1887

Abstract

In , the gene encodes a small non-translated RNA that regulates several genes involved in transport of amino acids and peptides (including , and ). Microarray analysis identified as an additional regulatory target of GcvB. The gene encodes a permease for the transport of glycine, -alanine, -serine and -cycloserine. RT-PCR confirmed that GcvB and the Hfq protein negatively regulate mRNA in cells grown in Luria–Bertani broth. In addition, deletion of the gene resulted in increased sensitivity to -cycloserine, consistent with increased expression of . A  : :  translational fusion confirmed that GcvB negatively regulates expression in Luria–Bertani broth and that Hfq is required for the GcvB effect. GcvB had no effect on  : :  expression in glucose minimal medium supplemented with glycine. However, Hfq still negatively regulated the fusion in the absence of GcvB. A set of transcriptional fusions of to identified a sequence in necessary for regulation by GcvB. Analysis of GcvB identified a region complementary to this region of mRNA. However, mutations predicted to disrupt base-pairing between mRNA and GcvB did not alter expression of  : : . A model for GcvB function in cell physiology is discussed.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.023598-0
2009-01-01
2019-08-23
Loading full text...

Full text loading...

/deliver/fulltext/micro/155/1/106.html?itemId=/content/journal/micro/10.1099/mic.0.023598-0&mimeType=html&fmt=ahah

References

  1. Altuvia, S., Zhang, A., Argaman, L., Tiwari, A. & Storz, G. ( 1998; ). The Escherichia coli OxyS regulatory RNA represses fhlA translation by blocking ribosome binding. EMBO J 17, 6069–6075.[CrossRef]
    [Google Scholar]
  2. Argaman, L. & Altuvia, S. ( 2000; ). fhlA repression by OxyS RNA: kissing complex formation at two sites results in a stable antisense-target RNA complex. J Mol Biol 300, 1101–1112.[CrossRef]
    [Google Scholar]
  3. Argaman, L., Hershberg, R., Vogel, J., Bejerano, G., Wagner, E. G., Margalit, H. & Altuvia, S. ( 2001; ). Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr Biol 11, 941–950.[CrossRef]
    [Google Scholar]
  4. Casadaban, M. J., Chou, J. & Cohen, S. N. ( 1980; ). In vitro gene fusions that join an enzymatically active β-galactosidase segment to amino-terminal fragments of exogenous proteins: Escherichia coli plasmid vectors for the detection and cloning of translational initiation signals. J Bacteriol 143, 971–980.
    [Google Scholar]
  5. Chen, S., Zhang, A., Blyn, L. B. & Storz, G. ( 2004; ). MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli. J Bacteriol 186, 6689–6697.[CrossRef]
    [Google Scholar]
  6. Chopra, I. & Ball, P. ( 1982; ). Transport of antibiotics into bacteria. Adv Microb Physiol 23, 183–240.
    [Google Scholar]
  7. Cosloy, S. D. ( 1973; ). d-Serine transport system in Escherichia coli K-12. J Bacteriol 114, 679–684.
    [Google Scholar]
  8. Gama-Castro, S., Jimenez-Jacinto, V., Peralta-Gil, M., Santos-Zavaleta, A., Peñaloza-Spinola, M. I., Contreras-Moreira, B., Segura-Salazar, J., Muñiz-Rascado, L., Martínez-Flores, I. & other authors ( 2008; ). RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res 36, D120–D124.[CrossRef]
    [Google Scholar]
  9. Gottesman, S. ( 2004; ). The small RNA regulators of Escherichia coli: roles and mechanisms. Annu Rev Microbiol 58, 303–328.[CrossRef]
    [Google Scholar]
  10. Hershberg, R., Altuvia, S. & Margalit, H. ( 2003; ). A survey of small RNA-encoding genes in Escherichia coli. . Nucleic Acids Res 31, 1813–1820.[CrossRef]
    [Google Scholar]
  11. Hiles, I. D., Gallagher, M. P., Jamieson, D. J. & Higgins, C. F. ( 1987; ). Molecular characterization of the oligopeptide permease of Salmonella typhimurium. J Mol Biol 195, 125–142.[CrossRef]
    [Google Scholar]
  12. Jourdan, A. D. & Stauffer, G. V. ( 1998; ). Mutational analysis of the transcriptional regulator GcvA: amino acids important for activation, repression, and DNA binding. J Bacteriol 180, 4865–4871.
    [Google Scholar]
  13. Jourdan, A. D. & Stauffer, G. V. ( 1999; ). Genetic analysis of the GcvA binding site in the gcvA control region. Microbiology 145, 2153–2162.[CrossRef]
    [Google Scholar]
  14. Kawamoto, H., Koide, Y., Morita, T. & Aiba, H. ( 2006; ). Base-pairing requirement for RNA silencing by a bacterial small RNA and acceleration of duplex formation by Hfq. Mol Microbiol 61, 1013–1022.[CrossRef]
    [Google Scholar]
  15. Lease, R. A. & Belfort, M. ( 2000; ). Riboregulation by DsrA RNA: trans-actions for global economy. Mol Microbiol 38, 667–672.[CrossRef]
    [Google Scholar]
  16. Ledeboer, N. A., Frye, J. G., McClelland, M. & Jones, B. D. ( 2006; ). Salmonella enterica serovar Typhimurium requires the Lpf, Pef, and Tafi fimbriae for biofilm formation on HEp-2 tissue culture cells and chicken intestinal epithelium. Infect Immun 74, 3156–3169.[CrossRef]
    [Google Scholar]
  17. Liu, M. Y., Gui, G., Wei, B., Preston, J. F., III, Oakford, L., Yuksel, U., Giedroc, D. P. & Romeo, T. ( 1997; ). The RNA molecule CsrB binds to the global regulatory protein CsrA and antagonizes its activity in Escherichia coli. J Biol Chem 272, 17502–17510.[CrossRef]
    [Google Scholar]
  18. Majdalani, N., Cunning, C., Sledjeski, D., Elliott, T. & Gottesman, S. ( 1998; ). DsrA RNA regulates translation of RpoS message by an anti-antisense mechanism, independent of its action as an antisilencer of transcription. Proc Natl Acad Sci U S A 95, 12462–12467.[CrossRef]
    [Google Scholar]
  19. Majdalani, N., Hernandez, D. & Gottesman, S. ( 2002; ). Regulation and mode of action of the second small RNA activator of RpoS translation, RprA. Mol Microbiol 46, 813–826.[CrossRef]
    [Google Scholar]
  20. Majdalani, N., Vanderpool, C. K. & Gottesman, S. ( 2005; ). Bacterial small RNA regulators. Crit Rev Biochem Mol Biol 40, 93–113.[CrossRef]
    [Google Scholar]
  21. Masse, E. & Gottesman, S. ( 2002; ). A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli. Proc Natl Acad Sci U S A 99, 4620–4625.[CrossRef]
    [Google Scholar]
  22. Mathews, D. H., Sabina, J., Zuker, M. & Turner, D. H. ( 1999; ). Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288, 911–940.[CrossRef]
    [Google Scholar]
  23. Miller, J. ( 1972; ). Experiments in Molecular Genetics. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
  24. Moller, T., Franch, T., Udesen, C., Gerdes, K. & Valentin-Hansen, P. ( 2002; ). Spot 42 RNA mediates discoordinate expression of the E. coli galactose operon. Genes Dev 16, 1696–1706.[CrossRef]
    [Google Scholar]
  25. Panasenko, S. M., Cameron, J. R., Davis, R. W. & Lehman, I. R. ( 1977; ). Five hundredfold overproduction of DNA ligase after induction of a hybrid lambda lysogen constructed in vitro. Science 196, 188–189.[CrossRef]
    [Google Scholar]
  26. Payne, J. W. ( 1986; ). Drug delivery systems: optimising the structure of peptide carriers for synthetic antimicrobial drugs. Drugs Exp Clin Res 12, 585–594.
    [Google Scholar]
  27. Pulvermacher, S. C., Stauffer, L. T. & Stauffer, G. V. ( 2008; ). The role of the small regulatory RNA GcvB in GcvB/mRNA posttranscriptional regulation of oppA and dppA in Escherichia coli. FEMS Microbiol Lett 281, 42–50.[CrossRef]
    [Google Scholar]
  28. Rasmussen, A. A., Eriksen, M., Gilany, K., Udesen, C., Franch, T., Petersen, C. & Valentin-Hansen, P. ( 2005; ). Regulation of ompA mRNA stability: the role of a small regulatory RNA in growth phase-dependent control. Mol Microbiol 58, 1421–1429.[CrossRef]
    [Google Scholar]
  29. Robbins, J. C. & Oxender, D. L. ( 1973; ). Transport systems for alanine, serine, and glycine in Escherichia coli K-12. J Bacteriol 116, 12–18.
    [Google Scholar]
  30. Romby, P., Vandenesch, F. & Wagner, E. G. ( 2006; ). The role of RNAs in the regulation of virulence-gene expression. Curr Opin Microbiol 9, 229–236.[CrossRef]
    [Google Scholar]
  31. Rudd, K. E. ( 2000; ). EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28, 60–64.[CrossRef]
    [Google Scholar]
  32. Russell, R. R. ( 1972; ). Mapping of a d-cycloserine resistance locus in Escherichia coli K-12. J Bacteriol 111, 622–624.
    [Google Scholar]
  33. Sarkar, G. & Sommer, S. S. ( 1990; ). The “megaprimer” method of site-directed mutagenesis. Biotechniques 8, 404–407.
    [Google Scholar]
  34. Schmidt, M., Zheng, P. & Delihas, N. ( 1995; ). Secondary structures of Escherichia coli antisense micF RNA, the 5′-end of the target ompF mRNA, and the RNA/RNA duplex. Biochemistry 34, 3621–3631.[CrossRef]
    [Google Scholar]
  35. Sharma, C. M., Darfeuille, F., Plantinga, T. H. & Vogel, J. ( 2007; ). A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites. Genes Dev 21, 2804–2817.[CrossRef]
    [Google Scholar]
  36. Shimada, K., Weisberg, R. A. & Gottesman, M. E. ( 1972; ). Prophage lambda at unusual chromosomal locations. I. Location of the secondary attachment sites and the properties of the lysogens. J Mol Biol 63, 483–503.[CrossRef]
    [Google Scholar]
  37. Sledjeski, D. D., Whitman, C. & Zhang, A. ( 2001; ). Hfq is necessary for regulation by the untranslated RNA DsrA. J Bacteriol 183, 1997–2005.[CrossRef]
    [Google Scholar]
  38. Smith, M. W. & Payne, J. W. ( 1990; ). Simultaneous exploitation of different peptide permeases by combinations of synthetic peptide smugglins can lead to enhanced antibacterial activity. FEMS Microbiol Lett 58, 311–316.
    [Google Scholar]
  39. Storz, G., Altuvia, S. & Wassarman, K. M. ( 2005; ). An abundance of RNA regulators. Annu Rev Biochem 74, 199–217.[CrossRef]
    [Google Scholar]
  40. Tao, H., Bausch, C., Richmond, C., Blattner, F. R. & Conway, T. ( 1999; ). Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media. J Bacteriol 181, 6425–6440.
    [Google Scholar]
  41. Tjaden, B., Goodwin, S. S., Opdyke, J. A., Guillier, M., Fu, D. X., Gottesman, S. & Storz, G. ( 2006; ). Target prediction for small, noncoding RNAs in bacteria. Nucleic Acids Res 34, 2791–2802.[CrossRef]
    [Google Scholar]
  42. Udekwu, K. I., Darfeuille, F., Vogel, J., Reimegard, J., Holmqvist, E. & Wagner, E. G. ( 2005; ). Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA. Genes Dev 19, 2355–2366.[CrossRef]
    [Google Scholar]
  43. Urbanowski, M. L. & Stauffer, G. V. ( 1986; ). Autoregulation by tandem promoters of the Salmonella typhimurium LT2 metJ gene. J Bacteriol 165, 740–745.
    [Google Scholar]
  44. Urbanowski, M. L., Stauffer, L. T. & Stauffer, G. V. ( 2000; ). The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli. Mol Microbiol 37, 856–868.[CrossRef]
    [Google Scholar]
  45. Valentin-Hansen, P., Eriksen, M. & Udesen, C. ( 2004; ). The bacterial Sm-like protein Hfq: a key player in RNA transactions. Mol Microbiol 51, 1525–1533.[CrossRef]
    [Google Scholar]
  46. Vogel, H. J. & Bonner, D. M. ( 1956; ). Acetylornithinase of Escherichia coli: partial purification and some properties. J Biol Chem 218, 97–106.
    [Google Scholar]
  47. Vogel, J. & Papenfort, K. ( 2006; ). Small non-coding RNAs and the bacterial outer membrane. Curr Opin Microbiol 9, 605–611.[CrossRef]
    [Google Scholar]
  48. Wagner, E. G. H. & Darfeuille, F. ( 2005; ). Small regulatory RNAs in bacteria. In Small RNAs: Analysis and Regulatory Functions (Nucleic Acids and Molecular Biology, vol. 17), pp. 1–29. Edited by W. Nellen & C. Hammann. Berlin: Springer-Verlag.
  49. Wagner, E. G. & Flardh, K. ( 2002; ). Antisense RNAs everywhere? Trends Genet 18, 223–226.[CrossRef]
    [Google Scholar]
  50. Wargel, R. J., Hadur, C. A. & Neuhaus, F. C. ( 1971; ). Mechanism of d-cycloserine action: transport mutants for d-alanine, d-cycloserine, and glycine. J Bacteriol 105, 1028–1035.
    [Google Scholar]
  51. Wassarman, K. M. ( 2002; ). Small RNAs in bacteria: diverse regulators of gene expression in response to environmental changes. Cell 109, 141–144.[CrossRef]
    [Google Scholar]
  52. Wassarman, K. M. & Storz, G. ( 2000; ). 6S RNA regulates E. coli RNA polymerase activity. Cell 101, 613–623.[CrossRef]
    [Google Scholar]
  53. Weilbacher, T., Suzuki, K., Dubey, A. K., Wang, X., Gudapaty, S., Morozov, I., Baker, C. S., Georgellis, D., Babitzke, P. & Romeo, T. ( 2003; ). A novel sRNA component of the carbon storage regulatory system of Escherichia coli. Mol Microbiol 48, 657–670.[CrossRef]
    [Google Scholar]
  54. Zhang, A., Altuvia, S., Tiwari, A., Argaman, L., Hengge-Aronis, R. & Storz, G. ( 1998; ). The OxyS regulatory RNA represses rpoS translation and binds the Hfq (HF-I) protein. EMBO J 17, 6061–6068.[CrossRef]
    [Google Scholar]
  55. Zhang, A., Wassarman, K. M., Rosenow, C., Tjaden, B. C., Storz, G. & Gottesman, S. ( 2003; ). Global analysis of small RNA and mRNA targets of Hfq. Mol Microbiol 50, 1111–1124.[CrossRef]
    [Google Scholar]
  56. Zuker, M. ( 2003; ). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31, 3406–3415.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.023598-0
Loading
/content/journal/micro/10.1099/mic.0.023598-0
Loading

Data & Media loading...

vol. , part 1, pp. 106 - 114

Genes shown to be significantly regulated in the WT versus the Δ strain by microarray analysis [PDF file](45 KB)



PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error