DNA Sequence Heterogeneity of Campylobacter jejuni CJIE4 Prophages and Expression of Prophage Genes

Abstract

Campylobacter jejuni carry temperate bacteriophages that can affect the biology or virulence of the host bacterium. Known effects include genomic rearrangements and resistance to DNA transformation. C. jejuni prophage CJIE1 shows sequence variability and variability in the content of morons. Homologs of the CJIE1 prophage enhance both adherence and invasion to cells in culture and increase the expression of a specific subset of bacterial genes. Other C. jejuni temperate phages have so far not been well characterized. In this study we describe investigations into the DNA sequence variability and protein expression in a second prophage, CJIE4. CJIE4 sequences were obtained de novo from DNA sequencing of five C. jejuni isolates, as well as from whole genome sequences submitted to GenBank by other research groups. These CJIE4 DNA sequences were heterogenous, with several different insertions/deletions (indels) in different parts of the prophage genome. Two variants of a 3–4 kb region inserted within CJIE4 had different gene content that distinguished two major conserved CJIE4 prophage families. Additional indels were detected throughout the prophage. Detection of proteins in the five isolates characterized in our laboratory in isobaric Tags for Relative and Absolute Quantitation (iTRAQ) experiments indicated that prophage proteins within each of the two large indel variants were expressed during growth of the bacteria on Mueller Hinton agar plates. These proteins included the extracellular DNase associated with resistance to DNA transformation and prophage repressor proteins. Other proteins associated with known or suspected roles in prophage biology were also expressed from CJIE4, including capsid protein, the phage integrase, and MazF, a type II toxin-antitoxin system protein. Together with the results previously obtained for the CJIE1 prophage these results demonstrate that sequence variability and expression of moron genes are both general properties of temperate bacteriophages in C. jejuni.

Comparison of genomes and proteomes of four whole genome-sequenced Campylobacter jejuni from different phylogenetic backgrounds

“…In addition, there are 29 gene differences between 00–0949 and 01–1512. Among these are 15 associated with the CJIE4 prophage (9 with the CJIE4 alternate indels discussed in previous work [ 33 ]). Three are associated with motility accessory factor proteins within the flagella glycosylation gene cluster, all of which are expressed.…”

“…A comparison of CJIE4 prophages in the 4 isolates, along with the proteins expressed from these prophages, has been discussed previously [ 33 ], though differences in protein detection levels was not included in that discussion. The most striking difference within CJIE4 is the presence of an indel, with one variant comprised of 5 genes (encoding the Cro/CI family transcriptional regulator, hypothetical protein PJ17_06640, 3′-5′ exonuclease, hypothetical protein PJ17_06650, NTPase KAP) present in isolates 00–0949 and 00–1597 and the alternate indel of 4 genes (encoding hypothetical protein PJ18_6440, peptidase S24, endonuclease, and hypothetical protein PJ18_06455) present in isolates 00–6200 and 01–1512 [ 33 ]. All proteins except hypothetical protein PJ18_06440 are detected at significantly higher log 2 fold change in the appropriate isolates, consistent with the presence or absence of the genes ( S2 Table ).…”

“…We previously used 4-plex iTRAQ proteomics to detect expression of proteins associated with the CJIE4 prophage in C . jejuni in isolates with different serotypes and multi-locus sequence types (STs) [ 33 ]. The main hypotheses underlying the current work is that we can specifically identify changes in protein expression that may be a consequence of regulatory differences between isolates as well as identify those protein expression changes that differentiate proteins encoded by genes that are unique to each isolate or serotype.…”

Prevention of Biofilm Formation and Removal of Existing Biofilms by Extracellular DNases of Campylobacter jejuni

“…One of the consequences is that C . jejuni shows a high level of genetic diversity, both at the sequence level and at the level of genetic content [ 29 , 53 ]. In this study we have used C .…”

A transferable plasticity region in Campylobacter coli allows isolates of an otherwise non‐glycolytic food‐borne pathogen to catabolize glucose

“…Several factors support our hypothesis that the glc ‐locus of glycolytic C. coli strains was acquired and can be spread between different Campylobacter species by HGT: (i) The glc ‐gene cluster of C. coli CHW470 is localized in a ribosomal RNA operon between the 16S rRNA and 23S rRNA adjacent to a isoleucyl‐tRNA gene, and tRNA‐loci are integration sites for horizontally acquired DNA (Ochman et al ., ). Similarly, phage‐like genomic islands were found at tRNA sites of C. jejuni strains (Fouts et al ., ; Parker et al ., ; Clark et al ., ), and a plasticity region with properties of an integrated plasmid was identified next to a leucyl‐tRNA of C. jejuni 81–176 (Hofreuter et al ., ). (ii) The genes of the ED pathway enzymes in glycolytic C. coli strains are assembled in one functional unit.…”