GadY, a small-RNA regulator of acid response genes in Escherichia coli

Journal of Bacteriology

Volumn 186, Issue 20, 2004, Pages 6698-6705

  Opdyke, Jason A ^a   Kang, Ju Gyeong ^a,c   Storz, Gisela ^a,b  

^a EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

^c NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLUTAMATE DECARBOXYLASE; MESSENGER RNA; NUCLEOTIDE DERIVATIVE; PROTEIN GADA; PROTEIN GADB; PROTEIN GADY; REGULATOR PROTEIN; RNA; SIGMA FACTOR; UNCLASSIFIED DRUG;

3' UNTRANSLATED REGION; ARTICLE; BACTERIAL GENE; BASE PAIRING; BIOINFORMATICS; ESCHERICHIA COLI; GADW GENE; GADX GENE; GADY GENE; GENE; GENE CLUSTER; GENE CONTROL; GENE EXPRESSION; GENE INDUCTION; GENE LOCATION; GENE MUTATION; GENE OVEREXPRESSION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN ANALYSIS; RNA STABILITY;

BASE PAIRING; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; HEAT-SHOCK RESPONSE; HOST FACTOR 1 PROTEIN; HYDROGEN-ION CONCENTRATION; MICRORNAS; RNA STABILITY; RNA, MESSENGER; TRANSCRIPTION FACTORS;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA; PROKARYOTA;

EID: 4944264194     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.186.20.6698-6705.2004     Document Type: Article

References (30)

1. Altuvia, S., A. Zhang, L. Argaman, A. Tiwari, and G. Storz. 1998. The Escherichia coli OxyS regulatory RNA represses fhl4 translation by blocking ribosome binding. EMBO J. 17:6069-6075.
2. Argaman, L., and S. Altuvia. 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.
3. Argaman, L., R. Hershberg, J. Vogel, G. Bejerano, E. G. H. Wagner, H. Margalit, and S. Altuvia. 2001. Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr. Biol. 11:941-950.
4. Bordi, C., L. Theraulaz, V. Mejean, and C. Jourlin-Castelli. 2003. Anticipating an alkaline stress through the Tor phosphorelay system in Escherichia coli. Mol. Microbiol. 48:211-223.
5. Castanie-Cornet, M. P., T. A. Penfound, D. Smith, J. F. Elliott, and J. W. Foster. 1999. Control of acid resistance in Escherichia coli. J. Bacteriol. 181:3525-3535.
6. Chen, S., E. A. Lesnik, T. A. Hall, R. Sampath, R. H. Griffey, D. J. Ecker, and L. B. Blyn. 2002. A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome. BioSystems 65:157-177.
7. Coburn, G. A., and G. A. Mackie. 1996. Overexpression, purification, and properties of Escherichia coli ribonuclease II. J. Biol. Chem. 271:1048-1053.
8. Court, D. L., S. Swaminathan, D. Yu, H. Wilson, T. Baker, M. Bubunenko, J. Sawitzke, and S. K. Sharan. 2003. Mini-lambda: a tractable system for chromosome and BAC engineering. Gene 315:63-69.
9. Datsenko, K. A., and B. L. Wanner. 2000. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. USA 97:6640-6645.
10. Homola, A. D., and E. E. Dekker. 1967. Decarboxylation of gamma-hydroxy-glutamate by glutamate decarboxylase of Escherichia coli (ATCC 11246). Biochemistry 6:2626-2634.
11. Loewen, P. C., and B. L. Triggs. 1984. Genetic mapping of katF, a locus that with katE affects the synthesis of a second catalase species in Escherichia coli. J. Bacteriol. 160:668-675.
12. Ma, Z., S. Gong, H. Richard, D. L. Tucker, T. Conway, and J. W. Foster. 2003. GadE (YhiE) activates glutamate decarboxylase-dependent acid resistance in Escherichia coli K-12. Mol. Microbiol. 49:1309-1320.
13. Ma, Z., H. Richard, and J. W. Foster. 2003. pH-dependent modulation of cyclic AMP levels and GadW-dependent repression of RpoS affect synthesis of the GadX regulator and Escherichia coli acid resistance. J. Bacteriol. 185:6852-6859.
14. Ma, Z., H. Richard, D. L. Tucker, T. Conway, and J. W. Foster. 2002. Collaborative regulation of Escherichia coli glutamate-dependent acid resistance by two AraC-like regulators, GadX and GadW (YhiW). J. Bacteriol. 184:7001-7012.
15. Majdalani, N., S. Chen, J. Murrow, K. St. John, and S. Gottesman. 2001. Regulation of RpoS by a novel small RNA: the characterization of RprA. Mol. Microbiol. 39:1382-1394.
16. Majdalani, N., C. Cunning, D. Sledjeski, T. Elliott, and S. Gottesman. 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. USA 95:12462-12467.
17. Majdalani, N., D. Hernandez, and S. Gottesman. 2002. Regulation and mode of action of the second small RNA activator of RpoS translation, RprA. Mol. Microbiol. 46:813-826.
18. Massé, E., F. E. Escorcia, and S. Gottesman. 2003. Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli. Genes Dev. 17:2374-2383.
19. Massé, E., and S. Gottesman. 2002. A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli. Proc. Natl. Acad. Sci. USA 99:4620-4625.
20. McLaren, R. S., S. F. Newbury, G. S. Dance, H. C. Causton, and C. F. Higgins. 1991. mRNA degradation by processive 3′-5′ exoribonucleases in vitro and the implications for prokaryotic mRNA decay in vivo. J. Mol. Biol. 221:81-95.
21. Møller, T., T. Franch, P. Hojrup, D. R. Keene, H. P. Bachinger, R. G. Brennan, and P. Valentin-Hansen. 2002. Hfq: a bacterial Sm-like protein that mediates RNA-RNA interaction. Mol. Cell 9:23-30.
22. Møller, T., T. Franch, C. Udesen, K. Gerdes, and P. Valentin-Hansen. 2002. Spot 42 RNA mediates discoordinate expression of the E. coli galactose operon. Genes Dev. 16:1696-1706.
23. Nelson, P., M. Kiriakidou, A. Sharma, E. Maniataki, and Z. Mourelatos. 2003. The microRNA world: small is mighty. Trends Biochem. Sci. 28:534-540.
24. Shin, S., M. P. Castanie-Cornet, J. W. Foster, J. A. Crawford, C. Brinkley, and J. B. Kaper. 2001. An activator of glutamate decarboxylase genes regulates the expression of enteropathogenic Escherichia coli virulence genes through control of the plasmid-encoded regulator, Per. Mol. Microbiol. 41:1133-1150.
25. Silhavy, T. J., M. L. Berman, and L. W. Enquist 1984. Experiments with gene fusions. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
26. Store, G., J. A. Opdyke, and A. Zhang. 2004. Controlling mRNA stability and translation with small, noncoding RNAs. Curr. Opin. Microbiol. 7:140-144.
27. Tramonti, A., P. Visca, M. De Canio, M. Falconi, and D. De Biase. 2002. Functional characterization and regulation of gadX, a gene encoding an AraC/XylS-like transcriptional activator of the Escherichia coli glutamic acid decarboxylase system. J. Bacteriol. 184:2603-2613.
28. Wassarman, K. M., F. Repoila, C. Rosenow, G. Store, and S. Gottesman. 2001. Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev. 15:1637-1651.
29. Zhang, A., K. M. Wassarman, J. Ortega, A. C. Steven, and G. Store. 2002. The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs. Mol. Cell 9:11-22.
30. Zhang, A., K. M. Wassarman, C. Rosenow, B. C. Tjaden, G. Store, and S. Gottesman. 2003. Global analysis of small RNA and mRNA targets of Hfq. Mol. Microbiol. 50:1111-1124.