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Valiauga B, Bagdžiūnas G, Sharrock AV, Ackerley DF, Čėnas N. The Catalysis Mechanism of E. coli Nitroreductase A, a Candidate for Gene-Directed Prodrug Therapy: Potentiometric and Substrate Specificity Studies. Int J Mol Sci 2024; 25:4413. [PMID: 38673999 PMCID: PMC11049802 DOI: 10.3390/ijms25084413] [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: 03/05/2024] [Revised: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
E. coli nitroreductase A (NfsA) is a candidate for gene-directed prodrug cancer therapy using bioreductively activated nitroaromatic compounds (ArNO2). In this work, we determined the standard redox potential of FMN of NfsA to be -215 ± 5 mV at pH 7.0. FMN semiquinone was not formed during 5-deazaflavin-sensitized NfsA photoreduction. This determines the two-electron character of the reduction of ArNO2 and quinones (Q). In parallel, we characterized the oxidant specificity of NfsA with an emphasis on its structure. Except for negative outliers nitracrine and SN-36506, the reactivity of ArNO2 increases with their electron affinity (single-electron reduction potential, E17) and is unaffected by their lipophilicity and Van der Waals volume up to 386 Å. The reactivity of quinoidal oxidants is not clearly dependent on E17, but 2-hydroxy-1,4-naphthoquinones were identified as positive outliers and a number of compounds with diverse structures as negative outliers. 2-Hydroxy-1,4-naphthoquinones are characterized by the most positive reaction activation entropy and the negative outlier tetramethyl-1,4-benzoquinone by the most negative. Computer modelling data showed that the formation of H bonds with Arg15, Arg133, and Ser40, plays a major role in the binding of oxidants to reduced NfsA, while the role of the π-π interaction of their aromatic structures is less significant. Typically, the calculated hydride-transfer distances during ArNO2 reduction are smallwer than for Q. This explains the lower reactivity of quinones. Another factor that slows down the reduction is the presence of positively charged aliphatic substituents.
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Affiliation(s)
- Benjaminas Valiauga
- Institute of Biochemistry of Life Sciences Center of Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (B.V.); (G.B.)
| | - Gintautas Bagdžiūnas
- Institute of Biochemistry of Life Sciences Center of Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (B.V.); (G.B.)
| | - Abigail V. Sharrock
- School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Wellington 6140, New Zealand; (A.V.S.); (D.F.A.)
| | - David F. Ackerley
- School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Wellington 6140, New Zealand; (A.V.S.); (D.F.A.)
| | - Narimantas Čėnas
- Institute of Biochemistry of Life Sciences Center of Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (B.V.); (G.B.)
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2
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Rahman Z, McLaws M, Thomas T. Genomic characterization of extended-spectrum beta-lactamase-producing and carbapenem-resistant Escherichia coli from urban wastewater in Australia. Microbiologyopen 2024; 13:e1403. [PMID: 38488803 PMCID: PMC10941799 DOI: 10.1002/mbo3.1403] [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: 10/05/2023] [Revised: 02/25/2024] [Accepted: 02/27/2024] [Indexed: 03/17/2024] Open
Abstract
This study investigates extended-spectrum beta-lactamase-producing and carbapenem-resistant Escherichia coli isolates from Sydney's wastewater. These isolates exhibit resistance to critical antibiotics and harbor novel resistance mechanisms. The findings highlight the importance of wastewater-based surveillance in monitoring resistance beyond the clinical setting.
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Affiliation(s)
- Zillur Rahman
- School of Biological, Earth and Environmental Sciences, Centre for Marine Science and InnovationUNSW SydneySydneyNew South WalesAustralia
| | - Mary‐Louise McLaws
- School of Population HealthUNSW SydneySydneyNew South WalesAustralia
- UNSW Global Water InstituteUNSW SydneySydneyNew South WalesAustralia
| | - Torsten Thomas
- School of Biological, Earth and Environmental Sciences, Centre for Marine Science and InnovationUNSW SydneySydneyNew South WalesAustralia
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3
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Day MA, Jarrom D, Rajah N, Searle PF, Hyde EI, White SA. Oxygen-insensitive nitroreductase E. coli NfsA, but not NfsB, is inhibited by fumarate. Proteins 2023; 91:585-592. [PMID: 36443029 PMCID: PMC10953011 DOI: 10.1002/prot.26451] [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: 08/19/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022]
Abstract
Escherichia coli NfsA and NfsB are founding members of two flavoprotein families that catalyze the oxygen-insensitive reduction of nitroaromatics and quinones by NAD(P)H. This reduction is required for the activity of nitrofuran antibiotics and the enzymes have also been proposed for use with nitroaromatic prodrugs in cancer gene therapy and biocatalysis, but the roles of the proteins in vivo in bacteria are not known. NfsA is NADPH-specific whereas NfsB can also use NADH. The crystal structures of E. coli NfsA and NfsB and several analogs have been determined previously. In our crystal trials, we unexpectedly observed NfsA bound to fumarate. We here present the X-ray structure of the E. coli NfsA-fumarate complex and show that fumarate acts as a weak inhibitor of NfsA but not of NfsB. The structural basis of this differential inhibition is conserved in the two protein families and occurs at fumarate concentrations found in vivo, so impacting the efficacy of these proteins.
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Affiliation(s)
- Martin A. Day
- School of BiosciencesUniversity of BirminghamBirminghamUK
- Institute for Cancer and Genomic SciencesUniversity of BirminghamBirminghamUK
| | - David Jarrom
- School of BiosciencesUniversity of BirminghamBirminghamUK
| | - Navina Rajah
- School of BiosciencesUniversity of BirminghamBirminghamUK
| | - Peter F. Searle
- Institute for Cancer and Genomic SciencesUniversity of BirminghamBirminghamUK
| | - Eva I. Hyde
- School of BiosciencesUniversity of BirminghamBirminghamUK
| | - Scott A. White
- School of BiosciencesUniversity of BirminghamBirminghamUK
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4
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Pimviriyakul P, Kapaothong Y, Tangsupatawat T. Heterologous Expression and Characterization of a Full-length Protozoan Nitroreductase from Leishmania orientalis isolate PCM2. Mol Biotechnol 2023; 65:556-569. [PMID: 36042106 DOI: 10.1007/s12033-022-00556-3] [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: 06/29/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022]
Abstract
Leishmaniasis, a parasitic disease found in parts of the tropics and subtropics, is caused by Leishmania protozoa infection. Nitroreductases (NTRs), enzymes involved in nitroaromatic prodrug activation, are attractive targets for leishmaniasis treatment development. In this study, a full-length recombinant NTR from the Leishmania orientalis isolate PCM2 (LoNTR), which causes severe leishmaniasis in Thailand, was successfully expressed in soluble form using chaperone co-expression in Escherichia coli BL21(DE3). The purified histidine-tagged enzyme (His6-LoNTR) had a subunit molecular mass of 36 kDa with no cofactor bound; however, the addition of exogenous flavin (either FMN or FAD) readily increased its enzyme activity. Bioinformatics analysis found that the unique N-terminal sequences of LoNTR is only present in Leishmania where the addition of this region might result in the loss of flavin binding. Either NADH or NADPH can serve as an electron donor to transfer electrons to nitrofurazone; however, NADPH was preferred. Molecular oxygen was identified as an additional electron acceptor resulting in wasteful electrons from NADPH for the main catalysis. Steady-state kinetic experiments revealed a ping-pong mechanism for His6-LoNTR with Km,NADPH, Km,NFZ, and kcat of 28 µM, 68 µM, and 0.84 min-1, respectively. Besides nitroreductase activity, His6-LoNTR also has the ability to reduce quinone derivatives. The properties of full-length His6-LoNTR were different from previously reported protozoa and bacterial NTRs in many respects. This study provides information of NTR catalysis to be developed as a potential future therapeutic target to treat leishmaniasis.
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Affiliation(s)
- Panu Pimviriyakul
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
| | - Yuvarun Kapaothong
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Theerapat Tangsupatawat
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
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5
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White SA, Christofferson AJ, Grainger AI, Day MA, Jarrom D, Graziano AE, Searle PF, Hyde EI. The 3D-structure, kinetics and dynamics of the E. coli nitroreductase NfsA with NADP + provide glimpses of its catalytic mechanism. FEBS Lett 2022; 596:2425-2440. [PMID: 35648111 PMCID: PMC9912195 DOI: 10.1002/1873-3468.14413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/20/2022] [Accepted: 05/25/2022] [Indexed: 11/12/2022]
Abstract
Nitroreductases activate nitroaromatic antibiotics and cancer prodrugs to cytotoxic hydroxylamines and reduce quinones to quinols. Using steady-state and stopped-flow kinetics, we show that the Escherichia coli nitroreductase NfsA is 20-50 fold more active with NADPH than with NADH and that product release may be rate-limiting. The crystal structure of NfsA with NADP+ shows that a mobile loop forms a phosphate-binding pocket. The nicotinamide ring and nicotinamide ribose are mobile, as confirmed in molecular dynamics (MD) simulations. We present a model of NADPH bound to NfsA. Only one NADP+ is seen bound to the NfsA dimers, and MD simulations show that binding of a second NADP(H) cofactor is unfavourable, suggesting that NfsA and other members of this protein superfamily may have a half-of-sites mechanism.
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Affiliation(s)
| | | | - Alastair I. Grainger
- School of BiosciencesUniversity of BirminghamUK,Present address:
School of Life and Health SciencesAston UniversityBirminghamB4 7ETUK
| | - Martin A. Day
- School of BiosciencesUniversity of BirminghamUK,Institute for Cancer and Genomic SciencesUniversity of BirminghamUK,Present address:
DurhamUK
| | - David Jarrom
- School of BiosciencesUniversity of BirminghamUK,Present address:
Health Technology WalesCardiffCF10 4PLUK
| | - Antonio E. Graziano
- School of BiosciencesUniversity of BirminghamUK,Present address:
Carlsberg Marstons Brewing CompanyNorthamptonNN1 1PZUK
| | - Peter F. Searle
- Institute for Cancer and Genomic SciencesUniversity of BirminghamUK
| | - Eva I. Hyde
- School of BiosciencesUniversity of BirminghamUK
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6
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Inhibition of Escherichia coli nitroreductase by the constituents in Syzygium aromaticum. Chin J Nat Med 2022; 20:506-517. [DOI: 10.1016/s1875-5364(22)60163-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Indexed: 11/23/2022]
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7
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Fortinez CM, Bloudoff K, Harrigan C, Sharon I, Strauss M, Schmeing TM. Structures and function of a tailoring oxidase in complex with a nonribosomal peptide synthetase module. Nat Commun 2022; 13:548. [PMID: 35087027 PMCID: PMC8795117 DOI: 10.1038/s41467-022-28221-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/19/2021] [Indexed: 12/15/2022] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) are large modular enzymes that synthesize secondary metabolites and natural product therapeutics. Most NRPS biosynthetic pathways include an NRPS and additional proteins that introduce chemical modifications before, during or after assembly-line synthesis. The bacillamide biosynthetic pathway is a common, three-protein system, with a decarboxylase that prepares an NRPS substrate, an NRPS, and an oxidase. Here, the pathway is reconstituted in vitro. The oxidase is shown to perform dehydrogenation of the thiazoline in the peptide intermediate while it is covalently attached to the NRPS, as the penultimate step in bacillamide D synthesis. Structural analysis of the oxidase reveals a dimeric, two-lobed architecture with a remnant RiPP recognition element and a dramatic wrapping loop. The oxidase forms a stable complex with the NRPS and dimerizes it. We visualized co-complexes of the oxidase bound to the elongation module of the NRPS using X-ray crystallography and cryo-EM. The three active sites (for adenylation, condensation/cyclization, and oxidation) form an elegant arc to facilitate substrate delivery. The structures enabled a proof-of-principle bioengineering experiment in which the BmdC oxidase domain is embedded into the NRPS.
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Affiliation(s)
- Camille Marie Fortinez
- Department of Biochemistry, McGill University, Montréal, QC, H3G 0B1, Canada.,Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada
| | - Kristjan Bloudoff
- Department of Biochemistry, McGill University, Montréal, QC, H3G 0B1, Canada.,Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada
| | - Connor Harrigan
- Department of Biochemistry, McGill University, Montréal, QC, H3G 0B1, Canada.,Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada
| | - Itai Sharon
- Department of Biochemistry, McGill University, Montréal, QC, H3G 0B1, Canada.,Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada
| | - Mike Strauss
- Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada.,Department of Anatomy and Cell Biology, McGill University, Montréal, QC, H3A 0C7, Canada
| | - T Martin Schmeing
- Department of Biochemistry, McGill University, Montréal, QC, H3G 0B1, Canada. .,Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada.
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8
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Wan Y, Mills E, Leung RC, Vieira A, Zhi X, Croucher NJ, Woodford N, Jauneikaite E, Ellington MJ, Sriskandan S. Alterations in chromosomal genes nfsA, nfsB, and ribE are associated with nitrofurantoin resistance in Escherichia coli from the United Kingdom. Microb Genom 2021; 7:000702. [PMID: 34860151 PMCID: PMC8767348 DOI: 10.1099/mgen.0.000702] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/01/2021] [Indexed: 01/18/2023] Open
Abstract
Antimicrobial resistance in enteric or urinary Escherichia coli is a risk factor for invasive E. coli infections. Due to widespread trimethoprim resistance amongst urinary E. coli and increased bacteraemia incidence, a national recommendation to prescribe nitrofurantoin for uncomplicated urinary tract infection was made in 2014. Nitrofurantoin resistance is reported in <6% urinary E. coli isolates in the UK, however, mechanisms underpinning nitrofurantoin resistance in these isolates remain unknown. This study aimed to identify the genetic basis of nitrofurantoin resistance in urinary E. coli isolates collected from north west London and then elucidate resistance-associated genetic alterations in available UK E. coli genomes. As a result, an algorithm was developed to predict nitrofurantoin susceptibility. Deleterious mutations and gene-inactivating insertion sequences in chromosomal nitroreductase genes nfsA and/or nfsB were identified in genomes of nine confirmed nitrofurantoin-resistant urinary E. coli isolates and additional 11 E. coli isolates that were highlighted by the prediction algorithm and subsequently validated to be nitrofurantoin-resistant. Eight categories of allelic changes in nfsA , nfsB , and the associated gene ribE were detected in 12412 E. coli genomes from the UK. Evolutionary analysis of these three genes revealed homoplasic mutations and explained the previously reported order of stepwise mutations. The mobile gene complex oqxAB , which is associated with reduced nitrofurantoin susceptibility, was identified in only one of the 12412 genomes. In conclusion, mutations and insertion sequences in nfsA and nfsB were leading causes of nitrofurantoin resistance in UK E. coli . As nitrofurantoin exposure increases in human populations, the prevalence of nitrofurantoin resistance in carriage E. coli isolates and those from urinary and bloodstream infections should be monitored.
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Affiliation(s)
- Yu Wan
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Ewurabena Mills
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Rhoda C.Y. Leung
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Present address: Department of Microbiology, Queen Mary Hospital, Hong Kong S.A.R., PR China
| | - Ana Vieira
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Xiangyun Zhi
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Nicholas J. Croucher
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, Colindale, London, United Kingdom
| | - Elita Jauneikaite
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Matthew J. Ellington
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, Colindale, London, United Kingdom
| | - Shiranee Sriskandan
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
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9
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Khamari B, Adak S, Chanakya PP, Lama M, Peketi ASK, Gurung SA, Chettri S, Kumar P, Bulagonda EP. Prediction of nitrofurantoin resistance among Enterobacteriaceae and mutational landscape of in vitro selected resistant E. coli. Res Microbiol 2021; 173:103889. [PMID: 34718096 DOI: 10.1016/j.resmic.2021.103889] [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: 06/03/2021] [Revised: 10/16/2021] [Accepted: 10/21/2021] [Indexed: 11/18/2022]
Abstract
Nitrofurantoin (NIT) has long been a drug of choice in the treatment of lower urinary tract infections. Recent emergence of NIT resistant Enterobacteriaceae is a global concern. An ordinal logistic regression model based on PCR amplification patterns of five genes associated with NIT resistance (nfsA, nfsB, ribE, oqxA, and oqxB) among 100 clinical Enterobacteriaceae suggested that a combination of oqxB, nfsB, ribE, and oqxA is ideal for NIT resistance prediction. In addition, four Escherichia coli NIT-resistant mutants were in vitro generated by exposing an NIT-susceptible E. coli to varying concentrations of NIT. The in vitro selected NIT resistant mutants (NI2, NI3, NI4 and NI5) were found to have mutations resulting in frameshifts, premature/lost stop codons or failed amplification of nfsA and/or nfsB genes. The in vitro selected NI5 and the transductant colonies with reconstructed NI5 genotype exhibited reduced fitness compared to their parent strain NS30, while growth of a resistant clinical isolate (NR42) was found to be unaffected in the absence of NIT. These results emphasize the importance of strict adherence to prescribed antibiotic treatment regimens and dosage duration. If left unchecked, these resistant bacteria may thrive at sub-therapeutic concentrations of NIT and spread in the community.
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Affiliation(s)
- Balaram Khamari
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, India
| | - Sudeshna Adak
- OmiX Research and Diagnostic Laboratories Private Limited, Bengaluru, India
| | - Pachi Pulusu Chanakya
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, India
| | - Manmath Lama
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, India
| | - Arun Sai Kumar Peketi
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, India
| | - Saurav Anand Gurung
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, India
| | - Sushil Chettri
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, India
| | - Prakash Kumar
- Department of Microbiology, Sri Sathya Sai Institute of Higher Medical Sciences, Prasanthigram, India
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Flavin oxidation state impacts on nitrofuran antibiotic binding orientation in nitroreductases. Biochem J 2021; 478:3423-3428. [PMID: 34554213 DOI: 10.1042/bcj20210489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 11/17/2022]
Abstract
Nitroreductases catalyse the NAD(P)H-dependent nitro reduction in nitrofuran antibiotics, which activates them into cytotoxic molecules leading to cell death. The design of new effective nitrofuran antibiotics relies on knowledge of the kinetic mechanism and nitrofuran binding mode of microbial nitroreductases NfsA and NfsB. This has been hampered by multiple co-crystallisation studies revealing ligand binding in non-electron transfer competent states. In a recent study by Day et al. (2021) the authors investigated the likely reaction mechanism and mode of nitrofurantoin binding to NfsA using potentiometry, global kinetics analysis, crystallography and molecular dynamics simulations. Their findings suggest nitrofurantoin reduction proceeds via a direct hydride transfer from reduced FMN, while the crystallographic binding orientation is an inhibitory complex. Molecular dynamics simulations suggest ligand binding orientations is dependent on the oxidation state of the FMN. This study highlights the importance of utilising computational studies alongside traditional crystallographic approaches, when multiple stable ligand binding orientations can occur.
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11
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Structure and substrate specificity determinants of NfnB, a dinitroaniline herbicide-catabolizing nitroreductase from Sphingopyxis sp. strain HMH. J Biol Chem 2021; 297:101143. [PMID: 34473996 PMCID: PMC8484813 DOI: 10.1016/j.jbc.2021.101143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/23/2021] [Accepted: 08/27/2021] [Indexed: 11/24/2022] Open
Abstract
Nitroreductases are emerging as attractive bioremediation enzymes, with substrate promiscuity toward both natural and synthetic compounds. Recently, the nitroreductase NfnB from Sphingopyxis sp. strain HMH exhibited metabolic activity for dinitroaniline herbicides including butralin and pendimethalin, triggering the initial steps of their degradation and detoxification. However, the determinants of the specificity of NfnB for these herbicides are unknown. In this study, we performed structural and biochemical analyses of NfnB to decipher its substrate specificity. The homodimer NfnB is a member of the PnbA subgroup of the nitroreductase family. Each monomer displays a central α + β fold for the core domain, with a protruding middle region and an extended C-terminal region. The protruding middle region of Val75–Tyr129 represents a structural extension that is a common feature to members of the PnbA subgroup and functions as an opening wall connecting the coenzyme FMN-binding site to the surface, therefore serving as a substrate binding site. We performed mutational, kinetic, and structural analyses of mutant enzymes and found that Tyr88 in the middle region plays a pivotal role in substrate specificity by determining the dimensions of the wall opening. The mutation of Tyr88 to phenylalanine or alanine caused significant changes in substrate selectivity toward bulkier dinitroaniline herbicides such as oryzalin and isopropalin without compromising its activity. These results provide a framework to modify the substrate specificity of nitroreductase in the PnbA subgroup, which has been a challenging issue for its biotechnological and bioremediation applications.
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12
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Čėnas N, Nemeikaitė-Čėnienė A, Kosychova L. Single- and Two-Electron Reduction of Nitroaromatic Compounds by Flavoenzymes: Mechanisms and Implications for Cytotoxicity. Int J Mol Sci 2021; 22:ijms22168534. [PMID: 34445240 PMCID: PMC8395237 DOI: 10.3390/ijms22168534] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 07/30/2021] [Accepted: 08/04/2021] [Indexed: 12/14/2022] Open
Abstract
Nitroaromatic compounds (ArNO2) maintain their importance in relation to industrial processes, environmental pollution, and pharmaceutical application. The manifestation of toxicity/therapeutic action of nitroaromatics may involve their single- or two-electron reduction performed by various flavoenzymes and/or their physiological redox partners, metalloproteins. The pivotal and still incompletely resolved questions in this area are the identification and characterization of the specific enzymes that are involved in the bioreduction of ArNO2 and the establishment of their contribution to cytotoxic/therapeutic action of nitroaromatics. This review addresses the following topics: (i) the intrinsic redox properties of ArNO2, in particular, the energetics of their single- and two-electron reduction in aqueous medium; (ii) the mechanisms and structure-activity relationships of reduction in ArNO2 by flavoenzymes of different groups, dehydrogenases-electrontransferases (NADPH:cytochrome P-450 reductase, ferredoxin:NADP(H) oxidoreductase and their analogs), mammalian NAD(P)H:quinone oxidoreductase, bacterial nitroreductases, and disulfide reductases of different origin (glutathione, trypanothione, and thioredoxin reductases, lipoamide dehydrogenase), and (iii) the relationships between the enzymatic reactivity of compounds and their activity in mammalian cells, bacteria, and parasites.
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Affiliation(s)
- Narimantas Čėnas
- Institute of Biochemistry of Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania;
- Correspondence: ; Tel.: +370-5-223-4392
| | - Aušra Nemeikaitė-Čėnienė
- State Research Institute Center for Innovative Medicine, Santariškių St. 5, LT-08406 Vilnius, Lithuania;
| | - Lidija Kosychova
- Institute of Biochemistry of Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania;
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13
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The structures of E. coli NfsA bound to the antibiotic nitrofurantoin; to 1,4-benzoquinone and to FMN. Biochem J 2021; 478:2601-2617. [PMID: 34142705 PMCID: PMC8286842 DOI: 10.1042/bcj20210160] [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: 03/11/2021] [Revised: 06/14/2021] [Accepted: 06/17/2021] [Indexed: 01/23/2023]
Abstract
NfsA is a dimeric flavoprotein that catalyses the reduction in nitroaromatics and quinones by NADPH. This reduction is required for the activity of nitrofuran antibiotics. The crystal structure of free Escherichia coli NfsA and several homologues have been determined previously, but there is no structure of the enzyme with ligands. We present here crystal structures of oxidised E. coli NfsA in the presence of several ligands, including the antibiotic nitrofurantoin. Nitrofurantoin binds with the furan ring, rather than the nitro group that is reduced, near the N5 of the FMN. Molecular dynamics simulations show that this orientation is only favourable in the oxidised enzyme, while potentiometry suggests that little semiquinone is formed in the free protein. This suggests that the reduction occurs by direct hydride transfer from FMNH− to nitrofurantoin bound in the reverse orientation to that in the crystal structure. We present a model of nitrofurantoin bound to reduced NfsA in a viable hydride transfer orientation. The substrate 1,4-benzoquinone and the product hydroquinone are positioned close to the FMN N5 in the respective crystal structures with NfsA, suitable for reaction, but are mobile within the active site. The structure with a second FMN, bound as a ligand, shows that a mobile loop in the free protein forms a phosphate-binding pocket. NfsA is specific for NADPH and a similar conformational change, forming a phosphate-binding pocket, is likely to also occur with the natural cofactor.
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Metabolites Potentiate Nitrofurans in Nongrowing Escherichia coli. Antimicrob Agents Chemother 2021; 65:AAC.00858-20. [PMID: 33361301 DOI: 10.1128/aac.00858-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 12/17/2020] [Indexed: 01/17/2023] Open
Abstract
Nitrofurantoin (NIT) is a broad-spectrum bactericidal antibiotic used in the treatment of urinary tract infections. It is a prodrug that once activated by nitroreductases goes on to inhibit bacterial DNA, RNA, cell wall, and protein synthesis. Previous work has suggested that NIT retains considerable activity against nongrowing bacteria. Here, we have found that Escherichia coli grown to stationary phase in minimal or artificial urine medium is not susceptible to NIT. Supplementation with glucose under conditions where cells remained nongrowing (other essential nutrients were absent) sensitized cultures to NIT. We conceptualized NIT sensitivity as a multi-input AND gate and lack of susceptibility as an insufficiency in one or more of those inputs. The inputs considered were an activating enzyme, cytoplasmic abundance of NIT, and reducing equivalents required for NIT activation. We systematically assessed the contribution of each of these inputs and found that NIT import and the level of activating enzyme were not contributing factors to the lack of susceptibility. Rather, evidence suggested that the low abundance of reducing equivalents is why stationary-phase E. coli are not killed by NIT and catabolites can resensitize those cells. We found that this phenomenon also occurred when using nitrofurazone, which established generality to the nitrofuran antibiotic class. In addition, we observed that NIT activity against stationary-phase uropathogenic E. coli (UPEC) could also be potentiated through metabolite supplementation. These findings suggest that the combination of nitrofurans with specific metabolites could improve the outcome of uncomplicated urinary tract infections.
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15
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Hall KR, Robins KJ, Williams EM, Rich MH, Calcott MJ, Copp JN, Little RF, Schwörer R, Evans GB, Patrick WM, Ackerley DF. Intracellular complexities of acquiring a new enzymatic function revealed by mass-randomisation of active-site residues. eLife 2020; 9:59081. [PMID: 33185191 PMCID: PMC7738182 DOI: 10.7554/elife.59081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/12/2020] [Indexed: 11/17/2022] Open
Abstract
Selection for a promiscuous enzyme activity provides substantial opportunity for competition between endogenous and newly-encountered substrates to influence the evolutionary trajectory, an aspect that is often overlooked in laboratory directed evolution studies. We selected the Escherichia coli nitro/quinone reductase NfsA for chloramphenicol detoxification by simultaneously randomising eight active-site residues and interrogating ~250,000,000 reconfigured variants. Analysis of every possible intermediate of the two best chloramphenicol reductases revealed complex epistatic interactions. In both cases, improved chloramphenicol detoxification was only observed after an R225 substitution that largely eliminated activity with endogenous quinones. Error-prone PCR mutagenesis reinforced the importance of R225 substitutions, found in 100% of selected variants. This strong activity trade-off demonstrates that endogenous cellular metabolites hold considerable potential to shape evolutionary outcomes. Unselected prodrug-converting activities were mostly unaffected, emphasising the importance of negative selection to effect enzyme specialisation, and offering an application for the evolved genes as dual-purpose selectable/counter-selectable markers. In the cell, most tasks are performed by big molecules called proteins, which behave like molecular machines. Although proteins are often described as having one job each, this is not always true, and many proteins can perform different roles. Enzymes are a type of protein that facilitate chemical reactions. They are often specialised to one reaction, but they can also accelerate other side-reactions. During evolution, these side-reactions can become more useful and, as a result, the role of the enzyme may change over time. The main role of the enzyme called NfsA in Escherichia coli bacteria is thought to be to convert molecules called quinones into hydroquinones, which can protect the cell from toxic molecules produced in oxidation reactions. As a side-reaction, NfsA has the potential to protect bacteria from an antibiotic called chloramphenicol, but it generally does this with such low efficacy that the effects are negligible. Producing hydroquinones is helpful to the cell in some situations, but if bacteria are regularly exposed to chloramphenicol, NfsA’s role aiding antibiotic resistance could become more important. Over time, the enzyme could evolve to become better at neutralising chloramphenicol. Therefore, NfsA provides an opportunity to study the evolution of proteins and how bacteria adapt to antibiotics. To see how evolution might affect the activity of NfsA, Hall et al. generated 250 million E. coli with either random or targeted changes to the gene that codes for the NfsA enzyme. The resulting variants of NfsA that were most effective against chloramphenicol all had a change that eliminated the enzyme’s ability to convert quinones. This result demonstrates a key trade-off between roles for NfsA, where one must be lost for the other to improve. These results demonstrate the interplay between a protein’s different roles and provide insight into bacterial drug resistance. Additionally, the experiments showed that the bacteria with improved resistance to chloramphenicol also became more sensitive to another antibiotic, metronidazole. These findings could inform the fight against drug-resistant bacterial infections and may also be helpful in guiding the design of proteins with different roles.
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Affiliation(s)
- Kelsi R Hall
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand.,Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Katherine J Robins
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand
| | - Elsie M Williams
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand.,Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Michelle H Rich
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand
| | - Mark J Calcott
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand.,Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Janine N Copp
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand
| | - Rory F Little
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand
| | - Ralf Schwörer
- Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand.,Ferrier Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Gary B Evans
- Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand.,Ferrier Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Wayne M Patrick
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand.,Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - David F Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand.,Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
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16
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Dabravolski SA. Evolutionary aspects of the Viridiplantae nitroreductases. J Genet Eng Biotechnol 2020; 18:60. [PMID: 33025290 PMCID: PMC7538488 DOI: 10.1186/s43141-020-00073-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/14/2020] [Indexed: 11/10/2022]
Abstract
Background Nitroreductases are a family of evolutionarily related proteins catalyzing the reduction of nitro-substituted compounds. Nitroreductases are widespread enzymes, but nearly all modern research and practical application have been concentrated on the bacterial proteins, mainly nitroreductases of Escherichia coli. The main aim of this study is to describe the phylogenic distribution of the nitroreductases in the photosynthetic eukaryotes (Viridiplantae) to highlight their structural similarity and areas for future research and application. Results This study suggests that homologs of nitroreductase proteins are widely presented also in Viridiplantae. Maximum likelihood phylogenetic tree reconstruction method and comparison of the structural models suggest close evolutional relation between cyanobacterial and Viridiplantae nitroreductases. Conclusions This study provides the first attempt to understand the evolution of nitroreductase protein family in Viridiplantae. Our phylogeny estimation and preservation of the chloroplasts/mitochondrial localization indicate the evolutional origin of the plant nitroreductases from the cyanobacterial endosymbiont. A defined high level of the similarity on the structural level suggests conservancy also for the functions. Directions for the future research and industrial application of the Viridiplantae nitroreductases are discussed.
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Affiliation(s)
- Siarhei A Dabravolski
- Department of Clinical Diagnostics, Vitebsk State Academy of Veterinary Medicine [UO VGAVM], 7/11 Dovatora St., 210026, Vitebsk, Belarus.
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17
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Pradhan SK, Singh NR, Dehury B, Panda D, Modi MK, Thatoi H. Insights into the mode of flavin mononucleotide binding and catalytic mechanism of bacterial chromate reductases: A molecular dynamics simulation study. J Cell Biochem 2019; 120:16990-17005. [PMID: 31131470 DOI: 10.1002/jcb.28960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/04/2019] [Accepted: 02/14/2019] [Indexed: 11/09/2022]
Abstract
Enzymes from natural sources protect the environment via complex biological mechanisms, which aid in reductive immobilization of toxic metals including chromium. Nevertheless, progress was being made in elucidating high-resolution crystal structures of reductases and their binding with flavin mononucleotide (FMN) to understand the underlying mechanism of chromate reduction. Therefore, herein, we employed molecular dynamics (MD) simulations, principal component analysis (PCA), and binding free energy calculations to understand the dynamics behavior of these enzymes with FMN. Six representative chromate reductases in monomeric and dimeric forms were selected to study the mode, dynamics, and energetic component that drive the FMN binding process. As evidenced by MD simulation, FMN prefers to bind the cervix formed between the catalytic domain surrounded by strong conserved hydrogen bonding, electrostatic, and hydrophobic contacts. The slight movement and reorientation of FMN resulted in breakage of some crucial H-bonds and other nonbonded contacts, which were well compensated with newly formed H-bonds, electrostatic, and hydrophobic interactions. The critical residues aiding in tight anchoring of FMN within dimer were found to be strongly conserved in the bacterial system. The molecular mechanics combined with the Poisson-Boltzmann surface area binding free energy of the monomer portrayed that the van der Waals and electrostatic energy contribute significantly to the total free energy, where, the polar solvation energy opposes the binding of FMN. The proposed proximity relationships between enzyme and FMN binding site presented in this study will open up better avenues to engineer enzymes with optimized chromate reductase activity for sustainable bioremediation of heavy metals.
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Affiliation(s)
- Sukanta Kumar Pradhan
- Department of Bioinformatics, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India.,Department of Biotechnology, School of Life Sciences, Ravenshaw University, Cuttack, Odisha, India
| | - Nihar Ranjan Singh
- Department of Botany, School of Life Sciences, Ravenshaw University, Cuttack, Odisha, India
| | - Budheswar Dehury
- Biomedical Informatics Centre, Regional Medical Research Centre (ICMR), Nalco Square, Chandrasekharpur, Bhubaneswar, Odisha, India.,Department of Chemistry, Technical University of Denmark, DK-2800 Kgs, Lyngby
| | - Debashis Panda
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Mahendra Kumar Modi
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Hrudayanath Thatoi
- Department of Biotechnology, North Orissa University, Sriram Chandra Vihar, Takatpur, Baripada, Odisha, India
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18
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Saghaug CS, Klotz C, Kallio JP, Brattbakk HR, Stokowy T, Aebischer T, Kursula I, Langeland N, Hanevik K. Genetic variation in metronidazole metabolism and oxidative stress pathways in clinical Giardia lamblia assemblage A and B isolates. Infect Drug Resist 2019; 12:1221-1235. [PMID: 31190910 PMCID: PMC6519707 DOI: 10.2147/idr.s177997] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/16/2019] [Indexed: 12/12/2022] Open
Abstract
Purpose: Treatment-refractory Giardia cases have increased rapidly within the last decade. No markers of resistance nor a standardized susceptibility test have been established yet, but several enzymes and their pathways have been associated with metronidazole (MTZ) resistant Giardia. Very limited data are available regarding genetic variation in these pathways. We aimed to investigate genetic variation in metabolic pathway genes proposed to be involved in MTZ resistance in recently acquired, cultured clinical isolates. Methods: Whole genome sequencing of 12 assemblage A2 and 8 assemblage B isolates was done, to decipher genomic variation in Giardia. Twenty-nine genes were identified in a literature search and investigated for their single nucleotide variants (SNVs) in the coding/non-coding regions of the genes, either as amino acid changing (non-synonymous SNVs) or non-changing SNVs (synonymous). Results: In Giardia assemblage B, several genes involved in MTZ activation or oxidative stress management were found to have higher numbers of non-synonymous SNVs (thioredoxin peroxidase, nitroreductase 1, ferredoxin 2, NADH oxidase, nitroreductase 2, alcohol dehydrogenase, ferredoxin 4 and ferredoxin 1) than the average variation. For Giardia assemblage A2, the highest genetic variability was found in the ferredoxin 2, ferredoxin 6 and in nicotinamide adenine dinucleotide phosphate (NADPH) oxidoreductase putative genes. SNVs found in the ferredoxins and nitroreductases were analyzed further by alignment and homology modeling. SNVs close to the iron-sulfur cluster binding sites in nitroreductase-1 and 2 and ferredoxin 2 and 4 could potentially affect protein function. Flavohemoprotein seems to be a variable-copy gene, due to higher, but variable coverage compared to other genes investigated. Conclusion: In clinical Giardia isolates, genetic variability is common in important genes in the MTZ metabolizing pathway and in the management of oxidative and nitrosative stress and includes high numbers of non-synonymous SNVs. Some of the identified amino acid changes could potentially affect the respective proteins important in the MTZ metabolism.
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Affiliation(s)
- Christina S Saghaug
- Department of Clinical Science, University of Bergen, Bergen, Hordaland, Norway.,Norwegian National Advisory Unit on Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Hordaland, Norway
| | - Christian Klotz
- Department of Infectious Diseases, Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Juha P Kallio
- Department of Biomedicine, University of Bergen, Bergen, Hordaland, Norway
| | - Hans-Richard Brattbakk
- Department of Clinical Science, University of Bergen, Bergen, Hordaland, Norway.,Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Hordaland, Norway
| | - Tomasz Stokowy
- Department of Clinical Science, University of Bergen, Bergen, Hordaland, Norway.,Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Hordaland, Norway
| | - Toni Aebischer
- Department of Infectious Diseases, Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Inari Kursula
- Department of Biomedicine, University of Bergen, Bergen, Hordaland, Norway.,Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Nina Langeland
- Department of Clinical Science, University of Bergen, Bergen, Hordaland, Norway.,Norwegian National Advisory Unit on Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Hordaland, Norway.,Department of Medicine, Haraldsplass Deaconess Hospital, Bergen, Hordaland, Norway
| | - Kurt Hanevik
- Department of Clinical Science, University of Bergen, Bergen, Hordaland, Norway.,Norwegian National Advisory Unit on Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Hordaland, Norway
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19
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Suzuki H. Remarkable diversification of bacterial azoreductases: primary sequences, structures, substrates, physiological roles, and biotechnological applications. Appl Microbiol Biotechnol 2019; 103:3965-3978. [PMID: 30941462 DOI: 10.1007/s00253-019-09775-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/13/2019] [Accepted: 03/15/2019] [Indexed: 12/12/2022]
Abstract
Azoreductases reductively cleave azo linkages by using NAD(P)H as an electron donor. The enzymes are widely found in bacteria and act on numerous azo dyes, which allow various unique applications. This review describes primary amino acid sequences, structures, substrates, physiological roles, and biotechnological applications of bacterial azoreductases to discuss their remarkable diversification. According to primary sequences, azoreductases were classified phylogenetically into four main clades. Most members of clades I-III are flavoproteins, whereas clade IV members include flavin-free azoreductases. Clades I and II prefer NADPH and NADH, respectively, as electron donors, whereas other members generally use both. Several enzymes formed no clades; moreover, some bacteria produce azoreductases with longer primary structures than those hitherto identified, which implies further diversification of bacterial azoreductases. The crystal structures commonly reveal the Rossmann folds; however, ternary structures are moderately varied with different quaternary conformation. Although physiological roles are obscure, several azoreductases have been shown to act on metabolites such as flavins, quinones, and metal ions more efficiently than on azo dyes. Considering that many homologs exclusively act on these metabolites, it is possible that azoreductases are actually side activities of versatile reductases that act on various substrates with different specificities. In parallel, this idea raises the possibility that homologous enzymes, even if these are already defined as other types of reductases, widely harbor azoreductase activities. Although azoreductases for which their genes have been identified are not abundant, it may be simple to identify azoreductases of biotechnological importance that have novel substrate specificities.
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Affiliation(s)
- Hirokazu Suzuki
- Faculty of Engineering, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8552, Japan. .,Center for Research on Green Sustainable Chemistry, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8552, Japan.
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20
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Yang J, Bai J, Qu M, Xie B, Yang Q. Biochemical characteristics of a nitroreductase with diverse substrate specificity from Streptomyces mirabilis DUT001. Biotechnol Appl Biochem 2018; 66:33-42. [PMID: 30231196 DOI: 10.1002/bab.1692] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/11/2018] [Indexed: 11/09/2022]
Abstract
A nitroreductase-encoded gene from an efficient nitro-reducing bacterium Streptomyces mirabilis DUT001, named snr, was cloned and heterogeneously expressed in Escherichia coli. The purified Streptomyces nitroreductase SNR was a homodimer with an apparent subunit molecular weight of 24 kDa and preferred NADH to NADPH as a cofactor. By enzyme incubation and isothermal calorimetry experiments, flavin mononucleotide (FMN) was found to be the preferred flavin cofactor; the binding process was exothermic and primarily enthalpy driven. The enzyme can reduce multiple nitro compounds and flavins, including antibacterial drug nitrofurazone, priority pollutants 2,4-dinitrotoluene and 2,4,6-trinitrotoluene, as well as key chemical intermediates 3-nitrophthalimide, 4-nitrophthalimide, and 4-nitro-1,8-naphthalic anhydride. Among the substrates tested, the highest activity of kcat(app) /Km(app) (0.234 μM-1 Sec-1 ) was observed for the reduction of FMN. Multiple sequence alignment revealed that the high FMN reduction activity of SNR may be due to the absence of a helix, constituting the entrance to the substrate pocket in other nitroreductases.
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Affiliation(s)
- Jun Yang
- State Key Laboratory of Fine Chemical Engineering and School of Life Science and Biotechnology, Dalian University of Technology, Dalian, People's Republic of China
| | - Jing Bai
- College of Bioscience and Bioengineering, Hebei University of Science & Technology, Hebei, People's Republic of China
| | - Mingbo Qu
- State Key Laboratory of Fine Chemical Engineering and School of Life Science and Biotechnology, Dalian University of Technology, Dalian, People's Republic of China
| | - Bo Xie
- State Key Laboratory of Fine Chemical Engineering and School of Life Science and Biotechnology, Dalian University of Technology, Dalian, People's Republic of China
| | - Qing Yang
- State Key Laboratory of Fine Chemical Engineering and School of Life Science and Biotechnology, Dalian University of Technology, Dalian, People's Republic of China
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21
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Copp JN, Akiva E, Babbitt PC, Tokuriki N. Revealing Unexplored Sequence-Function Space Using Sequence Similarity Networks. Biochemistry 2018; 57:4651-4662. [PMID: 30052428 DOI: 10.1021/acs.biochem.8b00473] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The rapidly expanding number of protein sequences found in public databases can improve our understanding of how protein functions evolve. However, our current knowledge of protein function likely represents a small fraction of the diverse repertoire that exists in nature. Integrative computational methods can facilitate the discovery of new protein functions and enzymatic reactions through the observation and investigation of the complex sequence-structure-function relationships within protein superfamilies. Here, we highlight the use of sequence similarity networks (SSNs) to identify previously unexplored sequence and function space. We exemplify this approach using the nitroreductase (NTR) superfamily. We demonstrate that SSN investigations can provide a rapid and effective means to classify groups of proteins, therefore exposing experimentally unexplored sequences that may exhibit novel functionality. Integration of such approaches with systematic experimental characterization will expand our understanding of the functional diversity of enzymes and their associated physiological roles.
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Affiliation(s)
- Janine N Copp
- Michael Smith Laboratories , University of British Columbia , 2185 East Mall , Vancouver , British Columbia V6T 1Z4 , Canada
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences , University of California , San Francisco , California 94158 , United States.,Quantitative Biosciences Institute , University of California , San Francisco , California 94143 , United States
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences , University of California , San Francisco , California 94158 , United States.,Quantitative Biosciences Institute , University of California , San Francisco , California 94143 , United States
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories , University of British Columbia , 2185 East Mall , Vancouver , British Columbia V6T 1Z4 , Canada
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22
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Zhang CL, Yu YY, Fang Z, Naraginti S, Zhang Y, Yong YC. Recent advances in nitroaromatic pollutants bioreduction by electroactive bacteria. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.04.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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23
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Pitsawong W, Haynes CA, Koder RL, Rodgers DW, Miller AF. Mechanism-Informed Refinement Reveals Altered Substrate-Binding Mode for Catalytically Competent Nitroreductase. Structure 2017; 25:978-987.e4. [PMID: 28578873 DOI: 10.1016/j.str.2017.05.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 04/02/2017] [Accepted: 05/05/2017] [Indexed: 01/25/2023]
Abstract
Nitroreductase (NR) from Enterobacter cloacae reduces diverse nitroaromatics including herbicides, explosives, and prodrugs, and holds promise for bioremediation, prodrug activation, and enzyme-assisted synthesis. We solved crystal structures of NR complexes with bound substrate or analog for each of its two half-reactions. We complemented these with kinetic isotope effect (KIE) measurements elucidating H-transfer steps essential to each half-reaction. KIEs indicate hydride transfer from NADH to the flavin consistent with our structure of NR with the NADH analog nicotinic acid adenine dinucleotide (NAAD). The KIE on reduction of p-nitrobenzoic acid (p-NBA) also indicates hydride transfer, and requires revision of prior computational mechanisms. Our mechanistic information provided a structural restraint for the orientation of bound substrate, placing the nitro group closer to the flavin N5 in the pocket that binds the amide of NADH. KIEs show that solvent provides a proton, enabling accommodation of different nitro group placements, consistent with the broad repertoire of NR.
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Affiliation(s)
- Warintra Pitsawong
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, KY 40506-0055, USA
| | - Chad A Haynes
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, 741 South Limestone Street, Lexington, KY 40536-0509, USA
| | - Ronald L Koder
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, KY 40506-0055, USA
| | - David W Rodgers
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, 741 South Limestone Street, Lexington, KY 40536-0509, USA.
| | - Anne-Frances Miller
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, KY 40506-0055, USA; Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, 741 South Limestone Street, Lexington, KY 40536-0509, USA.
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24
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Copp JN, Mowday AM, Williams EM, Guise CP, Ashoorzadeh A, Sharrock AV, Flanagan JU, Smaill JB, Patterson AV, Ackerley DF. Engineering a Multifunctional Nitroreductase for Improved Activation of Prodrugs and PET Probes for Cancer Gene Therapy. Cell Chem Biol 2017; 24:391-403. [DOI: 10.1016/j.chembiol.2017.02.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 12/31/2016] [Accepted: 02/01/2017] [Indexed: 12/20/2022]
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25
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Valiauga B, Williams EM, Ackerley DF, Čėnas N. Reduction of quinones and nitroaromatic compounds by Escherichia coli nitroreductase A (NfsA): Characterization of kinetics and substrate specificity. Arch Biochem Biophys 2016; 614:14-22. [PMID: 27986535 DOI: 10.1016/j.abb.2016.12.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 12/09/2016] [Accepted: 12/12/2016] [Indexed: 11/16/2022]
Abstract
NfsA, a major FMN-associated nitroreductase of E. coli, reduces nitroaromatic compounds via consecutive two-electron transfers. NfsA has potential applications in the biodegradation of nitroaromatic environment pollutants, e.g. explosives, and is also of interest for the anticancer strategy gene-directed enzyme prodrug therapy. However, the catalytic mechanism of NfsA is poorly characterized. Here we examined the NADPH-dependent reduction of quinones (n = 16) and nitroaromatic compounds (n = 12) by NfsA. We confirmed a general "ping-pong" reaction scheme, and preliminary rapid reaction studies of the enzyme reduction by NADPH showed that this step is much faster than the steady-state turnover number, i.e., the enzyme turnover is limited by the oxidative half-reaction. The reactivity of nitroaromatic compounds (log kcat/Km) followed a linear dependence on their single-electron reduction potential (E17), indicating a limited role for compound structure or active site flexibility in their reactivity. The reactivity of quinones was lower than that of nitroaromatics having similar E17 values, except for the significantly enhanced reactivity of 2-OH-1,4-naphthoquinones, consistent with observations previously made for the group B nitroreductase of Enterobacter cloacae. We present evidence that the reduction of quinones by NfsA is most consistent with a single-step (H-) hydride transfer mechanism.
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Affiliation(s)
- Benjaminas Valiauga
- Institute of Biochemistry of Vilnius University, Mokslininkų 12, LT-08662 Vilnius, Lithuania
| | - Elsie M Williams
- Victoria University of Wellington, School of Biological Sciences, Kelburn Parade, New Zealand
| | - David F Ackerley
- Victoria University of Wellington, School of Biological Sciences, Kelburn Parade, New Zealand
| | - Narimantas Čėnas
- Institute of Biochemistry of Vilnius University, Mokslininkų 12, LT-08662 Vilnius, Lithuania.
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26
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Ikeda M, Kamimura M, Hayakawa Y, Shibata A, Kitade Y. Reduction-Responsive Guanine Incorporated into G-Quadruplex-Forming DNA. Chembiochem 2016; 17:1304-7. [PMID: 27124306 DOI: 10.1002/cbic.201600164] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Indexed: 02/06/2023]
Abstract
Stimulus-responsive biomolecules are attractive targets to understand biomolecule behaviour as well as to explore their therapeutic and diagnostic applications. We demonstrate that a reduction-responsive cleavable group (chemically caged unit) introduced into the guanine ring enables modulation of the secondary structure transition of an oligonucleotide in a reduction-responsive and traceless manner leaving the unmodified oligonucleotide of interest. This simple but robust strategy could yield a variety of stimuli-responsive oligonucleotides.
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Affiliation(s)
- Masato Ikeda
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1, Yanagido, Gifu, 501-1193, Japan. .,Department of Biomolecular Science, Graduate School of Engineering, Gifu University, 1-1, Yanagido, Gifu, 501-1193, Japan. .,United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1, Yanagido, Gifu, 501-1193, Japan.
| | - Masahiro Kamimura
- Department of Biomolecular Science, Graduate School of Engineering, Gifu University, 1-1, Yanagido, Gifu, 501-1193, Japan
| | - Yukiko Hayakawa
- Department of Biomolecular Science, Graduate School of Engineering, Gifu University, 1-1, Yanagido, Gifu, 501-1193, Japan
| | - Aya Shibata
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1, Yanagido, Gifu, 501-1193, Japan.,Department of Biomolecular Science, Graduate School of Engineering, Gifu University, 1-1, Yanagido, Gifu, 501-1193, Japan
| | - Yukio Kitade
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1, Yanagido, Gifu, 501-1193, Japan. .,Department of Biomolecular Science, Graduate School of Engineering, Gifu University, 1-1, Yanagido, Gifu, 501-1193, Japan. .,United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1, Yanagido, Gifu, 501-1193, Japan.
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27
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Nitroreductase gene-directed enzyme prodrug therapy: insights and advances toward clinical utility. Biochem J 2015; 471:131-53. [PMID: 26431849 DOI: 10.1042/bj20150650] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This review examines the vast catalytic and therapeutic potential offered by type I (i.e. oxygen-insensitive) nitroreductase enzymes in partnership with nitroaromatic prodrugs, with particular focus on gene-directed enzyme prodrug therapy (GDEPT; a form of cancer gene therapy). Important first indications of this potential were demonstrated over 20 years ago, for the enzyme-prodrug pairing of Escherichia coli NfsB and CB1954 [5-(aziridin-1-yl)-2,4-dinitrobenzamide]. However, it has become apparent that both the enzyme and the prodrug in this prototypical pairing have limitations that have impeded their clinical progression. Recently, substantial advances have been made in the biodiscovery and engineering of superior nitroreductase variants, in particular development of elegant high-throughput screening capabilities to enable optimization of desirable activities via directed evolution. These advances in enzymology have been paralleled by advances in medicinal chemistry, leading to the development of second- and third-generation nitroaromatic prodrugs that offer substantial advantages over CB1954 for nitroreductase GDEPT, including greater dose-potency and enhanced ability of the activated metabolite(s) to exhibit a local bystander effect. In addition to forging substantial progress towards future clinical trials, this research is supporting other fields, most notably the development and improvement of targeted cellular ablation capabilities in small animal models, such as zebrafish, to enable cell-specific physiology or regeneration studies.
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28
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Plasmid-Mediated OqxAB Is an Important Mechanism for Nitrofurantoin Resistance in Escherichia coli. Antimicrob Agents Chemother 2015; 60:537-43. [PMID: 26552976 DOI: 10.1128/aac.02156-15] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 11/03/2015] [Indexed: 11/20/2022] Open
Abstract
Increasing consumption of nitrofurantoin (NIT) for treatment of acute uncomplicated urinary tract infections (UTI) highlights the need to monitor emerging NIT resistance mechanisms. This study investigated the molecular epidemiology of the multidrug-resistant efflux gene oqxAB and its contribution to nitrofurantoin resistance by using Escherichia coli isolates originating from patients with UTI (n = 205; collected in 2004 to 2013) and food-producing animals (n = 136; collected in 2012 to 2013) in Hong Kong. The oqxAB gene was highly prevalent among NIT-intermediate (11.5% to 45.5%) and -resistant (39.2% to 65.5%) isolates but rare (0% to 1.7%) among NIT-susceptible (NIT-S) isolates. In our isolates, the oqxAB gene was associated with IS26 and was carried by plasmids of diverse replicon types. Multilocus sequence typing revealed that the clones of oqxAB-positive E. coli were diverse. The combination of oqxAB and nfsA mutations was found to be sufficient for high-level NIT resistance. Curing of oqxAB-carrying plasmids from 20 NIT-intermediate/resistant UTI isolates markedly reduced the geometric mean MIC of NIT from 168.9 μg/ml to 34.3 μg/ml. In the plasmid-cured variants, 20% (1/5) of isolates with nfsA mutations were NIT-S, while 80% (12/15) of isolates without nfsA mutations were NIT-S (P = 0.015). The presence of plasmid-based oqxAB increased the mutation prevention concentration of NIT from 128 μg/ml to 256 μg/ml and facilitated the development of clinically important levels of nitrofurantoin resistance. In conclusion, plasmid-mediated oqxAB is an important nitrofurantoin resistance mechanism. There is a great need to monitor the dissemination of this transferable multidrug-resistant efflux pump.
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29
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Dauter Z, Wlodawer A. On the accuracy of unit-cell parameters in protein crystallography. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:2217-26. [PMID: 26527139 PMCID: PMC4631477 DOI: 10.1107/s1399004715015503] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Accepted: 08/19/2015] [Indexed: 11/10/2022]
Abstract
The availability in the Protein Data Bank (PDB) of a number of structures that are presented in space group P1 but in reality possess higher symmetry allowed the accuracy and precision of the unit-cell parameters of the crystals of macromolecules to be evaluated. In addition, diffraction images from crystals of several proteins, previously collected as part of in-house projects, were processed independently with three popular software packages. An analysis of the results, augmented by published serial crystallography data, suggests that the apparent precision of the presentation of unit-cell parameters in the PDB to three decimal points is not justified, since these parameters are subject to errors of not less than 0.2%. It was also noticed that processing data including full crystallographic symmetry does not lead to deterioration of the refinement parameters; thus, it is not beneficial to treat the crystals as belonging to space group P1 when higher symmetry can be seen.
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Affiliation(s)
- Zbigniew Dauter
- Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Alexander Wlodawer
- Protein Structure Section, MCL, National Cancer Institute, Frederick, MD 21702, USA
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30
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Tanokura M, Miyakawa T, Guan L, Hou F. Structural analysis of enzymes used for bioindustry and bioremediation. Biosci Biotechnol Biochem 2015; 79:1391-401. [DOI: 10.1080/09168451.2015.1052770] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Abstract
Microbial enzymes have been widely applied in the large-scale, bioindustrial manufacture of food products and pharmaceuticals due to their high substrate specificity and stereoselectivity, and their effectiveness under mild conditions with low environmental burden. At the same time, bioremedial techniques using microbial enzymes have been developed to solve the problem of industrial waste, particularly with respect to persistent chemicals and toxic substances. And finally, structural studies of these enzymes have revealed the mechanistic basis of enzymatic reactions, including the stereoselectivity and binding specificity of substrates and cofactors. The obtained structural insights are useful not only to deepen our understanding of enzymes with potential bioindustrial and/or bioremedial application, but also for the functional improvement of enzymes through rational protein engineering. This review shows the structural bases for various types of enzymatic reactions, including the substrate specificity accompanying cofactor-controlled and kinetic mechanisms.
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Affiliation(s)
- Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takuya Miyakawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Lijun Guan
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Feng Hou
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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31
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Transformation pathway of 2,4,6-trinitrotoluene by Escherichia coli nitroreductases and improvement of activity using structure-based mutagenesis. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.01.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Song HN, Jeong DG, Bang SY, Paek SH, Park BC, Park SG, Woo EJ. Crystal structure of the fungal nitroreductase Frm2 from Saccharomyces cerevisiae. Protein Sci 2015; 24:1158-63. [PMID: 25864423 DOI: 10.1002/pro.2686] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 03/31/2015] [Indexed: 11/09/2022]
Abstract
Nitroreductases are flavoenzymes that catalyze nitrocompounds and are widely utilized in industrial applications due to their detoxification potential and activation of biomedicinal prodrugs. Type I nitroreductases are classified into subgroups depending on the use of NADPH or NADH as the electron donor. Here, we report the crystal structure of the fungal nitroreductase Frm2 from Saccharomyces cerevisiae, one of the uncharacterized subgroups of proteins, to reveal its minimal architecture previously observed in bacterial nitroreductases such as CinD and YdjA. The structure lacks protruding helical motifs that form part of the cofactor and substrate binding site, resulting in an open and wide active site geometry. Arg82 is uniquely conserved in proximity to the substrate binding site in Frm2 homologues and plays a crucial role in the activity of the active site. Frm2 primarily utilizes NADH to reduce 4-NQO. Because missing helical elements are involved in the direct binding to the NAD(P)H in group A or group B in Type I family, Frm2 and its homologues may represent a distinctive subgroup with an altered binding mode for the reducing compound. This result provides a structural basis for the rational design of novel prodrugs with the ability to reduce nitrogen-containing hazardous molecules.
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Affiliation(s)
- Hyung-Nam Song
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Republic of Korea.,Department of Biotechnology and Bioinformatics, Korea University, Sejong, 339-700, Republic of Korea
| | - Dae-Gwin Jeong
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Republic of Korea.,Bio-Analytical Science Division, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Seo-Young Bang
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Republic of Korea
| | - Se-Hwan Paek
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, 339-700, Republic of Korea
| | - Byoung-Chul Park
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Republic of Korea.,Bio-Analytical Science Division, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Sung-Goo Park
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Republic of Korea.,Bio-Analytical Science Division, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Eui-Jeon Woo
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Republic of Korea.,Bio-Analytical Science Division, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
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33
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Park JT, Gómez Ramos LM, Bommarius AS. Engineering towards Nitroreductase Functionality in Ene-Reductase Scaffolds. Chembiochem 2015; 16:811-8. [DOI: 10.1002/cbic.201402667] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Indexed: 11/10/2022]
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34
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Megarity CF, Looi HK, Timson DJ. The Saccharomyces cerevisiae quinone oxidoreductase Lot6p: stability, inhibition and cooperativity. FEMS Yeast Res 2014; 14:797-807. [PMID: 24866129 DOI: 10.1111/1567-1364.12167] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 05/13/2014] [Accepted: 05/22/2014] [Indexed: 11/28/2022] Open
Abstract
Lot6p (EC 1.5.1.39; Ylr011wp) is the sole quinone oxidoreductase in the budding yeast, Saccharomyces cerevisiae. Using hexahistidine tagged, recombinant Lot6p, we determined the steady-state enzyme kinetic parameters with both NADH and NADPH as electron donors; no cooperativity was observed with these substrates. The NQO1 inhibitor curcumin, the NQO2 inhibitor resveratrol, the bacterial nitroreductase inhibitor nicotinamide and the phosphate mimic vanadate all stabilise the enzyme towards thermal denaturation as judged by differential scanning fluorimetry. All except vanadate have no observable effect on the chemical cross-linking of the two subunits of the Lot6p dimer. These compounds all inhibit Lot6p's oxidoreductase activity, and all except nicotinamide exhibit negative cooperativity. Molecular modelling suggests that curcumin, resveratrol and nicotinamide all bind over the isoalloxazine ring of the FMN cofactor in Lot6p. Resveratrol was predicted to contact an α-helix that links the two active sites. Mutation of Gly-142 (which forms part of this helix) to serine does not greatly affect the thermal stability of the enzyme. However, this variant shows less cooperativity towards resveratrol than the wild type. This suggests a plausible hypothesis for the transmission of information between the subunits and, thus, the molecular mechanism of negative cooperativity in Lot6p.
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Affiliation(s)
- Clare F Megarity
- School of Biological Sciences, Medical Biology Centre, Queen's University Belfast, Belfast, UK
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35
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Mercier C, Chalansonnet V, Orenga S, Gilbert C. Characteristics of major Escherichia coli reductases involved in aerobic nitro and azo reduction. J Appl Microbiol 2013; 115:1012-22. [PMID: 23795903 DOI: 10.1111/jam.12294] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 06/14/2013] [Accepted: 06/20/2013] [Indexed: 12/26/2022]
Abstract
AIMS Escherichia coli is able to reduce azo compounds such as methyl red (MR) and nitro compounds such as 7-nitrocoumarin-3-carboxylic acid (7NCCA). The aim of this study was to clarify the specificity of the major E. coli reductases. METHODS AND RESULTS Enzymatic assays with pure enzymes obtained after cloning, overproduction and purification under native or denaturing conditions were performed on three enzymes: AzoR, NfsA and NfsB. Their dependence on putative cofactors such as flavin mononucleotide (FMN), NADH and NADPH was studied as well as the reductase capacity of E. coli mutants depleted for one, two or three of the corresponding genes. CONCLUSIONS AzoR was able to reduce both MR and 7NCCA, whereas NfsA and NfsB could only reduce the nitro compound. AzoR and NfsB were strictly FMN dependent in contrast to NfsA. At a low oxygen concentration, the three proteins were not mandatory for azo reduction and nitro reduction, but in optimal aerobic conditions, azoR was essential for MR reduction, and an nfsA/nfsB combination was important for 7NCCA reduction. Overexpression of azoR gene was able to compensate for the loss of nfsA and nfsB under aerobic conditions. SIGNIFICANCE AND IMPACT OF STUDY These data provide new insights into the substrate specificity of major E. coli nitroreductases and demonstrate that oxygen is an important parameter to take into account in studies of nitroreductase activity.
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Affiliation(s)
- C Mercier
- BioMérieux, La Balme les Grottes, France; CIRI-U1111 INSERM- UMR5308 CNRS-UCBL-ENSL, Université de Lyon, Université Lyon 1, Villeurbanne, France
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36
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Residue Phe42 is critical for the catalytic activity of Escherichia coli major nitroreductase NfsA. Biotechnol Lett 2013; 35:1693-700. [PMID: 23801116 DOI: 10.1007/s10529-013-1262-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 05/31/2013] [Indexed: 10/26/2022]
Abstract
The major O2-insensitive nitroreductase (NfsA) of Escherichia coli shares low sequence homology but similar biochemical and structural features with NfsB, the E. coli minor O2-insensitive nitroreductase. A structural comparison revealed Phe42 was present in the active site of NfsA but not NfsB. F42Y, F42N and F42A were generated and had decreased activity toward nitrofurazone by 52, 96, and 99%, respectively. The kinetic parameters for other nitroaromatic substrates were also determined. Compared to wild type, the mutants did not have significantly altered K(m)s, but had dramatically decreased k(cat) and k(cat)/K(m) values. Far-UV CD spectral analysis of the mutants suggested that there were no significant conformational changes however F42A and F42N had changes from 208 to 222 nm, which was attributed to loss of helix content. These findings revealed that Phe42 is important for maintaining NfsA activity and structure.
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37
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Anusevičius Ž, Misevičienė L, Šarlauskas J, Rouhier N, Jacquot JP, Čėnas N. Quinone- and nitroreductase reactions of Thermotoga maritima peroxiredoxin-nitroreductase hybrid enzyme. Arch Biochem Biophys 2012; 528:50-6. [PMID: 22982531 DOI: 10.1016/j.abb.2012.08.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 08/29/2012] [Accepted: 08/31/2012] [Indexed: 10/27/2022]
Abstract
Thermotoga maritima peroxiredoxin-nitroreductase hybrid enzyme (Prx-NR) consists of a FMN-containing nitroreductase (NR) domain fused to a peroxiredoxin (Prx) domain. These domains seem to function independently as no electron transfer occurs between them. The reduction of quinones and nitroaromatics by NR proceeded in a two-electron manner, and follows a 'ping-pong' scheme with sometimes pronounced inhibition by quinone substrate. The comparison of steady- and presteady-state kinetic data shows that in most cases, the oxidative half-reaction may be rate-limiting in the catalytic cycle of NR. The enzyme was inhibited by dicumarol, a classical inhibitor of oxygen-insensitive nitroreductases. The reduction of quinones and nitroaromatic compounds by Prx-NR was characterized by the linear dependence of their reactivity (logk(cat)/K(m)) on their single-electron reduction potentials E(7)(1), while the reactivity of quinones markedly exceeded the one with nitroaromatics. It shows that NR lacks the specificity for the particular structure of these oxidants, except their single-electron accepting potency and the rate of electron self-exchange. It points to the possibility of a single-electron transfer step in a net two-electron reduction of quinones and nitroaromatics by T. maritima Prx-NR, and to a significant diversity of the structures of flavoenzymes which may perform the two-electron reduction of quinones and nitroaromatics.
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Affiliation(s)
- Žilvinas Anusevičius
- Institute of Biochemistry of Vilnius University, Mokslininkų 12, LT-08662 Vilnius, Lithuania
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38
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Alvarez-Fitz P, Alvarez L, Marquina S, Luna-Herrera J, Navarro-García VM. Enzymatic reduction of 9-methoxytariacuripyrone by Saccharomyces cerevisiae and its antimycobacterial activity. Molecules 2012; 17:8464-70. [PMID: 22790562 PMCID: PMC6268768 DOI: 10.3390/molecules17078464] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 07/05/2012] [Accepted: 07/05/2012] [Indexed: 11/20/2022] Open
Abstract
Biotransformation processes have been successfully utilized to obtain products of pharmaceutical, chemical, food, and agricultural interest, which are difficult to obtain by classic chemical methods. The compound with antituberculous activity, 9-methoxy-tariacuripyrone (1), isolated from Aristolochia brevipes, was submitted to biotransformation with the yeast Saccharomyces cerevisiae under culture, yielding 5-amino-9-methoxy-3,4-dihydro-2H-benzo[h]chromen-2-one (2). The structure of 2 was elucidated on the basis of spectroscopic analyses. The results mainly show the reduction of the double bond and the nitro group of compound 1. Metabolite 2 demonstrated an increase in anti-tuberculous activity (MIC = 3.12 µg/mL) against the drug-sensitive Mycobacterium tuberculosis (H37Rv) strain, with respect to that shown by 1.
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Affiliation(s)
- Patricia Alvarez-Fitz
- Laboratory of Microbiology, Biomedical Research Center of the South (IMSS), Argentina 1, Col. Centro, 62790 Xochitepec, Morelos, Mexico
- Center for Development of Biotic Products(IPN), Carretera Yautepec-Jojutla, Km. 6, Calle Ceprobi 8, Col San Isidro, Apdo. Postal 24, 62731 Yautepec, Morelos, Mexico
| | - Laura Alvarez
- Chemical Research Center, University of Morelos (UAEM), Av. Universidad 1001, Col. Chamilpa, 62209 Cuernavaca, Morelos, Mexico
| | - Silvia Marquina
- Chemical Research Center, University of Morelos (UAEM), Av. Universidad 1001, Col. Chamilpa, 62209 Cuernavaca, Morelos, Mexico
| | - Julieta Luna-Herrera
- Immunochemistry Laboratory II, Department of Immunology, National School of Sciences Biology (IPN), Prolongación Carpio y Plan de Ayala S/N, 11340, D.F., Mexico
| | - Víctor Manuel Navarro-García
- Laboratory of Microbiology, Biomedical Research Center of the South (IMSS), Argentina 1, Col. Centro, 62790 Xochitepec, Morelos, Mexico
- Author to whom correspondence should be addressed; ; Tel.: +52-777-361-21-94
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39
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Buss JM, McTamney PM, Rokita SE. Expression of a soluble form of iodotyrosine deiodinase for active site characterization by engineering the native membrane protein from Mus musculus. Protein Sci 2012; 21:351-61. [PMID: 22238141 DOI: 10.1002/pro.2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Reductive deiodination is critical for thyroid function and represents an unusual exception to the more common oxidative and hydrolytic mechanisms of dehalogenation in mammals. Studies on the reductive processes have been limited by a lack of convenient methods for heterologous expression of the appropriate proteins in large scale. The enzyme responsible for iodide salvage in the thyroid, iodotyrosine deodinase, is now readily generated after engineering its gene from Mus musculus. High expression of a truncated derivative lacking the membrane domain at its N-terminal was observed in Sf9 cells, whereas expression in Pichia pastoris remained low despite codon optimization. Ultimately, the desired expression in Escherichia coli was achieved after replacing the two conserved Cys residues of the deiodinase with Ala and fusing the resulting protein to thioredoxin. This final construct provided abundant enzyme for crystallography and mutagenesis. Utility of the E. coli system was demonstrated by examining a set of active site residues critical for binding to the zwitterionic portion of substrate.
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Affiliation(s)
- Jennifer M Buss
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742-2021, USA
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40
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Bang SY, Kim JH, Lee PY, Bae KH, Lee JS, Kim PS, Lee DH, Myung PK, Park BC, Park SG. Confirmation of Frm2 as a novel nitroreductase in Saccharomyces cerevisiae. Biochem Biophys Res Commun 2012; 423:638-41. [PMID: 22687599 DOI: 10.1016/j.bbrc.2012.05.156] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 05/28/2012] [Indexed: 11/18/2022]
Abstract
Nitroreductases comprise a group of FMN- or FAD-dependent enzymes that reduce nitrosubstituted compounds by using NAD(P)H, and are found in bacterial species and yeast. Although there is little information on the biological functions of nitroreductases, some studies suggest their possible involvement in oxidative stress responses. In the yeast Saccharomyces cerevisiae, a putative nitroreductase protein, Frm2, has been identified based on its sequence similarity with known bacterial nitroreductases. Frm2 has been reported to function in the lipid signaling pathway. To study the functions of Frm2, we measured the nitroreductase activity of purified Frm2 on 4-nitroquinoline-N-oxide (4-NQO) using NADH. LC-MS analysis of the reaction products revealed that Frm2 reduced NQO into 4-aminoquinoline-N-oxide (4-AQO) via 4-hydroxyaminoquinoline (4-HAQO). An Frm2 deletion mutant exhibited growth inhibition in the presence of 4-NQO. Thus, in this study, we demonstrate a novel nitroreductase activity of Frm2 and its involvement in the oxidative stress defense system.
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Affiliation(s)
- Seo Young Bang
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
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41
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Chung HW, Tu SC. Structure-function relationship of Vibrio harveyi NADPH-flavin oxidoreductase FRP: essential residues Lys167 and Arg15 for NADPH binding. Biochemistry 2012; 51:4880-7. [PMID: 22650604 DOI: 10.1021/bi3002314] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Vibrio harveyi NADPH-FMN oxidoreductase (FRP) catalyzes flavin reduction by NADPH. In comparing amino acid sequence and crystal structure with Escherichia coli NfsA, residues N134, R225, R133, K167, and R15 were targeted for investigation of their possible roles in the binding and utilization of the NADPH substrate. By mutation of each of these five residues to an alanine, steady-state rate analyses showed that the variants K167A and R15A had apparently greatly increased K(m,NADPH) and reduced k(cat)/K(m,NADPH), whereas little or much more modest changes were found for the other variants. The deuterium isotope effects (D)(V/K) for (4R)-[4-(2)H]-NADPH were markedly increased to 6.3 and 7.4 for K167A and R15A, respectively, indicating that the rate constants for NADPH and NADP(+) dissociation were greatly enhanced relative to the hydride transfer steps. Also, anaerobic stopped-flow analyses revealed that the equilibrium dissociation constant for NADPH binding (K(d)) to be 2.5-3.9 and 1.1 mM for K167A and R15A, respectively, much higher than the 0.4 μM K(d) for the native FRP, whereas the k(cat) of these two variants were similar to that of the wild-type enzyme. Moreover, the K167 to alanine mutation led to even a slight increase in k(cat)/K(m) for NADH. These results, taken together, provide a strong support to the conclusion that K167 and R15 each was critical in the binding of NADPH by FRP. Such a functional role may also exist for other FRP homologous proteins.
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Affiliation(s)
- Hae-Won Chung
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA
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Valle A, Le Borgne S, Bolívar J, Cabrera G, Cantero D. Study of the role played by NfsA, NfsB nitroreductase and NemA flavin reductase from Escherichia coli in the conversion of ethyl 2-(2'-nitrophenoxy)acetate to 4-hydroxy-(2H)-1,4-benzoxazin-3(4H)-one (D-DIBOA), a benzohydroxamic acid with interesting biological properties. Appl Microbiol Biotechnol 2011; 94:163-71. [PMID: 22173483 DOI: 10.1007/s00253-011-3787-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 11/06/2011] [Accepted: 11/23/2011] [Indexed: 10/14/2022]
Abstract
Benzohydroxamic acids, such as 4-hydroxy-(2H)-1,4-benzoxazin-3(4H)-one (D-DIBOA), exhibit interesting herbicidal, fungicidal and bactericidal properties. Recently, the chemical synthesis of D-DIBOA has been simplified to only two steps. In a previous paper, we demonstrated that the second step could be replaced by a biotransformation using Escherichia coli to reduce the nitro group of the precursor, ethyl 2-(2'-nitrophenoxy)acetate and obtain D-DIBOA. The NfsA and NfsB nitroreductases and the NemA xenobiotic reductase of E. coli have the capacity to reduce one or two nitro groups from a wide variety of nitroaromatic compounds, which are similar to the precursor. By this reason, we hypothesised that these three enzymes could be involved in this biotransformation. We have analysed the biotransformation yield (BY) of mutant strains in which one, two or three of these genes were knocked out, showing that only in the double nfsA/nfsB and in the triple nfsA/nfsB/nemA mutants, the BY was 0%. These results suggested that NfsA and NfsB are responsible for the biotransformation in the tested conditions. To confirm this, the nfsA and nfsB open reading frames were cloned into the pBAD expression vector and transformed into the nfsA and nfsB single mutants, respectively. In both cases, the biotransformation capacity of the strains was recovered (6.09 ± 0.06% as in the wild-type strain) and incremented considerably when NfsA and NfsB were overexpressed (40.33% ± 9.42% and 59.68% ± 2.0% respectively).
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Affiliation(s)
- Antonio Valle
- Department of Chemical Engineering and Food Technology, Campus de Excelencia Internacional Agroalimentario (ceiA3), University of Cádiz, Avda. República Saharaui s/n, 11510 Puerto Real, Cádiz, Spain.
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Miletti T, Farber PJ, Mittermaier A. Active site dynamics in NADH oxidase from Thermus thermophilus studied by NMR spin relaxation. JOURNAL OF BIOMOLECULAR NMR 2011; 51:71-82. [PMID: 21947916 DOI: 10.1007/s10858-011-9542-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 06/28/2011] [Indexed: 05/31/2023]
Abstract
We have characterized the backbone dynamics of NADH oxidase from Thermus thermophilus (NOX) using a recently-developed suite of NMR experiments designed to isolate exchange broadening, together with (15)N R (1), R (1ρ ), and {(1)H}-(15)N steady-state NOE relaxation measurements performed at 11.7 and 18.8 T. NOX is a 54 kDa homodimeric enzyme that belongs to a family of structurally homologous flavin reductases and nitroreductases with many potential biotechnology applications. Prior studies have suggested that flexibility is involved in the catalytic mechanism of the enzyme. The active site residue W47 was previously identified as being particularly important, as its level of solvent exposure correlates with enzyme activity, and it was observed to undergo "gating" motions in computer simulations. The NMR data are consistent with these findings. Signals from W47 are dynamically broadened beyond detection and several other residues in the active site have significant R ( ex ) contributions to transverse relaxation rates. In addition, the backbone of S193, whose side chain hydroxyl proton hydrogen bonds directly with the FMN cofactor, exhibits extensive mobility on the ns-ps timescale. We hypothesize that these motions may facilitate structural rearrangements of the active site that allow NOX to accept both FMN and FAD as cofactors.
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Affiliation(s)
- Teresa Miletti
- Department of Chemistry, McGill University, Montreal, QC H3A 2K6, Canada
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A kinetic analysis of three modified novel nitroreductases. Biodegradation 2010; 22:463-74. [PMID: 20862523 DOI: 10.1007/s10532-010-9418-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 09/14/2010] [Indexed: 10/19/2022]
Abstract
A kinetic comparison between three nitroreductase enzymes isolated from the genome of Bacillus licheniformis ATCC 14580 for prospective use as immobilised enzymes for explosives detection has been conducted. The genes encoding the three enzymes (yfkO [BLNfnB] encoding an NfsB-like enzyme; nfrA [BLNfrA1] and ycnD [BLNfrA2] encoding PnrA-like enzymes) have been PCR amplified from the native genome and cloned into pET-28a(+) and a modified cysteine((6))-tagged pET-28a(+) and subsequently over-expressed, purified, and biochemically characterised. The previously uncharacterised nitroreductases exhibited activity against a wide range of explosives, including cyclic nitramines. Amino acid alignments and overall structural comparisons with other nitroreductase family members suggest that the B. licheniformis enzymes are members of the NfsA-Frp/NfsB-FRase I family group. Despite the overall low amino acid identity, regions for flavin mononucleotide binding and active site residues were highly conserved.
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Nitroreductase activity of ferredoxin reductase BphA4 from Dyella ginsengisoli LA−4 by catalytic and structural properties analysis. Appl Microbiol Biotechnol 2010; 89:655-63. [DOI: 10.1007/s00253-010-2874-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 08/21/2010] [Accepted: 08/23/2010] [Indexed: 01/17/2023]
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Cortial S, Chaignon P, Iorga BI, Aymerich S, Truan G, Gueguen-Chaignon V, Meyer P, Moréra S, Ouazzani J. NADH oxidase activity of Bacillus subtilis nitroreductase NfrA1: insight into its biological role. FEBS Lett 2010; 584:3916-22. [PMID: 20727352 DOI: 10.1016/j.febslet.2010.08.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 08/06/2010] [Accepted: 08/12/2010] [Indexed: 10/19/2022]
Abstract
NfrA1 nitroreductase from the Gram-positive bacterium Bacillus subtilis is a member of the NAD(P)H/FMN oxidoreductase family. Here, we investigated the reactivity, the structure and kinetics of NfrA1, which could provide insight into the unclear biological role of this enzyme. We could show that NfrA1 possesses an NADH oxidase activity that leads to high concentrations of oxygen peroxide and an NAD(+) degrading activity leading to free nicotinamide. Finally, we showed that NfrA1 is able to rapidly scavenge H(2)O(2) produced during the oxidative process or added exogenously.
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Affiliation(s)
- Sylvie Cortial
- Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Gif-sur-Yvette, France
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Structure and function of CinD (YtjD) of Lactococcus lactis, a copper-induced nitroreductase involved in defense against oxidative stress. J Bacteriol 2010; 192:4172-80. [PMID: 20562311 DOI: 10.1128/jb.00372-10] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Lactococcus lactis IL1403, 14 genes are under the control of the copper-inducible CopR repressor. This so-called CopR regulon encompasses the CopR regulator, two putative CPx-type copper ATPases, a copper chaperone, and 10 additional genes of unknown function. We addressed here the function of one of these genes, ytjD, which we renamed cinD (copper-induced nitroreductase). Copper, cadmium, and silver induced cinD in vivo, as shown by real-time quantitative PCR. A knockout mutant of cinD was more sensitive to oxidative stress exerted by 4-nitroquinoline-N-oxide and copper. Purified CinD is a flavoprotein and reduced 2,6-dichlorophenolindophenol and 4-nitroquinoline-N-oxide with k(cat) values of 27 and 11 s(-1), respectively, using NADH as a reductant. CinD also exhibited significant catalase activity in vitro. The X-ray structure of CinD was resolved at 1.35 A and resembles those of other nitroreductases. CinD is thus a nitroreductase which can protect L. lactis against oxidative stress that could be exerted by nitroaromatic compounds and copper.
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LinWu SW, Wang AHJ, Peng FC. Flavin-containing reductase: new perspective on the detoxification of nitrobenzodiazepine. Expert Opin Drug Metab Toxicol 2010; 6:967-81. [DOI: 10.1517/17425255.2010.482928] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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de Oliveira IM, Zanotto-Filho A, Moreira JCF, Bonatto D, Henriques JAP. The role of two putative nitroreductases, Frm2p and Hbn1p, in the oxidative stress response in Saccharomyces cerevisiae. Yeast 2010; 27:89-102. [PMID: 19904831 DOI: 10.1002/yea.1734] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The nitroreductase family is comprised of a group of FMN- or FAD-dependent enzymes that are able to metabolize nitrosubstituted compounds using the reducing power of NAD(P)H. These nitroreductases can be found in bacterial species and, to a lesser extent, in eukaryotes. There is little information on the biochemical functions of nitroreductases. Some studies suggest their possible involvement in the oxidative stress response. In the yeast Saccharomyces cerevisiae, two nitroreductase proteins, Frm2p and Hbn1p, have been described. While Frm2p appears to act in the lipid signalling pathway, the function of Hbn1p is completely unknown. In order to elucidate the functions of Frm2p and Hbn1p, we evaluated the sensitivity of yeast strains, proficient and deficient in both oxidative stress proteins, for respiratory competence, antioxidant-enzyme activities, intracellular reactive oxygen species (ROS) production and lipid peroxidation. We found reduced basal activity of superoxide dismutase (SOD), ROS production, lipid peroxidation and petite induction and higher sensitivity to 4-nitroquinoline-oxide (4-NQO) and N-nitrosodiethylamine (NDEA), as well as higher basal activity of catalase (CAT) and glutathione peroxidase (GPx) and reduced glutathione (GSH) content in the single and double mutant strains frm2Delta and frm2Delta hbn1Delta. These strains exhibited less ROS accumulation and lipid peroxidation when exposed to peroxides, H(2)O(2) and t-BOOH. In summary, the Frm1p and Hbn1p nitroreductases influence the response to oxidative stress in S. cerevisae yeast by modulating the GSH contents and antioxidant enzymatic activities, such as SOD, CAT and GPx.
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Affiliation(s)
- Iuri Marques de Oliveira
- Departamento de Biofísica/Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av Bento Gonçalves 9500, 91507-970 Porto Alegre, RS, Brazil
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Vass SO, Jarrom D, Wilson WR, Hyde EI, Searle PF. E. coli NfsA: an alternative nitroreductase for prodrug activation gene therapy in combination with CB1954. Br J Cancer 2009; 100:1903-11. [PMID: 19455141 PMCID: PMC2690450 DOI: 10.1038/sj.bjc.6605094] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Prodrug activation gene therapy is a developing approach to cancer treatment, whereby prodrug-activating enzymes are expressed in tumour cells. After administration of a non-toxic prodrug, its conversion to cytotoxic metabolites directly kills tumour cells expressing the activating enzyme, whereas the local spread of activated metabolites can kill nearby cells lacking the enzyme (bystander cell killing). One promising combination that has entered clinical trials uses the nitroreductase NfsB from Escherichia coli to activate the prodrug, CB1954, to a potent bifunctional alkylating agent. NfsA, the major E. coli nitroreductase, has greater activity with nitrofuran antibiotics, but it has not been compared in the past with NfsB for the activation of CB1954. We show superior in vitro kinetics of CB1954 activation by NfsA using the NADPH cofactor, and show that the expression of NfsA in bacterial or human cells results in a 3.5- to 8-fold greater sensitivity to CB1954, relative to NfsB. Although NfsB reduces either the 2-NO2 or 4-NO2 positions of CB1954 in an equimolar ratio, we show that NfsA preferentially reduces the 2-NO2 group, which leads to a greater bystander effect with cells expressing NfsA than with NfsB. NfsA is also more effective than NfsB for cell sensitisation to nitrofurans and to a selection of alternative, dinitrobenzamide mustard (DNBM) prodrugs.
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Affiliation(s)
- S O Vass
- Cancer Research UK Institute for Cancer Studies, University of Birmingham, Birmingham, UK
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