Abstract
Dissimilatory nitrite reductase, a key enzyme in the denitrification pathway, catalyzes the reduction of nitrite to NO. Bioinformatic analysis showed that the genome of a novel nitrite-degrading haloarchaeon Halorussus sp. YCN54 possessed a gene encoding the Cu-containing dissimilatory nitrite reductase (NirKHrs). NirKHrs was heterologously expressed and purified. Protein sequencing indicated that two isoforms of NirKHrs monomer were produced intracellularly. UV–vis spectrum of the purified NirKHrs showed that it belonged to the blue NirK group. NirKHrs showed optimum activity at 4.5 M NaCl, 55 ℃ and pH 7.0, representing a halophilic, slightly thermophilic and neutral enzyme. It exhibited high stability at 30–50 ℃. NirKHrs activity was strongly inhibited by the copper chelating agent due to removal of copper. NirKHrs activity was activated by Mn2+ and Sr2+. It displayed good tolerance to some high polarity organic solvents and nonionic surfactants, such as glycerol, DMSO, DMF and tween-20. Na2S2O4 was an effective electron donor to NirKHrs. The Km and Vmax values of purified NirKHrs for nitrite were 3.2 mM and 477.2 U/mg, respectively, indicating its high activity. These results indicated that NirKHrs may have potential applications for nitrite degradation in high-salt industries, such as salted food and saline wastewater treatment.
Similar content being viewed by others
Abbreviations
- MV:
-
Methyl viologen
- NirK:
-
Cu-containing nitrite reductases
- NirS:
-
Cytochrome-c-dependent nitrite reductases
- DMSO:
-
Dimethyl sulfoxide
- DMF:
-
N,N-dimethylformamide
- DDC:
-
Diethyldithiocarbamate
- Tat:
-
Twin-arginine translocation
References
Adman ET, Godden JW, Turley S (1995) The structure of copper-nitrite reductase from Achromobacter cycloclastes at five pH values, with NO2− bound and with type II copper depleted. J Biol Chem 270:27458–27474. https://doi.org/10.1074/jbc.270.46.27458
Bonete MJ, Pire C, LLorca FI, Camacho ML (1996) Glucose dehydrogenase from the halophilic Archaeon Haloferax mediterranei: enzyme purification, characterisation and N-terminal sequence. FEBS Lett 383:227–229. https://doi.org/10.1016/0014-5793(96)00235-9
Boulanger MJ, Murphy ME (2003) Directing the mode of nitrite binding to a copper-containing nitrite reductase from Alcaligenes faecalis S-6: characterization of an active site isoleucine. Protein Sci 12:248–256. https://doi.org/10.1110/ps.0224503
Bradford MM (1976) A rapid and sensitive method for the quantization of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248–254
D'Amico S, Marx JC, Gerday C, Feller G (2003) Activity-stability relationships in extremophilic enzymes. J Biol Chem 278:7891–7896. https://doi.org/10.1074/jbc.M212508200
Dodd FE, Hasnain SS, Hunter WN, Abraham ZH, Debenham M, Kanzler H, Eldridge M, Eady RR, Ambler RP, Smith BE (1995) Evidence for two distinct azurins in Alcaligenes xylosoxidans (NCIMB 11015): potential electron donors to nitrite reductase. Biochemistry 34:10180–10186. https://doi.org/10.1021/bi00032a011
Esclapez J, Zafrilla B, Martínez-Espinosa RM, Bonete MJ (2013) Cu-NirK from Haloferax mediterranei as an example of metalloprotein maturation and exportation via Tat system. Biochim Biophys Acta 1834:1003–1009. https://doi.org/10.1016/j.bbapap.2013.03.002
Gao RC, Shi T, Liu XD, Zhao MQ, Cui HL, Yuan L (2017) Purification and characterisation of a salt-stable protease from the halophilic archaeon Halogranum rubrum. J Sci Food Agr 97:1412–1419. https://doi.org/10.1002/jsfa.7879
Han D, Zhu L, Cui HL (2019a) Halorussus litoreus sp. nov., isolated from the salted brown alga Laminaria. Int J Syst Evol Microbiol 69:767–772. https://doi.org/10.1099/ijsem.0.003233
Han SB, Hou XJ, Wu C, Zhao Z, Ju Z, Zhang R, Cui HL, Keen LJ, Xu L, Wu M (2019b) Complete genome sequence of Salinigranum rubrum GX10T, an extremely halophilic archaeon isolated from a marine solar saltern. Mar Genom 44:57–60. https://doi.org/10.1016/j.margen.2018.09.004
Hattori T, Shiba H, Ashiki K, Araki T, Nagashima YK, Yoshimatsu K, Fujiwara T (2016) Anaerobic growth of haloarchaeon Haloferax volcanii by denitrification is controlled by the transcription regulator NarO. J Bacteriol 198:1077–1086. https://doi.org/10.1128/Jb.00833-15
Heylen K, Gevers D, Vanparys B, Wittebolle L, Geets J, Boon N, De Vos P (2006) The incidence of nirS and nirK and their genetic heterogeneity in cultivated denitrifiers. Environ Microbiol 8:2012–2021. https://doi.org/10.1111/j.1462-2920.2006.01081.x
Horrell S, Kekilli D, Strange RW, Hough MA (2017) Recent structural insights into the function of copper nitrite reductases. Metallomics 9:1470–1482. https://doi.org/10.1039/c7mt00146k
Hou J, Zhao YJ, Zhu L, Cui HL (2018) Salinirubellus salinus gen. nov., sp. nov., isolated from a marine solar saltern. Int J Syst Evol Microbiol 68:1874–1878. https://doi.org/10.1099/ijsem.0.002757
Ichiki H, Tanaka Y, Mochizuki K, Yoshimatsu K, Sakurai T, Fujiwara T (2001) Purification, characterization, and genetic analysis of Cu-containing dissimilatory nitrite reductase from a denitrifying halophilic archaeon, Haloarcula marismortui. J Bacteriol 183:4149–4156. https://doi.org/10.1128/Jb.183.14.4149-4156.2001
Inatomi K, Hochstein LI (1996) The purification and properties of a copper nitrite reductase from Haloferax denitrificans. Curr Microbiol 32:5
Kobayashi M, Shoun H (1995) The copper-containing dissimilatory nitrite reductase involved in the denitrifying system of the fungus Fusarium oxysporum. J Biol Chem 270:4146–4151. https://doi.org/10.1074/jbc.270.8.4146
Kunz W (2010) Specific ion effects in colloidal and biological systems. Curr Opin Colloid Interface Sci 15:34–39. https://doi.org/10.1016/j.cocis.2009.11.008
Laemmli UK (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680–685. https://doi.org/10.1038/227680a0
Liu G, Hou J, Cai S, Zhao D, Cai L, Han J, Zhou J, Xiang H (2015) A patatin-like protein associated with the polyhydroxyalkanoate (PHA) granules of Haloferax mediterranei acts as an efficient depolymerase in the degradation of native PHA. Appl Environ Microbiol 81:3029–3038. https://doi.org/10.1128/AEM.04269-14
Liu MY, Liu MC, Payne WJ, Legall J (1986) Properties and electron transfer specificity of copper proteins from the denitrifier "Achromobacter cycloclastes". J Bacteriol 166:604–608. https://doi.org/10.1128/jb.166.2.604-608.1986
Madern D, Ebel C, Zaccai G (2000) Halophilic adaptation of enzymes. Extremophiles 4:91–98. https://doi.org/10.1007/s007920050142
Martínez-Espinosa RM, Cole JA, Richardson DJ, Watmough NJ (2011) Enzymology and ecology of the nitrogen cycle. Biochem Soc Trans 39:175–178. https://doi.org/10.1042/Bst0390175
Martínez-Espinosa RM, Marhuenda-Egea FC, Bonete MJ (2001) Purification and characterisation of a possible assimilatory nitrite reductase from the halophile archaeon Haloferax mediterranei. FEMS Microbiol Lett 196:113–118. https://doi.org/10.1016/S0378-1097(01)00044-1
Masuko M, Iwasaki H, Sakurai T, Suzuki S, Nakahara A (1984) Characterization of nitrite reductase from a denitrifier, Alcaligenes sp. NCIB 11015. A novel copper protein. J Biochem 96:447–454. https://doi.org/10.1093/oxfordjournals.jbchem.a134856
Prudêncio M, Eady RR, Sawers G (1999) The blue copper-containing nitrite reductase from Alcaligenes xylosoxidans: cloning of the nirA gene and characterization of the recombinant enzyme. J Bacteriol 181:2323–2329
Ruiz DM, De Castro RE (2007) Effect of organic solvents on the activity and stability of an extracellular protease secreted by the haloalkaliphilic archaeon Natrialba magadii. J Ind Microbiol Biotechnol 34:111–115. https://doi.org/10.1007/s10295-006-0174-4
Scharf B, Engelhard M (1993) Halocyanin, an archaebacterial blue copper protein (type I) from Natronobacterium pharaonis. Biochemistry 32:12894–12900. https://doi.org/10.1021/bi00210a043
Shevchenko A, Wilm M, Vorm O, Mann M (1996) Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal Chem 68:850–858. https://doi.org/10.1021/ac950914h
Snell FD, Snell CT (1949) Colorimetric methods of analysis. Van Nostrand, New York
Stroud A, Liddell S, Allers T (2012) Genetic and biochemical identification of a novel single-stranded DNA-binding complex in Haloferax volcanii. Front Microbiol 3:224. https://doi.org/10.3389/fmicb.2012.00224
Tosques IE, Kwiatkowski AV, Shi J, Shapleigh JP (1997) Characterization and regulation of the gene encoding nitrite reductase in Rhodobacter sphaeroides 2.4.3. J Bacteriol 179:1090–1095. https://doi.org/10.1128/jb.179.4.1090-1095.1997
Zeng J, Gao X, Dai Z, Tang B, Tang XF (2014) Effects of metal ions on stability and activity of hyperthermophilic pyrolysin and further stabilization of this enzyme by modification of a Ca2+-binding site. Appl Environ Microbiol 80:2763–2772. https://doi.org/10.1128/AEM.00006-14
Acknowledgements
This work was financially supported by grants from National Natural Science Foundation of China (No. 31600002 and No. 31770005) and the Advanced Talent Foundation of Jiangsu University (No. 15JDG062).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare no conflict of interest.
Compliance with ethics requirements
This article does not contain any studies with human or animal subjects.
Additional information
Communicated by S. Albers.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Hou, J., Yang, XY., Xu, Q. et al. Characterization of a novel Cu-containing dissimilatory nitrite reductase from the haloarchaeon Halorussus sp. YCN54. Extremophiles 24, 403–411 (2020). https://doi.org/10.1007/s00792-020-01164-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00792-020-01164-2