title: Nucleotide sequence and secondary structures of precursor 16S rRNA of slow-growing mycobacteria.
abstract: Slow-growing mycobacteria have a single ribosomal RNA (rrn) operon, with the genes for 16S, 23S and 5s rRNA being present in that order. The transcription start site of the rrn operon of Mycobacterium tuberculosis was identified in Escherichia coli. PCR methodology was used to amplify parts of the rrn operon, namely the leader region and the spacer-1 region separating the 16S rRNA and 23S rRNA genes of Mycobacterium avium, Mycobacterium paratuberculosis, Mycobacterium intracellulare, 'Mycobacterium lufu', Mycobacterium simiae and Mycobacterium marinum. The amplified DNA was sequenced. The sequence data, together with those obtained previously for Mycobacterium leprae and M. tuberculosis, were used to identify putative antitermination signals and RNase III processing sites within the leader region. Notable features include a highly conserved Box B element and a sequence of 31 nucleotides which is common to all eight slow-growers which were scrutinized. A secondary structure for mycobacterial precursor-16S rRNA was devised, based on sequence homologies and homologous nucleotide substitutions. The 18 nucleotides at the 5'-end of spacer-1 have the capacity of binding sequences close to the 5'- and 3'-ends of mature 16S rRNA, suggesting that secondary structure is important to the maturation process. All the slow-growers, including M. leprae, conform to the same scheme of secondary structure. The scheme proposed for M. tuberculosis is a variant of the main theme. The leader and spacer sequences may prove a useful supplement to 16S rRNA sequences in establishing phylogenetic relationships between very closely related species. 'M. lufu' appears to be a close relative of M. intracellulare.
authors.affiliation: Laboratory of Developmental Biochemistry, National Institute for Medical Research, Mill Hill, London, UK.
authors.forename: Y E
authors.initials: YE
authors.lastname: Ji
authors.forename: M J
authors.initials: MJ
authors.lastname: Colston
authors.forename: R A
authors.initials: RA
authors.lastname: Cox
mesh_terms: D001483:Base Sequence; D017931:DNA Primers / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D005798:Genes, Bacterial; D008969:Molecular Sequence Data; D009161:Mycobacterium / Q000737:chemistry / Q000235:genetics* / Q000254:growth & development; D009169:Mycobacterium tuberculosis / Q000235:genetics; D009690:Nucleic Acid Conformation; D009876:Operon; D010802:Phylogeny; D012322:RNA Precursors / Q000737:chemistry / Q000235:genetics*; D012323:RNA Processing, Post-Transcriptional; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity
chemical_list: D017931:DNA Primers; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012322:RNA Precursors; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S