RNA sequence requirements for NasR-mediated, nitrate-responsive transcription antitermination of the Klebsiella oxytoca M5al nasF operon leader

Journal of Molecular Biology

Volumn 292, Issue 2, 1999, Pages 203-216

  Chai, Weihang ^a   Stewart, Valley ^a,b  

^a Department of Obstetrics Gynecology   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

In vitro transcription; Nitrate assimilation; RNA protein interaction; Transcription antitermination; Transcription termination

Indexed keywords

BACTERIAL ENZYME; BACTERIAL PROTEIN; BACTERIAL RNA; GENE PRODUCT; NITRATE; NITRITE; PROTEIN NASR; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENE; CONTROLLED STUDY; DNA SEQUENCE; ELECTROPHORETIC MOBILITY; KLEBSIELLA OXYTOCA; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PHYLOGENY; PRIORITY JOURNAL; PROTEIN RNA BINDING; PROTEIN SECONDARY STRUCTURE; RNA SEQUENCE; TRANSCRIPTION INITIATION; TRANSCRIPTION TERMINATION;

KLEBSIELLA OXYTOCA;

EID: 0033578787     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3084     Document Type: Article

References (36)

1. Arnaud M., Débarbouillé M., Rapoport G., Saier M. H. Jr, Reizer J. In vitro reconstitution of transcriptional antitermination by the SacT and SacY proteins of Bacillus subtilis. J. Biol. Chem. 271:1996;18966-18972.
2. Babitzke P. Regulation of tryptophan biosynthesis: Trp-ing the TRAP or how Bacillus subtilis reinvented the wheel. Mol. Microbiol. 26, 1997;1-9.
3. Bartolomé B., Jubete Y., Martinez E., de la Cruz F. Construction and properties of a family of pACYC184-derived cloning vectors compatible with pBR322 and its derivatives. Gene. 102:1991;75-78.
4. Bender R. A., Friedrich B. Regulation of assimilatory nitrate reductase formation in Klebsiella aerogenes W70. J. Bacteriol. 172:1990;7256-7259.
5. Bloch M. A., Raibaud O. Comparison of the malA regions of Escherichia coli and Klebsiella pneumoniae. J. Bacteriol. 168:1986;1220-1227.
6. Cali B. M., Micca J. M., Stewart V. Genetic regulation of nitrate assimilation in Klebsiella pneumoniae M5al. J. Bacteriol. 171:1989;2666-2672.
7. Chai W. Antitermination control of nitrate assimilation gene expression in Klebsiella oxytoca M5al. Ph.D dissertation. 1999;Cornell University, Ithaca.
8. Chai W., Stewart V. NasR, a novel RNA-binding protein, mediates nitrate-responsive transcription antitermination of the Klebsiella oxytoca M5al nasF operon leader in vitro. J. Mol. Biol. 283:1998;339-351.
9. Drew R., Lowe N. Positive control of Pseudomonas aeruginosa amidase synthesis is mediated by a transcription anti-termination mechanism. J. Gen. Microbiol. 135:1989;817-823.
10. Goldman B. S., Lin J. T., Stewart V. Identification and structure of the nasR gene encoding a nitrate- and nitrite-responsive positive regulator ofnasFEDCBA (nitrate assimilation) operon expression in Klebsiella pneumoniae M5al. J. Bacteriol. 176:1994;5077-5085.
11. Groisman E. A., Casadaban M. J. Mini-Mu bacteriophage with plasmid replicons for in vivo cloning and lac gene fusing. J. Bacteriol. 168:1986;357-364.
12. Henkin T. M. Control of transcription termination in prokaryotes. Annu. Rev. Genet. 30:1996;35-57.
13. Jaeger J. A., Turner D. H., Zucker M. Improved predictions of secondary structures for RNA. Proc. Natl Acad. Sci. USA. 86:1989;7706-7710.
14. Jucker F. M., Heus H. A., Yip P. F., Moors E. H. M., Pardi A. A network of heterogeneous hydrogen bonds in GNRA tetraloops. J. Mol. Biol. 264:1996;968-980.
15. Lewis M. K., Thompson D. V. Efficient site directed in vitro mutagenesis using ampicillin selection. Nucl. Acids Res. 18:1990;3439-3443.
16. Lin J. T., Stewart V. Nitrate and nitrite-mediated transcription antitermination control of nasF (nitrate assimilation) operon expression in Klebsiella pneumoniae M5al. J. Mol. Biol. 256:1996;423-435.
17. Lin J. T., Stewart V. Nitrate assimilation by bacteria. Advan. Microb. Physiol. 39:1998;1-30.
18. Lin J. T., Goldman B. S., Stewart V. Structures of genes nasA and nasB, encoding assimilatory nitrate and nitrite reductases inKlebsiella pneumoniae M5al. J. Bacteriol. 175:1993;2370-2378.
19. Lin J. T., Goldman B. S., Stewart V. The nasFEDCBA operon for nitrate and nitrite assimilation in Klebsiella pneumoniae M5al. J. Bacteriol. 176:1994;2551-2559.
20. Magasanik B. Regulation of nitrogen utilization. Neidhardt F. C., Curtiss R. III, Ingraham J. L., Lin E. C. C., Low K. B., Magasanik B., Reznikoff W. S., Riley M., Schaechter M., Umbarger H. E. Escherichia coli and Salmonella. Cellular and Molecular Biology. 1996;1344-1356 ASM Press, Washington.
21. Maloy S. R., Stewart V. J., Taylor R. K. Genetic Analysis of Pathogenic Bacteria. A Laboratory Manual. 1996;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
22. Merrick M. J., Edwards R. A. Nitrogen control in bacteria. Microbiol. Rev. 59:1995;604-622.
23. Miller J. H. Experiments in Molecular Genetics. 1972;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
24. Mooney R. A., Artsimovitch I., Landick R. Information processing by RNA polymerase: recognition of regulatory signals during RNA chain elongation. J. Bacteriol. 180:1998;3265-3275.
25. Murray V. Improved double-stranded DNA sequencing using the linear polymerase chain reaction. Nucl. Acids Res. 17:1989;88-89.
26. IItwo-component system of enteric bacteria. Hoch J. A., Silhavy T. J. Two-component Signal Transduction. 1995;67-88 ASM Press, Washington DC.
27. Porter S. C., North A. K., Kustu S. Mechanism of transcriptional activation by NtrC. Hoch J. A., Silhavy T. J. Two-component Signal Transduction. 1995;147-158 ASM Press, Washington.
28. Rutberg B. Antitermination of transcription of catabolic operons. Mol. Microbiol. 23:1997;413-421.
29. Skorupski K., Taylor R. K. Positive selection vectors for allelic exchange. Gene. 169:1996;47-52.
30. St. Pierre R., Linn T. A refined vector system for the in vitro construction of single-copy transcriptional or translational fusions to lacZ. Gene. 169:1996;65-68.
31. Switzer R. L., Turner R. J., Lu Y. Regulation of the Bacillus subtilis pyrimidine biosynthetic operon by transcriptional attenuation: control of gene expression by an mRNA-binding protein. Prog. Nucl. Acid. Res. Mol. Biol. 62:1999;329-367.
32. Uhlenbeck O. C. Tetraloops and RNA folding. Nature. 346:1990;613-614.
33. Weisberg R. A., Gottesman M. E. Processive antitermination. J. Bacteriol. 181:1999;359-367.
34. Wilson S. A., Wachira S. J. M., Norman R. A., Pearl L. H., Drew R. E. Transcription antitermination regulation of the Pseudomonas aeruginosa amidase operon. EMBO J. 15:1996;5907-5916.
35. Yanofsky C. Comparison of regulatory and structural regions of genes of tryptophan metabolism. Mol. Biol. Evol. 1:1984;143-161.
36. Zuker M., Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucl. Acids Res. 9:1981;133-148.