Identification and Analysis of the Gap Region in the 23S Ribosomal RNA from Actinobacillus actinomycetemcomitans

Abstract

Actinobacillus actinomycetemcomitans is a Gram-negative coccobacillus which can cause certain severe extra-oral infections as well as forms of human periodontal disease such as localized juvenile periodontitis. In contrast to many prokaryotic and eukaryotic species which exhibit an intact 23S ribosomal RNA (rRNA) molecule, examination of six A. actinomycetemcomitans strains--including three serogroup representative strains and two strains from non-human primates--revealed that this micro-organism does not produce an intact 23S ribosomal RNA (rRNA) molecule but, rather, two smaller forms of 1.8 kb and 1.2 kb designated as 23S alpha and 23S beta fragments. On the other hand, 14 other strains of Actinobacillus, Haemophilus, and Pasteurella species demonstrated intact 23S rRNA. The sequence of the region of the 23S rRNA gene in A. actinomycetemcomitans strain ATCC 43718 containing the cleavage site was determined by dideoxynucleotide sequencing, while the location of the 3' and 5' termini of the 23S alpha and 23S beta fragments was resolved by S1 nuclease mapping and cDNA primer-extension. A deletion of 112 bases was noted in comparisons of base sequences from A. actinomycetemcomitans rRNA and rDNA. The DNA intervening sequence was localized to nucleotide 1180 of the Escherichia coli 23S rRNA map. While the primary structure of the gap region showed little homology with the gap regions described in other organisms, the secondary structure was similar to that previously described in the parasitic helminth Schistosoma japonicum. Restriction enzyme and nucleotide sequence analysis of the gap region in eight other A. actinomycetemcomitans strains showed it to be highly conserved.

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

“…The 1170 position is also at a position homologous to an expansion segment in eucaryotes (41). The five internal spacers reported by Van Camp et al (60) were also located in this helix, as were transcribed spacers of Salmonella (3), Yersinia (52), Actinobacillus (20), Leptospira (52), and Chlamydomonas chloroplasts (59) U-1859-C-1883 the true campylobacters, including C. coli, appear to belong to a previously undefined phylogenetic branch, on the basis of a signature sequence analysis and comparison of sequence data with partial sequences of representatives of 8 of the 10 major phylogenetic branches of the (eu)bacteria. Lau et al (30) subsequently suggested that while there is some evidence of affinity between an expanded division containing the purple photosynthetic bacteria and their relatives and the Campylobacter cluster, the Campylobacter cluster is not specifically positioned in either the alpha, beta, or gamma subdivision of the group.…”

“…2 and 3A). Similar sequence blocks have been shown to be present at this position in the 23S rRNA genes from a variety of bacteria (3,20,44,47,52,60) and chloroplasts (59), and these extra sequence blocks in the 23S rRNA genes have been termed intervening sequences (3) or transcribed spacers (60).…”

Mobile Elements in a Single-Filament Orange Guaymas Basin Beggiatoa (“Candidatus Maribeggiatoa”) sp. Draft Genome: Evidence for Genetic Exchange with Cyanobacteria

“…S1 in the supplemental material), at least so far as 23S rRNA sequences are available to date, but it contains two intervening elements (Fig. 1A) similar to ones found in the rRNA genes of diverse species (e.g., see references [30][31][32], including other giant sulfur bacteria (33). In orange Guaymas Beggiatoa, a putative group I catalytic intron is found at E. coli position 1917, in the loop of predicted helix 69, and a putative LAGLIDADG homing endonuclease at E. coli position 1931, in a predicted unstructured region between helices 69 and 71 (Fig.…”

Intervening sequence with conserved open reading frame in eubacterial 23S rRNA genes.

“…Eubacterial 23S rRNA genes (rrl) have been observed that carry small insertions of about 90-112 bases that are removed by cleavage but not religated (8)(9)(10). These IVSs have been found in only some strains within species in a few genera, implying that the IVS may be maintained by lateral transfer between strains but is not necessarily required for host survival.…”