Nucleotide sequences of the spacer-1, spacer-2 and trailer regions of the rrn operons and secondary structures of precursor 23S rRNAs and precursor 5S rRNAs of slow-growing mycobacteria

Abstract

Nucleotide sequences of the spacer-1, spacer-2 and trailer regions of the rrn operons and secondary structures of precursor 23s rRNAs and precursor 5s rRNAs of slow-growing rnyco bacter ia Yuan- The single ribosomal RNA (rrn) operons of slow-growing mycobacteria comprise the genes for 165, 235 and 55 rRNA, in that order. PCR methodology was used to amplify parts of the rrn operons, namely the spacer-1 region separating the 165 rRNA and 235 rRNA genes and the spacer-2 region separating the 235 rRNA and 55 rRNA genes of Mycobacterium avium, Mycobacterium intracellulare, 'Mycobacterium lufu ' and Mycobacterium simiae. The amplified DNA was sequenced. The spacer-2 region, the 55 rRNA gene, the trailer region and the downstream region of the rrn operon of Mycobacterium tuberculosis were cloned and sequenced. These data, together with those obtained previously for Mycobacterium leprae, were used to identify putative antitermination signals and RNase 111 processing sites within the spacer4 region. Notable features include two adjacent potential Box B elements and a Box A element. The latter is located within a sequence of 46 nucleotides which is very highly conserved among the slow-growers which were examined. The conserved sequence has the capacity to interact through base-pairing with part of the spacer-2 region. Secondary structures for mycobacterial precursor 235 rRNA and for precursor 55 rRNA were devised, based on sequence homologies and homologous nucleotide substitutions. All the slow-growers, including M. leprae, conform to the same scheme of secondary structure. A putative motif for the intrinsic termination of transcription was identified approximately 33 bp downstream from the 3'-end of the 55 rRNA gene. The spacer-1 and spacer-2 sequences may prove a useful supplement to 165 rRNA sequences in establishing phylogenetic relationships between very closely related species. The EMBL accession numbers for the nucleotide sequence data reported in this paper are X74056X74063 and X75599-X75602. (Shepard, 1960; K'inder & Rooney, 1970). Although ribosome biosynthesis is essential to cell proliferation, the strategy (or strategies) used by slow-growing mycobacteria to control the production of new ribosomes is not known. One facet of this strategy is the regulation of the biosynthesis of rRNA. The slow-growing mycobacteria have a single rRNA (rm) operon (Bercovier et a/., 1986) comprising genes for the rRNA family in the order 16s rRNA, 23s rRNA and 5s rRNA (see Fig. 1). The operon is transcribed as a single unit (precursor rRNA or prerRNA) which is cleaved by RNases to precursors of 16s rRNA (pre-16s rRNA), 23s rRNA (pre-23s rRNA) and Keywords

Ribosomal internal transcribed spacer sequences are identical among Mycobacterium avium-intracellulare complex isolates from AIDS patients, but vary among isolates from elderly pulmonary disease patients

“…Similarly, a recent publication has described the ITS sequence of M. habana, which is an older name for M. simiae (Ji et al, 1994). There were seven basepair differences between this published sequence and our Msi-A sequevar sequence, suggesting heterogeneity within this species as well.…”

“…A phylogenetic tree was constructed using the UPGMA algorithm with all the sequevars described here, all previously described Mav, MAC and Msc sequevars, as well as the Mtb-A sequevar and the published M. habana and M. paratubercdosis ITS sequences Ji et al, 1994; Van der Giessen e t al., 1994) (Fig. 2).…”

Strategies used by pathogenic and nonpathogenic mycobacteria to synthesize rRNA

“…The remaining 35 sequences, of approximately 65% similarity, were also found to be mycobacterial in origin and to be centered on the BoxA S motif of the spacer 1b region separating the 16S rRNA and 23S rRNA genes. The BoxA L and BoxA S sequences are closely related (15,16).…”

Primary and secondary structures of rRNA spacer regions in enterococci

“…faecium strains may contain no tRNA gene in the spacer region 1. A complete absence of tRNA gene in all spacer regions 1 of a given species is not a frequent situation, although it has been described for mycobacteria (Ji et al, 1994;van der Giessen et al, 1994).…”