Molecular analysis of the 16S-23S rDNA internal spacer region (ISR) and truncated tRNA(Ala) gene segments in Campylobacter lari.

Following PCR amplification and sequencing, nucleotide sequence alignment analyses demonstrated the presence of two kinds of 16S-23S rDNA internal spacer regions (ISRs), namely, long length ISRs of 837–844 base pair (bp) [n = six for urease-negative (UN) Campylobacter lari isolates, UN C. lari JCM2530T, RM2100, 176, 293, 299 and 448] and short length ISRs of 679–725 bp [n = six for UN C. lari: n = 14 for urease-positive thermophilic Campylobacter (UPTC) isolates]. The analyses also indicated that the short length ISRs mainly lacked the 156 bp sequence from the nucleotide positions 122–277 bp in long length ISRs for UN C. lari JCM2530T. The 156 bp sequences shared 94.9–96.8 % sequence similarity among six isolates. Surprisingly, atypical tRNAAla gene segment (5′ end 35 bp), which was extremely truncated, occurred within the 156 bp sequences in the long length ISRs, as an unexpected tRNAAla pseudogene. An order of the intercistronic tRNA genes within the short nucleotide spacer of 5′-16S rDNA-tRNAAla-tRNAIle-23S rDNA-3′ occurred in all the C. lari isolates examined.