Genome-Wide Identification of Binding Sites for the Nitric Oxide-Sensitive Transcriptional Regulator NsrR

Methods in Enzymology

Volumn 437, Issue , 2008, Pages 211-233

  Efromovich, Sam ^a   Grainger, David ^b   Bodenmiller, Diane ^c   Spiro, Stephen ^a  

^a UNIVERSITY OF TEXAS AT DALLAS   (United States)

^b UNIVERSITY OF BIRMINGHAM   (United Kingdom)

^c GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HEMOGLOBIN; NITRIC OXIDE; PROTEIN SUBUNIT; REGULATOR PROTEIN; DNA BINDING PROTEIN; ESCHERICHIA COLI PROTEIN; NSRR PROTEIN, E COLI; TRANSCRIPTION FACTOR;

BINDING SITE; CHROMATIN IMMUNOPRECIPITATION; CHROMOSOME ANALYSIS; DETOXIFICATION; DNA DETERMINATION; DNA HYBRIDIZATION; DNA MICROARRAY; ESCHERICHIA COLI; GENE IDENTIFICATION; GENE TARGETING; GENOME; METHODOLOGY; NONHUMAN; NSRR GENE; PRIORITY JOURNAL; REPRESSOR GENE; REVIEW; TRANSCRIPTION REGULATION; BACTERIAL GENOME; BIOLOGICAL MODEL; CHROMOSOME MAP; CLONING; DRUG EFFECT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; INFORMATION PROCESSING; METABOLISM; MICROBIOLOGICAL EXAMINATION; PHYSIOLOGY; PROTEIN BINDING; STAINING;

ESCHERICHIA COLI;

AUTOMATIC DATA PROCESSING; BINDING SITES; CHROMATIN IMMUNOPRECIPITATION; CHROMOSOME MAPPING; CLONING, ORGANISM; DNA-BINDING PROTEINS; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; MICROBIOLOGICAL TECHNIQUES; MODELS, BIOLOGICAL; NITRIC OXIDE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEIN BINDING; STAINING AND LABELING; TRANSCRIPTION FACTORS;

EID: 47049086640     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(07)37012-2     Document Type: Chapter

References (35)

1. Bang I.-S., Liu L., Vazquez-Torres A., Crouch M.-L., Stamler J.S., and Fang F.C. Maintenance of nitric oxide and redox homeostasis by the Salmonella flavohemoglobin Hmp. J. Biol. Chem. 281 (2006) 28039-28047
2. Bieda M., Xu X., Singer M.A., Green R., and Farnham P.J. Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome. Genome Res. 16 (2006) 595-605
3. Bodenmiller D.M., and Spiro S. The yjeB (nsrR) gene of Escherichia coli encodes a nitric oxide sensitive transcriptional regulator. J. Bacteriol. 188 (2006) 874-881
4. Buck M.J., and Lieb J.D. ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 83 (2004) 349-360
5. Buck M.J., Nobel A.B., and Lieb J.D. ChIPOTle: A user-friendly tool for the analysis of ChIP-chip data. Genome Biol. 6 (2005) R97
6. Cairrao F., Cruz A., Mori H., and Arraiano C.M. Cold shock induction of RNase R and its role in the maturation of the quality control mediator SsrA/tmRNA. Mol. Microbiol. 50 (2003) 1349-1360
7. Corker H., and Poole R.K. Nitric oxide formation by Escherichia coli: Dependence on nitrite reductase, the NO-sensing regulator Fnr, and flavohemoglobin Hmp. J. Biol. Chem. 278 (2003) 31584-31592
8. Datsenko K.A., and Wanner B.L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. USA 97 (2000) 6640-6645
9. D'Autréaux B., Tucker N.P., Dixon R., and Spiro S. A non-haem iron centre in the transcription factor NorR senses nitric oxide. Nature 437 (2005) 769-772
10. Efromovich S. "Nonparametric Curve Estimation: Methods, Theory and Applications." (1999), Springer, New York
11. Efromovich S. Multiwavelets and signal denoising. Sankhya 63 (2001) 367-393
12. Efromovich S., Lakey J., Pereyra M.C., and Tymes N. Data-driven and optimal denoising of a signal and recovery of its derivatives using multiwavelets. IEEE Trans. Signal Process. 52 (2004) 628-635
13. Filenko N., Spiro S., Browning D.F., Squire D., Overton T.W., Cole J., and Constantinidou C. The NsrR regular of Escherichia coli K12 includes genes encoding the hybrid cluster protein and the periplasmic, respiratory nitrite reductase. J. Bacteriol. 189 (2007) 4410-4417
14. 54 in the nitric oxide stress response. J. Biol. Chem. 278 (2003) 10081-10086
15. Gardner A.M., Helmick R.A., and Gardner P.R. Flavorubredoxin, an inducible catalyst for nitric oxide reduction and detoxification in Escherichia coli. J. Biol. Chem. 277 (2002) 8172-8177
16. Gomes C.M., Giuffre A., Forte E., Vicente J.B., Saraiva L.M., Brunori M., and Teixeira M. A novel type of nitric-oxide reductase. Escherichia coli flavorubredoxin. J. Biol. Chem. 277 (2002) 25273-25276
17. Grainger D.C., Aiba H., Hurd D., Browning D.F., and Busby S.J.W. Transcription factor distribution in Escherichia coli: Studies with FNR protein. Nucleic Acids Res. 35 (2006) 269-278
18. Grainger D.C., Hurd D., Harrison M., Holdstock J., and Busby S.J.W. Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome. Proc. Natl. Acad. Sci. USA 102 (2005) 17693-17698
19. Grainger D.C., Overton T.W., Reppas N., Wade J.T., Tamai E., Hobman J.L., Constantinidou C., Struhl K., Church G., and Busby S.J.W. Genomic studies with Escherichia coli MelR protein: Applications of chromatin immunoprecipitation and microarrays. J. Bacteriol. 186 (2004) 6938-6943
20. Ji X.B., and Hollocher T.C. Reduction of nitrite to nitric oxide by enteric bacteria. Biochem. Biophys. Res. Commun. 157 (1988) 106-108
21. Justino M.C., Almeida C.C., Goncalves V.L., Teixeira M., and Saraiva L.M. Escherichia coli YtfE is a di-iron protein with an important function in assembly of iron-sulphur clusters. FEMS Microbiol. Lett. 257 (2006) 278-284
22. Justino M.C., Vicente J.B., Teixeira M., and Saraiva L.M. New genes implicated in the protection of anaerobically grown Escherichia coli against nitric oxide. J. Biol. Chem. 280 (2005) 2636-2643
23. Kim T.H., Barrera L.O., Zheng M., Qu C., Singer M.A., Richmond T.A., Wu Y., Green R.D., and Ren B. A high-resolution map of active promoters in the human genome. Nature 436 (2005) 876-880
24. Molle V., Fujita M., Jensen S.T., Eichenberger P., Gonzalez-Pastor J.E., Liu J.S., and Losick R. The Spo0A regulon of Bacillus subtilis. Mol. Microbiol. 50 (2003) 1683-1701
25. Poock S.R., Leach E.R., Moir J.W., Cole J.A., and Richardson D.J. Respiratory detoxification of nitric oxide by the cytochrome c nitrite reductase of Escherichia coli. J. Biol. Chem. 277 (2002) 23664-23669
26. Poole R.K. Nitric oxide and nitrosative stress tolerance in bacteria. Biochem. Soc. Trans. 33 (2005) 176-180
27. Poole R.K., and Hughes M.N. New functions for the ancient globin family: Bacterial responses to nitric oxide and nitrosative stress. Mol. Microbiol. 36 (2000) 775-783
28. Rodionov D.A., Dubchak I.L., Arkin A.P., Alm E.J., and Gelfand M.S. Dissimilatory metabolim of nitrogen oxides in Bacteria: Comparative reconstruction of transcriptional networks. PLOS Comput. Biol. 1 (2005) e55
29. Rokop M.E., Auchtung J.M., and Grossman A.D. Control of DNA replication initiation by recruitment of an essential initiation protein to the membrane of Bacillus subtilis. Mol. Microbiol. 52 (2004) 1757-1767
30. Sebbane F., Lemaitre N., Sturdevant D.E., Rebeil R., Virtaneva K., Porcella S.F., and Hinnebusch B.J. Adaptive response of Yersinia pestis to extracellular effectors of innate immunity during bubonic plague. Proc. Natl. Acad. Sci. USA 103 (2006) 11766-11771
31. Shin D., and Groisman E.A. Signal-dependent binding of the response regulators PhoP and PmrA to their target promoters in vivo. J. Biol. Chem. 280 (2005) 4089-4094
32. Spiro S. Regulators of bacterial responses to nitric oxide. FEMS Microbiol. Rev. 31 (2007) 193-211
33. Stevanin T.M., Poole R.K., Demoncheaux E.A., and Read R.C. Flavohemoglobin Hmp protects Salmonella enterica serovar typhimurium from nitric oxide-related killing by human macrophages. Infect. Immun. 70 (2002) 4399-4405
34. Uzzau S., Figueroa-Bossi N., Rubino S., and Bossi L. Epitope tagging of chromosomal genes in Salmonella. Proc. Natl. Acad. Sci. USA 98 (2001) 15264-15269
35. Van Doorslaer S., Dewilde S., Kiger L., Nistor S.V., Goovaerts E., Marden M.C., and Moens L. Nitric oxide binding properties of neuroglobin: A characterization by EPR and flash photolysis. J. Biol. Chem. 278 (2003) 4919-4925