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
2020-04-07
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 J17:6069–6075
    [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 Biol300:1101–1112
    [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 Biol11:941–950
    [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 Bacteriol143:971–980
    [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 Bacteriol186:6689–6697
    [Google Scholar]
  6. Chopra I., Ball P.. 1982; Transport of antibiotics into bacteria. Adv Microb Physiol23:183–240
    [Google Scholar]
  7. Cosloy S. D.. 1973; d-Serine transport system in Escherichia coli K-12. J Bacteriol114:679–684
    [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 Res36:D120–D124
    [Google Scholar]
  9. Gottesman S.. 2004; The small RNA regulators of Escherichia coli: roles and mechanisms. Annu Rev Microbiol58:303–328
    [Google Scholar]
  10. Hershberg R., Altuvia S., Margalit H.. 2003; A survey of small RNA-encoding genes in Escherichia coli. Nucleic Acids Res31:1813–1820
    [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 Biol195:125–142
    [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 Bacteriol180:4865–4871
    [Google Scholar]
  13. Jourdan A. D., Stauffer G. V.. 1999; Genetic analysis of the GcvA binding site in the gcvA control region. Microbiology145:2153–2162
    [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 Microbiol61:1013–1022
    [Google Scholar]
  15. Lease R. A., Belfort M.. 2000; Riboregulation by DsrA RNA: trans-actions for global economy. Mol Microbiol38:667–672
    [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 Immun74:3156–3169
    [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 Chem272:17502–17510
    [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 A95:12462–12467
    [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 Microbiol46:813–826
    [Google Scholar]
  20. Majdalani N., Vanderpool C. K., Gottesman S.. 2005; Bacterial small RNA regulators. Crit Rev Biochem Mol Biol40:93–113
    [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 A99:4620–4625
    [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 Biol288:911–940
    [Google Scholar]
  23. Miller J.. 1972; Experiments in Molecular Genetics Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press;
    [Google Scholar]
  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 Dev16:1696–1706
    [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. Science196:188–189
    [Google Scholar]
  26. Payne J. W.. 1986; Drug delivery systems: optimising the structure of peptide carriers for synthetic antimicrobial drugs. Drugs Exp Clin Res12:585–594
    [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 Lett281:42–50
    [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 Microbiol58:1421–1429
    [Google Scholar]
  29. Robbins J. C., Oxender D. L.. 1973; Transport systems for alanine, serine, and glycine in Escherichia coli K-12. J Bacteriol116:12–18
    [Google Scholar]
  30. Romby P., Vandenesch F., Wagner E. G.. 2006; The role of RNAs in the regulation of virulence-gene expression. Curr Opin Microbiol9:229–236
    [Google Scholar]
  31. Rudd K. E.. 2000; EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res28:60–64
    [Google Scholar]
  32. Russell R. R.. 1972; Mapping of a d-cycloserine resistance locus in Escherichia coli K-12. J Bacteriol111:622–624
    [Google Scholar]
  33. Sarkar G., Sommer S. S.. 1990; The “megaprimer” method of site-directed mutagenesis. Biotechniques8:404–407
    [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. Biochemistry34:3621–3631
    [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 Dev21:2804–2817
    [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 Biol63:483–503
    [Google Scholar]
  37. Sledjeski D. D., Whitman C., Zhang A.. 2001; Hfq is necessary for regulation by the untranslated RNA DsrA. J Bacteriol183:1997–2005
    [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 Lett58:311–316
    [Google Scholar]
  39. Storz G., Altuvia S., Wassarman K. M.. 2005; An abundance of RNA regulators. Annu Rev Biochem74:199–217
    [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 Bacteriol181:6425–6440
    [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 Res34:2791–2802
    [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 Dev19:2355–2366
    [Google Scholar]
  43. Urbanowski M. L., Stauffer G. V.. 1986; Autoregulation by tandem promoters of the Salmonella typhimurium LT2 metJ gene. J Bacteriol165:740–745
    [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 Microbiol37:856–868
    [Google Scholar]
  45. Valentin-Hansen P., Eriksen M., Udesen C.. 2004; The bacterial Sm-like protein Hfq: a key player in RNA transactions. Mol Microbiol51:1525–1533
    [Google Scholar]
  46. Vogel H. J., Bonner D. M.. 1956; Acetylornithinase of Escherichia coli: partial purification and some properties. J Biol Chem218:97–106
    [Google Scholar]
  47. Vogel J., Papenfort K.. 2006; Small non-coding RNAs and the bacterial outer membrane. Curr Opin Microbiol9:605–611
    [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) pp1–29 Edited by Nellen W., Hammann C. Berlin: Springer-Verlag;
    [Google Scholar]
  49. Wagner E. G., Flardh K.. 2002; Antisense RNAs everywhere?. Trends Genet18:223–226
    [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 Bacteriol105:1028–1035
    [Google Scholar]
  51. Wassarman K. M.. 2002; Small RNAs in bacteria: diverse regulators of gene expression in response to environmental changes. Cell109:141–144
    [Google Scholar]
  52. Wassarman K. M., Storz G.. 2000; 6S RNA regulates E. coli RNA polymerase activity. Cell101:613–623
    [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 Microbiol48:657–670
    [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 J17:6061–6068
    [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 Microbiol50:1111–1124
    [Google Scholar]
  56. Zuker M.. 2003; Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res31:3406–3415
    [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...

Most cited this month

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