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Sharma G, Garg N, Hasan S, Saffarini D, Shirodkar S. Fumarate and nitrite reduction by Prevotella nigrescens and Prevotella buccae isolated from Chronic Periodontitis patients. Microb Pathog 2023; 176:106022. [PMID: 36739100 DOI: 10.1016/j.micpath.2023.106022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
OBJECTIVE This study is an investigation of anaerobic nitrite and fumarate reduction/respiration abilities of two characterised Prevotella species namely Prevotella nigrescens (SS6B) and Prevotella buccae (GS6B) isolated from the periodontal pockets of chronic periodontitis (ChP) patients. METHODS Isolation and identification of the periodontal bacteria from 20 patients showing clinical symptoms of ChP. Characterisation of anaerobic nitrite and fumarate reduction was done in P. nigrescens (SS6B) and P. buccae (GS6B) using reduction assays, inhibition assays with use of specific inhibitors, growth assays and enzyme activity assays. Degenerate PCR was used to detect and amplify nitrite reductase (nrfA) and fumarate reductase (frdA) gene sequences in these Prevotella isolates. In addition, molecular and in silico analysis of the amplified anaerobic reductase gene sequences was performed using NCBI conserved domain analysis, Interpro database and MegaX. RESULTS We provided experimental evidence for presence of active nitrite and fumarate reductase activities through enzyme activity, reduction, inhibitor and growth assays. Moreover, we were able to detect presence of 505 bps nrfA gene fragment and 400 bps frdA gene fragment in these Prevotella spp. These fragments show similarity to multiheme ammonia forming cytochrome c nitrite reductases and fumarate reductases flavoprotein subunit, respectively. CONCLUSION Anaerobic nitrite and fumarate respiration abilities in P. nigrescens and P. buccae isolates appear to be important for detoxification process and growth, respectively.
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Affiliation(s)
- Geetika Sharma
- Amity Institute of Biotechnology, Amity University Uttar Pradesh Noida Campus, Noida, 201313, India
| | - Nancy Garg
- Amity Institute of Biotechnology, Amity University Uttar Pradesh Noida Campus, Noida, 201313, India
| | - Shamimul Hasan
- Department of Oral Medicine and Radiology, Faculty of Dentistry, Jamia Millia Islamia, New Delhi, 110025, India
| | - Daad Saffarini
- Department of Biological Sciences, University of Wisconsin Milwaukee, 3209 N. Maryland Ave Milwaukee, WI, 53211, USA
| | - Sheetal Shirodkar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh Noida Campus, Noida, 201313, India.
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Homology modeling and virtual characterization of cytochrome c nitrite reductase (NrfA) in three model bacteria responsible for short-circuit pathway, DNRA in the terrestrial nitrogen cycle. World J Microbiol Biotechnol 2022; 38:168. [DOI: 10.1007/s11274-022-03352-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/04/2022] [Indexed: 11/26/2022]
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Monteiro T, Moreira M, Gaspar SBR, Almeida MG. Bilirubin oxidase as a single enzymatic oxygen scavenger for the development of reductase-based biosensors in the open air and its application on a nitrite biosensor. Biosens Bioelectron 2022; 217:114720. [PMID: 36148736 DOI: 10.1016/j.bios.2022.114720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/09/2022] [Accepted: 09/10/2022] [Indexed: 11/25/2022]
Abstract
The commercialization of amperometric or voltammetric biosensors that operate at potentials lower than -0.2 V vs SHE has been hindered by the need for anoxic working conditions due to the interference of molecular oxygen, whose electrochemical reduction can potentially mask other redox processes and generate reactive oxygen species (ROS). A deoxygenation step must be thus integrated into the analytical process. To this end, several (bio)chemical oxygen scavenging systems have been proposed, such as the bi-enzyme system, glucose oxidase/catalase. Still, a few issues persist owing to enzyme impurities and the formation of oxygen reactive species. Here in, we propose a new mono-enzymatic oxygen scavenging system composed of a multicopper oxidase as a single biocatalytic oxygen reducer. As a model, we used bilirubin oxidase (BOD), which catalyzes the direct reduction of oxygen to water in the presence of an electron donor substrate, without releasing hydrogen peroxide. Both the direct electron transfer and mediated electrochemical approach using different co-substrates were screened for the ability to promote the enzymatic reduction of oxygen. An optimal combination of BOD with sodium ascorbate proved to be quick (5 min) and effective. It was subsequently employed, as a proof-of-concept, in a voltammetric biosensor based on a multiheme cytochrome c nitrite reductase, which performs the reduction of nitrite to ammonia at potentials below -0.3 V vs SHE. The nitrite biosensor performed well under ambient air, with no need for a second enzyme to account for the build-up of oxygen reactive intermediaries.
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Affiliation(s)
- Tiago Monteiro
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry / Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Miguel Moreira
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry / Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Sara B R Gaspar
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry / Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Maria Gabriela Almeida
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry / Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal; Centro de investigação interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz, Campus Universitário, Quinta da Granja, 2829-511, Caparica, Portugal.
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Su Z, Zhang Y, Jia X, Xiang X, Zhou J. Research on enhancement of zero-valent iron on dissimilatory nitrate/nitrite reduction to ammonium of Desulfovibrio sp. CMX. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 746:141126. [PMID: 32750580 DOI: 10.1016/j.scitotenv.2020.141126] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/18/2020] [Accepted: 07/18/2020] [Indexed: 06/11/2023]
Abstract
The process of nitrate dissimilation to ammonium (DNRA) is an important way for storing nitrogen in nature and DNRA is a key step in efficient recovery of nitrogen in wastewater. However, in view of the low conversion efficiency of DNRA, zero-valent iron (ZVI) was used to enhance the DNRA process of Desulfovibrio sp. CMX. ZVI can obviously promote the nitrate/nitrite reduction. The experiment indicated that 5 g/L 300 mesh ZVI could convert 5 mmol/L nitrate or nitrite to ammonium in 48 h or 36 h respectively, and the conversion ratio of NO2- to NH4+ could reach more than 90%. The ZVI provided a suitable growth environment for the Desulfovibrio sp. CMX through chemical reduction of nitrite, production of divalent iron (Fe2+), reduction of oxidation-reduction potential (ORP) and adjustment of pH, which strengthened the DNRA performance. This experiment is advantageous for increasing efficiency of DNRA and provides a new idea for efficient recovery of nitrogen resources.
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Affiliation(s)
- Zhiqiang Su
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, China
| | - Yu Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, China.
| | - Xue Jia
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, China
| | - Xuemin Xiang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, China
| | - Jiti Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, China
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5
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Pan H, Qin Y, Wang Y, Liu S, Yu B, Song Y, Wang X, Zhu G. Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) pathway dominates nitrate reduction processes in rhizosphere and non-rhizosphere of four fertilized farmland soil. ENVIRONMENTAL RESEARCH 2020; 186:109612. [PMID: 32668552 DOI: 10.1016/j.envres.2020.109612] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 04/26/2020] [Accepted: 04/26/2020] [Indexed: 06/11/2023]
Abstract
Nitrate (NO3-) reduction partitioning between denitrification, anaerobic ammonium oxidation (anammox), denitrifying anaerobic methane oxidation (DAMO), and dissimilatory nitrate reduction to ammonium (DNRA), can influence the nitrogen (N) use efficiency and crop production in arid farmland. The microbial structure, function and potential rates of denitrification, anammox, DAMO and DNRA, and their respective contributions to total NO3- reduction were investigated in rhizosphere and non-rhizosphere soil of four typical crops in north China by functional gene amplification, high-throughput sequencing, network analysis and isotopic tracing technique. The measured denitrification and DNRA rate varied from 0.0294 to 20.769 nmol N g-1 h-1and 2.4125-58.682 nmol N g-1 h-1, respectively, based on which DNRA pathway contributed to 84.44 ± 14.40% of dissimilatory NO3- reduction, hence dominated NO3- reduction processes compared to denitrification. Anammox and DAMO were not detected. High-throughput sequencing analysis on DNRA nrfA gene, and denitrification nirS and nirK genes demonstrated that these two processes did not correlate to corresponding gene abundance or dominant genus. RDA and Pearson's correlation analysis illustrated that DNRA rate was significantly correlated with the abundance of Chthiniobacter, as well as total organic matter (TOM); denitrification rate was significantly correlated with the abundance of Lautropia, so did TOM. Network analysis showed that the genus performed DNRA was the key connector in the microbial community of dissimilatory nitrate reducers. This study simultaneously investigated the dissimilatory nitrate reduction processes in rhizosphere and non-rhizosphere soils in arid farmland, highlighting that DNRA dominated NO3- reduction processes against denitrification. As denitrification results in N loss, whereas DNRA contributes to N retention, the relative contributions of DNRA versus denitrification activities should be considered appropriately when assessing N transformation processes and N fertilizer management in arid farmland fields.
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Affiliation(s)
- Huawei Pan
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yu Qin
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuantao Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Shiguang Liu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Bin Yu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiping Song
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Xiaomin Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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Kim H, Park D, Yoon S. pH Control Enables Simultaneous Enhancement of Nitrogen Retention and N 2O Reduction in Shewanella loihica Strain PV-4. Front Microbiol 2017; 8:1820. [PMID: 28979255 PMCID: PMC5611402 DOI: 10.3389/fmicb.2017.01820] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/06/2017] [Indexed: 11/13/2022] Open
Abstract
pH has been recognized as one of the key environmental parameters with significant impacts on the nitrogen cycle in the environment. In this study, the effects of pH on NO3-/NO2- fate and N2O emission were examined with Shewanella loihica strain PV-4, an organism with complete denitrification and respiratory ammonification pathways. Strain PV-4 was incubated at varying pH with lactate as the electron donor and NO3-/NO2- and N2O as the electron acceptors. When incubated with NO3- and N2O at pH 6.0, transient accumulation of N2O was observed and no significant NH4+ production was observed. At pH 7.0 and 8.0, strain PV-4 served as a N2O sink, as N2O concentration decreased consistently without accumulation. Respiratory ammonification was upregulated in the experiments performed at these higher pH values. When NO2- was used in place of NO3-, neither growth nor NO2- reduction was observed at pH 6.0. NH4+ was the exclusive product from NO2- reduction at both pH 7.0 and 8.0 and neither production nor consumption of N2O was observed, suggesting that NO2- regulation superseded pH effects on the nitrogen-oxide dissimilation reactions. When NO3- was the electron acceptor, nirK transcription was significantly upregulated upon cultivation at pH 6.0, while nrfA transcription was significantly upregulated at pH 8.0. The highest level of nosZ transcription was observed at pH 6.0 and the lowest at pH 8.0. With NO2- as the electron acceptor, transcription profiles of nirK, nrfA, and nosZ were statistically indistinguishable between pH 7.0 and 8.0. The transcriptions of nirK and nosZ were severely downregulated regardless of pH. These observations suggested that the kinetic imbalance between N2O production and consumption, but neither decrease in expression nor activity of NosZ, was the major cause of N2O accumulation at pH 6.0. The findings also suggest that simultaneous enhancement of nitrogen retention and N2O emission reduction may be feasible through pH modulation, but only in environments where C:N or NO2-:NO3- ratio does not exhibit overarching control over the NO3-/NO2- reduction pathways.
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Affiliation(s)
- Hayeon Kim
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and TechnologyDaejeon, South Korea
| | - Doyoung Park
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and TechnologyDaejeon, South Korea
| | - Sukhwan Yoon
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and TechnologyDaejeon, South Korea
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A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Adv Microb Physiol 2015. [PMID: 26210106 DOI: 10.1016/bs.ampbs.2015.05.002] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.
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8
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Yoon S, Cruz-García C, Sanford R, Ritalahti KM, Löffler FE. Denitrification versus respiratory ammonification: environmental controls of two competing dissimilatory NO3(-)/NO2(-) reduction pathways in Shewanella loihica strain PV-4. THE ISME JOURNAL 2015; 9:1093-104. [PMID: 25350157 PMCID: PMC4409154 DOI: 10.1038/ismej.2014.201] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Revised: 08/30/2014] [Accepted: 09/05/2014] [Indexed: 11/09/2022]
Abstract
Denitrification and respiratory ammonification are two competing, energy-conserving NO3(-)/NO2(-) reduction pathways that have major biogeochemical consequences for N retention, plant growth and climate. Batch and continuous culture experiments using Shewanella loihica strain PV-4, a bacterium possessing both the denitrification and respiratory ammonification pathways, revealed factors that determine NO3(-)/NO2(-) fate. Denitrification dominated at low carbon-to-nitrogen (C/N) ratios (that is, electron donor-limiting growth conditions), whereas ammonium was the predominant product at high C/N ratios (that is, electron acceptor-limiting growth conditions). pH and temperature also affected NO3(-)/NO2(-) fate, and incubation above pH 7.0 and temperatures of 30 °C favored ammonium formation. Reverse-transcriptase real-time quantitative PCR analyses correlated the phenotypic observations with nirK and nosZ transcript abundances that decreased up to 1600-fold and 27-fold, respectively, under conditions favoring respiratory ammonification. Of the two nrfA genes encoded on the strain PV-4 genome, nrfA0844 transcription decreased only when the chemostat reactor received medium with the lowest C/N ratio of 1.5, whereas nrfA0505 transcription occurred at low levels (≤3.4 × 10(-2) transcripts per cell) under all growth conditions. At intermediate C/N ratios, denitrification and respiratory ammonification occurred concomitantly, and both nrfA0844 (5.5 transcripts per cell) and nirK (0.88 transcripts per cell) were transcribed. Recent findings suggest that organisms with both the denitrification and respiratory ammonification pathways are not uncommon in soil and sediment ecosystems, and strain PV-4 offers a tractable experimental system to explore regulation of dissimilatory NO3(-)/NO2(-) reduction pathways.
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Affiliation(s)
- Sukhwan Yoon
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Claribel Cruz-García
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Robert Sanford
- Department of Geology, University of Illinois, Urbana, IL, USA
| | - Kirsti M Ritalahti
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Frank E Löffler
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA
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9
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da Silva MLB, Soares HM, Furigo A, Schmidell W, Corseuil HX. Effects of Nitrate Injection on Microbial Enhanced Oil Recovery and Oilfield Reservoir Souring. Appl Biochem Biotechnol 2014; 174:1810-21. [DOI: 10.1007/s12010-014-1161-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 08/15/2014] [Indexed: 10/24/2022]
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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
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Welsh A, Chee-Sanford JC, Connor LM, Löffler FE, Sanford RA. Refined NrfA phylogeny improves PCR-based nrfA gene detection. Appl Environ Microbiol 2014; 80:2110-9. [PMID: 24463965 PMCID: PMC3993153 DOI: 10.1128/aem.03443-13] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 01/16/2014] [Indexed: 11/20/2022] Open
Abstract
Dissimilatory nitrate reduction to ammonium (DNRA) and denitrification are contrasting microbial processes in the terrestrial nitrogen (N) cycle, in that the former promotes N retention and the latter leads to N loss (i.e., the formation of gaseous products). The nitrite reductase NrfA catalyzes nitrite reduction to ammonium, the enzyme associated with respiratory nitrite ammonification and the key step in DNRA. Although well studied biochemically, the diversity and phylogeny of this enzyme had not been rigorously analyzed. A phylogenetic analysis of 272 full-length NrfA protein sequences distinguished 18 NrfA clades with robust statistical support (>90% Bayesian posterior probabilities). Three clades possessed a CXXCH motif in the first heme-binding domain, whereas all other clades had a CXXCK motif in this location. The analysis further identified a KXRH or KXQH motif between the third and fourth heme-binding motifs as a conserved and diagnostic feature of all pentaheme NrfA proteins. PCR primers targeting a portion of the heme-binding motifs that flank this diagnostic region yielded the expected 250-bp-long amplicons with template DNA from eight pure cultures and 16 new nrfA-containing isolates. nrfA amplicons obtained with template DNA from two geomorphically distinct agricultural soils could be assigned to one of the 18 NrfA clades, providing support for this expanded classification. The extended NrfA phylogeny revealed novel diagnostic features of DNRA populations and will be useful to assess nitrate/nitrite fate in natural and engineered ecosystems.
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Affiliation(s)
- Allana Welsh
- University of Illinois at Urbana Champaign, Urbana, Illinois, USA
| | - Joanne C. Chee-Sanford
- University of Illinois at Urbana Champaign, Urbana, Illinois, USA
- USDA-ARS, Urbana, Illinois, USA
| | | | - Frank E. Löffler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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Abstract
The global biogeochemical nitrogen cycle is essential for life on Earth. Many of the underlying biotic reactions are catalyzed by a multitude of prokaryotic and eukaryotic life forms whereas others are exclusively carried out by microorganisms. The last century has seen the rise of a dramatic imbalance in the global nitrogen cycle due to human behavior that was mainly caused by the invention of the Haber-Bosch process. Its main product, ammonia, is a chemically reactive and biotically favorable form of bound nitrogen. The anthropogenic supply of reduced nitrogen to the biosphere in the form of ammonia, for example during environmental fertilization, livestock farming, and industrial processes, is mandatory in feeding an increasing world population. In this chapter, environmental ammonia pollution is linked to the activity of microbial metalloenzymes involved in respiratory energy metabolism and bioenergetics. Ammonia-producing multiheme cytochromes c are discussed as paradigm enzymes.
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Affiliation(s)
- Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, D-64287, Darmstadt, Germany,
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13
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Zhao HP, Ilhan ZE, Ontiveros-Valencia A, Tang Y, Rittmann BE, Krajmalnik-Brown R. Effects of multiple electron acceptors on microbial interactions in a hydrogen-based biofilm. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:7396-7403. [PMID: 23721373 DOI: 10.1021/es401310j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
To investigate interactions among multiple electron acceptors in a H2-fed biofilm, we operated a membrane biofilm reactor with H2-delivery capacity sufficient to reduce all acceptors. ClO4(-) and O2 were input electron acceptors in all stages at surface loadings of 0.08 ± 0.006 g/m(2)-d (1.0 ± 0.7 e(-) meq/m(2)-d) for ClO4(-) and 0.51 g/m(2)-d (76 e(-) meq/m(2)-d) for O2. SO4(2-) was added in Stage 2 at 3.77 ± 0.39 g/m(2)-d (331 ± 34 e(-) meq/m(2)-d), and NO3(-) was further added in Stage 3 at 0.72 ± 0.03 g N/m(2)-d (312 ± 13 e(-) meq/m(2)-d). At steady state for each stage, ClO4(-), O2, and NO3(-) (when present in the influent) were completely reduced; measured SO4(2-) reduction decreased from 78 ± 4% in Stage 2 to 59 ± 4% in Stage 3, when NO3(-) was present. While perchlorate-reducing bacteria (PRB), assayed by qPCR targeting the pcrA gene, remained stable throughout, sulfate-reducing bacteria (SRB), assayed by the dsrA gene, increased almost 3 orders of magnitude when significant SO4(2-) reduction occurred in stage 2. The abundance of denitrifying bacteria (DB), assayed by the nirK and nirS genes, increased in Stage 3, while SRB remained at high numbers, but did not increase. Based on pyrosequencing analyses, β-Proteobacteria dominated in Stage 1, but ε-Proteobacteria became more important in Stages 2 and 3, when the input of multiple electron acceptors favored genera with broader electron-accepting capabilities. Sulfuricurvum (a sulfur oxidizer and NO3(-) reducer) and Desulfovibrio (a SO4(2-) reducer) become dominant in Stage 3, suggesting redox cycling of sulfur in the biofilm.
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Affiliation(s)
- He-Ping Zhao
- Swette Center for Environmental Biotechnology, Biodesign Institute at Arizona State University, P.O. Box 875701, Tempe, Arizona 85287-5701, United States
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Tikhonova TV, Trofimov AA, Popov VO. Octaheme nitrite reductases: Structure and properties. BIOCHEMISTRY (MOSCOW) 2012; 77:1129-38. [DOI: 10.1134/s0006297912100057] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Tikhonova T, Tikhonov A, Trofimov A, Polyakov K, Boyko K, Cherkashin E, Rakitina T, Sorokin D, Popov V. Comparative structural and functional analysis of two octaheme nitrite reductases from closely relatedThioalkalivibriospecies. FEBS J 2012; 279:4052-61. [DOI: 10.1111/j.1742-4658.2012.08811.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tamara Tikhonova
- Bach Institute of Biochemistry; Russian Academy of Sciences, Leninskii pr. 33; Moscow 119071; Russia
| | - Alexey Tikhonov
- Bach Institute of Biochemistry; Russian Academy of Sciences, Leninskii pr. 33; Moscow 119071; Russia
| | | | | | | | - Eugene Cherkashin
- National Research Centre ‘Kurchatov Institute’, Academic Kurchatov sq. 1; Moscow 123182; Russia
| | - Tatiana Rakitina
- National Research Centre ‘Kurchatov Institute’, Academic Kurchatov sq. 1; Moscow 123182; Russia
| | - Dmitry Sorokin
- Winogradsky Institute of Microbiology; Russian Academy of Sciences, Leninskii pr. 32a; Moscow 119991; Russia
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Rycovska A, Hatahet L, Fendler K, Michel H. The nitrite transport protein NirC from Salmonella typhimurium is a nitrite/proton antiporter. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:1342-50. [DOI: 10.1016/j.bbamem.2012.02.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 02/01/2012] [Accepted: 02/06/2012] [Indexed: 12/31/2022]
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Abstract
Dissimilatory sulfate and sulfur reduction evolved billions of years ago and while the bacteria and archaea that use this unique metabolism employ a variety of electron donors, H(2) is most commonly used as the energy source. These prokaryotes use multiheme c-type proteins to shuttle electrons from electron donors, and electron transport complexes presumed to contain b-type hemoproteins contribute to proton charging of the membrane. Numerous sulfate and sulfur reducers use an alternate pathway for heme synthesis and, frequently, uniquely specific axial ligands are used to secure c-type heme to the protein. This review presents some of the types and functional activities of hemoproteins involved in these two dissimilatory reduction pathways.
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18
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Kraft B, Strous M, Tegetmeyer HE. Microbial nitrate respiration – Genes, enzymes and environmental distribution. J Biotechnol 2011; 155:104-17. [DOI: 10.1016/j.jbiotec.2010.12.025] [Citation(s) in RCA: 223] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 12/07/2010] [Accepted: 12/20/2010] [Indexed: 01/13/2023]
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19
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Mota CS, Rivas MG, Brondino CD, Moura I, Moura JJG, González PJ, Cerqueira NMFSA. The mechanism of formate oxidation by metal-dependent formate dehydrogenases. J Biol Inorg Chem 2011; 16:1255-68. [DOI: 10.1007/s00775-011-0813-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Accepted: 06/20/2011] [Indexed: 10/18/2022]
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20
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Soils contaminated with explosives: Environmental fate and evaluation of state-of-the-art remediation processes (IUPAC Technical Report). PURE APPL CHEM 2011. [DOI: 10.1351/pac-rep-10-01-05] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
An explosion occurs when a large amount of energy is suddenly released. This energy may come from an over-pressurized steam boiler, from the products of a chemical reaction involving explosive materials, or from a nuclear reaction that is uncontrolled. In order for an explosion to occur, there must be a local accumulation of energy at the site of the explosion, which is suddenly released. This release of energy can be dissipated as blast waves, propulsion of debris, or by the emission of thermal and ionizing radiation. Modern explosives or energetic materials are nitrogen-containing organic compounds with the potential for self-oxidation to small gaseous molecules (N2, H2O, and CO2). Explosives are classified as primary or secondary based on their susceptibility of initiation. Primary explosives are highly susceptible to initiation and are often used to ignite secondary explosives, such as TNT (2,4,6-trinitrotoluene), RDX (1,3,5-trinitroperhydro-1,3,5-triazine), HMX (1,3,5,7-tetranitro-1,3,5,7-tetrazocane), and tetryl (N-methyl-N-2,4,6-tetranitro-aniline).
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21
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Tikhonova TV, Slutskaya ES, Filimonenkov AA, Boyko KM, Kleimenov SY, Konarev PV, Polyakov KM, Svergun DI, Trofimov AA, Khomenkov VG, Zvyagilskaya RA, Popov VO. Isolation and oligomeric composition of cytochrome c nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens. BIOCHEMISTRY (MOSCOW) 2011; 73:164-70. [DOI: 10.1134/s0006297908020077] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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22
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Einsle O. Structure and Function of Formate-Dependent Cytochrome c Nitrite Reductase, NrfA. Methods Enzymol 2011; 496:399-422. [DOI: 10.1016/b978-0-12-386489-5.00016-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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23
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Measuring the cytochrome C nitrite reductase activity-practical considerations on the enzyme assays. Bioinorg Chem Appl 2010. [PMID: 20689707 PMCID: PMC2905729 DOI: 10.1155/2010/634597] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2010] [Accepted: 05/03/2010] [Indexed: 11/20/2022] Open
Abstract
The cytochrome c nitrite reductase (ccNiR) from Desulfovibrio desulfuricans ATCC 27774 is
able to reduce nitrite to ammonia in a six-electron transfer reaction. Although extensively
characterized from the spectroscopic and structural points-of-view, some of its kinetic aspects
are still under explored. In this work the kinetic behaviour of ccNiR has been evaluated in a
systematic manner using two different spectrophotometric assays carried out in the presence of
different redox mediators and a direct electrochemical approach. Solution assays have proved
that the specific activity of ccNiR decreases with the reduction potential of the electronic carriers
and ammonium is always the main product of nitrite reduction. The catalytic parameters were
discussed on the basis of the mediator reducing power and also taking into account the location
of their putative docking sites with ccNiR. Due to the fast kinetics of ccNiR, electron delivering
from reduced electron donors is rate-limiting in all spectrophotometric assays, so the estimated
kinetic constants are apparent only. Nevertheless, this limitation could be overcome by using a
direct electrochemical approach which shows that the binding affinity for nitrite decreases whilst
turnover increases with the reductive driving force.
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24
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Moura I, Pauleta SR, Moura JJG. Enzymatic activity mastered by altering metal coordination spheres. J Biol Inorg Chem 2008; 13:1185-95. [PMID: 18719950 DOI: 10.1007/s00775-008-0414-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2008] [Accepted: 08/01/2008] [Indexed: 11/24/2022]
Abstract
Metalloenzymes control enzymatic activity by changing the characteristics of the metal centers where catalysis takes place. The conversion between inactive and active states can be tuned by altering the coordination number of the metal site, and in some cases by an associated conformational change. These processes will be illustrated using heme proteins (cytochrome c nitrite reductase, cytochrome c peroxidase and cytochrome cd1 nitrite reductase), non-heme proteins (superoxide reductase and [NiFe]-hydrogenase), and copper proteins (nitrite and nitrous oxide reductases) as examples. These examples catalyze electron transfer reactions that include atom transfer, abstraction and insertion.
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Affiliation(s)
- Isabel Moura
- REQUIMTE, Centro de Química Fina e Biotecnologia, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.
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25
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Zhao JS, Manno D, Hawari J. Regulation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) metabolism in Shewanella halifaxensis HAW-EB4 by terminal electron acceptor and involvement of c-type cytochrome. Microbiology (Reading) 2008; 154:1026-1037. [DOI: 10.1099/mic.0.2007/013409-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jian-Shen Zhao
- Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Ave., Montreal, Quebec H4P 2R2, Canada
| | - Dominic Manno
- Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Ave., Montreal, Quebec H4P 2R2, Canada
| | - Jalal Hawari
- Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Ave., Montreal, Quebec H4P 2R2, Canada
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26
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Najmudin S, González PJ, Trincão J, Coelho C, Mukhopadhyay A, Cerqueira NMFSA, Romão CC, Moura I, Moura JJG, Brondino CD, Romão MJ. Periplasmic nitrate reductase revisited: a sulfur atom completes the sixth coordination of the catalytic molybdenum. J Biol Inorg Chem 2008; 13:737-53. [PMID: 18327621 DOI: 10.1007/s00775-008-0359-6] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Accepted: 02/21/2008] [Indexed: 11/30/2022]
Abstract
Nitrate reductase from Desulfovibrio desulfuricans ATCC 27774 (DdNapA) is a monomeric protein of 80 kDa harboring a bis(molybdopterin guanine dinucleotide) active site and a [4Fe-4S] cluster. Previous electron paramagnetic resonance (EPR) studies in both catalytic and inhibiting conditions showed that the molybdenum center has high coordination flexibility when reacted with reducing agents, substrates or inhibitors. As-prepared DdNapA samples, as well as those reacted with substrates and inhibitors, were crystallized and the corresponding structures were solved at resolutions ranging from 1.99 to 2.45 A. The good quality of the diffraction data allowed us to perform a detailed structural study of the active site and, on that basis, the sixth molybdenum ligand, originally proposed to be an OH/OH(2) ligand, was assigned as a sulfur atom after refinement and analysis of the B factors of all the structures. This unexpected result was confirmed by a single-wavelength anomalous diffraction experiment below the iron edge (lambda = 1.77 A) of the as-purified enzyme. Furthermore, for six of the seven datasets, the S-S distance between the sulfur ligand and the Sgamma atom of the molybdenum ligand Cys(A140) was substantially shorter than the van der Waals contact distance and varies between 2.2 and 2.85 A, indicating a partial disulfide bond. Preliminary EPR studies under catalytic conditions showed an EPR signal designated as a turnover signal (g values 1.999, 1.990, 1.982) showing hyperfine structure originating from a nucleus of unknown nature. Spectropotentiometric studies show that reduced methyl viologen, the electron donor used in the catalytic reaction, does not interact directly with the redox cofactors. The turnover signal can be obtained only in the presence of the reaction substrates. With use of the optimized conditions determined by spectropotentiometric titration, the turnover signal was developed with (15)N-labeled nitrate and in D(2)O-exchanged DdNapA samples. These studies indicate that this signal is not associated with a Mo(V)-nitrate adduct and that the hyperfine structure originates from two equivalent solvent-exchangeable protons. The new coordination sphere of molybdenum proposed on the basis of our studies led us to revise the currently accepted reaction mechanism for periplasmic nitrate reductases. Proposals for a new mechanism are discussed taking into account a molybdenum and ligand-based redox chemistry, rather than the currently accepted redox chemistry based solely on the molybdenum atom.
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Affiliation(s)
- Shabir Najmudin
- Departamento de Química, FCT-UNL, REQUIMTE/CQFB, Monte de Caparica, 2829-516, Almada, Portugal.
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27
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Gavel OY, Bursakov SA, Di Rocco G, Trincão J, Pickering IJ, George GN, Calvete JJ, Shnyrov VL, Brondino CD, Pereira AS, Lampreia J, Tavares P, Moura JJG, Moura I. A new type of metal-binding site in cobalt- and zinc-containing adenylate kinases isolated from sulfate-reducers Desulfovibrio gigas and Desulfovibrio desulfuricans ATCC 27774. J Inorg Biochem 2008; 102:1380-95. [PMID: 18328566 DOI: 10.1016/j.jinorgbio.2008.01.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Revised: 01/13/2008] [Accepted: 01/18/2008] [Indexed: 11/28/2022]
Abstract
Adenylate kinase (AK) mediates the reversible transfer of phosphate groups between the adenylate nucleotides and contributes to the maintenance of their constant cellular level, necessary for energy metabolism and nucleic acid synthesis. The AK were purified from crude extracts of two sulfate-reducing bacteria (SRB), Desulfovibrio (D.) gigas NCIB 9332 and Desulfovibrio desulfuricans ATCC 27774, and biochemically and spectroscopically characterised in the native and fully cobalt- or zinc-substituted forms. These are the first reported adenylate kinases that bind either zinc or cobalt and are related to the subgroup of metal-containing AK found, in most cases, in Gram-positive bacteria. The electronic absorption spectrum is consistent with tetrahedral coordinated cobalt, predominantly via sulfur ligands, and is supported by EPR. The involvement of three cysteines in cobalt or zinc coordination was confirmed by chemical methods. Extended X-ray absorption fine structure (EXAFS) indicate that cobalt or zinc are bound by three cysteine residues and one histidine in the metal-binding site of the "LID" domain. The sequence 129Cys-X5-His-X15-Cys-X2-Cys of the AK from D. gigas is involved in metal coordination and represents a new type of binding motif that differs from other known zinc-binding sites of AK. Cobalt and zinc play a structural role in stabilizing the LID domain.
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Affiliation(s)
- Olga Yu Gavel
- REQUIMTE, Departamento de Química, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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28
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Chen H, Mousty C, Cosnier S, Silveira C, Moura J, Almeida M. Highly sensitive nitrite biosensor based on the electrical wiring of nitrite reductase by [ZnCr-AQS] LDH. Electrochem commun 2007. [DOI: 10.1016/j.elecom.2007.05.030] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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29
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Rial-Otero R, Carreira RJ, Cordeiro FM, Moro AJ, Santos HM, Vale G, Moura I, Capelo JL. Ultrasonic assisted protein enzymatic digestion for fast protein identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Chromatogr A 2007; 1166:101-7. [PMID: 17719595 DOI: 10.1016/j.chroma.2007.08.013] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Revised: 08/01/2007] [Accepted: 08/02/2007] [Indexed: 11/18/2022]
Abstract
Two different ultrasonic energy sources, the sonoreactor and the ultrasonic probe, are compared for enzymatic digestion of proteins for protein identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) using the peptide mass fingerprint (PMF) procedure. Variables such as (i) trypsin/protein ratio; (ii) sonication time; (iii) ultrasound amplitude; and (iv) protein concentration are studied and compared. As a general rule, the trypsin/protein ratio and the minimum protein concentration successfully digested are similar with both ultrasonic energy sources. Results showed that the time needed to digest proteins was shorter with the ultrasonic probe, 60s versus 120s, for the same amplitude of sonication, 50%. However, lower standard deviations and cleaner MALDI-TOF-MS spectra were obtained with the sonoreactor. In addition, the sonoreactor device provided higher sample throughput (6 samples for the sonoreactor versus 1 sample for the ultrasonic probe) and easier sample handling for lower sample volumes (25 microl). Finally, a comparison of both methodologies for the specific identification of the adenylylsulphate reductase alfa subunit from a complex protein mixture from Desulfovibrio desulfuricans ATCC 27774 was done as a proof of the procedure.
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Affiliation(s)
- R Rial-Otero
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829-516 Monte de Caparica, Portugal
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30
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Carreira RJ, Cordeiro FM, Moro AJ, Rivas MG, Rial-Otero R, Gaspar EM, Moura I, Capelo JL. New findings for in-gel digestion accelerated by high-intensity focused ultrasound for protein identification by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. J Chromatogr A 2007; 1153:291-9. [PMID: 17034802 DOI: 10.1016/j.chroma.2006.09.078] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2006] [Revised: 09/04/2006] [Accepted: 09/20/2006] [Indexed: 11/18/2022]
Abstract
New findings in sample treatment based on high-intensity focused ultrasound (HIFU) for protein digestion after polyacrylamide gel electrophoresis separation are presented. The following variables were studied: (i) sample volume; (ii) sonotrode diameter; (iii) previous protein denaturation; (iv) cooling; (v) enzyme concentration; and (vi) protein concentration. Results showed that positive protein identification could be done after protein separation by gel electrophoresis through peptide mass fingerprint (PMF) in a volume as low as 25 microL. The time needed was less than 2 min and no cooling was necessary. The importance of the sonotrode diameter was negligible. On the other hand, protein denaturation before sonication was a trade-off for the success of procedure here described. The protein coverage was raised from 5 to 30%, and the number of peptides matching the proteins was also increased in a percentage ranging 10-100% when the classical overnight treatment is compared with the proposed HIFU procedure. The minimum amount of protein that can be identified using the HIFU sample treatment by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) was 0.06 microg. The lower concentration of trypsin successfully used to obtain an adequate protein digestion was 3.6 microg/mL.
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Affiliation(s)
- R J Carreira
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829-516 Monte de Caparica, Portugal
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31
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32
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Lobo SAL, Melo AMP, Carita JN, Teixeira M, Saraiva LM. The anaerobeDesulfovibrio desulfuricansATCC 27774 grows at nearly atmospheric oxygen levels. FEBS Lett 2007; 581:433-6. [PMID: 17239374 DOI: 10.1016/j.febslet.2006.12.053] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Revised: 12/19/2006] [Accepted: 12/22/2006] [Indexed: 11/19/2022]
Abstract
Sulfate reducing bacteria of the Desulfovibrio genus are considered anaerobes, in spite of the fact that they are frequently isolated close to oxic habitats. However, until now, growth in the presence of high concentrations of oxygen was not reported for members of this genus. This work shows for the first time that the sulfate reducing bacterium Desulfovibrio desulfuricans ATCC 27774 is able to grow in the presence of nearly atmospheric oxygen levels. In addition, the activity and expression profile of several key enzymes was analyzed under different oxygen concentrations.
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Affiliation(s)
- Susana A L Lobo
- Instituto de Tecnologia Quimica e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
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33
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Cordeiro FM, Carreira RJ, Rial-Otero R, Rivas MG, Moura I, Capelo JL. Simplifying sample handling for protein identification by peptide mass fingerprint using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:3269-78. [PMID: 17879394 DOI: 10.1002/rcm.3214] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
An ultrasonic bath, an ultrasonic probe and a sonoreactor were used to speed up the kinetics of the reactions involved in each step of the sample handling for in-gel protein identification by peptide mass fingerprint, PMF, using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The following steps were successfully accelerated using ultrasonic energy: gel washing, protein reduction, and protein alkylation. As a result, a reduction comprising 80% to 90% of the total time involved in the classic approach was achieved. In addition the sample handling was also drastically simplified. The number of peptides identified and the protein sequence coverage obtained for the new procedure were comparable to those obtained with the traditional sample treatment for the following protein standards: glycogen phosphorylase b, BSA, ovalbumin, carbonic anhydrase, trypsin inhibitor and alpha-lactalbumin. Finally, as a proof of the procedure, specific proteins were identified from complex protein mixtures obtained from three different sulphate-reducing bacteria: Desulfovibrio desulfuricans G20, Desulfuvibrio gigas NCIB 9332, and Desulfuvibrio desulfuricans ATCC 27774.
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Affiliation(s)
- Francisco M Cordeiro
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Monte de Caparica, Portugal
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34
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López-Cortés A, Fardeau ML, Fauque G, Joulian C, Ollivier B. Reclassification of the sulfate- and nitrate-reducing bacterium Desulfovibrio vulgaris subsp. oxamicus as Desulfovibrio oxamicus sp. nov., comb. nov. Int J Syst Evol Microbiol 2006; 56:1495-1499. [PMID: 16825618 DOI: 10.1099/ijs.0.64074-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Desulfovibrio vulgaris subsp. oxamicus (type strain, DSM 1925(T)) was found to use nitrate as a terminal electron acceptor, the latter being reduced to ammonium. Phylogenetic studies indicated that strain DSM 1925(T) was distantly related to the type strain of Desulfovibrio vulgaris (95.4 % similarity of the small-subunit rRNA gene) and had as its closest phylogenetic relatives two other nitrate- and sulfate-reducing bacteria, namely Desulfovibrio termitidis (99.4 % similarity) and Desulfovibrio longreachensis (98.4 % similarity). Additional experiments were conducted to characterize better strain DSM 1925(T). This strain incompletely oxidized lactate and ethanol to acetate. It also oxidized butanol, pyruvate and citrate, but not glucose, fructose, acetate, propionate, butyrate, methanol, glycerol or peptone. The optimum temperature for growth was 37 degrees C (range 16-50 degrees C) and the optimum NaCl concentration for growth was 0.1 % (range 0-5 %). Because of significant genotypic and phenotypic differences from Desulfovibrio termitidis and Desulfovibrio longreachensis, reclassification of Desulfovibrio vulgaris subsp. oxamicus as Desulfovibrio oxamicus sp. nov., comb. nov., is proposed. The type strain is strain Monticello 2(T) (=DSM 1925(T)=NCIMB 9442(T)=ATCC 33405(T)).
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MESH Headings
- Carbohydrate Metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Desulfovibrio/classification
- Desulfovibrio/genetics
- Desulfovibrio/metabolism
- Desulfovibrio/physiology
- Desulfovibrio vulgaris/classification
- Desulfovibrio vulgaris/genetics
- Desulfovibrio vulgaris/metabolism
- Desulfovibrio vulgaris/physiology
- Genes, rRNA/genetics
- Growth Inhibitors/pharmacology
- Molecular Sequence Data
- Nitrates/metabolism
- Oxidation-Reduction
- Peptones/metabolism
- Phylogeny
- Quaternary Ammonium Compounds/metabolism
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Sodium Chloride/pharmacology
- Sulfates/metabolism
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Affiliation(s)
- Alejandro López-Cortés
- Laboratorio de Ecología Microbiana Molecular, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Mar Bermejo 195, Playa Palo Santa Rita, La Paz, Baja California Sur, 23090, Mexico
| | - Marie-Laure Fardeau
- Laboratoire de Microbiologie IRD, Universités de Provence et de la Méditerranée, 163 avenue de Luminy, ESIL-GBMA, Case 925, 13288 Marseille Cedex 9, France
| | - Guy Fauque
- Laboratoire de Microbiologie, Géochimie et Ecologie Marines, UMR CNRS 6117, Campus de Luminy, Case 901, 13288 Marseille Cedex 9, France
- Laboratoire de Microbiologie IRD, Universités de Provence et de la Méditerranée, 163 avenue de Luminy, ESIL-GBMA, Case 925, 13288 Marseille Cedex 9, France
| | - Catherine Joulian
- BRGM, Environment and Process Division, Biotechnology Unit, 2, avenue Claude Guillemin, 45060 Orléans Cedex 2, France
| | - Bernard Ollivier
- Laboratoire de Microbiologie IRD, Universités de Provence et de la Méditerranée, 163 avenue de Luminy, ESIL-GBMA, Case 925, 13288 Marseille Cedex 9, France
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35
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González PJ, Rivas MG, Brondino CD, Bursakov SA, Moura I, Moura JJG. EPR and redox properties of periplasmic nitrate reductase from Desulfovibrio desulfuricans ATCC 27774. J Biol Inorg Chem 2006; 11:609-16. [PMID: 16791644 DOI: 10.1007/s00775-006-0110-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2006] [Accepted: 04/13/2006] [Indexed: 11/30/2022]
Abstract
Nitrate reductases are enzymes that catalyze the conversion of nitrate to nitrite. We report here electron paramagnetic resonance (EPR) studies in the periplasmic nitrate reductase isolated from the sulfate-reducing bacteria Desulfovibrio desulfuricans ATCC 27774. This protein, belonging to the dimethyl sulfoxide reductase family of mononuclear Mo-containing enzymes, comprises a single 80-kDa subunit and contains a Mo bis(molybdopterin guanosine dinucleotide) cofactor and a [4Fe-4S] cluster. EPR-monitored redox titrations, carried out with and without nitrate in the potential range from 200 to -500 mV, and EPR studies of the enzyme, in both catalytic and inhibited conditions, reveal distinct types of Mo(V) EPR-active species, which indicates that the Mo site presents high coordination flexibility. These studies show that nitrate modulates the redox properties of the Mo active site, but not those of the [4Fe-4S] center. The possible structures and the role in catalysis of the distinct Mo(V) species detected by EPR are discussed.
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Affiliation(s)
- Pablo J González
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
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Tikhonova TV, Slutsky A, Antipov AN, Boyko KM, Polyakov KM, Sorokin DY, Zvyagilskaya RA, Popov VO. Molecular and catalytic properties of a novel cytochrome c nitrite reductase from nitrate-reducing haloalkaliphilic sulfur-oxidizing bacterium Thioalkalivibrio nitratireducens. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:715-23. [PMID: 16500161 DOI: 10.1016/j.bbapap.2005.12.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2005] [Revised: 12/26/2005] [Accepted: 12/28/2005] [Indexed: 10/25/2022]
Abstract
A highly active cytochrome c nitrite reductase from the haloalkaliphilic sulfur-oxidizing non-ammonifying bacterium Tv. nitratireducens strain ALEN 2 (TvNiR) was isolated and purified to apparent electrophoretic homogeneity. The enzyme catalyzes reductive conversion of nitrite and hydroxylamine to ammonia without release of any intermediates, as well as reduction of sulfite to sulfide. TvNiR also possesses peroxidase activity. In solution TvNiR exists as a stable hexamer with molecular mass of about 360kDa. Each TvNiR subunit with molecular mass of 64kDa contains, as defined from spectral properties and sequence analysis, eight c-type haems. Seven of them are coordinated by the characteristic CXXCH motifs for haem c binding, while one is bonded by the unique CXXCK motif. So far, this motif coordinating the catalytic haem was found only in bacterial cytochrome c nitrite reductases (ccNiRs). All the residues essential for catalysis in the known ccNiRs were also identified in TvNiR. However, TvNiR is only distantly related to known bacterial ammonifying dissimilatory ccNiRs, sharing no more than 20% homology.
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Spectroscopic characterization of a novel 2×[4Fe–4S] ferredoxin isolated from Desulfovibrio desulfuricans ATCC 27774. Inorganica Chim Acta 2003. [DOI: 10.1016/s0020-1693(03)00472-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Almeida MG, Macieira S, Gonçalves LL, Huber R, Cunha CA, Romão MJ, Costa C, Lampreia J, Moura JJG, Moura I. The isolation and characterization of cytochromecnitrite reductase subunits (NrfA and NrfH) fromDesulfovibrio desulfuricansATCC 27774. ACTA ACUST UNITED AC 2003; 270:3904-15. [PMID: 14511372 DOI: 10.1046/j.1432-1033.2003.03772.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The cytochrome c nitrite reductase is isolated from the membranes of the sulfate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774 as a heterooligomeric complex composed by two subunits (61 kDa and 19 kDa) containing c-type hemes, encoded by the genes nrfA and nrfH, respectively. The extracted complex has in average a 2NrfA:1NrfH composition. The separation of ccNiR subunits from one another is accomplished by gel filtration chromatography in the presence of SDS. The amino-acid sequence and biochemical subunits characterization show that NrfA contains five hemes and NrfH four hemes. These considerations enabled the revision of a vast amount of existing spectroscopic data on the NrfHA complex that was not originally well interpreted due to the lack of knowledge on the heme content and the oligomeric enzyme status. Based on EPR and Mössbauer parameters and their correlation to structural information recently obtained from X-ray crystallography on the NrfA structure [Cunha, C.A., Macieira, S., Dias, J.M., Almeida, M.G., Gonçalves, L.M.L., Costa, C., Lampreia, J., Huber, R., Moura, J.J.G., Moura, I. & Romão, M. (2003) J. Biol. Chem. 278, 17455-17465], we propose the full assignment of midpoint reduction potentials values to the individual hemes. NrfA contains the high-spin catalytic site (-80 mV) as well as a quite unusual high reduction potential (+150 mV)/low-spin bis-His coordinated heme, considered to be the site where electrons enter. In addition, the reassessment of the spectroscopic data allowed the first partial spectroscopic characterization of the NrfH subunit. The four NrfH hemes are all in a low-spin state (S = 1/2). One of them has a gmax at 3.55, characteristic of bis-histidinyl iron ligands in a noncoplanar arrangement, and has a positive reduction potential.
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Affiliation(s)
- Maria Gabriela Almeida
- REQUIMTE, CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Portugal
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Pires RH, Lourenço AI, Morais F, Teixeira M, Xavier AV, Saraiva LM, Pereira IAC. A novel membrane-bound respiratory complex from Desulfovibrio desulfuricans ATCC 27774. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1605:67-82. [PMID: 12907302 DOI: 10.1016/s0005-2728(03)00065-3] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In the anaerobic respiration of sulfate, performed by sulfate-reducing prokaryotes, reduction of the terminal electron acceptor takes place in the cytoplasm. The membrane-associated electron transport chain that feeds electrons to the cytoplasmic reductases is still very poorly characterized. In this study we report the isolation and characterization of a novel membrane-bound redox complex from Desulfovibrio desulfuricans ATCC 27774. This complex is formed by three subunits, and contains two hemes b, two FAD groups and several iron-sulfur centers. The two hemes b are low-spin, with macroscopic redox potentials of +75 and -20 mV at pH 7.6. Both hemes are reduced by menadiol, a menaquinone analogue, indicating a function for this complex in the respiratory electron-transport chain. EPR studies of the as-isolated and dithionite-reduced complex support the presence of a [3Fe-4S](1+/0) center and at least four [4Fe-4S](2+/1+) centers. Cloning of the genes coding for the complex subunits revealed that they form a putative transcription unit and have homology to subunits of heterodisulfide reductases (Hdr). The first and second genes code for soluble proteins that have homology to HdrA, whereas the third gene codes for a novel type of membrane-associated protein that contains both a hydrophobic domain with homology to the heme b protein HdrE and a hydrophilic domain with homology to the iron-sulfur protein HdrC. Homologous operons are found in the genomes of other sulfate-reducing organisms and in the genome of the green-sulfur bacterium Chlorobium tepidum TLS. The isolated complex is the first example of a new family of respiratory complexes present in anaerobic prokaryotes.
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Affiliation(s)
- Ricardo H Pires
- Instituto de Tecnologia Qui;mica e Biológica, Universidade Nova de Lisboa, R. da Quinta Grande 6, Oeiras 2780-156, Portugal
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40
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Greene EA, Hubert C, Nemati M, Jenneman GE, Voordouw G. Nitrite reductase activity of sulphate-reducing bacteria prevents their inhibition by nitrate-reducing, sulphide-oxidizing bacteria. Environ Microbiol 2003; 5:607-17. [PMID: 12823193 DOI: 10.1046/j.1462-2920.2003.00446.x] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Sulphate-reducing bacteria (SRB) can be inhibited by nitrate-reducing, sulphide-oxidizing bacteria (NR-SOB), despite the fact that these two groups are interdependent in many anaerobic environments. Practical applications of this inhibition include the reduction of sulphide concentrations in oil fields by nitrate injection. The NR-SOB Thiomicrospira sp. strain CVO was found to oxidize up to 15 mM sulphide, considerably more than three other NR-SOB strains that were tested. Sulphide oxidation increased the environmental redox potential (Eh) from -400 to +100 mV and gave 0.6 nitrite per nitrate reduced. Within the genus Desulfovibrio, strains Lac3 and Lac6 were inhibited by strain CVO and nitrate for the duration of the experiment, whereas inhibition of strains Lac15 and D. vulgaris Hildenborough was transient. The latter had very high nitrite reductase (Nrf) activity. Southern blotting with D. vulgaris nrf genes as a probe indicated the absence of homologous nrf genes from strains Lac3 and Lac6 and their presence in strain Lac15. With respect to SRB from other genera, inhibition of the known nitrite reducer Desulfobulbus propionicus by strain CVO and nitrate was transient, whereas inhibition of Desulfobacterium autotrophicum and Desulfobacter postgatei was long-lasting. The results indicate that inhibition of SRB by NR-SOB is caused by nitrite production. Nrf-containing SRB can overcome this inhibition by further reducing nitrite to ammonia, preventing a stalling of the favourable metabolic interactions between these two bacterial groups. Nrf, which is widely distributed in SRB, can thus be regarded as a resistance factor that prevents the inhibition of dissimilatory sulphate reduction by nitrite.
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Affiliation(s)
- E A Greene
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta, Canada, T2N 1N4
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41
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Cunha CA, Macieira S, Dias JM, Almeida G, Goncalves LL, Costa C, Lampreia J, Huber R, Moura JJG, Moura I, Romão MJ. Cytochrome c nitrite reductase from Desulfovibrio desulfuricans ATCC 27774. The relevance of the two calcium sites in the structure of the catalytic subunit (NrfA). J Biol Chem 2003; 278:17455-65. [PMID: 12618432 DOI: 10.1074/jbc.m211777200] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The gene encoding cytochrome c nitrite reductase (NrfA) from Desulfovibrio desulfuricans ATCC 27774 was sequenced and the crystal structure of the enzyme was determined to 2.3-A resolution. In comparison with homologous structures, it presents structural differences mainly located at the regions surrounding the putative substrate inlet and product outlet, and includes a well defined second calcium site with octahedral geometry, coordinated to propionates of hemes 3 and 4, and caged by a loop non-existent in the previous structures. The highly negative electrostatic potential in the environment around hemes 3 and 4 suggests that the main role of this calcium ion may not be electrostatic but structural, namely in the stabilization of the conformation of the additional loop that cages it and influences the solvent accessibility of heme 4. The NrfA active site is similar to that of peroxidases with a nearby calcium site at the heme distal side nearly in the same location as occurs in the class II and class III peroxidases. This fact suggests that the calcium ion at the distal side of the active site in the NrfA enzymes may have a similar physiological role to that reported for the peroxidases.
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Affiliation(s)
- Carlos A Cunha
- Departamento de Quimica, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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42
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Abreu IA, Lourenço AI, Xavier AV, LeGall J, Coelho AV, Matias PM, Pinto DM, Arménia Carrondo M, Teixeira M, Saraiva LM. A novel iron centre in the split-Soret cytochrome c from Desulfovibrio desulfuricans ATCC 27774. J Biol Inorg Chem 2003; 8:360-70. [PMID: 12589573 DOI: 10.1007/s00775-002-0426-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2002] [Accepted: 10/28/2002] [Indexed: 11/28/2022]
Abstract
The facultative sulfate/nitrate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774 harbours a split-Soret cytochrome c. This cytochrome is a homodimeric protein, having two bis-histidinyl c-type haems per monomer. It has an unique architecture at the haem domain: each haem has one of the coordinating histidines provided by the other monomer, and in each monomer the haems are parallel to each other, almost in van der Waals contact. This work reports the cloning and sequencing of the gene encoding for this cytochrome and shows, by transcriptional analysis, that it is more expressed in nitrate-grown cells than in sulfate-grown ones. In addition, the gene-deduced amino acid sequence revealed two new cysteine residues that could be involved in the binding of a non-haem iron centre. Indeed, the presence of a novel type of an iron-sulfur centre (possibly of the [2Fe-2S] type) was demonstrated by EPR spectroscopy, and putative models for its localization and structure in the cytochrome molecule are proposed on the basis of the so-far-known 3D crystallographic structure of the aerobically purified split-Soret cytochrome, which lacks this centre.
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Affiliation(s)
- Isabel A Abreu
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
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43
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Senko JM, Istok JD, Suflita JM, Krumholz LR. In-situ evidence for uranium immobilization and remobilization. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2002; 36:1491-1496. [PMID: 11999056 DOI: 10.1021/es011240x] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The in-situ microbial reduction and immobilization of uranium was assessed as a means of preventing the migration of this element in the terrestrial subsurface. Uranium immobilization (putatively identified as reduction) and microbial respiratory activities were evaluated in the presence of exogenous electron donors and acceptors with field push-pull tests using wells installed in an anoxic aquifer contaminated with landfill leachate. Uranium(VI) amended at 1.5 microM was reduced to less than 1 nM in groundwater in less than 8 d during all field experiments. Amendments of 0.5 mM sulfate or 5 mM nitrate slowed U(VI) immobilization and allowed for the recovery of 10% and 54% of the injected element, respectively, as compared to 4% in the unamended treatment. Laboratory incubations confirmed the field tests and showed that the majority of the U(VI) immobilized was due to microbial reduction. In these tests, nitrate treatment (7.5 mM) inhibited U(VI) reduction, and nitrite was transiently produced. Further push-pull tests were performed in which either 1 or 5 mM nitrate was added with 1.0 uM U(VI) to sediments that already contained immobilized uranium. After an initial loss of the amendments, the concentration of soluble U(VI) increased and eventually exceeded the injected concentration, indicating that previously immobilized uranium was remobilized as nitrate was reduced. Laboratory experiments using heat-inactivated sediment slurries suggested that the intermediates of dissimilatory nitrate reduction (denitrification or dissimilatory nitrate reduction to ammonia), nitrite, nitrous oxide, and nitric oxide were all capable of oxidizing and mobilizing U(IV). These findings indicate that in-situ subsurface U(VI) immobilization can be expected to take place under anaerobic conditions, but the permanence of the approach can be impaired by disimilatory nitrate reduction intermediates that can mobilize previously reduced uranium.
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Affiliation(s)
- John M Senko
- Department of Botany and Microbiology and Institute for Energy and the Environment, University of Oklahoma, Norman 73019, USA
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44
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Mancinelli RL, Cronin S, Hochstein LI. The purification and properties of a cd-cytochrome nitrite reductase from Paracoccus halodenitrificans. Arch Microbiol 2001; 145:202-8. [PMID: 11540874 DOI: 10.1007/bf00446781] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Paracoccus halodenitrificans, grown anaerobically in the presence of nitrite, contained membrane and cytoplasmic nitrite reductases. When assayed in the presence of phenazine methosulfate and ascorbate, the membrane-bound enzyme produced nitrous oxide whereas the cytoplasmic enzyme produced nitric oxide. When both enzymes were assayed in the presence of methyl viologen and dithionite, the cytoplasmic enzyme produced ammonia. Following solubilization, the membrane-bound enzyme behaved like the cytoplasmic enzyme, producing nitric oxide in the presence of phenazine methosulfate and ascorbate, and ammonia when assayed in the presence of methyl viologen and dithionite. The cytoplasmic and membrane-bound enzymes were purified to essentially the same specific activity. Only a single nitrite-reductase activity was detected on electrophoretic gels and the electrophoretic behavior of both enzymes suggested they were identical. The spectral properties of both enzymes suggested they were cd-type cytochromes. These data suggest that the products of nitrite reduction by the cd-cytochrome nitrite reductase are determined by the location of the enzyme and the redox potential of the electron donor.
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Affiliation(s)
- R L Mancinelli
- Planetary Biology Division, Ames Research Center, Moffett Field, CA 94035, USA
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45
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Senko JM, Stolz JF. Evidence for iron-dependent nitrate respiration in the dissimilatory iron-reducing bacterium Geobacter metallireducens. Appl Environ Microbiol 2001; 67:3750-2. [PMID: 11472960 PMCID: PMC93084 DOI: 10.1128/aem.67.8.3750-3752.2001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The dissimilatory iron-reducing bacterium Geobacter metallireducens was found to require iron at a concentration in excess of 50 microM for continuous cultivation on nitrate. Growth yield (approximately 3-fold), cytochrome c content (approximately 7-fold), and nitrate (approximately 4.5-fold) and nitrite (approximately 70-fold) reductase activities were all increased significantly when the growth medium was amended with 500 microM iron.
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Affiliation(s)
- J M Senko
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania 15219, USA
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46
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Saraiva LM, da Costa PN, Conte C, Xavier AV, LeGall J. In the facultative sulphate/nitrate reducer Desulfovibrio desulfuricans ATCC 27774, the nine-haem cytochrome c is part of a membrane-bound redox complex mainly expressed in sulphate-grown cells. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1520:63-70. [PMID: 11470160 DOI: 10.1016/s0167-4781(01)00250-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The bacterium Desulfovibrio desulfuricans ATCC 27774 belongs to the group of sulphate reducers also capable of utilising nitrate as its terminal electron acceptor for anaerobic growth. One of the complex multihaem proteins found in nitrate- or sulphate-grown cells of Desulfovibrio desulfuricans ATCC 27774 is the nine-haem cytochrome c. The present work shows that the gene encoding for Desulfovibrio desulfuricans ATCC 27774 nine-haem cytochrome c is part of an operon formed by the gene cluster 9hcA-D. Besides 9hcA, the gene encoding for the nine-haem cytochrome c, genes 9hcB to D encode for a protein containing four [4Fe-4S](2+/1+) centres, for a dihaem transmembrane cytochrome b and for an unknown hydrophobic protein, respectively. The four proteins have a predicted topology that is in accordance with the formation of a membrane-bound redox complex. Furthermore, the transcriptional studies show that not only the expression of the 9HcA-D complex is dependent on the growth phase, but also is markedly increased in sulphate-grown cells.
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Affiliation(s)
- L M Saraiva
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal.
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47
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da Costa PN, Romão CV, LeGall J, Xavier AV, Melo E, Teixeira M, Saraiva LM. The genetic organization of Desulfovibrio desulphuricans ATCC 27774 bacterioferritin and rubredoxin-2 genes: involvement of rubredoxin in iron metabolism. Mol Microbiol 2001; 41:217-27. [PMID: 11454214 DOI: 10.1046/j.1365-2958.2001.02509.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The anaerobic bacterium Desulfovibrio desulphuricans ATCC 27774 contains a unique bacterioferritin, isolated with a stable di-iron centre and having iron-coproporphyrin III as its haem cofactor, as well as a type 2 rubredoxin with an unusual spacing of four amino acid residues between the first two binding cysteines. The genes encoding for these two proteins were cloned and sequenced. The deduced amino acid sequence of the bacterioferritin shows that it is among the most divergent members of this protein family. Most interestingly, the bacterioferritin and rubredoxin-2 genes form a dicistronic operon, which reflects the direct interaction between the two proteins. Indeed, bacterioferritin and rubredoxin-2 form a complex in vitro, as shown by the significant increase in the anisotropy and decay times of the fluorescence of rubredoxin-2 tryptophan(s) when mixed with bacterioferritin. In addition, rubredoxin-2 donates electrons to bacterioferritin. This is the first identification of an electron donor to a bacterioferritin and shows the involvement of rubredoxin-2 in iron metabolism. Furthermore, analysis of the genomic data for anaerobes suggests that rubredoxins play a general role in iron metabolism and oxygen detoxification in these prokaryotes.
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Affiliation(s)
- P N da Costa
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, R. da Quinta Grande 6, 2780-156 Oeiras, Portugal
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48
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Metzler DE, Metzler CM, Sauke DJ. Transition Metals in Catalysis and Electron Transport. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50019-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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49
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Pereira IA, LeGall J, Xavier AV, Teixeira M. Characterization of a heme c nitrite reductase from a non-ammonifying microorganism, Desulfovibrio vulgaris Hildenborough. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1481:119-30. [PMID: 11004582 DOI: 10.1016/s0167-4838(00)00111-4] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A cytochrome c nitrite reductase (NiR) was purified for the first time from a microorganism not capable of growing on nitrate, the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. It was isolated from the membranes as a large heterooligomeric complex of 760 kDa, containing two cytochrome c subunits of 56 and 18 kDa. This complex has nitrite and sulfite reductase activities of 685 micromol NH(4)(+)/min/mg and 1.0 micromol H(2)/min/mg. The enzyme was studied by UV-visible and electron paramagnetic resonance (EPR) spectroscopies. The overall redox behavior was determined through a visible redox titration. The data were analyzed with a set of four redox transitions, with an E(0)' of +160 mV (12% of total absorption), -5 mV (38% of total absorption), -110 mV (38% of total absorption) and -210 mV (12% of total absorption) at pH 7.6. The EPR spectra of oxidized and partially reduced NiR show a complex pattern, indicative of multiple heme-heme magnetic interactions. It was found that D. vulgaris Hildenborough is not capable of using nitrite as a terminal electron acceptor. These results indicate that in this organism the NiR is not involved in the dissimilative reduction of nitrite, as is the case with the other similar enzymes isolated so far. The possible role of this enzyme in the detoxification of nitrite and/or in the reduction of sulfite is discussed.
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Affiliation(s)
- I A Pereira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Portugal.
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50
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Stach P, Einsle O, Schumacher W, Kurun E, Kroneck PM. Bacterial cytochrome c nitrite reductase: new structural and functional aspects. J Inorg Biochem 2000; 79:381-5. [PMID: 10830892 DOI: 10.1016/s0162-0134(99)00248-2] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Cytochrome c nitrite reductase catalyzes the six-electron reduction of nitrite to ammonia as a key step within the biological nitrogen cycle. Most recently, the crystal structure of the soluble enzyme from Sulfurospirillum deleyianum could be solved to 1.9 A resolution. This set the basis for new experiments on structural and functional aspects of the pentaheme protein which carries a Ca(2+) ion close to the active site heme. In the crystal, the protein was a homodimer with ten hemes in very close packing. The strong interaction between the nitrite reductase monomers also occurred in solution according to the dependence of the activity on the protein concentration. Addition of Ca(2+) to the enzyme as isolated had a stimulating effect on the activity. Ca(2+) could be removed from the enzyme by treatment with chelating agents such as EGTA or EDTA which led to a decrease in activity. In addition to nitrite, the enzyme converted NO, hydroxylamine and O-methyl hydroxylamine to ammonia at considerable rates. With N2O the activity was much lower; most likely dinitrogen was the product in this case. Cytochrome c nitrite reductase exhibited a remarkably high sulfite reductase activity, with hydrogen sulfide as the product. A paramagnetic Fe(II)-NO, S = 1/2 adduct was identified by rapid freeze EPR spectroscopy under turnover conditions with nitrite. This potential reaction intermediate of the reduction of nitrite to ammonia was also observed with PAPA NONOate and Spermine NONOate.
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Affiliation(s)
- P Stach
- Universität Konstanz, Fachbereich Biologie, Germany
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