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. 1997 Nov;179(22):6949–6958. doi: 10.1128/jb.179.22.6949-6958.1997

Strategies used by pathogenic and nonpathogenic mycobacteria to synthesize rRNA.

J A Gonzalez-y-Merchand 1, M J Garcia 1, S Gonzalez-Rico 1, M J Colston 1, R A Cox 1
PMCID: PMC179633  PMID: 9371439

Abstract

One rRNA operon of all mycobacteria studied so far is located downstream from a gene thought to code for the enzyme UDP-N-acetylglucosamine carboxyvinyl transferase (UNAcGCT), which is important to cell wall synthesis. This operon has been designated rrnAf for fast-growing mycobacteria and rrnAs for slow growers. We have investigated the upstream sequences and promoter activities of rrnA operons of typical fast growers which also possess a second rrn (rrnBf) operon and of the rrnA operons of the fast growers Mycobacterium abscessus and Mycobacterium chelonae, which each have a single rrn operon per genome. These fast growers have a common strategy for increasing the efficiency of transcription of their rrnA operons, thereby increasing the cells' potential for ribosome synthesis. This strategy involves the use of multiple (three to five) promoters which may have arisen through successive duplication events. Thus we have identified a hypervariable multiple promoter region (HMPR) located between the UNAcGCT gene and the 16S rRNA coding region. Two promoters, P1 and PCL1, appear to play pivotal roles in mycobacterial rRNA synthesis; they are present in all of the species examined and are the only promoters used for rRNA synthesis by the pathogenic slow growers. P1 is located within the coding region of the UNAcGCT gene, and PCL1 has a characteristic sequence that is related to but distinct from that of the additional promoters. In fast-growing species, P1 and PCL1 produce less than 10% of rRNA transcripts, so the additional promoters found in the HMPR are important in increasing the potential for rRNA synthesis during rapid growth. In contrast, rrnB operons appear to be regulated by a single promoter; because less divergence has taken place, rrnB appears to be younger than rrnA.

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Selected References

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  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  2. Bashyam M. D., Kaushal D., Dasgupta S. K., Tyagi A. K. A study of mycobacterial transcriptional apparatus: identification of novel features in promoter elements. J Bacteriol. 1996 Aug;178(16):4847–4853. doi: 10.1128/jb.178.16.4847-4853.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bercovier H., Kafri O., Sela S. Mycobacteria possess a surprisingly small number of ribosomal RNA genes in relation to the size of their genome. Biochem Biophys Res Commun. 1986 May 14;136(3):1136–1141. doi: 10.1016/0006-291x(86)90452-3. [DOI] [PubMed] [Google Scholar]
  4. Chan B., Busby S. Recognition of nucleotide sequences at the Escherichia coli galactose operon P1 promoter by RNA polymerase. Gene. 1989 Dec 14;84(2):227–236. doi: 10.1016/0378-1119(89)90496-4. [DOI] [PubMed] [Google Scholar]
  5. Condon C., Squires C., Squires C. L. Control of rRNA transcription in Escherichia coli. Microbiol Rev. 1995 Dec;59(4):623–645. doi: 10.1128/mr.59.4.623-645.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Domenech P., Menendez M. C., Garcia M. J. Restriction fragment length polymorphisms of 16S rRNA genes in the differentiation of fast-growing mycobacterial species. FEMS Microbiol Lett. 1994 Feb 1;116(1):19–24. doi: 10.1111/j.1574-6968.1994.tb06669.x. [DOI] [PubMed] [Google Scholar]
  8. Doukhan L., Predich M., Nair G., Dussurget O., Mandic-Mulec I., Cole S. T., Smith D. R., Smith I. Genomic organization of the mycobacterial sigma gene cluster. Gene. 1995 Nov 7;165(1):67–70. doi: 10.1016/0378-1119(95)00427-8. [DOI] [PubMed] [Google Scholar]
  9. Fassler J. S., Gussin G. N. Promoters and basal transcription machinery in eubacteria and eukaryotes: concepts, definitions, and analogies. Methods Enzymol. 1996;273:3–29. doi: 10.1016/s0076-6879(96)73003-3. [DOI] [PubMed] [Google Scholar]
  10. Garcia M. J., Guilhot C., Lathigra R., Menendez M. C., Domenech P., Moreno C., Gicquel B., Martin C. Insertion sequence IS1137, a new IS3 family element from Mycobacterium smegmatis. Microbiology. 1994 Oct;140(Pt 10):2821–2828. doi: 10.1099/00221287-140-10-2821. [DOI] [PubMed] [Google Scholar]
  11. Gonzalez-y-Merchand J. A., Colston M. J., Cox R. A. The rRNA operons of Mycobacterium smegmatis and Mycobacterium tuberculosis: comparison of promoter elements and of neighbouring upstream genes. Microbiology. 1996 Mar;142(Pt 3):667–674. doi: 10.1099/13500872-142-3-667. [DOI] [PubMed] [Google Scholar]
  12. González-y-Merchand J. A., Estrada-García I., Colston M. J., Cox R. A. A novel method for the isolation of mycobacterial DNA. FEMS Microbiol Lett. 1996 Jan 1;135(1):71–77. doi: 10.1111/j.1574-6968.1996.tb07968.x. [DOI] [PubMed] [Google Scholar]
  13. Honoré N., Bergh S., Chanteau S., Doucet-Populaire F., Eiglmeier K., Garnier T., Georges C., Launois P., Limpaiboon T., Newton S. Nucleotide sequence of the first cosmid from the Mycobacterium leprae genome project: structure and function of the Rif-Str regions. Mol Microbiol. 1993 Jan;7(2):207–214. doi: 10.1111/j.1365-2958.1993.tb01112.x. [DOI] [PubMed] [Google Scholar]
  14. Ji Y. E., Colston M. J., Cox R. A. Nucleotide sequence and secondary structures of precursor 16S rRNA of slow-growing mycobacteria. Microbiology. 1994 Jan;140(Pt 1):123–132. doi: 10.1099/13500872-140-1-123. [DOI] [PubMed] [Google Scholar]
  15. Ji Y. E., Colston M. J., Cox R. A. The ribosomal RNA (rrn) operons of fast-growing mycobacteria: primary and secondary structures and their relation to rrn operons of pathogenic slow-growers. Microbiology. 1994 Oct;140(Pt 10):2829–2840. doi: 10.1099/00221287-140-10-2829. [DOI] [PubMed] [Google Scholar]
  16. Ji Y. E., Kempsell K. E., Colston M. J., Cox R. A. 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. Microbiology. 1994 Jul;140(Pt 7):1763–1773. doi: 10.1099/13500872-140-7-1763. [DOI] [PubMed] [Google Scholar]
  17. Keilty S., Rosenberg M. Constitutive function of a positively regulated promoter reveals new sequences essential for activity. J Biol Chem. 1987 May 5;262(13):6389–6395. [PubMed] [Google Scholar]
  18. Kempsell K. E., Ji Y. E., Estrada I. C., Colston M. J., Cox R. A. The nucleotide sequence of the promoter, 16S rRNA and spacer region of the ribosomal RNA operon of Mycobacterium tuberculosis and comparison with Mycobacterium leprae precursor rRNA. J Gen Microbiol. 1992 Aug;138(Pt 8):1717–1727. doi: 10.1099/00221287-138-8-1717. [DOI] [PubMed] [Google Scholar]
  19. Kenney T. J., Churchward G. Genetic analysis of the Mycobacterium smegmatis rpsL promoter. J Bacteriol. 1996 Jun;178(12):3564–3571. doi: 10.1128/jb.178.12.3564-3571.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Krummel B., Chamberlin M. J. RNA chain initiation by Escherichia coli RNA polymerase. Structural transitions of the enzyme in early ternary complexes. Biochemistry. 1989 Sep 19;28(19):7829–7842. doi: 10.1021/bi00445a045. [DOI] [PubMed] [Google Scholar]
  21. Lederer E., Adam A., Ciorbaru R., Petit J. F., Wietzerbin J. Cell walls of Mycobacteria and related organisms; chemistry and immunostimulant properties. Mol Cell Biochem. 1975 May 30;7(2):87–104. doi: 10.1007/BF01792076. [DOI] [PubMed] [Google Scholar]
  22. Liesack W., Pitulle C., Sela S., Stackebrandt E. Nucleotide sequence of the 16S rRNA from Mycobacterium leprae. Nucleic Acids Res. 1990 Sep 25;18(18):5558–5558. doi: 10.1093/nar/18.18.5558. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Liesack W., Sela S., Bercovier H., Pitulle C., Stackebrandt E. Complete nucleotide sequence of the Mycobacterium leprae 23 S and 5 S rRNA genes plus flanking regions and their potential in designing diagnostic oligonucleotide probes. FEBS Lett. 1991 Apr 9;281(1-2):114–118. doi: 10.1016/0014-5793(91)80372-a. [DOI] [PubMed] [Google Scholar]
  24. Movahedzadeh F., Colston M. J., Davis E. O. Determination of DNA sequences required for regulated Mycobacterium tuberculosis RecA expression in response to DNA-damaging agents suggests that two modes of regulation exist. J Bacteriol. 1997 Jun;179(11):3509–3518. doi: 10.1128/jb.179.11.3509-3518.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Pitulle C., Dorsch M., Kazda J., Wolters J., Stackebrandt E. Phylogeny of rapidly growing members of the genus Mycobacterium. Int J Syst Bacteriol. 1992 Jul;42(3):337–343. doi: 10.1099/00207713-42-3-337. [DOI] [PubMed] [Google Scholar]
  26. Predich M., Doukhan L., Nair G., Smith I. Characterization of RNA polymerase and two sigma-factor genes from Mycobacterium smegmatis. Mol Microbiol. 1995 Jan;15(2):355–366. doi: 10.1111/j.1365-2958.1995.tb02249.x. [DOI] [PubMed] [Google Scholar]
  27. Rogall T., Wolters J., Flohr T., Böttger E. C. Towards a phylogeny and definition of species at the molecular level within the genus Mycobacterium. Int J Syst Bacteriol. 1990 Oct;40(4):323–330. doi: 10.1099/00207713-40-4-323. [DOI] [PubMed] [Google Scholar]
  28. Saiki R. K., Gelfand D. H., Stoffel S., Scharf S. J., Higuchi R., Horn G. T., Mullis K. B., Erlich H. A. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science. 1988 Jan 29;239(4839):487–491. doi: 10.1126/science.2448875. [DOI] [PubMed] [Google Scholar]
  29. Sela S., Clark-Curtiss J. E. Cloning and characterization of the Mycobacterium leprae putative ribosomal RNA promoter in Escherichia coli. Gene. 1991 Feb 1;98(1):123–127. doi: 10.1016/0378-1119(91)90114-q. [DOI] [PubMed] [Google Scholar]
  30. Springer B., Böttger E. C., Kirschner P., Wallace R. J., Jr Phylogeny of the Mycobacterium chelonae-like organism based on partial sequencing of the 16S rRNA gene and proposal of Mycobacterium mucogenicum sp. nov. Int J Syst Bacteriol. 1995 Apr;45(2):262–267. doi: 10.1099/00207713-45-2-262. [DOI] [PubMed] [Google Scholar]
  31. Stahl D. A., Urbance J. W. The division between fast- and slow-growing species corresponds to natural relationships among the mycobacteria. J Bacteriol. 1990 Jan;172(1):116–124. doi: 10.1128/jb.172.1.116-124.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Strohl W. R. Compilation and analysis of DNA sequences associated with apparent streptomycete promoters. Nucleic Acids Res. 1992 Mar 11;20(5):961–974. doi: 10.1093/nar/20.5.961. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Suzuki Y., Nagata A., Ono Y., Yamada T. Complete nucleotide sequence of the 16S rRNA gene of Mycobacterium bovis BCG. J Bacteriol. 1988 Jun;170(6):2886–2889. doi: 10.1128/jb.170.6.2886-2889.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Theissen G., Thelen L., Wagner R. Some base substitutions in the leader of an Escherichia coli ribosomal RNA operon affect the structure and function of ribosomes. Evidence for a transient scaffold function of the rRNA leader. J Mol Biol. 1993 Sep 20;233(2):203–218. doi: 10.1006/jmbi.1993.1500. [DOI] [PubMed] [Google Scholar]
  35. Verma A., Kinger A. K., Tyagi J. S. Functional analysis of transcription of the Mycobacterium tuberculosis 16S rDNA-encoding gene. Gene. 1994 Oct 11;148(1):113–118. doi: 10.1016/0378-1119(94)90243-7. [DOI] [PubMed] [Google Scholar]
  36. Winder F. G., Rooney S. A. Effects of nitrogenous components of the medium on the carbohydrate and nucleic acid content of Mycobacterium tuberculosis BCG. J Gen Microbiol. 1970 Sep;63(1):29–39. doi: 10.1099/00221287-63-1-29. [DOI] [PubMed] [Google Scholar]
  37. Yanisch-Perron C., Vieira J., Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene. 1985;33(1):103–119. doi: 10.1016/0378-1119(85)90120-9. [DOI] [PubMed] [Google Scholar]

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