Transcription regulation of the nir gene cluster encoding nitrite reductase of Paracoccus denitrificans involves NNR and NirI, a novel type of membrane protein

Molecular Microbiology

Volumn 34, Issue 1, 1999, Pages 24-36

  Saunders, Neil F W ^a   Houben, Edith N G ^a   Koefoed, Sarah ^a   De Weert, Sandra ^a   Reijnders, Willem N M ^a   Westerhoff, Hans V ^a   De Boer, Anthonius P N ^a   Van Spanning, Rob J M ^a  

^a VU UNIVERSITY AMSTERDAM   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN; NITRIC OXIDE REDUCTASE; NITRITE; NITRITE REDUCTASE; OXYGEN; REGULATOR PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GROWTH; CHROMOSOME; CONTROLLED STUDY; CULTURE MEDIUM; EXPRESSION VECTOR; GENE ACTIVATION; GENE CLUSTER; GENE EXPRESSION REGULATION; GENE INSERTION; GENE MUTATION; GENETIC COMPLEMENTATION; MOLECULAR CLONING; NONHUMAN; OPERON; PARACOCCUS DENITRIFICANS; PRIORITY JOURNAL; PROTEIN DOMAIN; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BASE SEQUENCE; DNA-BINDING PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; GENETIC COMPLEMENTATION TEST; MEMBRANE PROTEINS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; MUTATION; NITRITE REDUCTASES; PARACOCCUS DENITRIFICANS; PROTEIN STRUCTURE, SECONDARY; SEQUENCE HOMOLOGY, AMINO ACID; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

BACTERIA (MICROORGANISMS); PARACOCCUS DENITRIFICANS; POSIBACTERIA; PSEUDOMONAS; PSEUDOMONAS STUTZERI; SINORHIZOBIUM MELILOTI;

EID: 0032820729     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2958.1999.01563.x     Document Type: Article

References (48)

1. Aiba, H., Adhya, S., and de Crombrugghe, B. (1981) Evidence for two functional gal promoters in intact Escherichia coli cells. J Biol Chem 256: 11905-11910.
2. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
3. Arai, H., Igarashi, Y., and Kodama, T. (1994) Structure and ANR-dependent transcription of the nir genes for denitrification from Pseudomonas aeruginosa. Biosci Biotechnol Biochem 58: 1286-1291.
4. Arai, H., Igarashi, Y., and Kodama, T. (1995) Expression of the nir and nor genes for denitrification of Pseudomonas aeruginosa requires a novel CRP/FNR-related transcriptional regulator, DNR, in addition to ANR. FEBS Lett 371: 73-76.
5. Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A., et al. (1993) Current Protocols in Molecular Biology. New York: John Wiley & Sons.
6. Bell, L.C., Richardson, D.J., and Ferguson, S.J. (1990) Periplasmic and membrane-bound respiratory nitrate reductases in Thiosphaera pantotropha. The periplasmic enzyme catalyzes the first step in aerobic denitrification. FEBS Lett 265: 85-87.
7. Berks, B.C., Ferguson, S.J., Moir, J.W.B., and Richardson, D.J. (1995) Enzymes and associated electron transport systems that catalyse the respiratory reduction of nitrogen oxides and oxyanions. Bba-Bioenergetics 1232: 97-173.
8. Boogerd, F.C., van Verseveld, H.W., and Stouthamer, A.M. (1980) Electron transport to nitrous oxide in Paracoccus denitrificans. FEBS Lett 113: 279-284.
9. Boyer, H.W., and Roulland-Dussoix, D. (1969) A complementation analysis of the restriction and modification of DNA in Escherichia coli. J Mol Biol 41: 459-472.
10. Chan, Y., McCormick, W., and Watson, R. (1997) A new nos gene downstream from nosDFY is essential for dissimilatory reduction of nitrous oxide by Rhizobium (Sinorhizobium) meliloti. Microbiology 143: 2817-2824.
11. Chang, J.P., and Morris, J.G. (1962) Studies on the utilization of nitrate by Micrococcus denitrificans. J Gen Microbiol 29: 301-310.
12. Cuypers, H., Viebrock-Sambale, A., and Zumft, W.G. (1992) NosR, a membrane-bound regulatory component necessary for expression of nitrous oxide reductase in denitrifying Pseudomonas stutzeri. J Bacteriol 174: 5332-5339.
13. De Boer, A.P.N., Reijnders, W.N.M., Kuenen, J.G., Stouthamer, A.H., and Van Spanning, R.J.M. (1994) Isolation, sequencing and mutational analysis of a gene cluster involved in nitrite reduction in Paracoccus denitrificans. Antonie Van Leeuwenhoek 66: 111-127.
14. De Boer, A.P.N., Van der Oost, J., Reijnders, W.N.M., Westerhoff, H.V., Stouthamer, A.M., and Van Spanning, R.J.M. (1996) Mutational analysis of the nor gene cluster which encodes nitric-oxide reductase from Paracoccus denitrificans. Eur J Biochem 242: 592-600.
15. De Vries, G.E., Harms, N., Hoogendijk, J., and Stouthamer, A.M. (1989) Isolation and characterization of Paracoccus denitrificans mutants with increased conjugation frequencies and pleiotropic loss of a n(GATC)n DNA-modifying property. Arch Microbiol 152: 52-57.
16. Ditta, G., Stanfield, S., Corbin, D., and Helinski, D.R. (1985) Broad host range DNA cloning system for Gram-negative bacteria: construction of a gene bank of Rhizobium meliloti. Proc Natl Acad Sci USA 77: 7347-7351.
17. Frohman, M.A. (1993) Rapid amplification of complementary DNA ends for generation of full-length complementary DNAs: thermal RACE. Methods Enzymol 218: 340-356.
18. 1 gene replacement mutants. J Bacteriol 172: 2392-2400.
19. Hoeren, F.U., Berks, B.C., Ferguson, S.J., and McCarthy, J.E.G. (1993) Sequence and expression of the gene encoding the respiratory nitrous-oxide reductase from Paracoccus denitrificans. New and conserved structural and regulatory motifs. Eur J Biochem 218: 49-57.
20. Holloway, P., McCormick, W., Watson, R.J., and Chan, Y.K. (1996) Identification and analysis of the dissimilatory nitrous oxide reduction genes, nosRZDFY, of Rhizobium meliloti. J Bacteriol 178: 1505-1514.
21. Kessler, B., De Lorenzo, V., and Timmis, K.N. (1992) A general system to integrate lacZ fusions into the chromosomes of Gram-negative eubacteria; regulation of the Pm promoter of the TOL plasmid studied with all the controlling elements in monocopy. Mol Gen Genet 233: 293-301.
22. Kwiatkowski, A.V., Laratta, W.P., Toffanin, A., and Shapleigh, J.P. (1997) Analysis of the role of the nnrR gene product in the response of Rhodobacter sphaeroides 2.4.1 to exogenous nitric oxide. J Bacteriol 179: 5618-5620.
23. Kwiatkowski, A.V., and Shapleigh, J.P. (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.
24. Laemmli, U.K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227: 680-685.
25. Lam, Y., and Nicholas, D.J.D. (1969) A nitrite reductase with cytochrome oxidase activity from Micrococcus denitrificans. Biochim Biophys Acta 180: 459-472.
26. Lawford, H.G., Cox, J.C., Garland, P.B., and Hadock, B.A. (1976) Electron transport in aerobically grown Paracoccus denitrificans: kinetic characterization of the membrane-bound cytochromes and the stoichiometry of respiratory driven proton translocation. FEBS Lett 64: 369-374.
27. Matchová, I., Kucera, I., Janiczek, O., Van Spanning, R.J.M., and Oltmann, L.F. (1993) The existence of an alternative electron transfer pathway to the periplasmic nitrite reductase (cytochrome cd1) in Paracoccus denitrificans. Arch Microbiol 159: 272-275.
28. Miller, J.H. (1972) Experiments in Molecular Genetics. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
29. Nielsen, H., Engelbrecht, J., Brunak, S., and Vonheijne, G. (1997) Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng 10: 1-6.
30. Plumbridge, J., and Kolb, A. (1995) Nag represser-operator interactions: protein-DNA contacts cover more than two turns of the DMA helix [published erratum appears in J Mol Biol 1995 253: 219-220]. J Mol Biol 249: 890-902.
31. Rost, B., and Sander, C. (1994) Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 19: 55-72.
32. Rost, B., Casadio, R., Fariselli, P., and Sander, C. (1995) Prediction of helical transmembrane segments at 95% accuracy. Protein Sci 4: 521-533.
33. Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual. 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
34. Schmehl, M., Jahn, A., Meyer zu Vilsendorf, A., Hennecke, S., Masepohl, B., Schuppler, M., et al. (1993) Identification of a new class of nitrogen fixation genes in Rhodobacter capsulatus: a putative membrane complex involved in electron transport to nitrogenase. Mol Gen Genet 241: 602-615.
35. Simon, R., Priefer, U., and Pühler, A. (1983) Vector plasmids for in vivo and in vitro manipulations of Gram-negative bacteria. In Molecular Genetics of the Bacteria-Plant Interactions. Pühler, A. (ed.). Berlin: Springer, pp. 98-106.
36. Spiro, S. (1994) The FNR family of transcriptional regulators. Antonie van Leeuwenhoek Int J Gen Microbiol 66: 23-36.
37. Spiro, S., and Guest, J.R. (1990) FNR and its role in oxygen-regulated gene expression in Escherichia coli. FEMS Microbiol Rev 75: 399-428.
38. 450 on sodium dodecyl polyacrylamide gels. Anal Biochem 75: 168-176.
39. Tosques, I.E., Shi, J., and Shapleigh, J.P. (1996) Cloning and characterization of nnrR, whose product is required for the expression of proteins involved in nitric oxide metabolism in Rhodobacter sphaeroides 2.4.3. J Bacteriol 178: 4958-4964.
40. Van Spanning, R.J.M., Wansell, C.W., Harms, N., Oltmann, L.F., and Stouthamer, A.M. (1990) Mutagenesis of the gene encoding cytochrome c550 of Paracoccus denitrificans and analysis of the resultant physiological effects. J Bacteriol 172: 986-996.
41. 553i. J Bacteriol 173: 6962-6970.
42. Van Spanning, R.J.M., De Boer, A.P.N., Reijnders, W.N.M., Spiro, S., Westerhoff, H.V., Stouthamer, A.H., et al. (1995a) Nitrite and nitric oxide reduction in Paracoccus denitrificans is under the control of NNR, a regulatory protein that belongs to the FNR family of transcriptional activators. FEBS Lett 360: 151-154.
43. Van Spanning, R.J.M., De Boer, A.P.N., Slotboom, D.-J., Reijnders, W.N.M., and Stouthamer, A.M. (1995b) Isolation and characterization of a novel insertion sequence element, IS1248, in Paracoccus denitrificans. Plasmid 34: 11-21.
44. Van Spanning, R.J.M., De Boer, A.P.N., Reijnders, W.N.M., Westerhoff, H.V., Stouthamer, A.M., and Van der Oost, J. (1997) FnrP and NNR of Paracoccus denitrificans are both members of the FNR family of transcriptional activators but have distinct roles in respiratory adaptation in response to oxygen limitation. Mol Microbiol 23: 893-907.
45. Van Spanning, R.J.M., Houben, E.N.G., Reijnders, W.N.M., Spiro, S., Westerhoff, H.V., and Saunders, N. (1999) Nitric oxide is a signal for NNR-mediated transcription activation in Paracoccus denitrificans. J Bacteriol 181: 4129-4132.
46. Zimmer, W., Danneberg, G., and Bothe, H. (1985) Amperometric method for determining nitrous oxide in denitrification and in nitrogenase-catalyzed nitrous oxide reduction. Curr Microbiol 12: 341-346.
47. Zumft, W.G. (1997) Cell biology and molecular basis of denitrification. Microbiol Mol Biol Rev 61: 533-616.
48. Zumft, W.G., Dreusch, A., Lochelt, S., Cuypers, H., Friedrich, B., and Schneider, B. (1992) Derived amino acid sequences of the nosZ gene from Alcaligenes eutrophus, Pseudomonas aeruginosa and Pseudomonas stutzen reveal potential copper-binding residues. Eur J Biochem 208: 31-40.