A novel tRNA-associated locus (trl) from Helicobacter pylori is co-transcribed with tRNAGly and reveals genetic diversity

To date several genes have been identified in Helicobacter pylori that are expressed in only a proportion of strains, some of which are correlated with the pathogenicity of the bacterium. With this in mind, the present study was undertaken to identify other genes that are not expressed in all clinical isolates of H. pylori. Using arbitrarily primed PCR of RNA, a cDNA fragment of 187 bp (designated trl for transfer RNA-associated locus) was identified that was expressed in only one of two clinical isolates being tested. The fragment was purified, cloned and sequenced. A search of public databases prior to the release of the complete genome sequence of H. pylori strain 26695 showed no similarity with any other known genes or gene products. Inverse PCR was used to obtain further nucleotide sequence information surrounding the trl locus. A DNA probe derived from the trl locus hybridized with 32 (50%) of 64 clinical H. pylori isolates tested. Comparison of the nucleotide sequences of a trl-positive and trl-negative isolate showed that the locus is situated between two tRNA genes, tRNAGly and tRNALeu, in H. pylori. Primer extension analysis showed that the trl locus is co-transcribed with tRNAGly. Analysis of the region between tRNAGly and tRNALeu in trl-negative isolates revealed additional genetic diversity among these isolates.