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Galisteo C, de la Haba RR, Sánchez-Porro C, Ventosa A. A step into the rare biosphere: genomic features of the new genus Terrihalobacillus and the new species Aquibacillus salsiterrae from hypersaline soils. Front Microbiol 2023; 14:1192059. [PMID: 37228371 PMCID: PMC10203224 DOI: 10.3389/fmicb.2023.1192059] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 04/12/2023] [Indexed: 05/27/2023] Open
Abstract
Hypersaline soils are a source of prokaryotic diversity that has been overlooked until very recently. The phylum Bacillota, which includes the genus Aquibacillus, is one of the 26 phyla that inhabit the heavy metal contaminated soils of the Odiel Saltmarshers Natural Area (Southwest Spain), according to previous research. In this study, we isolated a total of 32 strains closely related to the genus Aquibacillus by the traditional dilution-plating technique. Phylogenetic studies clustered them into two groups, and comparative genomic analyses revealed that one of them represents a new species within the genus Aquibacillus, whereas the other cluster constitutes a novel genus of the family Bacillaceae. We propose the designations Aquibacillus salsiterrae sp. nov. and Terrihalobacillus insolitus gen. nov., sp. nov., respectively, for these two new taxa. Genome mining analysis revealed dissimilitude in the metabolic traits of the isolates and their closest related genera, remarkably the distinctive presence of the well-conserved pathway for the biosynthesis of molybdenum cofactor in the species of the genera Aquibacillus and Terrihalobacillus, along with genes that encode molybdoenzymes and molybdate transporters, scarcely found in metagenomic dataset from this area. In-silico studies of the osmoregulatory strategy revealed a salt-out mechanism in the new species, which harbor the genes for biosynthesis and transport of the compatible solutes ectoine and glycine betaine. Comparative genomics showed genes related to heavy metal resistance, which seem required due to the contamination in the sampling area. The low values in the genome recruitment analysis indicate that the new species of the two genera, Terrihalobacillus and Aquibacillus, belong to the rare biosphere of representative hypersaline environments.
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Hille R, Niks D. Application of EPR and related methods to molybdenum-containing enzymes. Methods Enzymol 2022; 666:373-412. [PMID: 35465925 DOI: 10.1016/bs.mie.2022.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A description is provided of the contributions made to our understanding of molybdenum-containing enzymes through the application of electron paramagnetic resonance spectroscopy and related methods, by way of illustrating how these can be applied to better understand enzyme structure and function. An emphasis is placed on the use of EPR to identify both the coordination environment of the molybdenum coordination sphere as well as the structures of paramagnetic intermediates observed transiently in the course of reaction that have led to the elucidation of reaction mechanism.
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Affiliation(s)
- Russ Hille
- Department of Biochemistry, University of California, Riverside, CA, United States.
| | - Dimitri Niks
- Department of Biochemistry, University of California, Riverside, CA, United States
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3
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Cabrerizo A, Bulteel D, Waligora J, Landrot G, Fonda E, Olard F. Chemical, mineralogical, and environmental characterization of tunnel boring muds for their valorization in road construction: a focus on molybdenum characterization. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:44314-44324. [PMID: 32761529 DOI: 10.1007/s11356-020-09969-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 06/30/2020] [Indexed: 06/11/2023]
Abstract
Tunnel boring muds, coming from underground works, are considered as specific materials due to their intrinsic characteristics (granularity, clay content, water content, presence of heavy metals). In order to determine if they can be valorized in road construction or civil engineering, a complete characterization, including their environmental behavior, is necessary. Thus, the aim of this study is to characterize a tunnel boring mud sample from chemical, mineralogical, and environmental point of view. The studied material, a limestone mud, was characterized using different analytical techniques. Some pollutants and heavy metals were identified, such as sulfates and molybdenum (Mo), and specific analyses were performed to identify molybdenum speciation. As molybdenum was detected as traces in the studied material, it was necessary to increase its concentration. Thus, a nitric acid extraction was specifically developed at a laboratory scale with the aim to remove its high-calcium carbonate content. Then, synchrotron analyses were performed, allowing to obtain data on the oxidation state of molybdenum.
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Affiliation(s)
- Adrien Cabrerizo
- Laboratoire de Génie Civil et Géo Environnement, département Génie Civil & Environnemental, IMT Lille Douai, Université Lille, EA 4515 LGCgE, F-59000, Lille, France.
| | - David Bulteel
- Laboratoire de Génie Civil et Géo Environnement, département Génie Civil & Environnemental, IMT Lille Douai, Université Lille, EA 4515 LGCgE, F-59000, Lille, France
| | - Julien Waligora
- EIFFAGE Infrastructures, Direction Recherche et Innovation, 8 rue du Dauphiné, CS 74005, 69964, Corbas Cedex, France
| | - Gautier Landrot
- Synchrotron SOLEIL, L'Orme des Meisiers-BP48, 91192, Saint-Aubin, France
| | - Emiliano Fonda
- Synchrotron SOLEIL, L'Orme des Meisiers-BP48, 91192, Saint-Aubin, France
| | - François Olard
- EIFFAGE Infrastructures, Direction Recherche et Innovation, 8 rue du Dauphiné, CS 74005, 69964, Corbas Cedex, France
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4
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Andrieu C, Vergnes A, Loiseau L, Aussel L, Ezraty B. Characterisation of the periplasmic methionine sulfoxide reductase (MsrP) from Salmonella Typhimurium. Free Radic Biol Med 2020; 160:506-512. [PMID: 32750406 DOI: 10.1016/j.freeradbiomed.2020.06.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 06/17/2020] [Indexed: 11/23/2022]
Abstract
The oxidation of free methionine (Met) and Met residues inside proteins leads to the formation of methionine sulfoxide (Met-O). The reduction of Met-O to Met is catalysed by a ubiquitous enzyme family: the methionine sulfoxide reductases (Msr). The importance of Msr systems in bacterial physiology and virulence has been reported in many species. Salmonella Typhimurium, a facultative intracellular pathogen, contains four cytoplasmic Msr. Recently, a periplasmic Msr enzyme (MsrP) has been identified in Escherichia coli. In the present study, the STM14_4072 gene from Salmonella was shown to encode the MsrP protein (StMsrP). We describe the experimental procedure and precautions for the production of this molybdo-enzyme. StMsrP was also demonstrated to reduce free Met-O and to catalyse the complete repair of an oxidized protein. More importantly, this study provides for the first time access to the exhaustive list of the Msr systems of a pathogen, including four cytoplasmic enzymes (MsrA, MsrB, MsrC, BisC) and one periplasmic enzyme (MsrP).
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Affiliation(s)
- Camille Andrieu
- Aix-Marseille Univ, CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Alexandra Vergnes
- Aix-Marseille Univ, CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Laurent Loiseau
- Aix-Marseille Univ, CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Laurent Aussel
- Aix-Marseille Univ, CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Benjamin Ezraty
- Aix-Marseille Univ, CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France.
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5
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Chatterjee S, Kumari S, Rath S, Priyadarshanee M, Das S. Diversity, structure and regulation of microbial metallothionein: metal resistance and possible applications in sequestration of toxic metals. Metallomics 2020; 12:1637-1655. [PMID: 32996528 DOI: 10.1039/d0mt00140f] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Metallothioneins (MTs) are a group of cysteine-rich, universal, low molecular weight proteins distributed widely in almost all major taxonomic groups ranging from tiny microbes to highly organized vertebrates. The primary function of this protein is storage, transportation and binding of metals, which enable microorganisms to detoxify heavy metals. In the microbial world, these peptides were first identified in a cyanobacterium Synechococcus as the SmtA protein which exhibits high affinity towards rising level of zinc and cadmium to preserve metal homeostasis in a cell. In yeast, MTs aid in reserving copper and confer protection against copper toxicity by chelating excess copper ions in a cell. Two MTs, CUP1 and Crs5, originating from Saccharomyces cerevisiae predominantly bind to copper though are capable of binding with zinc and cadmium ions. MT superfamily 7 is found in ciliated protozoa which show high affinity towards copper and cadmium. Several tools and techniques, such as western blot, capillary electrophoresis, inductively coupled plasma, atomic emission spectroscopy and high performance liquid chromatography, have been extensively utilized for the detection and quantification of microbial MTs which are utilized for the efficient remediation and sequestration of heavy metals from a contaminated environment.
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Affiliation(s)
- Shreosi Chatterjee
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India.
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6
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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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7
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Ingersol LJ, Yang J, Kc K, Pokhrel A, Astashkin AV, Weiner JH, Johnston CA, Kirk ML. Addressing Ligand-Based Redox in Molybdenum-Dependent Methionine Sulfoxide Reductase. J Am Chem Soc 2020; 142:2721-2725. [PMID: 31989824 DOI: 10.1021/jacs.9b11762] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A combination of pulsed EPR, CW EPR, and X-ray absorption spectroscopies has been employed to probe the geometric and electronic structure of the E. coli periplasmic molybdenum-dependent methionine sulfoxide reductase (MsrP). 17O and 1H pulsed EPR spectra show that the as-isolated Mo(V) enzyme form does not possess an exchangeable H2O/OH- ligand bound to Mo as found in the sulfite oxidizing enzymes of the same family. The nature of the unusual CW EPR spectrum has been re-evaluated in light of new data on the MsrP-N45R variant and related small-molecule analogues of the active site. These data point to a novel "thiol-blocked" [(PDT)MoVO(SCys)(thiolate)]- structure, which is supported by new EXAFS data. We discuss these new results in the context of ligand-based and metal-based redox chemistry in the enzymatic oxygen atom transfer reaction.
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Affiliation(s)
- Laura J Ingersol
- Department of Chemistry and Chemical Biology , The University of New Mexico , MSC03 2060, 1 University of New Mexico , Albuquerque , New Mexico 87131-0001 , United States
| | - Jing Yang
- Department of Chemistry and Chemical Biology , The University of New Mexico , MSC03 2060, 1 University of New Mexico , Albuquerque , New Mexico 87131-0001 , United States
| | - Khadanand Kc
- Department of Chemistry and Chemical Biology , The University of New Mexico , MSC03 2060, 1 University of New Mexico , Albuquerque , New Mexico 87131-0001 , United States
| | - Amrit Pokhrel
- Department of Chemistry and Chemical Biology , The University of New Mexico , MSC03 2060, 1 University of New Mexico , Albuquerque , New Mexico 87131-0001 , United States
| | - Andrei V Astashkin
- Department of Chemistry Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
| | - Joel H Weiner
- Department of Biochemistry , University of Alberta , 474 Medical Science Building , Edmonton , Alberta T6G 2H7 , Canada
| | - Christopher A Johnston
- Department of Biology , The University of New Mexico , MSC03 2060, 1 University of New Mexico , Albuquerque , New Mexico 87131-0001 , United States
| | - Martin L Kirk
- Department of Chemistry and Chemical Biology , The University of New Mexico , MSC03 2060, 1 University of New Mexico , Albuquerque , New Mexico 87131-0001 , United States
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8
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Duffus BR, Schrapers P, Schuth N, Mebs S, Dau H, Leimkühler S, Haumann M. Anion Binding and Oxidative Modification at the Molybdenum Cofactor of Formate Dehydrogenase from Rhodobacter capsulatus Studied by X-ray Absorption Spectroscopy. Inorg Chem 2019; 59:214-225. [PMID: 31814403 DOI: 10.1021/acs.inorgchem.9b01613] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Formate dehydrogenase (FDH) enzymes are versatile catalysts for CO2 conversion. The FDH from Rhodobacter capsulatus contains a molybdenum cofactor with the dithiolene functions of two pyranopterin guanine dinucleotide molecules, a conserved cysteine, and a sulfido group bound at Mo(VI). In this study, we focused on metal oxidation state and coordination changes in response to exposure to O2, inhibitory anions, and redox agents using X-ray absorption spectroscopy (XAS) at the Mo K-edge. Differences in the oxidative modification of the bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor relative to samples prepared aerobically without inhibitor, such as variations in the relative numbers of sulfido (Mo═S) and oxo (Mo═O) bonds, were observed in the presence of azide (N3-) or cyanate (OCN-). Azide provided best protection against O2, resulting in a quantitatively sulfurated cofactor with a displaced cysteine ligand and optimized formate oxidation activity. Replacement of the cysteine ligand by a formate (HCO2-) ligand at the molybdenum in active enzyme is compatible with our XAS data. Cyanide (CN-) inactivated the enzyme by replacing the sulfido ligand at Mo(VI) with an oxo ligand. Evidence that the sulfido group may become protonated upon molybdenum reduction was obtained. Our results emphasize the role of coordination flexibility at the molybdenum center during inhibitory and catalytic processes of FDH enzymes.
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Affiliation(s)
- Benjamin R Duffus
- Institut für Biochemie und Biologie, Molekulare Enzymologie , Universität Potsdam , Karl-Liebknecht Strasse 24-25 , 14476 Potsdam , Germany
| | - Peer Schrapers
- Institut für Experimentalphysik , Freie Universität Berlin , Arnimallee 14 , 14195 Berlin , Germany
| | - Nils Schuth
- Institut für Experimentalphysik , Freie Universität Berlin , Arnimallee 14 , 14195 Berlin , Germany
| | - Stefan Mebs
- Institut für Experimentalphysik , Freie Universität Berlin , Arnimallee 14 , 14195 Berlin , Germany
| | - Holger Dau
- Institut für Experimentalphysik , Freie Universität Berlin , Arnimallee 14 , 14195 Berlin , Germany
| | - Silke Leimkühler
- Institut für Biochemie und Biologie, Molekulare Enzymologie , Universität Potsdam , Karl-Liebknecht Strasse 24-25 , 14476 Potsdam , Germany
| | - Michael Haumann
- Institut für Experimentalphysik , Freie Universität Berlin , Arnimallee 14 , 14195 Berlin , Germany
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9
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Kappler U, Nasreen M, McEwan A. New insights into the molecular physiology of sulfoxide reduction in bacteria. Adv Microb Physiol 2019; 75:1-51. [PMID: 31655735 DOI: 10.1016/bs.ampbs.2019.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Sulfoxides occur in biology as products of the S-oxygenation of small molecules as well as in peptides and proteins and their formation is often associated with oxidative stress and can affect biological function. In bacteria, sulfoxide damage can be reversed by different types of enzymes. Thioredoxin-dependent peptide methionine sulfoxide reductases (MSR proteins) repair oxidized methionine residues and are found in all Domains of life. In bacteria MSR proteins are often found in the cytoplasm but in some bacteria, including pathogenic Neisseria, Streptococci, and Haemophilus they are extracytoplasmic. Mutants lacking MSR proteins are often sensitive to oxidative stress and in pathogens exhibit decreased virulence as indicated by reduced survival in host cell or animal model systems. Molybdenum enzymes are also known to reduce S-oxides and traditionally their physiological role was considered to be in anaerobic respiration using dimethylsulfoxide (DMSO) as an electron acceptor. However, it now appears that some enzymes (MtsZ) of the DMSO reductase family of Mo enzymes use methionine sulfoxide as preferred physiological substrate and thus may be involved in scavenging/recycling of this amino acid. Similarly, an enzyme (MsrP/YedY) of the sulfite oxidase family of Mo enzymes has been shown to be involved in repair of methionine sulfoxides in periplasmic proteins. Again, some mutants deficient in Mo-dependent sulfoxide reductases exhibit reduced virulence, and there is evidence that these Mo enzymes and some MSR systems are induced by hypochlorite produced by the innate immune system. This review describes recent advances in the understanding of the molecular microbiology of MSR systems and the broadening of the role of Mo-dependent sulfoxide reductase to encompass functions beyond anaerobic respiration.
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Affiliation(s)
- Ulrike Kappler
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Marufa Nasreen
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Alastair McEwan
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
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10
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Reschke S, Duffus BR, Schrapers P, Mebs S, Teutloff C, Dau H, Haumann M, Leimkühler S. Identification of YdhV as the First Molybdoenzyme Binding a Bis-Mo-MPT Cofactor in Escherichia coli. Biochemistry 2019; 58:2228-2242. [PMID: 30945846 DOI: 10.1021/acs.biochem.9b00078] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The oxidoreductase YdhV in Escherichia coli has been predicted to belong to the family of molybdenum/tungsten cofactor (Moco/Wco)-containing enzymes. In this study, we characterized the YdhV protein in detail, which shares amino acid sequence homology with a tungsten-containing benzoyl-CoA reductase binding the bis-W-MPT (for metal-binding pterin) cofactor. The cofactor was identified to be of a bis-Mo-MPT type with no guanine nucleotides present, which represents a form of Moco that has not been found previously in any molybdoenzyme. Our studies showed that YdhV has a preference for bis-Mo-MPT over bis-W-MPT to be inserted into the enzyme. In-depth characterization of YdhV by X-ray absorption and electron paramagnetic resonance spectroscopies revealed that the bis-Mo-MPT cofactor in YdhV is redox active. The bis-Mo-MPT and bis-W-MPT cofactors include metal centers that bind the four sulfurs from the two dithiolene groups in addition to a cysteine and likely a sulfido ligand. The unexpected presence of a bis-Mo-MPT cofactor opens an additional route for cofactor biosynthesis in E. coli and expands the canon of the structurally highly versatile molybdenum and tungsten cofactors.
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Affiliation(s)
- Stefan Reschke
- Institute of Biochemistry and Biology , University of Potsdam , Karl-Liebknecht-Strasse 24 , 14476 Potsdam , Germany
| | - Benjamin R Duffus
- Institute of Biochemistry and Biology , University of Potsdam , Karl-Liebknecht-Strasse 24 , 14476 Potsdam , Germany
| | | | | | - Christian Teutloff
- Institute of Experimental Physics, EPR Spectroscopy of Biological Systems , Freie Universität Berlin , Arnimallee 14 , 14195 Berlin , Germany
| | | | | | - Silke Leimkühler
- Institute of Biochemistry and Biology , University of Potsdam , Karl-Liebknecht-Strasse 24 , 14476 Potsdam , Germany
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11
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Zupok A, Iobbi-Nivol C, Méjean V, Leimkühler S. The regulation of Moco biosynthesis and molybdoenzyme gene expression by molybdenum and iron in bacteria. Metallomics 2019; 11:1602-1624. [DOI: 10.1039/c9mt00186g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The regulation of the operons involved in Moco biosynthesis is dependent on the availability of Fe–S clusters in the cell.
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Affiliation(s)
- Arkadiusz Zupok
- University of Potsdam
- Institute of Biochemistry and Biology
- Molecular Enzymology
- Potsdam-Golm
- Germany
| | - Chantal Iobbi-Nivol
- Aix-Marseille Université
- Institut de Microbiologie de la Méditerranée
- Laboratoire de Bioénergétique et Ingénierie des Protéines
- Centre National de la Recherche Scientifique
- Marseille
| | - Vincent Méjean
- Aix-Marseille Université
- Institut de Microbiologie de la Méditerranée
- Laboratoire de Bioénergétique et Ingénierie des Protéines
- Centre National de la Recherche Scientifique
- Marseille
| | - Silke Leimkühler
- University of Potsdam
- Institute of Biochemistry and Biology
- Molecular Enzymology
- Potsdam-Golm
- Germany
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12
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Maiti BK, Almeida RM, Moura I, Moura JJ. Rubredoxins derivatives: Simple sulphur-rich coordination metal sites and its relevance for biology and chemistry. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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13
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Reschke S, Mebs S, Sigfridsson-Clauss KGV, Kositzki R, Leimkühler S, Haumann M. Protonation and Sulfido versus Oxo Ligation Changes at the Molybdenum Cofactor in Xanthine Dehydrogenase (XDH) Variants Studied by X-ray Absorption Spectroscopy. Inorg Chem 2017; 56:2165-2176. [DOI: 10.1021/acs.inorgchem.6b02846] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Stefan Reschke
- Institut für
Biochemie und Biologie, Molekulare Enzymologie, Universität Potsdam, 14476 Potsdam, Germany
| | - Stefan Mebs
- Institut für Experimentalphysik, Freie Universität Berlin, 14195 Berlin, Germany
| | | | - Ramona Kositzki
- Institut für Experimentalphysik, Freie Universität Berlin, 14195 Berlin, Germany
| | - Silke Leimkühler
- Institut für
Biochemie und Biologie, Molekulare Enzymologie, Universität Potsdam, 14476 Potsdam, Germany
| | - Michael Haumann
- Institut für Experimentalphysik, Freie Universität Berlin, 14195 Berlin, Germany
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14
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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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15
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Juillan-Binard C, Picciocchi A, Andrieu JP, Dupuy J, Petit-Hartlein I, Caux-Thang C, Vivès C, Nivière V, Fieschi F. A Two-component NADPH Oxidase (NOX)-like System in Bacteria Is Involved in the Electron Transfer Chain to the Methionine Sulfoxide Reductase MsrP. J Biol Chem 2016; 292:2485-2494. [PMID: 28028176 DOI: 10.1074/jbc.m116.752014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 12/21/2016] [Indexed: 01/22/2023] Open
Abstract
MsrPQ is a newly identified methionine sulfoxide reductase system found in bacteria, which appears to be specifically involved in the repair of periplasmic proteins oxidized by hypochlorous acid. It involves two proteins: a periplasmic one, MsrP, previously named YedY, carrying out the Msr activity, and MsrQ, an integral b-type heme membrane-spanning protein, which acts as the specific electron donor to MsrP. MsrQ, previously named YedZ, was mainly characterized by bioinformatics as a member of the FRD superfamily of heme-containing membrane proteins, which include the NADPH oxidase proteins (NOX/DUOX). Here we report a detailed biochemical characterization of the MsrQ protein from Escherichia coli We optimized conditions for the overexpression and membrane solubilization of an MsrQ-GFP fusion and set up a purification scheme allowing the production of pure MsrQ. Combining UV-visible spectroscopy, heme quantification, and site-directed mutagenesis of histidine residues, we demonstrated that MsrQ is able to bind two b-type hemes through the histidine residues conserved between the MsrQ and NOX protein families. In addition, we identify the E. coli flavin reductase Fre, which is related to the dehydrogenase domain of eukaryotic NOX enzymes, as an efficient cytosolic electron donor to the MsrQ heme moieties. Cross-linking experiments as well as surface Plasmon resonance showed that Fre interacts with MsrQ to form a specific complex. Taken together, these data support the identification of the first prokaryotic two-component protein system related to the eukaryotic NOX family and involved in the reduction of periplasmic oxidized proteins.
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Affiliation(s)
- Céline Juillan-Binard
- From the Institut de Biologie Structurale (IBS), Université Grenoble Alpes, 38044 Grenoble.,the IBS, Commissariat à l'Energie Atomique (CEA), 38027 Grenoble.,the IBS, CNRS, 38027 Grenoble
| | - Antoine Picciocchi
- From the Institut de Biologie Structurale (IBS), Université Grenoble Alpes, 38044 Grenoble.,the IBS, Commissariat à l'Energie Atomique (CEA), 38027 Grenoble.,the IBS, CNRS, 38027 Grenoble
| | - Jean-Pierre Andrieu
- From the Institut de Biologie Structurale (IBS), Université Grenoble Alpes, 38044 Grenoble.,the IBS, Commissariat à l'Energie Atomique (CEA), 38027 Grenoble.,the IBS, CNRS, 38027 Grenoble
| | - Jerome Dupuy
- From the Institut de Biologie Structurale (IBS), Université Grenoble Alpes, 38044 Grenoble.,the IBS, Commissariat à l'Energie Atomique (CEA), 38027 Grenoble.,the IBS, CNRS, 38027 Grenoble
| | - Isabelle Petit-Hartlein
- From the Institut de Biologie Structurale (IBS), Université Grenoble Alpes, 38044 Grenoble.,the IBS, Commissariat à l'Energie Atomique (CEA), 38027 Grenoble.,the IBS, CNRS, 38027 Grenoble
| | - Christelle Caux-Thang
- the Université Grenoble Alpes, Grenoble.,CNRS LCBM UMR 5249, Grenoble, and.,CEA-DRF-BIG-Laboratoire de Chimie et Biologie des Métaux, 17 Rue des Martyrs, 38054 Grenoble, France
| | - Corinne Vivès
- From the Institut de Biologie Structurale (IBS), Université Grenoble Alpes, 38044 Grenoble.,the IBS, Commissariat à l'Energie Atomique (CEA), 38027 Grenoble.,the IBS, CNRS, 38027 Grenoble
| | - Vincent Nivière
- the Université Grenoble Alpes, Grenoble.,CNRS LCBM UMR 5249, Grenoble, and.,CEA-DRF-BIG-Laboratoire de Chimie et Biologie des Métaux, 17 Rue des Martyrs, 38054 Grenoble, France
| | - Franck Fieschi
- From the Institut de Biologie Structurale (IBS), Université Grenoble Alpes, 38044 Grenoble, .,the IBS, Commissariat à l'Energie Atomique (CEA), 38027 Grenoble.,the IBS, CNRS, 38027 Grenoble
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16
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Correia MAS, Otrelo-Cardoso AR, Schwuchow V, Sigfridsson Clauss KGV, Haumann M, Romão MJ, Leimkühler S, Santos-Silva T. The Escherichia coli Periplasmic Aldehyde Oxidoreductase Is an Exceptional Member of the Xanthine Oxidase Family of Molybdoenzymes. ACS Chem Biol 2016; 11:2923-2935. [PMID: 27622978 DOI: 10.1021/acschembio.6b00572] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The xanthine oxidase (XO) family comprises molybdenum-dependent enzymes that usually form homodimers (or dimers of heterodimers/trimers) organized in three domains that harbor two [2Fe-2S] clusters, one FAD, and a Mo cofactor. In this work, we crystallized an unusual member of the family, the periplasmic aldehyde oxidoreductase PaoABC from Escherichia coli. This is the first example of an E. coli protein containing a molybdopterin-cytosine-dinucleotide cofactor and is the only heterotrimer of the XO family so far structurally characterized. The crystal structure revealed the presence of an unexpected [4Fe-4S] cluster, anchored to an additional 40 residues subdomain. According to phylogenetic analysis, proteins containing this cluster are widely spread in many bacteria phyla, putatively through repeated gene transfer events. The active site of PaoABC is highly exposed to the surface with no aromatic residues and an arginine (PaoC-R440) making a direct interaction with PaoC-E692, which acts as a base catalyst. In order to understand the importance of R440, kinetic assays were carried out, and the crystal structure of the PaoC-R440H variant was also determined.
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Affiliation(s)
- Márcia A. S. Correia
- UCIBIO/Requimte,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Ana Rita Otrelo-Cardoso
- UCIBIO/Requimte,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Viola Schwuchow
- Institut
für Biologie und Biochemie, Universität Potsdam, Am Neuen Palais
10, 14469 Potsdam, Deutschland
| | | | - Michael Haumann
- Freie Universität Berlin, Fachbereich Physik, 14195 Berlin, Germany
| | - Maria João Romão
- UCIBIO/Requimte,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Silke Leimkühler
- Institut
für Biologie und Biochemie, Universität Potsdam, Am Neuen Palais
10, 14469 Potsdam, Deutschland
| | - Teresa Santos-Silva
- UCIBIO/Requimte,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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17
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Rochet A, Baubet B, Moizan V, Pichon C, Briois V. Co-K and Mo-K edges Quick-XAS study of the sulphidation properties of Mo/Al2O3 and CoMo/Al2O3 catalysts. CR CHIM 2016. [DOI: 10.1016/j.crci.2016.01.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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18
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Lee CC, Sickerman NS, Hu Y, Ribbe MW. YedY: A Mononuclear Molybdenum Enzyme with a Redox-Active Ligand? Chembiochem 2016; 17:453-5. [PMID: 26751730 DOI: 10.1002/cbic.201600004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Indexed: 11/07/2022]
Abstract
A recent electrochemical investigation suggests that the mononuclear molybdenum enzyme YdeY utilizes redox-active ligands during catalysis.
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Affiliation(s)
- Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California in Irvine, 2230/2236 McGaugh Hall, Irvine, CA, 92697-3900, USA
| | - Nathaniel S Sickerman
- Department of Molecular Biology and Biochemistry, University of California in Irvine, 2230/2236 McGaugh Hall, Irvine, CA, 92697-3900, USA
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California in Irvine, 2230/2236 McGaugh Hall, Irvine, CA, 92697-3900, USA.
| | - Markus W Ribbe
- Department of Molecular Biology and Biochemistry, University of California in Irvine, 2230/2236 McGaugh Hall, Irvine, CA, 92697-3900, USA. .,Department of Chemistry, University of California in Irvine, 2236 McGaugh Hall, Irvine, CA, 92697-2025, USA.
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19
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Electrochemical evidence that pyranopterin redox chemistry controls the catalysis of YedY, a mononuclear Mo enzyme. Proc Natl Acad Sci U S A 2015; 112:14506-11. [PMID: 26561582 DOI: 10.1073/pnas.1516869112] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A long-standing contradiction in the field of mononuclear Mo enzyme research is that small-molecule chemistry on active-site mimic compounds predicts ligand participation in the electron transfer reactions, but biochemical measurements only suggest metal-centered catalytic electron transfer. With the simultaneous measurement of substrate turnover and reversible electron transfer that is provided by Fourier-transformed alternating-current voltammetry, we show that Escherichia coli YedY is a mononuclear Mo enzyme that reconciles this conflict. In YedY, addition of three protons and three electrons to the well-characterized "as-isolated" Mo(V) oxidation state is needed to initiate the catalytic reduction of either dimethyl sulfoxide or trimethylamine N-oxide. Based on comparison with earlier studies and our UV-vis redox titration data, we assign the reversible one-proton and one-electron reduction process centered around +174 mV vs. standard hydrogen electrode at pH 7 to a Mo(V)-to-Mo(IV) conversion but ascribe the two-proton and two-electron transition occurring at negative potential to the organic pyranopterin ligand system. We predict that a dihydro-to-tetrahydro transition is needed to generate the catalytically active state of the enzyme. This is a previously unidentified mechanism, suggested by the structural simplicity of YedY, a protein in which Mo is the only metal site.
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20
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Novel mechanism for scavenging of hypochlorite involving a periplasmic methionine-rich Peptide and methionine sulfoxide reductase. mBio 2015; 6:e00233-15. [PMID: 25968643 PMCID: PMC4436054 DOI: 10.1128/mbio.00233-15] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
UNLABELLED Reactive chlorine species (RCS) defense mechanisms are important for bacterial fitness in diverse environments. In addition to the anthropogenic use of RCS in the form of bleach, these compounds are also produced naturally through photochemical reactions of natural organic matter and in vivo by the mammalian immune system in response to invading microorganisms. To gain insight into bacterial RCS defense mechanisms, we investigated Azospira suillum strain PS, which produces periplasmic RCS as an intermediate of perchlorate respiration. Our studies identified an RCS response involving an RCS stress-sensing sigma/anti-sigma factor system (SigF/NrsF), a soluble hypochlorite-scavenging methionine-rich periplasmic protein (MrpX), and a putative periplasmic methionine sulfoxide reductase (YedY1). We investigated the underlying mechanism by phenotypic characterization of appropriate gene deletions, chemogenomic profiling of barcoded transposon pools, transcriptome sequencing, and biochemical assessment of methionine oxidation. Our results demonstrated that SigF was specifically activated by RCS and initiated the transcription of a small regulon centering around yedY1 and mrpX. A yedY1 paralog (yedY2) was found to have a similar fitness to yedY1 despite not being regulated by SigF. Markerless deletions of yedY2 confirmed its synergy with the SigF regulon. MrpX was strongly induced and rapidly oxidized by RCS, especially hypochlorite. Our results suggest a mechanism involving hypochlorite scavenging by sacrificial oxidation of the MrpX in the periplasm. Reduced MrpX is regenerated by the YedY methionine sulfoxide reductase activity. The phylogenomic distribution of this system revealed conservation in several Proteobacteria of clinical importance, including uropathogenic Escherichia coli and Brucella spp., implying a putative role in immune response evasion in vivo. IMPORTANCE Bacteria are often stressed in the environment by reactive chlorine species (RCS) of either anthropogenic or natural origin, but little is known of the defense mechanisms they have evolved. Using a microorganism that generates RCS internally as part of its respiratory process allowed us to uncover a novel defense mechanism based on RCS scavenging by reductive reaction with a sacrificial methionine-rich peptide and redox recycling through a methionine sulfoxide reductase. This system is conserved in a broad diversity of organisms, including some of clinical importance, invoking a possible important role in innate immune system evasion.
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21
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Schrapers P, Hartmann T, Kositzki R, Dau H, Reschke S, Schulzke C, Leimkühler S, Haumann M. Sulfido and cysteine ligation changes at the molybdenum cofactor during substrate conversion by formate dehydrogenase (FDH) from Rhodobacter capsulatus. Inorg Chem 2015; 54:3260-71. [PMID: 25803130 DOI: 10.1021/ic502880y] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Formate dehydrogenase (FDH) enzymes are attractive catalysts for potential carbon dioxide conversion applications. The FDH from Rhodobacter capsulatus (RcFDH) binds a bis-molybdopterin-guanine-dinucleotide (bis-MGD) cofactor, facilitating reversible formate (HCOO(-)) to CO2 oxidation. We characterized the molecular structure of the active site of wildtype RcFDH and protein variants using X-ray absorption spectroscopy (XAS) at the Mo K-edge. This approach has revealed concomitant binding of a sulfido ligand (Mo=S) and a conserved cysteine residue (S(Cys386)) to Mo(VI) in the active oxidized molybdenum cofactor (Moco), retention of such a coordination motif at Mo(V) in a chemically reduced enzyme, and replacement of only the S(Cys386) ligand by an oxygen of formate upon Mo(IV) formation. The lack of a Mo=S bond in RcFDH expressed in the absence of FdsC implies specific metal sulfuration by this bis-MGD binding chaperone. This process still functioned in the Cys386Ser variant, showing no Mo-S(Cys386) ligand, but retaining a Mo=S bond. The C386S variant and the protein expressed without FdsC were inactive in formate oxidation, supporting that both Mo-ligands are essential for catalysis. Low-pH inhibition of RcFDH was attributed to protonation at the conserved His387, supported by the enhanced activity of the His387Met variant at low pH, whereas inactive cofactor species showed sulfido-to-oxo group exchange at the Mo ion. Our results support that the sulfido and S(Cys386) ligands at Mo and a hydrogen-bonded network including His387 are crucial for positioning, deprotonation, and oxidation of formate during the reaction cycle of RcFDH.
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Affiliation(s)
- Peer Schrapers
- †Institut für Experimentalphysik, Freie Universität Berlin, 14195 Berlin, Germany
| | - Tobias Hartmann
- ‡Institut für Biochemie und Biologie, Molekulare Enzymologie, Universität Potsdam, 14476 Potsdam, Germany
| | - Ramona Kositzki
- †Institut für Experimentalphysik, Freie Universität Berlin, 14195 Berlin, Germany
| | - Holger Dau
- †Institut für Experimentalphysik, Freie Universität Berlin, 14195 Berlin, Germany
| | - Stefan Reschke
- ‡Institut für Biochemie und Biologie, Molekulare Enzymologie, Universität Potsdam, 14476 Potsdam, Germany
| | - Carola Schulzke
- §Institut für Biochemie, Bioanorganische Chemie, Ernst-Moritz-Arndt-Universität Greifswald, 17487 Greifswald, Germany
| | - Silke Leimkühler
- ‡Institut für Biochemie und Biologie, Molekulare Enzymologie, Universität Potsdam, 14476 Potsdam, Germany
| | - Michael Haumann
- †Institut für Experimentalphysik, Freie Universität Berlin, 14195 Berlin, Germany
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22
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Nitrite reduction by molybdoenzymes: a new class of nitric oxide-forming nitrite reductases. J Biol Inorg Chem 2015; 20:403-33. [DOI: 10.1007/s00775-014-1234-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 12/14/2014] [Indexed: 02/07/2023]
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23
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Rothery RA, Weiner JH. Shifting the metallocentric molybdoenzyme paradigm: the importance of pyranopterin coordination. J Biol Inorg Chem 2014; 20:349-72. [PMID: 25267303 DOI: 10.1007/s00775-014-1194-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/15/2014] [Indexed: 01/10/2023]
Abstract
In this review, we test the hypothesis that pyranopterin coordination plays a critical role in defining substrate reactivities in the four families of mononuclear molybdenum and tungsten enzymes (Mo/W-enzymes). Enzyme families containing a single pyranopterin dithiolene chelate have been demonstrated to have reactivity towards two (sulfite oxidase, SUOX-fold) and five (xanthine dehydrogenase, XDH-fold) types of substrate, whereas the major family of enzymes containing a bis-pyranopterin dithiolene chelate (dimethylsulfoxide reductase, DMSOR-fold) is reactive towards eight types of substrate. A second bis-pyranopterin enzyme (aldehyde oxidoreductase, AOR-fold) family catalyzes a single type of reaction. The diversity of reactions catalyzed by each family correlates with active site variability, and also with the number of pyranopterins and their coordination by the protein. In the case of the AOR-fold enzymes, inflexibility of pyranopterin coordination correlates with their limited substrate specificity (oxidation of aldehydes). In examples of the SUOX-fold and DMSOR-fold enzymes, we observe three types of histidine-containing charge-transfer relays that can: (1) connect the piperazine ring of the pyranopterin to the substrate-binding site (SUOX-fold enzymes); (2) provide inter-pyranopterin communication (DMSOR-fold enzymes); and (3) connect a pyran ring oxygen to deeply buried water molecules (the DMSOR-fold NarGHI-type nitrate reductases). Finally, sequence data mining reveals a number of bacterial species whose predicted proteomes contain large numbers (up to 64) of Mo/W-enzymes, with the DMSOR-fold enzymes being dominant. These analyses also reveal an inverse correlation between Mo/W-enzyme content and pathogenicity.
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Affiliation(s)
- Richard A Rothery
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
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24
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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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25
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Reschke S, Niks D, Wilson H, Sigfridsson KGV, Haumann M, Rajagopalan KV, Hille R, Leimkühler S. Effect of Exchange of the Cysteine Molybdenum Ligand with Selenocysteine on the Structure and Function of the Active Site in Human Sulfite Oxidase. Biochemistry 2013; 52:8295-303. [DOI: 10.1021/bi4008512] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stefan Reschke
- Department
of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Dimitri Niks
- Department
of Biochemistry, University of California, Riverside, California 92521, United States
| | - Heather Wilson
- Department
of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
| | | | - Michael Haumann
- Institute
of Experimental Physics, Free University Berlin, 14195 Berlin, Germany
| | - K. V. Rajagopalan
- Department
of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Russ Hille
- Department
of Biochemistry, University of California, Riverside, California 92521, United States
| | - Silke Leimkühler
- Department
of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
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26
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Detrimental effect of the 6 His C-terminal tag on YedY enzymatic activity and influence of the TAT signal sequence on YedY synthesis. BMC BIOCHEMISTRY 2013; 14:28. [PMID: 24180491 PMCID: PMC4228395 DOI: 10.1186/1471-2091-14-28] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 10/25/2013] [Indexed: 11/21/2022]
Abstract
Background YedY, a molybdoenzyme belonging to the sulfite oxidase family, is found in most Gram-negative bacteria. It contains a twin-arginine signal sequence that is cleaved after its translocation into the periplasm. Despite a weak reductase activity with substrates such as dimethyl sulfoxide or trimethylamine N-oxide, its natural substrate and its role in the cell remain unknown. Although sequence conservation of the YedY family displays a strictly conserved hydrophobic C-terminal residue, all known studies on Escherichia coli YedY have been performed with an enzyme containing a 6 histidine-tag at the C-terminus which could hamper enzyme activity. Results In this study, we demonstrate that the tag fused to the C-terminus of Rhodobacter sphaeroides YedY is detrimental to the enzyme’s reductase activity and results in an eight-fold decrease in catalytic efficiency. Nonetheless this C-terminal tag does not influence the properties of the molybdenum active site, as assayed by EPR spectroscopy. When a cleavable His-tag was fused to the N-terminus of the mature enzyme in the absence of the signal sequence, YedY was expressed and folded with its cofactor. However, when the signal sequence was added upstream of the N-ter tag, the amount of enzyme produced was approximately ten-fold higher. Conclusion Our study thus underscores the risk of using a C-terminus tagged enzyme while studying YedY, and presents an alternative strategy to express signal sequence-containing enzymes with an N-terminal tag. It brings new insights into molybdoenzyme maturation in R. sphaeroides showing that for some enzymes, maturation can occur in the absence of the signal sequence but that its presence is required for high expression of active enzyme.
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27
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Reschke S, Sigfridsson KGV, Kaufmann P, Leidel N, Horn S, Gast K, Schulzke C, Haumann M, Leimkühler S. Identification of a bis-molybdopterin intermediate in molybdenum cofactor biosynthesis in Escherichia coli. J Biol Chem 2013; 288:29736-45. [PMID: 24003231 DOI: 10.1074/jbc.m113.497453] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The molybdenum cofactor is an important cofactor, and its biosynthesis is essential for many organisms, including humans. Its basic form comprises a single molybdopterin (MPT) unit, which binds a molybdenum ion bearing three oxygen ligands via a dithiolene function, thus forming Mo-MPT. In bacteria, this form is modified to form the bis-MPT guanine dinucleotide cofactor with two MPT units coordinated at one molybdenum atom, which additionally contains GMPs bound to the terminal phosphate group of the MPTs (bis-MGD). The MobA protein catalyzes the nucleotide addition to MPT, but the mechanism of the biosynthesis of the bis-MGD cofactor has remained enigmatic. We have established an in vitro system for studying bis-MGD assembly using purified compounds. Quantification of the MPT/molybdenum and molybdenum/phosphorus ratios, time-dependent assays for MPT and MGD detection, and determination of the numbers and lengths of Mo-S and Mo-O bonds by X-ray absorption spectroscopy enabled identification of a novel bis-Mo-MPT intermediate on MobA prior to nucleotide attachment. The addition of Mg-GTP to MobA loaded with bis-Mo-MPT resulted in formation and release of the final bis-MGD product. This cofactor was fully functional and reconstituted the catalytic activity of apo-TMAO reductase (TorA). We propose a reaction sequence for bis-MGD formation, which involves 1) the formation of bis-Mo-MPT, 2) the addition of two GMP units to form bis-MGD on MobA, and 3) the release and transfer of the mature cofactor to the target protein TorA, in a reaction that is supported by the specific chaperone TorD, resulting in an active molybdoenzyme.
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Affiliation(s)
- Stefan Reschke
- From the Institute for Biochemistry and Biology, Department of Molecular Enzymology, and
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28
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Mitra J, Sarkar S. Oxo-Mo(IV)(dithiolene)thiolato complexes: analogue of reduced sulfite oxidase. Inorg Chem 2013; 52:3032-42. [PMID: 23461669 DOI: 10.1021/ic302485c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A series of [Mo(IV)O(mnt)(SR)(N-N)](-) (mnt = maleonitriledithiolate; R = Ph, nap, p-Cl-Ph, p-CO2H-Ph, and p-NO2-Ph; N-N = 2,2'-bipyridine (bipy) and 1,10-phenanthroline (phen)) complexes analogous to the reduced active site of enzymes of the sulfite oxidase family has been synthesized and their participation in electron transfer reactions studied. Equatorial thiolate and dithiolene ligations have been used to closely simulate the three sulfur coordinations present in the native molybdenum active site. These synthetic analogues have been shown to participate in electron transfer via a pentavalent EPR-active Mo(V) intermediate with minimal structural change as observed electrochemically by reversible oxidative responses. The role of the redox-active dithiolene ligand as an electron transfer gate between external oxidants and the molybdenum center could be envisaged in one of the analogue systems where the initial transient EPR signal with <g> = 2.008 is replaced by the appearance of a typical Mo(V)-centered EPR (<g> = 1.976) signal. The appearance of such a ligand-based transient radical at the initial stage has been supported by the ligand-centered frontier orbital from DFT calculation. A stepwise rationale has been provided by computational study to show that the coupled effects of the diimine bite angle and the thiolato dihedral angle determine the metal- or ligand-based frontier orbital occupancy. DFT calculation has further supported the similarity between the reduced, semireduced, and oxidized resting state of the molybdenum center in Moco of SO with the synthesized complexes and their corresponding one-electron and fully oxidized species.
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Affiliation(s)
- Joyee Mitra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
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29
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Abstract
A perspective is provided of recent advances in our understanding of molybdenum-containing enzymes other than nitrogenase, a large and diverse group of enzymes that usually (but not always) catalyze oxygen atom transfer to or from a substrate, utilizing a Mo=O group as donor or acceptor. An emphasis is placed on the diversity of protein structure and reaction catalyzed by each of the three major families of these enzymes.
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Affiliation(s)
- Russ Hille
- Department of Biochemistry, University of California, 1643 Boyce Hall, Riverside, CA 92521, USA.
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30
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Iobbi-Nivol C, Leimkühler S. Molybdenum enzymes, their maturation and molybdenum cofactor biosynthesis in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012. [PMID: 23201473 DOI: 10.1016/j.bbabio.2012.11.007] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Molybdenum cofactor (Moco) biosynthesis is an ancient, ubiquitous, and highly conserved pathway leading to the biochemical activation of molybdenum. Moco is the essential component of a group of redox enzymes, which are diverse in terms of their phylogenetic distribution and their architectures, both at the overall level and in their catalytic geometry. A wide variety of transformations are catalyzed by these enzymes at carbon, sulfur and nitrogen atoms, which include the transfer of an oxo group or two electrons to or from the substrate. More than 50 molybdoenzymes were identified in bacteria to date. In molybdoenzymes Mo is coordinated to a dithiolene group on the 6-alkyl side chain of a pterin called molybdopterin (MPT). The biosynthesis of Moco can be divided into four general steps in bacteria: 1) formation of the cyclic pyranopterin monophosphate, 2) formation of MPT, 3) insertion of molybdenum into molybdopterin to form Moco, and 4) additional modification of Moco with the attachment of GMP or CMP to the phosphate group of MPT, forming the dinucleotide variant of Moco. This review will focus on molybdoenzymes, the biosynthesis of Moco, and its incorporation into specific target proteins focusing on Escherichia coli. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Affiliation(s)
- Chantal Iobbi-Nivol
- Institut de Microbiologie de la Méditerranée, Aix Marseille Université, Marseille, France
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31
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Leidel N, Chernev P, Havelius KGV, Ezzaher S, Ott S, Haumann M. Site-Selective X-ray Spectroscopy on an Asymmetric Model Complex of the [FeFe] Hydrogenase Active Site. Inorg Chem 2012; 51:4546-59. [DOI: 10.1021/ic2024154] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nils Leidel
- Freie Universität Berlin, Institut für Experimentalphysik, 14195
Berlin, Germany
| | - Petko Chernev
- Freie Universität Berlin, Institut für Experimentalphysik, 14195
Berlin, Germany
| | - Kajsa G. V. Havelius
- Freie Universität Berlin, Institut für Experimentalphysik, 14195
Berlin, Germany
| | - Salah Ezzaher
- University of Uppsala, Department of Chemistry, Ångström
Laboratories, 75120
Uppsala, Sweden
| | - Sascha Ott
- University of Uppsala, Department of Chemistry, Ångström
Laboratories, 75120
Uppsala, Sweden
| | - Michael Haumann
- Freie Universität Berlin, Institut für Experimentalphysik, 14195
Berlin, Germany
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Planas N, Vigara L, Cady C, Miró P, Huang P, Hammarström L, Styring S, Leidel N, Dau H, Haumann M, Gagliardi L, Cramer CJ, Llobet A. Electronic Structure of Oxidized Complexes Derived from cis-[RuII(bpy)2(H2O)2]2+ and Its Photoisomerization Mechanism. Inorg Chem 2011; 50:11134-42. [DOI: 10.1021/ic201686c] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nora Planas
- Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans 16, E-43007 Tarragona, Spain
| | - Laura Vigara
- Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans 16, E-43007 Tarragona, Spain
| | - Clyde Cady
- Department of Photochemistry and Molecular Science, Ångström Laboratory, Box 523, Uppsala University, SE-751 20 Uppsala, Sweden
| | - Pere Miró
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
| | - Ping Huang
- Department of Photochemistry and Molecular Science, Ångström Laboratory, Box 523, Uppsala University, SE-751 20 Uppsala, Sweden
| | - Leif Hammarström
- Department of Photochemistry and Molecular Science, Ångström Laboratory, Box 523, Uppsala University, SE-751 20 Uppsala, Sweden
| | - Stenbjörn Styring
- Department of Photochemistry and Molecular Science, Ångström Laboratory, Box 523, Uppsala University, SE-751 20 Uppsala, Sweden
| | - Nils Leidel
- Department of Physics, Free University Berlin, D-14195 Berlin, Germany
| | - Holger Dau
- Department of Physics, Free University Berlin, D-14195 Berlin, Germany
| | - Michael Haumann
- Department of Physics, Free University Berlin, D-14195 Berlin, Germany
| | - Laura Gagliardi
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
| | - Christopher J. Cramer
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
| | - Antoni Llobet
- Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans 16, E-43007 Tarragona, Spain
- Departament de Química, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, E-08193 Barcelona, Spain
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Samuel PP, Horn S, Döring A, Havelius KGV, Reschke S, Leimkühler S, Haumann M, Schulzke C. A Crystallographic and Mo K-Edge XAS Study of Molybdenum Oxo Bis-, Mono-, and Non-Dithiolene Complexes - First-Sphere Coordination Geometry and Noninnocence of Ligands. Eur J Inorg Chem 2011. [DOI: 10.1002/ejic.201100331] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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