Phylogenetic and molecular characterization of a 23S rRNA gene positions the genus Campylobacter in the epsilon subdivision of the Proteobacteria and shows that the presence of transcribed spacers is common in Campylobacter spp

Abstract

The nucleotide sequence of a 23S rRNA gene of Campylobacter coli VC167 was determined. The primary sequence of the C. coli 23S rRNA was deduced, and a secondary-structure model was constructed. Comparison with Escherichia coli 23S rRNA showed a major difference in the C. coli rRNA at approximately position 1170 (E. coli numbering) in the form of an extra sequence block approximately 147 bp long. PCR analysis of 31 other strains of C. coli and C. jejuni showed that 69%o carried a transcribed spacer of either ca. 147 or ca. 37 bp.Comparison of all sequenced Campylobacter transcribed spacers showed that the Campylobacter inserts were related in sequence and percent G+C content. All Campylobacter strains carrying transcribed spacers in their 23S rRNA genes produced fragmented 23S rRNAs. Other strains which produced unfragmented 23S rRNAs did not appear to carry transcribed spacers at this position in their 23S rRNA genes. At the 1850 region (E. coli numbering), Campylobacter 23S rRNA displayed a base pairing signature most like that of the beta and gamma subdivisions of the class Proteobacteria, but in the 270 region, Campylobacter 23S rRNA displayed a helix signature which distinguished it from the alpha, beta, and gamma subdivisions. Phylogenetic analysis comparing C. coli VC167 23S rRNA and a C.jejuni TGH9011 (ATCC 43431) 23S rRNA with 53 other completely sequenced (eu)bacterial 23S rRNAs showed that the two campylobacters form a sister group to the alpha, beta, and gamma proteobacterial 23S rRNAs, a positioning consistent with the idea that the genus Campylobacter belongs to the epsilon subdivision of the class Proteobacteria.The members of the Campylobacter group of organisms are important pathogens in human and veterinary medicine. This group includes Campylobacter, Arcobacter, Helicobacter, Wolinella, and "Flexispira" spp. and has been argued to constitute a separate bacterial lineage within the class Proteobacteria (62, 63). The most recently published phylogenetic tree based on small-subunit rRNA sequences has the group positioned in the delta and epsilon subdivisions of the Proteobacteria (purple bacteria) (39). There are 11 Campylobacter species (9, 56), and the roles of several of these species in diseases of humans and animals have been well described (43). Typically, these small, nutritionally fastidious, microaerophilic, gram-negative spiral bacteria colonize moist body surfaces, including the human gingival cavity, the small intestinal mucosa, and the vaginal mucosa of bovines and this colonization leads to disease. The two most important human pathogens in the genus are Campylobacterjejuni and C. coli, which cause enteritis.In keeping with their small size and limited nutritional properties, the campylobacters have a small genome (23,37,57). At 1.7 to 1.8 Mb, the C. jejuni and C. coli genomes are only 36% of the size of the Escherichia coli chromosome (53) (23,24,27,37,57). Unlike the characteristic continuous 16S-23S (eu)bacterial rRNA operon structure seen in E. coli (35), several studies have sug...

Molecular Basis of Bacterial Outer Membrane Permeability Revisited

“…More recently, Campylobacter and Helicobacter were recognized to form another deep branch in the Proteobacteria, with only very remote relationships to the other four subdivisions (365,678); this group is now called the ε-proteobacteria. Because of the clinical significance of these organisms, their porins have been investigated.…”

Prokaryotic introns and inteins: a panoply of form and function

“…The 23S and 16S rRNA genes of diverse bacterial species contain small (100 to 200 bp) IVSs, which are excised from the RNA without exon ligation, resulting in fragmented rRNAs (6,44,66). Analogous bacterial 23S rRNA IVSs that contain ORFs of 121 to 133 amino acids have also been found (58).…”

The Absence of Intervening Sequences in 23S rRNA Genes of Campylobacter coli Isolates from Turkeys Is a Unique Attribute of a Cluster of Related Strains Which Also Lack Resistance to Erythromycin

“…Genomic DNA was extracted from C. coli by use of a DNeasy kit (QIAGEN Inc., Valencia, CA) according to the manufacturer's protocol. Primers 1162 (5Ј-TGC GCG GAA AAT ATA ACG GGG CTA-3Ј) and CG1425 (5Ј-CTC ACA TTA ATT ATC GCT ACT CAT-3Ј) were used to amplify a segment of the 23S rRNA gene that has been reported to contain the IVS (41). PCR was done using Taq DNA polymerase (Takara).…”

“…(primarily C. jejuni, C. coli, C. upsaliensis, C. fetus, and C. sputorum) is the presence, in certain strains, of an intervening sequence (IVS) in at least one copy of the 23S rRNA gene (41). Following transcription, the IVS is excised, leading to fragmentation of the large-subunit (23S) rRNA.…”

“…jejuni and C. coli harbor three rRNA operons on their chromosomes. IVSs are absent from all three 23S rRNA gene copies of C. jejuni NCTC 11168 (32) but were detected in other strains of C. jejuni and C. coli (29,33,41) and were also identified in all three copies of the 23S rRNA gene in the recently sequenced genome of C. coli RM2228 (12). When present, the IVS is located only 891 nucleotides (nt) upstream from the site in the 23S rRNA gene where a point mutation (A2075G) has been associated with high-level resistance to erythromycin in Campylobacter (12,14,20).…”