1887

Microbiology Society logo

Volume 162, Issue 6

Functional roles of CymA and NapC in reduction of nitrate and nitrite by W3-18-1 Free

Abstract

W3-18-1 harbours two periplasmic nitrate reductase (Nap) gene clusters, NapC-associated EDABC) and CymA-dependent DAGHB), for dissimilatory nitrate respiration. CymA is a member of the NapC/NirT quinol dehydrogenase family and acts as a hub to support different respiratory pathways, including those on iron [Fe(III)] and manganese [Mn(III, IV)] (hydr)oxide, nitrate, nitrite, fumarate and arsenate in strains. However, in our analysis it was shown that another NapC/NirT family protein, NapC, was only involved in nitrate reduction, although both CymA and NapC can transfer quinol-derived electrons to a periplasmic terminal reductase or an electron acceptor. Furthermore, our results showed that NapC could only interact specifically with the Nap-alpha nitrate reductase while CymA could interact promiscuously with Nap-alpha, Nap-beta and the NrfA nitrite reductase for nitrate and nitrite reduction. To further explore the difference in specificity, site-directed mutagenesis on both CymA and NapC was conducted and the phenotypic changes in nitrate and nitrite reduction were tested. Our analyses demonstrated that the Lys-91 residue played a key role in nitrate reduction for quinol oxidation and the Asp-166 residue might influence the maturation of CymA. The Asp-97 residue might be one of the key factors that influence the interaction of CymA with the cytochromes NapB and NrfA.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): electron transfer , Nitrate reduction , nitrite reduction , Shewanella putrefaciens , specificity and tetraheme cytochromes
© 2016 The Authors
Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.000285
2016-06-01
2024-04-18
Loading full text...

Full text loading...

/deliver/fulltext/micro/162/6/930.html?itemId=/content/journal/micro/10.1099/mic.0.000285&mimeType=html&fmt=ahah

References

  1. Beliaev A. S., Klingeman D. M., Klappenbach J. A., Wu L., Romine M. F., Tiedje J. M., Nealson K. H., Fredrickson J. K., Zhou J. 2005; Global transcriptome analysis of Shewanella oneidensis MR-1 exposed to different terminal electron acceptors. J Bacteriol 187:7138–7145 [View Article][PubMed]
     [Google Scholar]
  2. Berks B. C., Richardson D. J., Reilly A., Willis A. C., Ferguson S. J. 1995; The napEDABC gene cluster encoding the periplasmic nitrate reductase system of Thiosphaera pantotropha . Biochem J 309:983–992[PubMed] [CrossRef]
     [Google Scholar]
  3. Botsford J. L., Harman J. G. 1992; Cyclic AMP in prokaryotes. Microbiol Rev 56:100–122[PubMed]
     [Google Scholar]
  4. Chen Y., Wang F., Xu J., Mehmood M. A., Xiao X. 2011; Physiological and evolutionary studies of NAP systems in Shewanella piezotolerans WP3. ISME J 5:843–855 [View Article][PubMed]
     [Google Scholar]
  5. China E P A. 2002 Water and Wastewater Monitoring Methods, 4th edn.266–274 Chinese Environmental Science Publishing House;
     [Google Scholar]
  6. Cordova C. D., Schicklberger M. F., Yu Y., Spormann A. M. 2011; Partial functional replacement of CymA by SirCD in Shewanella oneidensis MR-1. J Bacteriol 193:2312–2321 [View Article][PubMed]
     [Google Scholar]
  7. Cruz-García C., Murray A. E., Klappenbach J. A., Stewart V., Tiedje J. M. 2007; Respiratory nitrate ammonification by Shewanella oneidensis MR-1. J Bacteriol 189:656–662 [View Article][PubMed]
     [Google Scholar]
  8. Dong Y., Wang J., Fu H., Zhou G., Shi M., Gao H. 2012; A Crp-dependent two-component system regulates nitrate and nitrite respiration in Shewanella oneidensis . PLoS One 7:e51643 [View Article][PubMed]
     [Google Scholar]
  9. Fonseca B. M., Paquete C. M., Neto S. E., Pacheco I., Soares C. M., Louro R. O. 2013; Mind the gap: cytochrome interactions reveal electron pathways across the periplasm of Shewanella oneidensis MR-1 . Biochem J 449:101–108 [View Article][PubMed]
     [Google Scholar]
  10. Francis R. T., Becker R. R. 1984; Specific indication of hemoproteins in polyacrylamide gels using a double-staining process. Anal Biochem 136:509–514[PubMed] [CrossRef]
     [Google Scholar]
  11. Fredrickson, Romine M. F., Beliaev A. S., Auchtung J. M., Driscoll M. E., Gardner T. S., Nealson K. H., Osterman A. L., Pinchuk G. et al. 2008; Towards environmental systems biology of Shewanella . Nat Rev Microbiol 6:592–603 [View Article][PubMed]
     [Google Scholar]
  12. Fu H., Chen H., Wang J., Zhou G., Zhang H., Zhang L., Gao H. 2013; Crp-dependent cytochrome bd oxidase confers nitrite resistance to Shewanella oneidensis . Environ Microbiol 15:2198–2212 [View Article][PubMed]
     [Google Scholar]
  13. Fu H., Jin M., Ju L., Mao Y., Gao H. 2014; Evidence for function overlapping of CymA and the cytochrome bc1 complex in the Shewanella oneidensis nitrate and nitrite respiration. Environ Microbiol 16:3181–3195 [View Article][PubMed]
     [Google Scholar]
  14. Gao H., Wang X., Yang Z. K., Chen J., Liang Y., Chen H., Palzkill T., Zhou J. 2010; Physiological roles of ArcA, Crp, and EtrA and their interactive control on aerobic and anaerobic respiration in Shewanella oneidensis . PLoS One 5:e15295 [View Article][PubMed]
     [Google Scholar]
  15. Gao H., Yang Z. K., Barua S., Reed S. B., Romine M. F., Nealson K. H., Fredrickson J. K., Tiedje J. M., Zhou J. 2009; Reduction of nitrate in Shewanella oneidensis depends on atypical NAP and NRF systems with NapB as a preferred electron transport protein from CymA to NapA. ISME J 3:966–976 [View Article][PubMed]
     [Google Scholar]
  16. Gescher J. S., Cordova C. D., Spormann A. M. 2008; Dissimilatory iron reduction in Escherichia coli: identification of CymA of Shewanella oneidensis and NapC of E. coli as ferric reductases. Mol Microbiol 68:706–719 [View Article][PubMed]
     [Google Scholar]
  17. Gilda J. E., Gomes A. V. 2013; Stain-free total protein staining is a superior loading control to β-actin for Western blots. Anal Biochem 440:186–188 [View Article][PubMed]
     [Google Scholar]
  18. Hau H. H., Gralnick J. A. 2007; Ecology and biotechnology of the genus Shewanella . Annu Rev Microbiol 61:237–258 [View Article][PubMed]
     [Google Scholar]
  19. Kovach M. E., Elzer P. H., Hill D. S., Robertson G. T., Farris M. A., Roop R. M., Peterson K. M. 1995; Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes. Gene 166:175–176 [View Article][PubMed]
     [Google Scholar]
  20. Kovach M. E., Phillips R. W., Elzer P. H., Roop R. M., Peterson K. M. 1994; pBBR1MCS: a broad-host-range cloning vector. Biotechniques 16:800–802[PubMed]
     [Google Scholar]
  21. Li D.-B., Cheng Y.-Y., Wu C., Li W.-W., Li N., Yang Z.-C., Tong Z.-H., Yu H.-Q. 2014; Selenite reduction by Shewanella oneidensis MR-1 is mediated by fumarate reductase in periplasm. Sci Rep 4:[PubMed]
     [Google Scholar]
  22. Livak K. J., Schmittgen T. D. 2001; Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25:402–408 [View Article][PubMed]
     [Google Scholar]
  23. Marritt S. J., Lowe T. G., Bye J., McMillan D. G. G., Shi L., Fredrickson J., Zachara J., Richardson D. J., Cheesman M. R. et al. 2012a; A functional description of CymA, an electron-transfer hub supporting anaerobic respiratory flexibility in Shewanella . Biochem J 444:465–474 [CrossRef]
     [Google Scholar]
  24. Marritt S. J., McMillan D. G. G., Shi L., Fredrickson J. K., Zachara J. M., Richardson D. J., Jeuken L. J. C., Butt J. N. 2012b; The roles of cyma in support of the respiratory flexibility of shewanella oneidensis MR-1. Biochem Soc T 40:1217–1221 [CrossRef]
     [Google Scholar]
  25. McMillan D. G., Marritt S. J., Butt J. N., Jeuken L. J. 2012; Menaquinone-7 is specific cofactor in tetraheme quinol dehydrogenase CymA. J Biol Chem 287:14215–14225 [View Article][PubMed]
     [Google Scholar]
  26. Meyer T. E., Tsapin A. I., Vandenberghe I., de Smet L., Frishman D., Nealson K. H., Cusanovich M. A., van Beeumen J. J. 2004; Identification of 42 possible cytochrome C genes in the Shewanella oneidensis genome and characterization of six soluble cytochromes. OMICS 8:57–77 [View Article][PubMed]
     [Google Scholar]
  27. Murphy J. N., Saltikov C. W. 2007; The cymA gene, encoding a tetraheme c-type cytochrome, is required for arsenate respiration in Shewanella species. J Bacteriol 189:2283–2290 [View Article][PubMed]
     [Google Scholar]
  28. Murray A. E., Lies D., Li G., Nealson K., Zhou J., Tiedje J. M. 2001; DNA/DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes. P Natl Acad Sci USA 98:9853–9858 [CrossRef]
     [Google Scholar]
  29. Myers C. R., Myers J. M. 1997; Cloning and sequence of cymA, a gene encoding a tetraheme cytochrome C required for reduction of iron(III), fumarate, and nitrate by Shewanella putrefaciens MR-1. J Bacteriol 179:1143–1152[PubMed]
     [Google Scholar]
  30. Myers C. R., Nealson K. H. 1988; Bacterial manganese reduction and growth with manganese oxide as the sole electron acceptor. Science 240:1319–1321 [View Article][PubMed]
     [Google Scholar]
  31. Myers J. M., Myers C. R. 2000; Role of the tetraheme cytochrome CymA in anaerobic electron transport in cells of Shewanella putrefaciens MR-1 with normal levels of menaquinone. J Bacteriol 182:67–75[PubMed] [CrossRef]
     [Google Scholar]
  32. Neto S. E., Fonseca B. M., Maycock C., Louro R. O. 2014; Analysis of the residual alignment of a paramagnetic multiheme cytochrome by NMR. Chem Commun (Camb) 50:4561–4563 [View Article][PubMed]
     [Google Scholar]
  33. Nicholas D. J. D., Nason A. 1957; Determination of nitrate and nitrite. Method Enzymol 3:981–984 [CrossRef]
     [Google Scholar]
  34. Pinchuk G. E., Rodionov D. A., Yang C., Li X., Osterman A. L., Dervyn E., Geydebrekht O. V., Reed S. B., Romine M. F. et al. 2009; Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization. P Natl Acad Sci 106:2874–2879 [CrossRef]
     [Google Scholar]
  35. Potter L., Angove H., Richardson D., Cole J. 2001; Nitrate reduction in the periplasm of gram-negative bacteria. Adv Microb Physiol 45:51–112[PubMed] [CrossRef]
     [Google Scholar]
  36. Qiu D., Wei H., Tu Q., Yang Y., Xie M., Chen J., Pinkerton M. H., Jr., Liang Y., He Z., Zhou J. 2013; Combined genomics and experimental analyses of respiratory characteristics of Shewanella putrefaciens W3-18-1. Appl Environ Microbiol 79:5250–5257 [View Article][PubMed]
     [Google Scholar]
  37. Roldán M. D., Sears H. J., Cheesman M. R., Ferguson S. J., Thomson A. J., Berks B. C., Richardson D. J. 1998; Spectroscopic characterization of a novel multiheme c-type cytochrome widely implicated in bacterial electron transport. J Biol Chem 273:28785–28790[PubMed] [CrossRef]
     [Google Scholar]
  38. Saffarini D. A., Schultz R., Beliaev A. 2003; Involvement of cyclic AMP (cAMP) and cAMP receptor protein in anaerobic respiration of Shewanella oneidensis . J Bacteriol 185:3668–3671[PubMed] [CrossRef]
     [Google Scholar]
  39. Schmittgen T. D., Livak K. J. 2008; Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc 3:1101–1108[PubMed] [CrossRef]
     [Google Scholar]
  40. Schuetz B., Schicklberger M., Kuermann J., Spormann A. M., Gescher J. 2009; Periplasmic electron transfer via the c-type cytochromes MtrA and FccA of Shewanella oneidensis MR-1. Appl Environ Microbiol 75:7789–7796 [View Article][PubMed]
     [Google Scholar]
  41. Simon J., Gross R., Einsle O., Kroneck P. M., Kröger A., Klimmek O. 2000; A NapC/NirT-type cytochrome c (NrfH) is the mediator between the quinone pool and the cytochrome c nitrite reductase of Wolinella succinogenes . Mol Microbiol 35:686–696[PubMed] [CrossRef]
     [Google Scholar]
  42. Simpson P. J., Richardson D. J., Codd R. 2010; The periplasmic nitrate reductase in Shewanella: the resolution, distribution and functional implications of two NAP isoforms, NapEDABC and NapDAGHB. Microbiology 156:302–312 [View Article][PubMed]
     [Google Scholar]
  43. Stewart V., Bledsoe P. J., Chen L. L., Cai A. 2009; Catabolite repression control of napF (periplasmic nitrate reductase) operon expression in Escherichia coli K-12. J Bacteriol 191:996–1005 [View Article][PubMed]
     [Google Scholar]
  44. Sturm G., Richter K., Doetsch A., Heide H., Louro R. O., Gescher J. 2015; A dynamic periplasmic electron transfer network enables respiratory flexibility beyond a thermodynamic regulatory regime. ISME J 9:1802–1811 [View Article][PubMed]
     [Google Scholar]
  45. Szeinbaum N., Burns J. L., DiChristina T. J. 2014; Electron transport and protein secretion pathways involved in Mn(III) reduction by Shewanella oneidensis. Env Microbiol Rep 6:490–500 [CrossRef]
     [Google Scholar]
  46. Thomas P. E., Ryan D., Levin W. 1976; An improved staining procedure for the detection of the peroxidase activity of cytochrome P-450 on sodium dodecyl sulfate polyacrylamide gels. Anal Biochem 75:168–176[PubMed] [CrossRef]
     [Google Scholar]
  47. Wan X. F., Verberkmoes N. C., McCue L. A., Stanek D., Connelly H., Hauser L. J., Wu L., Liu X., Yan T. et al. 2004; Transcriptomic and proteomic characterization of the Fur modulon in the metal-reducing bacterium Shewanella oneidensis . J Bacteriol 186:8385–8400 [View Article][PubMed]
     [Google Scholar]
  48. Welinder C., Ekblad L. 2011; Coomassie staining as loading control in Western blot analysis. J Proteome Res 10:1416–1419 [View Article][PubMed]
     [Google Scholar]
  49. Wu L., Wang J., Tang P., Chen H., Gao H. 2011; Genetic and molecular characterization of flagellar assembly in Shewanella oneidensis . PLoS One 6:e21479 [View Article][PubMed]
     [Google Scholar]
  50. Zargar K., Saltikov C. W. 2009; Lysine-91 of the tetraheme c-type cytochrome CymA is essential for quinone interaction and arsenate respiration in Shewanella sp. strain ANA-3. Arch Microbiol 191:797–806 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.000285
Loading
Functional roles of CymA and NapC in reduction of nitrate and nitrite by Shewanella putrefaciens W3-18-1
Microbiology 162, 930 (2016); https://doi.org/10.1099/mic.0.000285
/content/journal/micro/10.1099/mic.0.000285
/content/journal/micro/10.1099/mic.0.000285
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited Most Cited RSS feed

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