Multiple small RNAs identified in Mycobacterium bovis BCG are also expressed in Mycobacterium tuberculosis and Mycobacterium smegmatis

Nucleic Acids Research

Volumn 38, Issue 12, 2010, Pages 4067-4078

  DiChiara, Jeanne M ^a   Contreras Martinez, Lydia M ^a   Livny, Jonathan ^b,c   Smith, Dorie ^a   McDonough, Kathleen A ^a,d   Belfort, Marlene ^a,d  

^a WADSWORTH CENTER   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^c BRIGHAM AND WOMEN S HOSPITAL   (United States)

^d STATE UNIVERSITY OF NEW YORK   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE IDENTIFICATION; HUMAN; HUMAN CELL; MYCOBACTERIUM SMEGMATIS; PRIORITY JOURNAL; GENETICS; METABOLISM; MOLECULAR CLONING; MOLECULAR EVOLUTION; MYCOBACTERIUM BOVIS; MYCOBACTERIUM TUBERCULOSIS;

MYCOBACTERIUM BOVIS BCG; MYCOBACTERIUM SMEGMATIS; MYCOBACTERIUM TUBERCULOSIS; STAPHYLOCOCCUS AUREUS; VIBRIO CHOLERAE;

BACTERIAL RNA; UNTRANSLATED RNA;

CLONING, MOLECULAR; EVOLUTION, MOLECULAR; MYCOBACTERIUM BOVIS; MYCOBACTERIUM SMEGMATIS; MYCOBACTERIUM TUBERCULOSIS; RNA, BACTERIAL; RNA, UNTRANSLATED;

EID: 77955077136     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq101     Document Type: Article

References (55)

1. Aziz, M.A., Wright, A., Laszlo, A., De Muynck, A., Portaels, F., Van Deun, A., Wells, C., Nunn, P., Blanc, L. and Raviglione, M. (2006) Epidemiology of antituberculosis drug resistance (the Global Project on Antituberculosis Drug Resistance Surveillance): an updated analysis. Lancet, 368, 2142-2154.
2. WHO Global Task Force on XDR-TB. Meeting (2006). Report of the meeting of the WHO Global Task Force on XDR-TB: Geneva, Switzerland, 9-10 October 2006. Geneva: World Health Organization, 2007. http://whqlibdoc.who.int/hq/2007/WHO_HTM_TB_2007.375_eng.pdf, doi: WHO/HTM/TB/2007.375.
3. Williams, N. (2006) Footprint fears for new TB threat. Curr. Biol., 16, R821-822.
4. Borgdorff, M. and Small, P.M. (2009) Scratching the surface of ignorance on MDR tuberculosis. Lancet, 373, 1822-1824.
5. Wright, A., Zignil, M., Van Deun, A., Falzon, D., Gerdes, S.R., Feldman, K., Hoffner, S., Drobniewski, F., Barrera, L., van Soolingen, D. et al. for the Global Project on Anti-Tuberculosis Drug Resistance Surveillance. (2009) Epidemiology of antituberculosis drug resistance 2002-07: an updated analysis of the Global Project on Anti-Tuberculosis Drug Resistance Surveillance. The Lancet, 373, 1861-1873.
6. Arnvig, K.B. and Young, D.B. (2009) Identification of small RNAs in Mycobacterium tuberculosis. Mol. Microbiol., 73, 397-408.
7. Vogel, J., Bartels, V., Tang, T.H., Churakov, G., Slater-Jager, J.G., Huttenhofer, A. and Wagner, E.G.H. (2003) RNomics in Escherichia coli detects new sRNA species and indiates parallel transcriptional output in bacteria. Nucleic Acids Res., 31, 6435-6643.
8. Gottesman, S. (2005) Micros for microbes: non-coding regulatory RNAs in bacteria. Trends Genet., 21, 399-404.
9. Lease, R.A., Smith, D., McDonough, K. and Belfort, M. (2004) The small noncoding DsrA RNA is an acid resistance regulator in Eschericia coli. J. Bacteriol., 186, 6179-6185.
10. Toledo-Arana, A., Repoila, F. and Cossart, P. (2007) Small noncoding RNAs controlling pathogenesis. Curr. Opin. Microbiol., 10, 182-188.
11. Johansson, J. (2005) RNA Molecules: More than Mere Information Intermediaries. ASM News, 71, 515-520.
12. Sun, X., Zhulin, I. and Wartell, R.M. (2002) Predicted structure and phyletic distribution of the RNA-binding protein Hfq. Nucleic Acids Res., 30, 3662-3671.
13. Chao, Y. and Vogel, J. (2010) The role of Hfq in bacterial pathogens. Curr. Opin. Microbiol., 13, 24-33.
14. Bohn, C., Rigoulay, C. and Bouloc, P. (2007) No detectable effect of RNA-binding protein Hfq absence in Staphylococcus aureus. BMC Microbiol., 7, 10.
15. Nielsen, J.S., Lei, L.K., Ebersbach, T., Olsen, A.S., Klitgaard, J.K., Valentin-Hansen, P. and Kallipolitis, B.H. (2009) Defining a role for Hfq in Gram-positive bacteria: evidence for Hfq-dependent antisense regulation in Listeria monocytogenes. Nucleic Acids Res, 28, 907-919.
16. Gottesman, S. (2004) The small RNA regulators of Escherichia coli: roles and mechanisms. Annu. Rev. Microbiol., 58, 303-328.
17. Perez-Bello, A., Munteanu, C.R., Ubeira, F.M., De Magalhães, A.L., Uriarte, E. and González-Díaz, H. (2009) Alignment-free prediction of mycobacterial DNA promoters based on pseudo-folding lattice network or star-graph topological indices. J. Theor. Biol, 256, 458-466.
18. Livny, J., Fogel, M.A., Davis, B.M. and Waldor, M.K. (2005) sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes. Nucleic Acids Res., 33, 4096-4105.
19. Livny, J. (2007) Efficient annotation of bacterial genomes for small, noncoding RNAs using the integrative computational tool sRNAPredict2. Methods Mol. Biol., 395, 475-488.
20. Livny, J., Teonadi, H., Livny, M. and Waldor, M.K. (2008) High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs. PLoS ONE, 3, e3197.
21. Purkayastha, A., McCue, L.A. and McDonough, K.A. (2002) Identification of a Mycobacterium tuberculosis putative classical nitroreductase gene whose expression is coregulated with that of the acr gene within macrophages, in standing versus shaking cultures, and under low oxygen conditions. Infect. Immun., 70, 1518-1529.
22. Florczyk, M.A., McCue, L.A., Purkayastha, A., Currenti, E., Wolin, M.J. and McDonough, K.A. (2003) A family of acr-coregulated Mycobacterium tuberculosis genes shares a common dna motif and requires Rv3133c (dosR or devR) for expression. Infect. Immun., 71, 5332-5343.
23. Gazdik, M.A., Bai, G., Wu, Y. and McDonough, K.A. (2009) Rv1675c (cmr) regulates intramacrophage and cAMP-induced gene expression in Mycobacterium tuberculosis-complex mycobacteria. Mol. Microbiol., 71, 434-448.
24. Lau, N.C., Lim, L.P., Wienstein, E.G. and Bartel, D.P. (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science, 294, 858-862.
25. Kempsell, K.E., Ji, Y., Estrada-G, I.C.E., Colston, M.J. and Cox, R.A. (1992) 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., 138, 1717-1727.
26. Roth, A., Fischer, M., Hamid, M.E., Michalke, S., Ludwig, W. and Mauch, H. (1998) Differentiation of phylogentetically related slowly growing mycobacteria based on 16s-23s rrna gene internal transcribed spacer sequences. J. Clin. Microbiol., 36, 139-147.
27. Awasthy, D., Gaonkar, S., Shandil, R.K., Yadav, R., Bharath, S., Marcel, N., Subbulakshmi, V. and Sharma, U. (2009) Inactivation of ilvB1 gene in Mycobacterium tuberculosis leads to branched chain amino acids auxotrophy and attenuation of virulence in mice. Microbiology, 155, 2978-2987.
28. Grandoni, J.A., Zahler, S.A. and Calvo, J.M. (1992) Transcriptional regulation of the ilv-leu operon of Bacillus subtilis. J. Bacteriol., 174, 3212-3219.
29. Grandoni, J.A., Fulmer, S.B., Brissio, V., Zahler, S.A. and Calvo, J.M. (1993) Regions of the Bacillus subtilis ilv-leu Operon Involved in Regulation by Leucine. J. Bacteriol., 175, 7581-7593.
30. Henkin, T.M. (1996) Control of Transciption Termination in Prokaryotes. Annu. Rev. Genet., 30, 35-57.
31. Kremer, L., Nampoothiri, K.M., Lesjean, S., Dover, L.G., Graham, S., Betts, J., Brennan, P.J., Minnikin, D.E., Locht, C. and Besra, G.S. (2001) Biochemical characterization of acyl carrier protein (AcpM) and malonyl-CoA:AcpM transacylase (mtFabD), two major components of Mycobacterium tuberculosis fatty acid synthase II. J. Biol. Chem., 276, 27967-27974.
32. Betts, J.C., Lukey, P.T., Robb, L.C., McAdam, R.A. and Duncan, K. (2002) Evaluation of a nutrient starvation model of Mycobcaterium tuberculosis persistence by gene and protein expression profiling. Mol. Microbiol., 43, 717-731.
33. Jungblut, P.R., Schaible, U.E., Mollenkopf, H.J., Zimny-Arndt, U., Raupach, B., Mattow, J., Halada, P., Lamer, S., Hagens, K. and Kaufmann, S.H. (1999) Comparative proteiome analysis of Mycobacterium tuberculosis and Mycobacterium bovis BCG strains: towards functional genomics of microbial pathogens. Mol. Microbiol., 33, 1103-1117.
34. Goldstone, R.M., Goonesekera, S.D., Bloom, B.R. and Sampson, S.L. (2009) The transcriptional regulator Rv0485 modulates the expresion of a pe/ppe gene pair and is required for Mycobcaterium tuberculosis virulence. Infect. Immun., 77, 4654-4667.
35. Choonee, N., Evan, S., Zig, L. and Putzer, H. (2007) Ribosomal protein L20 controls expression of the Bacillus subtilis infC operon via a transcription attenuation mechanism. Nucleic Acids Res., 35, 1578-1588.
36. Devulder, G., Pérouse de Montclos, M. and Flandrois, J.P. (2005) A multigene approach to phylogenetic analysis using the genus Mycobacterium as a model. Int. J. Syst. Evol. Microbiol., 55, 293-302.
37. Hobson, R.J., McBride, A.J., Kempsell, K.E. and Dale, J.W. (2002) Use of an arrayed promoter -probe library for the identification of macrophage-regulated genes in Mycobacterium tuberculosis. Microbiology, 148, 1571-1579.
38. Monohan, I.M., Bettes, J., Banerjee, D.K. and Butcher, P.D. (2001) Differential expression of mycobacterial proteins following phagocytosis by macrophages. Microbiology, 147, 459-471.
39. Smith, I. (2003) Mycobacterium tuberculosis pathogenesis and molecular determinants of virulence. Clin. Microbiol. Rev., 16, 463-496.
40. Sturgill-Koszycki, S., Schlesinger, P.H., Chakraborty, P., Haddix, P.L., Collins, H.L., Fok, A.K., Allen, R.D., Gluck, S.L., Heuser, J. and Russell, D.G. (1994) Lack of acidification in Mycobacterial phagosomes produced by exclusion of the vesicular proton-ATPase. Science, 263, 678-681.
41. Kawano, M., Reynolds, A.A., Miranda-Rios, J. and Storz, G. (2005) Detection of 5′- and 3′-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli. Nucleic Acids Res., 33, 1040-1050.
42. Liu, J.M., Livny, J., Lawrence, M.S., Kimball, M.D., Waldor, M.K. and Camilli, A. (2009) Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing. Nucleic Acids Res., 37, e46, 1-10.
43. Uzilov, A.V., Keegan, J.M. and Mathews, D.H. (2006) Detection of non-coding RNAs on the basis of predicted secondary structure formation and free energy change. BMC Bioinformatics, 7, 173.
44. Lee, J.H., Karakousis, P.C. and Bishai, W.R. (2008) Roles of SigB and SigF in the Mycobacterium tuberculosis sigma factor network. J. Bacteriol., 190, 699-707.
45. Agarwal, N. and Tyagi, A.K. (2006) Mycobacterial transcriptional signals: requirements for recognition by RNA polymerase and optimal transcriptional activity. Nucleic Acids Res., 34, 4245-4257.
46. Marchais, A., Naville, M., Bohn, C., Bouloc, P. and Gautheret, D. (2009) Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles. Genome Res., 19, 1084-1092.
47. Miller, C.D., Hall, K., Liang, Y.N., Nieman, K., Sorensen, D., Issa, B., Anderson, A.J. and Sims, R.C. (2004) Isolation and Characterization of polycyclic aromatic hydrocarbon-degrading mycobacterium isolates from soil. Microb. Ecol., 48, 230-238.
48. Khan, A.A., Kim, S.J., Paine, D.D. and Cerniglia, C.E. (2002) Classification of a polycyclic aromatic hydrocarbon-metabolizing bacterium, Mycobacterium sp. strain PYR-1, as Mycobacterium vanbaalenii sp. nov. Int. J. Syst. Evol. Microbiol., 52, 1997-2002.
49. Brezna, B., Khan, A.A. and Cerniglia, C.E. (2003) Molecular characterization of dioxygenases from polycyclic aromatic hydrocarbon-degrading Mycobacterium spp. FEMS Microbiol. Lett., 223, 177-183.
50. Ganguly, N., Siddiqui, I. and Sharma, P. (2008) Role of M. tuberculosis RD-1 region encoded secretory proteins in protective response and virulence. Tuberculosis, 88, 510-517.
51. van Ingen, J., de Zwaan, R., Dekhuijzen, R., Boeree, M. and van Soolingen, D. (2009) Region of difference 1 in nontuberculous Mycobacterium Species adds a phylogenetic and taxonomical character. J. Bacteriol., 191, 5865-5967.
52. Vogel, J. (2009) A rough guide to the non-coding RNA world of Salmonella. Mol. Microbiol., 71, 1-11.
53. Agarwal, N., Lamichhane, G., Gupta, R., Nolan, S. and Bishai, W.R. (2009) Cyclic AMP intoxication of macrophages by a Mycobacterium tuberculosis adenylate cyclase. Nature, 460, 98-102.
54. Bai, G., Schaak, D.D. and McDonough, K.A. (2009) cAMP levels within Mycobacterium tuberculosis and Mycobacterium bovis BCG increase upon infection of macrophages. FEMS Immunol. Med. Microbiol., 55, 68-73.
55. Mt), a cyclic AMP receptor protein-like DNA binding protein. J. Bacteriol., 187, 7795-7804.