1
|
Bai M, He J, Zheng F, Lv S, Wang Z, Hrynsphan D, Savitskaya T, Chen J. Gene cloning, expression and performance validation of nitric oxide dismutase. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 935:173455. [PMID: 38782282 DOI: 10.1016/j.scitotenv.2024.173455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/20/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
Nitrous oxide (N2O) is a significant contributor to global warming and possesses an ozone-depleting impact nearly 298 times that of CO2. To reduce N2O emissions, the newly-discovered nod gene which can directly convert NO into N2 and O2 was successfully cloned from the anaerobic denitrification sludge. The recombinant plasmid containing the nod gene was built, and the expression of nod gene in Escherichia coli was determined, leading to the construction of recombinant engineering bacteria. Results showed that the recombinant engineering bacteria E. coli BL21 (DE3)-pET28a-nod could autonomously degrade NO, with a degradation rate of 72 % within 48 h, and could produce 2479.72 ppm of N2 and 75.12 mL of O2. The cumulative O2 production of the sludge sample and recombinant E. coli within 8 h was 1.75 mL and 8.45 mL, respectively. The cumulative O2 production of recombinant E. coli was at least 4.82 times higher than that of the sludge sample. The investigation proposed a new biodegradation pathway for nitrogen pollution.
Collapse
Affiliation(s)
- Mengwei Bai
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jiamei He
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Fengzhen Zheng
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou 310015, China
| | - Sini Lv
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Zeyu Wang
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou 310015, China
| | - Dzmitry Hrynsphan
- Research Institute of Physical and Chemical Problems, Belarusian State University, Minsk 220030, Belarus
| | - Tatsiana Savitskaya
- Research Institute of Physical and Chemical Problems, Belarusian State University, Minsk 220030, Belarus
| | - Jun Chen
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou 310015, China.
| |
Collapse
|
2
|
Schmitz EV, Just CL, Schilling K, Streeter M, Mattes TE. Reconnaissance of Oxygenic Denitrifiers in Agriculturally Impacted Soils. mSphere 2023; 8:e0057122. [PMID: 37017537 PMCID: PMC10286720 DOI: 10.1128/msphere.00571-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/01/2023] [Indexed: 04/06/2023] Open
Abstract
Row crop production in the agricultural Midwest pollutes waterways with nitrate, and exacerbates climate change through increased emissions of nitrous oxide and methane. Oxygenic denitrification processes in agricultural soils mitigate nitrate and nitrous oxide pollution by short-circuiting the canonical pathway to avoid nitrous oxide formation. Furthermore, many oxygenic denitrifiers employ a nitric oxide dismutase (nod) to create molecular oxygen that is used by methane monooxygenase to oxidize methane in otherwise anoxic soils. The direct investigation of nod genes that could facilitate oxygenic denitrification processes in agricultural sites is limited, with no prior studies investigating nod genes at tile drainage sites. Thus, we performed a reconnaissance of nod genes at variably saturated surface sites, and within a variably to fully saturated soil core in Iowa to expand the known distribution of oxygenic denitrifiers. We identified new nod gene sequences from agricultural soil and freshwater sediments in addition to identifying nitric oxide reductase (qNor) related sequences. Surface and variably saturated core samples displayed a nod to 16S rRNA gene relative abundance of 0.004% to 0.1% and fully saturated core samples had relative nod gene abundance of 1.2%. The relative abundance of the phylum Methylomirabilota increased from 0.6% and 1% in the variably saturated core samples to 3.8% and 5.3% in the fully saturated core samples. The more than 10-fold increase in relative nod abundance and almost 9-fold increase in relative Methylomirabilota abundance in fully saturated soils suggests that potential oxygenic denitrifiers play a greater nitrogen cycling role under these conditions. IMPORTANCE The direct investigation of nod genes in agricultural sites is limited, with no prior studies investigating nod genes at tile drains. An improved understanding of nod gene diversity and distribution is significant to the field of bioremediation and ecosystem services. The expansion of the nod gene database will advance oxygenic denitrification as a potential strategy for sustainable nitrate and nitrous oxide mitigation, specifically for agricultural sites.
Collapse
Affiliation(s)
- Emily V. Schmitz
- Department of Civil and Environmental Engineering, 4105 Seamans Center, The University of Iowa, Iowa City, Iowa, USA
| | - Craig L. Just
- Department of Civil and Environmental Engineering, 4105 Seamans Center, The University of Iowa, Iowa City, Iowa, USA
| | - Keith Schilling
- Iowa Geological Survey, University of Iowa, Iowa City, Iowa, USA
| | - Matthew Streeter
- Iowa Geological Survey, University of Iowa, Iowa City, Iowa, USA
| | - Timothy E. Mattes
- Department of Civil and Environmental Engineering, 4105 Seamans Center, The University of Iowa, Iowa City, Iowa, USA
| |
Collapse
|
3
|
Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
Collapse
Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| |
Collapse
|
4
|
Salas A, Cabrera JJ, Jiménez-Leiva A, Mesa S, Bedmar EJ, Richardson DJ, Gates AJ, Delgado MJ. Bacterial nitric oxide metabolism: Recent insights in rhizobia. Adv Microb Physiol 2021; 78:259-315. [PMID: 34147187 DOI: 10.1016/bs.ampbs.2021.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nitric oxide (NO) is a reactive gaseous molecule that has several functions in biological systems depending on its concentration. At low concentrations, NO acts as a signaling molecule, while at high concentrations, it becomes very toxic due to its ability to react with multiple cellular targets. Soil bacteria, commonly known as rhizobia, have the capacity to establish a N2-fixing symbiosis with legumes inducing the formation of nodules in their roots. Several reports have shown NO production in the nodules where this gas acts either as a signaling molecule which regulates gene expression, or as a potent inhibitor of nitrogenase and other plant and bacteria enzymes. A better understanding of the sinks and sources of NO in rhizobia is essential to protect symbiotic nitrogen fixation from nitrosative stress. In nodules, both the plant and the microsymbiont contribute to the production of NO. From the bacterial perspective, the main source of NO reported in rhizobia is the denitrification pathway that varies significantly depending on the species. In addition to denitrification, nitrate assimilation is emerging as a new source of NO in rhizobia. To control NO accumulation in the nodules, in addition to plant haemoglobins, bacteroids also contribute to NO detoxification through the expression of a NorBC-type nitric oxide reductase as well as rhizobial haemoglobins. In the present review, updated knowledge about the NO metabolism in legume-associated endosymbiotic bacteria is summarized.
Collapse
Affiliation(s)
- Ana Salas
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Juan J Cabrera
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain; School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Andrea Jiménez-Leiva
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Socorro Mesa
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - David J Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Andrew J Gates
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - María J Delgado
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain.
| |
Collapse
|
5
|
Gomes FO, Maia LB, Cordas C, Moura I, Delerue-Matos C, Moura JJG, Morais S. Electroanalytical characterization of the direct Marinobacter hydrocarbonoclasticus nitric oxide reductase-catalysed nitric oxide and dioxygen reduction. Bioelectrochemistry 2018; 125:8-14. [PMID: 30176545 DOI: 10.1016/j.bioelechem.2018.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/15/2018] [Accepted: 08/19/2018] [Indexed: 02/07/2023]
Abstract
Understanding the direct electron transfer processes between redox proteins and electrode surface is fundamental to understand the proteins mechanistic properties and for development of novel biosensors. In this study, nitric oxide reductase (NOR) extracted from Marinobacter hydrocarbonoclasticus bacteria was adsorbed onto a pyrolytic graphite electrode (PGE) to develop an unmediated enzymatic biosensor (PGE/NOR)) for characterization of NOR direct electrochemical behaviour and NOR electroanalytical features towards NO and O2. Square-wave voltammetry showed the reduction potential of all the four NOR redox centers: 0.095 ± 0.002, -0.108 ± 0.008, -0.328 ± 0.001 and -0.635 ± 0.004 V vs. SCE for heme c, heme b, heme b3 and non-heme FeB, respectively. The determined sensitivity (-4.00 × 10-8 ± 1.84 × 10-9 A/μM and - 2.71 × 10-8 ± 1.44 × 10-9 A/μM for NO and O2, respectively), limit of detection (0.5 μM for NO and 1.0 μM for O2) and the Michaelis Menten constant (2.1 and 7.0 μM for NO and O2, respectively) corroborated the higher affinity of NOR for its natural substrate (NO). No significant interference on sensitivity towards NO was perceived in the presence of O2, while the O2 reduction was markedly and negatively impacted (3.6 times lower sensitivity) by the presence of NO. These results clearly demonstrate the high potential of NOR for the design of innovative NO biosensors.
Collapse
Affiliation(s)
- Filipa O Gomes
- REQUIMTE-LAQV, Instituto Superior de Engenharia do Instituto Politécnico do Porto, Rua Dr. António Bernardino de Almeida n° 451, 4249-015 Porto, Portugal; REQUIMTE-LAQV, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Luísa B Maia
- REQUIMTE-LAQV, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Cristina Cordas
- REQUIMTE-LAQV, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Isabel Moura
- REQUIMTE-LAQV, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Cristina Delerue-Matos
- REQUIMTE-LAQV, Instituto Superior de Engenharia do Instituto Politécnico do Porto, Rua Dr. António Bernardino de Almeida n° 451, 4249-015 Porto, Portugal
| | - José J G Moura
- REQUIMTE-LAQV, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Simone Morais
- REQUIMTE-LAQV, Instituto Superior de Engenharia do Instituto Politécnico do Porto, Rua Dr. António Bernardino de Almeida n° 451, 4249-015 Porto, Portugal.
| |
Collapse
|
6
|
Yamagiwa R, Kurahashi T, Takeda M, Adachi M, Nakamura H, Arai H, Shiro Y, Sawai H, Tosha T. Pseudomonas aeruginosa overexpression system of nitric oxide reductase for in vivo and in vitro mutational analyses. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:333-341. [PMID: 29499184 DOI: 10.1016/j.bbabio.2018.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/18/2018] [Accepted: 02/24/2018] [Indexed: 11/30/2022]
Abstract
Membrane-integrated nitric oxide reductase (NOR) reduces nitric oxide (NO) to nitrous oxide (N2O) with protons and electrons. This process is essential for the elimination of the cytotoxic NO that is produced from nitrite (NO2-) during microbial denitrification. A structure-guided mutagenesis of NOR is required to elucidate the mechanism for NOR-catalyzed NO reduction. We have already solved the crystal structure of cytochrome c-dependent NOR (cNOR) from Pseudomonas aeruginosa. In this study, we then constructed its expression system using cNOR-gene deficient and wild-type strains for further functional study. Characterizing the variants of the five conserved Glu residues located around the heme/non-heme iron active center allowed us to establish how the anaerobic growth rate of cNOR-deficient strains expressing cNOR variants correlates with the in vitro enzymatic activity of the variants. Since bacterial strains require active cNOR to eliminate cytotoxic NO and to survive under denitrification conditions, the anaerobic growth rate of a strain with a cNOR variant is a good indicator of NO decomposition capability of the variants and a marker for the screening of functionally important residues without protein purification. Using this in vivo screening system, we examined the residues lining the putative proton transfer pathways for NO reduction in cNOR, and found that the catalytic protons are likely transferred through the Glu57 located at the periplasmic protein surface. The homologous cNOR expression system developed here is an invaluable tool for facile identification of crucial residues in vivo, and for further in vitro functional and structural studies.
Collapse
Affiliation(s)
- Raika Yamagiwa
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan; RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan
| | - Takuya Kurahashi
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Mariko Takeda
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Mayuho Adachi
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Hiro Nakamura
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hiroyuki Arai
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Yoshitsugu Shiro
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan; RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan
| | - Hitomi Sawai
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan; RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan.
| | - Takehiko Tosha
- RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan.
| |
Collapse
|
7
|
Characterization of the quinol-dependent nitric oxide reductase from the pathogen Neisseria meningitidis, an electrogenic enzyme. Sci Rep 2018; 8:3637. [PMID: 29483528 PMCID: PMC5826923 DOI: 10.1038/s41598-018-21804-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/09/2018] [Indexed: 12/01/2022] Open
Abstract
Bacterial nitric oxide reductases (NORs) catalyse the reduction of NO to N2O and H2O. NORs are found either in denitrification chains, or in pathogens where their primary role is detoxification of NO produced by the immune defense of the host. Although NORs belong to the heme-copper oxidase superfamily, comprising proton-pumping O2-reducing enzymes, the best studied NORs, cNORs (cytochrome c-dependent), are non-electrogenic. Here, we focus on another type of NOR, qNOR (quinol-dependent). Recombinant qNOR from Neisseria meningitidis, a human pathogen, purified from Escherichia coli, showed high catalytic activity and spectroscopic properties largely similar to cNORs. However, in contrast to cNOR, liposome-reconstituted qNOR showed respiratory control ratios above two, indicating that NO reduction by qNOR was electrogenic. Further, we determined a 4.5 Å crystal structure of the N. meningitidis qNOR, allowing exploration of a potential proton transfer pathway from the cytoplasm by mutagenesis. Most mutations had little effect on the activity, however the E-498 variants were largely inactive, while the corresponding substitution in cNOR was previously shown not to induce significant effects. We thus suggest that, contrary to cNOR, the N. meningitidis qNOR uses cytoplasmic protons for NO reduction. Our results allow possible routes for protons to be discussed.
Collapse
|
8
|
Torregrosa-Crespo J, González-Torres P, Bautista V, Esclapez JM, Pire C, Camacho M, Bonete MJ, Richardson DJ, Watmough NJ, Martínez-Espinosa RM. Analysis of multiple haloarchaeal genomes suggests that the quinone-dependent respiratory nitric oxide reductase is an important source of nitrous oxide in hypersaline environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:788-796. [PMID: 28925557 DOI: 10.1111/1758-2229.12596] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Microorganisms, including Bacteria and Archaea, play a key role in denitrification, which is the major mechanism by which fixed nitrogen returns to the atmosphere from soil and water. While the enzymology of denitrification is well understood in Bacteria, the details of the last two reactions in this pathway, which catalyse the reduction of nitric oxide (NO) via nitrous oxide (N2 O) to nitrogen (N2 ), are little studied in Archaea, and hardly at all in haloarchaea. This work describes an extensive interspecies analysis of both complete and draft haloarchaeal genomes aimed at identifying the genes that encode respiratory nitric oxide reductases (Nors). The study revealed that the only nor gene found in haloarchaea is one that encodes a single subunit quinone dependent Nor homologous to the qNor found in bacteria. This surprising discovery is considered in terms of our emerging understanding of haloarchaeal bioenergetics and NO management.
Collapse
Affiliation(s)
- Javier Torregrosa-Crespo
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Pedro González-Torres
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88. 08003 Barcelona, Spain
| | - Vanesa Bautista
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Julia M Esclapez
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Carmen Pire
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Mónica Camacho
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - María José Bonete
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - David J Richardson
- Centre for Molecular Structure and Biochemistry, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Nicholas J Watmough
- Centre for Molecular Structure and Biochemistry, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Rosa María Martínez-Espinosa
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| |
Collapse
|
9
|
Zhu B, Bradford L, Huang S, Szalay A, Leix C, Weissbach M, Táncsics A, Drewes JE, Lueders T. Unexpected Diversity and High Abundance of Putative Nitric Oxide Dismutase (Nod) Genes in Contaminated Aquifers and Wastewater Treatment Systems. Appl Environ Microbiol 2017; 83:e02750-16. [PMID: 27986721 PMCID: PMC5288823 DOI: 10.1128/aem.02750-16] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/02/2016] [Indexed: 11/20/2022] Open
Abstract
It has recently been suggested that oxygenic dismutation of NO into N2 and O2 may occur in the anaerobic methanotrophic "Candidatus Methylomirabilis oxyfera" and the alkane-oxidizing gammaproteobacterium HdN1. It may represent a new pathway in microbial nitrogen cycling catalyzed by a putative NO dismutase (Nod). The formed O2 enables microbes to employ aerobic catabolic pathways in anoxic habitats, suggesting an ecophysiological niche space of substantial appeal for bioremediation and water treatment. However, it is still unknown whether this physiology is limited to "Ca Methylomirabilis oxyfera" and HdN1 and whether it can be coupled to the oxidation of electron donors other than alkanes. Here, we report insights into an unexpected diversity and remarkable abundance of nod genes in natural and engineered water systems. Phylogenetically diverse nod genes were recovered from a range of contaminated aquifers and N-removing wastewater treatment systems. Together with nod genes from "Ca Methylomirabilis oxyfera" and HdN1, the novel environmental nod sequences formed no fewer than 6 well-supported phylogenetic clusters, clearly distinct from canonical NO reductase (quinol-dependent NO reductase [qNor] and cytochrome c-dependent NO reductase [cNor]) genes. The abundance of nod genes in the investigated samples ranged from 1.6 × 107 to 5.2 × 1010 copies · g-1 (wet weight) of sediment or sludge biomass, accounting for up to 10% of total bacterial 16S rRNA gene counts. In essence, NO dismutation could be a much more widespread physiology than currently perceived. Understanding the controls of this emergent microbial capacity could offer new routes for nitrogen elimination or pollutant remediation in natural and engineered water systems. IMPORTANCE NO dismutation into N2 and O2 is a novel process catalyzed by putative NO dismutase (Nod). To date, only two bacteria, the anaerobic methane-oxidizing bacterium "Ca Methylomirabilis oxyfera" and the alkane-oxidizing gammaproteobacterium HdN1, are known to harbor nod genes. In this study, we report efficient molecular tools that can detect and quantify a wide diversity of nod genes in environmental samples. A surprisingly high diversity and abundance of nod genes were found in contaminated aquifers as well as wastewater treatment systems. This evidence indicates that NO dismutation may be a much more widespread physiology in natural and man-made environments than currently perceived. The molecular tools presented here will facilitate further studies on these enigmatic microbes in the future.
Collapse
Affiliation(s)
- Baoli Zhu
- Institute of Groundwater Ecology, Helmholtz-Zentrum München, Neuherberg, Germany
| | - Lauren Bradford
- Institute of Groundwater Ecology, Helmholtz-Zentrum München, Neuherberg, Germany
| | - Sichao Huang
- Institute of Groundwater Ecology, Helmholtz-Zentrum München, Neuherberg, Germany
| | - Anna Szalay
- Institute of Groundwater Ecology, Helmholtz-Zentrum München, Neuherberg, Germany
| | - Carmen Leix
- Chair of Urban Water Systems Engineering, Technical University of Munich, Munich, Germany
| | - Max Weissbach
- Chair of Urban Water Systems Engineering, Technical University of Munich, Munich, Germany
| | | | - Jörg E Drewes
- Chair of Urban Water Systems Engineering, Technical University of Munich, Munich, Germany
| | - Tillmann Lueders
- Institute of Groundwater Ecology, Helmholtz-Zentrum München, Neuherberg, Germany
| |
Collapse
|
10
|
Nitric oxide: a novel inducer for enhancement of microbial lipase production. Bioprocess Biosyst Eng 2016; 39:1671-8. [DOI: 10.1007/s00449-016-1642-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 06/14/2016] [Indexed: 10/21/2022]
|
11
|
Investigating the Proton Donor in the NO Reductase from Paracoccus denitrificans. PLoS One 2016; 11:e0152745. [PMID: 27030968 PMCID: PMC4816578 DOI: 10.1371/journal.pone.0152745] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/18/2016] [Indexed: 01/22/2023] Open
Abstract
Variant nomenclature: the variants were made in the NorB subunit if not indicated by the superscript c, which are variants in the NorC subunit (e.g. E122A = exchange of Glu-122 in NorB for an Ala, E71cD; exchange of Glu-71 in NorC for an Asp). Bacterial NO reductases (NORs) are integral membrane proteins from the heme-copper oxidase superfamily. Most heme-copper oxidases are proton-pumping enzymes that reduce O2 as the last step in the respiratory chain. With electrons from cytochrome c, NO reductase (cNOR) from Paracoccus (P.) denitrificans reduces NO to N2O via the following reaction: 2NO+2e-+2H+→N2O+H2O. Although this reaction is as exergonic as O2-reduction, cNOR does not contribute to the electrochemical gradient over the membrane. This means that cNOR does not pump protons and that the protons needed for the reaction are taken from the periplasmic side of the membrane (since the electrons are donated from this side). We previously showed that the P. denitrificans cNOR uses a single defined proton pathway with residues Glu-58 and Lys-54 from the NorC subunit at the entrance. Here we further strengthened the evidence in support of this pathway. Our further aim was to define the continuation of the pathway and the immediate proton donor for the active site. To this end, we investigated the region around the calcium-binding site and both propionates of heme b3 by site directed mutagenesis. Changing single amino acids in these areas often had severe effects on cNOR function, with many variants having a perturbed active site, making detailed analysis of proton transfer properties difficult. Our data does however indicate that the calcium ligation sphere and the region around the heme b3 propionates are important for proton transfer and presumably contain the proton donor. The possible evolutionary link between the area for the immediate donor in cNOR and the proton loading site (PLS) for pumped protons in oxygen-reducing heme-copper oxidases is discussed.
Collapse
|