Dissimilatory metabolism of nitrogen oxides in bacteria: Comparative reconstruction of transcriptional networks

PLoS Computational Biology

Volumn 1, Issue 5, 2005, Pages 0415-0431

  Rodionov, Dmitry A ^a,c   Dubchak, Inna L ^b   Arkin, Adam P ^b   Alm, Eric J ^b   Gelfand, Mikhail S ^a,c,d  

^a INSTITUTE FOR INFORMATION TRANSMISSION PROBLEMS   (Russian Federation)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c STATE RESEARCH INSTITUTE OF GENETICS AND SELECTION OF INDUSTRIAL MICROORGANISMS   (Russian Federation)

^d MOSCOW STATE UNIVERSITY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; DETOXIFICATION; ENZYMES; METABOLISM; NITRIC OXIDE; NITROGEN OXIDES; PHYSIOLOGY;

AMINO-ACIDS; ANAEROBIC BACTERIUM; BINDING MOTIF; COMPARATIVE GENOMICS; HYBRID CLUSTERS; NITROSOMONAS; PROTEOBACTERIA; REDOX ENZYME; TRANSCRIPTIONAL NETWORKS; TWO COMPONENT SYSTEMS;

TRANSCRIPTION;

BACTERIAL PROTEIN; ESCHERICHIA COLI PROTEIN; NITRITE; NITROGEN OXIDE;

ARTICLE; BACTERIUM; BIOLOGICAL MODEL; BIOLOGY; CHEMISTRY; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENOMICS; METABOLISM; METHODOLOGY; MULTIGENE FAMILY; OXIDATION REDUCTION REACTION; PHYLOGENY; PROTEIN MOTIF;

AMINO ACID MOTIFS; BACTERIA; BACTERIAL PROTEINS; COMPUTATIONAL BIOLOGY; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; GENOMICS; MODELS, BIOLOGICAL; MULTIGENE FAMILY; NITRITES; NITROGEN OXIDES; OXIDATION-REDUCTION; PHYLOGENY; TRANSCRIPTION, GENETIC;

EID: 85044710067     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0010055     Document Type: Article

References (64)

1. Simon J (2002) Enzymology and bioenergetics of respiratory nitrite ammonification. FEMS Microbiol Rev 26: 285-309.
2. Shapleigh JP (2000) The denitrifying prokaryotes. In: Dworkin M, Falkow N, Rosenberg H, Schleifer KH, Stackebrandt E, editors. The prokaryotes: An evolving electronic resource for the microbiological community, 3rd edition. New York: Springer-Verlag.
3. Poole RK (2005) Nitric oxide and nitrosative stress tolerance in bacteria. Biochem Soc Trans 33: 176-180.
4. Rudolf M, Einsle O, Neese F, Kroneck PM (2002) Pentahaem cytochrome c nitrite reductase: Reaction with hydroxylamine, a potential reaction intermediate and substrate. Biochem Soc Trans 30: 649-653.
5. Kuznetsova S, Knaff DB, Hirasawa M, Setif P, Mattioli TA (2004) Reactions of spinach nitrite reductase with its substrate, nitrite, and a putative intermediate, hydroxylamine. Biochemistry 43: 10765-10774.
6. Gomes CM, Giuffre A, Forte E, Vicente JB, Saraiva LM, et al. (2002) A novel type of nitric-oxide reductase. Escherichia coli flavorubredoxin. J Biol Chem 277: 25273-25276.
7. Gardner PR, Gardner AM, Martin LA, Salzman AL (1998) Nitric oxide dioxygenase: An enzymic function for flavohemoglobin. Proc Natl Acad Sci U S A 95: 10378-10383.
8. Cramm R, Siddiqui RA, Friedrich B (1994) Primary sequence and evidence for a physiological function of the flavohemoprotein of Alcaligenes eutrophus. J Biol Chem 269: 7349-7354.
9. LaCelle M, Kumano M, Kurita K, Yamane K, Zuber P, et al. (1996) Oxygencontrolled regulation of the flavohemoglobin gene in Bacillus subtilis. J Bacteriol 178: 3803-3808.
10. Beliaev AS, Thompson DK, Khare T, Lim H, Brandt CC, et al. (2002) Gene and protein expression profiles of Shewanella oneidensis during anaerobic growth with different electron acceptors. OMICS 6: 39-60.
11. van den Berg WA, Hagen WR, van Dongen WM (2000) The hybrid-cluster protein ('prismane protein') from Escherichia coli. Characterization of the hybrid-cluster protein, redox properties of the [2Fe-2S] and [4Fe-2S-2O] clusters and identification of an associated NADH oxidoreductase containing FAD and [2Fe-2S]. Eur J Biochem 267: 666-676.
12. Kim CC, Monack D, Falkow S (2003) Modulation of virulence by two acidified nitrite-responsive loci of Salmonella enterica serovar Typhimurium. Infect Immun 71: 3196-3205.
13. Dominy CN, Deane SM, Rawlings DE (1997) A geographically widespread plasmid from Thiobacillus ferrooxidans has genes for ferredoxin-, FNR-, prismane- and NADH-oxidoreductase-like proteins which are also located on the chromosome. Microbiology 143: 3123-3136.
14. Haveman SA, Greene EA, Stilwell CP, Voordouw JK, Voordouw G (2004) Physiological and gene expression analysis of inhibition of Desulfovibrio vulgaris hildenborough by nitrite. J Bacteriol 186: 7944-7950.
15. Cooper SJ, Garner CD, Hagen WR, Lindley PF, Bailey S (2000) Hybridcluster protein (HCP) from Desulfovibrio vulgaris (Hildenborough) at 1.6 A resolution. Biochemistry 39: 15044-15054.
16. Wolfe MT, Heo J, Garavelli JS, Ludden PW (2002) Hydroxylamine reductase activity of the hybrid cluster protein from Escherichia coli. J Bacteriol 184: 5898-5902.
17. Cabello P, Pino C, Olmo-Mira MF, Castillo F, Roldan MD, et al. (2004) Hydroxylamine assimilation by Rhodobacter capsulatus E1F1. requirement of the hcp gene (hybrid cluster protein) located in the nitrate assimilation nas gene region for hydroxylamine reduction. J Biol Chem 279: 45485-45494.
18. Zumft WG (2002) Nitric oxide signaling and NO dependent transcriptional control in bacterial denitrification by members of the FNR-CRP regulator family. J Mol Microbiol Biotechnol 4: 277-286.
19. Stewart V (1993) Nitrate regulation of anaerobic respiratory gene expression in Escherichia coli. Mol Microbiol 9: 425-434.
20. Korner H, Sofia HJ, Zumft WG (2003) Phylogeny of the bacteria l superfamily of Crp-Fnr transcription regulators: Exploiting the metabolic spectrum by controlling alternative gene programs. FEMS Microbiol Rev 27: 559-592.
21. Tucker NP, D'Autreaux B, Studholme DJ, Spiro S, Dixon R (2004) DNA binding activity of the Escherichia coli nitric oxide sensor NorR suggests a conserved target sequence in diverse proteobacteria. J Bacteriol 186: 6656-6660.
22. Pohlmann A, Cramm R, Schmelz K, Friedrich B (2000) A novel NOresponding regulator controls the reduction of nitric oxide in Ralstonia eutropha. Mol Microbiol 38: 626-638.
23. Busch A, Pohlmann A, Friedrich B, Cramm R (2004) A DNA region recognized by the nitric oxide-responsive transcriptional activator NorR is conserved in beta- and gamma-proteobacteria. J Bacteriol 186: 7980-7987.
24. Beaumont HJ, Lens SI, Reijnders WN, Westerhoff HV, van Spanning RJ (2004) Expression of nitrite reductase in Nitrosomonas europaea involves NsrR, a novel nitrite-sensitive transcription repressor. Mol Microbiol 54: 148-158.
25. Keon RG, Fu R, Voordouw G (1997) Deletion of two downstream genes alters expression of the hmc operon of Desulfovibrio vulgaris subsp. vulgaris Hildenborough. Arch Microbiol 167: 376-383.
26. Todd JD, Wexler M, Sawers G, Yeoman KH, Poole PS, et al. (2001) RirA, an iron-responsive regulator in the symbiotic bacterium Rhizobium leguminosarum. Microbiology 148: 4059-4071.
27. Schwartz CJ, Giel JL, Patschkowski T, Luther C, Ruzicka FJ, et al. (2001) IscR, an Fe-S cluster-containing transcription factor, represses expression of Escherichia coli genes encoding Fe-S cluster assembly proteins. Proc Natl Acad Sci U S A 98: 14895-14900.
28. Poole RK, Anjum MF, Membrillo-Hernandez J, Kim SO, Hughes MN, et al. (1996) Nitric oxide, nitrite, and Fnr regulation of hmp (flavohemoglobin) gene expression in Escherichia coli K-12. J Bacteriol 178: 5487-5492.
29. Moore CM, Nakano MM, Wang T, Ye RW, Helmann JD (2004) Response of Bacillus subtilis to nitric oxide and the nitrosating agent sodium nitroprusside. J Bacteriol 186: 4655-4664.
30. Householder TC, Fozo EM, Cardinale JA, Clark VL (2000) Gonococcal nitric oxide reductase is encoded by a single gene, norB, which is required for anaerobic growth and is induced by nitric oxide. Infect Immun 68: 5241-5246.
31. Osterman A, Overbeek R (2003) Missing genes in metabolic pathways: A comparative genomics approach. Curr Opin Chem Biol 7: 238-251.
32. Gelfand MS, Novichkov PS, Novichkova ES, Mironov AA (2000) Comparative analysis of regulatory patterns in bacterial genomes. Brief Bioinform 1: 357-371.
33. Rodionov DA, Dubchak I, Arkin A, Alm E, Gelfand MS (2004) Reconstruction of regulatory and metabolic pathways in metal-reducing deltaproteobacteria. Genome Biol 5: R90.
34. Vollack KU, Zumft WG (2001) Nitric oxide signaling and transcriptional control of denitrification genes in Pseudomonas stutzeri. J Bacteriol 183: 2516-2526.
35. Arai H, Mizutani M, Igarashi Y (2003) Transcriptional regulation of the nos genes for nitrous oxide reductase in Pseudomonas aeruginosa. Microbiology 149:
36. Bartnikas TB, Wang Y, Bobo T, Veselov A, Scholes CP, et al. (2002) Characterization of a member of the NnrR regulon in Rhodobacter sphaeroides 2.4.3 encoding a haem-copper protein. Microbiology 148: 825-833.
37. Kwiatkowski AV, Shapleigh JP (1996) Requirement of nitric oxide for induction of genes whose products are involved in nitric oxide metabolism in Rhodobacter sphaeroides 2.4.3. J Biol Chem 271: 24382-24388.
38. Mesa S, Bedmar EJ, Chanfon A, Hennecke H, Fischer HM (2003) Bradyrhizobium japonicum NnrR, a denitrification regulator, expands the FixLJ-FixK2 regulatory cascade. J Bacteriol 185: 3978-3982.
39. Schultz SC, Shields GC, Steitz TA (1991) Crystal structure of a CAP-DNA complex: The DNA is bent by 90 degrees. Science 253: 1001-1007.
40. Luscombe NM, Thornton JM (2002) Protein-DNA interactions: Amino acid conservation and the effects of mutations on binding specificity. J Mol Biol 320: 991-1009.
41. Korner H, Sofia HJ, Zumft WG (2003) Phylogeny of the bacterial superfamily of Crp-Fnr transcription regulators: Exploiting the metabolic spectrum by controlling alternative gene programs. FEMS Microbiol Rev 27: 559-592.
42. Crack J, Green J, Thomson AJ (2004) Mechanism of oxygen sensing by the bacterial transcription factor fumarate-nitrate reduction (FNR). J Biol Chem 279: 9278-9286.
43. Korbel JO, Jensen LJ, von Mering C, Bork P (2004) Analysis of genomic context: Prediction of functional associations from conserved bidirectionally transcribed gene pairs. Nat Biotechnol 22: 911-917.
44. LaCelle M, Kumano M, Kurita K, Yamane K, Zuber P, et al. (1996) Oxygencontrolled regulation of the flavohemoglobin gene in Bacillus subtilis. J Bacteriol 178: 3803-3808.
45. Filenko NA, Browning DF, Cole JA (2005) Transcriptional regulation of a hybrid cluster (prismane) protein. Biochem Soc Trans 33: 195-197.
46. Zumft WG (1997) Cell biology and molecular basis of denitrification. Microbiol Mol Biol Rev 61: 533-616.
47. Lee HS, Abdelal AH, Clark MA, Ingraham JL (1991) Molecular characterization of nosA, a Pseudomonas stutzeri gene encoding an outer membrane protein required to make copper-containing N2O reductase. J Bacterio l 173: 5406-5413.
48. Elvers KT, Wu G, Gilberthorpe NJ, Poole RK, Park SF (2004) Role of an inducible single-domain hemoglobin in mediating resistance to nitric oxide and nitrosative stress in Campylobacter jejuni and Campylobacter coli. J Bacteriol 186: 5332-5341.
49. Lissenden S, Mohan S, Overton T, Regan T, Crooke H, et al. (2000) Identification of transcription activators that regulate gonococcal adaptation from aerobic to anaerobic or oxygen-limited growth. Mol Microbiol 37: 839-855.
50. Cruz-Ramos H, Crack J, Wu G, Hughes MN, Scott C, et al. (2002) NO sensing by FNR: Regulation of the Escherichia coli NO-detoxifying flavohaemoglobin, Hmp. EMBO J 21: 3235-3244.
51. Arai H, Hayashi M, Kuroi A, Ishii M, Igarashi Y (2005) Transcriptional regulation of the flavohemoglobin gene for aerobic nitric oxide detoxification by the second nitric oxide-responsive regulator of Pseudomonas aeruginosa. J Bacteriol 187: 3960-3968.
52. Elvers KT, Turner SM, Wainwright LM, Marsden G, Hinds J, et al. (2005) NssR, a member of the Crp-Fnr superfamily from Campylobacter jejuni, regulates a nitrosative stress-responsive regulon that includes both a singledomain and a truncated haemoglobin. Mol Microbiol 57: 735-750.
53. Levine JS, Augustsson TR, Anderson IC, Hoell JM Jr (1984) Tropospheric sources of NOx: Lightning and biology. Atmos Environ 18: 1797-1804.
54. Fang FC (1997) Perspectives series: Host/pathogen interactions. Mechanisms of nitric oxide-related antimicrobial activity. J Clin Invest 99: 28182825.
55. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL (2005) GenBank. Nucleic Acids Res 33: D34-38.
56. Mironov AA, Vinokurova NP, Gelfand MS (2000) GenomeExplorer: Software for analysis of complete bacterial genomes. Mol Biol 34: 222-231.
57. Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, et al. (2001) The COG database: New developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 29: 22-28.
58. Altschul SF, Koonin EV (1998) Iterated profile searches with PSI-BLASTA tool for discovery in protein databases. Trends Biochem Sci 23: 444-447.
59. Felsenstein J (1981) Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 17: 368-376.
60. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882.
61. Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, et al. (2001) The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res 29: 37-40.
62. Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, et al. (2002) The Pfam protein families database. Nucleic Acids Res 30: 276-280.
63. Gelfand MS, Koonin EV, Mironov AA (2000) Prediction of transcription regulatory sites in Archaea by a comparative genomic approach. Nucleic Acids Res 28: 695-705.
64. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: A sequence logo generator. Genome Res 14: 1188-1190.