were ionized by electrospray ionization by applying a positive 2 kV potential to a laser pulled spray tip at the end of the analytical column. The Velos-FTICR mass spectrometer was operated using data dependent method consisting of a high resolution MS 1 measurement in the ICR cell at 50K resolving power followed by low resolution MS 2 scans in the ion trap on the 20 most intense ions with charge state of 2+ or greater. MS 2 settings included a normalized collision energy of 35, and isolation width of 2 m/ z, and an activation time of 10 ms. Ions selected for MS2 were placed on a dynamic exclusion list for 45 seconds. A total of four biological samples were analyzed in triplicate.
Tandem mass spectra data were searched against a protein database for C. jejuni strain 11168 (UniProt entry CAMJE) containing forward and reverse sequences (3246 total protein sequences) as well as a database containing forward and reverse sequences for C. jejuni strain F38011 (3368 total protein sequences), using SEQUEST (version UWPR2012.01). SEQUEST search parameters included: consideration of only fully tryptic peptide sequences, a 25 ppm precursor ion mass tolerance, a 0.36 Da fragment ion mass tolerance, the static modification of carbamidomethylation of Cys residues (57.021464 Da), and the variable modification of oxidation on Met residues (15.9949 Da). A 1% false discovery rate (FDR) threshold was applied to the resulting peptide spectrum matches. All proteins were analyzed and sorted based on subcellular locations using PSORTb v.2.0 [24]. Enzymatic functional class annotations were obtained from the UniProt database for 485 enzymes identified in this study [25].

Tissue culture
INT 407 human intestinal epithelial cells (ATCC CCL6; American Type Culture Collection, Manassas, VA, USA) were cultured as previously described [26].

Binding and internalization assays
Determination of C. jejuni adherence and internalization by INT 407 cells was assessed as previously described [27]. Assays were performed using a multiplicity of infection of 50-500 and reproduced at least 3 times. Statistical analyses were performed using GraphPad Prism 6 (La Jolla, CA. USA) and statistical significance (P 0.05) was determined by one-way analysis of variance (ANOVA) using Tukey's post-test.
Growth characterization of C. jejuni strains and survival in deoxycholate (DOC) Overnight MHB plate cultures of C. jejuni strains were used to inoculate fresh MH broth, with and without 0.05% DOC concentration, at an OD 540 of 0.01 and bacterial density was monitored at the indicated time points using a spectrophotometer. Survival was assessed by plating 10-fold serial dilutions of the broth cultures on MHB plates, at the indicated time points, and colonies were counted to determine CFU/ml. Statistical analyses were performed using GraphPad Prism 6 and statistical significance (P 0.05) was determined by ANOVA using Tukey's post-test.

Results and Discussion
The C. jejuni F38011 clinical strain (biotype I, serotype 90) was isolated from an individual with bloody diarrhea [28,29]. Given that this C. jejuni strain has been used for more than two decades to dissect the virulence proteins and associated factors necessary for Campylobacter pathogenesis, we sought to more fully characterize this strain. The genome of the C. jejuni F38011 strain was sequenced using Pacific Biosciences sequencing technology. The C. jejuni F38011 genome was determined to be 1.69 Mb (1,691,939) with 1613 predicted protein coding sequences (CDSs) (Fig. 1). The genome was sequenced with 100% of bases called, forming a single circular genome from library preparation (99.9999% consensus accuracy) and average nucleotide coverage of 396. No plasmids were identified. The mol.% (G+C) content was 30.5% and the change in GC skew demonstrates origin of replication for the C. jejuni F38011 strain, as observed elsewhere [30]. Genomic regions associated with the largest changes in mol.% (G+C) content reflect points in the genome encoding tRNAs or rRNAs. Using the Artemis Comparison Tool (ACT), the genomes of the C. jejuni F38011 and NCTC 11168 strains were compared (Fig. 2). C. jejuni NCTC 11168 is 1.6 Mb (1,641,481) with a mol.% (G+C content) of 30.5% [31]. There is substantial synteny between strains and similarity in mol.% (G+C) content, even though the C. jejuni F38011 genome is greater in size. Furthermore, the C. jejuni F38011 strain contained 122 putative CDSs with little similarity to genes found in NCTC 11168 strain; however, the C. jejuni F38011 strain also lacked 58 CDSs present in the NCTC 11168 genome (S1 Table). Many of the CDSs unique to either strain fall within the hypervariable plasticity regions of the organism, as discussed below. Additionally, the C. jejuni F38011 strain does not harbor plasmids that confer resistance to antibiotics, including the tetracycline resistance plasmid found in C. jejuni 81-176 (pTet plasmid) [32].  Genes are shown in blue with the gray bar below each PR indicating the gap fraction of pairwise alignment with black columns representing absence of genetic information in the C. jejuni F38011 strain. PR parameters were determined as described elsewhere [33]. The pan genome, which is comprised of both the core and variable genes, was evaluated in the C. jejuni F38011 strain. Previous comparative genomic hybridization analysis using microarrays to assess the genomic content of 11 C. jejuni clinical isolates identified the common or core genes despite extensive genetic variability between isolates [34]. The common genes, which were nearly 84% of the total genes, encoded proteins involved in metabolic, biosynthetic, cellular, and regulatory processes. The regions of the genome that were variable included genes encoding the biosynthesis and modification of the flagella, LOS and capsular polysaccharide. It was later determined that the variable regions were generally found in seven clusters termed hypervariable plasticity regions (PR; PR1-PR7) [33]. The genetic content of PR1 encodes proteins associated with molybdenum reduction and transport and biotin synthesis; PR2 contains putative membrane transporters and hypothetical proteins; PR3 contains ABC transporters, membrane, and hypothetical proteins; PR4 encodes N-Acetyl Neuraminic Acid (NANA) synthase genes; PR5 contains components of the LOS biosynthesis and flagellar genes (including posttranslational modification); PR6 harbors components responsible for capsule biosynthesis; and PR7 contains genes that encode membrane proteins. Using the PR parameters determined by Pearson and colleagues [33], we compared each variable region of the C. jejuni F38011 strain to the C. jejuni NCTC 11168 strain (Fig. 2). While PR1, PR2, PR3 were nearly identical between these two C. jejuni strains, differences were observed in PR4, PR5, PR6, and PR7. Others have also observed considerable genomic diversity between C. jejuni isolates recovered from a similar biological source [35,36]. Additional research is needed to assess the contribution of the gene products located within these hypervariable regions to the phenotypic variation, microbial adaptation to an environmental niche, and/or an isolate's virulence.

Methylation motifs in the C. jejuni F38011 genome
PacBio sequencing is a reliable and robust method to determine modified bases due to changes in the kinetics of the DNA polymerase as it incorporates the appropriate nucleotide opposite a modified base [37]. DNA methylation was determined in the C. jejuni F38011 strain using the PacBio RS sequencing platform and total base modifications were detected during SMRT sequencing. The modified bases were clustered into five consensus sequences (plus additional modified bases that were not clustered) and were distributed throughout the genome (Fig. 3). The motifs identified were consistent with two types of methylation: four motifs are recognized by m6 A methyltransferases (N-6 adenine-specific DNA methylases) and a single motif is recognized by m4 C methyltransferases (N-4 cytosine-specific DNA methylases). Motifs 1, 3 and 4 contained bases methylated on both strands, whereas bases on motifs 2 and 5 were modified on only one strand at each site. The dominant m6 A methylation motifs were abundant and nearly completely methylated, as the percent of methylated motifs detected range from 99.5 to 100% for motifs 1, 2, 3 and 4. The m4 C modification (motif 5) had a consensus sequence of ANNNNCGNAAATTY and was methylated on 34 of 77 motifs (44.2% percent of motifs detected). The mean modification quality value (QV = 122) and the mean coverage was 188, which is necessary for a confident base modification call at this level of coverage (Table 1). However, because the modification signatures can vary due to the dynamic nature of the kinetic signal, we cannot rule out the possibility that Motif 5 is a false positive motif overcalled by PacBio software, as described elsewhere [38].
The C. jejuni F38011 strain genome was assessed by REBASE (www.rebase.neb.com) to determine putative C. jejuni F38011 enzymes (Cje) involved with each motif and for comparisons with known modification systems ( Table 2). Motif 1 (RAATTY) identified in the C. jejuni F38011 genome is associated with a Type II restriction-modification system common to Gram-positive and Gram-negative bacteria. REBASE analysis indicated that the RM enzyme pair CjeF38011P and M.CjeF38011I is predicted to be responsible for RAATTY modification.
Motif 3 (GAGNNNNNRTG) has been identified in C. jejuni strain RFL1 and is digested by the restriction enzyme CjuII. The Type II RM system responsible for Motif 3 likely consists of Cje-F38011ORFDP, based on 87% identity to CjeNII. Motif 4 (CTANNNNNNNNTAYC) is a Type I RM and predicted to be modified by the RM enzymes CjeF38011IIP, S.CjeF38011II, and M.CjeF38011II. Motifs 2 (GKAAYC) and 5 (ANNNNCGNAAATTY) are both predicted to be part of the Type II restriction modification system. CjeF38011ORFCP is the likely gene candidate responsible for modification at the consensus sequence GKAAYC based on 98% identity to CjeNIII (GKAAYG). There are two candidate enzymes that may be responsible for modification at Motif 5 (ANNNNCGNAAATTY): 1) M.CjeF38011ORFEP and 2) Cje-F38011ORFAP. M.CjeF38011ORFEP shares 98.9% amino acid identity with CJE0220 from C. jejuni RM1221, as judged by BLAST analysis, and is annotated as a DNA adenine methylase (http://microbesonline.org/). The second candidate enzyme, CjeF38011ORFAP, shares similarity with Cj0031 (originally designated Cj0031/Cj0032) from C. jejuni NCTC 11168 that contains a hypervariable homopolymeric tract. CjeF38011ORFAP may or may not be a member of a new class of split DNA methyltransferases [39] (Dr. Richard J. Roberts, personal communication). The split DNA methyltransferases usually consist of 2 or 3 subunit enzymes necessary for full activity, although there is evidence that they demonstrate partial activity with just one subunit [40]. Furthermore, there are members of this family that are not split and are single polypeptide enzymes including CjeFV, which recognizes GGRCA but only as a methylase [41].
Presence of the ANNNNCGNAAATTY motif in C. jejuni strains and analysis of the CJH00185 sequence REBASE predicted that the gene CJH00185 (CjeF38011ORFAP) is one of two putative Type IIG methylases in C. jejuni F38011 that could be responsible for DNA methylation of the N-4 cytosine ( m4 C) at the ANNNNCGNAAATTY motif. All of these sites also contain the RAATTY motif. Considering this m4 C motif was previously not recognized in C. jejuni as a site of DNA methylation, we first inspected the genomes of three additional C. jejuni strains (NCTC 11168, 81-176, and RM1221) for the presence of the m4 C methylated motif. The C. jejuni NCTC 11168 and 81-176 strains were recovered from the stools of individuals with campylobacteriosis whereas the C. jejuni RM1221 strain was recovered from the skin of a chicken [42][43][44]. All three C. jejuni strains shared 23 of the 34 genomic regions associated with the m4 C motif in the C. jejuni F38011 strain ( Table 3). The only m4 C site that was unique to the C. jejuni F38011 genome was associated with a hypothetical protein (CJH01365). Inspection of the CJH00185 sequence revealed a frameshift mutation within the 3491 nucleotides that splits the sequence into two ORFs and could prevent the translation of the full-length CDS of the CjeF38011ORFAP (S1 Fig.). Noteworthy is that the Cj0031 gene of C. jejuni NCTC 11168, which is a putative homologue of CJH00185, contains a hypervariable homopolymeric tract [41]. In contrast to the Cj0031 gene that has a polymorphic poly-G tract within the CDS (8-10 bases), we identified a tract of four bases in a similar location within the CJH00185 gene.

Proteomic analysis of the C. jejuni F38011 strain
Total protein was assessed in the C. jejuni F38011 strain to determine the putative restrictionmodification enzymes that are synthesized. The proteins produced by the C. jejuni F38011 strain were collected after 48 h growth in rich broth medium and analyzed by LC-MS/MS. A total of 1336 proteins (82% of the 1613 predicted CDSs) were identified when mapped to C. jejuni NCTC 11168 (listed in S2 and S3 Tables). Interestingly, peptides matched uniquely to more than 30 CDSs in the C. jejuni F38011 database compared to NCTC 11168 (S3 Table). Only the proteins with peptides identified at less than 1% false discovery rate were included in the analysis. The identified proteins were assessed by the PSORTb v.2.035 program (http:// www.psort.org/psortb/index.html) to classify subcellular locations. The subcellular localization of proteins was predicted to group into three major classes: cytoplasmic proteins (53%), cytoplasmic membrane proteins (21%), and proteins of unknown location (21%) (Fig. 4). Comparing the 1336 proteins identified against the UniProt entry for the C. jejuni 11168 strain, we identified 485 enzymes that were grouped into six functional classes, with transferases (34%) representing the most abundant group (Fig. 4).
Consistent with the results of genomic sequence and methylation profiles, peptide fragments corresponding to the C. jejuni putative RM enzymes (Table 2) were identified by LC-MS/MS. For example, four peptide fragments corresponding to the deduced amino acid sequence of CjeF38011ORFAP protein were detected (S3 Table). However, the CjeF38011OR-FAP peptide fragments identified were localized within the amino-terminal region of the CDS (S1 Fig.). While this finding indicates that CJH00185 is expressed and a protein is synthesized, it is not possible to determine the true CDS from the LC-MS/MS analysis. In summary, the LC-MS/MS data indicates that the RM enzymes listed in Table 2 are synthesized.

Preliminary characterization of a C. jejuni F38011 CJH00185 deletion mutant
We chose to assess the contribution of the gene CJH00185, as it is predicted to encode a putative Type II RM methylase. A C. jejuni CJH00185 mutant was constructed in which the entire CDS was deleted and the mutant was analyzed by PacBio sequencing. The C. jejuni CJH00185 mutant mapped to the wild-type reference strain at all positions (except where the gene deletion occurred), with 100% of bases called with 99.99% consensus accuracy and an average nucleotide coverage of 342.4. Interestingly, the modified bases found in the mutant clustered into only four consensus sequences (Table 4). Specifically, PacBio SMRT analysis did not identify modified bases corresponding to motif 5 in the CJH00185 mutant. However, based on the data in-hand, we cannot rule out the possibility that the PacBio SMRT analysis failed to identify motif 5 in the C. jejuni CJH00185 mutant due to the relative difficulty in identifying partially methylated DNA.
Although many m4 C modifications protect bacteria from foreign DNA, the majority of m4 C modifications do not have known biological roles [45]. We initially hypothesized that m4 C methylation could play a role in gene regulation. However, the methyl-cytosine consensus sequence was distributed throughout the entire genome without statistical correlation to the nearest putative methionine initiation codon (Fig. 5). Therefore, we have no evidence for methylation altering gene expression in C. jejuni. Another possibility is that the methylation Table 3. m4 C Methylation motif (ANNNNCGNAAATTY) associated with CDSs in 4 C. jejuni strains. influences C. jejuni fitness, as has been shown for Brucella, Escherichia coli, Haemophilus, Salmonella, Vibrio, and Yersinia [16]. To test this possibility, several phenotypic assays were performed. Malik-Kale and colleagues identified a set of C. jejuni genes upregulated in the presence of a physiologically relevant concentration of the bile acid DOC [46]. More specifically, microarray data from C. jejuni grown in the presence of DOC revealed that multiple genes were upregulated compared to growth without DOC [46]. C. jejuni inoculation of growth medium supplemented with DOC increases the kinetics of cellular invasion and increases the secretion and delivery of key virulence proteins to the cytosol of host cells, as compared to growth in non-supplemented growth medium. Thus, we characterized the C. jejuni CJH00185  deletion mutant in assays with and without physiological concentrations of DOC (0.05%) and determined whether this mutant is capable of binding to and invading epithelial cells. Bacterial growth rates were similar between strains in MH broth with and without 0.05% DOC (S2 Fig.). Bacterial survival over time was also similar between strains in MH broth with and without 0.05% DOC, as determined by CFU analysis (S2 Fig.). Furthermore, adherence to and invasion of INT 407 cells by C. jejuni following 30 and 180 min incubation period, respectively, demonstrated no statistical difference between the wild-type and the mutant isolate (S2 Fig.). Thus, the C. jejuni F38011 CJH00185 mutant is phenotypically indistinguishable from the wild-type strain in these assays.

Summary
The goal of this study was to analyze the genomic content, methylome profile, and proteomic capacity of the C. jejuni F38011 clinical strain to gain insight into microbial processes. In this study, we have further characterized the C. jejuni F38011 strain using PacBio's SMRT sequencing coupled with methylome analysis. While this sequencing method provides insight into the DNA methylation status of the C. jejuni genome, additional work is necessary to confirm the observation of the m4 C modification. Nonetheless, peptides corresponding to all of the enzymes predicted to be responsible for methylation in C. jejuni were detected using proteomic analysis. This study provides the foundation for studies to determine the functions of the putative restriction-modification enzymes in C. jejuni.