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Engrola F, Correia MAS, Watson C, Romão CC, Veiros LF, Romão MJ, Santos-Silva T, Santini JM. Arsenite oxidase in complex with antimonite and arsenite oxyanions: Insights into the catalytic mechanism. J Biol Chem 2023; 299:105036. [PMID: 37442232 PMCID: PMC10448176 DOI: 10.1016/j.jbc.2023.105036] [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: 04/11/2023] [Revised: 06/27/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
Arsenic contamination of groundwater is among one of the biggest health threats affecting millions of people in the world. There is an urgent need for efficient arsenic biosensors where the use of arsenic metabolizing enzymes can be explored. In this work, we have solved four crystal structures of arsenite oxidase (Aio) in complex with arsenic and antimony oxyanions and the structures determined correspond to intermediate states of the enzymatic mechanism. These structural data were complemented with density-functional theory calculations providing a unique view of the molybdenum active site at different time points that, together with mutagenesis data, enabled to clarify the enzymatic mechanism and the molecular determinants for the oxidation of As(III) to the less toxic As(V) species.
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Affiliation(s)
- Filipa Engrola
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Márcia A S Correia
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Cameron Watson
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, United Kingdom
| | | | - Luis F Veiros
- Centro de Química Estrutural, Institute of Molecular Sciences, Lisboa, Portugal; Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Maria João Romão
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.
| | - Teresa Santos-Silva
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.
| | - Joanne M Santini
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, United Kingdom.
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2
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Hu M, Li F, Qiao J, Yuan C, Yu H, Zhuang L. New Arsenite Oxidase Gene ( aioA) PCR Primers for Assessing Arsenite-Oxidizer Diversity in the Environment Using High-Throughput Sequencing. Front Microbiol 2021; 12:691913. [PMID: 34690945 PMCID: PMC8527091 DOI: 10.3389/fmicb.2021.691913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 09/16/2021] [Indexed: 11/13/2022] Open
Abstract
Gene encoding the large subunit of As(III) oxidase (AioA), an important component of the microbial As(III) oxidation system, is a widely used biomarker to characterize As(III)-oxidizing communities in the environment. However, many studies were restricted to a few sequences generated by clone libraries and Sanger sequencing, which may have underestimated the diversity of As(III)-oxidizers in natural environments. In this study, we designed a primer pair, 1109F (5'-ATC TGG GGB AAY RAC AAY TA-3') and 1548R (5'-TTC ATB GAS GTS AGR TTC AT-3'), targeting gene sequence encoding for the conserved molybdopterin center of the AioA protein, yielding amplicons approximately 450 bp in size that are feasible for highly parallel amplicon sequencing. By utilizing in silico analyses and the experimental construction of clone libraries using Sanger sequencing, the specificity and resolution of 1109F/1548R are approximated with two other previously published and commonly used primers, i.e., M1-2F/M3-2R and deg1F/deg1R. With the use of the 1109F/1548R primer pair, the taxonomic composition of the aioA genes was similar both according to the Sanger and next-generation sequencing (NGS) platforms. Furthermore, high-throughput amplicon sequencing using the primer pair, 1109F/1548R, successfully identified the well-known As(III)-oxidizers in paddy soils and sediments, and they also revealed the differences in the community structure and composition of As(III)-oxidizers in above two biotopes. The random forest analysis showed that the dissolved As(III) had the highest relative influence on the Chao1 index of the aioA genes. These observations demonstrate that the newly designed PCR primers enhanced the ability to detect the diversity of aioA-encoding microorganisms in environments using highly parallel short amplicon sequencing.
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Affiliation(s)
- Min Hu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China.,National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, China
| | - Fangbai Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China.,National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, China
| | - Jiangtao Qiao
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China.,National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, China
| | - Chaolei Yuan
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Huanyun Yu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China.,National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, China
| | - Li Zhuang
- School of Environment, Jinan University, Guangzhou, China
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3
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Herrera C, Moraga R, Bustamante B, Vilo C, Aguayo P, Valenzuela C, Smith CT, Yáñez J, Guzmán-Fierro V, Roeckel M, Campos VL. Characterization of Arsenite-Oxidizing Bacteria Isolated from Arsenic-Rich Sediments, Atacama Desert, Chile. Microorganisms 2021; 9:microorganisms9030483. [PMID: 33668956 PMCID: PMC7996500 DOI: 10.3390/microorganisms9030483] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 12/29/2020] [Accepted: 12/29/2020] [Indexed: 11/16/2022] Open
Abstract
Arsenic (As), a semimetal toxic for humans, is commonly associated with serious health problems. The most common form of massive and chronic exposure to As is through consumption of contaminated drinking water. This study aimed to isolate an As resistant bacterial strain to characterize its ability to oxidize As (III) when immobilized in an activated carbon batch bioreactor and to evaluate its potential to be used in biological treatments to remediate As contaminated waters. The diversity of bacterial communities from sediments of the As-rich Camarones River, Atacama Desert, Chile, was evaluated by Illumina sequencing. Dominant taxonomic groups (>1%) isolated were affiliated with Proteobacteria and Firmicutes. A high As-resistant bacterium was selected (Pseudomonas migulae VC-19 strain) and the presence of aio gene in it was investigated. Arsenite detoxification activity by this bacterial strain was determined by HPLC/HG/AAS. Particularly when immobilized on activated carbon, P. migulae VC-19 showed high rates of As(III) conversion (100% oxidized after 36 h of incubation). To the best of our knowledge, this is the first report of a P. migulae arsenite oxidizing strain that is promising for biotechnological application in the treatment of arsenic contaminated waters.
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Affiliation(s)
- Constanza Herrera
- Laboratory of Environmental Microbiology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepcion, Concepcion 4070386, Chile; (C.H.); (B.B.); (C.V.); (P.A.); (C.V.); (C.T.S.)
| | - Ruben Moraga
- Microbiology Laboratory, Faculty of Renewable Natural Resources, Arturo Prat University, Iquique 1100000, Chile
- Correspondence: (R.M.); (V.L.C.)
| | - Brian Bustamante
- Laboratory of Environmental Microbiology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepcion, Concepcion 4070386, Chile; (C.H.); (B.B.); (C.V.); (P.A.); (C.V.); (C.T.S.)
| | - Claudia Vilo
- Laboratory of Environmental Microbiology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepcion, Concepcion 4070386, Chile; (C.H.); (B.B.); (C.V.); (P.A.); (C.V.); (C.T.S.)
| | - Paulina Aguayo
- Laboratory of Environmental Microbiology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepcion, Concepcion 4070386, Chile; (C.H.); (B.B.); (C.V.); (P.A.); (C.V.); (C.T.S.)
- Faculty of Environmental Sciences, EULA-Chile, Universidad de Concepcion, Concepcion 4070386, Chile
- Institute of Natural Resources, Faculty of Veterinary Medicine and Agronomy, Universidad de Las Américas, Sede Concepcion, Campus El Boldal, Av. Alessandri N°1160, Concepcion 4090940, Chile
| | - Cristian Valenzuela
- Laboratory of Environmental Microbiology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepcion, Concepcion 4070386, Chile; (C.H.); (B.B.); (C.V.); (P.A.); (C.V.); (C.T.S.)
| | - Carlos T. Smith
- Laboratory of Environmental Microbiology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepcion, Concepcion 4070386, Chile; (C.H.); (B.B.); (C.V.); (P.A.); (C.V.); (C.T.S.)
| | - Jorge Yáñez
- Faculty of Chemical Sciences, Department of Analytical and Inorganic Chemistry, University of Concepción, Concepción 4070386, Chile;
| | - Victor Guzmán-Fierro
- Department of Chemical Engineering, Faculty of Engineering, University of Concepción, Concepcion 4070386, Chile; (V.G.-F.); (M.R.)
| | - Marlene Roeckel
- Department of Chemical Engineering, Faculty of Engineering, University of Concepción, Concepcion 4070386, Chile; (V.G.-F.); (M.R.)
| | - Víctor L. Campos
- Laboratory of Environmental Microbiology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepcion, Concepcion 4070386, Chile; (C.H.); (B.B.); (C.V.); (P.A.); (C.V.); (C.T.S.)
- Correspondence: (R.M.); (V.L.C.)
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4
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Szyttenholm J, Chaspoul F, Bauzan M, Ducluzeau AL, Chehade MH, Pierrel F, Denis Y, Nitschke W, Schoepp-Cothenet B. The controversy on the ancestral arsenite oxidizing enzyme; deducing evolutionary histories with phylogeny and thermodynamics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148252. [PMID: 32569664 DOI: 10.1016/j.bbabio.2020.148252] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 06/07/2020] [Accepted: 06/12/2020] [Indexed: 12/12/2022]
Abstract
The three presently known enzymes responsible for arsenic-using bioenergetic processes are arsenite oxidase (Aio), arsenate reductase (Arr) and alternative arsenite oxidase (Arx), all of which are molybdoenzymes from the vast group referred to as the Mo/W-bisPGD enzyme superfamily. Since arsenite is present in substantial amounts in hydrothermal environments, frequently considered as vestiges of primordial biochemistry, arsenite-based bioenergetics has long been predicted to be ancient. Conflicting scenarios, however, have been put forward proposing either Arr/Arx or Aio as operating in the ancestral metabolism. Phylogenetic data argue in favor of Aio whereas biochemical and physiological data led several authors to propose Arx/Arr as the most ancient anaerobic arsenite metabolizing enzymes. Here we combine phylogenetic approaches with physiological and biochemical experiments to demonstrate that the Arx/Arr enzymes could not have been functional in the Archaean geological eon. We propose that Arr reacts with menaquinones to reduce arsenate whereas Arx reacts with ubiquinone to oxidize arsenite, in line with thermodynamic considerations. The distribution of the quinone biosynthesis pathways, however, clearly indicates that the ubiquinone pathway is recent. An updated phylogeny of Arx furthermore reinforces the hypothesis of a recent emergence of this enzyme. We therefore conclude that anaerobic arsenite redox conversion in the Archaean must have been performed in a metabolism involving Aio.
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Affiliation(s)
- Julie Szyttenholm
- Aix-Marseille Univ., CNRS, BIP UMR 7281, FR 3479, IMM, 13402 Marseille Cedex 20, France
| | - Florence Chaspoul
- Aix Marseille Univ., CNRS, IRD, IMBE UMR 7263, Faculté de Pharmacie, 13005 Marseille, France
| | - Marielle Bauzan
- Aix-Marseille Univ., CNRS, Plateforme Fermentation, FR3479, IMM, 13402 Marseille Cedex 20, France
| | - Anne-Lise Ducluzeau
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775-7220, USA
| | | | - Fabien Pierrel
- Univ. Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000 Grenoble, France
| | - Yann Denis
- Aix-Marseille Univ., CNRS, Plateforme Transcriptomique, FR3479, IMM, 13402 Marseille Cedex 20, France
| | - Wolfgang Nitschke
- Aix-Marseille Univ., CNRS, BIP UMR 7281, FR 3479, IMM, 13402 Marseille Cedex 20, France
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5
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Ayala-Muñoz D, Burgos WD, Sánchez-España J, Couradeau E, Falagán C, Macalady JL. Metagenomic and Metatranscriptomic Study of Microbial Metal Resistance in an Acidic Pit Lake. Microorganisms 2020; 8:microorganisms8091350. [PMID: 32899650 PMCID: PMC7563247 DOI: 10.3390/microorganisms8091350] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 08/18/2020] [Accepted: 09/02/2020] [Indexed: 11/16/2022] Open
Abstract
Cueva de la Mora (CM) is an acidic, meromictic pit lake in the Iberian Pyrite Belt characterized by extremely high metal(loid) concentrations and strong gradients in oxygen, metal, and nutrient concentrations. We hypothesized that geochemical variations with depth would result in differences in community composition and in metal resistance strategies among active microbial populations. We also hypothesized that metal resistance gene (MRG) expression would correlate with toxicity levels for dissolved metal species in the lake. Water samples were collected in the upper oxic layer, chemocline, and deep anoxic layer of the lake for shotgun metagenomic and metatranscriptomic sequencing. Metagenomic analyses revealed dramatic differences in the composition of the microbial communities with depth, consistent with changing geochemistry. Based on relative abundance of taxa identified in each metagenome, Eukaryotes (predominantly Coccomyxa) dominated the upper layer, while Archaea (predominantly Thermoplasmatales) dominated the deep layer, and a combination of Bacteria and Eukaryotes were abundant at the chemocline. We compared metal resistance across communities using a curated list of protein-coding MRGs with KEGG Orthology identifiers (KOs) and found that there were broad differences in the metal resistance strategies (e.g., intracellular metal accumulation) expressed by Eukaryotes, Bacteria, and Archaea. Although normalized abundances of MRG and MRG expression were generally higher in the deep layer, expression of metal-specific genes was not strongly related to variations in specific metal concentrations, especially for Cu and As. We also compared MRG potential and expression in metagenome assembled genomes (MAGs) from the deep layer, where metal concentrations are highest. Consistent with previous work showing differences in metal resistance mechanisms even at the strain level, MRG expression patterns varied strongly among MAG populations from the same depth. Some MAG populations expressed very few MRG known to date, suggesting that novel metal resistance strategies remain to be discovered in uncultivated acidophiles.
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Affiliation(s)
- Diana Ayala-Muñoz
- Department of Civil and Environmental Engineering, The Pennsylvania State University, 212 Sackett Building, University Park, PA 16802, USA;
- Correspondence:
| | - William D. Burgos
- Department of Civil and Environmental Engineering, The Pennsylvania State University, 212 Sackett Building, University Park, PA 16802, USA;
| | - Javier Sánchez-España
- Geochemistry and Sustainable Mining Unit, Instituto Geológico y Minero de España (IGME), Calera 1, Tres Cantos, 28760 Madrid, Spain;
| | - Estelle Couradeau
- Department of Ecosystem Science and Management, The Pennsylvania State University, 450 ASI, University Park, PA 16802, USA;
| | - Carmen Falagán
- Environment & Sustainability Institute and Camborne School of Mines, University of Exeter, Penryn Campus, Penryn TR10 9FE, UK;
| | - Jennifer L. Macalady
- Department of Geosciences, The Pennsylvania State University, 211 Deike Building, University Park, PA 16802, USA;
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Yamazaki C, Kashiwa S, Horiuchi A, Kasahara Y, Yamamura S, Amachi S. A novel dimethylsulfoxide reductase family of molybdenum enzyme, Idr, is involved in iodate respiration by Pseudomonas sp. SCT. Environ Microbiol 2020; 22:2196-2212. [PMID: 32190953 DOI: 10.1111/1462-2920.14988] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/30/2020] [Accepted: 03/16/2020] [Indexed: 10/24/2022]
Abstract
Pseudomonas sp. strain SCT is capable of using iodate (IO3 - ) as a terminal electron acceptor for anaerobic respiration. A possible key enzyme, periplasmic iodate reductase (Idr), was visualized by active staining on non-denaturing gel electrophoresis. Liquid chromatography-tandem mass spectrometry analysis revealed that at least four proteins, designated as IdrA, IdrB, IdrP1 , and IdrP2 , were involved in Idr. IdrA and IdrB were homologues of catalytic and electron transfer subunits of respiratory arsenite oxidase (Aio); however, IdrA defined a novel clade within the dimethylsulfoxide (DMSO) reductase family. IdrP1 and IdrP2 were closely related to each other and distantly related to cytochrome c peroxidase. The idr genes (idrABP 1 P 2 ) formed an operon-like structure, and their transcription was upregulated under iodate-respiring conditions. Comparative proteomic analysis also revealed that Idr proteins and high affinity terminal oxidases (Cbb3 and Cyd), various H2 O2 scavengers, and chlorite (ClO2 - ) dismutase-like proteins were expressed specifically or abundantly under iodate-respiring conditions. These results suggest that Idr is a respiratory iodate reductase, and that both O2 and H2 O2 are formed as by-products of iodate respiration. We propose an electron transport chain model of strain SCT, in which iodate, H2 O2 , and O2 are used as terminal electron acceptors.
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Affiliation(s)
- Chihiro Yamazaki
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo-city, Chiba, 271-8510, Japan
| | - Sumie Kashiwa
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo-city, Chiba, 271-8510, Japan
| | - Ayaka Horiuchi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo-city, Chiba, 271-8510, Japan
| | - Yasuhiro Kasahara
- Institute of Low Temperature Science, Hokkaido University, Sapporo, 060-0819, Japan
| | - Shigeki Yamamura
- Center for Regional Environmental Research, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Seigo Amachi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo-city, Chiba, 271-8510, Japan
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7
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Lescure T, Joulian C, Charles C, Ben Ali Saanda T, Charron M, Breeze D, Bauda P, Battaglia-Brunet F. Simple or complex organic substrates inhibit arsenite oxidation and aioA gene expression in two β-Proteobacteria strains. Res Microbiol 2020; 171:13-20. [DOI: 10.1016/j.resmic.2019.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/04/2019] [Accepted: 09/06/2019] [Indexed: 11/30/2022]
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8
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Pandey N, Bhatt R. Improved biotransformation of arsenic by arsenite oxidase – Chitosan nanoparticle conjugates. Int J Biol Macromol 2018; 106:258-265. [DOI: 10.1016/j.ijbiomac.2017.08.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 08/02/2017] [Accepted: 08/02/2017] [Indexed: 10/19/2022]
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9
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Watson C, Niks D, Hille R, Vieira M, Schoepp-Cothenet B, Marques AT, Romão MJ, Santos-Silva T, Santini JM. Electron transfer through arsenite oxidase: Insights into Rieske interaction with cytochrome c. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2017; 1858:865-872. [PMID: 28801050 PMCID: PMC5574378 DOI: 10.1016/j.bbabio.2017.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 07/05/2017] [Accepted: 08/05/2017] [Indexed: 11/25/2022]
Abstract
Arsenic is a widely distributed environmental toxin whose presence in drinking water poses a threat to >140 million people worldwide. The respiratory enzyme arsenite oxidase from various bacteria catalyses the oxidation of arsenite to arsenate and is being developed as a biosensor for arsenite. The arsenite oxidase from Rhizobium sp. str. NT-26 (a member of the Alphaproteobacteria) is a heterotetramer consisting of a large catalytic subunit (AioA), which contains a molybdenum centre and a 3Fe-4S cluster, and a small subunit (AioB) containing a Rieske 2Fe-2S cluster. Stopped-flow spectroscopy and isothermal titration calorimetry (ITC) have been used to better understand electron transfer through the redox-active centres of the enzyme, which is essential for biosensor development. Results show that oxidation of arsenite at the active site is extremely fast with a rate of >4000s-1 and reduction of the electron acceptor is rate-limiting. An AioB-F108A mutation results in increased activity with the artificial electron acceptor DCPIP and decreased activity with cytochrome c, which in the latter as demonstrated by ITC is not due to an effect on the protein-protein interaction but instead to an effect on electron transfer. These results provide further support that the AioB F108 is important in electron transfer between the Rieske subunit and cytochrome c and its absence in the arsenite oxidases from the Betaproteobacteria may explain the inability of these enzymes to use this electron acceptor.
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Affiliation(s)
- Cameron Watson
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, WC1E 6BT, United Kingdom
| | - Dimitri Niks
- Department of Biochemistry, University of California; Riverside, Riverside, CA 92521, USA
| | - Russ Hille
- Department of Biochemistry, University of California; Riverside, Riverside, CA 92521, USA
| | - Marta Vieira
- UCIBIO-Requimte, Department of Chemistry, Faculty of Sciences and Technology, Universidade Nova de Lisboa, Portugal
| | | | - Alexandra T Marques
- UCIBIO-Requimte, Department of Chemistry, Faculty of Sciences and Technology, Universidade Nova de Lisboa, Portugal
| | - Maria João Romão
- UCIBIO-Requimte, Department of Chemistry, Faculty of Sciences and Technology, Universidade Nova de Lisboa, Portugal
| | - Teresa Santos-Silva
- UCIBIO-Requimte, Department of Chemistry, Faculty of Sciences and Technology, Universidade Nova de Lisboa, Portugal
| | - Joanne M Santini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, WC1E 6BT, United Kingdom.
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10
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Kumari N, Jagadevan S. Genetic identification of arsenate reductase and arsenite oxidase in redox transformations carried out by arsenic metabolising prokaryotes - A comprehensive review. CHEMOSPHERE 2016; 163:400-412. [PMID: 27565307 DOI: 10.1016/j.chemosphere.2016.08.044] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 08/04/2016] [Accepted: 08/08/2016] [Indexed: 06/06/2023]
Abstract
Arsenic (As) contamination in water is a cause of major concern to human population worldwide, especially in Bangladesh and West Bengal, India. Arsenite (As(III)) and arsenate (As(V)) are the two common forms in which arsenic exists in soil and groundwater, the former being more mobile and toxic. A large number of arsenic metabolising microorganisms play a crucial role in microbial transformation of arsenic between its different states, thus playing a key role in remediation of arsenic contaminated water. This review focuses on advances in biochemical, molecular and genomic developments in the field of arsenic metabolising bacteria - covering recent developments in the understanding of structure of arsenate reductase and arsenite oxidase enzymes, their gene and operon structures and their mechanism of action. The genetic and molecular studies of these microbes and their proteins may lead to evolution of successful strategies for effective implementation of bioremediation programs.
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Affiliation(s)
- Nisha Kumari
- Department of Environmental Science and Engineering, Indian School of Mines, Dhanbad, Jharkhand, 826004, India
| | - Sheeja Jagadevan
- Department of Environmental Science and Engineering, Indian School of Mines, Dhanbad, Jharkhand, 826004, India.
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11
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Andres J, Bertin PN. The microbial genomics of arsenic. FEMS Microbiol Rev 2016; 40:299-322. [DOI: 10.1093/femsre/fuv050] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2015] [Indexed: 12/17/2022] Open
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12
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Jiang Z, Li P, Jiang D, Dai X, Zhang R, Wang Y, Wang Y. Microbial Community Structure and Arsenic Biogeochemistry in an Acid Vapor-Formed Spring in Tengchong Geothermal Area, China. PLoS One 2016; 11:e0146331. [PMID: 26761709 PMCID: PMC4711897 DOI: 10.1371/journal.pone.0146331] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 12/16/2015] [Indexed: 11/24/2022] Open
Abstract
Arsenic biogeochemistry has been studied extensively in acid sulfate-chloride hot springs, but not in acid sulfate hot springs with low chloride. In this study, Zhenzhuquan in Tengchong geothermal area, a representative acid sulfate hot spring with low chloride, was chosen to study arsenic geochemistry and microbial community structure using Illumina MiSeq sequencing. Over 0.3 million 16S rRNA sequence reads were obtained from 6-paired parallel water and sediment samples along its outflow channel. Arsenic oxidation occurred in the Zhenxhuquan pool, with distinctly high ratios of arsenate to total dissolved arsenic (0.73–0.86). Coupled with iron and sulfur oxidation along the outflow channel, arsenic accumulated in downstream sediments with concentrations up to 16.44 g/kg and appeared to significantly constrain their microbial community diversity. These oxidations might be correlated with the appearance of some putative functional microbial populations, such as Aquificae and Pseudomonas (arsenic oxidation), Sulfolobus (sulfur and iron oxidation), Metallosphaera and Acidicaldus (iron oxidation). Temperature, total organic carbon and dissolved oxygen significantly shaped the microbial community structure of upstream and downstream samples. In the upstream outflow channel region, most microbial populations were microaerophilic/anaerobic thermophiles and hyperthermophiles, such as Sulfolobus, Nocardia, Fervidicoccus, Delftia, and Ralstonia. In the downstream region, aerobic heterotrophic mesophiles and thermophiles were identified, including Ktedonobacteria, Acidicaldus, Chthonomonas and Sphingobacteria. A total of 72.41–95.91% unassigned-genus sequences were derived from the downstream high arsenic sediments 16S rRNA clone libraries. This study could enable us to achieve an integrated understanding on arsenic biogeochemistry in acid hot springs.
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Affiliation(s)
- Zhou Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, People's Republic of China
- School of Environmental Studies, China University of Geosciences, Wuhan, People's Republic of China
| | - Ping Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, People's Republic of China
- * E-mail: (PL); (YXW)
| | - Dawei Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, People's Republic of China
| | - Xinyue Dai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, People's Republic of China
- School of Environmental Studies, China University of Geosciences, Wuhan, People's Republic of China
| | - Rui Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, People's Republic of China
| | - Yanhong Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, People's Republic of China
| | - Yanxin Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, People's Republic of China
- School of Environmental Studies, China University of Geosciences, Wuhan, People's Republic of China
- * E-mail: (PL); (YXW)
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13
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Corsini A, Colombo M, Muyzer G, Cavalca L. Characterization of the arsenite oxidizer Aliihoeflea sp. strain 2WW and its potential application in the removal of arsenic from groundwater in combination with Pf-ferritin. Antonie van Leeuwenhoek 2015; 108:673-84. [PMID: 26149126 DOI: 10.1007/s10482-015-0523-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/29/2015] [Indexed: 10/23/2022]
Abstract
A heterotrophic arsenite-oxidizing bacterium, strain 2WW, was isolated from a biofilter treating arsenic-rich groundwater. Comparative analysis of 16S rRNA gene sequences showed that it was closely related (98.7 %) to the alphaproteobacterium Aliihoeflea aesturari strain N8(T). However, it was physiologically different by its ability to grow at relatively low substrate concentrations, low temperatures and by its ability to oxidize arsenite. Here we describe the physiological features of strain 2WW and compare these to its most closely related relative, A. aestuari strain N8(T). In addition, we tested its efficiency to remove arsenic from groundwater in combination with Pf-ferritin. Strain 2WW oxidized arsenite to arsenate between pH 5.0 and 8.0, and from 4 to 30 °C. When the strain was used in combination with a Pf-ferritin-based material for arsenic removal from natural groundwater, the removal efficiency was significantly higher (73 %) than for Pf-ferritin alone (64 %). These results showed that arsenite oxidation by strain 2WW combined with Pf-ferritin-based material has a potential in arsenic removal from contaminated groundwater.
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Affiliation(s)
- Anna Corsini
- DeFENS - Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, via Celoria 2, 20133, Milan, Italy
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14
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Wang Q, Qin D, Zhang S, Wang L, Li J, Rensing C, McDermott TR, Wang G. Fate of arsenate following arsenite oxidation in Agrobacterium tumefaciens GW4. Environ Microbiol 2014; 17:1926-40. [PMID: 24673976 DOI: 10.1111/1462-2920.12465] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/20/2014] [Indexed: 10/25/2022]
Abstract
The fate of arsenate (As(V) ) generated by microbial arsenite (As(III) ) oxidation is poorly understood. Agrobacterium tumefaciens wild-type strain (GW4) was studied to determine how the cell copes with As(V) generated in batch culture. GW4 grown heterotrophically with mannitol used As(III) as a supplemental energy supply as reflected by enhanced growth and increased cellular levels of NADH and ATP. Under low phosphate (Pi) conditions and presence of As(III) oxidation, up to ∼ 50% of the resulting As(V) was taken up and found associated with the periplasm, membrane or cytoplasm fractions of the cells. Arsenic was found associated with proteins and polar lipids, but not in nucleic acids or sugars. Thin-layer chromatography and gas chromatography-mass spectrometry analysis suggested the presence of arsenolipids in membranes, presumably as part of the bilayer structure of the cell membrane and replacing Pi under Pi-limiting conditions. The potential role of a Pi-binding protein (PstS) for As(V) uptake was assessed with the His-tag purified protein. Intrinsic tryptophan fluorescence spectra analysis suggests that PstS can bind As(V) , but with lower affinity as compared with Pi. In early stationary phase cells, the As(V) : Pi ratio was approximately 4.3 and accompanied by an altered cell ultrastructure.
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Affiliation(s)
- Qian Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dong Qin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shengzhe Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lu Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jingxin Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Christopher Rensing
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Timothy R McDermott
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, 59717, USA
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
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15
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Kang YS, Shi Z, Bothner B, Wang G, McDermott TR. Involvement of the Acr3 and DctA anti-porters in arsenite oxidation in Agrobacterium tumefaciens 5A. Environ Microbiol 2014; 17:1950-62. [PMID: 24674103 DOI: 10.1111/1462-2920.12468] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 03/22/2014] [Indexed: 12/01/2022]
Abstract
Microbial arsenite (AsIII) oxidation forms a critical piece of the arsenic cycle in nature, though our understanding of how and why microorganisms oxidize AsIII remains rudimentary. Our model organism Agrobacterium tumefaciens 5A contains two distinct ars operons (ars1 and ars2) that are similar in their coding region content. The ars1 operon is located nearby the aio operon that is essential for AsIII oxidation. The AsIII/H(+) anti-porters encoded by acr3-1 and acr3-2 are required for maximal AsIII and antimonite (SbIII) resistance, but acr3-1 (negatively regulated by ArsR-1) appears more active in this regard and also required for AsIII oxidation and expression of aioBA. A malate-phosphate anti-porter DctA is regulated by RpoN and AsIII, and is required for normal growth with malate as a sole carbon source. Qualitatively, a ΔdctA mutant was normal for AsIII oxidation and AsIII/SbIII resistance at metalloid concentrations inhibitory to the Δacr3-1 mutant; however, aioBA induction kinetics was significantly phase-shift delayed. Acr3 involvement in AsIII/SbIII resistance is reasonably well understood, but the role of Acr3 and DctA anti-porters in AsIII oxidation and its regulation is unexpected, and suggests that controlled AsIII trafficking across the cytoplasmic membrane is important to a process understood to occur in the periplasm.
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Affiliation(s)
- Yoon-Suk Kang
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, 59717, USA
| | - Zunji Shi
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, 59717, USA.,State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Timothy R McDermott
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, 59717, USA
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Affiliation(s)
- Russ Hille
- Department of Biochemistry, University of California, Riverside, Riverside, California 92521, United States
| | - James Hall
- Department of Biochemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Partha Basu
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
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Andres J, Arsène-Ploetze F, Barbe V, Brochier-Armanet C, Cleiss-Arnold J, Coppée JY, Dillies MA, Geist L, Joublin A, Koechler S, Lassalle F, Marchal M, Médigue C, Muller D, Nesme X, Plewniak F, Proux C, Ramírez-Bahena MH, Schenowitz C, Sismeiro O, Vallenet D, Santini JM, Bertin PN. Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium rhizobium sp. NT-26. Genome Biol Evol 2013; 5:934-53. [PMID: 23589360 PMCID: PMC3673622 DOI: 10.1093/gbe/evt061] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Arsenic is widespread in the environment and its presence is a result of natural or anthropogenic activities. Microbes have developed different mechanisms to deal with toxic compounds such as arsenic and this is to resist or metabolize the compound. Here, we present the first reference set of genomic, transcriptomic and proteomic data of an Alphaproteobacterium isolated from an arsenic-containing goldmine: Rhizobium sp. NT-26. Although phylogenetically related to the plant-associated bacteria, this organism has lost the major colonizing capabilities needed for symbiosis with legumes. In contrast, the genome of Rhizobium sp. NT-26 comprises a megaplasmid containing the various genes, which enable it to metabolize arsenite. Remarkably, although the genes required for arsenite oxidation and flagellar motility/biofilm formation are carried by the megaplasmid and the chromosome, respectively, a coordinate regulation of these two mechanisms was observed. Taken together, these processes illustrate the impact environmental pressure can have on the evolution of bacterial genomes, improving the fitness of bacterial strains by the acquisition of novel functions.
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Affiliation(s)
- Jérémy Andres
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS Université de Strasbourg, Strasbourg, France
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18
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Li H, Li M, Huang Y, Rensing C, Wang G. In silico analysis of bacterial arsenic islands reveals remarkable synteny and functional relatedness between arsenate and phosphate. Front Microbiol 2013; 4:347. [PMID: 24312089 PMCID: PMC3834237 DOI: 10.3389/fmicb.2013.00347] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 10/31/2013] [Indexed: 11/18/2022] Open
Abstract
In order to construct a more universal model for understanding the genetic requirements for bacterial AsIII oxidation, an in silico examination of the available sequences in the GenBank was assessed and revealed 21 conserved 5–71 kb arsenic islands within phylogenetically diverse bacterial genomes. The arsenic islands included the AsIII oxidase structural genes aioBA, ars operons (e.g., arsRCB) which code for arsenic resistance, and pho, pst, and phn genes known to be part of the classical phosphate stress response and that encode functions associated with regulating and acquiring organic and inorganic phosphorus. The regulatory genes aioXSR were also an island component, but only in Proteobacteria and orientated differently depending on whether they were in α-Proteobacteria or β-/γ-Proteobacteria. Curiously though, while these regulatory genes have been shown to be essential to AsIII oxidation in the Proteobacteria, they are absent in most other organisms examined, inferring different regulatory mechanism(s) yet to be discovered. Phylogenetic analysis of the aio, ars, pst, and phn genes revealed evidence of both vertical inheritance and horizontal gene transfer (HGT). It is therefore likely the arsenic islands did not evolve as a whole unit but formed independently by acquisition of functionally related genes and operons in respective strains. Considering gene synteny and structural analogies between arsenate and phosphate, we presumed that these genes function together in helping these microbes to be able to use even low concentrations of phosphorus needed for vital functions under high concentrations of arsenic, and defined these sequences as the arsenic islands.
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Affiliation(s)
- Hang Li
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University Wuhan, P. R. of China
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19
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Bahar MM, Megharaj M, Naidu R. Kinetics of arsenite oxidation by Variovorax sp. MM-1 isolated from a soil and identification of arsenite oxidase gene. JOURNAL OF HAZARDOUS MATERIALS 2013; 262:997-1003. [PMID: 23290483 DOI: 10.1016/j.jhazmat.2012.11.064] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 11/29/2012] [Accepted: 11/30/2012] [Indexed: 06/01/2023]
Abstract
A Gram-negative, arsenite-oxidizing bacterial strain, MM-1 tolerant to 20mM arsenite and 200 mM arsenate was isolated from a heavy metal contaminated soil which contained only 8.8 mg kg(-1) of arsenic. Based on 16S rRNA analysis, the strain was closely related to the genus Variovorax. This strain completely oxidized 500 μM of arsenite to arsenate within 3h of incubation in minimal salts medium. Kinetic studies of arsenite oxidation by the cells showed one of the lowest Km (17 μM) and highest Vmax (1.23 × 10(-7) μM min(-1) cell(-1)) values reported to date for whole cell suspension. PCR analysis using degenerate primers confirmed the presence of arsenite oxidase gene and its amino acid sequence was 70-91% identical to the large subunit of most reported arsenite oxidases. The significant arsenite oxidation capacity shown by the strain opens the way to its potential application in arsenic remediation process.
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Affiliation(s)
- Md Mezbaul Bahar
- Centre for Environmental Risk Assessment and Remediation (CERAR), University of South Australia, Mawson Lakes Boulevard, Mawson Lakes, SA 5095, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), Mawson Lakes Bvd., Mawson lakes, SA 5095, Australia
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21
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Osborne TH, Heath MD, Martin ACR, Pankowski JA, Hudson-Edwards KA, Santini JM. Cold-adapted arsenite oxidase from a psychrotolerant Polaromonas species. Metallomics 2013; 5:318-24. [PMID: 23150098 DOI: 10.1039/c2mt20180a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Polaromonas sp. str. GM1 is an aerobic, psychrotolerant, heterotrophic member of the Betaproteobacteria and is the only isolate capable of oxidising arsenite at temperatures below 10 °C. Sequencing of the aio gene cluster in GM1 revealed the presence of the aioB and aioA genes, which encode the arsenite oxidase but the regulatory genes typically found upstream of aioB in other members of the Proteobacteria were absent. The GM1 Aio was purified to homogeneity and was found to be a heterodimer. The enzyme contained Mo and Fe as cofactors and had, using the artificial electron acceptor 2,6-dichlorophenolindophenol, a Km for arsenite of 111.70 ± 0.88 μM and a Vmax of 12.16 ± 0.30 U mg(-1), which is the highest reported specific activity for any known Aio. The temperature-activity profiles of the arsenite oxidases from GM1 and the mesophilic betaproteobacterium Alcaligenes faecalis were compared and showed that the GM1 Aio was more active at low temperatures than that of A. faecalis. A homology model of the GM1 Aio was made using the X-ray crystal structure of the Aio from A. faecalis as the template. Structural changes that account for cold adaptation were identified and it was found that these resulted in increased enzyme flexibility and a reduction in the hydrophobicity of the core.
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Affiliation(s)
- Thomas H Osborne
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
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22
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Warelow TP, Oke M, Schoepp-Cothenet B, Dahl JU, Bruselat N, Sivalingam GN, Leimkühler S, Thalassinos K, Kappler U, Naismith JH, Santini JM. The respiratory arsenite oxidase: structure and the role of residues surrounding the rieske cluster. PLoS One 2013; 8:e72535. [PMID: 24023621 PMCID: PMC3758308 DOI: 10.1371/journal.pone.0072535] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Accepted: 07/10/2013] [Indexed: 11/18/2022] Open
Abstract
The arsenite oxidase (Aio) from the facultative autotrophic Alphaproteobacterium Rhizobium sp. NT-26 is a bioenergetic enzyme involved in the oxidation of arsenite to arsenate. The enzyme from the distantly related heterotroph, Alcaligenes faecalis, which is thought to oxidise arsenite for detoxification, consists of a large α subunit (AioA) with bis-molybdopterin guanine dinucleotide at its active site and a 3Fe-4S cluster, and a small β subunit (AioB) which contains a Rieske 2Fe-2S cluster. The successful heterologous expression of the NT-26 Aio in Escherichia coli has resulted in the solution of its crystal structure. The NT-26 Aio, a heterotetramer, shares high overall similarity to the heterodimeric arsenite oxidase from A. faecalis but there are striking differences in the structure surrounding the Rieske 2Fe-2S cluster which we demonstrate explains the difference in the observed redox potentials (+225 mV vs. +130/160 mV, respectively). A combination of site-directed mutagenesis and electron paramagnetic resonance was used to explore the differences observed in the structure and redox properties of the Rieske cluster. In the NT-26 AioB the substitution of a serine (S126 in NT-26) for a threonine as in the A. faecalis AioB explains a -20 mV decrease in redox potential. The disulphide bridge in the A. faecalis AioB which is conserved in other betaproteobacterial AioB subunits and the Rieske subunit of the cytochrome bc 1 complex is absent in the NT-26 AioB subunit. The introduction of a disulphide bridge had no effect on Aio activity or protein stability but resulted in a decrease in the redox potential of the cluster. These results are in conflict with previous data on the betaproteobacterial AioB subunit and the Rieske of the bc 1 complex where removal of the disulphide bridge had no effect on the redox potential of the former but a decrease in cluster stability was observed in the latter.
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Affiliation(s)
- Thomas P. Warelow
- Institute of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Muse Oke
- Centre for Biomolecular Sciences, University of St Andrews, St Andrews, United Kingdom
| | - Barbara Schoepp-Cothenet
- Laboratoire de Bioénergétique et Ingénierie des Protéines, BIP/CNRS, UMR7281, AMU, Marseille, France
| | - Jan U. Dahl
- Universität Potsdam, Institut für Biochemie and Biologie, Potsdam, Germany
| | - Nicole Bruselat
- Institute of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Ganesh N. Sivalingam
- Institute of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Silke Leimkühler
- Universität Potsdam, Institut für Biochemie and Biologie, Potsdam, Germany
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Ulrike Kappler
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - James H. Naismith
- Centre for Biomolecular Sciences, University of St Andrews, St Andrews, United Kingdom
| | - Joanne M. Santini
- Institute of Structural and Molecular Biology, University College London, London, United Kingdom
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Slyemi D, Moinier D, Talla E, Bonnefoy V. Organization and regulation of the arsenite oxidase operon of the moderately acidophilic and facultative chemoautotrophic Thiomonas arsenitoxydans. Extremophiles 2013; 17:911-20. [DOI: 10.1007/s00792-013-0573-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 07/30/2013] [Indexed: 10/26/2022]
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Kalimuthu P, Heath MD, Santini JM, Kappler U, Bernhardt PV. Electrochemically driven catalysis of Rhizobium sp. NT-26 arsenite oxidase with its native electron acceptor cytochrome c552. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:112-20. [PMID: 23891971 DOI: 10.1016/j.bbabio.2013.07.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 07/05/2013] [Accepted: 07/19/2013] [Indexed: 10/26/2022]
Abstract
We describe the catalytic voltammograms of the periplasmic arsenite oxidase (Aio) from the chemolithoautotrophic bacterium Rhizobium sp. str. NT-26 that oxidizes arsenite to arsenate. Electrochemistry of the enzyme was accomplished using its native electron transfer partner, cytochrome c552 (cyt c552), as a mediator. The protein cyt c552 adsorbed on a mercaptoundecanoic acid (MUA) modified Au electrode exhibited a stable, reversible one-electron voltammetric response at +275mV vs NHE (pH6). In the presence of arsenite and Aio the voltammetry of cyt c552 is transformed from a transient response to an amplified sigmoidal (steady state) wave consistent with an electro-catalytic system. Digital simulation was performed using a single set of parameters for all catalytic voltammetries obtained at different sweep rates and various substrate concentrations. The obtained kinetic constants from digital simulation provide new insight into the kinetics of the NT-26 Aio catalytic mechanism.
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Affiliation(s)
- Palraj Kalimuthu
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia
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Poirel J, Joulian C, Leyval C, Billard P. Arsenite-induced changes in abundance and expression of arsenite transporter and arsenite oxidase genes of a soil microbial community. Res Microbiol 2013; 164:457-65. [DOI: 10.1016/j.resmic.2013.01.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 01/26/2013] [Indexed: 11/15/2022]
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26
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Cavalca L, Corsini A, Zaccheo P, Andreoni V, Muyzer G. Microbial transformations of arsenic: perspectives for biological removal of arsenic from water. Future Microbiol 2013; 8:753-68. [DOI: 10.2217/fmb.13.38] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Arsenic is present in many environments and is released by various natural processes and anthropogenic actions. Although arsenic is recognized to cause a wide range of adverse health effects in humans, diverse bacteria can metabolize it by detoxification and energy conservation reactions. This review highlights the current understanding of the ecology, biochemistry and genomics of these bacteria, and their potential application in the treatment of arsenic-polluted water.
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Affiliation(s)
- Lucia Cavalca
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milano, Italy.
| | - Anna Corsini
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milano, Italy
| | - Patrizia Zaccheo
- Dipartimento di Scienze Agrarie e Ambientali – Produzione, Territorio, Agroenergia (DiSAA), Università degli Studi di Milano, Milano, Italy
| | - Vincenza Andreoni
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milano, Italy
| | - Gerard Muyzer
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milano, Italy
- Institute for Biodiversity & Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands
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The prokaryotic Mo/W-bisPGD enzymes family: a catalytic workhorse in bioenergetic. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1048-85. [PMID: 23376630 DOI: 10.1016/j.bbabio.2013.01.011] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 01/21/2013] [Accepted: 01/23/2013] [Indexed: 01/05/2023]
Abstract
Over the past two decades, prominent importance of molybdenum-containing enzymes in prokaryotes has been put forward by studies originating from different fields. Proteomic or bioinformatic studies underpinned that the list of molybdenum-containing enzymes is far from being complete with to date, more than fifty different enzymes involved in the biogeochemical nitrogen, carbon and sulfur cycles. In particular, the vast majority of prokaryotic molybdenum-containing enzymes belong to the so-called dimethylsulfoxide reductase family. Despite its extraordinary diversity, this family is characterized by the presence of a Mo/W-bis(pyranopterin guanosine dinucleotide) cofactor at the active site. This review highlights what has been learned about the properties of the catalytic site, the modular variation of the structural organization of these enzymes, and their interplay with the isoprenoid quinones. In the last part, this review provides an integrated view of how these enzymes contribute to the bioenergetics of prokaryotes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Slyemi D, Bonnefoy V. How prokaryotes deal with arsenic(†). ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:571-586. [PMID: 23760928 DOI: 10.1111/j.1758-2229.2011.00300.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Arsenic is a notorious poison classified as a carcinogen, a teratogen and a clastogen that ranks number one on the Environmental Protection Agency's priority list of drinking water contaminants. It is ubiquitous and relatively abundant in the Earth's crust. Its mobilization in waters by weathering, volcanic, anthropogenic or biological activities represents a major hazard to public health, exemplified in India and Bangladesh where 50 million people are acutely at risk. Since basically the origin of life, microorganisms have been exposed to this toxic compound and have evolved a variety of resistance mechanisms, such as extracellular precipitation, chelation, intracellular sequestration, active extrusion from the cell or biochemical transformation (redox or methylation). Arsenic efflux systems are widespread and are found in nearly all organisms. Some microorganisms are also able to utilize this metalloid as a metabolic energy source through either arsenite oxidation or arsenate reduction. The energy metabolism involving redox reactions of arsenic has been suggested to have evolved during early life on Earth. This review highlights the different systems evolved by prokaryotes to cope with arsenic and how they participate in its biogeochemical cycle.
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Affiliation(s)
- Djamila Slyemi
- Laboratoire de Chimie Bactérienne, UPR-CNRS 9043, Institut de Microbiologie de la Méditerranée, 31 chemin Joseph Aiguier, 13402, Marseille, Cedex 20, France. Aix-Marseille Université, Marseille, France
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Engel AS, Johnson LR, Porter ML. Arsenite oxidase gene diversity among Chloroflexi and Proteobacteria from El Tatio Geyser Field, Chile. FEMS Microbiol Ecol 2012; 83:745-56. [PMID: 23066664 DOI: 10.1111/1574-6941.12030] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 10/05/2012] [Accepted: 10/07/2012] [Indexed: 11/29/2022] Open
Abstract
Arsenic concentrations (450-600 μmol L(-1)) at the El Tatio Geyser Field in northern Chile are an order of magnitude greater than at other natural geothermal sites, making El Tatio an ideal location to investigate unique microbial diversity and metabolisms associated with the arsenic cycle in low sulfide, > 50 °C, and circumneutral pH waters. 16S rRNA gene and arsenite oxidase gene (aioA) diversities were evaluated from biofilms and microbial mats from two geyser-discharge stream transects. Chloroflexi was the most prevalent bacterial phylum at flow distances where arsenite was converted to arsenate, corresponding to roughly 60 °C. Among aioA-like gene sequences retrieved, most had homology to whole genomes of Chloroflexus aurantiacus, but others were homologous to alphaproteobacterial and undifferentiated beta- and gammaproteobacterial groups. No Deinococci, Thermus, Aquificales, or Chlorobi aioA-like genes were retrieved. The functional importance of amino acid sites was evaluated from evolutionary trace analyses of all retrieved aioA genes. Fifteen conserved residue sites identified across all phylogenetic groups highlight a conserved functional core, while six divergent sites demonstrate potential differences in electron transfer modes. This research expands the known distribution and diversity of arsenite oxidation in natural geothermal settings, and provides information about the evolutionary history of microbe-arsenic interactions.
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Affiliation(s)
- Annette Summers Engel
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, USA.
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Kang YS, Heinemann J, Bothner B, Rensing C, McDermott TR. Integrated co-regulation of bacterial arsenic and phosphorus metabolisms. Environ Microbiol 2012; 14:3097-109. [PMID: 23057575 DOI: 10.1111/j.1462-2920.2012.02881.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Revised: 08/19/2012] [Accepted: 08/20/2012] [Indexed: 11/30/2022]
Abstract
Arsenic ranks first on the US Environmental Protection Agency Superfund List of Hazardous Substances. Its mobility and toxicity depend upon chemical speciation, which is significantly driven by microbial redox transformations. Genome sequence-enabled surveys reveal that in many microorganisms genes essential to arsenite (AsIII) oxidation are located immediately adjacent to genes coding for functions associated with phosphorus (Pi) acquisition, implying some type of functional importance to the metabolism of As, Pi or both. We extensively document how expression of genes key to AsIII oxidation and the Pi stress response are intricately co-regulated in the soil bacterium Agrobacterium tumefaciens. These observations significantly expand our understanding of how environmental factors influence microbial AsIII metabolism and contribute to the current discussion of As and P metabolism in the microbial cell.
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Affiliation(s)
- Yoon-Suk Kang
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA
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van Lis R, Nitschke W, Duval S, Schoepp-Cothenet B. Arsenics as bioenergetic substrates. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:176-88. [PMID: 22982475 DOI: 10.1016/j.bbabio.2012.08.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 08/28/2012] [Accepted: 08/31/2012] [Indexed: 01/24/2023]
Abstract
Although at low concentrations, arsenic commonly occurs naturally as a local geological constituent. Whereas both arsenate and arsenite are strongly toxic to life, a number of prokaryotes use these compounds as electron acceptors or donors, respectively, for bioenergetic purposes via respiratory arsenate reductase, arsenite oxidase and alternative arsenite oxidase. The recent burst in discovered arsenite oxidizing and arsenate respiring microbes suggests the arsenic bioenergetic metabolisms to be anything but exotic. The first goal of the present review is to bring to light the widespread distribution and diversity of these metabolizing pathways. The second goal is to present an evolutionary analysis of these diverse energetic pathways. Taking into account not only the available data on the arsenic metabolizing enzymes and their phylogenetical relatives but also the palaeogeochemical records, we propose a crucial role of arsenite oxidation via arsenite oxidase in primordial life. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.
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Affiliation(s)
- Robert van Lis
- Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 CNRS/AMU, FR3479, F-13402 Marseille Cedex 20, France
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Heterologously expressed arsenite oxidase: A system to study biogenesis and structure/function relationships of the enzyme family. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1701-8. [DOI: 10.1016/j.bbabio.2012.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 05/31/2012] [Accepted: 06/01/2012] [Indexed: 11/19/2022]
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Abstract
In this study with the model organism Agrobacterium tumefaciens, we used a combination of lacZ gene fusions, reverse transcriptase PCR (RT-PCR), and deletion and insertional inactivation mutations to show unambiguously that the alternative sigma factor RpoN participates in the regulation of As(III) oxidation. A deletion mutation that removed the RpoN binding site from the aioBA promoter and an aacC3 (gentamicin resistance) cassette insertional inactivation of the rpoN coding region eliminated aioBA expression and As(III) oxidation, although rpoN expression was not related to cell exposure to As(III). Putative RpoN binding sites were identified throughout the genome and, as examples, included promoters for aioB, phoB1, pstS1, dctA, glnA, glnB, and flgB that were examined by using qualitative RT-PCR and lacZ reporter fusions to assess the relative contribution of RpoN to their transcription. The expressions of aioB and dctA in the wild-type strain were considerably enhanced in cells exposed to As(III), and both genes were silent in the rpoN::aacC3 mutant regardless of As(III). The expression level of glnA was not influenced by As(III) but was reduced (but not silent) in the rpoN::aacC3 mutant and further reduced in the mutant under N starvation conditions. The rpoN::aacC3 mutation had no obvious effect on the expression of glnB, pstS1, phoB1, or flgB. These experiments provide definitive evidence to document the requirement of RpoN for As(III) oxidation but also illustrate that the presence of a consensus RpoN binding site does not necessarily link the associated gene with regulation by As(III) or by this sigma factor.
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Bachate SP, Khapare RM, Kodam KM. Oxidation of arsenite by two β-proteobacteria isolated from soil. Appl Microbiol Biotechnol 2011; 93:2135-45. [PMID: 21983709 DOI: 10.1007/s00253-011-3606-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 08/29/2011] [Accepted: 09/22/2011] [Indexed: 10/17/2022]
Abstract
Two heterotrophic As(III)-oxidizing bacteria, SPB-24 and SPB-31 were isolated from garden soil. Based on 16S rRNA gene sequence analysis, strain SPB-24 was closely related to genus Bordetella, and strain SPB-31 was most closely related to genus Achromobacter. Both strains exhibited high As(III) (15 mM for SPB-24 and 40 mM for SPB-31) and As(V) (>300 mM for both strains) resistance. Both strains oxidized 5 mM As(III) in minimal medium with oxidation rate of 554 and 558 μM h(-1) for SPB-24 and SPB-31, respectively. Washed cells of both strains oxidized As(III) over broad pH and temperature range with optimum pH 6 and temperature 42°C for both strains. The As(III) oxidation kinetic by washed cells showed K (m) and V (max) values of 41.7 μM and 1,166 μM h(-1) for SPB-24, 52 μM and 1,186 μM h(-1) for SPB-31. In the presence of minimal amount of carbon source, the strains showed high As(III) oxidation rate and high specific arsenite oxidase activity. The ability of strains to resist high concentration of arsenic and oxidize As(III) with highest rates reported so far makes them potential candidates for bioremediation of arsenic-contaminated environment.
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Affiliation(s)
- Sachin P Bachate
- Division of Biochemistry, Department of Chemistry, University of Pune, Pune, 411007, India
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Unsuspected diversity of arsenite-oxidizing bacteria as revealed by widespread distribution of the aoxB gene in prokaryotes. Appl Environ Microbiol 2011; 77:4685-92. [PMID: 21571879 DOI: 10.1128/aem.02884-10] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, new strains were isolated from an environment with elevated arsenic levels, Sainte-Marie-aux-Mines (France), and the diversity of aoxB genes encoding the arsenite oxidase large subunit was investigated. The distribution of bacterial aoxB genes is wider than what was previously thought. AoxB subfamilies characterized by specific signatures were identified. An exhaustive analysis of AoxB sequences from this study and from public databases shows that horizontal gene transfer has likely played a role in the spreading of aoxB in prokaryotic communities.
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Duval S, Santini JM, Nitschke W, Hille R, Schoepp-Cothenet B. The small subunit AroB of arsenite oxidase: lessons on the [2Fe-2S] Rieske protein superfamily. J Biol Chem 2010; 285:20442-51. [PMID: 20421651 DOI: 10.1074/jbc.m110.113811] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Here, we describe the characterization of the [2Fe-2S] clusters of arsenite oxidases from Rhizobium sp. NT-26 and Ralstonia sp. 22. Both reduced Rieske proteins feature EPR signals similar to their homologs from Rieske-cyt b complexes, with g values at 2.027, 1.88, and 1.77. Redox titrations in a range of pH values showed that both [2Fe-2S] centers have constant E(m) values up to pH 8 at approximately +210 mV. Above this pH value, the E(m) values of both centers are pH-dependent, similar to what is observed for the Rieske-cyt b complexes. The redox properties of these two proteins, together with the low E(m) value (+160 mV) of the Alcaligenes faecalis arsenite oxidase Rieske (confirmed herein), are in line with the structural determinants observed in the primary sequences, which have previously been deduced from the study of Rieske-cyt b complexes. Since the published E(m) value of the Chloroflexus aurantiacus Rieske (+100 mV) is in conflict with this sequence analysis, we re-analyzed membrane samples of this organism and obtain a new value (+200 mV). Arsenite oxidase activity was affected by quinols and quinol analogs, which is similar to what is found with the Rieske-cyt b complexes. Together, these results show that the Rieske protein of arsenite oxidase shares numerous properties with its counterpart in the Rieske-cyt b complex. However, two cysteine residues, strictly conserved in the Rieske-cyt b-Rieske and considered to be crucial for its function, are not conserved in the arsenite oxidase counterpart. We discuss the role of these residues.
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Affiliation(s)
- Simon Duval
- Laboratoire de Bioénergétique et Ingénierie des Protéines UPR 9036, Institut de Biologie Structurale et Microbiologie, CNRS, F-13402 Marseille Cedex 20, France
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