Table of Contents
ISRN Microbiology
Volume 2012 (2012), Article ID 636273, 10 pages
http://dx.doi.org/10.5402/2012/636273
Research Article

The Escherichia coli GcvB sRNA Uses Genetic Redundancy to Control cycA Expression

Department of Microbiology, University of Iowa, Iowa City, IA 52242, USA

Received 25 February 2012; Accepted 19 March 2012

Academic Editors: H. Asakura, P. D. Ghiringhelli, G. Koraimann, F. Navarro-Garcia, J. Theron, and K. Trulzsch

Copyright © 2012 Lorraine T. Stauffer and George V. Stauffer. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. M. L. Urbanowski, L. T. Stauffer, and G. V. Stauffer, “The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli,” Molecular Microbiology, vol. 37, no. 4, pp. 856–868, 2000. View at Publisher · View at Google Scholar · View at Scopus
  2. S. C. Pulvermacher, L. T. Stauffer, and G. V. Stauffer, “Role of the sRNA GcvB in regulation of cycA in Escherichia coli,” Microbiology, vol. 155, no. 1, pp. 106–114, 2009. View at Publisher · View at Google Scholar · View at Scopus
  3. S. C. Pulvermacher, L. T. Stauffer, and G. V. Stauffer, “The role of the small regulatory RNA GcvB in GcvB/mRNA posttranscriptional regulation of oppA and dppA in Escherichia coli,” FEMS Microbiology Letters, vol. 281, no. 1, pp. 42–50, 2008. View at Publisher · View at Google Scholar · View at Scopus
  4. S. C. Pulvermacher, L. T. Stauffer, and G. V. Stauffer, “The small RNA GcvB regulates sstT mRNA expression in Escherichia coli,” Journal of Bacteriology, vol. 91, no. 1, pp. 238–248, 2009. View at Publisher · View at Google Scholar · View at Scopus
  5. C. M. Sharma, F. Darfeuille, T. H. Plantinga, and J. Vogel, “A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites,” Genes and Development, vol. 21, no. 21, pp. 2804–2817, 2007. View at Publisher · View at Google Scholar · View at Scopus
  6. C. M. Sharma, K. Papenfort, S. R. Pernitzsch, H. J. Mollenkopf, J. C. D. Hinton, and J. Vogel, “Pervasive post-transcriptional control of genes involved in amino acid metabolism by the Hfq-dependent GcvB small RNA,” Molecular Microbiology, vol. 81, no. 5, pp. 1144–1165, 2011. View at Publisher · View at Google Scholar · View at Scopus
  7. S. Gottesman, “The small RNA regulators of Escherichia coli: roles and mechanisms,” Annual Review of Microbiology, vol. 58, pp. 303–328, 2004. View at Publisher · View at Google Scholar · View at Scopus
  8. H. Aiba, “Mechanism of RNA silencing by Hfq-binding small RNAs,” Current Opinion in Microbiology, vol. 10, no. 2, pp. 134–139, 2007. View at Publisher · View at Google Scholar · View at Scopus
  9. R. G. Brennan and T. M. Link, “Hfq structure, function and ligand binding,” Current Opinion in Microbiology, vol. 10, no. 2, pp. 125–133, 2007. View at Publisher · View at Google Scholar · View at Scopus
  10. P. Valentin-Hansen, M. Eriksen, and C. Udesen, “The bacterial Sm-like protein Hfq: a key player in RNA transactions,” Molecular Microbiology, vol. 51, no. 6, pp. 1525–1533, 2004. View at Publisher · View at Google Scholar · View at Scopus
  11. A. Zhang, K. M. Wassarman, C. Rosenow, B. C. Tjaden, G. Storz, and S. Gottesman, “Global analysis of small RNA and mRNA targets of Hfq,” Molecular Microbiology, vol. 50, no. 4, pp. 1111–1124, 2003. View at Publisher · View at Google Scholar · View at Scopus
  12. A. Sittka, S. Lucchini, K. Papenfort et al., “Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq,” PLoS Genetics, vol. 4, no. 8, Article ID e1000163, 2008. View at Publisher · View at Google Scholar · View at Scopus
  13. S. C. Pulvermacher, L. T. Stauffer, and G. V. Stauffer, “Role of the Escherichia coli Hfq protein in GcvB regulation of oppA and dppA mRNAs,” Microbiology, vol. 155, no. 1, pp. 115–123, 2009. View at Publisher · View at Google Scholar · View at Scopus
  14. H. Kawamoto, Y. Koide, T. Morita, and H. Aiba, “Base-pairing requirement for RNA silencing by a bacterial small RNA and acceleration of duplex formation by Hfq,” Molecular Microbiology, vol. 61, no. 4, pp. 1013–1022, 2006. View at Publisher · View at Google Scholar · View at Scopus
  15. R. L. Wilson and G. V. Stauffer, “DNA sequence and characterization of GcvA, a LysR family regulatory protein for the Escherichia coli glycine cleavage enzyme system,” Journal of Bacteriology, vol. 176, no. 10, pp. 2862–2868, 1994. View at Google Scholar · View at Scopus
  16. R. L. Wilson, M. L. Urbanowski, and G. V. Stauffer, “DNA binding sites of the LysR-type regulator GcvA in the gcv and gcvA control regions of Escherichia coli,” Journal of Bacteriology, vol. 177, no. 17, pp. 4940–4946, 1995. View at Google Scholar · View at Scopus
  17. A. D. Jourdan and G. V. Stauffer, “Mutational analysis of the transcriptional regulator GcvA: amino acids important for activation, repression, and DNA binding,” Journal of Bacteriology, vol. 180, no. 18, pp. 4865–4871, 1998. View at Google Scholar · View at Scopus
  18. S. M. Panasenko, J. R. Cameron, R. W. Davis, and I. R. Lehman, “Five hundredfold overproduction of DNA ligase after induction of a hybrid lambda lysogen constructed in vitro,” Science, vol. 196, no. 4286, pp. 188–189, 1977. View at Google Scholar · View at Scopus
  19. J. Miller, Experiments in Molecular Genetics, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA, 1972.
  20. H. J. Vogel and D. M. Bonner, “Acetylornithinase of Escherichia coli: partial purification and some properties.,” The Journal of Biological Chemistry, vol. 218, no. 1, pp. 97–106, 1956. View at Google Scholar · View at Scopus
  21. Y. Zhou, X. Zhang, and R. H. Ebright, “Random mutagenesis of gene-sized DNA molecules by use of PCR with Taq DNA polymerase,” Nucleic Acids Research, vol. 19, no. 21, p. 6052, 1991. View at Google Scholar · View at Scopus
  22. G. Sarkar and S. S. Sommer, “The 'megaprimer' method of site-directed mutagenesis,” BioTechniques, vol. 8, no. 4, pp. 404–407, 1990. View at Google Scholar · View at Scopus
  23. D. H. Mathews, J. Sabina, M. Zuker, and D. H. Turner, “Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure,” Journal of Molecular Biology, vol. 288, no. 5, pp. 911–940, 1999. View at Publisher · View at Google Scholar · View at Scopus
  24. M. Zuker, “Mfold web server for nucleic acid folding and hybridization prediction,” Nucleic Acids Research, vol. 31, no. 13, pp. 3406–3415, 2003. View at Publisher · View at Google Scholar · View at Scopus
  25. M. L. Urbanowski and G. V. Stauffer, “Autoregulation by tandem promoters of the Salmonella typhimurium LT2 metJ gene,” Journal of Bacteriology, vol. 165, no. 3, pp. 740–745, 1986. View at Google Scholar · View at Scopus
  26. K. Shimada, R. A. Weisberg, and M. E. Gottesman, “Prophage lambda at unusual chromosomal locations. I. Location of the secondary attachment sites and the properties of the lysogens,” Journal of Molecular Biology, vol. 63, no. 3, pp. 483–503, 1972. View at Google Scholar · View at Scopus
  27. K. C. Tu and B. L. Bassler, “Multiple small RNAs act additively to integrate sensory information and control quorum sensing in Vibrio harveyi,” Genes and Development, vol. 21, no. 2, pp. 221–233, 2007. View at Publisher · View at Google Scholar · View at Scopus
  28. M. Guillier and S. Gottesman, “The 5 end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator,” Nucleic Acids Research, vol. 36, no. 21, pp. 6781–6794, 2008. View at Publisher · View at Google Scholar · View at Scopus
  29. E. Massé, C. K. Vanderpool, and S. Gottesman, “Effect of RyhB small RNA on global iron use in Escherichia coli,” Journal of Bacteriology, vol. 187, no. 20, pp. 6962–6971, 2005. View at Publisher · View at Google Scholar · View at Scopus
  30. E. Massé and S. Gottesman, “A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 7, pp. 4620–4625, 2002. View at Publisher · View at Google Scholar · View at Scopus
  31. R. A. Lease and M. Belfort, “Riboregulation by DsrA RNA: Trans-actions for global economy,” Molecular Microbiology, vol. 38, no. 4, pp. 667–672, 2000. View at Publisher · View at Google Scholar · View at Scopus
  32. N. Majoalani, C. Cunning, D. Sledjeski, T. Elliott, and S. Gottesman, “DsrA RNA regulates translation of RpoS message by an anti-antisense mechanism, independent of its action as an antisilencer of transcription,” Proceedings of the National Academy of Sciences of the United States of America, vol. 95, no. 21, pp. 12462–12467, 1998. View at Publisher · View at Google Scholar · View at Scopus
  33. S. Durand and G. Storz, “Reprogramming of anaerobic metabolism by the FnrS small RNA,” Molecular Microbiology, vol. 75, no. 5, pp. 1215–1231, 2010. View at Publisher · View at Google Scholar · View at Scopus
  34. Y. Jin, R. M. Watt, A. Danchin, and J. D. Huang, “Small noncoding RNA GcvB is a novel regulator of acid resistance in Escherichia coli,” BMC Genomics, vol. 10, article 165, 2009. View at Publisher · View at Google Scholar · View at Scopus