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Liunardo JJ, Messerli S, Gregotsch A, Lang S, Schlosser K, Rückert‐Reed C, Busche T, Kalinowski J, Zischka M, Weller P, Nouioui I, Neumann‐Schaal M, Risdian C, Wink J, Mack M. Isolation, characterisation and description of the roseoflavin producer Streptomyces berlinensis sp. nov. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13266. [PMID: 38653477 PMCID: PMC11039241 DOI: 10.1111/1758-2229.13266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/06/2024] [Indexed: 04/25/2024]
Abstract
The Gram-positive bacteria Streptomyces davaonensis and Streptomyces cinnabarinus have been the only organisms known to produce roseoflavin, a riboflavin (vitamin B2) derived red antibiotic. Using a selective growth medium and a phenotypic screening, we were able to isolate a novel roseoflavin producer from a German soil sample. The isolation procedure was repeated twice, that is, the same strain could be isolated from the same location in Berlin 6 months and 12 months after its first isolation. Whole genome sequencing of the novel roseoflavin producer revealed an unusual chromosomal arrangement and the deposited genome sequence of the new isolate (G + C content of 71.47%) contains 897 genes per inverted terminal repeat, 6190 genes in the core and 107 genes located on an illegitimate terminal end. We identified the roseoflavin biosynthetic genes rosA, rosB and rosC and an unusually high number of riboflavin biosynthetic genes. Overexpression of rosA, rosB and rosC in Escherichia coli and enzyme assays confirmed their predicted functions in roseoflavin biosynthesis. A full taxonomic analysis revealed that the isolate represents a previously unknown Streptomyces species and we propose the name Streptomyces berlinensis sp. nov. for this roseoflavin producer.
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Affiliation(s)
- Jimmy Jonathan Liunardo
- Institute for Technical Microbiology, Department of BiotechnologyMannheim University of Applied SciencesMannheimGermany
| | - Sebastien Messerli
- Institute for Technical Microbiology, Department of BiotechnologyMannheim University of Applied SciencesMannheimGermany
| | - Ann‐Kathrin Gregotsch
- Institute for Technical Microbiology, Department of BiotechnologyMannheim University of Applied SciencesMannheimGermany
| | - Sonja Lang
- Institute for Technical Microbiology, Department of BiotechnologyMannheim University of Applied SciencesMannheimGermany
| | - Kerstin Schlosser
- Institute for Technical Microbiology, Department of BiotechnologyMannheim University of Applied SciencesMannheimGermany
| | - Christian Rückert‐Reed
- Medical School East Westphalia‐LippeBielefeld UniversityBielefeldGermany
- Technology Platform Genomics, Center for BiotechnologyBielefeld UniversityBielefeldGermany
| | - Tobias Busche
- Medical School East Westphalia‐LippeBielefeld UniversityBielefeldGermany
| | - Jörn Kalinowski
- Technology Platform Genomics, Center for BiotechnologyBielefeld UniversityBielefeldGermany
| | - Martin Zischka
- Institute for Instrumental Analytics and Bioanalytics, Department of BiotechnologyMannheim University of Applied SciencesMannheimGermany
| | - Philipp Weller
- Institute for Instrumental Analytics and Bioanalytics, Department of BiotechnologyMannheim University of Applied SciencesMannheimGermany
| | - Imen Nouioui
- Leibniz‐Institute DSMZ‐German Collection of Microorganisms and Cell CulturesBraunschweigGermany
| | - Meina Neumann‐Schaal
- Leibniz‐Institute DSMZ‐German Collection of Microorganisms and Cell CulturesBraunschweigGermany
| | - Chandra Risdian
- Department of Microbial Strain CollectionHelmholtz Centre for Infection ResearchBraunschweigGermany
- Research Center for Applied MicrobiologyNational Research and Innovation Agency (BRIN)BandungIndonesia
| | - Joachim Wink
- Department of Microbial Strain CollectionHelmholtz Centre for Infection ResearchBraunschweigGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐BraunschweigBraunschweigGermany
| | - Matthias Mack
- Institute for Technical Microbiology, Department of BiotechnologyMannheim University of Applied SciencesMannheimGermany
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Lei J, Xin C, Xiao W, Chen W, Song Z. The promise of endogenous and exogenous riboflavin in anti-infection. Virulence 2021; 12:2314-2326. [PMID: 34490839 PMCID: PMC8425684 DOI: 10.1080/21505594.2021.1963909] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
To resolve the growing problem of drug resistance in the treatment of bacterial and fungal pathogens, specific cellular targets and pathways can be used as targets for new antimicrobial agents. Endogenous riboflavin biosynthesis is a conserved pathway that exists in most bacteria and fungi. In this review, the roles of endogenous and exogenous riboflavin in infectious disease as well as several antibacterial agents, which act as analogues of the riboflavin biosynthesis pathway, are summarized. In addition, the effects of exogenous riboflavin on immune cells, cytokines, and heat shock proteins are described. Moreover, the immune response of endogenous riboflavin metabolites in infectious diseases, recognized by MHC-related protein-1, and then presented to mucosal associated invariant T cells, is highlighted. This information will provide a strategy to identify novel drug targets as well as highlight the possible clinical use of riboflavin.
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Affiliation(s)
- Junwen Lei
- Molecular Biotechnology Platform, Public Center of Experimental Technology, School of Basic Medical Sciences, Southwest Medical University, Luzhou People's Republic of China
| | - Caiyan Xin
- Molecular Biotechnology Platform, Public Center of Experimental Technology, School of Basic Medical Sciences, Southwest Medical University, Luzhou People's Republic of China
| | - Wei Xiao
- Molecular Biotechnology Platform, Public Center of Experimental Technology, School of Basic Medical Sciences, Southwest Medical University, Luzhou People's Republic of China
| | - Wenbi Chen
- Molecular Biotechnology Platform, Public Center of Experimental Technology, School of Basic Medical Sciences, Southwest Medical University, Luzhou People's Republic of China
| | - Zhangyong Song
- Molecular Biotechnology Platform, Public Center of Experimental Technology, School of Basic Medical Sciences, Southwest Medical University, Luzhou People's Republic of China
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3
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Schneider C, Konjik V, Kißling L, Mack M. The novel phosphatase RosC catalyzes the last unknown step of roseoflavin biosynthesis in Streptomyces davaonensis. Mol Microbiol 2020; 114:609-625. [PMID: 32621340 DOI: 10.1111/mmi.14567] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/31/2022]
Abstract
The bacterium Streptomyces davaonensis produces the antibiotic roseoflavin, which is a riboflavin (vitamin B2 ) analog. The key enzyme of roseoflavin biosynthesis is the 8-demethyl-8-amino-riboflavin-5'-phosphate (AFP) synthase RosB which synthesizes AFP from riboflavin-5'-phosphate. AFP is not a substrate for the last enzyme of roseoflavin biosynthesis the N, N-dimethyltransferase RosA, which generates roseoflavin from 8-demethyl-8-amino-riboflavin (AF). Consequently, the roseoflavin biosynthetic pathway depends on a phosphatase, which dephosphorylates AFP to AF. Here, we report on the identification and characterization of such an AFP phosphatase which we named RosC. The gene rosC is located immediately downstream of rosA and both genes are part of a cluster comprising 10 genes. Deletion of rosC from the chromosome of S. davaonensis led to reduced roseoflavin levels in the corresponding recombinant strain. In contrast to wild-type S. davaonensis, cell-free extracts of the rosC deletion strain did not catalyze dephosphorylation of AFP. RosC was purified from an overproducing Escherichia coli strain. RosC is the fastest enzyme of roseoflavin biosynthesis (kcat 31.3 ± 1.4 min-1 ). The apparent KM for the substrate AFP was 34.5 µM. Roseoflavin biosynthesis is now completely understood--it takes three enzymes (RosB, RosC, and RosA) to convert the flavin cofactor riboflavin-5'-phosphate into a potent antibiotic.
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Affiliation(s)
- Carmen Schneider
- Department of Biotechnology, Institute for Technical Microbiology, Mannheim University of Applied Sciences, Mannheim, Germany
| | - Valentino Konjik
- Department of Biotechnology, Institute for Technical Microbiology, Mannheim University of Applied Sciences, Mannheim, Germany
| | - Lena Kißling
- Department of Biotechnology, Institute for Technical Microbiology, Mannheim University of Applied Sciences, Mannheim, Germany
| | - Matthias Mack
- Department of Biotechnology, Institute for Technical Microbiology, Mannheim University of Applied Sciences, Mannheim, Germany
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4
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Ludwig P, Sévin DC, Busche T, Kalinowski J, Bourdeaux F, Grininger M, Mack M. Characterization of the small flavin-binding dodecin in the roseoflavin producer Streptomyces davawensis. MICROBIOLOGY-SGM 2019; 164:908-919. [PMID: 29856311 DOI: 10.1099/mic.0.000662] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Genes encoding dodecin proteins are present in almost 20 % of archaeal and in more than 50 % of bacterial genomes. Archaeal dodecins bind riboflavin (vitamin B2), are thought to play a role in flavin homeostasis and possibly also help to protect cells from radical or oxygenic stress. Bacterial dodecins were found to bind riboflavin-5'-phosphate (also called flavin mononucleotide or FMN) and coenzyme A, but their physiological function remained unknown. In this study, we set out to investigate the relevance of dodecins for flavin metabolism and oxidative stress management in the phylogenetically related bacteria Streptomyces coelicolor and Streptomyces davawensis. Additionally, we explored the role of dodecins with regard to resistance against the antibiotic roseoflavin, a riboflavin analogue produced by S. davawensis. Our results show that the dodecin of S. davawensis predominantly binds FMN and is neither involved in roseoflavin biosynthesis nor in roseoflavin resistance. In contrast to S. davawensis, growth of S. coelicolor was not reduced in the presence of plumbagin, a compound, which induces oxidative stress. Plumbagin treatment stimulated expression of the dodecin gene in S. davawensis but not in S. coelicolor. Deletion of the dodecin gene in S. davawensis generated a recombinant strain which, in contrast to the wild-type, was fully resistant to plumbagin. Subsequent metabolome analyses revealed that the S. davawensis dodecin deletion strain exhibited a very different stress response when compared to the wild-type indicating that dodecins broadly affect cellular physiology.
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Affiliation(s)
- Petra Ludwig
- Institute for Technical Microbiology, Mannheim University of Applied Sciences, 68163 Mannheim, Germany
| | - Daniel C Sévin
- Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Tobias Busche
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Florian Bourdeaux
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Matthias Mack
- Institute for Technical Microbiology, Mannheim University of Applied Sciences, 68163 Mannheim, Germany
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Sepúlveda Cisternas I, Salazar JC, García-Angulo VA. Overview on the Bacterial Iron-Riboflavin Metabolic Axis. Front Microbiol 2018; 9:1478. [PMID: 30026736 PMCID: PMC6041382 DOI: 10.3389/fmicb.2018.01478] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 06/13/2018] [Indexed: 01/10/2023] Open
Abstract
Redox reactions are ubiquitous in biological processes. Enzymes involved in redox metabolism often use cofactors in order to facilitate electron-transfer reactions. Common redox cofactors include micronutrients such as vitamins and metals. By far, while iron is the main metal cofactor, riboflavin is the most important organic cofactor. Notably, the metabolism of iron and riboflavin seem to be intrinsically related across life kingdoms. In bacteria, iron availability influences expression of riboflavin biosynthetic genes. There is documented evidence for riboflavin involvement in surpassing iron-restrictive conditions in some species. This is probably achieved through increase in iron bioavailability by reduction of extracellular iron, improvement of iron uptake pathways and boosting hemolytic activity. In some cases, riboflavin may also work as replacement of iron as enzyme cofactor. In addition, riboflavin is involved in dissimilatory iron reduction during extracellular respiration by some species. The main direct metabolic relationships between riboflavin and iron in bacterial physiology are reviewed here.
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Affiliation(s)
- Ignacio Sepúlveda Cisternas
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Juan C Salazar
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Víctor A García-Angulo
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
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Landwehr W, Kämpfer P, Glaeser SP, Rückert C, Kalinowski J, Blom J, Goesmann A, Mack M, Schumann P, Atasayar E, Hahnke RL, Rohde M, Martin K, Stadler M, Wink J. Taxonomic analyses of members of the Streptomyces cinnabarinus cluster, description of Streptomyces cinnabarigriseus sp. nov. and Streptomyces davaonensis sp. nov. Int J Syst Evol Microbiol 2018; 68:382-393. [DOI: 10.1099/ijsem.0.002519] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Wiebke Landwehr
- Department of Microbial Strain Collection, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Peter Kämpfer
- University of Gießen, Heinrich-Buff-Ring 26, 35392 Gießen, Germany
| | | | - Christian Rückert
- University of Bielefeld, Centere for Biotechnology, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- University of Bielefeld, Centere for Biotechnology, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Jochen Blom
- University of Gießen, Heinrich-Buff-Ring 26, 35392 Gießen, Germany
| | | | - Matthias Mack
- Biotechnology Department, Institute for Technical Microbiology, Hochschule Mannheim, Paul-Wittsack-Str.10, 68163 Mannheim, Germany
| | - Peter Schumann
- Leibnitz Institute, DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Ewelina Atasayar
- Leibnitz Institute, DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Richard L. Hahnke
- Leibnitz Institute, DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Karin Martin
- Hans Knöll Institut für Wirkstoffforschung, 07743 Jena, Germany
| | - Marc Stadler
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
- Department of Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Joachim Wink
- Department of Microbial Strain Collection, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
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7
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Konjik V, Brünle S, Demmer U, Vanselow A, Sandhoff R, Ermler U, Mack M. Die Kristallstruktur von RosB: Einblicke in den Reaktionsmechanismus des ersten Mitglieds einer flavodoxinähnlichen Enzymfamilie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201610292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Valentino Konjik
- Hochschule Mannheim; Paul-Wittsack-Straße 10 68163 Mannheim Deutschland
| | - Steffen Brünle
- Max-Planck-Institut für Biophysik; Max-von-Laue-Straße 3 60438 Frankfurt am Main Deutschland
| | - Ulrike Demmer
- Max-Planck-Institut für Biophysik; Max-von-Laue-Straße 3 60438 Frankfurt am Main Deutschland
| | - Amanda Vanselow
- Hochschule Mannheim; Paul-Wittsack-Straße 10 68163 Mannheim Deutschland
| | - Roger Sandhoff
- Deutsches Krebsforschungszentrum (DKFZ); Im Neuenheimer Feld 280 69120 Heidelberg Deutschland
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik; Max-von-Laue-Straße 3 60438 Frankfurt am Main Deutschland
| | - Matthias Mack
- Hochschule Mannheim; Paul-Wittsack-Straße 10 68163 Mannheim Deutschland
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Konjik V, Brünle S, Demmer U, Vanselow A, Sandhoff R, Ermler U, Mack M. The Crystal Structure of RosB: Insights into the Reaction Mechanism of the First Member of a Family of Flavodoxin-like Enzymes. Angew Chem Int Ed Engl 2016; 56:1146-1151. [DOI: 10.1002/anie.201610292] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Valentino Konjik
- Mannheim University of Applied Sciences; Paul-Wittsack-Strasse 10 68163 Mannheim Germany
| | - Steffen Brünle
- Max-Planck-Institute for Biophysics; Max-von-Laue-Strasse 3 60438 Frankfurt am Main Germany
| | - Ulrike Demmer
- Max-Planck-Institute for Biophysics; Max-von-Laue-Strasse 3 60438 Frankfurt am Main Germany
| | - Amanda Vanselow
- Mannheim University of Applied Sciences; Paul-Wittsack-Strasse 10 68163 Mannheim Germany
| | - Roger Sandhoff
- German Cancer Research Center (DKFZ); Im Neuenheimer Feld 280 69120 Heidelberg Germany
| | - Ulrich Ermler
- Max-Planck-Institute for Biophysics; Max-von-Laue-Strasse 3 60438 Frankfurt am Main Germany
| | - Matthias Mack
- Mannheim University of Applied Sciences; Paul-Wittsack-Strasse 10 68163 Mannheim Germany
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Uptake and Metabolism of Antibiotics Roseoflavin and 8-Demethyl-8-Aminoriboflavin in Riboflavin-Auxotrophic Listeria monocytogenes. J Bacteriol 2016; 198:3233-3243. [PMID: 27672192 DOI: 10.1128/jb.00388-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 09/14/2016] [Indexed: 01/12/2023] Open
Abstract
The riboflavin analogs roseoflavin (RoF) and 8-demethyl-8-aminoriboflavin (AF) are produced by the bacteria Streptomyces davawensis and Streptomyces cinnabarinus Riboflavin analogs have the potential to be used as broad-spectrum antibiotics, and we therefore studied the metabolism of riboflavin (vitamin B2), RoF, and AF in the human pathogen Listeria monocytogenes, a bacterium which is a riboflavin auxotroph. We show that the L. monocytogenes protein Lmo1945 is responsible for the uptake of riboflavin, RoF, and AF. Following import, these flavins are phosphorylated/adenylylated by the bifunctional flavokinase/flavin adenine dinucleotide (FAD) synthetase Lmo1329 and adenylylated by the unique FAD synthetase Lmo0728, the first monofunctional FAD synthetase to be described in bacteria. Lmo1329 generates the cofactors flavin mononucleotide (FMN) and FAD, whereas Lmo0728 produces FAD only. The combined activities of Lmo1329 and Lmo0728 are responsible for the intracellular formation of the toxic cofactor analogs roseoflavin mononucleotide (RoFMN), roseoflavin adenine dinucleotide (RoFAD), 8-demethyl-8-aminoriboflavin mononucleotide (AFMN), and 8-demethyl-8-aminoriboflavin adenine dinucleotide (AFAD). In vivo reporter gene assays and in vitro transcription/translation experiments show that the L. monocytogenes FMN riboswitch Rli96, which controls expression of the riboflavin transport gene lmo1945, is negatively affected by riboflavin/FMN and RoF/RoFMN but not by AF/AFMN. Treatment of L. monocytogenes with RoF or AF leads to drastically reduced FMN/FAD levels. We suggest that the reduced flavin cofactor levels in combination with concomitant synthesis of inactive cofactor analogs (RoFMN, RoFAD, AFMN, and AFAD) explain why RoF and AF contribute to antibiotic activity in L. monocytogenes IMPORTANCE: The riboflavin analogs roseoflavin (RoF) and 8-demethyl-8-aminoriboflavin (AF) are small molecules which are produced by Streptomyces davawensis and Streptomyces cinnabarinus RoF and AF were reported to have antibacterial activity, and we studied how these compounds are metabolized by the human bacterial pathogen Listeria monocytogenes We found that the L. monocytogenes protein Lmo1945 mediates uptake of AF and RoF and that the combined activities of the enzymes Lmo1329 and Lmo0728 are responsible for the conversion of AF and RoF to toxic cofactor analogs. Comparative studies with RoF and AF (a weaker antibiotic) suggest that the reduction in FMN/FAD levels and the formation of inactive FMN/FAD analogs explain to a large extent the antibiotic activity of AF and RoF.
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Tongsook C, Uhl MK, Jankowitsch F, Mack M, Gruber K, Macheroux P. Structural and kinetic studies on RosA, the enzyme catalysing the methylation of 8-demethyl-8-amino-d-riboflavin to the antibiotic roseoflavin. FEBS J 2016; 283:1531-49. [PMID: 26913589 PMCID: PMC4982073 DOI: 10.1111/febs.13690] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/26/2016] [Accepted: 02/18/2016] [Indexed: 11/28/2022]
Abstract
N,N‐8‐demethyl‐8‐amino‐d‐riboflavin dimethyltransferase (RosA) catalyses the final dimethylation of 8‐demethyl‐8‐amino‐d‐riboflavin (AF) to the antibiotic roseoflavin (RoF) in Streptomyces davawensis. In the present study, we solved the X‐ray structure of RosA, and determined the binding properties of substrates and products. Moreover, we used steady‐state and rapid reaction kinetic studies to obtain detailed information on the reaction mechanism. The structure of RosA was found to be similar to that of previously described S‐adenosylmethionine (SAM)‐dependent methyltransferases, featuring two domains: a mainly α‐helical ‘orthogonal bundle’ and a Rossmann‐like domain (α/β twisted open sheet). Bioinformatics studies and molecular modelling enabled us to predict the potential SAM and AF binding sites in RosA, suggesting that both substrates, AF and SAM, bind independently to their respective binding pocket. This finding was confirmed by kinetic experiments that demonstrated a random‐order ‘bi‐bi’ reaction mechanism. Furthermore, we determined the dissociation constants for substrates and products by either isothermal titration calorimetry or UV/Vis absorption spectroscopy, revealing that both products, RoF and S‐adenosylhomocysteine (SAH), bind more tightly to RosA compared with the substrates, AF and SAM. This suggests that RosA may contribute to roseoflavin resistance in S. davawensis. The tighter binding of products is also reflected by the results of inhibition experiments, in which RoF and SAH behave as competitive inhibitors for AF and SAM, respectively. We also showed that formation of a ternary complex of RosA, RoF and SAH (or SAM) leads to drastic spectral changes that are indicative of a hydrophobic environment. Database Structural data are available in the Protein Data Bank under accession number 4D7K.
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Affiliation(s)
| | - Michael K Uhl
- Institute of Molecular Biosciences, University of Graz, Austria
| | - Frank Jankowitsch
- Department of Biotechnology, Institute for Technical Microbiology, Mannheim University of Applied Sciences, Germany
| | - Matthias Mack
- Department of Biotechnology, Institute for Technical Microbiology, Mannheim University of Applied Sciences, Germany
| | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Austria
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Brannan AM, Whelan WA, Cole E, Booth V. Differential scanning calorimetry of whole Escherichia coli treated with the antimicrobial peptide MSI-78 indicate a multi-hit mechanism with ribosomes as a novel target. PeerJ 2015; 3:e1516. [PMID: 26713257 PMCID: PMC4690349 DOI: 10.7717/peerj.1516] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 11/27/2015] [Indexed: 11/20/2022] Open
Abstract
Differential Scanning Calorimetry (DSC) of intact Escherichia coli (E. coli) was used to identify non-lipidic targets of the antimicrobial peptide (AMP) MSI-78. The DSC thermograms revealed that, in addition to its known lytic properties, MSI-78 also has a striking effect on ribosomes. MSI-78’s effect on DSC scans of bacteria was similar to that of kanamycin, an antibiotic drug known to target the 30S small ribosomal subunit. An in vitro transcription/translation assay helped confirm MSI-78’s targeting of ribosomes. The scrambled version of MSI-78 also affected the ribosome peak of the DSC scans, but required greater amounts of peptide to cause a similar effect to the unscrambled peptide. Furthermore, the effect of the scrambled peptide was not specific to the ribosomes; other regions of the DSC thermogram were also affected. These results suggest that MSI-78’s effects on E. coli are at least somewhat dependent on its particular structural features, rather than a sole function of its overall charge and hydrophobicity. When considered along with earlier work detailing MSI-78’s membrane lytic properties, it appears that MSI-78 operates via a multi-hit mechanism with multiple targets.
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Affiliation(s)
- Alexander M Brannan
- Department of Biochemistry, Memorial University of Newfoundland , St. John's Newfoundland and Labrador , Canada
| | - William A Whelan
- Department of Biochemistry, Memorial University of Newfoundland , St. John's Newfoundland and Labrador , Canada
| | - Emma Cole
- Department of Biochemistry, Memorial University of Newfoundland , St. John's Newfoundland and Labrador , Canada
| | - Valerie Booth
- Department of Biochemistry, Memorial University of Newfoundland , St. John's Newfoundland and Labrador , Canada ; Department of Physics and Physical Oceanography, Memorial University of Newfoundland , St. John's Newfoundland and Labrador , Canada
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12
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A dual control mechanism synchronizes riboflavin and sulphur metabolism in Bacillus subtilis. Proc Natl Acad Sci U S A 2015; 112:14054-9. [PMID: 26494285 DOI: 10.1073/pnas.1515024112] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Flavin mononucleotide (FMN) riboswitches are genetic elements, which in many bacteria control genes responsible for biosynthesis and/or transport of riboflavin (rib genes). Cytoplasmic riboflavin is rapidly and almost completely converted to FMN by flavokinases. When cytoplasmic levels of FMN are sufficient ("high levels"), FMN binding to FMN riboswitches leads to a reduction of rib gene expression. We report here that the protein RibR counteracts the FMN-induced "turn-off" activities of both FMN riboswitches in Bacillus subtilis, allowing rib gene expression even in the presence of high levels of FMN. The reason for this secondary metabolic control by RibR is to couple sulfur metabolism with riboflavin metabolism.
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Pedrolli D, Langer S, Hobl B, Schwarz J, Hashimoto M, Mack M. The ribB FMN riboswitch from Escherichia coli operates at the transcriptional and translational level and regulates riboflavin biosynthesis. FEBS J 2015; 282:3230-42. [PMID: 25661987 DOI: 10.1111/febs.13226] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 01/29/2015] [Accepted: 02/03/2015] [Indexed: 01/13/2023]
Abstract
FMN riboswitches are genetic elements that, in many bacteria, control genes responsible for biosynthesis and/or transport of riboflavin (vitamin B2 ). We report that the Escherichia coli ribB FMN riboswitch controls expression of the essential gene ribB coding for the riboflavin biosynthetic enzyme 3,4-dihydroxy-2-butanone-4-phosphate synthase (RibB; EC 4.1.99.12). Our data show that the E. coli ribB FMN riboswitch is unusual because it operates at the transcriptional and also at the translational level. Expression of ribB is negatively affected by FMN and by the FMN analog roseoflavin mononucleotide, which is synthesized enzymatically from roseoflavin and ATP. Consequently, in addition to flavoenzymes, the E. coli ribB FMN riboswitch constitutes a target for the antibiotic roseoflavin produced by Streptomyces davawensis.
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Affiliation(s)
- Danielle Pedrolli
- Department of Biotechnology, Institute for Technical Microbiology, Mannheim University of Applied Sciences, Germany.,Department of Bioprocessing and Biotechnology, School of Pharmaceutical Sciences, Univ Estadual Paulista - UNESP, Araraquara, Brazil
| | - Simone Langer
- Department of Biotechnology, Institute for Technical Microbiology, Mannheim University of Applied Sciences, Germany
| | - Birgit Hobl
- Department of Biotechnology, Institute for Technical Microbiology, Mannheim University of Applied Sciences, Germany
| | - Julia Schwarz
- Department of Biotechnology, Institute for Technical Microbiology, Mannheim University of Applied Sciences, Germany
| | - Masayuki Hashimoto
- Institute of Molecular Medicine, Medical School, National Chengkung University, Tainan City, Taiwan.,Center for Infectious Disease and Signal Transduction, Medical School, National Chengkung University, Tainan City, Taiwan
| | - Matthias Mack
- Department of Biotechnology, Institute for Technical Microbiology, Mannheim University of Applied Sciences, Germany
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