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Giri NC, Mintmier B, Radhakrishnan M, Mielke JW, Wilcoxen J, Basu P. The critical role of a conserved lysine residue in periplasmic nitrate reductase catalyzed reactions. J Biol Inorg Chem 2024; 29:395-405. [PMID: 38782786 DOI: 10.1007/s00775-024-02057-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/10/2024] [Indexed: 05/25/2024]
Abstract
Periplasmic nitrate reductase NapA from Campylobacter jejuni (C. jejuni) contains a molybdenum cofactor (Moco) and a 4Fe-4S cluster and catalyzes the reduction of nitrate to nitrite. The reducing equivalent required for the catalysis is transferred from NapC → NapB → NapA. The electron transfer from NapB to NapA occurs through the 4Fe-4S cluster in NapA. C. jejuni NapA has a conserved lysine (K79) between the Mo-cofactor and the 4Fe-4S cluster. K79 forms H-bonding interactions with the 4Fe-4S cluster and connects the latter with the Moco via an H-bonding network. Thus, it is conceivable that K79 could play an important role in the intramolecular electron transfer and the catalytic activity of NapA. In the present study, we show that the mutation of K79 to Ala leads to an almost complete loss of activity, suggesting its role in catalytic activity. The inhibition of C. jejuni NapA by cyanide, thiocyanate, and azide has also been investigated. The inhibition studies indicate that cyanide inhibits NapA in a non-competitive manner, while thiocyanate and azide inhibit NapA in an uncompetitive manner. Neither inhibition mechanism involves direct binding of the inhibitor to the Mo-center. These results have been discussed in the context of the loss of catalytic activity of NapA K79A variant and a possible anion binding site in NapA has been proposed.
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Affiliation(s)
- Nitai C Giri
- Department of Chemistry and Chemical Biology, Indiana University Indianapolis, Indianapolis, IN, USA
| | - Breeanna Mintmier
- Department of Chemistry and Chemical Biology, Indiana University Indianapolis, Indianapolis, IN, USA
| | - Manohar Radhakrishnan
- Department of Chemistry and Chemical Biology, Indiana University Indianapolis, Indianapolis, IN, USA
| | - Jonathan W Mielke
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Jarett Wilcoxen
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
| | - Partha Basu
- Department of Chemistry and Chemical Biology, Indiana University Indianapolis, Indianapolis, IN, USA.
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2
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Ahmad I, Singh AK, Mohd S, Katari SK, Nalamolu RM, Ahmad A, Baothman OA, Hosawi SA, Altayeb H, Nadeem MS, Ahmad V. In Silico Insights into the Arsenic Binding Mechanism Deploying Application of Computational Biology-Based Toolsets. ACS OMEGA 2024; 9:7529-7544. [PMID: 38405466 PMCID: PMC10882604 DOI: 10.1021/acsomega.3c06313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/27/2024]
Abstract
An assortment of environmental matrices includes arsenic (As) in its different oxidation states, which is often linked to concerns that pose a threat to public health worldwide. The current difficulty lies in addressing toxicological concerns and achieving sustained detoxification of As. Multiple conventional degradation methods are accessible; however, they are indeed labor-intensive, expensive, and reliant on prolonged laboratory evaluations. Molecular interaction and atomic level degradation mechanisms for enzyme-As exploration are, however, underexplored in those approaches. A feasible approach in this case for tackling this accompanying concern of As might be to cope with undertaking multivalent computational methodologies and tools. This work aimed to provide molecular-level insight into the enzyme-aided As degradation mechanism. AutoDock Vina, CABS-flex 2.0, and Desmond high-performance molecular dynamics simulation (MDS) were utilized in the current investigation to simulate multivalent molecular processes on two protein sets: arsenate reductase (ArsC) and laccase (LAC) corresponding arsenate (ART) and arsenite (AST), which served as model ligands to comprehend binding, conformational, and energy attributes. The structural configurations of both proteins exhibited variability in flexibility and structure framework within the range of 3.5-4.5 Å. The LAC-ART complex exhibited the lowest calculated binding affinity, measuring -5.82 ± 0.01 kcal/mol. Meanwhile, active site residues ILE-200 and HIS-206 were demonstrated to engage in H-bonding with the ART ligand. In contrast to ArsC, the ligand binding affinity of this bound complex was considerably greater. Additional validation of docked complexes was carried out by deploying Desmond MDS of 100 ns to capture protein and ligand conformation behavior. The system achieved stability during the 100 ns simulation run, as confirmed by the average P-L RMSD, which was ∼1 Å. As a preliminary test of the enzyme's ability to catalyze As species, corresponding computational insights might be advantageous for bridging gaps and regulatory consideration.
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Affiliation(s)
- Imran Ahmad
- Department
of Biochemistry, King George’s Medical
University, Lucknow, Uttar Pradesh 226003, India
- Environmental
Toxicology Group, CSIR-Indian Institute
of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Anil Kumar Singh
- Environmental
Toxicology Group, CSIR-Indian Institute
of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shayan Mohd
- Department
of Bioengineering, Faculty of Engineering, Integral University, Dasauli, Kursi Road, Lucknow 226026, India
| | - Sudheer Kumar Katari
- Department
of Biotechnology, Vignan’s Foundation
for Science, Technology & Research, Vadlamudi, Andhra Pradesh 522213, India
| | - Ravina Madhulitha Nalamolu
- Department
of Biotechnology, Vignan’s Foundation
for Science, Technology & Research, Vadlamudi, Andhra Pradesh 522213, India
| | - Abrar Ahmad
- Department
of Biochemistry, Faculty of Sciences, King
Abdulaziz University, Jeddah 21589, Kingdom
of Saudi Arabia
| | - Othman A. Baothman
- Department
of Biochemistry, Faculty of Sciences, King
Abdulaziz University, Jeddah 21589, Kingdom
of Saudi Arabia
| | - Salman A. Hosawi
- Department
of Biochemistry, Faculty of Sciences, King
Abdulaziz University, Jeddah 21589, Kingdom
of Saudi Arabia
| | - Hisham Altayeb
- Department
of Biochemistry, Faculty of Sciences, King
Abdulaziz University, Jeddah 21589, Kingdom
of Saudi Arabia
| | - Muhammad Shahid Nadeem
- Department
of Biochemistry, Faculty of Sciences, King
Abdulaziz University, Jeddah 21589, Kingdom
of Saudi Arabia
| | - Varish Ahmad
- Department
of Health Information Technology, Faculty of Applied Studies, King Abdulaziz University, Jeddah 21589, Kingdom of Saudi Arabia
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William VU, Magpantay HD. Arsenic and Microorganisms: Genes, Molecular Mechanisms, and Recent Advances in Microbial Arsenic Bioremediation. Microorganisms 2023; 12:74. [PMID: 38257901 PMCID: PMC10820871 DOI: 10.3390/microorganisms12010074] [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: 11/30/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
Throughout history, cases of arsenic poisoning have been reported worldwide, and the highly toxic effects of arsenic to humans, plants, and animals are well documented. Continued anthropogenic activities related to arsenic contamination in soil and water, as well as its persistency and lethality, have allowed arsenic to remain a pollutant of high interest and concern. Constant scrutiny has eventually resulted in new and better techniques to mitigate it. Among these, microbial remediation has emerged as one of the most important due to its reliability, safety, and sustainability. Over the years, numerous microorganisms have been successfully shown to remove arsenic from various environmental matrices. This review provides an overview of the interactions between microorganisms and arsenic, the different mechanisms utilized by microorganisms to detoxify arsenic, as well as current trends in the field of microbial-based bioremediation of arsenic. While the potential of microbial bioremediation of arsenic is notable, further studies focusing on the field-scale applicability of this technology is warranted.
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Affiliation(s)
| | - Hilbert D. Magpantay
- Department of Chemistry, De La Salle University, 2401 Taft Avenue, Manila 0922, Philippines;
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Runda ME, de Kok NAW, Schmidt S. Rieske Oxygenases and Other Ferredoxin-Dependent Enzymes: Electron Transfer Principles and Catalytic Capabilities. Chembiochem 2023; 24:e202300078. [PMID: 36964978 DOI: 10.1002/cbic.202300078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 03/27/2023]
Abstract
Enzymes that depend on sophisticated electron transfer via ferredoxins (Fds) exhibit outstanding catalytic capabilities, but despite decades of research, many of them are still not well understood or exploited for synthetic applications. This review aims to provide a general overview of the most important Fd-dependent enzymes and the electron transfer processes involved. While several examples are discussed, we focus in particular on the family of Rieske non-heme iron-dependent oxygenases (ROs). In addition to illustrating their electron transfer principles and catalytic potential, the current state of knowledge on structure-function relationships and the mode of interaction between the redox partner proteins is reviewed. Moreover, we highlight several key catalyzed transformations, but also take a deeper dive into their engineerability for biocatalytic applications. The overall findings from these case studies highlight the catalytic capabilities of these biocatalysts and could stimulate future interest in developing additional Fd-dependent enzyme classes for synthetic applications.
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Affiliation(s)
- Michael E Runda
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Niels A W de Kok
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Sandy Schmidt
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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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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6
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Mohsin H, Shafique M, Zaid M, Rehman Y. Microbial biochemical pathways of arsenic biotransformation and their application for bioremediation. Folia Microbiol (Praha) 2023:10.1007/s12223-023-01068-6. [PMID: 37326815 DOI: 10.1007/s12223-023-01068-6] [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: 12/17/2022] [Accepted: 05/19/2023] [Indexed: 06/17/2023]
Abstract
Arsenic is a ubiquitous toxic metalloid, the concentration of which is beyond WHO safe drinking water standards in many areas of the world, owing to many natural and anthropogenic activities. Long-term exposure to arsenic proves lethal for plants, humans, animals, and even microbial communities in the environment. Various sustainable strategies have been developed to mitigate the harmful effects of arsenic which include several chemical and physical methods, however, bioremediation has proved to be an eco-friendly and inexpensive technique with promising results. Many microbes and plant species are known for arsenic biotransformation and detoxification. Arsenic bioremediation involves different pathways such as uptake, accumulation, reduction, oxidation, methylation, and demethylation. Each of these pathways has a certain set of genes and proteins to carry out the mechanism of arsenic biotransformation. Based on these mechanisms, various studies have been conducted for arsenic detoxification and removal. Genes specific for these pathways have also been cloned in several microorganisms to enhance arsenic bioremediation. This review discusses different biochemical pathways and the associated genes which play important roles in arsenic redox reactions, resistance, methylation/demethylation, and accumulation. Based on these mechanisms, new methods can be developed for effective arsenic bioremediation.
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Affiliation(s)
- Hareem Mohsin
- Department of Life Sciences, School of Science, University of Management and Technology, Lahore, Pakistan
| | - Maria Shafique
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan
| | - Muhammad Zaid
- Department of Life Sciences, School of Science, University of Management and Technology, Lahore, Pakistan
| | - Yasir Rehman
- Department of Life Sciences, School of Science, University of Management and Technology, Lahore, Pakistan.
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7
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Al-Ansari MM. Influence of blue light on effective removal of arsenic by photosynthetic bacterium Rhodobacter sp. BT18. CHEMOSPHERE 2022; 292:133399. [PMID: 34952019 DOI: 10.1016/j.chemosphere.2021.133399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Arsenic (As) contamination in an ecosystem has been a serious threat for the ecosystem as well as human health. Thus, the present study was established an eco-friendly remediation of As by using As resistant Rhodobacter sp. Accordingly, the growth of Rhodobacter sp. in As stress environment was assessed. Expectedly, enhanced growth order of the Rhodobacter sp., under As stress was found to be control >50 > 100 > 200 > 300 > 400 > 500 mg/L of As. In addition, the present study explored the influence of various light sources (Yellow, light blue, red, green and white) on growth and As removal mechanisms of Rhodobacter sp. The growth profile of the bacteria indicated that the light blue source showed an enhanced growth at 72 h of incubation. Based on optimization experiments, an increased As removal percentage rate was found to be at 87.5% at pH 7.0, 3% of glucose, 1% of citrate supplemented in the medium. The As resistant genetic pattern for arsenic transformation, the genes arsenate reductase (arsC), arsenite oxidase (aio) was investigated. To study the transcript level expression of arsC and aio genes were performed after exposure to different concentrations of As (50, 100, 150, and 200 mg/L) at different time intervals (24, 48, 72 and 96 h). The results showed that both arsC and aio were up regulated from 24 to 72 h and the down regulation was observed at 96 h. The obtained results indicated that the Rhodobacter sp., possess significant AS tolerance and removal potential would make it is a noteworthy candidate for future As remediation practices.
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Affiliation(s)
- Mysoon M Al-Ansari
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.
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8
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Pal S, Sengupta K. In silico analysis of phylogeny, structure, and function of arsenite oxidase from unculturable microbiome of arsenic contaminated soil. J Genet Eng Biotechnol 2021; 19:47. [PMID: 33779860 PMCID: PMC8006529 DOI: 10.1186/s43141-021-00146-x] [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: 10/23/2020] [Accepted: 03/12/2021] [Indexed: 11/10/2022]
Abstract
Background Arsenite oxidase (EC 1.20.2.1) is a metalloenzyme that catalyzes the oxidation of arsenite into lesser toxic arsenate. In this study, 78 amino acid sequences of arsenite oxidase from unculturable bacteria available in metagenomic data of arsenic-contaminated soil have been characterized by using standard bioinformatics tools to investigate its phylogenetic relationships, three-dimensional structure and functional parameters. Results The phylogenetic relationship of all arsenite oxidase from unculturable microorganisms was revealed their closeness to bacterial order Rhizobiales. The higher aliphatic content showed that these enzymes are thermostable and could be used for in situ bioremediation. A representative protein from each phylogenetic cluster was analysed for secondary structure arrangements which indicated the presence of α-helices (~63%), β-sheets (57–60%) and turns (13–15%). The validated 3D models suggested that these proteins are hetero-dimeric with two chains whereas alpha chain is the main catalytic subunit which binds with arsenic oxides. Three representative protein models were deposited in Protein Model Database. The query enzymes were predicted with two conserved motifs, one is Rieske 3Fe-4S and the other is molybdopterin protein. Conclusions Computational analysis of protein interactome revealed the protein partners might be involved in the whole process of arsenic detoxification by Rhizobiales. The overall report is unique to the best of our knowledge, and the importance of this study is to understand the theoretical aspects of the structure and functions of arsenite oxidase in unculturable bacteria residing in arsenic-contaminated sites. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-021-00146-x.
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Affiliation(s)
- Siddhartha Pal
- National Centre for Cell Science, Ganeshkhind, Pune, 411007, India
| | - Kriti Sengupta
- Bioenergy Group, Agharkar Research Institute, Gopal Ganesh Agarkar Road, Pune, 411004, India.
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9
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Zhong Q, Kobe B, Kappler U. Molybdenum Enzymes and How They Support Virulence in Pathogenic Bacteria. Front Microbiol 2020; 11:615860. [PMID: 33362753 PMCID: PMC7759655 DOI: 10.3389/fmicb.2020.615860] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 11/23/2020] [Indexed: 12/11/2022] Open
Abstract
Mononuclear molybdoenzymes are highly versatile catalysts that occur in organisms in all domains of life, where they mediate essential cellular functions such as energy generation and detoxification reactions. Molybdoenzymes are particularly abundant in bacteria, where over 50 distinct types of enzymes have been identified to date. In bacterial pathogens, all aspects of molybdoenzyme biology such as molybdate uptake, cofactor biosynthesis, and function of the enzymes themselves, have been shown to affect fitness in the host as well as virulence. Although current studies are mostly focused on a few key pathogens such as Escherichia coli, Salmonella enterica, Campylobacter jejuni, and Mycobacterium tuberculosis, some common themes for the function and adaptation of the molybdoenzymes to pathogen environmental niches are emerging. Firstly, for many of these enzymes, their role is in supporting bacterial energy generation; and the corresponding pathogen fitness and virulence defects appear to arise from a suboptimally poised metabolic network. Secondly, all substrates converted by virulence-relevant bacterial Mo enzymes belong to classes known to be generated in the host either during inflammation or as part of the host signaling network, with some enzyme groups showing adaptation to the increased conversion of such substrates. Lastly, a specific adaptation to bacterial in-host survival is an emerging link between the regulation of molybdoenzyme expression in bacterial pathogens and the presence of immune system-generated reactive oxygen species. The prevalence of molybdoenzymes in key bacterial pathogens including ESKAPE pathogens, paired with the mounting evidence of their central roles in bacterial fitness during infection, suggest that they could be important future drug targets.
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Affiliation(s)
- Qifeng Zhong
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Bostjan Kobe
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.,Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, Australia
| | - Ulrike Kappler
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
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10
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Mintmier B, McGarry JM, Bain DJ, Basu P. Kinetic consequences of the endogenous ligand to molybdenum in the DMSO reductase family: a case study with periplasmic nitrate reductase. J Biol Inorg Chem 2020; 26:13-28. [PMID: 33131003 DOI: 10.1007/s00775-020-01833-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/20/2020] [Indexed: 11/24/2022]
Abstract
The molybdopterin enzyme family catalyzes a variety of substrates and plays a critical role in the cycling of carbon, nitrogen, arsenic, and selenium. The dimethyl sulfoxide reductase (DMSOR) subfamily is the most diverse family of molybdopterin enzymes and the members of this family catalyze a myriad of reactions that are important in microbial life processes. Enzymes in the DMSOR family can transform multiple substrates; however, quantitative information about the substrate preference is sparse, and, more importantly, the reasons for the substrate selectivity are not clear. Molybdenum coordination has long been proposed to impact the catalytic activity of the enzyme. Specifically, the molybdenum-coordinating residue may tune substrate preference. As such, molybdopterin enzyme periplasmic nitrate reductase (Nap) is utilized as a vehicle to understand the substrate preference and delineate the kinetic underpinning of the differences imposed by exchanging the molybdenum ligands. To this end, NapA from Campylobacter jejuni has been heterologously overexpressed, and a series of variants, where the molybdenum coordinating cysteine has been replaced with another amino acid, has been produced. The kinetic properties of these variants are discussed and compared with those of the native enzyme, providing quantitative information to understand the function of the molybdenum-coordinating residue.
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Affiliation(s)
- Breeanna Mintmier
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N Blackford St, Indianapolis, IN, 46202, USA
| | - Jennifer M McGarry
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N Blackford St, Indianapolis, IN, 46202, USA
| | - Daniel J Bain
- Department of Geology and Environmental Science, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Partha Basu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N Blackford St, Indianapolis, IN, 46202, USA.
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11
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Functional mononuclear molybdenum enzymes: challenges and triumphs in molecular cloning, expression, and isolation. J Biol Inorg Chem 2020; 25:547-569. [PMID: 32279136 DOI: 10.1007/s00775-020-01787-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/30/2020] [Indexed: 10/24/2022]
Abstract
Mononuclear molybdenum enzymes catalyze a variety of reactions that are essential in the cycling of nitrogen, carbon, arsenic, and sulfur. For decades, the structure and function of these crucial enzymes have been investigated to develop a fundamental knowledge for this vast family of enzymes and the chemistries they carry out. Therefore, obtaining abundant quantities of active enzyme is necessary for exploring this family's biochemical capability. This mini-review summarizes the methods for overexpressing mononuclear molybdenum enzymes in the context of the challenges encountered in the process. Effective methods for molybdenum cofactor synthesis and incorporation, optimization of expression conditions, improving isolation of active vs. inactive enzyme, incorporation of additional prosthetic groups, and inclusion of redox enzyme maturation protein chaperones are discussed in relation to the current molybdenum enzyme literature. This article summarizes the heterologous and homologous expression studies providing underlying patterns and potential future directions.
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12
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Zeamari K, Gerbaud G, Grosse S, Fourmond V, Chaspoul F, Biaso F, Arnoux P, Sabaty M, Pignol D, Guigliarelli B, Burlat B. Tuning the redox properties of a [4Fe-4S] center to modulate the activity of Mo-bisPGD periplasmic nitrate reductase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:402-413. [DOI: 10.1016/j.bbabio.2019.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 11/30/2018] [Accepted: 01/25/2019] [Indexed: 11/15/2022]
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13
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Abstract
Two factors, climate change brought on by rising atmospheric CO2 levels and the accelerating shift toward renewable energy sources, have together worked to heighten interest in understanding how biological catalysts so effectively bring about the reduction of CO2 to formate, with potential applications for both bioremediation and energy storage. Most metal-dependent formate dehydrogenases, containing either molybdenum or tungsten in their active sites, function physiologically in the direction of formate oxidation to CO2, but it has become clear that many, if not all, are also effective in catalyzing the reverse reaction. In this chapter, we describe methods for isolating and characterizing these enzymes.
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Affiliation(s)
- Dimitri Niks
- Department of Biochemistry, University of California, Riverside, CA, United States
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, CA, United States.
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14
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Molybdenum-Containing Enzymes. Methods Mol Biol 2018. [PMID: 30317474 DOI: 10.1007/978-1-4939-8864-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
An overview of modern methods used in the preparation and characterization of molybdenum-containing enzymes is presented, with an emphasis on those methods that have been developed over the past decade to address specific difficulties frequently encountered in studies of these enzymes.
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15
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Unraveling the inner workings of respiratory arsenate reductase. Proc Natl Acad Sci U S A 2018; 115:9051-9053. [PMID: 30150409 DOI: 10.1073/pnas.1812841115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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16
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Structural and mechanistic analysis of the arsenate respiratory reductase provides insight into environmental arsenic transformations. Proc Natl Acad Sci U S A 2018; 115:E8614-E8623. [PMID: 30104376 DOI: 10.1073/pnas.1807984115] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Arsenate respiration by bacteria was discovered over two decades ago and is catalyzed by diverse organisms using the well-conserved Arr enzyme complex. Until now, the mechanisms underpinning this metabolism have been relatively opaque. Here, we report the structure of an Arr complex (solved by X-ray crystallography to 1.6-Å resolution), which was enabled by an improved Arr expression method in the genetically tractable arsenate respirer Shewanella sp. ANA-3. We also obtained structures bound with the substrate arsenate (1.8 Å), the product arsenite (1.8 Å), and the natural inhibitor phosphate (1.7 Å). The structures reveal a conserved active-site motif that distinguishes Arr [(R/K)GRY] from the closely related arsenite respiratory oxidase (Arx) complex (XGRGWG). Arr activity assays using methyl viologen as the electron donor and arsenate as the electron acceptor display two-site ping-pong kinetics. A Mo(V) species was detected with EPR spectroscopy, which is typical for proteins with a pyranopterin guanine dinucleotide cofactor. Arr is an extraordinarily fast enzyme that approaches the diffusion limit (Km = 44.6 ± 1.6 μM, kcat = 9,810 ± 220 seconds-1), and phosphate is a competitive inhibitor of arsenate reduction (Ki = 325 ± 12 μM). These observations, combined with knowledge of typical sedimentary arsenate and phosphate concentrations and known rates of arsenate desorption from minerals in the presence of phosphate, suggest that (i) arsenate desorption limits microbiologically induced arsenate reductive mobilization and (ii) phosphate enhances arsenic mobility by stimulating arsenate desorption rather than by inhibiting it at the enzymatic level.
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Leon CG, Moraga R, Valenzuela C, Gugliandolo C, Lo Giudice A, Papale M, Vilo C, Dong Q, Smith CT, Rossello-Mora R, Yañez J, Campos VL. Effect of the natural arsenic gradient on the diversity and arsenic resistance of bacterial communities of the sediments of Camarones River (Atacama Desert, Chile). PLoS One 2018; 13:e0195080. [PMID: 29715297 PMCID: PMC5929503 DOI: 10.1371/journal.pone.0195080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 03/17/2018] [Indexed: 12/20/2022] Open
Abstract
Arsenic (As), a highly toxic metalloid, naturally present in Camarones River (Atacama Desert, Chile) is a great health concern for the local population and authorities. In this study, the taxonomic and functional characterization of bacterial communities associated to metal-rich sediments from three sites of the river (sites M1, M2 and M3), showing different arsenic concentrations, were evaluated using a combination of approaches. Diversity of bacterial communities was evaluated by Illumina sequencing. Strains resistant to arsenic concentrations varying from 0.5 to 100 mM arsenite or arsenate were isolated and the presence of genes coding for enzymes involved in arsenic oxidation (aio) or reduction (arsC) investigated. Bacterial communities showed a moderate diversity which increased as arsenic concentrations decreased along the river. Sequences of the dominant taxonomic groups (abundances ≥1%) present in all three sites were affiliated to Proteobacteria (range 40.3–47.2%), Firmicutes (8.4–24.8%), Acidobacteria (10.4–17.1%), Actinobacteria (5.4–8.1%), Chloroflexi (3.9–7.5%), Planctomycetes (1.2–5.3%), Gemmatimonadetes (1.2–1.5%), and Nitrospirae (1.1–1.2%). Bacterial communities from sites M2 and M3 showed no significant differences in diversity between each other (p = 0.9753) but they were significantly more diverse than M1 (p<0.001 and p<0.001, respectively). Sequences affiliated with Proteobacteria, Firmicutes, Acidobacteria, Chloroflexi and Actinobacteria at M1 accounted for more than 89% of the total classified bacterial sequences present but these phyla were present in lesser proportions in M2 and M3 sites. Strains isolated from the sediment of sample M1, having the greatest arsenic concentration (498 mg kg-1), showed the largest percentages of arsenic oxidation and reduction. Genes aio were more frequently detected in isolates from M1 (54%), whereas arsC genes were present in almost all isolates from all three sediments, suggesting that bacterial communities play an important role in the arsenic biogeochemical cycle and detoxification of arsenical compounds. Overall, results provide further knowledge on the microbial diversity of arsenic contaminated fresh-water sediments.
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Affiliation(s)
- Carla G. Leon
- Environmental Microbiology Laboratory, Department of Microbiology, Faculty of Biological Sciences, University of Concepción, Concepción, Chile
| | - Ruben Moraga
- Microbiology Laboratory, Faculty of Renewable Natural Resources, Arturo Prat University, Iquique, Chile
| | - Cristian Valenzuela
- Environmental Microbiology Laboratory, Department of Microbiology, Faculty of Biological Sciences, University of Concepción, Concepción, Chile
| | - Concetta Gugliandolo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Angelina Lo Giudice
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
- Institute for the Coastal Marine Environment, National Research Council (IAMC-CNR), Messina, Italy
| | - Maria Papale
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Claudia Vilo
- Environmental Microbiology Laboratory, Department of Microbiology, Faculty of Biological Sciences, University of Concepción, Concepción, Chile
| | - Qunfeng Dong
- Center for Biomedical Informatics, Department of Public Health Sciences, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Carlos T. Smith
- Environmental Microbiology Laboratory, Department of Microbiology, Faculty of Biological Sciences, University of Concepción, Concepción, Chile
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Institut Mediterrani d’Estudis Avancats (CSIC-UIB), Esporles, Spain
| | - Jorge Yañez
- Department of Analytical and Inorganic Chemistry, Faculty of Chemical Sciences, University of Concepcion, Concepcion, Chile
| | - Victor L. Campos
- Environmental Microbiology Laboratory, Department of Microbiology, Faculty of Biological Sciences, University of Concepción, Concepción, Chile
- * E-mail:
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18
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Badilla C, Osborne TH, Cole A, Watson C, Djordjevic S, Santini JM. A new family of periplasmic-binding proteins that sense arsenic oxyanions. Sci Rep 2018; 8:6282. [PMID: 29674678 PMCID: PMC5908839 DOI: 10.1038/s41598-018-24591-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 04/06/2018] [Indexed: 01/21/2023] Open
Abstract
Arsenic contamination of drinking water affects more than 140 million people worldwide. While toxic to humans, inorganic forms of arsenic (arsenite and arsenate), can be used as energy sources for microbial respiration. AioX and its orthologues (ArxX and ArrX) represent the first members of a new sub-family of periplasmic-binding proteins that serve as the first component of a signal transduction system, that’s role is to positively regulate expression of arsenic metabolism enzymes. As determined by X-ray crystallography for AioX, arsenite binding only requires subtle conformational changes in protein structure, providing insights into protein-ligand interactions. The binding pocket of all orthologues is conserved but this alone is not sufficient for oxyanion selectivity, with proteins selectively binding either arsenite or arsenate. Phylogenetic evidence, clearly demonstrates that the regulatory proteins evolved together early in prokaryotic evolution and had a separate origin from the metabolic enzymes whose expression they regulate.
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Affiliation(s)
- Consuelo Badilla
- Institute of Structural & Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Thomas H Osborne
- Institute of Structural & Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Ambrose Cole
- Institute of Structural & Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, WC1E 7HX, London, UK
| | - Cameron Watson
- Institute of Structural & Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Snezana Djordjevic
- Institute of Structural & Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK.
| | - Joanne M Santini
- Institute of Structural & Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK.
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19
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Taguchi AT, Miyajima-Nakano Y, Fukazawa R, Lin MT, Baldansuren A, Gennis RB, Hasegawa K, Kumasaka T, Dikanov SA, Iwasaki T. Unpaired Electron Spin Density Distribution across Reduced [2Fe-2S] Cluster Ligands by 13Cβ-Cysteine Labeling. Inorg Chem 2017; 57:741-746. [DOI: 10.1021/acs.inorgchem.7b02676] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander T. Taguchi
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Sendagi, Tokyo 113-8602, Japan
| | - Yoshiharu Miyajima-Nakano
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Sendagi, Tokyo 113-8602, Japan
| | - Risako Fukazawa
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Sendagi, Tokyo 113-8602, Japan
| | | | - Amgalanbaatar Baldansuren
- Department of Veterinary
Clinical Medicine, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Robert B. Gennis
- Department of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Kazuya Hasegawa
- Japan Synchrotron Radiation Research Institute (SPring-8/JASRI), Sayo, Hyogo 679-5198, Japan
| | - Takashi Kumasaka
- Japan Synchrotron Radiation Research Institute (SPring-8/JASRI), Sayo, Hyogo 679-5198, Japan
| | - Sergei A. Dikanov
- Department of Veterinary
Clinical Medicine, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Toshio Iwasaki
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Sendagi, Tokyo 113-8602, Japan
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20
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Corsini PM, Walker KT, Santini JM. Expression of the arsenite oxidation regulatory operon in Rhizobium sp. str. NT-26 is under the control of two promoters that respond to different environmental cues. Microbiologyopen 2017; 7:e00567. [PMID: 29250936 PMCID: PMC6011840 DOI: 10.1002/mbo3.567] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/31/2017] [Accepted: 11/03/2017] [Indexed: 12/04/2022] Open
Abstract
Rhizobium sp. str. NT‐26 is a Gram‐negative facultative chemolithoautotrophic arsenite oxidizer that has been used as a model organism to study various aspects of arsenite oxidation including the regulation of arsenite oxidation. The three regulatory genes, aioX, aioS, and aioR, are cotranscribed when NT‐26 was grown in the presence or absence of arsenite. The aioXSR operon is upregulated in stationary phase but not by the presence of arsenite in the growth medium. The two transcription start sites upstream of aioX were determined which led to the identification of two promoters, the housekeeping promoter RpoD and the growth‐phase‐dependent promoter RpoE2. Promoter–lacZ fusions confirmed their constitutive and stationary phase expressions. The involvement of the NT‐26 sigma factor RpoE2 in acting on the NT‐26 RpoE2 promoter was confirmed in vivo in Escherichia coli, which lacks a rpoE2 homolog, using a strain carrying both the promoter–lacZ fusion and the NT‐26 rpoE2 gene. An in silico approach was used to search for other RpoE2 promoters and AioR‐binding motifs and led to the identification of other genes that could be regulated by these proteins including those involved in quorum sensing, chemotaxis, and motility expanding the signaling networks important for the microbial metabolism of arsenite.
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Affiliation(s)
- Paula M Corsini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Kenneth T Walker
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Joanne M Santini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
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21
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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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22
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Dong G, Ryde U. Effect of the protein ligand in DMSO reductase studied by computational methods. J Inorg Biochem 2017; 171:45-51. [DOI: 10.1016/j.jinorgbio.2017.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 02/07/2017] [Accepted: 03/19/2017] [Indexed: 11/27/2022]
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23
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Warelow TP, Pushie MJ, Cotelesage JJH, Santini JM, George GN. The active site structure and catalytic mechanism of arsenite oxidase. Sci Rep 2017; 7:1757. [PMID: 28496149 PMCID: PMC5432002 DOI: 10.1038/s41598-017-01840-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/04/2017] [Indexed: 11/09/2022] Open
Abstract
Arsenite oxidase is thought to be an ancient enzyme, originating before the divergence of the Archaea and the Bacteria. We have investigated the nature of the molybdenum active site of the arsenite oxidase from the Alphaproteobacterium Rhizobium sp. str. NT-26 using a combination of X-ray absorption spectroscopy and computational chemistry. Our analysis indicates an oxidized Mo(VI) active site with a structure that is far from equilibrium. We propose that this is an entatic state imposed by the protein on the active site through relative orientation of the two molybdopterin cofactors, in a variant of the Rây-Dutt twist of classical coordination chemistry, which we call the pterin twist hypothesis. We discuss the implications of this hypothesis for other putatively ancient molybdopterin-based enzymes.
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Affiliation(s)
- Thomas P Warelow
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom
| | - M Jake Pushie
- Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada.,Molecular and Environmental Sciences Research Group, Department of Geological Sciences, University of Saskatchewan, SK, S7N 5E2, Canada
| | - Julien J H Cotelesage
- Molecular and Environmental Sciences Research Group, Department of Geological Sciences, University of Saskatchewan, SK, S7N 5E2, Canada
| | - Joanne M Santini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom
| | - Graham N George
- Molecular and Environmental Sciences Research Group, Department of Geological Sciences, University of Saskatchewan, SK, S7N 5E2, Canada. .,Department of Chemistry, University of Saskatchewan, Saskatoon, SK, S7N 5C9, Canada.
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24
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Nookongbut P, Kantachote D, Krishnan K, Megharaj M. Arsenic resistance genes of As-resistant purple nonsulfur bacteria isolated from As-contaminated sites for bioremediation application. J Basic Microbiol 2017; 57:316-324. [DOI: 10.1002/jobm.201600584] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/26/2016] [Accepted: 12/16/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Phitthaya Nookongbut
- Faculty of Science; Department of Microbiology; Prince of Songkla University; Hat Yai Thailand
| | - Duangporn Kantachote
- Faculty of Science; Department of Microbiology; Prince of Songkla University; Hat Yai Thailand
- Center of Excellence on Hazardous Substance Management (HSM); Bangkok Thailand
| | - Kannan Krishnan
- Faculty of Science and Information Technology; Global Centre for Environmental Remediation; The University of Newcastle; Callaghan NSW Australia
- Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC-CARE); The University of Newcastle; Callaghan NSW Australia
| | - Mallavarapu Megharaj
- Faculty of Science and Information Technology; Global Centre for Environmental Remediation; The University of Newcastle; Callaghan NSW Australia
- Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC-CARE); The University of Newcastle; Callaghan NSW Australia
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25
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Maia LB, Moura I, Moura JJ. EPR Spectroscopy on Mononuclear Molybdenum-Containing Enzymes. FUTURE DIRECTIONS IN METALLOPROTEIN AND METALLOENZYME RESEARCH 2017. [DOI: 10.1007/978-3-319-59100-1_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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26
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The competition between chemistry and biology in assembling iron-sulfur derivatives. Molecular structures and electrochemistry. Part IV. {[Fe3S4](SγCys)3} proteins. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2016.09.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Veit S, Takeda K, Tsunoyama Y, Baymann F, Nevo R, Reich Z, Rögner M, Miki K, Rexroth S. Structural and functional characterisation of the cyanobacterial PetC3 Rieske protein family. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1879-1891. [DOI: 10.1016/j.bbabio.2016.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/12/2016] [Accepted: 09/17/2016] [Indexed: 11/30/2022]
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28
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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: 42] [Impact Index Per Article: 5.3] [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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29
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The H-bond network surrounding the pyranopterins modulates redox cooperativity in the molybdenum- bis PGD cofactor in arsenite oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1353-1362. [DOI: 10.1016/j.bbabio.2016.05.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 05/12/2016] [Accepted: 05/16/2016] [Indexed: 11/19/2022]
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30
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The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part III. {[Fe2S2](Cys)3(X)} (X=Asp, Arg, His) and {[Fe2S2](Cys)2(His)2} proteins. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2015.07.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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31
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Leimkühler S, Iobbi-Nivol C. Bacterial molybdoenzymes: old enzymes for new purposes. FEMS Microbiol Rev 2015; 40:1-18. [PMID: 26468212 DOI: 10.1093/femsre/fuv043] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2015] [Indexed: 02/06/2023] Open
Abstract
Molybdoenzymes are widespread in eukaryotic and prokaryotic organisms where they play crucial functions in detoxification reactions in the metabolism of humans and bacteria, in nitrate assimilation in plants and in anaerobic respiration in bacteria. To be fully active, these enzymes require complex molybdenum-containing cofactors, which are inserted into the apoenzymes after folding. For almost all the bacterial molybdoenzymes, molybdenum cofactor insertion requires the involvement of specific chaperones. In this review, an overview on the molybdenum cofactor biosynthetic pathway is given together with the role of specific chaperones dedicated for molybdenum cofactor insertion and maturation. Many bacteria are involved in geochemical cycles on earth and therefore have an environmental impact. The roles of molybdoenzymes in bioremediation and for environmental applications are presented.
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Affiliation(s)
- Silke Leimkühler
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, 14476 Potsdam, Germany
| | - Chantal Iobbi-Nivol
- The Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS, Aix Marseille Université, 13402 Marseille cedex 20, France
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32
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Coelho C, Romão MJ. Structural and mechanistic insights on nitrate reductases. Protein Sci 2015; 24:1901-11. [PMID: 26362109 DOI: 10.1002/pro.2801] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 09/04/2015] [Indexed: 01/31/2023]
Abstract
Nitrate reductases (NR) belong to the DMSO reductase family of Mo-containing enzymes and perform key roles in the metabolism of the nitrogen cycle, reducing nitrate to nitrite. Due to variable cell location, structure and function, they have been divided into periplasmic (Nap), cytoplasmic, and membrane-bound (Nar) nitrate reductases. The first crystal structure obtained for a NR was that of the monomeric NapA from Desulfovibrio desulfuricans in 1999. Since then several new crystal structures were solved providing novel insights that led to the revision of the commonly accepted reaction mechanism for periplasmic nitrate reductases. The two crystal structures available for the NarGHI protein are from the same organism (Escherichia coli) and the combination with electrochemical and spectroscopic studies also lead to the proposal of a reaction mechanism for this group of enzymes. Here we present an overview on the current advances in structural and functional aspects of bacterial nitrate reductases, focusing on the mechanistic implications drawn from the crystallographic data.
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Affiliation(s)
- Catarina Coelho
- Departamento de Química, Faculdade de Ciências e Tecnologia, UCIBIO@REQUIMTE, Universidade Nova de Lisboa, Caparica, 2829-516, Portugal
| | - Maria João Romão
- Departamento de Química, Faculdade de Ciências e Tecnologia, UCIBIO@REQUIMTE, Universidade Nova de Lisboa, Caparica, 2829-516, Portugal
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Abstract
Arsenic and antimony are toxic metalloids and are considered priority environmental pollutants by the U.S. Environmental Protection Agency. Significant advances have been made in understanding microbe-arsenic interactions and how they influence arsenic redox speciation in the environment. However, even the most basic features of how and why a microorganism detects and reacts to antimony remain poorly understood. Previous work with Agrobacterium tumefaciens strain 5A concluded that oxidation of antimonite [Sb(III)] and arsenite [As(III)] required different biochemical pathways. Here, we show with in vivo experiments that a mutation in aioA [encoding the large subunit of As(III) oxidase] reduces the ability to oxidize Sb(III) by approximately one-third relative to the ability of the wild type. Further, in vitro studies with the purified As(III) oxidase from Rhizobium sp. strain NT-26 (AioA shares 94% amino acid sequence identity with AioA of A. tumefaciens) provide direct evidence of Sb(III) oxidation but also show a significantly decreased Vmax compared to that of As(III) oxidation. The aioBA genes encoding As(III) oxidase are induced by As(III) but not by Sb(III), whereas arsR gene expression is induced by both As(III) and Sb(III), suggesting that detection and transcriptional responses for As(III) and Sb(III) differ. While Sb(III) and As(III) are similar with respect to cellular extrusion (ArsB or Acr3) and interaction with ArsR, they differ in the regulatory mechanisms that control the expression of genes encoding the different Ars or Aio activities. In summary, this study documents an enzymatic basis for microbial Sb(III) oxidation, although additional Sb(III) oxidation activity also is apparent in this bacterium.
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Zhu YG, Yoshinaga M, Zhao FJ, Rosen BP. Earth Abides Arsenic Biotransformations. ANNUAL REVIEW OF EARTH AND PLANETARY SCIENCES 2014; 42:443-467. [PMID: 26778863 PMCID: PMC4712701 DOI: 10.1146/annurev-earth-060313-054942] [Citation(s) in RCA: 314] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Arsenic is the most prevalent environmental toxic element and causes health problems throughout the world. The toxicity, mobility, and fate of arsenic in the environment are largely determined by its speciation, and arsenic speciation changes are driven, at least to some extent, by biological processes. In this article, biotransformation of arsenic is reviewed from the perspective of the formation of Earth and the evolution of life, and the connection between arsenic geochemistry and biology is described. The article provides a comprehensive overview of molecular mechanisms of arsenic redox and methylation cycles as well as other arsenic biotransformations. It also discusses the implications of arsenic biotransformation in environmental remediation and food safety, with particular emphasis on groundwater arsenic contamination and arsenic accumulation in rice.
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Affiliation(s)
- Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People’s Republic of China
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People’s Republic of China
| | - Masafumi Yoshinaga
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida 33199
| | - Fang-Jie Zhao
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | - Barry P. Rosen
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida 33199
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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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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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