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Cirqueira ML, Bortot LO, Bolean M, Aleixo MAA, Luccas PH, Costa-Filho AJ, Ramos AP, Ciancaglini P, Nonato MC. Trypanosoma cruzi nitroreductase: Structural features and interaction with biological membranes. Int J Biol Macromol 2022; 221:891-899. [PMID: 36100001 DOI: 10.1016/j.ijbiomac.2022.09.073] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/28/2022] [Accepted: 09/08/2022] [Indexed: 11/05/2022]
Abstract
Due to its severe burden and geographic distribution, Chagas disease (CD) has a significant social and economic impact on low-income countries. Benznidazole and nifurtimox are currently the only drugs available for CD. These are prodrugs activated by reducing the nitro group, a reaction catalyzed by nitroreductase type I enzyme from Trypanosoma cruzi (TcNTR), with no homolog in the human host. The three-dimensional structure of TcNTR, and the molecular and chemical bases of the selective activation of nitro drugs, are still unknown. To understand the role of TcNTR in the basic parasite biology, investigate its potential as a drug target, and contribute to the fight against neglected tropical diseases, a combined approach using multiple biophysical and biochemical methods together with in silico studies was employed in the characterization of TcNTR. For the first time, the interaction of TcNTR with membranes was demonstrated, with a preference for those containing cardiolipin, a unique dimeric phospholipid that exists almost exclusively in the inner mitochondrial membrane in eukaryotic cells. Prediction of TcNTR's 3D structure suggests that a 23-residue long insertion (199 to 222), absent in the homologous bacterial protein and identified as conserved in protozoan sequences, mediates enzyme specificity, and is involved in protein-membrane interaction.
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Affiliation(s)
- Marília L Cirqueira
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (FCFRP-USP), Ribeirão Preto, SP, Brazil
| | - Leandro O Bortot
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (FCFRP-USP), Ribeirão Preto, SP, Brazil; Laboratory of Computational Biology (LBC), Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Maytê Bolean
- Chemistry Dept., Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo (FFCLRP-USP), Ribeirão Preto, SP, Brazil
| | - Mariana A A Aleixo
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (FCFRP-USP), Ribeirão Preto, SP, Brazil; Brazilian Nanotechnology National Laboratory (LNNano), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Pedro H Luccas
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (FCFRP-USP), Ribeirão Preto, SP, Brazil
| | - Antonio J Costa-Filho
- Physics Dept., Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo (FFCLRP-USP), Ribeirão Preto, SP, Brazil
| | - Ana Paula Ramos
- Chemistry Dept., Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo (FFCLRP-USP), Ribeirão Preto, SP, Brazil
| | - Pietro Ciancaglini
- Chemistry Dept., Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo (FFCLRP-USP), Ribeirão Preto, SP, Brazil
| | - M Cristina Nonato
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (FCFRP-USP), Ribeirão Preto, SP, Brazil.
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2
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Yan Y, Yu Z, Zhong W, Hou X, Tao Q, Cao M, Wang L, Cai X, Rao Y, Huang SX. Characterization of Multifunctional and Non-stereoselective Oxidoreductase RubE7/IstO, Expanding the Functional Diversity of the Flavoenzyme Superfamily. Angew Chem Int Ed Engl 2022; 61:e202200189. [PMID: 35191152 DOI: 10.1002/anie.202200189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Indexed: 12/23/2022]
Abstract
Flavin-dependent enzymes enable a broad range of redox transformations and generally act as monofunctional and stereoselective catalysts. Herein, we report the investigation of a multifunctional and non-stereoselective FMN-dependent oxidoreductase RubE7 from the rubrolone biosynthetic pathway. Our study outlines a single RubE7-catalysed sequential reduction of three spatially distinct bonds in a tropolone ring and a reversible double-bond reduction and dehydrogenation. The crystal structure of IstO (a RubE7 homologue) with 2.0 Å resolution reveals the location of the active site at the interface of two monomers, and the size of active site is large enough to permit both flipping and free rotation of the substrate, resulting in multiple nonselective reduction reactions. Molecular docking and site mutation studies demonstrate that His106 is oriented towards the substrate and is important for the reverse dehydrogenation reaction.
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Affiliation(s)
- Yijun Yan
- State Key Laboratory of Phytochemistry and Plant Resources in West China, CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zhiyin Yu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Wei Zhong
- State Key Laboratory of Phytochemistry and Plant Resources in West China, CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaodong Hou
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Qiaoqiao Tao
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Minhang Cao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Li Wang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xiaofeng Cai
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yijian Rao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Sheng-Xiong Huang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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3
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Xu T, Zhou F, Wang L, Wu S, Huang H. Metronidazole-Resistant Clostridioides difficile: Genomic and Transcriptomic Traits Acquired under In vitro Metronidazole Induction. Int J Antimicrob Agents 2022; 59:106570. [DOI: 10.1016/j.ijantimicag.2022.106570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/02/2022] [Accepted: 03/06/2022] [Indexed: 11/05/2022]
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4
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Yan Y, Yu Z, Zhong W, Hou X, Tao Q, Cao M, Wang L, Cai X, Rao Y, Huang S. Characterization of Multifunctional and Non‐stereoselective Oxidoreductase RubE7/IstO, Expanding the Functional Diversity of the Flavoenzyme Superfamily. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yijun Yan
- State Key Laboratory of Phytochemistry and Plant Resources in West China CAS Center for Excellence in Molecular Plant Sciences Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 China
| | - Zhiyin Yu
- State Key Laboratory of Phytochemistry and Plant Resources in West China CAS Center for Excellence in Molecular Plant Sciences Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 China
| | - Wei Zhong
- State Key Laboratory of Phytochemistry and Plant Resources in West China CAS Center for Excellence in Molecular Plant Sciences Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 China
- University of the Chinese Academy of Sciences Beijing 100049 China
| | - Xiaodong Hou
- Key Laboratory of Carbohydrate Chemistry and Biotechnology Ministry of Education School of Biotechnology Jiangnan University Wuxi 214122 China
| | - Qiaoqiao Tao
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation School of Pharmacy Tongji Medical College Huazhong University of Science and Technology Wuhan 430030 China
| | - Minhang Cao
- State Key Laboratory of Phytochemistry and Plant Resources in West China CAS Center for Excellence in Molecular Plant Sciences Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 China
| | - Li Wang
- State Key Laboratory of Phytochemistry and Plant Resources in West China CAS Center for Excellence in Molecular Plant Sciences Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 China
| | - Xiaofeng Cai
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation School of Pharmacy Tongji Medical College Huazhong University of Science and Technology Wuhan 430030 China
| | - Yijian Rao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology Ministry of Education School of Biotechnology Jiangnan University Wuxi 214122 China
| | - Sheng‐Xiong Huang
- State Key Laboratory of Phytochemistry and Plant Resources in West China CAS Center for Excellence in Molecular Plant Sciences Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 China
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Madeira CL, Menezes O, Park D, Jog KV, Hatt JK, Gavazza S, Krzmarzick MJ, Sierra-Alvarez R, Spain JC, Konstantinidis KT, Field JA. Bacteria Make a Living Breathing the Nitroheterocyclic Insensitive Munitions Compound 3-Nitro-1,2,4-triazol-5-one (NTO). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:5806-5814. [PMID: 33835790 DOI: 10.1021/acs.est.0c07161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The nitroheterocyclic 3-nitro-1,2,4-triazol-5-one (NTO) is an ingredient of insensitive explosives increasingly used by the military, becoming an emergent environmental pollutant. Cometabolic biotransformation of NTO occurs in mixed microbial cultures in soils and sludges with excess electron-donating substrates. Herein, we present the unusual energy-yielding metabolic process of NTO respiration, in which the NTO reduction to 3-amino-1,2,4-triazol-5-one (ATO) is linked to the anoxic acetate oxidation to CO2 by a culture enriched from municipal anaerobic digester sludge. Cell growth was observed simultaneously with NTO reduction, whereas the culture was unable to grow in the presence of acetate only. Extremely low concentrations (0.06 mg L-1) of the uncoupler carbonyl cyanide m-chlorophenyl hydrazone inhibited NTO reduction, indicating that the process was linked to respiration. The ultimate evidence of NTO respiration was adenosine triphosphate production due to simultaneous exposure to NTO and acetate. Metagenome sequencing revealed that the main microorganisms (and relative abundances) were Geobacter anodireducens (89.3%) and Thauera sp. (5.5%). This study is the first description of a nitroheterocyclic compound being reduced by anaerobic respiration, shedding light on creative microbial processes that enable bacteria to make a living reducing NTO.
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Affiliation(s)
- Camila L Madeira
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona 85721-0011, United States
| | - Osmar Menezes
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona 85721-0011, United States
- Laboratório de Saneamento Ambiental, Departamento de Engenharia Civil e Ambiental, Universidade Federal de Pernambuco, Recife, Pernambuco 50740-530, Brazil
| | - Doyoung Park
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0355, United States
| | - Kalyani V Jog
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona 85721-0011, United States
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0355, United States
| | - Savia Gavazza
- Laboratório de Saneamento Ambiental, Departamento de Engenharia Civil e Ambiental, Universidade Federal de Pernambuco, Recife, Pernambuco 50740-530, Brazil
| | - Mark J Krzmarzick
- School of Civil and Environmental Engineering, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Reyes Sierra-Alvarez
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona 85721-0011, United States
| | - Jim C Spain
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0355, United States
- Center for Environmental Diagnostics & Bioremediation, University of West Florida, Pensacola, Florida 32514, United States
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0355, United States
| | - Jim A Field
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona 85721-0011, United States
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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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7
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A novel cold-adapted nitroreductase from Psychrobactersp. ANT206: Heterologous expression, characterization and nitrobenzene reduction capacity. Enzyme Microb Technol 2019; 131:109434. [DOI: 10.1016/j.enzmictec.2019.109434] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 01/20/2023]
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8
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Dingsdag SA, Hunter N. Metronidazole: an update on metabolism, structure-cytotoxicity and resistance mechanisms. J Antimicrob Chemother 2019; 73:265-279. [PMID: 29077920 DOI: 10.1093/jac/dkx351] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Metronidazole, a nitroimidazole, remains a front-line choice for treatment of infections related to inflammatory disorders of the gastrointestinal tract including colitis linked to Clostridium difficile. Despite >60 years of research, the metabolism of metronidazole and associated cytotoxicity is not definitively characterized. Nitroimidazoles are prodrugs that are reductively activated (the nitro group is reduced) under low oxygen tension, leading to imidazole fragmentation and cytotoxicity. It remains unclear if nitroimidazole reduction (activation) contributes to the cytotoxicity profile, or whether subsequent fragmentation of the imidazole ring and formed metabolites alone mediate cytotoxicity. A molecular mechanism underpinning high level (>256 mg/L) bacterial resistance to metronidazole also remains elusive. Considering the widespread use of metronidazole and other nitroimidazoles, this review was undertaken to emphasize the structure-cytotoxicity profile of the numerous metabolites of metronidazole in human and murine models and to examine conflicting reports regarding metabolite-DNA interactions. An alternative hypothesis, that DNA synthesis and repair of existing DNA is indirectly inhibited by metronidazole is proposed. Prokaryotic metabolism of metronidazole is detailed to discuss new resistance mechanisms. Additionally, the review contextualizes the history and current use of metronidazole, rates of metronidazole resistance including metronidazole MDR as well as the biosynthesis of azomycin, the natural precursor of metronidazole. Changes in the gastrointestinal microbiome and the host after metronidazole administration are also reviewed. Finally, novel nitroimidazoles and new antibiotic strategies are discussed.
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Affiliation(s)
- Simon A Dingsdag
- Institute of Dental Research and Westmead Centre for Oral Health, Westmead, NSW 2145, Australia.,Department of Life Sciences Faculty of Dentistry, The University of Sydney, NSW 2006, Australia.,The Westmead Institute for Medical Research, The University of Sydney, NSW 2145, Australia
| | - Neil Hunter
- Institute of Dental Research and Westmead Centre for Oral Health, Westmead, NSW 2145, Australia.,Department of Life Sciences Faculty of Dentistry, The University of Sydney, NSW 2006, Australia.,The Westmead Institute for Medical Research, The University of Sydney, NSW 2145, Australia
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Alauzet C, Aujoulat F, Lozniewski A, Marchandin H. A sequence database analysis of 5-nitroimidazole reductase and related proteins to expand knowledge on enzymes responsible for metronidazole inactivation. Anaerobe 2018; 55:29-34. [PMID: 30315962 DOI: 10.1016/j.anaerobe.2018.10.005] [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: 07/06/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 01/13/2023]
Abstract
nim genes are associated, in combination with other factors, with acquired resistance to metronidazole (MTZ) in anaerobes. These genes encode 5-nitroimidazole reductase enzymes (Nim proteins) that reduce MTZ into an inactive compound. Eleven variants (nimA to nimK) are currently described in anaerobes with either a chromosomal or a plasmidic location. Mostly found in members of the Bacteroides fragilis group, nim genes were demonstrated in anaerobic taxa outside the phylum Bacteroidetes. Nitroreductase enzymes, weakly related to those found in Bacteroidetes but associated with MTZ inactivation, were also characterized both in anaerobic and non-anaerobic taxa. Published data only poorly reflect the growing number of data from cultivation-independent studies and sequences deposited in databases. Considering this limitation, we performed herein an analysis of the sequence databases with the aim to increase the current knowledge on Nim protein distribution and diversity. The 250 sequences the most closely related to the 11 known Nim proteins were selected and analyzed for identity level and phylogenetic relationships with Nim A to K proteins. The analysis revealed a larger diversity of anaerobic species harboring known Nim proteins than that currently described in the literature. Putative new variants of known Nim proteins and novel Nim proteins were found. In addition, nitroreductase proteins and homologs related to the pyridoxamine 5'-phosphate oxidase family were found in highly diverse anaerobic and aerobic taxa of human but also animal and environmental origin. On the other hand, we found a very low number of sequences recovered from metagenomic studies. Considering the different databases currently available to identify antimicrobial resistance genes (ARG) among metagenomic sequences, we hypothesized that this may, at least in part, be related to the incompleteness of ARG databases because none of them includes the 11 described nim genes at the time of our study. Both the wide distribution of proteins with potential MTZ inactivation ability within the bacterial world and a wider diversity of Nim determinants than expected from published literature is underlined in this sequence database analysis.
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Affiliation(s)
- Corentine Alauzet
- Université de Lorraine, EA 7300 Stress Immunité Pathogènes SIMPA, F-54000 Nancy, France; Université de Lorraine, CHRU-Nancy, Laboratoire de Bactériologie, F-54000, France
| | - Fabien Aujoulat
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, Montpellier, France
| | - Alain Lozniewski
- Université de Lorraine, EA 7300 Stress Immunité Pathogènes SIMPA, F-54000 Nancy, France; Université de Lorraine, CHRU-Nancy, Laboratoire de Bactériologie, F-54000, France
| | - Hélène Marchandin
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, Département de Microbiologie, CHU Nîmes, Nîmes, France.
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Akiva E, Copp JN, Tokuriki N, Babbitt PC. Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily. Proc Natl Acad Sci U S A 2017; 114:E9549-E9558. [PMID: 29078300 PMCID: PMC5692541 DOI: 10.1073/pnas.1706849114] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Insight regarding how diverse enzymatic functions and reactions have evolved from ancestral scaffolds is fundamental to understanding chemical and evolutionary biology, and for the exploitation of enzymes for biotechnology. We undertook an extensive computational analysis using a unique and comprehensive combination of tools that include large-scale phylogenetic reconstruction to determine the sequence, structural, and functional relationships of the functionally diverse flavin mononucleotide-dependent nitroreductase (NTR) superfamily (>24,000 sequences from all domains of life, 54 structures, and >10 enzymatic functions). Our results suggest an evolutionary model in which contemporary subgroups of the superfamily have diverged in a radial manner from a minimal flavin-binding scaffold. We identified the structural design principle for this divergence: Insertions at key positions in the minimal scaffold that, combined with the fixation of key residues, have led to functional specialization. These results will aid future efforts to delineate the emergence of functional diversity in enzyme superfamilies, provide clues for functional inference for superfamily members of unknown function, and facilitate rational redesign of the NTR scaffold.
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Affiliation(s)
- Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
| | - Janine N Copp
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4;
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158;
- California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158
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