Common and divergent features in transcriptional control of the homologous small RNAs GlmY and GlmZ in Enterobacteriaceae

Nucleic Acids Research

Volumn 39, Issue 4, 2011, Pages 1294-1309

  Göpel, Yvonne ^a   Lüttmann, Denise ^a   Heroven, Ann Kathrin ^a   Reichenbach, Birte ^a   Dersch, Petra ^a   Görke, Boris ^a,b  

^a UNIVERSITY OF GÖTTINGEN   (Germany)

^b HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; GENE PRODUCT; GLUTAMINE FRUCTOSE 6 PHOSPHATE AMINOTRANSFERASE; INTEGRATION HOST FACTOR; RESPONSE REGULATOR; SMALL RNA GLMY; SMALL RNA GLMZ; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; ENTEROBACTERIACEAE; ENZYME SYNTHESIS; ESCHERICHIA COLI; GENETIC CONSERVATION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; PROTEIN EXPRESSION; PROTEIN PHOSPHORYLATION; SALMONELLA TYPHIMURIUM; SYNTENY; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; YERSINIA PSEUDOTUBERCULOSIS;

BACTERIAL PROTEINS; BINDING SITES; DNA-BINDING PROTEINS; ENTEROBACTERIACEAE; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; INTEGRATION HOST FACTORS; PROMOTER REGIONS, GENETIC; RNA POLYMERASE SIGMA 54; RNA, BACTERIAL; RNA, SMALL UNTRANSLATED; SALMONELLA TYPHIMURIUM; SYNTENY; TRANSCRIPTION, GENETIC; YERSINIA PSEUDOTUBERCULOSIS;

ENTEROBACTERIACEAE; ESCHERICHIA COLI; SALMONELLA TYPHIMURIUM; YERSINIA PSEUDOTUBERCULOSIS;

EID: 79952327376     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq986     Document Type: Article

References (40)

1. Gorke, B. and Vogel, J. (2008) Noncoding RNA control of the making and breaking of sugars. Genes Dev., 22, 2914-2925.
2. Repoila, F. and Darfeuille, F. (2009) Small regulatory non-coding RNAs in bacteria: physiology and mechanistic aspects. Biol. Cell, 101, 117-131.
3. Guillier, M., Gottesman, S. and Storz, G. (2006) Modulating the outer membrane with small RNAs. Genes Dev., 20, 2338-2348. (Pubitemid 44320382)
4. Brantl, S. (2009) Bacterial chromosome-encoded small regulatory RNAs. Future Microbiol., 4, 85-103.
5. Vanderpool, C.K. (2007) Physiological consequences of small RNA-mediated regulation of glucose-phosphate stress. Curr. Opin. Microbiol., 10, 146-151. (Pubitemid 46590051)
6. Waters, L.S. and Storz, G. (2009) Regulatory RNAs in bacteria. Cell, 136, 615-628.
7. Frohlich, K.S. and Vogel, J. (2009) Activation of gene expression by small RNA. Curr. Opin. Microbiol., 12, 674-682.
8. Reichenbach, B., Maes, A., Kalamorz, F., Hajnsdorf, E. and Gorke, B. (2008) The small RNA GlmY acts upstream of the sRNA GlmZ in the activation of glmS expression and is subject to regulation by polyadenylation in Escherichia coli. Nucleic Acids Res., 36, 2570-2580. (Pubitemid 351659572)
9. Urban, J.H. and Vogel, J. (2008) Two seemingly homologous noncoding RNAs act hierarchically to activate glmS mRNA translation. PLoS Biol., 6, e64.
10. Kalamorz, F., Reichenbach, B., Marz, W., Rak, B. and Gorke, B. (2007) Feedback control of glucosamine-6-phosphate synthase GlmS expression depends on the small RNA GlmZ and involves the novel protein YhbJ in Escherichia coli. Mol. Microbiol., 65, 1518-1533. (Pubitemid 47347835)
11. Urban, J.H., Papenfort, K., Thomsen, J., Schmitz, R.A. and Vogel, J. (2007) A conserved small RNA promotes discoordinate expression of the glmUS operon mRNA to activate GlmS synthesis. J. Mol. Biol., 373, 521-528. (Pubitemid 47488389)
12. Valverde, C. and Haas, D. (2008) Small RNAs controlled by two-component systems. Adv. Exp. Med. Biol., 631, 54-79.
13. Vogel, J. (2009) A rough guide to the non-coding RNA world of Salmonella. Mol. Microbiol., 71, 1-11.
14. Sonnleitner, E., Abdou, L. and Haas, D. (2009) Small RNA as global regulator of carbon catabolite repression in Pseudomonas aeruginosa. Proc. Natl Acad. Sci. USA, 106, 21866-21871.
15. Tu, K.C. and Bassler, B.L. (2007) Multiple small RNAs act additively to integrate sensory information and control quorum sensing in Vibrio harveyi. Genes Dev., 21, 221-233. (Pubitemid 46155815)
16. Reitzer, L. and Schneider, B.L. (2001) Metabolic context and possible physiological themes of sigma(54)-dependent genes in Escherichia coli. Microbiol. Mol. Biol. Rev., 65, 422-444. (Pubitemid 32881714)
17. Zhao, K., Liu, M. and Burgess, R.R. (2010) Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis. Nucleic Acids Res., 38, 1273-1283.
18. Wigneshweraraj, S., Bose, D., Burrows, P.C., Joly, N., Schumacher, J., Rappas, M., Pape, T., Zhang, X., Stockley, P. Severinov, K. et al. (2008) Modus operandi of the bacterial RNA polymerase containing the sigma54 promoter-specificity factor. Mol. Microbiol., 68, 538-546. (Pubitemid 351490187)
19. Mendoza-Vargas, A., Olvera, L., Olvera, M., Grande, R., Vega-Alvarado, L., Taboada, B., Jimenez-Jacinto, V., Salgado, H., Juarez, K., Contreras-Moreira, B. et al. (2009) Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli. PLoS ONE, 4, e7526.
20. Wade, J.T., Roa, D.C., Grainger, D.C., Hurd, D., Busby, S.J., Struhl, K. and Nudler, E. (2006) Extensive functional overlap between sigma factors in Escherichia coli. Nat. Struct. Mol. Biol., 13, 806-814. (Pubitemid 44338775)
21. Darfeuille, F., Unoson, C., Vogel, J. and Wagner, E.G. (2007) An antisense RNA inhibits translation by competing with standby ribosomes. Mol. Cell., 26, 381-392. (Pubitemid 46687099)
22. Reichenbach, B., Gopel, Y. and Gorke, B. (2009) Dual control by perfectly overlapping sigma 54- and sigma 70- promoters adjusts small RNA GlmY expression to different environmental signals. Mol. Microbiol., 74, 1054-1070.
23. Wilson, G.G., Young, K.Y., Edlin, G.J. and Konigsberg, W. (1979) High-frequency generalised transduction by bacteriophage T4. Nature, 280, 80-82. (Pubitemid 10231991)
24. Diederich, L., Rasmussen, L.J. and Messer, W. (1992) New cloning vectors for integration in the lambda attachment site attB of the Escherichia coli chromosome. Plasmid, 28, 14-24.
25. Miller, J. (1972) Experiments in Molecular Genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
26. Heroven, A.K., Bohme, K., Rohde, M. and Dersch, P. (2008) A Csr-type regulatory system, including small non-coding RNAs, regulates the global virulence regulator RovA of Yersinia pseudotuberculosis through RovM. Mol. Microbiol., 68, 1179-1195. (Pubitemid 351670194)
27. Stratmann, T., Madhusudan, S. and Schnetz, K. (2008) Regulation of the yjjQ-bglJ operon, encoding LuxR-type transcription factors, and the divergent yjjP gene by H-NS and LeuO. J. Bacteriol., 190, 926-935. (Pubitemid 351170936)
28. Dehal, P.S., Joachimiak, M.P., Price, M.N., Bates, J.T., Baumohl, J.K., Chivian, D., Friedland, G.D., Huang, K.H., Keller, K., Novichkov, P.S. et al. (2009) MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Res., 38, D396-400.
29. Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T. et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res., 36, D480-D484. (Pubitemid 351149770)
30. Swinger, K.K. and Rice, P.A. (2004) IHF and HU: flexible architects of bent DNA. Curr. Opin. Struct. Biol., 14, 28-35. (Pubitemid 38249589)
31. Paradis, S., Boissinot, M., Paquette, N., Belanger, S.D., Martel, E.A., Boudreau, D.K., Picard, F.J., Ouellette, M., Roy, P.H. and Bergeron, M.G. (2005) Phylogeny of the Enterobacteriaceae based on genes encoding elongation factor Tu and F-ATPase beta-subunit. Int. J. Syst. Evol. Microbiol., 55, 2013-2025. (Pubitemid 41410419)
32. Yamamoto, K., Hirao, K., Oshima, T., Aiba, H., Utsumi, R. and Ishihama, A. (2005) Functional characterization in vitro of all two-component signal transduction systems from Escherichia coli. J. Biol. Chem., 280, 1448-1456.
33. Stock, A.M., Robinson, V.L. and Goudreau, P.N. (2000) Two-component signal transduction. Annu. Rev. Biochem., 69, 183-215.
34. Zakikhany, K., Harrington, C.R., Nimtz, M., Hinton, J.C. and Romling, U. (2010) Unphosphorylated CsgD controls biofilm formation in Salmonella enterica serovar Typhimurium. Mol. Microbiol., 77, 771-786.
35. Scharf, B.E. (2010) Summary of useful methods for two-component system research. Curr. Opin. Microbiol., 13, 246-252.
36. Flamez, C., Ricard, I., Arafah, S., Simonet, M. and Marceau, M. (2008) Phenotypic analysis of Yersinia pseudotuberculosis 32777 response regulator mutants: new insights into two-component system regulon plasticity in bacteria. Int. J. Med. Microbiol., 298, 193-207. (Pubitemid 351318364)
37. Reading, N.C., Torres, A.G., Kendall, M.M., Hughes, D.T., Yamamoto, K. and Sperandio, V. (2007) A novel two-component signaling system that activates transcription of an enterohemorrhagic Escherichia coli effector involved in remodeling of host actin. J. Bacteriol., 189, 2468-2476. (Pubitemid 46411361)
38. Reading, N.C., Rasko, D.A., Torres, A.G. and Sperandio, V. (2009) The two-component system QseEF and the membrane protein QseG link adrenergic and stress sensing to bacterial pathogenesis. Proc. Natl Acad. Sci. USA, 106, 5889-5894.
39. Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K.A., Tomita, M., Wanner, B.L. and Mori, H. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol., 2, 1-11.
40. Gorke, B. and Rak, B. (1999) Catabolite control of Escherichia coli regulatory protein BglG activity by antagonistically acting phosphorylations. EMBO J., 18, 3370-3379. (Pubitemid 29276583)