1887

Abstract

Nitrous oxide (NO) is a potent greenhouse gas that is produced naturally as an intermediate during the process of denitrification carried out by some soil bacteria. It is consumed by nitrous oxide reductase (NOR), the terminal enzyme of the denitrification pathway, which catalyses a reduction reaction to generate dinitrogen. NOR contains two important copper cofactors (Cu and Cu centres) that are essential for activity, and in copper-limited environments, NOR fails to function, contributing to rising levels of atmospheric NO and a major environmental challenge. Here we report studies of , one of eight genes in the cluster of the soil dwelling α-proteobaterium . A Δ deletion mutant failed to reduce NO under both copper-sufficient and copper-limited conditions, demonstrating that NosX plays an essential role in NOR activity. NOR isolated from -deficient cells was found to be unaffected in terms of the assembly of its copper cofactors, and to be active in assays, indicating that NosX is not required for the maturation of the enzyme; in particular, it plays no part in the assembly of either of the Cu and Cu centres. Furthermore, quantitative Reverse Transcription PCR (qRT-PCR) studies showed that NosX does not significantly affect the expression of the NOR-encoding gene. NosX is a homologue of the FAD-binding protein ApbE from , which functions in the flavinylation of another NOR accessory protein, NosR. Thus, it is likely that NosX is a system-specific maturation factor of NosR, and so is indirectly involved in maintaining the reaction cycle of NOR and cellular NO reduction.

Funding
This study was supported by the:
  • Biotechnology and Biological Sciences Research Council (Award NRP DTP)
    • Principle Award Recipient: Sophie P Bennett
  • EU (Award 316472)
    • Principle Award Recipient: Manuel J Soriano-Laguna
  • Biotechnology and Biological Sciences Research Council (Award BB/S008942/1)
    • Principle Award Recipient: Andrew J Gates
  • Biotechnology and Biological Sciences Research Council (Award BB/M00256X/1)
    • Principle Award Recipient: Andrew J Gates
  • Biotechnology and Biological Sciences Research Council (Award BB/L022796/1)
    • Principle Award Recipient: David J Richardson
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.000955
2020-09-04
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/micro/166/10/909.html?itemId=/content/journal/micro/10.1099/mic.0.000955&mimeType=html&fmt=ahah

References

  1. Ravishankara AR, Daniel JS, Portmann RW. Nitrous oxide N2O: the dominant ozone-depleting substance emitted in the 21st century . Science 2009; 326:123–125 [View Article][PubMed]
    [Google Scholar]
  2. Fowler D, Coyle M, Skiba U, Sutton MA, Cape JN et al. The global nitrogen cycle in the twenty-first century. Philos Trans R Soc Lond B Biol Sci 2013; 368:20130164 [View Article][PubMed]
    [Google Scholar]
  3. Thomson AJ, Giannopoulos G, Pretty J, Baggs EM, Richardson DJ. Biological sources and sinks of nitrous oxide and strategies to mitigate emissions. Philos Trans R Soc Lond B Biol Sci 2012; 367:1157–1168 [View Article][PubMed]
    [Google Scholar]
  4. Hu H-W, Chen D, He J-Z, HW H, JZ H. Microbial regulation of terrestrial nitrous oxide formation: understanding the biological pathways for prediction of emission rates. FEMS Microbiol Rev 2015; 39:729–749 [View Article][PubMed]
    [Google Scholar]
  5. Hallin S, Philippot L, Löffler FE, Sanford RA, Jones CM. Genomics and ecology of Novel N2O-reducing microorganisms. Trends Microbiol 2018; 26:43–55 [View Article][PubMed]
    [Google Scholar]
  6. Jones CM, Graf DRH, Bru D, Philippot L, Hallin S. The unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink. ISME J 2013; 7:417–426 [View Article][PubMed]
    [Google Scholar]
  7. Stein LY. Insights into the physiology of ammonia-oxidizing microorganisms. Curr Opin Chem Biol 2019; 49:9–15 [View Article][PubMed]
    [Google Scholar]
  8. Domeignoz-Horta LA, Philippot L, Peyrard C, Bru D, Breuil M-C et al. Peaks of in situ N2O emissions are influenced by N2O-producing and reducing microbial communities across arable soils. Glob Chang Biol 2018; 24:360–370 [View Article]
    [Google Scholar]
  9. Griffis TJ, Chen Z, Baker JM, Wood JD, Millet DB et al. Nitrous oxide emissions are enhanced in a warmer and wetter world. Proc Natl Acad Sci U S A 2017; 114:12081–12085 [View Article][PubMed]
    [Google Scholar]
  10. Liu B, Frostegård Åsa, Bakken LR. Impaired reduction of N2O to N2 in acid soils is due to a posttranscriptional interference with the expression of nosZ . mBio 2014; 5:e01383–01314 [View Article][PubMed]
    [Google Scholar]
  11. Brown K, Djinovic-Carugo K, Haltia T, Cabrito I, Saraste M et al. Revisiting the catalytic CuZ cluster of nitrous oxide (N2O) reductase. Evidence of a bridging inorganic sulfur. J Biol Chem 2000; 275:41133–41136 [View Article][PubMed]
    [Google Scholar]
  12. Pomowski A, Zumft WG, Kroneck PMH, Einsle O. . N2O binding at a [4Cu:2S] copper-sulphur cluster in nitrous oxide reductase. Nature 2011; 477:234–237 [View Article][PubMed]
    [Google Scholar]
  13. Rasmussen T, Berks BC, Butt JN, Thomson AJ. Multiple forms of the catalytic centre, CuZ, in the enzyme nitrous oxide reductase from Paracoccus pantotrophus . Biochem J 2002; 364:807–815 [View Article][PubMed]
    [Google Scholar]
  14. Mattatall NR, Jazairi J, Hill BC. Characterization of YpmQ, an accessory protein required for the expression of cytochrome c oxidase in Bacillus subtilis . J Biol Chem 2000; 275:28802–28809 [View Article][PubMed]
    [Google Scholar]
  15. Heikkilä MP, Honisch U, Wunsch P, Zumft WG. Role of the Tat ransport system in nitrous oxide reductase translocation and cytochrome cd 1 biosynthesis in Pseudomonas stutzeri . J Bacteriol 2001; 183:1663–1671 [View Article][PubMed]
    [Google Scholar]
  16. Simon J, Einsle O, Kroneck PMH, Zumft WG. The unprecedented nos gene cluster of Wolinella succinogenes encodes a novel respiratory electron transfer pathway to cytochrome c nitrous oxide reductase. FEBS Lett 2004; 569:7–12 [View Article][PubMed]
    [Google Scholar]
  17. Sullivan MJ, Gates AJ, Appia-Ayme C, Rowley G, Richardson DJ. Copper control of bacterial nitrous oxide emission and its impact on vitamin B12-dependent metabolism. Proc Natl Acad Sci U S A 2013; 110:19926–19931 [View Article][PubMed]
    [Google Scholar]
  18. Wunsch P, Zumft WG. Functional domains of NosR, a novel transmembrane iron-sulfur flavoprotein necessary for nitrous oxide respiration. J Bacteriol 2005; 187:1992–2001 [View Article][PubMed]
    [Google Scholar]
  19. Riester J, Zumft WG, Kroneck PM. Nitrous oxide reductase from Pseudomonas stutzeri. Redox properties and spectroscopic characterization of different forms of the multicopper enzyme. Eur J Biochem 1989; 178:751–762 [View Article][PubMed]
    [Google Scholar]
  20. Zumft WG. Biogenesis of the bacterial respiratory CuA, Cu-S enzyme nitrous oxide reductase. J Mol Microbiol Biotech 2005; 10:154–166 [View Article][PubMed]
    [Google Scholar]
  21. Bennett SP, Soriano-Laguna MJ, Bradley JM, Svistunenko DA, Richardson DJ et al. NosL is a dedicated copper chaperone for assembly of the CuZ center of nitrous oxide reductase. Chem Sci 2019; 10:4985–4993 [View Article][PubMed]
    [Google Scholar]
  22. Saunders NF, Hornberg JJ, Reijnders WN, Westerhoff HV, de Vries S et al. The NosX and NirX proteins of Paracoccus denitrificans are functional homologues: their role in maturation of nitrous oxide reductase. J Bacteriol 2000; 182:5211–5217 [View Article][PubMed]
    [Google Scholar]
  23. Zhang L, Trncik C, Andrade SLA, Einsle O. The flavinyl transferase ApbE of Pseudomonas stutzeri matures the NosR protein required for nitrous oxide reduction. Biochim Biophys Acta Bioenerg 2017; 1858:95–102 [View Article][PubMed]
    [Google Scholar]
  24. Vishniac W, Santer M. The thiobacilli. Bacteriol Rev 1957; 21:195–213 [View Article][PubMed]
    [Google Scholar]
  25. Bradford MM. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 1976; 72:248–254 [View Article][PubMed]
    [Google Scholar]
  26. Ghosh S, Gorelsky SI, Chen P, Cabrito I, Moura JJG et al. Activation of N2O reduction by the fully reduced µ4-sulfide bridged tetranuclear CuZ cluster in nitrous oxide reductase. J Am Chem Soc 2003; 125:15708–15709 [View Article][PubMed]
    [Google Scholar]
  27. Kristjansson JK, Hollocher TC. First practical assay for soluble nitrous oxide reductase of denitrifying bacteria and a partial kinetic characterization. J Biol Chem 1980; 255:704–707[PubMed]
    [Google Scholar]
  28. Pfaffl MW. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 2001; 29:e4545 [View Article][PubMed]
    [Google Scholar]
  29. Coyle CL, Zumft WG, Kroneck PM, Körner H, Jakob W. Nitrous oxide reductase from denitrifying Pseudomonas perfectomarina. Purification and properties of a novel multicopper enzyme. Eur J Biochem 1985; 153:459–467 [View Article][PubMed]
    [Google Scholar]
  30. Prudêncio M, Pereira AS, Tavares P, Besson S, Cabrito I et al. Purification, characterization, and preliminary crystallographic study of copper-containing nitrous oxide reductase from Pseudomonas nautica 617. Biochemistry 2000; 39:3899–3907 [View Article][PubMed]
    [Google Scholar]
  31. Paraskevopoulos K, Antonyuk SV, Sawers RG, Eady RR, Hasnain SS. Insight into catalysis of nitrous oxide reductase from high-resolution structures of resting and inhibitor-bound enzyme from Achromobacter cycloclastes . J Mol Biol 2006; 362:55–65 [View Article][PubMed]
    [Google Scholar]
  32. Dell'Acqua S, Pauleta SR, Moura JJG, Moura I. Biochemical characterization of the purple form of Marinobacter hydrocarbonoclasticus nitrous oxide reductase. Philos Trans R Soc Lond B Biol Sci 2012; 367:1204–1212 [View Article][PubMed]
    [Google Scholar]
  33. Bertsova YV, Fadeeva MS, Kostyrko VA, Serebryakova MV, Baykov AA et al. Alternative pyrimidine biosynthesis protein ApbE is a flavin transferase catalyzing covalent attachment of FMN to a threonine residue in bacterial flavoproteins. J Biol Chem 2013; 288:14276–14286 [View Article][PubMed]
    [Google Scholar]
  34. Boyd JM, Endrizzi JA, Hamilton TL, Christopherson MR, Mulder DW et al. FAD binding by ApbE protein from Salmonella enterica: a new class of FAD-binding proteins. J Bacteriol 2011; 193:887–895 [View Article][PubMed]
    [Google Scholar]
  35. Hayashi M, Nakayama Y, Yasui M, Maeda M, Furuishi K et al. FMN is covalently attached to a threonine residue in the NqrB and NqrC subunits of Na(+)-translocating NADH-quinone reductase from Vibrio alginolyticus . FEBS Lett 2001; 488:5–8 [View Article][PubMed]
    [Google Scholar]
  36. Chan YK, McCormick WA, Watson RJ. A new nos gene downstream from nosDFY is essential for dissimilatory reduction of nitrous oxide by Rhizobium (Sinorhizobium) meliloti . Microbiology 1997; 143:2817–2824 [View Article][PubMed]
    [Google Scholar]
  37. Wunsch P, Körner H, Neese F, van Spanning RJM, Kroneck PMH et al. NosX function connects to nitrous oxide (N2O) reduction by affecting the CuZ center of NosZ and its activity in vivo . FEBS Lett 2005; 579:4605–4609 [View Article][PubMed]
    [Google Scholar]
  38. Carreira C, Pauleta SR, Moura I. The catalytic cycle of nitrous oxide reductase - The enzyme that catalyzes the last step of denitrification. J Inorg Biochem 2017; 177:423–434 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.000955
Loading
/content/journal/micro/10.1099/mic.0.000955
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error