Role of the Escherichia coli Hfq protein in GcvB regulation of oppA and dppA mRNAs

Microbiology

Volumn 155, Issue 1, 2009, Pages 115-123

  Pulvermacher, Sarah C ^a   Stauffer, Lorraine T ^a   Stauffer, George V ^a  

^a UNIVERSITY OF IOWA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI PROTEIN; MESSENGER RNA; PROTEIN DPPA; PROTEIN GCVB; PROTEIN HFQ; PROTEIN OPPA; RNA BINDING PROTEIN; UNCLASSIFIED DRUG; BACTERIAL RNA; CARRIER PROTEIN; DPPA PROTEIN, E COLI; HFQ PROTEIN, E COLI; HOST FACTOR 1; LIPOPROTEIN; OPPA PROTEIN, E COLI; PERIPLASMIC BINDING PROTEIN; UNTRANSLATED RNA;

ARTICLE; BACTERIAL GENETICS; BASE PAIRING; CONTROLLED STUDY; CULTURE MEDIUM; ESCHERICHIA COLI; GENE INTERACTION; GENE MUTATION; GENE REPRESSION; GENE TARGETING; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN RNA BINDING; TRANSCRIPTION REGULATION; CHEMISTRY; CONFORMATION; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

ESCHERICHIA COLI; LURIA;

BASE SEQUENCE; CARRIER PROTEINS; CULTURE MEDIA; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; HOST FACTOR 1 PROTEIN; LIPOPROTEINS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PERIPLASMIC BINDING PROTEINS; RNA, BACTERIAL; RNA, MESSENGER; RNA, UNTRANSLATED;

EID: 61449128339     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/mic.0.023432-0     Document Type: Article

References (41)

1. Ali Azam, T., Iwata, A., Nishimura, A., Ueda, S. & Ishihama, A. (1999). Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J Bacteriol 181, 6361-6370.
2. 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.
3. Brescia, C. C., Mikulecky, P. J., Feig, A. L. & Sledjeski, D. D. (2003). Identification of the Hfq-binding site on DsrA RNA: Hfq binds without altering DsrA secondary structure. RNA 9, 33-43.
4. Brickman, E. & Beckwith, J. (1975). Analysis of the regulation of Escherichia coli alkaline phosphatase synthesis using deletions and 80 transducing phages. J Mol Biol 96, 307-316.
5. Chang, A. C. & Cohen, S. N. (1978). Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J Bacteriol 134, 1141-1156.
6. 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.
7. 32P-based hybridizations. Anal Biochem 210, 235-244.
8. Franze de Fernandez, M. T., Eoyang, L. & August, J. T. (1968). Factor fraction required for the synthesis of bacteriophage Qβ-RNA. Nature 219, 588-590.
9. Gottesman, S. (2004). The small RNA regulators of Escherichia coli: roles and mechanisms. Annu Rev Microbiol 58, 303-328.
10. 32-mediated cytoplasmic stress response in Escherichia coli. J Bacteriol 189, 1963-1973.
11. Hershberg, R., Altuvia, S. & Margalit, H. (2003). A survey of small RNA-encoding genes in Escherichia coli. Nucleic Acids Res 31, 1813-1820.
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.
13. Kikuchi, G. (1973). The glycine cleavage system: composition, reaction mechanism, and physiological significance. Mol Cell Biochem 1, 169-187.
14. Lease, R. A. & Belfort, M. (2000). A trans-acting RNA as a control switch in Escherichia coli: DsrA modulates function by forming alternative structures. Proc Natl Acad Sci U S A 97, 9919-9924.
15. 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.
16. 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.
17. Miller, J. (1972). A Short Course in Bacterial Genetics. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
18. Moll, I., Afonyushkin, T., Vytvytska, O., Kaberdin, V. R. & Blasi, U. (2003). Coincident Hfq binding and RNase E cleavage sites on mRNA and small regulatory RNAs. RNA 9, 1308-1314.
19. Moller, T., Franch, T., Hojrup, P., Keene, D. R., Bachinger, H. P., Brennan, R. G. & Valentin-Hansen, P. (2002). Hfq: a bacterial Sm-like protein that mediates RNA-RNA interaction. Mol Cell 9, 23-30.
20. Opdyke, J. A., Kang, J. G. & Storz, G. (2004). GadY, a small-RNA regulator of acid response genes in Escherichia coli. J Bacteriol 186, 6698-6705.
21. 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.
22. 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.
23. Sambrook, J., Fritsch, E. & Maniatis, T. (1989). Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
24. Schumacher, M. A., Pearson, R. F., Moller, T., Valentin-Hansen, P. & Brennan, R. G. (2002). Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein. EMBO J 21, 3546-3556.
25. 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.
26. 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.
27. Sledjeski, D. D., Whitman, C. & Zhang, A. (2001). Hfq is necessary for regulation by the untranslated RNA DsrA. J Bacteriol 183, 1997-2005.
28. Stauffer, L. T. & Stauffer, G. V. (1994). Characterization of the gcv control region from Escherichia coli. J Bacteriol 176, 6159-6164.
29. Urbanowski, M. L. & Stauffer, G. V. (1986). Autoregulation by tandem promoters of the Salmonella typhimurium LT2 metJ gene. J Bacteriol 165, 740-745.
30. 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.
31. Vecerek, B., Moll, I., Afonyushkin, T., Kaberdin, V. & Blasi, U. (2003). Interaction of the RNA chaperone Hfq with mRNAs: direct and indirect roles of Hfq in iron metabolism of Escherichia coli. Mol Microbiol 50, 897-909.
32. Vogel, H. J. & Bonner, D. M. (1956). Acetylornithinase of Escherichia coli: partial purification and some properties. J Biol Chem 218, 97-106.
33. Wagner, E. G. & Flardh, K. (2002). Antisense RNAs everywhere? Trends Genet 18, 223-226.
34. Wassarman, K. M. (2002). Small RNAs in bacteria: diverse regulators of gene expression in response to environmental changes. Cell 109, 141-144.
35. Wassarman, K. M., Zhang, A. & Storz, G. (1999). Small RNAs in Escherichia coli. Trends Microbiol 7, 37-45.
36. Wassarman, K. M., Repoila, F., Rosenow, C., Storz, G. & Gottesman, S. (2001). Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev 15, 1637-1651.
37. Wilson, R. L., Stauffer, L. T. & Stauffer, G. V. (1993). Roles of the GcvA and PurR proteins in negative regulation of the Escherichia coli glycine cleavage enzyme system. J Bacteriol 175, 5129-5134.
38. 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.
39. Zhang, A., Wassarman, K. M., Ortega, J., Steven, A. C. & Storz, G. (2002). The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs. Mol Cell 9, 11-22.
40. 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.
41. Zuker, M. (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31, 3406-3415.