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PMID: 8718455 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't Review

Regulation of oxidative phosphorylation: the flexible respiratory network of Paracoccus denitrificans.

Journal of bioenergetics and biomembranes ·Vol. 27 ·No. 5 ·1995-10-00 ·Pages 499-512

Van Spanning RJ, de Boer AP, Reijnders WN, De Gier JW, Delorme CO, Stouthamer AH, Westerhoff HV, Harms N, van der Oost J

Abstract

Paracoccus denitrificans is a facultative anaerobic bacterium that has the capacity to adjust its metabolic infrastructure, quantitatively and/or qualitatively, to the prevailing growth condition. In this bacterium the relative activity of distinct catabolic pathways is subject to a hierarchical control. In the presence of oxygen the aerobic respiration, the most efficient way of electron transfer-linked phosphorylation, has priority. At high oxygen tensions P. denitrificans synthesizes an oxidase with a relatively low affinity for oxygen, whereas under oxygen limitation a high-affinity oxidase appears specifically induced. During anaerobiosis, the pathways with lower free energy-transducing efficiency are induced. In the presence of nitrate, the expression of a number of dehydrogenases ensures the continuation of oxidative phosphorylation via denitrification. After identification of the structural components that are involved in both the aerobic and the anaerobic respiratory networks of P. denitrificans, the intriguing next challenge is to get insight in its regulation. Two transcription regulators have recently been demonstrated to be involved in the expression of a number of aerobic and/or anaerobic respiratory complexes in P. denitrificans. Understanding of the regulation machinery is beginning to emerge and promises much excitement in discovery.

MeSH Terms
Aerobiosis Anaerobiosis Gene Expression Regulation, Bacterial Genes, Bacterial Homeostasis Models, Biological Mutagenesis Oxidative Phosphorylation Paracoccus denitrificans/genetics,growth & development,metabolism
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Van Spanning R J
Department of Microbial Physiology, Vrije Universiteit, Amsterdam, Netherlands.
de Boer A P
Reijnders W N
De Gier J W
Delorme C O
Stouthamer A H
Westerhoff H V
Harms N
van der Oost J
References (72)
72 references, click to expand
  1. Physical mapping of transposon Tn5 insertions defines a gene cluster functional in nitrous oxide respiration by Pseudomonas stutzeri.
    J Bacteriol. 1987 Oct;169(10):4577-80 PMID: 2820935
  2. Respiratory nitrate reductase from Paracoccus denitrificans. Evidence for two b-type haems in the gamma subunit and properties of a water-soluble active enzyme containing alpha and beta subunits.
    Eur J Biochem. 1988 May 16;174(1):207-12 PMID: 3371362
  3. 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. 1995 Feb 27;360(2):151-4 PMID: 7875319
  4. Metabolic regulation including anaerobic metabolism in Paracoccus denitrificans.
    J Bioenerg Biomembr. 1991 Apr;23(2):163-85 PMID: 2050653
  5. The molecule of the year.
    Science. 1992 Dec 18;258(5090):1861 PMID: 1470903
  6. Derived amino acid sequences of the nosZ gene (respiratory N2O reductase) from Alcaligenes eutrophus, Pseudomonas aeruginosa and Pseudomonas stutzeri reveal potential copper-binding residues. Implications for the CuA site of N2O reductase and cytochrome-c oxidase.
    Eur J Biochem. 1992 Aug 15;208(1):31-40 PMID: 1324835
  7. Nitrate respiration in relation to facultative metabolism in enterobacteria.
    Microbiol Rev. 1988 Jun;52(2):190-232 PMID: 3045516
  8. Genetic regulation of nitrogen fixation in rhizobia.
    Microbiol Rev. 1994 Sep;58(3):352-86 PMID: 7968919
  9. Purification and characterization of the periplasmic nitrate reductase from Thiosphaera pantotropha.
    Eur J Biochem. 1994 Feb 15;220(1):117-24 PMID: 8119278
  10. A cytochrome ba3 functions as a quinol oxidase in Paracoccus denitrificans. Purification, cloning, and sequence comparison.
    J Biol Chem. 1994 Sep 16;269(37):23079-86 PMID: 8083210
  11. Adaptation of Escherichia coli to respiratory conditions: regulation of gene expression.
    Cell. 1991 Jul 12;66(1):5-7 PMID: 2070418
  12. Aerobic and anaerobic bacterial respiration monitored by electrodes.
    J Gen Microbiol. 1977 Jan;98(1):231-8 PMID: 319200
  13. Site-directed mutagenesis of residues within helix VI in subunit I of the cytochrome bo3 ubiquinol oxidase from Escherichia coli suggests that tyrosine 288 may be a CuB ligand.
    Biochemistry. 1994 Nov 8;33(44):13013-21 PMID: 7947706
  14. The heme-copper oxidase family consists of three distinct types of terminal oxidases and is related to nitric oxide reductase.
    FEMS Microbiol Lett. 1994 Aug 1;121(1):1-9 PMID: 8082820
  15. The NADH:ubiquinone oxidoreductase (complex I) of respiratory chains.
    Q Rev Biophys. 1992 Aug;25(3):253-324 PMID: 1470679
  16. A method for introduction of unmarked mutations in the genome of Paracoccus denitrificans: construction of strains with multiple mutations in the genes encoding periplasmic cytochromes c550, c551i, and c553i.
    J Bacteriol. 1991 Nov;173(21):6962-70 PMID: 1657872
  17. Nitrate reductase of Escherichia coli: completion of the nucleotide sequence of the nar operon and reassessment of the role of the alpha and beta subunits in iron binding and electron transfer.
    Mol Gen Genet. 1989 Aug;218(2):249-56 PMID: 2674654
  18. Oxygen regulated gene expression in facultatively anaerobic bacteria.
    Antonie Van Leeuwenhoek. 1994;66(1-3):3-22 PMID: 7747938
  19. Isolation, sequencing and mutational analysis of a gene cluster involved in nitrite reduction in Paracoccus denitrificans.
    Antonie Van Leeuwenhoek. 1994;66(1-3):111-27 PMID: 7747927
  20. Restoration of a lost metal-binding site: construction of two different copper sites into a subunit of the E. coli cytochrome o quinol oxidase complex.
    EMBO J. 1992 Sep;11(9):3209-17 PMID: 1324168
  21. Oxygen control in Rhizobium.
    Antonie Van Leeuwenhoek. 1994;66(1-3):129-50 PMID: 7747928
  22. Oxygen reaction and proton uptake in helix VIII mutants of cytochrome bo3.
    Biochemistry. 1995 Apr 18;34(15):5252-8 PMID: 7711046
  23. Genes for a microaerobically induced oxidase complex in Bradyrhizobium japonicum are essential for a nitrogen-fixing endosymbiosis.
    Proc Natl Acad Sci U S A. 1993 Apr 15;90(8):3309-13 PMID: 8386371
  24. Expression of denitrification enzymes in response to the dissolved oxygen level and respiratory substrate in continuous culture of Pseudomonas stutzeri.
    Appl Environ Microbiol. 1989 Jul;55(7):1670-6 PMID: 2764573
  25. narI region of the Escherichia coli nitrate reductase (nar) operon contains two genes.
    J Bacteriol. 1988 Apr;170(4):1721-9 PMID: 2832376
  26. The FNR family of transcriptional regulators.
    Antonie Van Leeuwenhoek. 1994;66(1-3):23-36 PMID: 7747934
  27. NarK is a nitrite-extrusion system involved in anaerobic nitrate respiration by Escherichia coli.
    Mol Microbiol. 1994 May;12(4):579-86 PMID: 7934881
  28. The oxidation of methylamine in Paracoccus denitrificans.
    Eur J Biochem. 1995 Apr 1;229(1):148-54 PMID: 7744026
  29. FNR and its role in oxygen-regulated gene expression in Escherichia coli.
    FEMS Microbiol Rev. 1990 Aug;6(4):399-428 PMID: 2248796
  30. Nitric oxide reductase from Pseudomonas stutzeri. Primary structure and gene organization of a novel bacterial cytochrome bc complex.
    Eur J Biochem. 1994 Jan 15;219(1-2):481-90 PMID: 7508388
  31. Insight into the active-site structure and function of cytochrome oxidase by analysis of site-directed mutants of bacterial cytochrome aa3 and cytochrome bo.
    J Bioenerg Biomembr. 1993 Apr;25(2):121-36 PMID: 8389745
  32. Proton pump coupled to cytochrome c oxidase in Paracoccus denitrificans.
    Biochim Biophys Acta. 1981 May 13;635(3):525-34 PMID: 6263335
  33. Cytochrome oxidase evolved by tinkering with denitrification enzymes.
    FEBS Lett. 1994 Mar 14;341(1):1-4 PMID: 8137905
  34. 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. 1993 Nov 15;218(1):49-57 PMID: 8243476
  35. The nitric oxide reductase of Paracoccus denitrificans.
    Biochem J. 1990 Jul 15;269(2):423-9 PMID: 2167070
  36. Electron transfer between cytochrome c and the isolated CuA domain: identification of substrate-binding residues in cytochrome c oxidase.
    Biochemistry. 1995 May 2;34(17):5824-30 PMID: 7727443
  37. Isolation and characterization of the moxJ, moxG, moxI, and moxR genes of Paracoccus denitrificans: inactivation of moxJ, moxG, and moxR and the resultant effect on methylotrophic growth.
    J Bacteriol. 1991 Nov;173(21):6948-61 PMID: 1657871
  38. Formation of the N-N bond from nitric oxide by a membrane-bound cytochrome bc complex of nitrate-respiring (denitrifying) Pseudomonas stutzeri.
    J Bacteriol. 1989 Jun;171(6):3288-97 PMID: 2542222
  39. Pseudomonas stutzeri N2O reductase contains CuA-type sites.
    Proc Natl Acad Sci U S A. 1989 Jun;86(11):4082-6 PMID: 2542963
  40. Regulation of nitrate and nitrite reductase synthesis in enterobacteria.
    Antonie Van Leeuwenhoek. 1994;66(1-3):37-45 PMID: 7747939
  41. Possible proton relay pathways in cytochrome c oxidase.
    Proc Natl Acad Sci U S A. 1995 Feb 28;92(5):1604-8 PMID: 7878026
  42. Sequence and genetic characterization of etrA, an fnr analog that regulates anaerobic respiration in Shewanella putrefaciens MR-1.
    J Bacteriol. 1993 Dec;175(24):7938-44 PMID: 8253682
  43. Nitrate reductases of Escherichia coli: sequence of the second nitrate reductase and comparison with that encoded by the narGHJI operon.
    Mol Gen Genet. 1990 Jun;222(1):104-11 PMID: 2233673
  44. The terminal oxidases of Paracoccus denitrificans.
    Mol Microbiol. 1994 Jul;13(2):183-96 PMID: 7984100
  45. Denitrification: production and consumption of nitric oxide.
    Appl Environ Microbiol. 1994 Apr;60(4):1053-8 PMID: 8017903
  46. Sequence analysis of subunits of the membrane-bound nitrate reductase from a denitrifying bacterium: the integral membrane subunit provides a prototype for the dihaem electron-carrying arm of a redox loop.
    Mol Microbiol. 1995 Jan;15(2):319-31 PMID: 7746153
  47. Oxidation of methylamine by a Paracoccus denitrificans mutant impaired in the synthesis of the bc1 complex and the aa3-type oxidase. Evidence for the existence of an alternative cytochrome c oxidase in this bacterium.
    FEBS Lett. 1992 Jul 13;306(1):23-6 PMID: 1321057
  48. Isolation, sequencing, and mutagenesis of the gene encoding cytochrome c553i of Paracoccus denitrificans and characterization of the mutant strain.
    J Bacteriol. 1991 Nov;173(21):6971-9 PMID: 1657873
  49. Interdependence of respiratory NO reduction and nitrite reduction revealed by mutagenesis of nirQ, a novel gene in the denitrification gene cluster of Pseudomonas stutzeri.
    FEBS Lett. 1992 Dec 21;314(3):308-14 PMID: 1468562
  50. The three-subunit cytochrome bc1 complex of Paracoccus denitrificans. Its physiological function, structure, and mechanism of electron transfer and energy transduction.
    J Bioenerg Biomembr. 1991 Apr;23(2):241-55 PMID: 1646795
  51. The cupric site in nitrous oxide reductase contains a mixed-valence [Cu(II),Cu(I)] binuclear center: a multifrequency electron paramagnetic resonance investigation.
    FEBS Lett. 1988 Dec 19;242(1):70-4 PMID: 2849565
  52. Mutational analysis of mau genes involved in methylamine metabolism in Paracoccus denitrificans.
    Eur J Biochem. 1995 Jun 15;230(3):860-71 PMID: 7601147
  53. Formation of a potent respiratory inhibitor at nitrite reduction by nitrite reductase isolated from the bacterium Paracoccus denitrificans.
    J Basic Microbiol. 1990;30(7):515-22 PMID: 2266492
  54. Mutagenesis of the gene encoding cytochrome c550 of Paracoccus denitrificans and analysis of the resultant physiological effects.
    J Bacteriol. 1990 Feb;172(2):986-96 PMID: 2153663
  55. Anaerobic control of denitrification in Pseudomonas stutzeri escapes mutagenesis of an fnr-like gene.
    J Bacteriol. 1993 Nov;175(22):7236-46 PMID: 8226670
  56. Variable stoichiometry of proton pumping by the mitochondrial respiratory chain.
    Nature. 1987 Sep 10-16;329(6135):170-2 PMID: 3041231
  57. Denitrification and its control.
    Antonie Van Leeuwenhoek. 1994;66(1-3):89-110 PMID: 7747942
  58. Isolation of ubiquinol oxidase from Paracoccus denitrificans and resolution into cytochrome bc1 and cytochrome c-aa3 complexes.
    J Biol Chem. 1985 Feb 25;260(4):2458-67 PMID: 2982819
  59. Nitrite reductase from Pseudomonas aeruginosa: sequence of the gene and the protein.
    FEBS Lett. 1989 Aug 28;254(1-2):33-8 PMID: 2506077
  60. Isolation, sequencing, and mutagenesis of the gene encoding NAD- and glutathione-dependent formaldehyde dehydrogenase (GD-FALDH) from Paracoccus denitrificans, in which GD-FALDH is essential for methylotrophic growth.
    J Bacteriol. 1995 Jan;177(1):247-51 PMID: 7798140
  61. Paracoccus denitrificans cytochrome c1 gene replacement mutants.
    J Bacteriol. 1990 May;172(5):2392-400 PMID: 2158969
  62. C1 metabolism in Paracoccus denitrificans: genetics of Paracoccus denitrificans.
    J Bioenerg Biomembr. 1991 Apr;23(2):187-210 PMID: 2050654
  63. Isolation and characterization of a nitrite reductase gene and its use as a probe for denitrifying bacteria.
    Appl Environ Microbiol. 1992 Jan;58(1):376-84 PMID: 1539983
  64. Characterization of the paramagnetic iron-containing redox centres of Thiosphaera pantotropha periplasmic nitrate reductase.
    FEBS Lett. 1994 May 23;345(1):76-80 PMID: 8194605
  65. Proton transfer in cytochrome bo3 ubiquinol oxidase of Escherichia coli: second-site mutations in subunit I that restore proton pumping in the mutant Asp135-->Asn.
    Biochemistry. 1995 Apr 4;34(13):4428-33 PMID: 7703256
  66. Isolation and nucleotide sequence of the methanol dehydrogenase structural gene from Paracoccus denitrificans.
    J Bacteriol. 1987 Sep;169(9):3969-75 PMID: 3114231
  67. Periplasmic and membrane-bound respiratory nitrate reductases in Thiosphaera pantotropha. The periplasmic enzyme catalyzes the first step in aerobic denitrification.
    FEBS Lett. 1990 Jun 4;265(1-2):85-7 PMID: 2365057
  68. Copper protein structures.
    Adv Protein Chem. 1991;42:145-97 PMID: 1793005
  69. Respiration-driven proton translocation with nitrite and nitrous oxide in Paracoccus denitrificans.
    Biochim Biophys Acta. 1981 Dec 14;638(2):181-91 PMID: 7317386
  70. The genes of the Paracoccus denitrificans bc1 complex. Nucleotide sequence and homologies between bacterial and mitochondrial subunits.
    J Biol Chem. 1987 Oct 5;262(28):13805-11 PMID: 2820981
  71. Purification of Paracoccus denitrificans cytochrome c552 and sequence analysis of the gene.
    Eur J Biochem. 1995 Jul 1;231(1):259-65 PMID: 7628479
  72. Mutagenesis of the gene encoding amicyanin of Paracoccus denitrificans and the resultant effect on methylamine oxidation.
    FEBS Lett. 1990 Nov 26;275(1-2):217-20 PMID: 2261991
Article Info
Journal
Journal of bioenergetics and biomembranes
Abbr.
J Bioenerg Biomembr
ISSN
0145-479X
Published
1995-10-00
Pages
499-512
Language
English
Region
United States
NLM ID
7701859
Subset
IM
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