1
|
Liu X, Dang Y, Sun D, Holmes DE. Identification of optimal parameters for treatment of high-strength ammonium leachate by mixed communities of heterotrophic nitrifying/aerobic denitrifying bacteria. BIORESOURCE TECHNOLOGY 2021; 336:125415. [PMID: 34198239 DOI: 10.1016/j.biortech.2021.125415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
Heterotrophic nitrifying and aerobic denitrifying bacteria (HNADB) are important for partial nitrification treatment of high strength ammonium leachate. However, conditions for their optimal performance in mixed reactor systems have yet to be determined. In this study, optimal parameters were identified and included free ammonia (FA) concentrations below 40 mg/L, a dissolved oxygen concentration of 1.2 mg/L, a carbon to nitrogen ratio of 5 and a reflux ratio of 4. These conditions were applied to a continuous anoxic/oxic membrane moving biofilm reactor treating raw incineration leachate with high total ammonium nitrogen (TAN = 1400 mg/L). Ammonium conversion and nitrogen removal efficiencies of 99% and 86% were achieved. Autotrophic ammonia oxidizing bacteria were inhibited at FA concentrations above 25 mg/L. HNADB, particularly Paracoccus species, contributed to ammonium conversion at high FA (25-40 mg/L). These results show that leachate with high TAN and FA can be treated using parameters that support the growth of HNADB.
Collapse
Affiliation(s)
- Xinying Liu
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China; Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, Beijing Forestry University, Beijing 100083, China
| | - Yan Dang
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China; Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, Beijing Forestry University, Beijing 100083, China
| | - Dezhi Sun
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China; Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, Beijing Forestry University, Beijing 100083, China.
| | - Dawn E Holmes
- Department of Physical and Biological Sciences, Western New England University, 1215 Wilbraham Rd, Springfield, MA 01119, United States
| |
Collapse
|
2
|
Zhao B, Ran XC, An Q, Huang YS, Lv QH, Dan Q. N 2O production from hydroxylamine oxidation and corresponding hydroxylamine oxidoreductase involved in a heterotrophic nitrifier A. faecalis strain NR. Bioprocess Biosyst Eng 2019; 42:1983-1992. [PMID: 31420725 DOI: 10.1007/s00449-019-02191-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 08/03/2019] [Accepted: 08/04/2019] [Indexed: 10/26/2022]
Abstract
N2O production from NH2OH oxidation involved in a heterotrophic nitrifier Alcaligenes faecalis strain NR was studied. 15N-labeling experiments showed that biological NH2OH consumption by strain NR played a dominant role in N2O production, although chemical reaction between NH2OH and O2 indeed existed. Hydroxylamine oxidoreductase (HAO) from strain NR was partially purified by (NH4)2SO4 fractionation and DEAE Cartridge chromatography. The maximum activity of HAO was 9.60 mU with a specific activity of 92.04 mU/(mg protein) when K3Fe(CN)6 was used as an electron acceptor. The addition of Ca2+ promoted the HAO activity, while the presence of Mn2+ inhibited the enzyme activity. The optimal temperature and pH for HAO activity were 30 °C and 8. Analysis of enzyme-catalyzed products demonstrated that NH2OH oxidation catalyzed by HAO from strain NR played significant role in the production of N2O.
Collapse
Affiliation(s)
- Bin Zhao
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, People's Republic of China
| | - Xiao Chuan Ran
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, People's Republic of China
| | - Qiang An
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, People's Republic of China.
| | - Yuan Sheng Huang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, People's Republic of China
| | - Qing Hao Lv
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, People's Republic of China
| | - Qiao Dan
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, People's Republic of China
| |
Collapse
|
3
|
Liu Y, Yuan X, Liu Z. Optimization, purification, and characterization of hydroxylamine oxidoreductase from Acinetobacter sp. Y1. Biotechnol Appl Biochem 2019; 66:494-501. [PMID: 30905079 DOI: 10.1002/bab.1745] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 03/11/2019] [Indexed: 01/14/2023]
Abstract
Hydroxylamine oxidoreductase (HAO) is a key enzyme involved in ammonium removal pathway. To further study the enzyme, HAO was purified from heterotrophic nitrifier Acinetobacter sp. Y1 and its property was investigated. Results of single-factor experiments showed that the optimal carbon source, nitrogen source, and C/N ratio were trisodium citrate, ammonium sulfate, and 14, respectively, with incubation time of 16 H. DEAE SefinoseTM FF anion-exchange chromatography was used to purify HAO, followed by SefinoseTM CL-6B gel filtration chromatography. SDS-PAGE revealed that a 47 kDa enzyme was purified successfully, with a purification fold of 7.32 and a recovery rate of 19.40%. The optimized enzyme activity of purified HAO was tested at pH 8.0 and 30 °C. The results showed that the activity was increased by 43.78% and 25.64% in the presence of 1 mM Fe2+ and Fe3+ , respectively. HAO activity was increased with the increase of Na+ and K+ , Mn2+ , Zn2+ , Cu2+ , Ca2+ , Ba2+ inhibited the HAO activity at three concentrations. In addition, HAO activity was activated by ethylenediaminetetraacetic acid at 0.4 mM, and a negative effect arose as the dose increased. The purified enzyme from Y1 is different from other reported HAOs. Further study should be conducted to investigate the enzyme.
Collapse
Affiliation(s)
- Yuxiang Liu
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, Shanxi, People's Republic of China
| | - Xin Yuan
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, Shanxi, People's Republic of China
| | - Zeying Liu
- Key Laboratory of Coal Science and Technology of Shanxi Province and Ministry of Education, Taiyuan University of Technology, Taiyuan, Shanxi, People's Republic of China
| |
Collapse
|
4
|
Yang Y, Lin E, Huang S. Heterotrophic nitrogen removal in Bacillus sp. K5: involvement of a novel hydroxylamine oxidase. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2017; 76:3461-3467. [PMID: 29236024 DOI: 10.2166/wst.2017.510] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
An aerobic denitrifying bacterium isolated from a bio-trickling filter treating NOx, Bacillus sp. K5, is able to convert ammonium to nitrite, in which hydroxylamine oxidase (HAO) plays a critical role. In the present study, the performance for simultaneous nitrification and denitrification was investigated with batch experiments and an HAO was purified by an anion-exchange and gel-filtration chromatography from strain K5. The purified HAO's molecular mass was determined by SDS-PAGE and its activity by measuring the change in the concentration of ferricyanide, the electron acceptor. Results showed that as much as 87.8 mg L-1 ammonium-N was removed without nitrite accumulation within 24 hours in the sodium citrate medium at C/N of 15. The HAO isolated from the strain K5 was approximately 71 KDa. With hydroxylamine (NH2OH) as a substrate and potassium ferricyanide as an electron acceptor, the enzyme was capable of oxidizing NH2OH to nitrite in vitro when the pH varied from 7 to 9 and temperature ranged from 25 °C to 40 °C. This is the first time that an HAO has been purified from the Bacillus genus, and the findings revealed that it is distinctive in its molecular mass and enzyme properties.
Collapse
Affiliation(s)
- Yunlong Yang
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ershu Lin
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shaobin Huang
- The Key Laboratory of Environmental Protection and Eco-Remediation of Guangdong Regular Higher Education Institutions, Guangzhou 510006, China and School of Environment and Energy, South China University of Technology, Guangzhou 510006, China E-mail:
| |
Collapse
|
5
|
Irisa T, Hira D, Furukawa K, Fujii T. Reduction of nitric oxide catalyzed by hydroxylamine oxidoreductase from an anammox bacterium. J Biosci Bioeng 2014; 118:616-21. [DOI: 10.1016/j.jbiosc.2014.05.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 05/25/2014] [Accepted: 05/27/2014] [Indexed: 11/29/2022]
|
6
|
Attia AAA, Silaghi-Dumitrescu R. Computational investigation of the initial two-electron, two-proton steps in the reaction mechanism of hydroxylamine oxidoreductase. J Phys Chem B 2014; 118:12140-5. [PMID: 25277374 DOI: 10.1021/jp507023a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reported here is a computational study based on density functional theory that presents the first attempt to investigate the 2-electron 2-proton reaction of Fe(III)-H2NOH to Fe(III)-HNO in the catalytic cycle of hydroxylamine oxidoreductase-a multiheme-containing enzyme that catalyzes the conversion of hydroxylamine (HA) to nitrite in nitrifying bacteria. Two subsequent protonation events are proposed to initiate the process, of which the second is suggested to be concerted with a one-electron oxidation. The final one-electron oxidation is further proposed to be accompanied by a third deprotonation process, suggesting that Fe(III)-HNO may not be an isolable intermediate in the HAO catalytic cycle. Further explorations are suggested to be focused on the following steps in the catalytic cycle, the influence of the lateral substituents of the heme (and especially of the Cys and Tyr cross-links), the comparative study of hydrazine oxidation, the proton delivery network in the distal site and, possibly, on linkage isomerism.
Collapse
Affiliation(s)
- Amr A A Attia
- Department of Chemistry, Babes-Bolyai University , Cluj-Napoca, RO-400028 Romania
| | | |
Collapse
|
7
|
Affiliation(s)
- Luisa B. Maia
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - José J. G. Moura
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| |
Collapse
|
8
|
Keluskar R, Desai A. Evaluation of hydroxylamine oxidoreductase as a functional and phylogenetic marker to differentiate Nitrosomonas spp. J Basic Microbiol 2013; 54:261-8. [PMID: 23553651 DOI: 10.1002/jobm.201200378] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/26/2012] [Indexed: 11/12/2022]
Abstract
Nitrosomonas genus belongs to beta-subclass of Proteobacteria and encompasses closely related species. Sequence independent techniques like single strand confirmation polymorphism (SSCP) was attempted in the present study to resolve AOB using ammonia monooxygenase (amoA) and hydroxylamine oxidoreductase (hao) gene fragments, unique to AOB. Variation in hydroxylamine oxidoreductase (HAO) enzyme zymogram of isolates observed in the study was also explored as an additional sequence independent method to substantiate the observations. Nitrosomonas europaea (standard strain) and 12 isolates, obtained by enriching environmental samples, were differentiated into six and four groups by SSCP analyses of amoA and hao gene fragments, respectively, whereas they could be resolved into six distinct groups through activity staining of HAO enzyme. amoA gene fragment was therefore found to be better than hao gene fragment in resolving the studied AOB based on richness and evenness with Simpson's index of diversity - 0.85. However, the ensembled use of these molecular methods (SSCP of amoA and hao gene fragments) and HAO enzyme zymogram in fingerprinting AOB provide better resolution and evenness, contributing significantly in AOB diversity studies. Grouping of AOB isolates by hao gene SSCP analysis followed almost the same pattern as that by 16S rRNA gene based sequence analysis, hence it is suitable as a phylogenetic marker.
Collapse
Affiliation(s)
- Radhika Keluskar
- Faculty of Science, Department of Microbiology and Biotechnology Centre, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | | |
Collapse
|
9
|
Bewley KD, Ellis KE, Firer-Sherwood MA, Elliott SJ. Multi-heme proteins: nature's electronic multi-purpose tool. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:938-48. [PMID: 23558243 DOI: 10.1016/j.bbabio.2013.03.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 03/20/2013] [Accepted: 03/25/2013] [Indexed: 02/06/2023]
Abstract
While iron is often a limiting nutrient to Biology, when the element is found in the form of heme cofactors (iron protoporphyrin IX), living systems have excelled at modifying and tailoring the chemistry of the metal. In the context of proteins and enzymes, heme cofactors are increasingly found in stoichiometries greater than one, where a single protein macromolecule contains more than one heme unit. When paired or coupled together, these protein associated heme groups perform a wide variety of tasks, such as redox communication, long range electron transfer and storage of reducing/oxidizing equivalents. Here, we review recent advances in the field of multi-heme proteins, focusing on emergent properties of these complex redox proteins, and strategies found in Nature where such proteins appear to be modular and essential components of larger biochemical pathways. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
Collapse
Affiliation(s)
- Kathryn D Bewley
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | | | | | | |
Collapse
|
10
|
Global analysis of the Nitrosomonas europaea iron starvation stimulon. Arch Microbiol 2011; 194:305-13. [DOI: 10.1007/s00203-011-0778-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 09/28/2011] [Accepted: 12/02/2011] [Indexed: 10/14/2022]
|
11
|
Vajrala N, Sayavedra-Soto LA, Bottomley PJ, Arp DJ. Role of a Fur homolog in iron metabolism in Nitrosomonas europaea. BMC Microbiol 2011; 11:37. [PMID: 21338516 PMCID: PMC3050691 DOI: 10.1186/1471-2180-11-37] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Accepted: 02/21/2011] [Indexed: 11/24/2022] Open
Abstract
Background In response to environmental iron concentrations, many bacteria coordinately regulate transcription of genes involved in iron acquisition via the ferric uptake regulation (Fur) system. The genome of Nitrosomonas europaea, an ammonia-oxidizing bacterium, carries three genes (NE0616, NE0730 and NE1722) encoding proteins belonging to Fur family. Results Of the three N. europaea fur homologs, only the Fur homolog encoded by gene NE0616 complemented the Escherichia coli H1780 fur mutant. A N. europaea fur:kanP mutant strain was created by insertion of kanamycin-resistance cassette in the promoter region of NE0616 fur homolog. The total cellular iron contents of the fur:kanP mutant strain increased by 1.5-fold compared to wild type when grown in Fe-replete media. Relative to the wild type, the fur:kanP mutant exhibited increased sensitivity to iron at or above 500 μM concentrations. Unlike the wild type, the fur:kanP mutant was capable of utilizing iron-bound ferrioxamine without any lag phase and showed over expression of several outer membrane TonB-dependent receptor proteins irrespective of Fe availability. Conclusions Our studies have clearly indicated a role in Fe regulation by the Fur protein encoded by N. europaea NE0616 gene. Additional studies are required to fully delineate role of this fur homolog.
Collapse
Affiliation(s)
- Neeraja Vajrala
- Department of Botany and Plant Pathology, 2082 Cordley, Oregon State University, Corvallis, OR 97331, USA
| | | | | | | |
Collapse
|
12
|
Kostera J, McGarry J, Pacheco AA. Enzymatic Interconversion of Ammonia and Nitrite: The Right Tool for the Job. Biochemistry 2010; 49:8546-53. [DOI: 10.1021/bi1006783] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joshua Kostera
- Department of Chemistry and Biochemistry, University of Wisconsin, Milwaukee, Wisconsin 53211
| | - Jennifer McGarry
- Department of Chemistry and Biochemistry, University of Wisconsin, Milwaukee, Wisconsin 53211
| | - A. Andrew Pacheco
- Department of Chemistry and Biochemistry, University of Wisconsin, Milwaukee, Wisconsin 53211
| |
Collapse
|
13
|
Klotz MG, Schmid MC, Strous M, op den Camp HJM, Jetten MSM, Hooper AB. Evolution of an octahaem cytochromecprotein family that is key to aerobic and anaerobic ammonia oxidation by bacteria. Environ Microbiol 2008; 10:3150-63. [DOI: 10.1111/j.1462-2920.2008.01733.x] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
14
|
Kostera J, Youngblut MD, Slosarczyk JM, Pacheco AA. Kinetic and product distribution analysis of NO* reductase activity in Nitrosomonas europaea hydroxylamine oxidoreductase. J Biol Inorg Chem 2008; 13:1073-83. [PMID: 18553112 DOI: 10.1007/s00775-008-0393-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2007] [Accepted: 05/25/2008] [Indexed: 10/22/2022]
Abstract
Hydroxylamine oxidoreductase (HAO) from the ammonia-oxidizing bacterium Nitrosomonas europaea normally catalyzes the four-electron oxidation of hydroxylamine to nitrite, which is the second step in ammonia-dependent respiration. Here we show that, in the presence of methyl viologen monocation radical (MV(red)), HAO can catalyze the reduction of nitric oxide to ammonia. The process is analogous to that catalyzed by cytochrome c nitrite reductase, an enzyme found in some bacteria that use nitrite as a terminal electron acceptor during anaerobic respiration. The availability of a reduction pathway to ammonia is an important factor to consider when designing in vitro studies of HAO, and may also have some physiological relevance. The reduction of nitric oxide to ammonia proceeds in two kinetically distinct steps: nitric oxide is first reduced to hydroxylamine, and then hydroxylamine is reduced to ammonia at a tenfold slower rate. The second step was investigated independently in solutions initially containing hydroxylamine, MV(red), and HAO. Both steps show first-order dependence on nitric oxide and HAO concentrations, and zero-order dependence on MV(red) concentration. The rate constants governing each reduction step were found to have values of (4.7 +/- 0.3) x 10(5) and (2.06 +/- 0.04) x 10(4) M(-1) s(-1), respectively. A second reduction pathway, with second-order dependence on nitric oxide, may become available as the concentration of nitric oxide is increased. Such a pathway might lead to production of nitrous oxide. We estimate a maximum value of (1.5 +/- 0.05) x 10(10) M(-2) s(-1) for the rate constant of the alternative pathway, which is small and suggests that the pathway is not physiologically important.
Collapse
Affiliation(s)
- Joshua Kostera
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | | | | | | |
Collapse
|
15
|
Shimamura M, Nishiyama T, Shinya K, Kawahara Y, Furukawa K, Fujii T. Another multiheme protein, hydroxylamine oxidoreductase, abundantly produced in an anammox bacterium besides the hydrazine-oxidizing enzyme. J Biosci Bioeng 2008; 105:243-8. [DOI: 10.1263/jbb.105.243] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Accepted: 12/17/2007] [Indexed: 11/17/2022]
|
16
|
Fernández ML, Estrin DA, Bari SE. Theoretical insight into the hydroxylamine oxidoreductase mechanism. J Inorg Biochem 2008; 102:1523-30. [PMID: 18336913 DOI: 10.1016/j.jinorgbio.2008.01.032] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2007] [Revised: 01/18/2008] [Accepted: 01/21/2008] [Indexed: 10/22/2022]
Abstract
The multiheme enzyme hydroxylamine oxidoreductase from the autotrophic bacteria Nitrosomonas europaea catalyzes the conversion of hydroxylamine to nitrite, with a complicate arrangement of heme groups in three subunits. As a distinctive feature, the protein has a covalent linkage between a tyrosyl residue of one subunit and a meso carbon atom of the heme active site of another. We studied the influence of this bond in the catalysis from a theoretical perspective through electronic structure calculations at the density functional theory level, starting from the crystal structure of the protein. Geometry optimizations of proposed reaction intermediates were used to calculate the dissociation energy of different nitrogen containing ligands, considering the presence and absence of the meso tyrosyl residue. The results indicate that the tyrosine residue enhances the binding of hydroxylamine, and increases the stability of a Fe(III)NO intermediate, while behaving indifferently in the Fe(II)NO form. The calculations performed on model systems including neighboring aminoacids revealed the probable formation of a bidentate hydrogen bond between the Fe(III)H(2)O complex and Asp 257, in a high-spin aquo complex as the resting state. Characterization of non-planar heme distortions showed that the meso-substituent induces significant ruffling in the evaluated intermediates.
Collapse
Affiliation(s)
- M Laura Fernández
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, C1428EHA, Argentina
| | | | | |
Collapse
|
17
|
Pearson AR, Elmore BO, Yang C, Ferrara JD, Hooper AB, Wilmot CM. The crystal structure of cytochrome P460 of Nitrosomonas europaea reveals a novel cytochrome fold and heme-protein cross-link. Biochemistry 2007; 46:8340-9. [PMID: 17583915 PMCID: PMC2527454 DOI: 10.1021/bi700086r] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have determined the 1.8 A X-ray crystal structure of a monoheme c-type cytochrome, cytochrome P460, from Nitrosomonas europea. The chromophore possesses unusual spectral properties analogous to those of the catalytic heme P460 of hydroxylamine oxidoreductase (HAO), the only known heme in biology to withdraw electrons from an iron-coordinated substrate. The analysis reveals a homodimeric structure and elucidates a new c-type cytochrome fold that is predominantly beta-sheet. In addition to the two cysteine thioether links to the porphyrin typical of c-type hemes, there is a third proteinaceous link involving a conserved lysine. The covalent bond is between the lysine side-chain nitrogen and the 13'-meso carbon of the heme, which, following cross-link formation, is sp3-hybridized, demonstrating the loss of conjugation at this position within the porphyrin. The structure has implications for the analogous tyrosine-heme meso carbon cross-link observed in HAO.
Collapse
Affiliation(s)
- Arwen R. Pearson
- Department of Biochemistry, Molecular Biology and Biophysics, The University of Minnesota, Minneapolis, MN, 55455, U. S. A
| | - Bradley O. Elmore
- Department of Biochemistry, Molecular Biology and Biophysics, The University of Minnesota, Minneapolis, MN, 55455, U. S. A
| | - Cheng Yang
- Rigaku Americas Corp. 9009 New Trails Drive, The Woodlands, TX, 77381, U. S. A
| | - Joseph D. Ferrara
- Rigaku Americas Corp. 9009 New Trails Drive, The Woodlands, TX, 77381, U. S. A
| | - Alan B. Hooper
- Department of Biochemistry, Molecular Biology and Biophysics, The University of Minnesota, Minneapolis, MN, 55455, U. S. A
| | - Carrie M. Wilmot
- Department of Biochemistry, Molecular Biology and Biophysics, The University of Minnesota, Minneapolis, MN, 55455, U. S. A
- Corresponding Author: Carrie M. Wilmot, e-mail: , tel: +1-612-624-2406, fax: +1-612-624-5121
| |
Collapse
|
18
|
Shimamura M, Nishiyama T, Shigetomo H, Toyomoto T, Kawahara Y, Furukawa K, Fujii T. Isolation of a multiheme protein with features of a hydrazine-oxidizing enzyme from an anaerobic ammonium-oxidizing enrichment culture. Appl Environ Microbiol 2006; 73:1065-72. [PMID: 17172456 PMCID: PMC1828659 DOI: 10.1128/aem.01978-06] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A multiheme protein having hydrazine-oxidizing activity was purified from enriched culture from a reactor in which an anammox bacterium, strain KSU-1, was dominant. The enzyme has oxidizing activity toward hydrazine but not hydroxylamine and is a 130-kDa homodimer composed of a 62-kDa polypeptide containing eight hemes. It was therefore named hydrazine-oxidizing enzyme (HZO). With cytochrome c as an electron acceptor, the V(max) and K(m) for hydrazine are 6.2 +/- 0.3 micromol/min.mg and 5.5 +/- 0.6 microM, respectively. Hydrazine (25 microM) induced an increase in the proportion of reduced form in the spectrum, whereas hydroxylamine (500 microM) did not. Two genes coding for HZO, hzoA and hzoB, were identified within the metagenomic DNA from the culture. The genes encode the same amino acid sequence except for two residues. The sequences deduced from these genes showed low-level identities (<30%) to those of all of the hydroxylamine oxidoreductases reported but are highly homologous to two hao genes found by sequencing the genome of "Candidatus Kuenenia stuttgartiensis" (88% and 89% identities). The purified enzyme might therefore be a novel hydrazine-oxidizing enzyme having a critical role in anaerobic ammonium oxidation.
Collapse
Affiliation(s)
- Munetaka Shimamura
- Department of Applied Life Science, Faculty of Biotechnology and Life Science, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan
| | | | | | | | | | | | | |
Collapse
|
19
|
Wei X, Vajrala N, Hauser L, Sayavedra-Soto LA, Arp DJ. Iron nutrition and physiological responses to iron stress in Nitrosomonas europaea. Arch Microbiol 2006; 186:107-18. [PMID: 16802173 DOI: 10.1007/s00203-006-0126-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2005] [Revised: 04/11/2006] [Accepted: 05/18/2006] [Indexed: 10/24/2022]
Abstract
Nitrosomonas europaea, as an ammonia-oxidizing bacterium, has a high Fe requirement and has 90 genes dedicated to Fe acquisition. Under Fe-limiting conditions (0.2 microM Fe), N. europaea was able to assimilate up to 70% of the available Fe in the medium even though it is unable to produce siderophores. Addition of exogenous siderophores to Fe-limited medium increased growth (final cell mass). Fe-limited cells had lower heme and cellular Fe contents, reduced membrane layers, and lower NH3- and NH2OH-dependent O2 consumption activities than Fe-replete cells. Fe acquisition-related proteins, such as a number of TonB-dependent Fe-siderophore receptors for ferrichrome and enterobactin and diffusion protein OmpC, were expressed to higher levels under Fe limitation, providing biochemical evidence for adaptation of N. europaea to Fe-limited conditions.
Collapse
Affiliation(s)
- Xueming Wei
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331-2902, USA
| | | | | | | | | |
Collapse
|
20
|
Fiencke C, Bock E. Immunocytochemical localization of membrane-bound ammonia monooxygenase in cells of ammonia oxidizing bacteria. Arch Microbiol 2006; 185:99-106. [PMID: 16395553 DOI: 10.1007/s00203-005-0074-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2005] [Revised: 10/19/2005] [Accepted: 12/06/2005] [Indexed: 11/24/2022]
Abstract
The intracellular location of the membrane-bound ammonia monooxygenase (AMO) in all genera of ammonia oxidizing bacteria (Nitrosomonas, Nitrosococcus and Nitrosospira) was determined by electron microscopic immunocytochemistry. Polyclonal antibodies recognizing the two subunits, AmoA- and AmoB-proteins, were used for post-embedding labeling. Ultrathin sections revealed that the AmoB-protein was located in all genera on the cytoplasmic membrane. In cells of Nitrosomonas and Nitrosococus additional but less AmoB-labeling was found on the intracytoplasmic membrane (ICM). In contrast to the detection of AmoB-protein, the AmoA-antibodies failed to detect the AmoA-protein. Based on quantitative immunoblots the extent of ICM in Nitrosomonas eutropha was correlated with the amount of AmoA in the cells. The highest extent of ICM and amount of AmoA was found at low ammonium substrate concentrations.
Collapse
Affiliation(s)
- Claudia Fiencke
- Biocenter Klein Flottbek, Section for Microbiology, University of Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany,
| | | |
Collapse
|
21
|
Bergmann DJ, Hooper AB, Klotz MG. Structure and sequence conservation of hao cluster genes of autotrophic ammonia-oxidizing bacteria: evidence for their evolutionary history. Appl Environ Microbiol 2005; 71:5371-82. [PMID: 16151127 PMCID: PMC1214698 DOI: 10.1128/aem.71.9.5371-5382.2005] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Comparison of the organization and sequence of the hao (hydroxylamine oxidoreductase) gene clusters from the gammaproteobacterial autotrophic ammonia-oxidizing bacterium (aAOB) Nitrosococcus oceani and the betaproteobacterial aAOB Nitrosospira multiformis and Nitrosomonas europaea revealed a highly conserved gene cluster encoding the following proteins: hao, hydroxylamine oxidoreductase; orf2, a putative protein; cycA, cytochrome c(554); and cycB, cytochrome c(m)(552). The deduced protein sequences of HAO, c(554), and c(m)(552) were highly similar in all aAOB despite their differences in species evolution and codon usage. Phylogenetic inference revealed a broad family of multi-c-heme proteins, including HAO, the pentaheme nitrite reductase, and tetrathionate reductase. The c-hemes of this group also have a nearly identical geometry of heme orientation, which has remained conserved during divergent evolution of function. High sequence similarity is also seen within a protein family, including cytochromes c(m)(552), NrfH/B, and NapC/NirT. It is proposed that the hydroxylamine oxidation pathway evolved from a nitrite reduction pathway involved in anaerobic respiration (denitrification) during the radiation of the Proteobacteria. Conservation of the hydroxylamine oxidation module was maintained by functional pressure, and the module expanded into two separate narrow taxa after a lateral gene transfer event between gamma- and betaproteobacterial ancestors of extant aAOB. HAO-encoding genes were also found in six non-aAOB, either singly or tandemly arranged with an orf2 gene, whereas a c(554) gene was lacking. The conservation of the hao gene cluster in general and the uniqueness of the c(554) gene in particular make it a suitable target for the design of primers and probes useful for molecular ecology approaches to detect aAOB.
Collapse
Affiliation(s)
- David J Bergmann
- University of Louisville, Department of Biology, 139 Life Science Building, Louisville, KY 40292, USA
| | | | | |
Collapse
|
22
|
Kurnikov IV, Ratner MA, Pacheco AA. Redox equilibria in hydroxylamine oxidoreductase. Electrostatic control of electron redistribution in multielectron oxidative processes. Biochemistry 2005; 44:1856-63. [PMID: 15697211 DOI: 10.1021/bi048060v] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report results of continuum electrostatics calculations of the cofactor redox potentials, and of the titratable group pK(a) values, in hydroxylamine oxidoreductase (HAO). A picture of a sophisticated multicomponent control of electron flow in the protein emerged from the studies. First, we found that neighboring heme cofactors strongly interact electrostatically, with energies of 50-100 mV. Thus, cofactor redox potentials depend on the oxidation state of other cofactors, and cofactor redox potentials in the active (partially oxidized) enzyme differ substantially from the values obtained in electrochemical redox titration experiments. We found that, together, solvent-exposed heme 1 (having a large negative redox potential) and heme 2 (having a large positive redox potential) form a lock for electrons generated during the oxidation reaction The attachment of HAO's physiological electron transfer partner cytochrome c(554) results in a positive shift in the redox potential of heme 1, and "opens the electron gate". Electrons generated as a result of hydroxylamine oxidation travel to heme 3 and heme 8, which have redox potentials close to 0 mV versus NHE (this result is in partial disagreement with an existing experimental redox potential assignment). The closeness of hemes 3 and 8 from different enzyme subunits allows redistribution of the four electrons generated as a result of hydroxylamine oxidation, among the three enzyme subunits. For the multielectron oxidation process to be maximally efficient, the redox potentials of the electron-accepting cofactors should be roughly equal, and electrostatic interactions between extra electrons on these cofactors should be minimal. The redox potential assignments presented in the paper satisfy this general rule.
Collapse
Affiliation(s)
- Igor V Kurnikov
- Chemistry Department, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA.
| | | | | |
Collapse
|
23
|
Cabail MZ, Kostera J, Pacheco AA. Laser photoinitiated nitrosylation of 3-electron reduced Nm europaea hydroxylamine oxidoreductase: kinetic and thermodynamic properties of the nitrosylated enzyme. Inorg Chem 2005; 44:225-31. [PMID: 15651867 DOI: 10.1021/ic048822a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydroxylamine-cytochrome c554 oxidoreductase (HAO) catalyzes the 4-e(-) oxidation of NH(2)OH to NO(2)(-) by cytochrome c554. The electrons are transferred from NH(2)OH to a 5-coordinate heme known as P(460), the active site of HAO. From P(460), c-type hemes transport the electrons through the enzyme to a remote solvent-exposed c-heme, where cyt c554 reduction occurs. When 3-60 microM NO* are photogenerated by laser flash photolysis of N,N'-bis-(carboxymethyl)-N,N'-dinitroso-1,4-phenylenediamine, in a solution containing approximately 1 microM HAO prereduced by 3 e(-)/subunit, the HAO c-heme pool is subsequently oxidized by up to 1 e(-)/HAO subunit. The reaction rate for HAO oxidation shows first-order dependence on [HAO], and zero-order dependence on [NO*] (k(obs) = 1250 +/- 150 s(-)(1)). However, the total HAO oxidized shows hyperbolic dependence on [NO*]. We suggest that NO* first binds reversibly to P(460) giving a {Fe(NO)}(6) moiety. Intramolecular electron transfer (IET) from the c-heme pool then reduces P(460) to {Fe(NO)}.(7) The overall binding constant (K) for formation of {Fe(NO)}(7) from free NO* and 3-e(-) reduced HAO was measured at (7.7 +/- 0.6) x10(4) M(-1). This value is larger than that for typical ferriheme proteins ( approximately 10(4) M(-1)), but much smaller than that for the corresponding ferroheme proteins ( approximately 10(11) M(-1)). The final product generated by nitrosylating 3-e(-) reduced HAO is believed to be the same species obtained by adding NH(2)OH to the fully oxidized enzyme. The experiments described herein suggest that when NH(2)OH and HAO first react, only two of the NH(2)OH electrons end up in the c-heme pool. The other two remain at P(460) as part of an {Fe(NO)}(7) moiety. These results are discussed in relation to earlier studies that investigated the effect of putting fully oxidized and fully reduced HAO under 1 atm of NO*.
Collapse
Affiliation(s)
- Maria Zulema Cabail
- Department of Chemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, USA
| | | | | |
Collapse
|
24
|
Schmidt I, Look C, Bock E, Jetten MSM. Ammonium and hydroxylamine uptake and accumulation in Nitrosomonas. MICROBIOLOGY-SGM 2004; 150:1405-1412. [PMID: 15133102 DOI: 10.1099/mic.0.26719-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Starved cells of Nitrosomonas europaea and further ammonia oxidizers were able to rapidly accumulate ammonium and hydroxylamine to an internal concentration of about 1 and 0.8 M, respectively. In kinetic studies, the uptake/accumulation rates for ammonium [3.1 mmol (g protein)(-1) min(-1)] and hydroxylamine [4.39 mmol (g protein)(-1) min(-1)] were determined. The uptake and accumulation process of ammonium and hydroxylamine was not coupled to ammonia or hydroxylamine oxidation and nitrite was not produced. In the presence of uncouplers the ammonium accumulation was completely inhibited, indicating an active, membrane-potential-driven transport mechanism. When the external ammonium or hydroxylamine pool was depleted, the internal ammonium and hydroxylamine was consumed within 12 h or 20 min, respectively. The binding of ammonium/ammonia was correlated with an energized membrane system, and hydroxylamine may bind to the hydroxylamine oxidoredutase.
Collapse
Affiliation(s)
- Ingo Schmidt
- Department of Microbiology, University of Bayreuth, Universitaetsstrasse 30, 95447 Bayreuth, Germany
| | - Christiane Look
- Department of Microbiology, University of Hamburg, Ohnhorststrasse 18, 22609 Hamburg, Germany
| | - Eberhard Bock
- Department of Microbiology, University of Hamburg, Ohnhorststrasse 18, 22609 Hamburg, Germany
| | - Mike S M Jetten
- Department of Microbiology, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
| |
Collapse
|
25
|
Schmidt I, Steenbakkers PJM, op den Camp HJM, Schmidt K, Jetten MSM. Physiologic and proteomic evidence for a role of nitric oxide in biofilm formation by Nitrosomonas europaea and other ammonia oxidizers. J Bacteriol 2004; 186:2781-8. [PMID: 15090520 PMCID: PMC387797 DOI: 10.1128/jb.186.9.2781-2788.2004] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
NO, a free radical gas, is the signal for Nitrosomonas europaea cells to switch between different growth modes. At an NO concentration of more than 30 ppm, biofilm formation by N. europaea was induced. NO concentrations below 5 ppm led to a reversal of the biofilm formation, and the numbers of motile and planktonic (motile-planktonic) cells increased. In a proteomics approach, the proteins expressed by N. europaea were identified. Comparison studies of the protein patterns of motile-planktonic and attached (biofilm) cells revealed several clear differences. Eleven proteins were found to be up or down regulated. Concentrations of other compounds such as ammonium, nitrite, and oxygen as well as different temperatures and pH values had no significant effect on the growth mode of and the proteins expressed by N. europaea.
Collapse
Affiliation(s)
- Ingo Schmidt
- Department of Microbiology, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany.
| | | | | | | | | |
Collapse
|
26
|
Bergmann DJ, Hooper AB. Cytochrome P460 of Nitrosomonas europaea. Formation of the heme-lysine cross-link in a heterologous host and mutagenic conversion to a non-cross-linked cytochrome c'. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:1935-41. [PMID: 12709052 DOI: 10.1046/j.1432-1033.2003.03550.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The heme of cytochrome P460 of Nitrosomonas europaea, which is covalently crosslinked to two cysteines of the polypeptide as with all c-type cytochromes, has an additional novel covalent crosslink to lysine 70 of the polypeptide [Arciero, D.M. & Hooper, A.B. (1997) FEBS Lett.410, 457-460]. The protein can catalyze the oxidation of hydroxylamine. The gene for this protein, cyp, was expressed in Pseudomonas aeruginosa strain PAO lacI, resulting in formation of a holo-cytochrome P460 which closely resembled native cytochrome P460 purified from N. europaea in its UV-visible spectroscopic, ligand binding and catalytic properties. Mutant versions of cytochrome P460 of N. europaea in which Lys70 70 was replaced by Arg, Ala, or Tyr, retained ligand-binding ability but lost catalytic ability and differed in optical spectra which, instead, closely resembled those of cytochromes c'. Tryptic fragments containing the c-heme joined only by two thioether linkages were observed by MALDI-TOF for the mutant cytochromes P460 K70R and K70A but not in wild-type cytochrome P460, consistent with the structural modification of the c-heme only in the wild-type cytochrome. The present observations support the hypothesized evolutionary relationship between cytochromes P460 and cytochromes c' in N. europaea and M. capsulatus[Bergmann, D.J., Zahn, J.A., & DiSpirito, A.A. (2000) Arch. Microbiol. 173, 29-34], confirm the importance of a heme-crosslink to the spectroscopic properties and catalysis and suggest that the crosslink might form auto-catalytically.
Collapse
Affiliation(s)
- David J Bergmann
- Department of Biology, Black Hills State University, Spearfish, SD, USA
| | | |
Collapse
|
27
|
Cabail MZ, Pacheco AA. Selective one-electron reduction of Nitrosomonas europaea hydroxylamine oxidoreductase with nitric oxide. Inorg Chem 2003; 42:270-2. [PMID: 12693206 DOI: 10.1021/ic025779n] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydroxylamine oxidoreductase (HAO) from the autotrophic bacterium Nitrosomonas europaea catalyzes the 4-e- oxidation of NH2-OH to NO2-. The e- are transferred from NH2OH to an unusual 5-coordinate heme known as P460, which is the active site of HAO, and from there to an array of seven c-type hemes. NO., generated by laser flash photolysis of N,N'-bis(carboxymethyl)-N,N'-dinitroso-1,4-phenylenediamine, is found to act as a 1-e- donor to HAO. Most likely NO. binds P460 to yield a [Fe(NO)]6 moiety, which then hydrolyzes to give the reduced enzyme and NO2-. The [Fe(NO)]6 moiety is also a plausible final intermediate in the oxidation of NH2OH.
Collapse
Affiliation(s)
- Maria Zulema Cabail
- Department of Chemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, USA
| | | |
Collapse
|
28
|
Hendrich MP, Upadhyay AK, Riga J, Arciero DM, Hooper AB. Spectroscopic characterization of the NO adduct of hydroxylamine oxidoreductase. Biochemistry 2002; 41:4603-11. [PMID: 11926822 DOI: 10.1021/bi011332z] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydroxylamine oxidoreductase (HAO) from the autotrophic nitrifying bacterium Nitrosomonas europaea catalyzes the oxidation of NH2OH to NO2-. The enzyme contains eight hemes per subunit which participate in catalysis and electron transport. NO is found to bind to the enzyme and inhibit electron flow to the acceptor protein, cytochrome c554. NO is found to oxidize either partially or fully reduced HAO, but NO will not reduce ferric HAO. Since NO can be reduced but not oxidized to product by HAO, NO is not considered to be a long-lived intermediate in the catalytic mechanism. Substrate oxidation occurs in the presence of bound NO or cyanide, suggesting a second interaction site for substrate with HAO and providing a means for recovery of the NO-inhibited form of the enzyme. Upon addition of NO to oxidized HAO, the integer-spin EPR signal from the active site vanishes, an IR band from NO appears at 1920 cm(-1), and a diamagnetic quadrupole iron doublet appears in Mössbauer spectroscopy with delta = 0.06 mm/s and DeltaEq = 2.1 mm/s. The NO stretching frequency and Mössbauer parameters are characteristic of an [FeNO]6 heme complex. New Mössbauer data on ferric myoglobin-NO are also presented for comparison. The results indicate that NO binds to heme P460 and that the loss of the integer-spin EPR signal is due to the conversion of heme P460 to a diamagnetic S = 0 state and concomitant loss of magnetic interaction with neighboring heme 6. In previous studies where the heme P460-heme 6 interaction was affected by substrate or cyanide binding, a signal attributable to heme 6 was not observable. In contrast, in this work, the NO-induced loss of the signal is accompanied by the appearance of a previously unobserved large g(max) (or HALS) low-spin EPR signal from heme 6.
Collapse
Affiliation(s)
- Michael P Hendrich
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA.
| | | | | | | | | |
Collapse
|
29
|
Schmidt I, Bock E, Jetten MSM. Ammonia oxidation by Nitrosomonas eutropha with NO(2) as oxidant is not inhibited by acetylene. MICROBIOLOGY (READING, ENGLAND) 2001; 147:2247-2253. [PMID: 11496001 DOI: 10.1099/00221287-147-8-2247] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The effect of acetylene ((14)C(2)H(2)) on aerobic and anaerobic ammonia oxidation by Nitrosomonas eutropha was investigated. Ammonia monooxygenase (AMO) was inhibited and a 27 kDa polypeptide (AmoA) was labelled during aerobic ammonia oxidation. In contrast, anaerobic, NO(2)-dependent ammonia oxidation (NO(2)/N(2)O(4) as oxidant) was not affected by acetylene. Further studies gave evidence that the inhibition as well as the labelling reaction were O(2)-dependent. Cells pretreated with acetylene under oxic conditions were unable to oxidize ammonia with O(2) as oxidant. After these cell suspensions were supplemented with gaseous NO(2), ammonia oxidation activity of about 140 micromol NH(4)(+) (g protein)(-1) h(-1) was detectable under both oxic and anoxic conditions. A significantly reduced acetylene inhibition of the ammonia oxidation activity was observed for cells incubated in the presence of NO. This suggests that NO and acetylene compete for the same binding site on AMO. On the basis of these results a new hypothetical model of ammonia oxidation by N. eutropha was developed.
Collapse
Affiliation(s)
- Ingo Schmidt
- Department of Microbiology, University of Nijmegen, Toernooidveld 1, 6525 ED Nijmegen, The Netherlands1
| | - Eberhard Bock
- Institute for General Botany, Department of Microbiology, University of Hamburg, Ohnhorststraße 18, 22609 Hamburg, Germany2
| | - Mike S M Jetten
- Department of Microbiology, University of Nijmegen, Toernooidveld 1, 6525 ED Nijmegen, The Netherlands1
| |
Collapse
|
30
|
Hendrich MP, Petasis D, Arciero DM, Hooper AB. Correlations of structure and electronic properties from EPR spectroscopy of hydroxylamine oxidoreductase. J Am Chem Soc 2001; 123:2997-3005. [PMID: 11457010 DOI: 10.1021/ja002982d] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydroxylamine oxidoreductase (HAO) from the autotrophic nitrifying bacterium Nitrosomonas europaea catalyzes the oxidation of NH(2)OH to HNO(2). The enzyme contains eight hemes per subunit which participate in catalytic function and electron transport. The structure of the enzyme shows a unique spatial arrangement of the eight hemes, subsets of which are now observed in four other proteins. The spatial arrangement displays three types of diheme pairing motifs. At least four of the eight hemes are electronically coupled in two distinguishable pairs and one of these pairs is at the active site of the enzyme. Here, the use of quantitative simulation of the EPR signals allows determination of exchange couplings, and assignments of signals and reduction potentials to hemes of the crystal structure. The absence of any obvious heme-to-heme bonding pathway in the crystal structure suggests that the observed exchange interactions are derived from direct electronic overlap of porphyrin orbitals. This provides evidence for heme pairs which function as biological two-electron redox centers in electron-transfer processes.
Collapse
Affiliation(s)
- M P Hendrich
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA.
| | | | | | | |
Collapse
|
31
|
Pinck C, Coeur C, Potier P, Bock E. Polyclonal antibodies recognizing the AmoB protein of ammonia oxidizers of the beta-subclass of the class Proteobacteria. Appl Environ Microbiol 2001; 67:118-24. [PMID: 11133435 PMCID: PMC92528 DOI: 10.1128/aem.67.1.118-124.2001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2000] [Accepted: 09/22/2000] [Indexed: 11/20/2022] Open
Abstract
A 41-kDa protein of Nitrosomonas eutropha was purified, and the N-terminal amino acid sequence was found to be nearly identical with the sequence of AmoB, a subunit of ammonia monooxygenase. This protein was used to develop polyclonal antibodies, which were highly specific for the detection of the four genera of ammonia oxidizers of the beta-subclass of Proteobacteria (Nitrosomonas, including Nitrosococcus mobilis, which belongs phylogenetically to Nitrosomonas; Nitrosospira; Nitrosolobus; and Nitrosovibrio). In contrast, the antibodies did not react with ammonia oxidizers affiliated with the gamma-subclass of Proteobacteria (Nitrosococcus oceani and Nitrosococcus halophilus). Moreover, methane oxidizers (Methylococcus capsulatus, Methylocystis parvus, and Methylomonas methanica) containing the related particulate methane monooxygenase were not detected. Quantitative immunoblot analysis revealed that total cell protein of N. eutropha consisted of approximately 6% AmoB, when cells were grown using standard conditions (mineral medium containing 10 mM ammonium). This AmoB amount was shown to depend on the ammonium concentration in the medium. About 14% AmoB of total protein was found when N. eutropha was grown with 1 mM ammonium, whereas 4% AmoB was detected when 100 mM ammonium were used. In addition, the cellular amount of AmoB was influenced by the absence of the substrate. Cells starved for more than 2 months contained nearly twice as much AmoB as actively growing cells, although these cells possessed low ammonia-oxidizing activity. AmoB was always present and could even be detected in cells of Nitrosomonas after 1 year of ammonia starvation.
Collapse
Affiliation(s)
- C Pinck
- Institut für Allgemeine Botanik, Universität Hamburg, D-22609 Hamburg, Germany.
| | | | | | | |
Collapse
|
32
|
Hamamura N, Storfa RT, Semprini L, Arp DJ. Diversity in butane monooxygenases among butane-grown bacteria. Appl Environ Microbiol 1999; 65:4586-93. [PMID: 10508093 PMCID: PMC91611 DOI: 10.1128/aem.65.10.4586-4593.1999] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Butane monooxygenases of butane-grown Pseudomonas butanovora, Mycobacterium vaccae JOB5, and an environmental isolate, CF8, were compared at the physiological level. The presence of butane monooxygenases in these bacteria was indicated by the following results. (i) O(2) was required for butane degradation. (ii) 1-Butanol was produced during butane degradation. (iii) Acetylene inhibited both butane oxidation and 1-butanol production. The responses to the known monooxygenase inactivator, ethylene, and inhibitor, allyl thiourea (ATU), discriminated butane degradation among the three bacteria. Ethylene irreversibly inactivated butane oxidation by P. butanovora but not by M. vaccae or CF8. In contrast, butane oxidation by only CF8 was strongly inhibited by ATU. In all three strains of butane-grown bacteria, specific polypeptides were labeled in the presence of [(14)C]acetylene. The [(14)C]acetylene labeling patterns were different among the three bacteria. Exposure of lactate-grown CF8 and P. butanovora and glucose-grown M. vaccae to butane induced butane oxidation activity as well as the specific acetylene-binding polypeptides. Ammonia was oxidized by all three bacteria. P. butanovora oxidized ammonia to hydroxylamine, while CF8 and M. vaccae produced nitrite. All three bacteria oxidized ethylene to ethylene oxide. Methane oxidation was not detected by any of the bacteria. The results indicate the presence of three distinct butane monooxygenases in butane-grown P. butanovora, M. vaccae, and CF8.
Collapse
Affiliation(s)
- N Hamamura
- Department of Botany and Plant Pathology, Construction, and Environmental Engineering, Oregon State University, Corvallis, Oregon 97331-2902, USA
| | | | | | | |
Collapse
|
33
|
Bergmann DJ, Zahn JA, Hooper AB, DiSpirito AA. Cytochrome P460 genes from the methanotroph Methylococcus capsulatus bath. J Bacteriol 1998; 180:6440-5. [PMID: 9851984 PMCID: PMC107742 DOI: 10.1128/jb.180.24.6440-6445.1998] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
P460 cytochromes catalyze the oxidation of hydroxylamine to nitrite. They have been isolated from the ammonia-oxidizing bacterium Nitrosomonas europaea (R. H. Erickson and A. B. Hooper, Biochim. Biophys. Acta 275:231-244, 1972) and the methane-oxidizing bacterium Methylococcus capsulatus Bath (J. A. Zahn et al., J. Bacteriol. 176:5879-5887, 1994). A degenerate oligonucleotide probe was synthesized based on the N-terminal amino acid sequence of cytochrome P460 and used to identify a DNA fragment from M. capsulatus Bath that contains cyp, the gene encoding cytochrome P460. cyp is part of a gene cluster that contains three open reading frames (ORFs), the first predicted to encode a 59,000-Da membrane-bound polypeptide, the second predicted to encode a 12, 000-Da periplasmic protein, and the third (cyp) encoding cytochrome P460. The products of the first two ORFs have no apparent similarity to any proteins in the GenBank database. The overall sequence similarity of the P460 cytochromes from M. capsulatus Bath and N. europaea was low (24.3% of residues identical), although short regions of conserved residues are present in the two proteins. Both cytochromes have a C-terminal, c-heme binding motif (CXXCH) and a conserved lysine residue (K61) that may provide an additional covalent cross-link to the heme (D. M. Arciero and A. B. Hooper, FEBS Lett. 410:457-460, 1997). Gene probing using cyp indicated that a cytochrome P460 similar to that from M. capsulatus Bath may be present in the type II methanotrophs Methylosinus trichosporium OB3b and Methylocystis parvus OBBP but not in the type I methanotrophs Methylobacter marinus A45, Methylomicrobium albus BG8, and Methylomonas sp. strains MN and MM2. Immunoblot analysis with antibodies against cytochrome P460 from M. capsulatus Bath indicated that the expression level of cytochrome P460 was not affected either by expression of the two different methane monooxygenases or by addition of ammonia to the culture medium.
Collapse
Affiliation(s)
- D J Bergmann
- Department of Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | | | | | | |
Collapse
|
34
|
Arciero DM, Golombek A, Hendrich MP, Hooper AB. Correlation of optical and EPR signals with the P460 heme of hydroxylamine oxidoreductase from Nitrosomonas europaea. Biochemistry 1998; 37:523-9. [PMID: 9425072 DOI: 10.1021/bi972187l] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Hydroxylamine oxidoreductase (HAO) of Nitrosomonas europaea catalyzes the four-electron oxidation of NH2OH to NO2-. Each subunit of the trimeric enzyme contains seven c-hemes and one heme P460. In previous work [Hendrich, M. P., et al. (1994) J. Am. Chem. Soc. 116, 11961-11968], an integer-spin EPR signal at g = 7.7 was discovered from the active site of the resting enzyme. This new signal was assigned to an exchange-coupled cluster containing ferric heme P460 and a ferric c-heme. An electrochemical titration of HAO is presented here in which EPR signals and optical bands, believed to be associated with the P460 heme, are monitored. In the EPR titration, as a redox center with Em8 = -140 mV becomes reduced, the integer-spin signal disappears. Then, upon reduction of a redox center with Em8 = -190 mV, a g = 6 type signal, which has been previously assigned to a high-spin form of the ferric P460 heme of HAO, appears. However, in the -140 to -190 mV range, we have been unable to identify an additional EPR signal attributable to the P460 center. Thus, the electronic environment of oxidized P460 heme of HAO appears to pass through three states before reduction in a titration experiment, with an intermediate state that is not readily detectable by X-band EPR. The best candidate for the c-heme partner of the P460 heme is the heme at -190 mV, which would correspond to heme 6 of the crystal structure. A possible function of the exchange-coupled heme cluster is to facilitate two-electron oxidation steps of the substrate. An earlier spectropotentiometric titration of HAO [Collins, M. J., et al. (1993) J. Biol. Chem. 268, 14655-14662] identified a broad, weak optical band, centered near 740 nm, that was tentatively assigned to the oxidized P460 heme. This assignment has been strengthened by additional spectropotentiometric titrations at several values of pH and also by rapid kinetic experiments following the reduction of HAO by dithionite. The 740 nm band is not observed in fully oxidized HAO. In the spectropotentiometric titrations, its appearance cannot be correlated with reduction of a specific c-heme nor modeled to a Nernstian one-electron redox center. Instead, the range of potential in which the 740 nm band is present depends on whether the titration is carried out in an oxidative or reductive direction. One possible interpretation is that the 740 nm band is a property of the oxidized high-spin P460 heme but not of the low-spin state, and that the transition between the two spin states occurs at different potentials depending on the direction of the electrochemical titration.
Collapse
Affiliation(s)
- D M Arciero
- Department of Genetics and Cell Biology, University of Minnesota, St. Paul, Minnesota 55108, USA
| | | | | | | |
Collapse
|
35
|
Crossman LC, Moir JWB, Enticknap JJ, Richardson DJ, Spiro S. Heterologous expression of heterotrophic nitrification genes. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 12):3775-3783. [PMID: 9421902 DOI: 10.1099/00221287-143-12-3775] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Paracoccus denitrificans is a heterotrophic organism capable of oxidizing ammonia to nitrite during growth on an organic carbon and energy source. This pathway, termed heterotrophic nitrification, requires the concerted action of an ammonia monooxygenase (AMO) and hydroxylamine oxidase (HAO). The genes required for heterotrophic nitrification have been isolated by introducing a Pa. denitrificans genomic library into Pseudomonas putida and screening for the accumulation of nitrite. In contrast to the situation in chemolithoautotrophic ammonia oxidizers, the genes encoding AMO and HAO are present in single linked copies in the genome of Pa. denitrificans. AMO from Pa. denitrificans expressed in Ps. putida is capable of oxidizing ethene (ethylene) to epoxyethane (ethylene oxide), which is indicative of a relaxed substrate specificity. Further, when expressed in the methylotroph Methylobacterium extorquens AM1, the AMO endows on this organism the ability to grow on ethene and methane. Thus, the Pa. denitrificans AMO is capable of oxidizing methane to methanol, as is the case for the AMO from Nitrosomonas europaea. The heterotrophic nitrification genes are moderately toxic in M. extorquens, more toxic in Ps. putida, and non-toxic in Escherichia coli. Toxicity is due to the activity of the gene products in M. extorquens, and both expression and activity in Ps. putida. This is the first time that the genes encoding an active AMO have been expressed in a heterologous host.
Collapse
Affiliation(s)
- Lisa C Crossman
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | | | | | - David J Richardson
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Stephen Spiro
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| |
Collapse
|
36
|
Abstract
Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1. An important class of regulators for the anaerobic expression of the denitrification apparatus are transcription factors of the greater FNR family. Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.
Collapse
Affiliation(s)
- W G Zumft
- Lehrstuhl für Mikrobiologie, Universität Fridericiana, Karlsruhe, Germany
| |
Collapse
|
37
|
Pereira IA, Pacheco I, Liu MY, Legall J, Xavier AV, Teixeira M. Multiheme cytochromes from the sulfur-reducing bacterium Desulfuromonas acetoxidans. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 248:323-8. [PMID: 9346284 DOI: 10.1111/j.1432-1033.1997.00323.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Two new multiheme cytochromes were isolated from the anaerobic sulfur reducing bacterium Desulfuromonas acetoxidans. They have monomeric molecular masses of 50 and 65 kDa and contain six and eight hemes, respectively. Visible and EPR spectroscopies, in the as-isolated (oxidised) cytochromes, show the presence of only low-spin hemes in the 50-kDa cytochrome, and of high-spin and low-spin hemes in the 65-kDa cytochrome. The EPR spectra of the native 65-kDa cytochrome indicate multiple heme-heme interactions, including integer-spin systems as judged by parallel-mode EPR. The 50-kDa cytochrome has a complex redox pattern, as shown by EPR redox titrations, and contains one heme with unusual characteristics. Both cytochromes cover an extremely wide range of reduction potentials, which go from +100 mV to -375 mV for the 50-kDa cytochrome, and +185 mV to -235 mV for the 65-kDa cytochrome. The two cytochromes were tested for hydroxylamine oxidoreductase activity and polysulfide reductase activity, but neither displayed any activity. In contrast, it was found for the first time that the previously characterised cytochrome c551.5, from the same bacterium is very active in the reduction of polysulfide, which suggests that it acts as a terminal reductase in D. acetoxidans.
Collapse
Affiliation(s)
- I A Pereira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | | | | | | | | | | |
Collapse
|
38
|
Arciero DM, Hooper AB. Evidence for a crosslink between c-heme and a lysine residue in cytochrome P460 of Nitrosomonas europaea. FEBS Lett 1997; 410:457-60. [PMID: 9237682 DOI: 10.1016/s0014-5793(97)00635-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Cytochrome P460 and hydroxylamine oxidoreductase (HAO) of Nitrosomonas europaea catalyze the oxidation of hydroxylamine. Cytochrome P460 contains an unidentified heme-like chromophore whose distinctive spectroscopic properties are similar to those for the P460 heme found in HAO. The heme P460 of HAO has previously been shown by protein chemistry and NMR structural analysis to be a c-heme with an additional covalent crosslink between the C2 ring carbon of a tyrosine residue of the polypeptide chain and a meso carbon of the porphyrin [Arciero, D.M. et al. (1993) Biochemistry 32, 9370-9378]. The recent determination of the gene sequence for cytochrome P460 [Bergmann, D.J. and Hooper, A.B. (1994) FEBS Lett. 353, 324-326] indicates that the heme in this protein also possesses a c-heme binding site and provides the basis for determining whether an HAO-like crosslink exists to the porphyrin. Sequence analysis of a purified heme-containing tryptic chromopeptide from cytochrome P460 revealed two predominant amino acid residues per cycle. Two peptides present in the chromopeptide with the sequences NLPTAEXAAXHK and DGTVTVXELVSV. Comparison of the data to the gene sequence for the protein revealed that the gaps in the first peptide (indicated by X's) code for C residues, confirming the prediction of a c-heme binding motif. The gap in the sequence in the second peptide at cycle 7 is predicted by the gene sequence to be a K. The results suggest that the lysine residue is crosslinked in some manner to the porphyrin macrocycle, possibly mimicking the tyrosine crosslink found for the heme P460 of HAO. While a common role for the crosslinked residues in HAO and cytochrome P460 is difficult to ascertain due to the dissimilarities in side chain structure, it may be related to the similar pKa values for lysine and tyrosine.
Collapse
Affiliation(s)
- D M Arciero
- Department of Genetics and Cell Biology, University of Minnesota, St. Paul 55108, USA
| | | |
Collapse
|
39
|
Klotz MG, Alzerreca J, Norton JM. A gene encoding a membrane protein exists upstream of the amoA/amoB genes in ammonia oxidizing bacteria: a third member of the amo operon? FEMS Microbiol Lett 1997; 150:65-73. [PMID: 9163908 DOI: 10.1111/j.1574-6968.1997.tb10351.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The gene cluster encoding ammonia monooxygenase (AMO) in the chemolithotrophic soil bacterium Nitrosospira sp. NpAV was found to contain a third open reading frame, termed amoC, upstream of the genes amoA and amoB that encode the subunits of AMO. The amoC gene and its flanking regions were isolated and sequenced from a 4.4 kb EcoRI fragment that contains one of three copies of the ammonia monooxygenase gene cluster. The presence of this gene upstream of the other two amoA gene copies in Nitrosospira NpAV as well as upstream of amoA genes in the genomes of other ammonia oxidizing nitrifiers (strains in the genera Nitrosomonas, Nitrosopira, Nitrosolobus and Nitrosovibrio) was confirmed using genomic DNA, oligodeoxyribonucleotide primers and the PCR. The amoC gene in Nitrosospira sp. NpAV encodes a 270 amino acid polypeptide of approximately 36 kDa. Topological analysis of the predicted primary structure revealed 6 membrane spanning domains. The amoC gene was expressed in recombinant Escherichia coli from its indigenous promoter.
Collapse
Affiliation(s)
- M G Klotz
- Department of Biology, University of Colorado, Denver 80217-3364, USA.
| | | | | |
Collapse
|
40
|
Igarashi N, Moriyama H, Fujiwara T, Fukumori Y, Tanaka N. The 2.8 A structure of hydroxylamine oxidoreductase from a nitrifying chemoautotrophic bacterium, Nitrosomonas europaea. NATURE STRUCTURAL BIOLOGY 1997; 4:276-84. [PMID: 9095195 DOI: 10.1038/nsb0497-276] [Citation(s) in RCA: 163] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The 2.8 A crystal structure of hydroxylamine oxidoreductase of a nitrifying chemoautotrophic bacterium, Nitrosomonas europaea, is described. Twenty-four haems lie in the centre bottom of the trimeric molecule, localized in four clusters within each monomer. The haem clusters within the trimer are aligned to form a ring that has inlet and outlet sites. The inlet is occupied by a novel haem, P460, and there are two possible outlet sites per monomer formed by paired haems lying within a cavity or cleft on the protein surface. The structure suggests pathways by which electron transfer may occur through the precisely arranged haems and provides a framework for the interpretation of previous and future biochemical and genetic observations.
Collapse
Affiliation(s)
- N Igarashi
- Department of Life Science, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | | | | | | | | |
Collapse
|
41
|
Wehrfritz J, Carter JP, Spiro S, Richardson DJ. Hydroxylamine oxidation in heterotrophic nitrate-reducing soil bacteria and purification of a hydroxylamine-cytochrome c oxidoreductase from a Pseudomonas species. Arch Microbiol 1996; 166:421-4. [PMID: 9082922 DOI: 10.1007/bf01682991] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Hydroxylamine oxidation was measured in four recently isolated heterotrophic nitrate-reducing bacteria belonging to the genera Pseudomonas, Moraxella, Arthrobacter and Aeromonas. A hydroxylamine-cytochrome c oxidoreductase activity was detected in periplasmic fractions of the Pseudomonas and Aeromonas spp. and in total soluble fractions of the Arthrobacter sp. A monomeric 19-kDa non-haem iron hydroxylamine-cytochrome c oxidoreductase was purified from the Pseudomonas species and shown to be similar to hydroxylamine-cytochrome c oxidoreductase of Paracoccus denitrificans.
Collapse
Affiliation(s)
- J Wehrfritz
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | | | | | | |
Collapse
|
42
|
Ono Y, Makino N, Hoshino Y, Shoji K, Yamanaka T. An iron dioxygenase from Alcaligenes faecalis catalyzing the oxidation of pyruvic oxime to nitrite. FEMS Microbiol Lett 1996; 139:103-8. [PMID: 8674977 DOI: 10.1111/j.1574-6968.1996.tb08187.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
An enzyme which participated in the oxidation of hydroxylamine to nitrite from was partially purified Alcaligenes faecalis, and some of its properties were studied. The enzyme oxidized aerobically pyruvic oxime to nitrite in the presence of hydroxylamine or ascorbate. As molecular oxygen equimolar to nitrite formed was consumed in the enzymatic oxidation of pyruvic oxime to nitrite, the enzyme was thought to be a dioxygenase. It was an iron protein, and a reducing reagent was required to keep the iron in the ferrous state for the action of the enzyme.
Collapse
Affiliation(s)
- Y Ono
- Department of Industrial Chemistry, College of Science and Technology, Nihon University, Tokyo, Japan
| | | | | | | | | |
Collapse
|
43
|
Moir JW, Crossman LC, Spiro S, Richardson DJ. The purification of ammonia monooxygenase from Paracoccus denitrificans. FEBS Lett 1996; 387:71-4. [PMID: 8654570 DOI: 10.1016/0014-5793(96)00463-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The heterotrophic nitrifier Paracoccus denitrificans expresses a membrane-associated ammonia monooxygenase. The active enzyme has been solubilized in the detergent dodecyl-beta-D-maltoside and purified by standard chromatographic techniques. This is the first purification of an ammonia monooxygenase. The enzyme consists of two subunits with molecular masses of 38 and 46 kDa. The purified enzyme is a quinol oxidase, is inhibited by light and a variety of chelating agents and is activated by cupric ions. These properties indicate that this enzyme has similarities to a family of enzymes including the ammonia monooxygenase from Nitrosomonas europaea and the particulate methane monooxygenase from Methylococcus capsulatus (Bath).
Collapse
Affiliation(s)
- J W Moir
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | | | | | | |
Collapse
|
44
|
Quaternary structure of the hydroxylamine oxidoreductase from Nitrosomonas europaea. Arch Microbiol 1995. [DOI: 10.1007/bf00393384] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
45
|
Zahn JA, Duncan C, DiSpirito AA. Oxidation of hydroxylamine by cytochrome P-460 of the obligate methylotroph Methylococcus capsulatus Bath. J Bacteriol 1994; 176:5879-87. [PMID: 7928947 PMCID: PMC196803 DOI: 10.1128/jb.176.19.5879-5887.1994] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
An enzyme capable of the oxidation of hydroxylamine to nitrite was isolated from the obligate methylotroph Methylococcus capsulatus Bath. The absorption spectra in cell extracts, electron paramagnetic resonance spectra, molecular weight, covalent attachment of heme group to polypeptide, and enzymatic activities suggest that the enzyme is similar to cytochrome P-460, a novel iron-containing protein previously observed only in Nitrosomonas europaea. The native and subunit molecular masses of the M. capsulatus Bath protein were 38,900 and 16,390 Da, respectively; the isoelectric point was 6.98. The enzyme has approximately one iron and one copper atom per subunit. The electron paramagnetic resonance spectrum of the protein showed evidence for a high-spin ferric heme. In contrast to the enzyme from N. europaea, a 13-nm blue shift in the soret band of the ferrocytochrome (463 nm in cell extracts to 450 nm in the final sample) occurred during purification. The amino acid composition and N-terminal amino acid sequence of the enzyme from M. capsulatus Bath was similar but not identical to those of cytochrome P-460 of N. europaea. In cell extracts, the identity of the biological electron acceptor is as yet unestablished. Cytochrome c-555 is able to accept electrons from cytochrome P-460, although the purified enzyme required phenazine methosulfate for maximum hydroxylamine oxidation activity (specific activity, 366 mol of O2 per s per mol of enzyme). Hydroxylamine oxidation rates were stimulated approximately 2-fold by 1 mM cyanide and 1.5-fold by 0.1 mM 8-hydroxyquinoline.
Collapse
Affiliation(s)
- J A Zahn
- Department of Microbiology, Immunology, and Preventive Medicine, Iowa State University, Ames 50011
| | | | | |
Collapse
|
46
|
Bergmann DJ, Arciero DM, Hooper AB. Organization of the hao gene cluster of Nitrosomonas europaea: genes for two tetraheme c cytochromes. J Bacteriol 1994; 176:3148-53. [PMID: 8195067 PMCID: PMC205482 DOI: 10.1128/jb.176.11.3148-3153.1994] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The organization of genes for three proteins involved in ammonia oxidation in Nitrosomonas europaea has been investigated. The amino acid sequence of the N-terminal region and four heme-containing peptides produced by proteolysis of the tetraheme cytochrome c554 of N. europaea were determined by Edman degradation. The gene (cycA) encoding this cytochrome is present in three copies per genome (H. McTavish, F. LaQuier, D. Arciero, M. Logan, G. Mundfrom, J.A. Fuchs, and A. B. Hooper, J. Bacteriol. 175:2445-2447, 1993). Three clones, representing at least two copies of cycA, were isolated and sequenced by the dideoxy-chain termination procedure. In both copies, the sequences of 211 amino acids derived from the gene sequence are identical and include all amino acids predicted by the proteolytic peptides. In two copies, the cycA open reading frame (ORF) is followed closely (three bases in one copy) by a second ORF predicted to encode a 28-kDa tetraheme c cytochrome not previously characterized but similar to the nirT gene product of Pseudomonas stutzeri. In one copy of the cycA gene cluster, the second ORF is absent.
Collapse
Affiliation(s)
- D J Bergmann
- Department of Genetics and Cell Biology, University of Minnesota, St. Paul 55108
| | | | | |
Collapse
|
47
|
Arciero D, Hooper A. A di-heme cytochrome c peroxidase from Nitrosomonas europaea catalytically active in both the oxidized and half-reduced states. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)32655-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
48
|
Sayavedra-Soto LA, Hommes NG, Arp DJ. Characterization of the gene encoding hydroxylamine oxidoreductase in Nitrosomonas europaea. J Bacteriol 1994; 176:504-10. [PMID: 8288544 PMCID: PMC205074 DOI: 10.1128/jb.176.2.504-510.1994] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Hydroxylamine oxidoreductase (HAO) catalyzes the oxidation of hydroxylamine to nitrite in Nitrosomonas europaea. The electrons released in the reaction are partitioned to ammonium monooxygenase and to the respiratory chain. The immediate acceptor of electrons from HAO is believed to be cytochrome c-554 (Cyt c-554). We have isolated a genomic DNA fragment containing the structural gene encoding HAO (hao) and a part of the gene for Cyt c-554. The nucleotide sequence of hao was determined, and its transcription was analyzed. The open reading frame (ORF) encodes amino acid sequences matching the purified peptides of HAO. A 64.28-kDa protein is encoded in this ORF, in close agreement with the empirically determined molecular mass of 63 kDa. The N terminus was located 24 amino acids from the start codon, suggesting the presence of a leader sequence. The putative eight heme-binding peptides were localized in this ORF. The gene for Cyt c-554 was located 1,200 bp downstream from the 3' end of hao. An ORF was identified in the upstream region from hao and may encode a protein of unknown function. Data bank searches did not reveal proteins with substantial similarities to HAO, but they did reveal similarities between Cyt c-554 and other c-type cytochromes.
Collapse
Affiliation(s)
- L A Sayavedra-Soto
- Laboratory for Nitrogen Fixation Research, Oregon State University, Corvallis 97331-2902
| | | | | |
Collapse
|
49
|
Shimura M, Hirota F, Yagi T. Functional sites of cytochrome c and other electron carrier proteins: semi-empirical molecular orbital program PM3 applied to the conformational analysis of Cys-X1-X2-Cys peptides. Biochimie 1994; 76:614-21. [PMID: 7893813 DOI: 10.1016/0300-9084(94)90138-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The semi-empirical molecular orbital program, MOPAC version 6.0, PM3 was applied to estimate the distance between two sulfur atoms of two Cys side chains in optimized conformers of Cys-X1-X2-Cys sequences, as well as the total energy of that conformer relative to the most stable one. Some Cys-X1-X2-Cys tetrapeptides found in cytochrome c were optimized to conformers whose sulfur-sulfur distances were just suitable for binding to heme, whereas some tetrapeptides not found in cytochrome c were unable to be optimized to heme-binding conformers. Similarly, Cys-X1-X2-Cys tetrapeptides found in [4Fe-4S]ferredoxin were optimized to [4Fe-4S]-binding conformers, etc. The tetrapeptides found in the redox site of thioredoxin were optimized to conformers in which the two sulfur atoms were in van der Waals contact, so that a disulfide bond may be formed during the function. The conclusion has been drawn that the combination of X1 and X2 in a Cys-X1-X2-Cys sequence may be determining for that sequence to be a functional redox site in an electron carrier protein.
Collapse
Affiliation(s)
- M Shimura
- Department of Chemistry, Shizuoka University, Japan
| | | | | |
Collapse
|
50
|
Wehrfritz JM, Reilly A, Spiro S, Richardson DJ. Purification of hydroxylamine oxidase from Thiosphaera pantotropha. Identification of electron acceptors that couple heterotrophic nitrification to aerobic denitrification. FEBS Lett 1993; 335:246-50. [PMID: 8253206 DOI: 10.1016/0014-5793(93)80739-h] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Thiosphaera pantotropha, a Gram-negative heterotrophic nitrifying bacterium, expresses a soluble 20 kDa monomeric periplasmic hydroxylamine oxidase that differs markedly from the hydroxylamine oxidase found in autotrophic bacteria. This enzyme can use the periplasmic redox proteins, cytochrome c551 and pseudoazurin as electron acceptors, both of which can also donate electrons to denitrification enzymes. A model of electron transfer is proposed, that suggests a coupling of nitrification and provides a mechanism by which nitrification can play a role in dissipating reductant.
Collapse
Affiliation(s)
- J M Wehrfritz
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | | | | | | |
Collapse
|