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Jaroensuk J, Chuaboon L, Kesornpun C, Chaiyen P. Enzymes in riboflavin biosynthesis: Potential antibiotic drug targets. Arch Biochem Biophys 2023; 748:109762. [PMID: 37739114 DOI: 10.1016/j.abb.2023.109762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/13/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
The rapid resistance of pathogens to antibiotics has emerged as a major threat to global health. Identification of new antibiotic targets is thus needed for developing alternative drugs. Genes encoding enzymes involved in the biosynthesis of riboflavin and flavin cofactors (FMN/FAD) are attractive targets because these enzymatic reactions are necessary for most bacteria to synthesize flavin cofactors for use in their central metabolic reactions. Moreover, humans lack most of these enzymes because we uptake riboflavin from our diet. This review discusses the current knowledge of enzymes involved in bacterial biosynthesis of riboflavin and other flavin cofactors, as well as the functions of the FMN riboswitch. Here, we highlight recent progress in the structural and mechanistic characterization, and inhibition of GTP cyclohydrolase II (GCH II), lumazine synthase (LS), riboflavin synthase (RFS), FAD synthetase (FADS), and FMN riboswitch, which have been identified as plausible antibiotic targets. As the structures and functions of these enzymes and regulatory systems are not completely understood, they are attractive as subjects for future in-depth biochemical and biophysical analysis.
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Affiliation(s)
- Juthamas Jaroensuk
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Wangchan, Rayong, 21210, Thailand
| | - Litavadee Chuaboon
- School of Pharmacy and Biomass and Oil Palm Center of Excellence, Walailak University, Nakhon Si Thammarat, 80160, Thailand
| | - Chatchai Kesornpun
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Wangchan, Rayong, 21210, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Wangchan, Rayong, 21210, Thailand.
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2
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Karazan ZM, Roushani M. Selective determination of cadmium and lead ions in different food samples by poly (riboflavin)/carbon black-modified glassy carbon electrode. Food Chem 2023; 423:136283. [PMID: 37187010 DOI: 10.1016/j.foodchem.2023.136283] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 04/27/2023] [Accepted: 04/27/2023] [Indexed: 05/17/2023]
Abstract
In this research, a poly (riboflavin)/carbon black-modified glassy carbon electrode (PRF/CB/GCE) is introduced as a novel electrochemical sensor toward Cd2+ and Pb2+ simultaneous measurement in presence of bismuth ions, applying differential pulse anodic stripping voltammetry (DPASV). Regarding the optimized conditions, the linear ranges were achieved from 0.5 to 600 nM for Cd2+ and Pb2+. The detection limit (LOD) was found to be 0.16 nM for Cd2+ and 0.13 nM for Pb2+. In order to perform the technique in real application, the proposed electrode was used to simultaneously detect ions in rice, honey, and vegetable samples with satisfactory recoveries - indicating that the sensor possesses good practicability to determine Cd2+ and Pb2+. Moreover, an atomic absorption spectrometry (AAS) was used in order to detect the concentration of ions as a reference technique in rice, honey, and vegetable samples.
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Affiliation(s)
| | - Mahmoud Roushani
- Department of Chemistry, Faculty of Sciences, Ilam University, Ilam 69315-516, Iran.
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3
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Zhao J, Li F, Kong S, Chen T, Song H, Wang Z. Elongated Riboflavin-Producing Shewanella oneidensis in a Hybrid Biofilm Boosts Extracellular Electron Transfer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206622. [PMID: 36710254 PMCID: PMC10037984 DOI: 10.1002/advs.202206622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/05/2023] [Indexed: 06/18/2023]
Abstract
Shewanella oneidensis is able to carry out extracellular electron transfer (EET), although its EET efficiency is largely limited by low flavin concentrations, poor biofilm forming-ability, and weak biofilm conductivity. After identifying an important role for riboflavin (RF) in EET via in vitro experiments, the synthesis of RF is directed to 837.74 ± 11.42 µm in S. oneidensis. Molecular dynamics simulation reveals RF as a cofactor that binds strongly to the outer membrane cytochrome MtrC, which is correspondingly further overexpressed to enhance EET. Then the cell division inhibitor sulA, which dramatically enhanced the thickness and biomass of biofilm increased by 155% and 77%, respectively, is overexpressed. To reduce reaction overpotential due to biofilm thickness, a spider-web-like hybrid biofilm comprising RF, multiwalled carbon nanotubes (MWCNTs), and graphene oxide (GO) with adsorption-optimized elongated S. oneidensis, achieve a 77.83-fold increase in power (3736 mW m-2 ) relative to MR-1 and dramatically reduce the charge-transfer resistance and boosted biofilm electroactivity. This work provides an elegant paradigm to boost EET based on a synthetic biology strategy and materials science strategy, opens up further opportunities for other electrogenic bacteria.
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Affiliation(s)
- Juntao Zhao
- Frontier Science Center for Synthetic BiologyTianjin UniversityTianjin300072P. R. China
- Key Laboratory of Systems Bioengineering (Ministry of Education)Tianjin UniversityTianjin300072P. R. China
- School of Chemical Engineering and TechnologyTianjin UniversityTianjin300072P. R. China
| | - Feng Li
- Frontier Science Center for Synthetic BiologyTianjin UniversityTianjin300072P. R. China
- Key Laboratory of Systems Bioengineering (Ministry of Education)Tianjin UniversityTianjin300072P. R. China
- School of Chemical Engineering and TechnologyTianjin UniversityTianjin300072P. R. China
| | - Shutian Kong
- Frontier Science Center for Synthetic BiologyTianjin UniversityTianjin300072P. R. China
- Key Laboratory of Systems Bioengineering (Ministry of Education)Tianjin UniversityTianjin300072P. R. China
- School of Chemical Engineering and TechnologyTianjin UniversityTianjin300072P. R. China
| | - Tao Chen
- Frontier Science Center for Synthetic BiologyTianjin UniversityTianjin300072P. R. China
- Key Laboratory of Systems Bioengineering (Ministry of Education)Tianjin UniversityTianjin300072P. R. China
- School of Chemical Engineering and TechnologyTianjin UniversityTianjin300072P. R. China
| | - Hao Song
- Frontier Science Center for Synthetic BiologyTianjin UniversityTianjin300072P. R. China
- Key Laboratory of Systems Bioengineering (Ministry of Education)Tianjin UniversityTianjin300072P. R. China
- School of Chemical Engineering and TechnologyTianjin UniversityTianjin300072P. R. China
| | - Zhiwen Wang
- Frontier Science Center for Synthetic BiologyTianjin UniversityTianjin300072P. R. China
- Key Laboratory of Systems Bioengineering (Ministry of Education)Tianjin UniversityTianjin300072P. R. China
- School of Chemical Engineering and TechnologyTianjin UniversityTianjin300072P. R. China
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4
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Moreno A, Taleb V, Sebastián M, Anoz-Carbonell E, Martínez-Júlvez M, Medina M. Cofactors and pathogens: Flavin mononucleotide and flavin adenine dinucleotide (FAD) biosynthesis by the FAD synthase from Brucella ovis. IUBMB Life 2021; 74:655-671. [PMID: 34813144 PMCID: PMC9299109 DOI: 10.1002/iub.2576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/14/2021] [Accepted: 10/26/2021] [Indexed: 02/02/2023]
Abstract
The biosynthesis of the flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), cofactors used by 2% of proteins, occurs through the sequential action of two ubiquitous activities: a riboflavinkinase (RFK) that phosphorylates the riboflavin (RF) precursor to FMN, and a FMN:adenylyltransferase (FMNAT) that transforms FMN into FAD. In most mammals two different monofunctional enzymes have each of these activities, but in prokaryotes a single bifunctional enzyme, FAD synthase (FADS), holds them. Differential structural and functional traits for RFK and FMNAT catalysis between bacteria and mammals, as well as within the few bacterial FADSs so far characterized, has envisaged the potentiality of FADSs from pathogens as targets for the development of species‐specific inhibitors. Here, we particularly characterize the FADS from the ovine pathogen Brucella ovis (BoFADS), causative agent of brucellosis. We show that BoFADS has RFK activity independently of the media redox status, but its FMNAT activity (in both forward and reverse senses) only occurs under strong reducing conditions. Moreover, kinetics for flavin and adenine nucleotides binding to the RFK site show that BoFADS binds preferentially the substrates of the RFK reaction over the products and that the adenine nucleotide must bind prior to flavin entrapment. These results, together with multiple sequence alignments and phylogenetic analysis, point to variability in the less conserved regions as contributing to the species‐specific features in prokaryotic FADSs, including those from pathogens, that allow them to adopt alternative strategies in FMN and FAD biosynthesis and overall flavin homeostasis.
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Affiliation(s)
- Andrea Moreno
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza, Spain.,Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | - Victor Taleb
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza, Spain
| | - María Sebastián
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza, Spain
| | - Ernesto Anoz-Carbonell
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza, Spain
| | - Marta Martínez-Júlvez
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza, Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza, Spain
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5
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Zhou G, Pan Q, Hu Z, Qiu J, Yu Z. Heterologous Expression and Characterization of Flavinadenine Dinucleotide Synthetase from Candida famata for Flavin Adenine Dinucleotide Production. Protein Pept Lett 2021; 28:229-239. [PMID: 32640951 DOI: 10.2174/0929866527666200708151327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/02/2020] [Accepted: 06/05/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Flavin adenine dinucleotide (FAD) is a redox-active coenzyme that regulates several important enzymatic reactions during metabolism. FAD is used in the medicinal and food industries and FAD supplements have been used to treat some inheritable diseases. FAD can be biosynthesized from flavin mononucleotide (FMN) and adenosine triphosphate (ATP), catalyzed by FAD synthetase (FADS). OBJECTIVE The aim of this study was to heterologously express the gene encoding FADS from the flavinogenic yeast Candida famata (FADSCf) for biosynthesis of FAD. METHODS The sequence encoding FADSCf was retrieved and heterologously expressed in Escherichia coli. The structure and enzymatic properties of recombinant FADSCf were characterized. RESULTS FADSCf (279 amino acids) was successfully expressed in E. coli BL21 (DE3), with a theoretical molecular weight of 32299.79 Da and an isoelectric point of 6.09. Secondary structural analysis showed that the number of α-helices was 2-fold higher than the number of β-sheets, indicating that the protein was highly hydrophilic. Under fixed ATP concentration, FADSCf had a Km of 0.04737±0.03158 mM and a Vmax of 3.271±0.79 μM/min/mg. Under fixed FMN concentration, FADSCf had a Km of 0.1214±0.07464 mM and a Vmax of 2.6695±0.3715 μM/min/mg. Enzymatic reactions in vitro showed that expressed FADSCf could form 80 mM of FAD per mg of enzyme after 21 hours under the following conditions: 0.5 mM FMN, 5 mM ATP and 10 mM Mg2+. CONCLUSION Under optimized conditions (0.5 mM FMN, 5 mM ATP and 10 mM Mg2+), the production of FAD reached 80 mM per mg of FADSCf after a 21-hour reaction. Our results indicate that purified recombinant FADSCf can be used for the biosynthesis of FAD.
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Affiliation(s)
- Guoqiang Zhou
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou-310014, China
| | - Qiaoqiao Pan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou-310014, China
| | - Zeyu Hu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou-310014, China
| | - Juanping Qiu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou-310014, China
| | - Zhiliang Yu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou-310014, China
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Molecular insights into the mechanism of substrate binding and catalysis of bifunctional FAD synthetase from Staphylococcus aureus. Biochimie 2021; 182:217-227. [PMID: 33516756 DOI: 10.1016/j.biochi.2021.01.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/05/2021] [Accepted: 01/19/2021] [Indexed: 11/24/2022]
Abstract
Flavin adenine dinucleotide synthetase (FADS), a bifunctional prokaryotic enzyme, is involved in the synthesis of two vital cofactors, flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). Here, we investigated the biochemical characteristics of FADS from Staphylococcus aureus (Sa), a pathogenic bacteria causing food-borne diseases. The SaFADS possesses riboflavin kinase (RFK) and FMN adenylyltransferase (FMNAT) activities that transforms riboflavin to FMN and FMN to FAD, respectively. The FMNAT domain also exhibits reversible FAD pyrophosphorylase activity (FADpp). Further, we show that the FMNAT and FADpp activities are dependent on the reducing environment. Mutations of the conserved K289 and F290 residues present on the RFK domain affect the kinetic parameters of both the RFK and FMNAT domains. Additionally, the molecular dynamics analysis of apo and riboflavin: ATP: Mg2+ ternary complex of SaFADS shows that F290 is involved in stabilizing the active site geometry to hold the enzyme-substrate complex. In addition, the deletion of the αh2 helix that acts as a connecting linker between the FMNAT and RFK domains showed substantial loss of their activities. The helix deletion could have affected the flap motion of L2c, L4c, β4n and L3n present in the close proximity resulting in the distortion of the active site geometry. In conclusion, our study has characterized the RFK and FMNAT activities of SaFADS and shown the importance of conserved K289 and F290 in RFK activity. As FADSs are potential drug targets, understanding their mechanism of action might help in discovering species-specific antibacterial drugs.
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7
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Riboflavin-mediated radical polymerization – Outlook for eco-friendly synthesis of functional materials. Eur Polym J 2021. [DOI: 10.1016/j.eurpolymj.2020.110152] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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8
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Lans I, Anoz-Carbonell E, Palacio-Rodríguez K, Aínsa JA, Medina M, Cossio P. In silico discovery and biological validation of ligands of FAD synthase, a promising new antimicrobial target. PLoS Comput Biol 2020; 16:e1007898. [PMID: 32797038 PMCID: PMC7449411 DOI: 10.1371/journal.pcbi.1007898] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/26/2020] [Accepted: 07/09/2020] [Indexed: 01/06/2023] Open
Abstract
New treatments for diseases caused by antimicrobial-resistant microorganisms can be developed by identifying unexplored therapeutic targets and by designing efficient drug screening protocols. In this study, we have screened a library of compounds to find ligands for the flavin-adenine dinucleotide synthase (FADS) -a potential target for drug design against tuberculosis and pneumonia- by implementing a new and efficient virtual screening protocol. The protocol has been developed for the in silico search of ligands of unexplored therapeutic targets, for which limited information about ligands or ligand-receptor structures is available. It implements an integrative funnel-like strategy with filtering layers that increase in computational accuracy. The protocol starts with a pharmacophore-based virtual screening strategy that uses ligand-free receptor conformations from molecular dynamics (MD) simulations. Then, it performs a molecular docking stage using several docking programs and an exponential consensus ranking strategy. The last filter, samples the conformations of compounds bound to the target using MD simulations. The MD conformations are scored using several traditional scoring functions in combination with a newly-proposed score that takes into account the fluctuations of the molecule with a Morse-based potential. The protocol was optimized and validated using a compound library with known ligands of the Corynebacterium ammoniagenes FADS. Then, it was used to find new FADS ligands from a compound library of 14,000 molecules. A small set of 17 in silico filtered molecules were tested experimentally. We identified five inhibitors of the activity of the flavin adenylyl transferase module of the FADS, and some of them were able to inhibit growth of three bacterial species: C. ammoniagenes, Mycobacterium tuberculosis, and Streptococcus pneumoniae, where the last two are human pathogens. Overall, the results show that the integrative VS protocol is a cost-effective solution for the discovery of ligands of unexplored therapeutic targets.
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Affiliation(s)
- Isaias Lans
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, Medellin, Colombia
| | - Ernesto Anoz-Carbonell
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (Unidades Asociadas BIFI-IQFR y CBsC-CSIC), Universidad de Zaragoza, Spain
- Grupo de Genética de Micobacterias, Departamento de Microbiología, Pediatría, Radiología y Salud Pública. Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
| | - Karen Palacio-Rodríguez
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, Medellin, Colombia
| | - José Antonio Aínsa
- Instituto de Biocomputación y Física de Sistemas Complejos (Unidades Asociadas BIFI-IQFR y CBsC-CSIC), Universidad de Zaragoza, Spain
- Grupo de Genética de Micobacterias, Departamento de Microbiología, Pediatría, Radiología y Salud Pública. Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (Unidades Asociadas BIFI-IQFR y CBsC-CSIC), Universidad de Zaragoza, Spain
| | - Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, Medellin, Colombia
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany
- * E-mail:
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Insights into the FMNAT Active Site of FAD Synthase: Aromaticity is Essential for Flavin Binding and Catalysis. Int J Mol Sci 2020; 21:ijms21103738. [PMID: 32466340 PMCID: PMC7279473 DOI: 10.3390/ijms21103738] [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: 05/01/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 11/17/2022] Open
Abstract
The last step in the biosynthesis of flavin adenine dinucleotide (FAD) is considered a target for the design of antimicrobial drugs because it is carried out by two non-homologous proteins in eukaryotic and prokaryotic organisms. Monofunctional FMN: adenylyltransferases (FMNAT) in Eukarya and FMNAT modules of bifunctional FAD synthases (FADS) in Prokarya belong to different structural families with dissimilar chemistry and binding modes for the substrates. In this study, we analyzed the relevance of the hydrophobic environment of the flavin isoalloxazine in the FMNAT active site of Corynebacterium ammoniagenes FADS (CaFADS) through the mutational analysis of its F62, Y106, and F128 residues. They form the isoalloxazine binding cavity and are highly conserved in the prokaryotic FADS family. The spectroscopic, steady-state kinetics and thermodynamic data presented indicate that distortion of aromaticity at the FMNAT isoalloxazine binding cavity prevents FMN and FAD from correct accommodation in their binding cavity and, as a consequence, decreases the efficiency of the FMNAT activity. Therefore, the side-chains of F62, Y106 and F128 are relevant in the formation of the catalytic competent complex during FMNAT catalysis in CaFADS. The introduced mutations also modulate the activity occurring at the riboflavin kinase (RFK) module of CaFADS, further evidencing the formation of quaternary assemblies during catalysis.
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Arilla-Luna S, Serrano A, Medina M. Specific Features for the Competent Binding of Substrates at the FMN Adenylyltransferase Site of FAD Synthase from Corynebacterium ammoniagenes. Int J Mol Sci 2019; 20:ijms20205083. [PMID: 31614972 PMCID: PMC6829536 DOI: 10.3390/ijms20205083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 10/07/2019] [Accepted: 10/09/2019] [Indexed: 11/16/2022] Open
Abstract
Bifunctional FAD synthases (FADSs) catalyze FMN (flavin mononucleotide) and FAD (flavinadenine dinucleotide) biosynthesis at their C-riboflavin kinase (RFK) and N-FMN:adenylyltransferase (FMNAT) modules, respectively. Biophysical properties and requirements for their FMNAT activity differ among species. Here, we evaluate the relevance of the integrity of the binding site of the isoalloxazine of flavinic substrates for FMNAT catalysis in Corynebacterium ammoniagenes FADS (CaFADS). We have substituted P56 and P58, belonging to a conserved motif, as well as L98. These residues shape the isoalloxazine FMNAT site, although they are not expected to directly contact it. All substitutions override enzyme ability to transform substrates at the FMNAT site, although most variants are able to bind them. Spectroscopic properties and thermodynamic parameters for the binding of ligands indicate that mutations alter their interaction modes. Substitutions also modulate binding and kinetic properties at the RFK site, evidencing the crosstalk of different protomers within CaFADS assemblies during catalysis. In conclusion, despite the FMNAT site for the binding of substrates in CaFADS appearing as a wide open cavity, it is finely tuned to provide the competent binding conformation of substrates. In particular, P56, P58 and L98 shape the isoalloxazine site to place the FMN- and FAD-reacting phosphates in optimal geometry for catalysis.
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Affiliation(s)
- Sonia Arilla-Luna
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, and Institute of Biocomputation and Physics of Complex Systems (Joint Units: BIFI-IQFR and GBsC-CSIC), University of Zaragoza, 50009 Zaragoza, Spain.
| | - Ana Serrano
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, and Institute of Biocomputation and Physics of Complex Systems (Joint Units: BIFI-IQFR and GBsC-CSIC), University of Zaragoza, 50009 Zaragoza, Spain.
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain.
| | - Milagros Medina
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, and Institute of Biocomputation and Physics of Complex Systems (Joint Units: BIFI-IQFR and GBsC-CSIC), University of Zaragoza, 50009 Zaragoza, Spain.
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11
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Shang F, Lan J, Wang L, Liu W, Chen Y, Chen J, Ha NC, Quan C, Nam KH, Xu Y. Crystal structure of the Siderophore-interacting protein SIP from Aeromonas hydrophila. Biochem Biophys Res Commun 2019; 519:23-28. [PMID: 31477273 DOI: 10.1016/j.bbrc.2019.08.085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 08/14/2019] [Indexed: 11/30/2022]
Abstract
Siderophores acquire iron from hosts under iron-limiting conditions and play an essential role in the survival of microorganisms. Siderophore-interacting proteins (SIPs) from microbes release iron from the siderophore complex by reducing ferric iron to ferrous iron, but the molecular mechanism of iron reduction remains unclear. To better understand the molecular mechanism of SIPs, we herein report the crystal structure of Aeromonas hydrophila SIP (AhSIP) in complex with flavin adenine dinucleotide (FAD) as a cofactor. AhSIP consists of an N-terminal FAD binding domain and a C-terminal NADH binding domain, which are connected by a linker region. AhSIP showed unique structural differences in the orientation of the cofactor binding lobes when compared with SIP homologs. This study identified a cluster of three basic residues (Lys48, His259 and Arg262) in AhSIP distributed around a potential substrate binding pocket. In addition, AhSIP, containing the NADH binding motif E(L)VL-X3-GE, belongs to the group I subfamily. Our results show the diverse cofactor and substrate binding sites of the SIP family.
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Affiliation(s)
- Fei Shang
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China
| | - Jing Lan
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China
| | - Lulu Wang
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China; School of Life Science and Biotechnology, Dalian University of Technology, No 2 Linggong Road, Dalian, 116024, Liaoning, China
| | - Wei Liu
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China
| | - Yuanyuan Chen
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China
| | - Jinli Chen
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China
| | - Nam-Chul Ha
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Chunshan Quan
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China.
| | - Ki Hyun Nam
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea; Institute of Life Science and Natural Resources, Korea University, Seoul, 02841, Republic of Korea.
| | - Yongbin Xu
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China.
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12
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Sebastián M, Arilla-Luna S, Bellalou J, Yruela I, Medina M. The Biosynthesis of Flavin Cofactors in Listeria monocytogenes. J Mol Biol 2019; 431:2762-2776. [PMID: 31132361 DOI: 10.1016/j.jmb.2019.05.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/20/2019] [Accepted: 05/20/2019] [Indexed: 11/26/2022]
Abstract
Listeria monocytogenes is riboflavin auxotrophic, but it has two genes envisaged to transform riboflavin into FMN and FAD after its uptaked by specialized transporters. One encodes a bifunctional type I FAD synthase (FADS, herein LmFADS-1), while the other produces a protein similar to type I at the FMN:ATP adenylyltransferase (FMNAT) site but with a shorter C-terminal that lacks any riboflavin kinase (RFK) motif. This second protein is rare among bacteria and has been named FADS type II (LmFADS-2). Here we present a biochemical and biophysical study of LmFADS-1 and LmFADS-2 by integrating kinetic and thermodynamic data together with sequence and structural prediction methods to evaluate their occurrence in Listeria, as well as their function and molecular properties. Despite LmFADS-1 similarities to other type I FADSs, (i) its RFK activity has not riboflavin substrate inhibition and occurs under reducing and oxidizing conditions, (ii) its FMNAT activity requires strong reducing environment, and (iii) binding of reaction products, but not substrates, favors binding of the second ligand. LmFADS-2 produces FAD under oxidizing and reducing environments, but its C-terminus module function remains unknown. Listeria species conserve both FADSs, being sequence identity high within L. monocytogenes strains. Our data exemplify alternative strategies for FMN and FAD biosynthesis and homeostasis, envisaging that in Listeria two FADSs might be required to fulfill the supply of flavin cofactors under niches that can go from saprophytism to virulence. As FADSs are attractive antimicrobial targets, understanding of FADSs traits in different species is essential to help in the discovery of specific antimicrobials.
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Affiliation(s)
- Maria Sebastián
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias and Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Sonia Arilla-Luna
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias and Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Jacques Bellalou
- Plateforme de Protéines Recombinantes, Institut Pasteur, CNRS-UMR 3528, Paris, France
| | - Inmaculada Yruela
- Estación Experimental de Aula Dei, National Spanish Research Council (CSIC), Zaragoza, Spain; Group of Biochemistry, Biophysics and Computational Biology (BIFI-Unizar) Joint Unit to CSIC Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias and Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, 50009 Zaragoza, Spain; Group of Biochemistry, Biophysics and Computational Biology (BIFI-Unizar) Joint Unit to CSIC Spain.
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13
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Sebastián M, Velázquez-Campoy A, Medina M. The RFK catalytic cycle of the pathogen Streptococcus pneumoniae shows species-specific features in prokaryotic FMN synthesis. J Enzyme Inhib Med Chem 2018; 33:842-849. [PMID: 29693467 PMCID: PMC6010069 DOI: 10.1080/14756366.2018.1461857] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 03/31/2018] [Accepted: 04/03/2018] [Indexed: 02/03/2023] Open
Abstract
Emergence of multidrug-resistant bacteria forces us to explore new therapeutic strategies, and proteins involved in key metabolic pathways are promising anti-bacterial targets. Bifunctional flavin-adenine dinucleotide (FAD) synthetases (FADS) are prokaryotic enzymes that synthesise the flavin mononucleotide (FMN) and FAD cofactors. The FADS from the human pathogen Streptococcus pneumoniae (SpnFADS)-causative agent of pneumonia in humans - shows relevant catalytic dissimilarities compared to other FADSs. Here, by integrating thermodynamic and kinetic data, we present a global description of the riboflavin kinase activity of SpnFADS, as well as of the inhibition mechanisms regulating this activity. Our data shed light on biophysical determinants that modulate species-specific conformational changes leading to catalytically competent conformations, as well as binding rates and affinities of substrates versus products. This knowledge paves the way for the development of tools - that taking advantage of the regulatory dissimilarities during FMN biosynthesis in different species - might be used in the discovery of specific anti-pneumococcal drugs.
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Affiliation(s)
- María Sebastián
- Facultad de Ciencias, Departamento de Bioquímica y Biología Molecular y Celular, and Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC-CSIC and BIFI-CSIC Joint Units), Universidad de Zaragoza, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Facultad de Ciencias, Departamento de Bioquímica y Biología Molecular y Celular, and Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC-CSIC and BIFI-CSIC Joint Units), Universidad de Zaragoza, Zaragoza, Spain
- Fundación ARAID, Diputación General de Aragón, Zaragoza, Spain
- Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain
| | - Milagros Medina
- Facultad de Ciencias, Departamento de Bioquímica y Biología Molecular y Celular, and Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC-CSIC and BIFI-CSIC Joint Units), Universidad de Zaragoza, Zaragoza, Spain
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14
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The Dimer-of-Trimers Assembly Prevents Catalysis at the Transferase Site of Prokaryotic FAD Synthase. Biophys J 2018; 115:988-995. [PMID: 30177440 DOI: 10.1016/j.bpj.2018.08.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/26/2018] [Accepted: 08/13/2018] [Indexed: 12/18/2022] Open
Abstract
Flavin mononucleotide (FMN) and flavin-adenine dinucleotide (FAD) are essential flavoprotein cofactors. A riboflavin kinase (RFK) activity catalyzes riboflavin phosphorylation to FMN, which can then be transformed into FAD by an FMN:adenylyltransferase (FMNAT) activity. Two enzymes are responsible for each one of these activities in eukaryotes, whereas prokaryotes have a single bifunctional enzyme, FAD synthase (FADS). FADS folds in two independent modules: the C-terminal with RFK activity and the N-terminal with FMNAT activity. Differences in structure and chemistry for the FMNAT catalysis among prokaryotic and eukaryotic enzymes pointed to the FMNAT activity of prokaryotic FADS as a potential antimicrobial target, making the structural model of the bacterial FMNAT module in complex with substrates relevant to understand the FADS catalytic mechanism and to the discovery of antimicrobial drugs. However, such a crystallographic complex remains elusive. Here, we have used molecular docking and molecular dynamics simulations to generate energetically stable interactions of the FMNAT module of FADS from Corynebacterium ammoniagenes with ATP/Mg2+ and FMN in both the monomeric and dimer-of-trimers assemblies reported for this protein. For the monomer, we have identified the residues that accommodate the reactive phosphates in a conformation compatible with catalysis. Interestingly, for the dimer-of-trimers conformation, we have found that the RFK module negatively influences FMN binding at the interacting FMNAT module. These results agree with calorimetric data of purified samples containing nearly 100% monomer or nearly 100% dimer-of-trimers, indicating that FMN binds to the monomer but not to the dimer-of-trimers. Such observations support regulation of flavin homeostasis by quaternary C. ammoniagenes FADS assemblies.
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15
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Two-Component Flavin-Dependent Riboflavin Monooxygenase Degrades Riboflavin in Devosia riboflavina. J Bacteriol 2018; 200:JB.00022-18. [PMID: 29610214 DOI: 10.1128/jb.00022-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/28/2018] [Indexed: 12/22/2022] Open
Abstract
The actinobacterium Microbacterium maritypicum splits riboflavin (vitamin B2) into lumichrome and d-ribose. However, such degradation by other bacteria and the involvement of a two-component flavin-dependent monooxygenase (FMO) in the reaction remain unknown. Here we investigated the mechanism of riboflavin degradation by the riboflavin-assimilating alphaproteobacterium Devosia riboflavina (formerly Pseudomonas riboflavina). We found that adding riboflavin to bacterial cultures induced riboflavin-degrading activity and a protein of the FMO family that had 67% amino acid identity with the predicted riboflavin hydrolase (RcaE) of M. maritypicum MF109. The D. riboflavina genome clustered genes encoding the predicted FMO, flavin reductase (FR), ribokinase, and flavokinase, and riboflavin induced their expression. This finding suggests that these genes constitute a mechanism for utilizing riboflavin as a carbon source. Recombinant FMO (rFMO) protein of D. riboflavina oxidized riboflavin in the presence of reduced flavin mononucleotide (FMN) provided by recombinant FR (rFR), oxidized FMN and NADH, and produced stoichiometric amounts of lumichrome and d-ribose. Further investigation of the enzymatic properties of D. riboflavina rFMO indicated that rFMO-rFR coupling accompanied O2 consumption and the generation of enzyme-bound hydroperoxy-FMN, which are characteristic of two-component FMOs. These results suggest that D. riboflavina FMO is involved in hydroperoxy-FMN-dependent mechanisms to oxygenize riboflavin and a riboflavin monooxygenase is necessary for the initial step of riboflavin degradation.IMPORTANCE Whether bacteria utilize either a monooxygenase or a hydrolase for riboflavin degradation has remained obscure. The present study found that a novel riboflavin monooxygenase, not riboflavin hydrolase, facilitated this process in D. riboflavina The riboflavin monooxygenase gene was clustered with flavin reductase, flavokinase, and ribokinase genes, and riboflavin induced their expression and riboflavin-degrading activity. The gene cluster is uniquely distributed in Devosia species and actinobacteria, which have exploited an environmental niche by developing adaptive mechanisms for riboflavin utilization.
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Oraei M, Razavi SH, Khodaiyan F. Optimization of Effective Minerals on Riboflavin Production by Bacillus subtilis subsp. subtilis ATCC 6051 Using Statistical Designs. Avicenna J Med Biotechnol 2018; 10:49-55. [PMID: 29296267 PMCID: PMC5742654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
BACKGROUND Riboflavin (vitamin B2) is an essential component of the basic metabolism, and an important nutritional and growth factor in humans, animals, plants and micro-organisms. It has been widely used in the fields of pharmaceuticals, feed and food additives. The industrial production of riboflavin mostly relies on the microbial fermentation. Designing an appropriate fermentation medium is of crucial importance to improve the riboflavin production. METHODS In this study, sequential methodology combining a screening test of minerals by Plackett-Burman (PB) and an optimization test by Central Composite Design (CCD) was applied to enhance riboflavin production by Bacillus subtilis ATCC 6051 in shake flasks. RESULTS Initially, one-factor-at-a-time approach was applied to evaluate the effect of different carbon sources. The results showed that fructose was significantly most effective on biomass and riboflavin production. After that, 13 minerals [CaCl2, CuCl, FeCl3, FeSO4, AlCl3, Na3MoO4, Co(NO3)2, NaCl, KH2PO4, K2HPO4, MgSO4, ZnSO4, and MnSO4] were studied with the screening test. The results revealed that concentration of MgSO4, K2HPO4, and FeSO4 had greater influence on riboflavin production (p< 0.05). A CCD with five factors (concentration of fructose, MgSO4, K2HPO4, FeSO4, and yeast extract) at five levels was then used to determine the maximum riboflavin concentration. The optimal concentrations (g/l) of these variables determined by Response Surface Methodology (RSM) were fructose, 38.10; MgSO4, 0.85; K2HPO4, 2.27; FeSO4, 0.02; and yeast extract, 4.37. CONCLUSION Statistical experimental design offers a practicable approach to the implementation of medium optimization. From an industrial view point, our optimum medium, besides fructose and a small amount of yeast extract, is mainly composed of common and cheap inorganic salts, which are available to the industrial riboflavin production.
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Affiliation(s)
| | - Seyed Hadi Razavi
- Corresponding author: Seyed Hadi Razavi, Ph.D., Bioprocess Engineering Laboratory (BPEL), Department of Food Science, Engineering and Technology, Faculty of Agricultural Engineering and Technology, University of Tehran, Karaj, Iran, Tel: +98 26 32248804, Fax: +98 26 32249453, E-mail:
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17
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Sebastián M, Anoz-Carbonell E, Gracia B, Cossio P, Aínsa JA, Lans I, Medina M. Discovery of antimicrobial compounds targeting bacterial type FAD synthetases. J Enzyme Inhib Med Chem 2017; 33:241-254. [PMID: 29258359 PMCID: PMC7012052 DOI: 10.1080/14756366.2017.1411910] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The increase of bacterial strains resistant to most of the available antibiotics shows a need to explore novel antibacterial targets to discover antimicrobial drugs. Bifunctional bacterial FAD synthetases (FADSs) synthesise the flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). These cofactors act in vital processes as part of flavoproteins, making FADS an essential enzyme. Bacterial FADSs are potential antibacterial targets because of differences to mammalian enzymes, particularly at the FAD producing site. We have optimised an activity-based high throughput screening assay targeting Corynebacterium ammoniagenes FADS (CaFADS) that identifies inhibitors of its different activities. We selected the three best high-performing inhibitors of the FMN:adenylyltransferase activity (FMNAT) and studied their inhibition mechanisms and binding properties. The specificity of the CaFADS hits was evaluated by studying also their effect on the Streptococcus pneumoniae FADS activities, envisaging differences that can be used to discover species-specific antibacterial drugs. The antimicrobial effect of these compounds was also evaluated on C. ammoniagenes, S. pneumoniae, and Mycobacterium tuberculosis cultures, finding hits with favourable antimicrobial properties.
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Affiliation(s)
- María Sebastián
- a Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias , Universidad de Zaragoza , Zaragoza , Spain.,b Institute of Biocomputation and Physics of Complex Systems (BIFI-IQFR and CBsC-CSIC Joint Units) , Universidad de Zaragoza , Zaragoza , Spain
| | - Ernesto Anoz-Carbonell
- a Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias , Universidad de Zaragoza , Zaragoza , Spain.,b Institute of Biocomputation and Physics of Complex Systems (BIFI-IQFR and CBsC-CSIC Joint Units) , Universidad de Zaragoza , Zaragoza , Spain.,c Grupo de Genética de Micobacterias, Departamento de Microbiología, Medicina Preventiva y Salud Pública. Facultad de Medicina , Universidad de Zaragoza , Zaragoza , Spain
| | - Begoña Gracia
- c Grupo de Genética de Micobacterias, Departamento de Microbiología, Medicina Preventiva y Salud Pública. Facultad de Medicina , Universidad de Zaragoza , Zaragoza , Spain.,d CIBER Enfermedades Respiratorias (CIBERES) , Instituto de Salud Carlos III , Madrid , Spain
| | - Pilar Cossio
- e Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Frankfurt , Germany.,f Biophysics of Tropical Diseases, Max Planck Tandem Group , University of Antioquia , Medellín , Colombia
| | - José Antonio Aínsa
- b Institute of Biocomputation and Physics of Complex Systems (BIFI-IQFR and CBsC-CSIC Joint Units) , Universidad de Zaragoza , Zaragoza , Spain.,c Grupo de Genética de Micobacterias, Departamento de Microbiología, Medicina Preventiva y Salud Pública. Facultad de Medicina , Universidad de Zaragoza , Zaragoza , Spain.,d CIBER Enfermedades Respiratorias (CIBERES) , Instituto de Salud Carlos III , Madrid , Spain
| | - Isaías Lans
- f Biophysics of Tropical Diseases, Max Planck Tandem Group , University of Antioquia , Medellín , Colombia
| | - Milagros Medina
- a Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias , Universidad de Zaragoza , Zaragoza , Spain.,b Institute of Biocomputation and Physics of Complex Systems (BIFI-IQFR and CBsC-CSIC Joint Units) , Universidad de Zaragoza , Zaragoza , Spain
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18
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Sebastián M, Lira-Navarrete E, Serrano A, Marcuello C, Velázquez-Campoy A, Lostao A, Hurtado-Guerrero R, Medina M, Martínez-Júlvez M. The FAD synthetase from the human pathogen Streptococcus pneumoniae: a bifunctional enzyme exhibiting activity-dependent redox requirements. Sci Rep 2017; 7:7609. [PMID: 28790457 PMCID: PMC5548840 DOI: 10.1038/s41598-017-07716-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/28/2017] [Indexed: 11/12/2022] Open
Abstract
Prokaryotic bifunctional FAD synthetases (FADSs) catalyze the biosynthesis of FMN and FAD, whereas in eukaryotes two enzymes are required for the same purpose. FMN and FAD are key cofactors to maintain the flavoproteome homeostasis in all type of organisms. Here we shed light to the properties of the hitherto unstudied bacterial FADS from the human pathogen Streptococcus pneumoniae (SpnFADS). As other members of the family, SpnFADS catalyzes the three typical activities of prokaryotic FADSs: riboflavin kinase (RFK), ATP:FMN:adenylyltransferase (FMNAT), and FAD pyrophosphorylase (FADpp). However, several SpnFADS biophysical properties differ from those of other family members. In particular; i) the RFK activity is not inhibited by the riboflavin (RF) substrate, ii) the FMNAT and FADSpp activities require flavin substrates in the reduced state, iii) binding of adenine nucleotide ligands is required for the binding of flavinic substrates/products and iv) the monomer is the preferred state. Collectively, our results add interesting mechanistic differences among the few prokaryotic bifunctional FADSs already characterized, which might reflect the adaptation of the enzyme to relatively different environments. In a health point of view, differences among FADS family members provide us with a framework to design selective compounds targeting these enzymes for the treatment of diverse infectious diseases.
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Affiliation(s)
- María Sebastián
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) and GBsC-CSIC and BIFI-CSIC Joint Units, Universidad de Zaragoza, Zaragoza, Spain
| | - Erandi Lira-Navarrete
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) and GBsC-CSIC and BIFI-CSIC Joint Units, Universidad de Zaragoza, Zaragoza, Spain.,Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Ana Serrano
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) and GBsC-CSIC and BIFI-CSIC Joint Units, Universidad de Zaragoza, Zaragoza, Spain.,Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040, Madrid, Spain
| | - Carlos Marcuello
- Laboratorio de Microscopías Avanzadas (LMA), Instituto de Nanociencia de Aragón (INA), and Fundación INA, Universidad de Zaragoza, Zaragoza, Spain.,Univ Reims, Lab Rech Nanosci, EA4682, F-51100 Reims and INRA, FARE Lab, F-51100, Reims, France
| | - Adrián Velázquez-Campoy
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) and GBsC-CSIC and BIFI-CSIC Joint Units, Universidad de Zaragoza, Zaragoza, Spain.,Fundación ARAID, Diputación General de Aragón, Aragón, Spain.,Aragon Institute for Health Research (IIS Aragon), Zaragoza, 50009, Spain
| | - Anabel Lostao
- Laboratorio de Microscopías Avanzadas (LMA), Instituto de Nanociencia de Aragón (INA), and Fundación INA, Universidad de Zaragoza, Zaragoza, Spain.,Fundación ARAID, Diputación General de Aragón, Aragón, Spain
| | - Ramón Hurtado-Guerrero
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) and GBsC-CSIC and BIFI-CSIC Joint Units, Universidad de Zaragoza, Zaragoza, Spain.,Fundación ARAID, Diputación General de Aragón, Aragón, Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain. .,Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) and GBsC-CSIC and BIFI-CSIC Joint Units, Universidad de Zaragoza, Zaragoza, Spain.
| | - Marta Martínez-Júlvez
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain. .,Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) and GBsC-CSIC and BIFI-CSIC Joint Units, Universidad de Zaragoza, Zaragoza, Spain.
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Sebastián M, Serrano A, Velázquez-Campoy A, Medina M. Kinetics and thermodynamics of the protein-ligand interactions in the riboflavin kinase activity of the FAD synthetase from Corynebacterium ammoniagenes. Sci Rep 2017; 7:7281. [PMID: 28779158 PMCID: PMC5544777 DOI: 10.1038/s41598-017-07875-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 07/04/2017] [Indexed: 01/20/2023] Open
Abstract
Enzymes known as bifunctional and bimodular prokaryotic type-I FAD synthetase (FADS) exhibit ATP:riboflavin kinase (RFK) and FMN:ATP adenylyltransferase (FMNAT) activities in their C-terminal and N-terminal modules, respectively, and produce flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). These act as cofactors of a plethora of flavoproteins in all organisms. Therefore, regulation of their production maintains the cellular flavoproteome homeostasis. Here, we focus on regulation of the FMN synthesis in Corynebacterium ammoniagenes (Ca) by the inhibition of its RFK activity by substrates and products of the reaction. We use a truncated CaFADS variant consisting in the isolated C-terminal RFK module, whose RFK activity is similar to that of the full-length enzyme. Inhibition of the RFK activity by the RF substrate is independent of the FMNAT module, and FMN production, in addition to being inhibited by an excess of RF, is also inhibited by both of the reaction products. Pre-steady-state kinetic and thermodynamic studies reveal key aspects to the substrates induced fit to produce the catalytically competent complex. Among them, the role of Mg2+ in the concerted allocation of substrates for catalysis and the ensemble of non-competent complexes that contribute to the regulated inhibition of the RFK activity are particularly relevant.
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Affiliation(s)
- María Sebastián
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, and Institute of Biocomputation and Physics of Complex Systems (Joint Units: BIFI-IQFR and GBsC-CSIC), University of Zaragoza, Zaragoza, Spain
| | - Ana Serrano
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, and Institute of Biocomputation and Physics of Complex Systems (Joint Units: BIFI-IQFR and GBsC-CSIC), University of Zaragoza, Zaragoza, Spain.,Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, Madrid, Spain
| | - Adrián Velázquez-Campoy
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, and Institute of Biocomputation and Physics of Complex Systems (Joint Units: BIFI-IQFR and GBsC-CSIC), University of Zaragoza, Zaragoza, Spain.,ARAID Foundation, Diputación General de Aragón, Zaragoza, Spain.,Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain
| | - Milagros Medina
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, and Institute of Biocomputation and Physics of Complex Systems (Joint Units: BIFI-IQFR and GBsC-CSIC), University of Zaragoza, Zaragoza, Spain.
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The trimer interface in the quaternary structure of the bifunctional prokaryotic FAD synthetase from Corynebacterium ammoniagenes. Sci Rep 2017; 7:404. [PMID: 28341845 PMCID: PMC5428420 DOI: 10.1038/s41598-017-00402-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 02/27/2017] [Indexed: 12/25/2022] Open
Abstract
Bifunctional FAD synthetases (FADSs) fold in two independent modules; The C-terminal riboflavin kinase (RFK) catalyzes the RFK activity, while the N-terminal FMN-adenylyltransferase (FMNAT) exhibits the FMNAT activity. The search for macromolecular interfaces in the Corynebacterium ammoniagenes FADS (CaFADS) crystal structure predicts a dimer of trimers organization. Within each trimer, a head-to-tail arrangement causes the RFK and FMNAT catalytic sites of the two neighboring protomers to approach, in agreement with active site residues of one module influencing the activity at the other. We analyze the relevance of the CaFADS head-to-tail macromolecular interfaces to stabilization of assemblies, catalysis and ligand binding. With this aim, we evaluate the effect of point mutations in loop L1c-FlapI, loop L6c, and helix α1c of the RFK module (positions K202, E203, F206, D298, V300, E301 and L304), regions at the macromolecular interface between two protomers within the trimer. Although none of the studied residues is critical in the formation and dissociation of assemblies, residues at L1c-FlapI and helix α1c particularly modulate quaternary architecture, as well as ligand binding and kinetic parameters involved with RFK and FMNAT activities. These data support the influence of transient oligomeric structures on substrate accommodation and catalysis at both CaFADS active sites.
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Shen K, Huang XE. Clinical investigation in effect of riboflavin sodium phosphate on prevention and treatment for patients with radiotherapy related esophagitis. Asian Pac J Cancer Prev 2015; 16:1525-7. [PMID: 25743825 DOI: 10.7314/apjcp.2015.16.4.1525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE To investigate the clinical effect of riboflavin sodium phosphate on prevention of radiotherapy related esophagitis (RRE). METHODS This retrospective study involved 55 patients with middle and advanced esophageal cancer who were divided into an experimental group of 28 and a control group of 27 patients. Those in the experimental group were treated with riboflavin sodium phosphate combined with conventional symptomatic treatment during radiotherapy; while patients in control group received the latter alone. The incidence and degree of RRE were compared after radiotherapy. RESULTS The incidences of RRE in experimental and control group were 53.5% and 81.4%, respectively (p<0.05); the incidence of stages III and IV RRE in the experimental group was 17.8%, while in the control group it was 44.4% (p<0.05). CONCLUSION Riboflavin sodium phosphate could significantly prevent RRE and reduce the incidence of stage III and IV disease. These results were worthy of further confirmation by randomized controlled trials.
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Affiliation(s)
- Kang Shen
- Oncology Department, Siyang County People's Hospital, Suqian, China E-mail :
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Herguedas B, Lans I, Sebastián M, Hermoso JA, Martínez-Júlvez M, Medina M. Structural insights into the synthesis of FMN in prokaryotic organisms. ACTA ACUST UNITED AC 2015; 71:2526-42. [PMID: 26627660 DOI: 10.1107/s1399004715019641] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/16/2015] [Indexed: 11/10/2022]
Abstract
Riboflavin kinases (RFKs) catalyse the phosphorylation of riboflavin to produce FMN. In most bacteria this activity is catalysed by the C-terminal module of a bifunctional enzyme, FAD synthetase (FADS), which also catalyses the transformation of FMN into FAD through its N-terminal FMN adenylyltransferase (FMNAT) module. The RFK module of FADS is a homologue of eukaryotic monofunctional RFKs, while the FMNAT module lacks homologyto eukaryotic enzymes involved in FAD production. Previously, the crystal structure of Corynebacterium ammoniagenes FADS (CaFADS) was determined in its apo form. This structure predicted a dimer-of-trimers organization with the catalytic sites of two modules of neighbouring protomers approaching each other, leading to a hypothesis about the possibility of FMN channelling in the oligomeric protein. Here, two crystal structures of the individually expressed RFK module of CaFADS in complex with the products of the reaction, FMN and ADP, are presented. Structures are complemented with computational simulations, binding studies and kinetic characterization. Binding of ligands triggers dramatic structural changes in the RFK module, which affect large portions of the protein. Substrate inhibition and molecular-dynamics simulations allowed the conformational changes that take place along the RFK catalytic cycle to be established. The influence of these conformational changes in the FMNAT module is also discussed in the context of the full-length CaFADS protomer and the quaternary organization.
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Affiliation(s)
- Beatriz Herguedas
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, and Instituto de Biocomputación y Física de Sistemas Complejos (Joint Unit BIFI-IQFR), Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Isaias Lans
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, and Instituto de Biocomputación y Física de Sistemas Complejos (Joint Unit BIFI-IQFR), Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - María Sebastián
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, and Instituto de Biocomputación y Física de Sistemas Complejos (Joint Unit BIFI-IQFR), Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Juan A Hermoso
- GCMBE - Instituto Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Marta Martínez-Júlvez
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, and Instituto de Biocomputación y Física de Sistemas Complejos (Joint Unit BIFI-IQFR), Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, and Instituto de Biocomputación y Física de Sistemas Complejos (Joint Unit BIFI-IQFR), Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
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Serrano A, Sebastián M, Arilla-Luna S, Baquedano S, Pallarés MC, Lostao A, Herguedas B, Velázquez-Campoy A, Martínez-Júlvez M, Medina M. Quaternary organization in a bifunctional prokaryotic FAD synthetase: Involvement of an arginine at its adenylyltransferase module on the riboflavin kinase activity. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:897-906. [DOI: 10.1016/j.bbapap.2015.03.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 03/11/2015] [Accepted: 03/15/2015] [Indexed: 01/14/2023]
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Mahalingam R, Peng HP, Yang AS. Prediction of FMN-binding residues with three-dimensional probability distributions of interacting atoms on protein surfaces. J Theor Biol 2013; 343:154-61. [PMID: 24211525 DOI: 10.1016/j.jtbi.2013.10.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 10/29/2013] [Accepted: 10/30/2013] [Indexed: 12/12/2022]
Abstract
Flavin mono-nucleotide (FMN) is a cofactor which is involved in many biological reactions. The insights on protein-FMN interactions aid the protein functional annotation and also facilitate in drug design. In this study, we have established a new method, making use of an encoding scheme of the three-dimensional probability density maps that describe the distributions of 40 non-covalent interacting atom types around protein surfaces, to predict FMN-binding sites on protein surfaces. One machine learning model was trained for each of the 30 protein atom types to predict tentative FMN-binding sites on protein structures. The method's capability was evaluated by five-fold cross-validation on a dataset containing 81 non-redundant FMN-binding protein structures and further tested on independent datasets of 30 and 15 non-redundant protein structures respectively. These predictions achieved an accuracy of 0.94, 0.94 and 0.96 with the Matthews correlation coefficient (MCC) of 0.53, 0.53 and 0.65 respectively for the three protein structure sets. The prediction capability is superior to the existing method. This is the first structure-based approach that does not rely on evolutionary information for predicting FMN-interacting residues. The webserver for the prediction is available at http://ismblab.genomics.sinica.edu.tw/.
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Affiliation(s)
- Rajasekaran Mahalingam
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei 115, Taiwan.
| | - Hung-Pin Peng
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei 115, Taiwan; Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan; Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - An-Suei Yang
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei 115, Taiwan.
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Xuan Z, An Y, Yang D, Wang S, Xu Q, Yuan S. Exploration of the protection of riboflavin laurate on oral mucositis induced by chemotherapy or radiotherapy at the cellular level: what is the leading contributor? Int J Mol Sci 2013; 14:4722-33. [PMID: 23446867 PMCID: PMC3634417 DOI: 10.3390/ijms14034722] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 02/21/2013] [Accepted: 02/22/2013] [Indexed: 01/24/2023] Open
Abstract
Oral or gastrointestinal mucositis is a frequent phenomenon in cancer patients receiving chemotherapy or radiotherapy. In addition, several clinical investigations have demonstrated in recent years that riboflavin laurate has the potential to protect the patients from the disease induced by chemotherapy or radiotherapy. In our studies, it is observed that riboflavin laurate can ameliorate either chemotherapy- or radiotherapy-induced toxicities on Helf cells, and the effect is greater than that of riboflavin. In addition, riboflavin laurate is able to transport through the Caco-2 cell monolayer as the prototype, indicating the protective effects may be produced by the prototype of riboflavin laurate, rather than simply by the released riboflavin.
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Affiliation(s)
- Zixue Xuan
- School of Graduate Studies, Anhui Medical University, Hefei 230032, Anhui, China; E-Mail: (Z.X.)
- Department of Pharmacology and Toxicology, Beijing Institute of Radiation Medicine, Beijing 100850, China; E-Mails: (Y.A.); (D.Y.); (S.W.); (Q.X.)
| | - Yinghong An
- Department of Pharmacology and Toxicology, Beijing Institute of Radiation Medicine, Beijing 100850, China; E-Mails: (Y.A.); (D.Y.); (S.W.); (Q.X.)
| | - Dexuan Yang
- Department of Pharmacology and Toxicology, Beijing Institute of Radiation Medicine, Beijing 100850, China; E-Mails: (Y.A.); (D.Y.); (S.W.); (Q.X.)
| | - Shanshan Wang
- Department of Pharmacology and Toxicology, Beijing Institute of Radiation Medicine, Beijing 100850, China; E-Mails: (Y.A.); (D.Y.); (S.W.); (Q.X.)
| | - Qishou Xu
- Department of Pharmacology and Toxicology, Beijing Institute of Radiation Medicine, Beijing 100850, China; E-Mails: (Y.A.); (D.Y.); (S.W.); (Q.X.)
| | - Shoujun Yuan
- Department of Pharmacology and Toxicology, Beijing Institute of Radiation Medicine, Beijing 100850, China; E-Mails: (Y.A.); (D.Y.); (S.W.); (Q.X.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +86-10-6693-0271
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Marcuello C, Arilla-Luna S, Medina M, Lostao A. Detection of a quaternary organization into dimer of trimers of Corynebacterium ammoniagenes FAD synthetase at the single-molecule level and at the in cell level. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:665-76. [PMID: 23291469 DOI: 10.1016/j.bbapap.2012.12.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Revised: 12/11/2012] [Accepted: 12/21/2012] [Indexed: 01/24/2023]
Abstract
Biochemical characterization of Corynebacterium ammoniagenes FADS (CaFADS) pointed to certain confusion about the stoichiometry of this bifunctional enzyme involved in the production of FMN and FAD in prokaryotes. Resolution of its crystal structure suggested that it might produce a hexameric ensemble formed by a dimer of trimers. We used atomic force microscopy (AFM) to direct imaging single CaFADS molecules bound to mica surfaces, while preserving their catalytic properties. AFM allowed solving individual CaFADS monomers, for which it was even possible to distinguish their sub-molecular individual N- and C-terminal modules in the elongated enzyme. Differences between monomers and higher stoichiometries were easily imaged, enabling us to detect formation of oligomeric species induced by ligand binding. The presence of ATP:Mg(2+) particularly induced the appearance of the hexameric assembly whose mean molecular volume resembles the crystallographic dimer of trimers. Finally, the AFM results are confirmed in cross-linking solution, and the presence of such oligomeric CaFADS species detected in cell extracts. All these results are consistent with the formation of a dimer of trimers during the enzyme catalytic cycle that might bear biological relevance.
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Affiliation(s)
- Carlos Marcuello
- Laboratorio de Microscopías Avanzadas (LMA), Instituto de Nanociencia de Aragón (INA), Universidad de Zaragoza, Spain
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