Transcriptome of a Nitrosomonas europaea mutant with a disrupted nitrite reductase gene (nirK)

Applied and Environmental Microbiology

Volumn 72, Issue 6, 2006, Pages 4450-4454

  Cho, Catherine Mee Hie ^a   Yan, Tingfen ^b   Liu, Xueduan ^b   Wu, Liyou ^b,c   Zhou, Jizhong ^b,c   Stein, Lisa Y ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF OKLAHOMA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYMES; GENETIC ENGINEERING; IRON; MICROBIOLOGY;

CYTOCHROME C OXIDASE; GENOMIC MICROARRAY; MUTANT; NIRK OPERON; NITRITE REDUCTASE GENE (NIRK);

GENES;

CYTOCHROME C OXIDASE; IRON; NITRITE REDUCTASE; TRANSCRIPTOME;

GENE EXPRESSION; GENOMICS; NITRIFYING BACTERIUM;

ARTICLE; BACTERIAL GENE; BACTERIUM MUTANT; DNA MICROARRAY; GENE DISRUPTION; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENOMIC MICROARRAY; IRON TRANSPORT; NIRK GENE; NITROSOMONAS EUROPAEA; NONHUMAN; OPERON; PHENOTYPE; WILD TYPE;

ELECTRON TRANSPORT COMPLEX IV; GENE DELETION; GENES, BACTERIAL; MUTATION; NITRITE REDUCTASES; NITROSOMONAS EUROPAEA; OPERON; TRANSCRIPTION, GENETIC;

NITROSOMONAS EUROPAEA;

EID: 33745172807     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.02958-05     Document Type: Article

References (25)

1. Beaumont, H. J. E., N. G. Hommes, L. A. Sayavedra-Soto, D. J. Arp, D. M. Arciero, A. B. Hooper, H. V. Westerhoff, and R. J. M. van Spanning. 2002. Nitrite reductase of Nitrosomonas europaea is not essential for production of gaseous nitrogen oxides and confers tolerance to nitrite. J. Bacteriol. 184:2557-2560.
2. Beaumont, H. J. E., S. I. Lens, W. N. M. Reijnders, H. V. Westerhoff, and R. J. M. van Spanning. 2004. Expression of nitrite reductase in Nitrosomonas europaea involves NsrR, a novel nitrite-sensitive transcription repressor. Mol. Microbiol. 54:148-158.
3. Beaumont, H. J. E., S. I. Lens, H. V. Westerhoff, and R. J. M. van Spanning. 2005. Novel nirK cluster genes in Nitrosomonas europaea are required for NirK-dependent tolerance to nitrite. J. Bacteriol. 187:6849-6851.
4. Beaumont, H. J. E., B. van Schooten, S. I. Lens, H. V. Westerhoff, and R. J. M. van Spanning. 2004. Nitrosomonas europaea expresses a nitric oxide reductase during nitrification. J. Bacteriol. 186:4417-1421.
5. Bothe, H., G. Jost, M. Schloter, B. B. Ward, and K.-P. Witzel. 2000. Molecular analysis of ammonia oxidation and denitrification in natural environments. FEMS Microbiol. Rev. 24:673-690.
6. Brittain, T., R. Blackmore, C. Greenwood, and A. J. Thomson. 1992. Bacterial nitrite-reducing enzymes. Eur. J. Biochem. 209:793-802.
7. Chain, P., J. Lamerdin, F. Larimer, W. Regala, V. Lao, M. Land, L. Hauser, A. B. Hooper, M. G. Klotz, J. M. Norton, L. A. Sayavedra-Soto, D. M. Arciero, N. G. Hommes, M. R. Whittaker, and D. J. Arp. 2003. Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. J. Bacteriol. 185:2759-2773.
8. Cole, J. 1996. Nitrate reduction to ammonia by enteric bacteria: redundancy, or a strategy for survival during oxygen starvation? FEMS Microbiol. Lett. 136:1-11.
9. Colliver, B. B., and T. Stephenson. 2000. Production of nitrogen oxide and dinitrogen oxide by autotrophic nitrifiers. Biotechnol. Adv. 18:219-232.
10. Cruz-Ramos, H., J. Crack, G. Wu, M. N. Hughes, C. Scott, A. J. Thomson, J. Green, and R. K. Poole. 2002. NO sensing by FNR: regulation of the Escherichia coli NO-detoxifying flavohaemoglobin, Hmp. EMBO J. 21:3235-3244.
11. Gao, H., Y. Wang, X. Liu, T. Yan, L. Wu, E. Alm, A. Arkin, D. K. Thompson, and J. Zhou. 2004. Global transcriptome analysis of the heat shock response of Shewanella oneidensis. J. Bacteriol. 186:7796-7803.
12. Hendriks, J., A. Warne, U. Gohlke, T. Haltia, C. Ludovici, M. Lubben, and M. Saraste. 1998. The active site of the bacterial nitric oxide reductase is a dinuclear iron center. Biochemistry 37:13102-13109.
13. Jiang, Q. Q., and L. R. Bakken. 1999. Nitrous oxide production and methane oxidation by different ammonia-oxidizing bacteria. Appl. Environ. Microbiol. 65:2679-2684.
14. Justino, M. C., J. B. Vicente, M. Teixeira, and L. M. Saraiva. 2005. New genes implicated in the protection of anaerobically grown Escherichia coli against nitric oxide. J. Biol. Chem. 280:2636-2643.
15. Page, L., L. Griffiths, and J. A. Cole. 1990. Different physiological roles of two independent pathways for nitrite reduction to ammonia by enteric bacteria. Arch. Microbiol. 154:349-354.
16. Rodionov, D. A., A. A. Mironov, and M. S. Gelfand. 2002. Conservation of the biotin regulon and the BirA regulatory signal in eubacteria and archaea. Genome Res. 12:1507-1516.
17. Sambrook, J., and D. W. Russell. 2001. Molecular cloning: a laboratory manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
18. Schmidt, I., R. J. M. van Spanning, and M. S. M. Jetten. 2004. Denitrification and ammonia oxidation by Nitrosomonas europaea wild-type, and NirK- and NorB-deficient mutants. Microbiology 150:4107-4114.
19. Spiro, S., and J. R. Guest. 1990. FNR and its role in oxygen-regulated gene expression in Escherichia coli. FEMS Microbiol. Rev. 75:399-428.
20. Stein, L. Y., and D. J. Arp. 1998. Ammonium limitation results in the loss of ammonia-oxidizing activity in Nitrosomonas europaea. Appl. Environ. Microbiol. 64:1514-1521.
21. Suzuki, T., H. F. Mower, M. D. Friesen, I. Gilibert, T. Sawa, and H. Ohshima. 2004. Nitration and nitrosation of N-acetyl-L-tryptophan and tryptophan residues in proteins by various reactive nitrogen species. Free Radic. Biol. Med. 37:671-681.
22. Torres, J., M. A. Sharpe, A. Rosquist, C. E. Cooper, and M. T. Wilson. 2000. Cytochrome c oxidase rapidly metabolises nitric oxide to nitrite. FEBS Lett. 475:263-266.
23. Wei, X., T. Van, N. G. Hommes, X. Liu, L. Wu, C. McAlvin, M. G. Klotz, L. A. Sayavedra-Soto, J. Zhou, and D. J. Arp. 2006. Transcript profiles of Nitrosomonas europaea during growth and upon deprivation of ammonia and carbonate. FEMS Microbiol. Lett. 257:76-83.
24. Xu, D., G. Li, L. Wu, J. Zhou, and Y. Xu. 2002. PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis. Bioinformatics 18:1432-1437.
25. Zumft, W. G. 1997. Cell biology and molecular basis of denitrification. Microbiol. Mol. Biol. Rev. 61:533-616.