An intervening sequence (IVS) in the 16S rRNA gene of the eubacteriumHelicobacter canis

Abstract

PCR amplicons enlarged by approximately 250bp were generated from the 16S rRNA (rrs) genes of certain strains of the recently described Helicobacter species, H. canis. The DNA sequence of the rrs gene of one such strain was determined, and it was shown that an intervening sequence (IVS) of 235bp followed nucleotide 199 in the rrs sequence. In four other H. canis strains, identical or similar IVSs were found, always at the same location in the rrs gene. The secondary structures of the RNA transcripts of the IVSs were predicted. They were characterised by the presence of a conserved stem-loop structure, a potential recognition site for RNA processing enzymes. Ribosomal RNA was compared from a strain of H. canis with and without the IVS-containing rrs gene. In the former 16S rRNA appeared as two fragments, whose sizes were consistent with cleavage at either side of the IVS, and which were not subsequently religated. The IVS sequence was not represented elsewhere in the H. canis genome. Its evolutionary significance is discussed.

Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria

“…Intervening sequences, in contrast to introns, cannot self-splice from precursor RNA and, upon removal by cellular maturation enzymes, leave the ribosomal RNA fragmented (3)(4)(5)(6)(7). In this study, we also showed that true selfsplicing introns can be present in bacterial 16S rRNA genes, leading to the conclusion that the 16S rRNA genes of bacteria can indeed be far longer than ∼1,500 nucleotides.…”

“…The possibility that the 16S rRNA gene may not have a conserved size has not been sufficiently considered in designing and applying techniques for diversity studies, even though elongations of 16S rRNA genes due to intervening sequences have been reported before (3)(4)(5)(6)(7). Intervening sequences, in contrast to introns, cannot self-splice from precursor RNA and, upon removal by cellular maturation enzymes, leave the ribosomal RNA fragmented (3)(4)(5)(6)(7).…”

“…In the past decades, these techniques have become fundamental tools in molecular ecology, and the 16S rRNA gene is the most frequently sequenced and analyzed gene today. The universality of this gene has never been questioned, even though in some studies unusual 16S rRNA genes, which contained, e.g., intervening sequences, were encountered (3)(4)(5)(6)(7).…”

Source of variation detected in ribotyping patterns of Haemophilus influenzae: comparison of traditional ribotyping, PCR-ribotyping and rDNA restriction analysis

“…4 and 5), suggesting variation between rrn copies within a genome. Variation in the length of 23s rDNA and 16s rDNA between strains within species has been reported previously and has been shown to result from the presence of intervening sequences [27]. The results of the present study suggest the presence of variant rrn operons within the genomes of some H. inJuenzae strains.…”

Obligate bacterial endosymbionts of Acanthamoeba spp. related to the beta-Proteobacteria: proposal of 'Candidatus Procabacter acanthamoebae' gen. nov., sp. nov.

“…The presence of IVS within rRNA genes has previously been reported for several bacterial genera of other phylogenetic groupings. IVS were, for example, re- ported in the 23S rDNA of Haemophilus (Song et al, 1999), Salmonella (Pabbaraju & Sanderson, 2000) and Leptospira (Ralph & McClelland, 1993) and in the 16S rDNA of Helicobacter (Linton et al, 1994) and ' Candidatus Blochmannia ' (Sauer et al, 2000). The highly variable extended stem-loop structures formed by the IVS are excised from the rRNA post-transcriptionally (Burgin et al, 1990).…”