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Iacobucci I, Monaco V, Hovasse A, Dupouy B, Keumoe R, Cichocki B, Elhabiri M, Meunier B, Strub JM, Monti M, Cianférani S, Blandin SA, Schaeffer-Reiss C, Davioud-Charvet E. Proteomic Profiling of Antimalarial Plasmodione Using 3-Benz(o)ylmenadione Affinity-Based Probes. Chembiochem 2024; 25:e202400187. [PMID: 38639212 DOI: 10.1002/cbic.202400187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/20/2024]
Abstract
Understanding the mechanisms of drug action in malarial parasites is crucial for the development of new drugs to combat infection and to counteract drug resistance. Proteomics is a widely used approach to study host-pathogen systems and to identify drug protein targets. Plasmodione is an antiplasmodial early-lead drug exerting potent activities against young asexual and sexual blood stages in vitro with low toxicity to host cells. To elucidate its molecular mechanisms, an affinity-based protein profiling (AfBPP) approach was applied to yeast and P. falciparum proteomes. New (pro-) AfBPP probes based on the 3-benz(o)yl-6-fluoro-menadione scaffold were synthesized. With optimized conditions of both photoaffinity labeling and click reaction steps, the AfBPP protocol was then applied to a yeast proteome, yielding 11 putative drug-protein targets. Among these, we found four proteins associated with oxidoreductase activities, the hypothesized type of targets for plasmodione and its metabolites, and other proteins associated with the mitochondria. In Plasmodium parasites, the MS analysis revealed 44 potential plasmodione targets that need to be validated in further studies. Finally, the localization of a 3-benzyl-6-fluoromenadione AfBPP probe was studied in the subcellular structures of the parasite at the trophozoite stage.
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Affiliation(s)
- Ilaria Iacobucci
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic & Medicinal Chemistry, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, 25, rue Becquerel, F-67087, Strasbourg, France
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, F-67087, Strasbourg, France
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant' Angelo, Via Cintia 26, I-80126, Napoli, Italy
| | - Vittoria Monaco
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic & Medicinal Chemistry, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, 25, rue Becquerel, F-67087, Strasbourg, France
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, F-67087, Strasbourg, France
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant' Angelo, Via Cintia 26, I-80126, Napoli, Italy
| | - Agnès Hovasse
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, F-67087, Strasbourg, France
| | - Baptiste Dupouy
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic & Medicinal Chemistry, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, 25, rue Becquerel, F-67087, Strasbourg, France
| | - Rodrigue Keumoe
- Institut de Biologie Moléculaire et Cellulaire, INSERM U1257 - CNRS UPR9022 - Université de Strasbourg, 2, Allée Konrad Roentgen, -67084, Strasbourg, France
| | - Bogdan Cichocki
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic & Medicinal Chemistry, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, 25, rue Becquerel, F-67087, Strasbourg, France
| | - Mourad Elhabiri
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic & Medicinal Chemistry, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, 25, rue Becquerel, F-67087, Strasbourg, France
| | - Brigitte Meunier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-Sur-Yvette Cedex, France
| | - Jean-Marc Strub
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, F-67087, Strasbourg, France
| | - Maria Monti
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant' Angelo, Via Cintia 26, I-80126, Napoli, Italy
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, F-67087, Strasbourg, France
| | - Stéphanie A Blandin
- Institut de Biologie Moléculaire et Cellulaire, INSERM U1257 - CNRS UPR9022 - Université de Strasbourg, 2, Allée Konrad Roentgen, -67084, Strasbourg, France
| | - Christine Schaeffer-Reiss
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, F-67087, Strasbourg, France
| | - Elisabeth Davioud-Charvet
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic & Medicinal Chemistry, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, 25, rue Becquerel, F-67087, Strasbourg, France
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2
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Nowrouzi B, Torres-Montero P, Kerkhoven EJ, Martínez JL, Rios-Solis L. Rewiring Saccharomyces cerevisiae metabolism for optimised Taxol® precursors production. Metab Eng Commun 2024; 18:e00229. [PMID: 38098801 PMCID: PMC10716015 DOI: 10.1016/j.mec.2023.e00229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/09/2023] [Accepted: 11/04/2023] [Indexed: 12/17/2023] Open
Abstract
Saccharomyces cerevisiae has been conveniently used to produce Taxol® anticancer drug early precursors. However, the harmful impact of oxidative stress by the first cytochrome P450-reductase enzymes (CYP725A4-POR) of Taxol® pathway has hampered sufficient progress in yeast. Here, we evolved an oxidative stress-resistant yeast strain with three-fold higher titre of their substrate, taxadiene. The performance of the evolved and parent strains were then evaluated in galactose-limited chemostats before and under the oxidative stress by an oxidising agent. The interaction of evolution and oxidative stress was comprehensively evaluated through transcriptomics and metabolite profiles integration in yeast enzyme-constrained genome scale model. Overall, the evolved strain showed improved respiration, reduced overflow metabolites production and oxidative stress re-induction tolerance. The cross-protection mechanism also potentially contributed to better heme, flavin and NADPH availability, essential for CYP725A4 and POR optimal activity in yeast. The results imply that the evolved strain is a robust cell factory for future efforts towards Taxol© production.
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Affiliation(s)
- Behnaz Nowrouzi
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
- Centre for Engineering Biology, The University of Edinburgh, Edinburgh, EH9 3BD, United Kingdom
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Pablo Torres-Montero
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Eduard J. Kerkhoven
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- SciLifeLab, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - José L. Martínez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
- Centre for Engineering Biology, The University of Edinburgh, Edinburgh, EH9 3BD, United Kingdom
- School of Natural and Environmental Sciences, Molecular Biology and Biotechnology Division, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
- Department of Biochemical Engineering, The Advanced Centre for Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, United Kingdom
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Kato T, Azegami J, Kano M, El Enshasy HA, Park EY. Induction of Oxidative Stress in Sirtuin Gene-Disrupted Ashbya gossypii Mutants Overproducing Riboflavin. Mol Biotechnol 2024; 66:1144-1153. [PMID: 38184809 DOI: 10.1007/s12033-023-01012-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/27/2023] [Indexed: 01/08/2024]
Abstract
AgHST1 and AgHST3 genes encode sirtuins that are NAD+-dependent protein deacetylases. According to previous reports, their disruption leads to the overproduction of riboflavin in Ashbya gossypii. In this study, we investigated the potential causes of riboflavin overproduction in the AgHST1Δ and AgHST3Δ mutant strains of A. gossypii. The generation of reactive oxygen species was increasd in the mutants compared to in WT. Additionally, membrane potential was lower in the mutants than in WT. The NAD+/NADH ratio in AgHST1Δ mutant strain was lower than that in WT; however, the NAD+/NADH ratio in AgHST3Δ was slightly higher than that in WT. AgHST1Δ mutant strain was more sensitive to high temperatures and hydroxyurea treatment than WT or AgHST3Δ. Expression of the AgGLR1 gene, encoding glutathione reductase, was substantially decreased in AgHST1Δ and AgHST3Δ mutant strains. The addition of N-acetyl-L-cysteine, an antioxidant, suppressed the riboflavin production in the mutants, indicating that it was induced by oxidative stress. Therefore, high oxidative stress resulting from the disruption of sirtuin genes induces riboflavin overproduction in AgHST1Δ and AgHST3Δ mutant strains. This study established that oxidative stress is an important trigger for riboflavin overproduction in sirtuin gene-disrupted mutant strains of A. gossypii and helped to elucidate the mechanism of riboflavin production in A. gossypii.
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Affiliation(s)
- Tatsuya Kato
- Molecular and Biological Function Research Core, Research Institute of Green Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan.
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan.
- Department of Applied Life Science, Faculty of Agriculture, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan.
| | - Junya Azegami
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan
| | - Mai Kano
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan
| | - Hesham A El Enshasy
- Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia (UTM), 81310 UTM, Johor Bahru, Malaysia
- City of Scientific Research and Technology Applications, New Borg Al Arab, Alexandria, Egypt
| | - Enoch Y Park
- Molecular and Biological Function Research Core, Research Institute of Green Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan
- Department of Applied Life Science, Faculty of Agriculture, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan
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Rivero M, Boneta S, Novo N, Velázquez-Campoy A, Polo V, Medina M. Riboflavin kinase and pyridoxine 5′-phosphate oxidase complex formation envisages transient interactions for FMN cofactor delivery. Front Mol Biosci 2023; 10:1167348. [PMID: 37056721 PMCID: PMC10086132 DOI: 10.3389/fmolb.2023.1167348] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Enzymes catalysing sequential reactions have developed different mechanisms to control the transport and flux of reactants and intermediates along metabolic pathways, which usually involve direct transfer of metabolites from an enzyme to the next one in a cascade reaction. Despite the fact that metabolite or substrate channelling has been widely studied for reactant molecules, such information is seldom available for cofactors in general, and for flavins in particular. Flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) act as cofactors in flavoproteins and flavoenzymes involved in a wide range of physiologically relevant processes in all type of organisms. Homo sapiens riboflavin kinase (RFK) catalyses the biosynthesis of the flavin mononucleotide cofactor, and might directly interplay with its flavin client apo-proteins prior to the cofactor transfer. Non-etheless, none of such complexes has been characterized at molecular or atomic level so far. Here, we particularly evaluate the interaction of riboflavin kinase with one of its potential FMN clients, pyridoxine-5′-phosphate oxidase (PNPOx). The interaction capacity of both proteins is assessed by using isothermal titration calorimetry, a methodology that allows to determine dissociation constants for interaction in the micromolar range (in agreement with the expected transient nature of the interaction). Moreover, we show that; i) both proteins become thermally stabilized upon mutual interaction, ii) the tightly bound FMN product can be transferred from RFK to the apo-form of PNPOx producing an efficient enzyme, and iii) the presence of the apo-form of PNPOx slightly enhances RFK catalytic efficiency. Finally, we also show a computational study to predict likely RFK-PNPOx binding modes that can envisage coupling between the FMN binding cavities of both proteins for the potential transfer of FMN.
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Affiliation(s)
- Maribel Rivero
- 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), Universidad de Zaragoza, Zaragoza, Spain
| | - Sergio Boneta
- 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), Universidad de Zaragoza, Zaragoza, Spain
| | - Nerea Novo
- 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), Universidad de Zaragoza, Zaragoza, Spain
| | - 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), Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
- Group of Biochemistry, Biophysics and Computational Biology “GBsC” (BIFI, Unizar) Joint Unit to CSIC, Zaragoza, Spain
| | - Victor Polo
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain
- Departamento de Química Física, 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), Universidad de Zaragoza, Zaragoza, Spain
- Group of Biochemistry, Biophysics and Computational Biology “GBsC” (BIFI, Unizar) Joint Unit to CSIC, Zaragoza, Spain
- *Correspondence: Milagros Medina,
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Minjárez-Sáenz M, Martínez-Júlvez M, Yruela I, Medina M. Mining the Flavoproteome of Brucella ovis, the Brucellosis Causing Agent in Ovis aries. Microbiol Spectr 2022; 10:e0229421. [PMID: 35315701 PMCID: PMC9045290 DOI: 10.1128/spectrum.02294-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/19/2022] [Indexed: 11/20/2022] Open
Abstract
Flavoproteins are a diverse class of proteins that are mostly enzymes and contain as cofactors flavin mononucleotide (FMN) and/or flavin adenine dinucleotide (FAD), which enable them to participate in a wide range of physiological reactions. We have compiled 78 potential proteins building the flavoproteome of Brucella ovis (B. ovis), the causative agent of ovine brucellosis. The curated list of flavoproteins here reported is based on (i) the analysis of sequence, structure and function of homologous proteins, and their classification according to their structural domains, clans, and expected enzymatic functions; (ii) the constructed phylogenetic trees of enzyme functional classes using 19 Brucella strains and 26 pathogenic and/or biotechnological relevant alphaproteobacteria together with B. ovis; and (iii) the evaluation of the genetic context for each entry. Candidates account for ∼2.7% of the B. ovis proteome, and 75% of them use FAD as cofactor. Only 55% of these flavoproteins belong to the core proteome of Brucella and contribute to B. ovis processes involved in maintenance activities, survival and response to stress, virulence, and/or infectivity. Several of the predicted flavoproteins are highly divergent in Brucella genus from revised proteins and for them it is difficult to envisage a clear function. This might indicate modified catalytic activities or even divergent processes and mechanisms still not identified. We have also detected the lack of some functional flavoenzymes in B. ovis, which might contribute to it being nonzoonotic. Finally, potentiality of B. ovis flavoproteome as the source of antimicrobial targets or biocatalyst is discussed. IMPORTANCE Some microorganisms depend heavily on flavin-dependent activities, but others maintain them at a minimum. Knowledge about flavoprotein content and functions in different microorganisms will help to identify their metabolic requirements, as well as to benefit either industry or health. Currently, most flavoproteins from the sheep pathogen Brucella ovis are only automatically annotated in databases, and only two have been experimentally studied. Indeed, certain homologues with unknown function are not characterized, and they might relate to still not identified mechanisms or processes. Our research has identified 78 members that comprise its flavoproteome, 76 of them flavoenzymes, which mainly relate to bacteria survival, virulence, and/or infectivity. The list of flavoproteins here presented allows us to better understand the peculiarities of Brucella ovis and can be applied as a tool to search for candidates as new biocatalyst or antimicrobial targets.
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Affiliation(s)
- Martha Minjárez-Sáenz
- 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), 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), Universidad de Zaragoza, Zaragoza, Spain
- Group of Biochemistry, Biophysics and Computational Biology “GBsC” (BIFI, Unizar) Joint Unit to CSIC, Zaragoza, Spain
| | - Inmaculada Yruela
- Estación Experimental de Aula Dei, CSIC, Zaragoza, Spain
- Group of Biochemistry, Biophysics and Computational Biology “GBsC” (BIFI, Unizar) Joint Unit to CSIC, 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), Universidad de Zaragoza, Zaragoza, Spain
- Group of Biochemistry, Biophysics and Computational Biology “GBsC” (BIFI, Unizar) Joint Unit to CSIC, Zaragoza, Spain
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Palma M, Mondo S, Pereira M, Vieira É, Grigoriev IV, Sá-Correia I. Genome Sequence and Analysis of the Flavinogenic Yeast Candida membranifaciens IST 626. J Fungi (Basel) 2022; 8:jof8030254. [PMID: 35330255 PMCID: PMC8955749 DOI: 10.3390/jof8030254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/26/2022] [Accepted: 02/27/2022] [Indexed: 02/04/2023] Open
Abstract
The ascomycetous yeast Candida membranifaciens has been isolated from diverse habitats, including humans, insects, and environmental sources, exhibiting a remarkable ability to use different carbon sources that include pentoses, melibiose, and inulin. In this study, we isolated four C. membranifaciens strains from soil and investigated their potential to overproduce riboflavin. C. membranifaciens IST 626 was found to produce the highest concentrations of riboflavin. The volumetric production of this vitamin was higher when C. membranifaciens IST 626 cells were cultured in a commercial medium without iron and when xylose was the available carbon source compared to the same basal medium with glucose. Supplementation of the growth medium with 2 g/L glycine favored the metabolization of xylose, leading to biomass increase and consequent enhancement of riboflavin volumetric production that reached 120 mg/L after 216 h of cultivation. To gain new insights into the molecular basis of riboflavin production and carbon source utilization in this species, the first annotated genome sequence of C. membranifaciens is reported in this article, as well as the result of a comparative genomic analysis with other relevant yeast species. A total of 5619 genes were predicted to be present in C. membranifaciens IST 626 genome sequence (11.5 Mbp). Among them are genes involved in riboflavin biosynthesis, iron homeostasis, and sugar uptake and metabolism. This work put forward C. membranifaciens IST 626 as a riboflavin overproducer and provides valuable molecular data for future development of superior producing strains capable of using the wide range of carbon sources, which is a characteristic trait of the species.
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Affiliation(s)
- Margarida Palma
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; (M.P.); (É.V.); (I.S.-C.)
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- Correspondence:
| | - Stephen Mondo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.M.); (I.V.G.)
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Mariana Pereira
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; (M.P.); (É.V.); (I.S.-C.)
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Érica Vieira
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; (M.P.); (É.V.); (I.S.-C.)
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.M.); (I.V.G.)
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; (M.P.); (É.V.); (I.S.-C.)
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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Lee M, Drenth J, Trajkovic M, de Jong RM, Fraaije MW. Introducing an Artificial Deazaflavin Cofactor in Escherichia coli and Saccharomyces cerevisiae. ACS Synth Biol 2022; 11:938-952. [PMID: 35044755 PMCID: PMC8859854 DOI: 10.1021/acssynbio.1c00552] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Deazaflavin-dependent
whole-cell conversions in well-studied and
industrially relevant microorganisms such as Escherichia coli and Saccharomyces cerevisiae have high potential
for the biocatalytic production of valuable compounds. The artificial
deazaflavin FOP (FO-5′-phosphate) can functionally substitute
the natural deazaflavin F420 and can be synthesized in
fewer steps, offering a solution to the limited availability of the
latter due to its complex (bio)synthesis. Herein we set out to produce
FOP in vivo as a scalable FOP production method and as a means for
FOP-mediated whole-cell conversions. Heterologous expression of the
riboflavin kinase from Schizosaccharomyces pombe enabled
in vivo phosphorylation of FO, which was supplied by either organic
synthesis ex vivo, or by a coexpressed FO synthase in vivo, producing
FOP in E. coli as well as in S. cerevisiae. Through combined approaches of enzyme engineering as well as optimization
of expression systems and growth media, we further improved the in
vivo FOP production in both organisms. The improved FOP production
yield in E. coli is comparable to the F420 yield of native F420-producing organisms such
as Mycobacterium smegmatis, but the former can be
achieved in a significantly shorter time frame. Our E. coli expression system has an estimated production rate of 0.078 μmol
L–1 h–1 and results in an intracellular
FOP concentration of about 40 μM, which is high enough to support
catalysis. In fact, we demonstrate the successful FOP-mediated whole-cell
conversion of ketoisophorone using E. coli cells.
In S. cerevisiae, in vivo FOP production by SpRFK using supplied FO was improved through media optimization
and enzyme engineering. Through structure-guided enzyme engineering,
a SpRFK variant with 7-fold increased catalytic efficiency
compared to the wild type was discovered. By using this variant in
optimized media conditions, FOP production yield in S. cerevisiae was 20-fold increased compared to the very low initial yield of
0.24 ± 0.04 nmol per g dry biomass. The results show that bacterial
and eukaryotic hosts can be engineered to produce the functional deazaflavin
cofactor mimic FOP.
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Affiliation(s)
- Misun Lee
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Jeroen Drenth
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Milos Trajkovic
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - René M. de Jong
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
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8
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Role of quinone reductases in extracellular redox cycling in lichenized ascomycetes. Fungal Biol 2021; 125:879-885. [PMID: 34649674 DOI: 10.1016/j.funbio.2021.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/25/2021] [Accepted: 06/01/2021] [Indexed: 11/24/2022]
Abstract
Our previous work showed that many lichenized Ascomycetes can generate hydroxyl radicals using quinone-based extracellular redox cycling. During cycling, hydroquinones must be formed and subsequently regenerated from quinones using a quinone reductase (QR). However, we also showed that no simple correlation exists between QR activity and rates of hydroxyl radical formation. To further investigate the role of QR in hydroxyl radical formation, three model lichen species, Leptogium furfuraceum, Lasallia pustulata and Peltigera membranacea were selected for further investigation. All possessed QR activity and could metabolize quinones, and both Leptogium furfuraceum and Lasallia pustulata actively produced hydroxyl radicals. By contrast, P. membranacea produced almost no hydroxyl radicals, and although the lichen readily metabolized quinones, no hydroquinone production was detected. Peltigera had laccase (LAC) activity that was c. 50 times higher than in the other two species, suggesting that LAC rapidly oxidizes the hydroquinones, preventing radical formation deriving from auto-oxidation. It appears that in some lichens hydroxyl radical formation is blocked by the presence of high redox enzyme activity. QR from P. didactyla was studied further and found to display similar properties to the enzyme from free-living fungi, although it possessed an unusually high molecular mass (c. 62 kDa).
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9
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Sedenho GC, Modenez I, Mendes GR, Crespilho FN. The role of extracellular polymeric substance matrix on Saccharomyces cerevisiae bioelectricity. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2021.139080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Kato T, Azegami J, Kano M, El Enshasy HA, Park EY. Effects of sirtuins on the riboflavin production in Ashbya gossypii. Appl Microbiol Biotechnol 2021; 105:7813-7823. [PMID: 34559286 DOI: 10.1007/s00253-021-11595-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 09/08/2021] [Accepted: 09/11/2021] [Indexed: 12/01/2022]
Abstract
This study focuses on sirtuins, which catalyze the reaction of NAD+-dependent protein deacetylase, for riboflavin production in A. gossypii. Nicotinamide, a known inhibitor of sirtuin, made the color of A. gossypii colonies appear a deeper yellow at 5 mM. A. gossypii has 4 sirtuin genes (AgHST1, AgHST2, AgHST3, AgHST4) and these were disrupted to investigate the role of sirtuins in riboflavin production in A. gossypii. AgHST1∆, AgHST3∆, and AgHST4∆ strains were obtained, but AgHST2∆ was not. The AgHST1∆ and AgHST3∆ strains produced approximately 4.3- and 2.9-fold higher amounts of riboflavin than the WT strain. The AgHST3∆ strain showed a lower human sirtuin 6 (SIRT6)-like activity than the WT strain and only in the AgHST3∆ strain was a higher amount of acetylation of histone H3 K9 and K56 (H3K9ac and H3K56ac) observed compared to the WT strain. These results indicate that AgHst3 is SIRT6-like sirtuin in A. gossypii and the activity has an influence on the riboflavin production in A. gossypii. In the presence of 5 mM hydroxyurea and 50 µM camptothecin, which causes DNA damage, especially double-strand DNA breaks, the color of the WT strain colonies turned a deeper yellow. Additionally, hydroxyurea significantly led to the production of approximately 1.5 higher amounts of riboflavin and camptothecin also enhanced the riboflavin production even through the significant difference was not detected. Camptothecin tended to increase the amount of H3K56ac, but the amount of H3K56ac was not increased by hydroxyurea treatment. This study revealed that AgHst1 and AgHst3 are involved in the riboflavin production in A. gossypii through NAD metabolism and the acetylation of H3, respectively. This new finding is a step toward clarifying the role of sirtuins in riboflavin over-production by A. gossypii.Key points• Nicotinamide enhanced the riboflavin production in Ashbya gossypii.• Disruption of AgHST1 or AgHST3 gene also enhanced the riboflavin production in Ashbya gossypii.• Acetylation of H3K56 led to the enhancement of the riboflavin production in Ashbya gossypii.
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Affiliation(s)
- Tatsuya Kato
- Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan. .,Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan. .,Department of Applied Life Science, Faculty of Agriculture, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan.
| | - Junya Azegami
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan
| | - Mai Kano
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan
| | - Hesham A El Enshasy
- Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia (UTM), 81310 UTM, Johor Bahru, Malaysia.,City of Scientific Research and Technology Applications, New Borg Al Arab, Alexandria, Egypt
| | - Enoch Y Park
- Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan.,Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan.,Department of Applied Life Science, Faculty of Agriculture, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan
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11
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Bruni F, Giancaspero TA, Oreb M, Tolomeo M, Leone P, Boles E, Roberti M, Caselle M, Barile M. Subcellular Localization of Fad1p in Saccharomyces cerevisiae: A Choice at Post-Transcriptional Level? Life (Basel) 2021; 11:life11090967. [PMID: 34575116 PMCID: PMC8470081 DOI: 10.3390/life11090967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/06/2021] [Accepted: 09/13/2021] [Indexed: 11/24/2022] Open
Abstract
FAD synthase is the last enzyme in the pathway that converts riboflavin into FAD. In Saccharomyces cerevisiae, the gene encoding for FAD synthase is FAD1, from which a sole protein product (Fad1p) is expected to be generated. In this work, we showed that a natural Fad1p exists in yeast mitochondria and that, in its recombinant form, the protein is able, per se, to both enter mitochondria and to be destined to cytosol. Thus, we propose that FAD1 generates two echoforms—that is, two identical proteins addressed to different subcellular compartments. To shed light on the mechanism underlying the subcellular destination of Fad1p, the 3′ region of FAD1 mRNA was analyzed by 3′RACE experiments, which revealed the existence of (at least) two FAD1 transcripts with different 3′UTRs, the short one being 128 bp and the long one being 759 bp. Bioinformatic analysis on these 3′UTRs allowed us to predict the existence of a cis-acting mitochondrial localization motif, present in both the transcripts and, presumably, involved in protein targeting based on the 3′UTR context. Here, we propose that the long FAD1 transcript might be responsible for the generation of mitochondrial Fad1p echoform.
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Affiliation(s)
- Francesco Bruni
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (F.B.); (T.A.G.); (M.T.); (P.L.); (M.R.)
| | - Teresa Anna Giancaspero
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (F.B.); (T.A.G.); (M.T.); (P.L.); (M.R.)
| | - Mislav Oreb
- Institute of Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; (M.O.); (E.B.)
| | - Maria Tolomeo
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (F.B.); (T.A.G.); (M.T.); (P.L.); (M.R.)
| | - Piero Leone
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (F.B.); (T.A.G.); (M.T.); (P.L.); (M.R.)
| | - Eckhard Boles
- Institute of Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; (M.O.); (E.B.)
| | - Marina Roberti
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (F.B.); (T.A.G.); (M.T.); (P.L.); (M.R.)
| | - Michele Caselle
- Physics Department, University of Turin and INFN, Via P. Giuria 1, 10125 Turin, Italy;
| | - Maria Barile
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (F.B.); (T.A.G.); (M.T.); (P.L.); (M.R.)
- Correspondence: ; Tel.: +39-080-544-3604
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12
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Kato T, Yokomori A, Suzuki R, Azegami J, El Enshasy HA, Park EY. Effects of a proteasome inhibitor on the riboflavin production in Ashbya gossypii. J Appl Microbiol 2021; 132:1176-1184. [PMID: 34496097 DOI: 10.1111/jam.15296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/01/2021] [Accepted: 09/01/2021] [Indexed: 10/20/2022]
Abstract
AIMS Effects of a proteasome inhibitor, MG-132, on the riboflavin production in Ashbya gossypii were investigated to elucidate the relationship of the riboflavin production with flavoprotein homeostasis. METHODS AND RESULTS The addition of MG-132 to the liquid medium reduced the specific riboflavin production by 79% in A. gossypii at 25 μM after 24 h. The addition of the inhibitor also caused the accumulation of reactive oxygen species and ubiquitinated proteins. These results indicated that MG-132 works in A. gossypii without any genetic engineering and reduces riboflavin production. In the presence of 25 μM MG-132, specific NADH dehydrogenase activity was increased by 1.4-fold compared to DMSO, but specific succinate dehydrogenase (SDH) activity was decreased to 52% compared to DMSO. Additionally, the amount of AgSdh1p (ACR052Wp) was also reduced. Specific riboflavin production was reduced to 22% when 20 mM malonate, a SDH inhibitor, was added to the culture medium. The riboflavin production in heterozygous AgSDH1 gene-disrupted mutant (AgSDH1-/+ ) was reduced to 63% compared to that in wild type. CONCLUSIONS MG-132 suppresses the riboflavin production and SDH activity in A. gossypii. SDH is one of the flavoproteins involved in the riboflavin production in A. gossypii. SIGNIFICANCE AND IMPACT OF THE STUDY This study shows that MG-132 has a negative influence on the riboflavin production and SDH activity in A. gossypii and leads to the elucidation of the connection of the riboflavin production with flavoproteins.
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Affiliation(s)
- Tatsuya Kato
- Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan.,Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan.,Department of Applied Life Science, Faculty of Agriculture, Shizuoka University, Shizuoka, Japan
| | - Ami Yokomori
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Riho Suzuki
- Department of Applied Life Science, Faculty of Agriculture, Shizuoka University, Shizuoka, Japan
| | - Junya Azegami
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Hesham A El Enshasy
- Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia (UTM), Johor Bahru, Malaysia.,City of Scientific Research and Technology Applications, New Borg Al Arab, Alexandria, Egypt
| | - Enoch Y Park
- Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan.,Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan.,Department of Applied Life Science, Faculty of Agriculture, Shizuoka University, Shizuoka, Japan
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13
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Fracassetti D, Di Canito A, Bodon R, Messina N, Vigentini I, Foschino R, Tirelli A. Light-struck taste in white wine: Reaction mechanisms, preventive strategies and future perspectives to preserve wine quality. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.04.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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14
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Groth B, Venkatakrishnan P, Lin SJ. NAD + Metabolism, Metabolic Stress, and Infection. Front Mol Biosci 2021; 8:686412. [PMID: 34095234 PMCID: PMC8171187 DOI: 10.3389/fmolb.2021.686412] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/05/2021] [Indexed: 12/26/2022] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+) is an essential metabolite with wide-ranging and significant roles in the cell. Defects in NAD+ metabolism have been associated with many human disorders; it is therefore an emerging therapeutic target. Moreover, NAD+ metabolism is perturbed during colonization by a variety of pathogens, either due to the molecular mechanisms employed by these infectious agents or by the host immune response they trigger. Three main biosynthetic pathways, including the de novo and salvage pathways, contribute to the production of NAD+ with a high degree of conservation from bacteria to humans. De novo biosynthesis, which begins with l-tryptophan in eukaryotes, is also known as the kynurenine pathway. Intermediates of this pathway have various beneficial and deleterious effects on cellular health in different contexts. For example, dysregulation of this pathway is linked to neurotoxicity and oxidative stress. Activation of the de novo pathway is also implicated in various infections and inflammatory signaling. Given the dynamic flexibility and multiple roles of NAD+ intermediates, it is important to understand the interconnections and cross-regulations of NAD+ precursors and associated signaling pathways to understand how cells regulate NAD+ homeostasis in response to various growth conditions. Although regulation of NAD+ homeostasis remains incompletely understood, studies in the genetically tractable budding yeast Saccharomyces cerevisiae may help provide some molecular basis for how NAD+ homeostasis factors contribute to the maintenance and regulation of cellular function and how they are regulated by various nutritional and stress signals. Here we present a brief overview of recent insights and discoveries made with respect to the relationship between NAD+ metabolism and selected human disorders and infections, with a particular focus on the de novo pathway. We also discuss how studies in budding yeast may help elucidate the regulation of NAD+ homeostasis.
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Affiliation(s)
- Benjamin Groth
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, Davis, CA, United States
| | - Padmaja Venkatakrishnan
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, Davis, CA, United States
| | - Su-Ju Lin
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, Davis, CA, United States
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15
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Evers MS, Roullier-Gall C, Morge C, Sparrow C, Gobert A, Alexandre H. Vitamins in wine: Which, what for, and how much? Compr Rev Food Sci Food Saf 2021; 20:2991-3035. [PMID: 33884746 DOI: 10.1111/1541-4337.12743] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/11/2021] [Accepted: 03/01/2021] [Indexed: 12/01/2022]
Abstract
Vitamins are essential compounds to yeasts, and notably in winemaking contexts. Vitamins are involved in numerous yeast metabolic pathways, including those of amino acids, fatty acids, and alcohols, which suggests their notable implication in fermentation courses, as well as in the development of aromatic compounds in wines. Although they are major components in the course of those microbial processes, their significance and impact have not been extensively studied in the context of winemaking and wine products, as most of the studies focusing on the subject in the past decades have relied on relatively insensitive and imprecise analytical methods. Therefore, this review provides an extensive overview of the current knowledge regarding the impacts of vitamins on grape must fermentations, wine-related yeast metabolisms, and requirements, as well as on the profile of wine sensory characteristics. We also highlight the methodologies and techniques developed over time to perform vitamin analysis in wines, and assess the importance of precisely defining the role played by vitamins in winemaking processes, to ensure finer control of the fermentation courses and product characteristics in a highly complex matrix.
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Affiliation(s)
- Marie Sarah Evers
- Institut Universitaire de la Vigne et du Vin Jules Guyot, Université de Bourgogne, Dijon, France.,SAS Sofralab, Magenta, France
| | - Chloé Roullier-Gall
- Institut Universitaire de la Vigne et du Vin Jules Guyot, Université de Bourgogne, Dijon, France
| | | | | | | | - Hervé Alexandre
- Institut Universitaire de la Vigne et du Vin Jules Guyot, Université de Bourgogne, Dijon, France
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16
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Molin M, Logg K, Bodvard K, Peeters K, Forsmark A, Roger F, Jörhov A, Mishra N, Billod JM, Amir S, Andersson M, Eriksson LA, Warringer J, Käll M, Blomberg A. Protein kinase A controls yeast growth in visible light. BMC Biol 2020; 18:168. [PMID: 33198745 PMCID: PMC7667738 DOI: 10.1186/s12915-020-00867-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/09/2020] [Indexed: 01/07/2023] Open
Abstract
Background A wide variety of photosynthetic and non-photosynthetic species sense and respond to light, having developed protective mechanisms to adapt to damaging effects on DNA and proteins. While the biology of UV light-induced damage has been well studied, cellular responses to stress from visible light (400–700 nm) remain poorly understood despite being a regular part of the life cycle of many organisms. Here, we developed a high-throughput method for measuring growth under visible light stress and used it to screen for light sensitivity in the yeast gene deletion collection. Results We found genes involved in HOG pathway signaling, RNA polymerase II transcription, translation, diphthamide modifications of the translational elongation factor eEF2, and the oxidative stress response to be required for light resistance. Reduced nuclear localization of the transcription factor Msn2 and lower glycogen accumulation indicated higher protein kinase A (cAMP-dependent protein kinase, PKA) activity in many light-sensitive gene deletion strains. We therefore used an ectopic fluorescent PKA reporter and mutants with constitutively altered PKA activity to show that repression of PKA is essential for resistance to visible light. Conclusion We conclude that yeast photobiology is multifaceted and that protein kinase A plays a key role in the ability of cells to grow upon visible light exposure. We propose that visible light impacts on the biology and evolution of many non-photosynthetic organisms and have practical implications for how organisms are studied in the laboratory, with or without illumination.
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Affiliation(s)
- Mikael Molin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden. .,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Katarina Logg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.,Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Kristofer Bodvard
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Ken Peeters
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Annabelle Forsmark
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Friederike Roger
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Anna Jörhov
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Neha Mishra
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.,Horizon Discovery, Cambridge, CB25 9TL, UK
| | - Jean-Marc Billod
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.,Bio-Me A/S, Oslo Science Park, Gaustadalléen, 210349, Oslo, Norway
| | - Sabiha Amir
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Mikael Andersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Mikael Käll
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Anders Blomberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
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17
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Abstract
Flavin-dependent enzymes catalyze a wide variety of biological reactions that are important for all types of living organisms. Knowledge gained from studying the chemistry and biological functions of flavins and flavin-dependent enzymes has continuously made significant contributions to the development of the fields of enzymology and metabolism from the 1970s until now. The enzymes have been applied in various applications such as use as biocatalysts in synthetic processes for the chemical and pharmaceutical industries or in the biodetoxification and bioremediation of toxic or unwanted compounds, and as biosensors or biodetection tools for quantifying various agents of interest. Many flavin-dependent enzymes are also prime targets for drug development. Based on their reaction mechanisms, they can be classified into five categories: oxidase, dehydrogenase, monooxygenase, reductase, and redox neutral flavin-dependent enzymes. In this chapter, the general properties of flavin-dependent enzymes and the nature of their chemical reactions are discussed, along with their practical applications.
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18
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Molecular Elucidation of Riboflavin Production and Regulation in Candida albicans, toward a Novel Antifungal Drug Target. mSphere 2020; 5:5/4/e00714-20. [PMID: 32759338 PMCID: PMC7407072 DOI: 10.1128/msphere.00714-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Candida albicans is an important fungal pathogen causing common superficial infections as well as invasive diseases with an extremely high morbidity and mortality. Antifungal therapies are limited in efficiency and availability. In this research, we describe the regulation of riboflavin production in C. albicans. Since riboflavin biosynthesis is essential to this organism, we can appreciate that targeting it would be a promising new strategy to combat these fungal infections. We provide evidence that one particular enzyme in the production process, CaRib1, would be most promising as an antifungal drug target, as it plays a central role in regulation and proves to be essential in a mouse model of systemic infection. Candida albicans is a major cause of fungal infections, both superficial and invasive. The economic costs as well as consequences for patient welfare are substantial. Only a few treatment options are available due to the high resemblance between fungal targets and host molecules, as both are eukaryotes. Riboflavin is a yellow pigment, also termed vitamin B2. Unlike animals, fungi can synthesize this essential component themselves, thereby leading us to appreciate that targeting riboflavin production is a promising novel strategy against fungal infections. Here, we report that the GTP cyclohydrolase encoded by C. albicansRIB1 (CaRIB1) is essential and rate-limiting for production of riboflavin in the fungal pathogen. We confirm the high potential of CaRib1 as an antifungal drug target, as its deletion completely impairs in vivo infectibility by C. albicans in model systems. Furthermore, the stimulating effect of iron deprivation and PKA activation on riboflavin production seems to involve CaRib1 and the upstream transcription factor CaSef1. Gathering insights in the synthesis mechanism of riboflavin in pathogenic fungi, like C. albicans, will allow us to design a novel strategy and specifically target this process to combat fungal infections. IMPORTANCECandida albicans is an important fungal pathogen causing common superficial infections as well as invasive diseases with an extremely high morbidity and mortality. Antifungal therapies are limited in efficiency and availability. In this research, we describe the regulation of riboflavin production in C. albicans. Since riboflavin biosynthesis is essential to this organism, we can appreciate that targeting it would be a promising new strategy to combat these fungal infections. We provide evidence that one particular enzyme in the production process, CaRib1, would be most promising as an antifungal drug target, as it plays a central role in regulation and proves to be essential in a mouse model of systemic infection.
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Schall P, Marutschke L, Grimm B. The Flavoproteome of the Model Plant Arabidopsis thaliana. Int J Mol Sci 2020; 21:ijms21155371. [PMID: 32731628 PMCID: PMC7432721 DOI: 10.3390/ijms21155371] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/22/2020] [Accepted: 07/25/2020] [Indexed: 12/17/2022] Open
Abstract
Flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) are essential cofactors for enzymes, which catalyze a broad spectrum of vital reactions. This paper intends to compile all potential FAD/FMN-binding proteins encoded by the genome of Arabidopsis thaliana. Several computational approaches were applied to group the entire flavoproteome according to (i) different catalytic reactions in enzyme classes, (ii) the localization in subcellular compartments, (iii) different protein families and subclasses, and (iv) their classification to structural properties. Subsequently, the physiological significance of several of the larger flavoprotein families was highlighted. It is conclusive that plants, such as Arabidopsis thaliana, use many flavoenzymes for plant-specific and pivotal metabolic activities during development and for signal transduction pathways in response to biotic and abiotic stress. Thereby, often two up to several homologous genes are found encoding proteins with high protein similarity. It is proposed that these gene families for flavoproteins reflect presumably their need for differential transcriptional control or the expression of similar proteins with modified flavin-binding properties or catalytic activities.
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Tolomeo M, Nisco A, Leone P, Barile M. Development of Novel Experimental Models to Study Flavoproteome Alterations in Human Neuromuscular Diseases: The Effect of Rf Therapy. Int J Mol Sci 2020; 21:ijms21155310. [PMID: 32722651 PMCID: PMC7432027 DOI: 10.3390/ijms21155310] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 02/07/2023] Open
Abstract
Inborn errors of Riboflavin (Rf) transport and metabolism have been recently related to severe human neuromuscular disorders, as resulting in profound alteration of human flavoproteome and, therefore, of cellular bioenergetics. This explains why the interest in studying the “flavin world”, a topic which has not been intensively investigated before, has increased much over the last few years. This also prompts basic questions concerning how Rf transporters and FAD (flavin adenine dinucleotide) -forming enzymes work in humans, and how they can create a coordinated network ensuring the maintenance of intracellular flavoproteome. The concept of a coordinated cellular “flavin network”, introduced long ago studying humans suffering for Multiple Acyl-CoA Dehydrogenase Deficiency (MADD), has been, later on, addressed in model organisms and more recently in cell models. In the frame of the underlying relevance of a correct supply of Rf in humans and of a better understanding of the molecular rationale of Rf therapy in patients, this review wants to deal with theories and existing experimental models in the aim to potentiate possible therapeutic interventions in Rf-related neuromuscular diseases.
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21
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Kato T, Azegami J, Yokomori A, Dohra H, El Enshasy HA, Park EY. Genomic analysis of a riboflavin-overproducing Ashbya gossypii mutant isolated by disparity mutagenesis. BMC Genomics 2020; 21:319. [PMID: 32326906 PMCID: PMC7181572 DOI: 10.1186/s12864-020-6709-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 03/30/2020] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Ashbya gossypii naturally overproduces riboflavin and has been utilized for industrial riboflavin production. To improve riboflavin production, various approaches have been developed. In this study, to investigate the change in metabolism of a riboflavin-overproducing mutant, namely, the W122032 strain (MT strain) that was isolated by disparity mutagenesis, genomic analysis was carried out. RESULTS In the genomic analysis, 33 homozygous and 1377 heterozygous mutations in the coding sequences of the genome of MT strain were detected. Among these heterozygous mutations, the proportion of mutated reads in each gene was different, ranging from 21 to 75%. These results suggest that the MT strain may contain multiple nuclei containing different mutations. We tried to isolate haploid spores from the MT strain to prove its ploidy, but this strain did not sporulate under the conditions tested. Heterozygous mutations detected in genes which are important for sporulation likely contribute to the sporulation deficiency of the MT strain. Homozygous and heterozygous mutations were found in genes encoding enzymes involved in amino acid metabolism, the TCA cycle, purine and pyrimidine nucleotide metabolism and the DNA mismatch repair system. One homozygous mutation in AgILV2 gene encoding acetohydroxyacid synthase, which is also a flavoprotein in mitochondria, was found. Gene ontology (GO) enrichment analysis showed heterozygous mutations in all 22 DNA helicase genes and genes involved in oxidation-reduction process. CONCLUSION This study suggests that oxidative stress and the aging of cells were involved in the riboflavin over-production in A. gossypii riboflavin over-producing mutant and provides new insights into riboflavin production in A. gossypii and the usefulness of disparity mutagenesis for the creation of new types of mutants for metabolic engineering.
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Affiliation(s)
- Tatsuya Kato
- Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan
| | - Junya Azegami
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan
| | - Ami Yokomori
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan
| | - Hideo Dohra
- Instrumental Research Support Office, Research Institute of Green Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan
| | - Hesham A. El Enshasy
- Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia (UTM), 81310 UTM, Johor Bahru, Malaysia
| | - Enoch Y. Park
- Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan
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22
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Anam K, Nasuno R, Takagi H. A Novel Mechanism for Nitrosative Stress Tolerance Dependent on GTP Cyclohydrolase II Activity Involved in Riboflavin Synthesis of Yeast. Sci Rep 2020; 10:6015. [PMID: 32265460 PMCID: PMC7138843 DOI: 10.1038/s41598-020-62890-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 03/20/2020] [Indexed: 11/23/2022] Open
Abstract
The biological functions of nitric oxide (NO) depend on its concentration, and excessive levels of NO induce various harmful situations known as nitrosative stress. Therefore, organisms possess many kinds of strategies to regulate the intracellular NO concentration and/or to detoxify excess NO. Here, we used genetic screening to identify a novel nitrosative stress tolerance gene, RIB1, encoding GTP cyclohydrolase II (GTPCH2), which catalyzes the first step in riboflavin biosynthesis. Our further analyses demonstrated that the GTPCH2 enzymatic activity of Rib1 is essential for RIB1-dependent nitrosative stress tolerance, but that riboflavin itself is not required for this tolerance. Furthermore, the reaction mixture of a recombinant purified Rib1 was shown to quench NO or its derivatives, even though formate or pyrophosphate, which are byproducts of the Rib1 reaction, did not, suggesting that the reaction product of Rib1, 2,5-diamino-6-(5-phospo-d-ribosylamino)-pyrimidin-4(3 H)-one (DARP), scavenges NO or its derivatives. Finally, it was revealed that 2,4,5-triamino-1H-pyrimidin-6-one, which is identical to a pyrimidine moiety of DARP, scavenged NO or its derivatives, suggesting that DARP reacts with N2O3 generated via its pyrimidine moiety.
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Affiliation(s)
- Khairul Anam
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara, 630-0192, Japan.,Research Center for Biotechnology, Indonesian Institute of Sciences, Jl. Raya Bogor KM 46, Cibinong, 16911, Bogor, West Java, Indonesia
| | - Ryo Nasuno
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara, 630-0192, Japan
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara, 630-0192, Japan.
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Chen X, Ji B, Hao X, Li X, Eisele F, Nyström T, Petranovic D. FMN reduces Amyloid-β toxicity in yeast by regulating redox status and cellular metabolism. Nat Commun 2020; 11:867. [PMID: 32054832 PMCID: PMC7018843 DOI: 10.1038/s41467-020-14525-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 01/07/2020] [Indexed: 01/09/2023] Open
Abstract
Alzheimer's disease (AD) is defined by progressive neurodegeneration, with oligomerization and aggregation of amyloid-β peptides (Aβ) playing a pivotal role in its pathogenesis. In recent years, the yeast Saccharomyces cerevisiae has been successfully used to clarify the roles of different human proteins involved in neurodegeneration. Here, we report a genome-wide synthetic genetic interaction array to identify toxicity modifiers of Aβ42, using yeast as the model organism. We find that FMN1, the gene encoding riboflavin kinase, and its metabolic product flavin mononucleotide (FMN) reduce Aβ42 toxicity. Classic experimental analyses combined with RNAseq show the effects of FMN supplementation to include reducing misfolded protein load, altering cellular metabolism, increasing NADH/(NADH + NAD+) and NADPH/(NADPH + NADP+) ratios and increasing resistance to oxidative stress. Additionally, FMN supplementation modifies Htt103QP toxicity and α-synuclein toxicity in the humanized yeast. Our findings offer insights for reducing cytotoxicity of Aβ42, and potentially other misfolded proteins, via FMN-dependent cellular pathways.
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Affiliation(s)
- Xin Chen
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE41296, Gothenburg, Sweden
| | - Boyang Ji
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE41296, Gothenburg, Sweden
| | - Xinxin Hao
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, SE40530, Gothenburg, Sweden
| | - Xiaowei Li
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296, Gothenburg, Sweden
| | - Frederik Eisele
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, SE40530, Gothenburg, Sweden
| | - Thomas Nyström
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, SE40530, Gothenburg, Sweden
| | - Dina Petranovic
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296, Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE41296, Gothenburg, Sweden.
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Moosavi B, Berry EA, Zhu XL, Yang WC, Yang GF. The assembly of succinate dehydrogenase: a key enzyme in bioenergetics. Cell Mol Life Sci 2019; 76:4023-4042. [PMID: 31236625 PMCID: PMC11105593 DOI: 10.1007/s00018-019-03200-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/30/2019] [Accepted: 06/17/2019] [Indexed: 12/12/2022]
Abstract
Succinate dehydrogenase (SDH) also known as complex II or succinate:quinone oxidoreductase is an enzyme involved in both oxidative phosphorylation and tricarboxylic acid cycle; the processes that generate energy. SDH is a multi-subunit enzyme which requires a series of proteins for its proper assembly at several steps. This enzyme has medical significance as there is a broad range of human diseases from cancers to neurodegeneration related to SDH malfunction. Some of these disorders have recently been linked to defective assembly factors, reinvigorating further research in this area. Apart from that this enzyme has agricultural importance as many fungicides have been/will be designed targeting specifically this enzyme in plant fungal pathogens. In addition, we speculate it might be possible to design novel fungicides specifically targeting fungal assembly factors. Considering the medical and agricultural implications of SDH, the aim of this review is an overview of the SDH assembly factors and critical analysis of controversial issues around them.
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Affiliation(s)
- Behrooz Moosavi
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Edward A Berry
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Xiao-Lei Zhu
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Wen-Chao Yang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China.
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25
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Lindahl PA. A comprehensive mechanistic model of iron metabolism in Saccharomyces cerevisiae. Metallomics 2019; 11:1779-1799. [PMID: 31531508 DOI: 10.1039/c9mt00199a] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ironome of budding yeast (circa 2019) consists of approximately 139 proteins and 5 nonproteinaceous species. These proteins were grouped according to location in the cell, type of iron center(s), and cellular function. The resulting 27 groups were used, along with an additional 13 nonprotein components, to develop a mesoscale mechanistic model that describes the import, trafficking, metallation, and regulation of iron within growing yeast cells. The model was designed to be simultaneously mutually autocatalytic and mutually autoinhibitory - a property called autocatinhibitory that should be most realistic for simulating cellular biochemical processes. The model was assessed at the systems' level. General conclusions are presented, including a new perspective on understanding regulatory mechanisms in cellular systems. Some unsettled issues are described. This model, once fully developed, has the potential to mimic the phenotype (at a coarse-grain level) of all iron-related genetic mutations in this simple and well-studied eukaryote.
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Affiliation(s)
- Paul A Lindahl
- Departments of Chemistry and of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-3255, USA.
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26
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Toplak M, Brunner J, Tabib CR, Macheroux P. Closing the gap: yeast electron-transferring flavoprotein links the oxidation of d-lactate and d-α-hydroxyglutarate to energy production via the respiratory chain. FEBS J 2019; 286:3611-3628. [PMID: 31081204 PMCID: PMC6771786 DOI: 10.1111/febs.14924] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/19/2019] [Accepted: 05/10/2019] [Indexed: 01/07/2023]
Abstract
Electron-transferring flavoproteins (ETFs) have been found in all kingdoms of life, mostly assisting in shuttling electrons to the respiratory chain for ATP production. While the human (h) ETF has been studied in great detail, very little is known about the biochemical properties of the homologous protein in the model organism Saccharomyces cerevisiae (yETF). In view of the absence of client dehydrogenases, for example, the acyl-CoA dehydrogenases involved in the β-oxidation of fatty acids, d-lactate dehydrogenase 2 (Dld2) appeared to be the only relevant enzyme that is serviced by yETF for electron transfer to the mitochondrial electron transport chain. However, this hypothesis was never tested experimentally. Here, we report the biochemical properties of yETF and Dld2 as well as the electron transfer reaction between the two proteins. Our study revealed that Dld2 oxidizes d-α-hydroxyglutarate more efficiently than d-lactate exhibiting kcatapp /KMapp values of 1200 ± 300 m-1 ·s-1 and 11 ± 2 m-1 ·s-1 , respectively. As expected, substrate-reduced Dld2 very slowly reacted with oxygen or the artificial electron acceptor 2,6-dichlorophenol indophenol. However, photoreduced Dld2 was rapidly reoxidized by oxygen, suggesting that the reaction products, that is, α-ketoglutarate and pyruvate, 'lock' the reduced enzyme in an unreactive state. Interestingly, however, we could demonstrate that substrate-reduced Dld2 rapidly transfers electrons to yETF. Therefore, we conclude that the formation of a product-reduced Dld2 complex suppresses electron transfer to dioxygen but favors the rapid reduction in yETF, thus preventing the loss of electrons and the generation of reactive oxygen species.
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Affiliation(s)
- Marina Toplak
- Institute of BiochemistryGraz University of TechnologyAustria
| | - Julia Brunner
- Institute of BiochemistryGraz University of TechnologyAustria
| | | | - Peter Macheroux
- Institute of BiochemistryGraz University of TechnologyAustria
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27
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Integrated transcriptomic and proteomic analysis of the ethanol stress response in Saccharomyces cerevisiae Sc131. J Proteomics 2019; 203:103377. [DOI: 10.1016/j.jprot.2019.103377] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 04/12/2019] [Accepted: 05/12/2019] [Indexed: 12/29/2022]
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28
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Koch K, Strandback E, Jha S, Richter G, Bourgeois B, Madl T, Macheroux P. Oxidative stress-induced structural changes in the microtubule-associated flavoenzyme Irc15p from Saccharomyces cerevisiae. Protein Sci 2019; 28:176-190. [PMID: 30267443 PMCID: PMC6296175 DOI: 10.1002/pro.3517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 11/07/2022]
Abstract
The genome of the yeast Saccharomyces cerevisiae encodes a canonical lipoamide dehydrogenase (Lpd1p) as part of the pyruvate dehydrogenase complex and a highly similar protein termed Irc15p (increased recombination centers 15). In contrast to Lpd1p, Irc15p lacks a pair of redox active cysteine residues required for the reduction of lipoamide and thus it is very unlikely that Irc15p performs a similar dithiol-disulfide exchange reaction as reported for lipoamide dehydrogenases. We expressed IRC15 in Escherichia coli and purified the produced protein to conduct a detailed biochemical characterization. Here, we show that Irc15p is a dimeric protein with one FAD per protomer. Photoreduction of the protein generates the fully reduced hydroquinone without the occurrence of a flavin semiquinone radical. Similarly, reduction with NADH or NADPH yields the flavin hydroquinone without the occurrence of intermediates as observed for lipoamide dehydrogenase. The redox potential of Irc15p was -313 ± 1 mV and is thus similar to lipoamide dehydrogenase. Reduced Irc15p is oxidized by several artificial electron acceptors such as potassium ferricyanide, 2,6-dichlorophenol-indophenol, 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide, and menadione. However, disulfides such as cystine, glutathione, and lipoamide were unable to react with reduced Irc15p. Limited proteolysis and SAXS-measurements revealed that the NADH-dependent formation of hydrogen peroxide caused a substantial structural change in the dimeric protein. Therefore, we hypothesize that Irc15p undergoes a conformational change in the presence of elevated levels of hydrogen peroxide, which is a putative biomarker of oxidative stress. This conformational change may in turn modulate the interaction of Irc15p with other key players involved in regulating microtubule dynamics.
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Affiliation(s)
- Karin Koch
- Institute of BiochemistryGraz University of TechnologyGrazAustria
| | | | - Shalinee Jha
- Institute of BiochemistryGraz University of TechnologyGrazAustria
| | - Gesa Richter
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and BiochemistryMedical University of GrazGrazAustria
| | - Benjamin Bourgeois
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and BiochemistryMedical University of GrazGrazAustria
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and BiochemistryMedical University of GrazGrazAustria
- BioTechMed‐GrazGrazAustria
| | - Peter Macheroux
- Institute of BiochemistryGraz University of TechnologyGrazAustria
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29
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Autofluorescence of yeast Saccharomyces cerevisiae cells caused by glucose metabolism products and its methodological implications. J Microbiol Methods 2018; 146:55-60. [DOI: 10.1016/j.mimet.2018.01.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 01/26/2018] [Accepted: 01/26/2018] [Indexed: 11/23/2022]
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30
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Decreased aluminium tolerance in the growth of Saccharomyces cerevisiae with SSO2 gene disruption. Biometals 2018; 31:203-215. [PMID: 29383568 DOI: 10.1007/s10534-017-0069-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 11/20/2017] [Indexed: 01/06/2023]
Abstract
Aluminium ions inhibit growth of the budding yeast Saccharomyces cerevisiae. Disruption of the SSO2 gene increased the susceptibility to aluminium. Sso2p belongs to the soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE) family. SSO2 has one paralogue, SSO1, which encodes Sso1p. The SNARE complex containing Sso1/2p plays a role in the recognition of plasma membrane targeted vesicle transport. The susceptibility to aluminium stress was not increased in the Δsso1 strain. The phenotype of aluminium ion influx between the wild-type and Δsso2 strains was not different, suggesting that Sso2p was involved in the elimination of cellular aluminium. However, the cellular lipid constitution of Δsso2 was richer in unsaturated fatty acids than the wild type, indicating that Sso2p is associated with lipid homeostasis of the plasma membrane. Aluminium treatment increased the production of reactive oxygen species (ROS) during proliferation. ROS production was increased in the Δsso2 strain after 3 h of aluminium treatment compared with the wild type. These results suggested that Sso2p plays a role in maintaining the lipid composition of the plasma membrane and the increase in unsaturated fatty acids amplified the production of ROS in the acute phase of aluminium stress. ROS derived from aluminium stress inhibited growth and resulted in the susceptibility of the Δsso2 strain.
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31
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Dietl AM, Meir Z, Shadkchan Y, Osherov N, Haas H. Riboflavin and pantothenic acid biosynthesis are crucial for iron homeostasis and virulence in the pathogenic mold Aspergillus fumigatus. Virulence 2018; 9:1036-1049. [PMID: 30052132 PMCID: PMC6068542 DOI: 10.1080/21505594.2018.1482181] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/22/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Aspergillus fumigatus is the most prevalent airborne fungal pathogen, causing invasive fungal infections mainly in immunosuppressed individuals. Death rates from invasive aspergillosis remain high because of limited treatment options and increasing antifungal resistance. The aim of this study was to identify key fungal-specific genes participating in vitamin B biosynthesis in A. fumigatus. Because these genes are absent in humans they can serve as possible novel targets for antifungal drug development. METHODS By sequence homology we identified, deleted and analysed four key A. fumigatus genes (riboB, panA, pyroA, thiB) involved respectively in the biosynthesis of riboflavin (vitamin B2), pantothenic acid (vitamin B5), pyridoxine (vitamin B6) and thiamine (vitamin B1). RESULTS Deletion of riboB, panA, pyroA or thiB resulted in respective vitamin auxotrophy. Lack of riboflavin and pantothenic acid biosynthesis perturbed many cellular processes including iron homeostasis. Virulence in murine pulmonary and systemic models of infection was severely attenuated following deletion of riboB and panA, strongly reduced after pyroA deletion and weakly attenuated after thiB deletion. CONCLUSIONS This study reveals the biosynthetic pathways of the vitamins riboflavin and pantothenic acid as attractive targets for novel antifungal therapy. Moreover, the virulence studies with auxotrophic mutants serve to identify the availability of nutrients to pathogens in host niches. ABBREVIATIONS BPS: bathophenanthrolinedisulfonate; BSA: bovine serum albumin; CFU: colony forming unit; -Fe: iron starvation; +Fe: iron sufficiency; hFe: high iron; NRPSs: nonribosomal peptide synthetases; PKSs: polyketide synthaseses; wt: wild type.
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Affiliation(s)
- Anna-Maria Dietl
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Zohar Meir
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine Ramat-Aviv, Tel-Aviv, Israel
| | - Yona Shadkchan
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine Ramat-Aviv, Tel-Aviv, Israel
| | - Nir Osherov
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine Ramat-Aviv, Tel-Aviv, Israel
| | - Hubertus Haas
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
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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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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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SLC25 Family Member Genetic Interactions Identify a Role for HEM25 in Yeast Electron Transport Chain Stability. G3-GENES GENOMES GENETICS 2017; 7:1861-1873. [PMID: 28404662 PMCID: PMC5473764 DOI: 10.1534/g3.117.041194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The SLC25 family member SLC25A38 (Hem25 in yeast) was recently identified as a mitochondrial glycine transporter that provides substrate to initiate heme/hemoglobin synthesis. Mutations in the human SLC25A38 gene cause congenital sideroblastic anemia. The full extent to which SLC25 family members coregulate heme synthesis with other mitochondrial functions is not clear. In this study, we surveyed 29 nonessential SLC25 family members in Saccharomyces cerevisiae for their ability to support growth in the presence and absence of HEM25. Six SLC25 family members were identified that were required for growth or for heme synthesis in cells lacking Hem25 function. Importantly, we determined that loss of function of the SLC25 family member Flx1, which imports FAD into mitochondria, together with loss of function of Hem25, resulted in inability to grow on media that required yeast cells to supply energy using mitochondrial respiration. We report that specific components of complexes of the electron transport chain are decreased in the absence of Flx1 and Hem25 function. In addition, we show that mitochondria from flx1Δ hem25Δ cells contain uncharacterized Cox2-containing high molecular weight aggregates. The functions of Flx1 and Hem25 provide a facile explanation for the decrease in heme level, and in specific electron transport chain complex components.
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The role of flavin-containing enzymes in mitochondrial membrane hyperpolarization and ROS production in respiring Saccharomyces cerevisiae cells under heat-shock conditions. Sci Rep 2017; 7:2586. [PMID: 28566714 PMCID: PMC5451409 DOI: 10.1038/s41598-017-02736-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 04/19/2017] [Indexed: 01/01/2023] Open
Abstract
Heat shock is known to accelerate mitochondrial ROS production in Saccharomyces cerevisiae cells. But how yeast mitochondria produce ROS under heat-shock condition is not completely clear. Previously, it was shown that ROS production in heat-stressed fermenting yeast cells was accompanied by mitochondrial membrane potential (MMP) increase. In the current investigation the relationship between ROS production and MMP was studied in respiring yeast cells in stationary phase, using diphenyleneiodonium chloride (DPI), an inhibitor of flavin-containing proteins, as well as the mutants deleted for NDE1, NDE2 and NDI1 genes, encoding flavin-containing external and internal NADH dehydrogenases. It was shown that heat shock induced a transient burst in mitochondrial ROS production, which was paralleled by MMP rise. ROS production and MMP was significantly suppressed by DPI addition and deletion of NDE1. The effect of DPI on ROS production and MMP rise was specific for respiring cells. The results obtained suggest that the functioning of mitochondrial flavin-binding enzymes, Nde1p for instance, is required for the hyperpolarization of inner mitochondrial membrane and ROS production in respiring S. cerevisiae cells under heat-shock conditions.
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Structure, biochemical and kinetic properties of recombinant Pst2p from Saccharomyces cerevisiae, a FMN-dependent NAD(P)H:quinone oxidoreductase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1046-1056. [PMID: 28499769 DOI: 10.1016/j.bbapap.2017.05.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 05/05/2017] [Accepted: 05/08/2017] [Indexed: 01/09/2023]
Abstract
The genome of the yeast Saccharomyces cerevisiae encodes four flavodoxin-like proteins, namely Lot6p, Pst2p, Rfs1p and Ycp4p. Thus far only Lot6p was characterized in detail demonstrating that the enzyme possesses NAD(P)H:quinone oxidoreductase activity. In the present study, we heterologously expressed PST2 in Escherichia coli and purified the produced protein to conduct a detailed biochemical and structural characterization. Determination of the three-dimensional structure by X-ray crystallography revealed that Pst2p adopts the flavodoxin-like fold and forms tetramers independent of cofactor binding. The lack of electron density for FMN indicated weak binding, which was confirmed by further biochemical analysis yielding a dissociation constant of 20±1μM. The redox potential of FMN bound to Pst2p was determined to -89±3mV and is thus 119mV more positive than that of free FMN indicating that reduced FMN binds ca. five orders of magnitude tighter to Pst2p than oxidized FMN. Due to this rather positive redox potential Pst2p is unable to reduce free FMN or azo dyes as reported for other members of the flavodoxin-like protein family. On the other hand, Pst2p efficiently catalyzes the NAD(P)H dependent two-electron reduction of natural and artificial quinones. The kinetic mechanism follows a ping-pong bi-bi reaction scheme. In vivo experiments with a PST2 knock out and overexpressing strain demonstrated that Pst2p enables yeast cells to cope with quinone-induced damage suggesting a role of the enzyme in managing oxidative stress.
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Ye JS, Liu J, Ou HS, Wang LL. Degradation of ciprofloxacin by 280 nm ultraviolet-activated persulfate: Degradation pathway and intermediate impact on proteome of Escherichia coli. CHEMOSPHERE 2016; 165:311-319. [PMID: 27664520 DOI: 10.1016/j.chemosphere.2016.09.031] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 09/08/2016] [Accepted: 09/08/2016] [Indexed: 06/06/2023]
Abstract
In this study, the degradation of ciprofloxacin (CIP) was explored using ultraviolet activated persulfate (UV/PS) with 280 nm ultraviolet light-emitting diodes (UV-LEDs), and the toxicological assessment of degrading intermediates was performed using iTRAQ labeling quantitative proteomic technology. The quantitative mass spectrum results showed that 280 nm UV/PS treatment had a high transformation efficiency of CIP ([CIP] = 3 μM, [S2O82-] = 210 μM, apparent rate constants 0.2413 min-1). The high resolution mass spectrum analyses demonstrated that the primary intermediates included C15H16FN3O3 (m/z 306.1248) and C17H18FN3O4 (m/z 348.1354). The former one was formed by the cleavage of piperazine ring, while the later one was generated by the addition of a hydroxyl on the quinolone backbone. The toxicological assessment demonstrated that 56 and 110 proteins had significant up regulations and down regulations, respectively, in the Escherichia coli exposed to degraded CIP compared to untreated CIP. The majority of up-regulated proteins, such as GapA, SodC, were associated with primary metabolic process rather than responses to stress and toxic substance, inferring that the moderate UV/PS treatment can reduce the antibacterial activity of CIP by incomplete mineralization. Consequently, these results provided a novel insight into the application of UV-LED/PS treatment as a promising removal methodology for quinolones.
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Affiliation(s)
- Jin-Shao Ye
- School of Environment, Guangzhou Key Laboratory of Environmental Exposure and Health, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China; Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek 94598, CA, USA
| | - Juan Liu
- School of Environment, Guangzhou Key Laboratory of Environmental Exposure and Health, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Hua-Se Ou
- School of Environment, Guangzhou Key Laboratory of Environmental Exposure and Health, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China.
| | - Lin-Lin Wang
- School of Environment, Guangzhou Key Laboratory of Environmental Exposure and Health, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China; Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek 94598, CA, USA
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Chemogenetic E-MAP in Saccharomyces cerevisiae for Identification of Membrane Transporters Operating Lipid Flip Flop. PLoS Genet 2016; 12:e1006160. [PMID: 27462707 PMCID: PMC4962981 DOI: 10.1371/journal.pgen.1006160] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 06/10/2016] [Indexed: 01/12/2023] Open
Abstract
While most yeast enzymes for the biosynthesis of glycerophospholipids, sphingolipids and ergosterol are known, genes for several postulated transporters allowing the flopping of biosynthetic intermediates and newly made lipids from the cytosolic to the lumenal side of the membrane are still not identified. An E-MAP measuring the growth of 142'108 double mutants generated by systematically crossing 543 hypomorphic or deletion alleles in genes encoding multispan membrane proteins, both on media with or without an inhibitor of fatty acid synthesis, was generated. Flc proteins, represented by 4 homologous genes encoding presumed FAD or calcium transporters of the ER, have a severe depression of sphingolipid biosynthesis and elevated detergent sensitivity of the ER. FLC1, FLC2 and FLC3 are redundant in granting a common function, which remains essential even when the severe cell wall defect of flc mutants is compensated by osmotic support. Biochemical characterization of some other genetic interactions shows that Cst26 is the enzyme mainly responsible for the introduction of saturated very long chain fatty acids into phosphatidylinositol and that the GPI lipid remodelase Cwh43, responsible for introducing ceramides into GPI anchors having a C26:0 fatty acid in sn-2 of the glycerol moiety can also use lyso-GPI protein anchors and various base resistant lipids as substrates. Furthermore, we observe that adjacent deletions in several chromosomal regions show strong negative genetic interactions with a single gene on another chromosome suggesting the presence of undeclared suppressor mutations in certain chromosomal regions that need to be identified in order to yield meaningful E-map data. All living cells define their boundaries by lipid-containing membranes, which are impermeable to ions and water-soluble metabolic intermediates, and thus allow maintaining constant conditions inside the cells and stopping metabolic intermediates from diffusing away. Membranes are formed by amphiphilic lipids that have a hydrophilic and a hydrophobic component. Such lipids form flat double-layered sheets (bilayers) wherein the hydrophilic components of the constituent lipids are directed towards the aqueous surroundings, the hydrophobic ones populate the center of the bilayer. Membranes grow when enzymes resident in the bilayer synthesize new amphiphilic lipids. These enzymes have their active site on one side of the membrane and insert the newly made lipids in only one of the two layers. To ensure symmetric growth of membranes, cells need flippases catalyzing the transfer of lipids from one into the other layer. To identify unknown flippases we performed a chemogenetic interaction screen able to bring to light functions of unknown proteins through their genetic interaction with genes of known function. The data point to Flc proteins as potential lipid flippases of the endoplasmic reticulum, reveal novel lipid modifying activities of Cst26 and Cwh43 and suggest that undeclared suppressor mutations in certain chromosomal regions can generate false genetic interactions.
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Rußmayer H, Buchetics M, Gruber C, Valli M, Grillitsch K, Modarres G, Guerrasio R, Klavins K, Neubauer S, Drexler H, Steiger M, Troyer C, Al Chalabi A, Krebiehl G, Sonntag D, Zellnig G, Daum G, Graf AB, Altmann F, Koellensperger G, Hann S, Sauer M, Mattanovich D, Gasser B. Systems-level organization of yeast methylotrophic lifestyle. BMC Biol 2015; 13:80. [PMID: 26400155 PMCID: PMC4580311 DOI: 10.1186/s12915-015-0186-5] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 09/03/2015] [Indexed: 12/20/2022] Open
Abstract
Background Some yeasts have evolved a methylotrophic lifestyle enabling them to utilize the single carbon compound methanol as a carbon and energy source. Among them, Pichia pastoris (syn. Komagataella sp.) is frequently used for the production of heterologous proteins and also serves as a model organism for organelle research. Our current knowledge of methylotrophic lifestyle mainly derives from sophisticated biochemical studies which identified many key methanol utilization enzymes such as alcohol oxidase and dihydroxyacetone synthase and their localization to the peroxisomes. C1 assimilation is supposed to involve the pentose phosphate pathway, but details of these reactions are not known to date. Results In this work we analyzed the regulation patterns of 5,354 genes, 575 proteins, 141 metabolites, and fluxes through 39 reactions of P. pastoris comparing growth on glucose and on a methanol/glycerol mixed medium, respectively. Contrary to previous assumptions, we found that the entire methanol assimilation pathway is localized to peroxisomes rather than employing part of the cytosolic pentose phosphate pathway for xylulose-5-phosphate regeneration. For this purpose, P. pastoris (and presumably also other methylotrophic yeasts) have evolved a duplicated methanol inducible enzyme set targeted to peroxisomes. This compartmentalized cyclic C1 assimilation process termed xylose-monophosphate cycle resembles the principle of the Calvin cycle and uses sedoheptulose-1,7-bisphosphate as intermediate. The strong induction of alcohol oxidase, dihydroxyacetone synthase, formaldehyde and formate dehydrogenase, and catalase leads to high demand of their cofactors riboflavin, thiamine, nicotinamide, and heme, respectively, which is reflected in strong up-regulation of the respective synthesis pathways on methanol. Methanol-grown cells have a higher protein but lower free amino acid content, which can be attributed to the high drain towards methanol metabolic enzymes and their cofactors. In context with up-regulation of many amino acid biosynthesis genes or proteins, this visualizes an increased flux towards amino acid and protein synthesis which is reflected also in increased levels of transcripts and/or proteins related to ribosome biogenesis and translation. Conclusions Taken together, our work illustrates how concerted interpretation of multiple levels of systems biology data can contribute to elucidation of yet unknown cellular pathways and revolutionize our understanding of cellular biology. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0186-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hannes Rußmayer
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria
| | - Markus Buchetics
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria
| | - Clemens Gruber
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria
| | - Minoska Valli
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria
| | - Karlheinz Grillitsch
- Institute of Biochemistry, Graz University of Technology, A-8010 Graz, Austria.,Austrian Centre of Industrial Biotechnology, A-8010 Graz, Austria
| | - Gerda Modarres
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,School of Bioengineering, University of Applied Sciences FH Campus, A-1190 Vienna, Austria
| | - Raffaele Guerrasio
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria.,Present addresses: Sandoz GmbH, A-6250 Kundl, Austria
| | - Kristaps Klavins
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria.,Present addresses: BIOCRATES Life Sciences AG, A-6020 Innsbruck, Austria
| | - Stefan Neubauer
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria.,University of Tübingen, D-72076 Tübingen, Germany
| | - Hedda Drexler
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria
| | - Matthias Steiger
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria
| | - Christina Troyer
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria
| | | | | | | | - Günther Zellnig
- Institute of Plant Sciences, NAWI Graz, University of Graz, A-8010 Graz, Austria
| | - Günther Daum
- Institute of Biochemistry, Graz University of Technology, A-8010 Graz, Austria.,Austrian Centre of Industrial Biotechnology, A-8010 Graz, Austria
| | - Alexandra B Graf
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-8010 Graz, Austria
| | - Friedrich Altmann
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria
| | | | - Stephan Hann
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria
| | - Michael Sauer
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria. .,Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.
| | - Brigitte Gasser
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria
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Li L, Naseem S, Sharma S, Konopka JB. Flavodoxin-Like Proteins Protect Candida albicans from Oxidative Stress and Promote Virulence. PLoS Pathog 2015; 11:e1005147. [PMID: 26325183 PMCID: PMC4556627 DOI: 10.1371/journal.ppat.1005147] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 08/13/2015] [Indexed: 12/26/2022] Open
Abstract
The fungal pathogen Candida albicans causes lethal systemic infections in humans. To better define how pathogens resist oxidative attack by the immune system, we examined a family of four Flavodoxin-Like Proteins (FLPs) in C. albicans. In agreement with previous studies showing that FLPs in bacteria and plants act as NAD(P)H quinone oxidoreductases, a C. albicans quadruple mutant lacking all four FLPs (pst1Δ, pst2Δ, pst3Δ, ycp4Δ) was more sensitive to benzoquinone. Interestingly, the quadruple mutant was also more sensitive to a variety of oxidants. Quinone reductase activity confers important antioxidant effects because resistance to oxidation was restored in the quadruple mutant by expressing either Escherichia coli wrbA or mammalian NQO1, two distinct types of quinone reductases. FLPs were detected at the plasma membrane in C. albicans, and the quadruple mutant was more sensitive to linolenic acid, a polyunsaturated fatty acid that can auto-oxidize and promote lipid peroxidation. These observations suggested that FLPs reduce ubiquinone (coenzyme Q), enabling it to serve as an antioxidant in the membrane. In support of this, a C. albicans coq3Δ mutant that fails to synthesize ubiquinone was also highly sensitive to oxidative stress. FLPs are critical for survival in the host, as the quadruple mutant was avirulent in a mouse model of systemic candidiasis under conditions where infection with wild type C. albicans was lethal. The quadruple mutant cells initially grew well in kidneys, the major site of C. albicans growth in mice, but then declined after the influx of neutrophils and by day 4 post-infection 33% of the mice cleared the infection. Thus, FLPs and ubiquinone are important new antioxidant mechanisms that are critical for fungal virulence. The potential of FLPs as novel targets for antifungal therapy is further underscored by their absence in mammalian cells.
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Affiliation(s)
- Lifang Li
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, United States of America
| | - Shamoon Naseem
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, United States of America
| | - Sahil Sharma
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, United States of America
| | - James B. Konopka
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, United States of America
- * E-mail:
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Hamdane D, Bou-Nader C, Cornu D, Hui-Bon-Hoa G, Fontecave M. Flavin-Protein Complexes: Aromatic Stacking Assisted by a Hydrogen Bond. Biochemistry 2015; 54:4354-64. [PMID: 26120776 DOI: 10.1021/acs.biochem.5b00501] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enzyme-catalyzed reactions often rely on a noncovalently bound cofactor whose reactivity is tuned by its immediate environment. Flavin cofactors, the most versatile catalyst encountered in biology, are often maintained within the protein throughout numbers of complex ionic and aromatic interactions. Here, we have investigated the role of π-π stacking and hydrogen bond interactions between a tyrosine and the isoalloxazine moiety of the flavin adenine dinucleotide (FAD) in an FAD-dependent RNA methyltransferase. Combining several static and time-resolved spectroscopies as well as biochemical approaches, we showed that aromatic stacking is assisted by a hydrogen bond between the phenol group and the amide of an adjacent active site loop. A mechanism of recognition and binding of the redox cofactor is proposed.
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Affiliation(s)
- Djemel Hamdane
- †Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, France 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Charles Bou-Nader
- †Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, France 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - David Cornu
- ‡INSERM U779, 78 Rue du Général Leclerc, 94275 Le Kremlin-Bicêtre, France
| | - Gaston Hui-Bon-Hoa
- §Plateforme IMAGIF, Centre de Recherche de Gif, Centre National de la Recherche Scientifique, 1 avenue de le terrasse, 91191 Gif Sur Yvette, France
| | - Marc Fontecave
- †Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, France 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
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Steinkellner G, Gruber CC, Pavkov-Keller T, Binter A, Steiner K, Winkler C, Łyskowski A, Schwamberger O, Oberer M, Schwab H, Faber K, Macheroux P, Gruber K. Identification of promiscuous ene-reductase activity by mining structural databases using active site constellations. Nat Commun 2014; 5:4150. [PMID: 24954722 PMCID: PMC4083419 DOI: 10.1038/ncomms5150] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 05/15/2014] [Indexed: 12/03/2022] Open
Abstract
The exploitation of catalytic promiscuity and the application of de novo design have recently opened the access to novel, non-natural enzymatic activities. Here we describe a structural bioinformatic method for predicting catalytic activities of enzymes based on three-dimensional constellations of functional groups in active sites ('catalophores'). As a proof-of-concept we identify two enzymes with predicted promiscuous ene-reductase activity (reduction of activated C-C double bonds) and compare them with known ene-reductases, that is, members of the Old Yellow Enzyme family. Despite completely different amino acid sequences, overall structures and protein folds, high-resolution crystal structures reveal equivalent binding modes of typical Old Yellow Enzyme substrates and ligands. Biochemical and biocatalytic data show that the two enzymes indeed possess ene-reductase activity and reveal an inverted stereopreference compared with Old Yellow Enzymes for some substrates. This method could thus be a tool for the identification of viable starting points for the development and engineering of novel biocatalysts.
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Affiliation(s)
- Georg Steinkellner
- ACIB GmbH, Petersgasse 14, 8010 Graz, Austria
- These authors contributed equally to this work
| | - Christian C. Gruber
- ACIB GmbH, Petersgasse 14, 8010 Graz, Austria
- These authors contributed equally to this work
| | | | | | | | - Christoph Winkler
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria
| | | | - Orsolya Schwamberger
- ACIB GmbH, Petersgasse 14, 8010 Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
| | - Monika Oberer
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
| | - Helmut Schwab
- ACIB GmbH, Petersgasse 14, 8010 Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
| | - Kurt Faber
- ACIB GmbH, Petersgasse 14, 8010 Graz, Austria
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria
| | - Peter Macheroux
- ACIB GmbH, Petersgasse 14, 8010 Graz, Austria
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Karl Gruber
- ACIB GmbH, Petersgasse 14, 8010 Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
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Giancaspero TA, Dipalo E, Miccolis A, Boles E, Caselle M, Barile M. Alteration of ROS homeostasis and decreased lifespan in S. cerevisiae elicited by deletion of the mitochondrial translocator FLX1. BIOMED RESEARCH INTERNATIONAL 2014; 2014:101286. [PMID: 24895546 PMCID: PMC4033422 DOI: 10.1155/2014/101286] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 03/20/2014] [Accepted: 04/01/2014] [Indexed: 01/15/2023]
Abstract
This paper deals with the control exerted by the mitochondrial translocator FLX1, which catalyzes the movement of the redox cofactor FAD across the mitochondrial membrane, on the efficiency of ATP production, ROS homeostasis, and lifespan of S. cerevisiae. The deletion of the FLX1 gene resulted in respiration-deficient and small-colony phenotype accompanied by a significant ATP shortage and ROS unbalance in glycerol-grown cells. Moreover, the flx1Δ strain showed H2O2 hypersensitivity and decreased lifespan. The impaired biochemical phenotype found in the flx1Δ strain might be justified by an altered expression of the flavoprotein subunit of succinate dehydrogenase, a key enzyme in bioenergetics and cell regulation. A search for possible cis-acting consensus motifs in the regulatory region upstream SDH1-ORF revealed a dozen of upstream motifs that might respond to induced metabolic changes by altering the expression of Flx1p. Among these motifs, two are present in the regulatory region of genes encoding proteins involved in flavin homeostasis. This is the first evidence that the mitochondrial flavin cofactor status is involved in controlling the lifespan of yeasts, maybe by changing the cellular succinate level. This is not the only case in which the homeostasis of redox cofactors underlies complex phenotypical behaviours, as lifespan in yeasts.
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Affiliation(s)
| | - Emilia Dipalo
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari “A. Moro”, Via Orabona 4, 70126 Bari, Italy
| | - Angelica Miccolis
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari “A. Moro”, Via Orabona 4, 70126 Bari, Italy
| | - Eckhard Boles
- Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Straße 9, 60438 Frankfurt am Main, Germany
| | - Michele Caselle
- Dipartimento di Fisica, Via P. Giuria 1, 10125 Torino, Italy
| | - Maria Barile
- Istituto di Biomembrane e Bioenergetica, CNR, Via Amendola 165/A, 70126 Bari, Italy
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari “A. Moro”, Via Orabona 4, 70126 Bari, Italy
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