1
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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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2
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Xu J, Hou J, Ding M, Wang Z, Chen T. Riboswitches, from cognition to transformation. Synth Syst Biotechnol 2023; 8:357-370. [PMID: 37325181 PMCID: PMC10265488 DOI: 10.1016/j.synbio.2023.05.008] [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: 03/01/2023] [Revised: 05/20/2023] [Accepted: 05/25/2023] [Indexed: 06/17/2023] Open
Abstract
Riboswitches are functional RNA elements that regulate gene expression by directly detecting metabolites. Twenty years have passed since it was first discovered, researches on riboswitches are becoming increasingly standardized and refined, which could significantly promote people's cognition of RNA function as well. Here, we focus on some representative orphan riboswitches, enumerate the structural and functional transformation and artificial design of riboswitches including the coupling with ribozymes, hoping to attain a comprehensive understanding of riboswitch research.
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Affiliation(s)
- Jingdong Xu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, 300350, China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300350, China
| | - Junyuan Hou
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, 300350, China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300350, China
| | - Mengnan Ding
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, 300350, China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300350, China
| | - Zhiwen Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, 300350, China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300350, China
| | - Tao Chen
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, 300350, China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300350, China
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3
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Agrawal A, Chanana P, Yadav V, Bhutani V, Subbarao N, Srivastava A. Vitamin derivatives as potential drugs for Influenza Hemagglutinin. J Biomol Struct Dyn 2023; 41:11781-11795. [PMID: 36629034 DOI: 10.1080/07391102.2022.2163698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/23/2022] [Indexed: 01/12/2023]
Abstract
The objective of the study was to identify potential inhibitors of Influenza surface Hemagglutinin (HA), which plays key role in the entry and replication of Influenza virus into the host cell. As ligands, seven vitamins and their derivatives were selected after initial screening based on their metabolizable capacity with no reported side effects, for in silico studies. Docking, and Post docking analysis (X Score and Ligplot+) were performed against nine Influenza HA targets for the vitamins and its derivatives. 'Vitamin Derivatives' with top docking score were further analysed by MD Simulations and free energy was calculated using MMGBSA module. FMNNa and FMNCa displayed high binding free energy with Influenza HA, thereby exhibiting potential as HA inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ananyaa Agrawal
- University School of Chemical Technology, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, India
| | - Pratibha Chanana
- University School of Chemical Technology, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, India
| | - Vikas Yadav
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Vilakshan Bhutani
- University School of Chemical Technology, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, India
| | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Aradhana Srivastava
- University School of Chemical Technology, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, India
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4
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Expanding the Functionality of an Autoinduction Device for Repression of Gene Expression in Bacillus subtilis. Int J Mol Sci 2022; 24:ijms24010084. [PMID: 36613548 PMCID: PMC9820800 DOI: 10.3390/ijms24010084] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022] Open
Abstract
Autonomous control of gene expression through engineered quorum-sensing processes is broadly applicable to biosynthetic pathways, including simultaneous control of different genes. It is also a powerful tool for balancing growth and production. We had previously engineered a modular autoinduction device for the control of gene expression in B. subtilis. Now, we expand its functionality to repress gene expression autonomously. The engineered R8 promoter responds to AHL accumulation in the culture medium. In a riboflavin-producing strain, the AHL-Lux complex exerts 5-fold repression on the R8-driven expression of the flavokinase/FAD synthetase gene ribC, resulting in a higher titer of the vitamin. We engineered a strain able to autonomously induce and repress different genes simultaneously, demonstrating the potential of the device for use in metabolic engineering.
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5
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Roseoflavin, a Natural Riboflavin Analogue, Possesses In Vitro and In Vivo Antiplasmodial Activity. Antimicrob Agents Chemother 2022; 66:e0054022. [PMID: 36094195 PMCID: PMC9578400 DOI: 10.1128/aac.00540-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ability of the human malaria parasite Plasmodium falciparum to access and utilize vital nutrients is critical to its growth and proliferation. Molecules that interfere with these processes could potentially serve as antimalarials. We found that two riboflavin analogues, roseoflavin and 8-aminoriboflavin, inhibit malaria parasite proliferation by targeting riboflavin metabolism and/or the utilization of the riboflavin metabolites flavin mononucleotide and flavin adenine dinucleotide. An additional eight riboflavin analogues were evaluated, but none were found to be more potent than roseoflavin, nor was their activity on target. Focusing on roseoflavin, we tested its antimalarial activity in vivo against Plasmodium vinckei vinckei in mice. We found that roseoflavin decreased the parasitemia by 46-fold following a 4 day suppression test and, on average, increased the survival of mice by 4 to 5 days. Our data are consistent with riboflavin metabolism and/or the utilization of riboflavin-derived cofactors being viable drug targets for the development of new antimalarials and that roseoflavin could serve as a potential starting point.
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6
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Giarimoglou N, Kouvela A, Maniatis A, Papakyriakou A, Zhang J, Stamatopoulou V, Stathopoulos C. A Riboswitch-Driven Era of New Antibacterials. Antibiotics (Basel) 2022; 11:antibiotics11091243. [PMID: 36140022 PMCID: PMC9495366 DOI: 10.3390/antibiotics11091243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/01/2022] [Accepted: 09/08/2022] [Indexed: 11/26/2022] Open
Abstract
Riboswitches are structured non-coding RNAs found in the 5′ UTR of important genes for bacterial metabolism, virulence and survival. Upon the binding of specific ligands that can vary from simple ions to complex molecules such as nucleotides and tRNAs, riboswitches change their local and global mRNA conformations to affect downstream transcription or translation. Due to their dynamic nature and central regulatory role in bacterial metabolism, riboswitches have been exploited as novel RNA-based targets for the development of new generation antibacterials that can overcome drug-resistance problems. During recent years, several important riboswitch structures from many bacterial representatives, including several prominent human pathogens, have shown that riboswitches are ideal RNA targets for new compounds that can interfere with their structure and function, exhibiting much reduced resistance over time. Most interestingly, mainstream antibiotics that target the ribosome have been shown to effectively modulate the regulatory behavior and capacity of several riboswitches, both in vivo and in vitro, emphasizing the need for more in-depth studies and biological evaluation of new antibiotics. Herein, we summarize the currently known compounds that target several main riboswitches and discuss the role of mainstream antibiotics as modulators of T-box riboswitches, in the dawn of an era of novel inhibitors that target important bacterial regulatory RNAs.
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Affiliation(s)
- Nikoleta Giarimoglou
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Adamantia Kouvela
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Alexandros Maniatis
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Athanasios Papakyriakou
- Institute of Biosciences & Applications, National Centre for Scientific Research “Demokritos”, Ag. Paraskevi, 15341 Athens, Greece
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | | | - Constantinos Stathopoulos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
- Correspondence: ; Tel.: +30-2610-997932
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7
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Moreno A, Taleb V, Sebastián M, Anoz-Carbonell E, Martínez-Júlvez M, Medina M. Cofactors and pathogens: Flavin mononucleotide and flavin adenine dinucleotide (FAD) biosynthesis by the FAD synthase from Brucella ovis. IUBMB Life 2021; 74:655-671. [PMID: 34813144 PMCID: PMC9299109 DOI: 10.1002/iub.2576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/14/2021] [Accepted: 10/26/2021] [Indexed: 02/02/2023]
Abstract
The biosynthesis of the flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), cofactors used by 2% of proteins, occurs through the sequential action of two ubiquitous activities: a riboflavinkinase (RFK) that phosphorylates the riboflavin (RF) precursor to FMN, and a FMN:adenylyltransferase (FMNAT) that transforms FMN into FAD. In most mammals two different monofunctional enzymes have each of these activities, but in prokaryotes a single bifunctional enzyme, FAD synthase (FADS), holds them. Differential structural and functional traits for RFK and FMNAT catalysis between bacteria and mammals, as well as within the few bacterial FADSs so far characterized, has envisaged the potentiality of FADSs from pathogens as targets for the development of species‐specific inhibitors. Here, we particularly characterize the FADS from the ovine pathogen Brucella ovis (BoFADS), causative agent of brucellosis. We show that BoFADS has RFK activity independently of the media redox status, but its FMNAT activity (in both forward and reverse senses) only occurs under strong reducing conditions. Moreover, kinetics for flavin and adenine nucleotides binding to the RFK site show that BoFADS binds preferentially the substrates of the RFK reaction over the products and that the adenine nucleotide must bind prior to flavin entrapment. These results, together with multiple sequence alignments and phylogenetic analysis, point to variability in the less conserved regions as contributing to the species‐specific features in prokaryotic FADSs, including those from pathogens, that allow them to adopt alternative strategies in FMN and FAD biosynthesis and overall flavin homeostasis.
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Affiliation(s)
- Andrea Moreno
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza, Spain.,Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | - Victor Taleb
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza, Spain
| | - María Sebastián
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza, Spain
| | - Ernesto Anoz-Carbonell
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza, Spain
| | - Marta Martínez-Júlvez
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza, Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza, Spain
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8
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Silvis MR, Rajendram M, Shi H, Osadnik H, Gray AN, Cesar S, Peters JM, Hearne CC, Kumar P, Todor H, Huang KC, Gross CA. Morphological and Transcriptional Responses to CRISPRi Knockdown of Essential Genes in Escherichia coli. mBio 2021; 12:e0256121. [PMID: 34634934 PMCID: PMC8510551 DOI: 10.1128/mbio.02561-21] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 09/09/2021] [Indexed: 01/03/2023] Open
Abstract
CRISPR interference (CRISPRi) has facilitated the study of essential genes in diverse organisms using both high-throughput and targeted approaches. Despite the promise of this technique, no comprehensive arrayed CRISPRi library targeting essential genes exists for the model bacterium Escherichia coli, or for any Gram-negative species. Here, we built and characterized such a library. Each of the ∼500 strains in our E. coli library contains an inducible, chromosomally integrated single guide RNA (sgRNA) targeting an essential (or selected nonessential) gene and can be mated with a pseudo-Hfr donor strain carrying a dcas9 cassette to create a CRISPRi knockdown strain. Using this system, we built an arrayed library of CRISPRi strains and performed population and single-cell growth and morphology measurements as well as targeted follow-up experiments. These studies found that inhibiting translation causes an extended lag phase, identified new modulators of cell morphology, and revealed that the morphogene mreB is subject to transcriptional feedback regulation, which is critical for the maintenance of morphology. Our findings highlight canonical and noncanonical roles for essential genes in numerous aspects of cellular homeostasis. IMPORTANCE Essential genes make up only ∼5 to 10% of the genetic complement in most organisms but occupy much of their protein synthesis and account for almost all antibiotic targets. Despite the importance of essential genes, their intractability has, until recently, hampered efforts to study them. CRISPRi has facilitated the study of essential genes by allowing inducible and titratable depletion. However, all large-scale CRISPRi studies in Gram-negative bacteria thus far have used plasmids to express CRISPRi components and have been constructed in pools, limiting their utility for targeted assays and complicating the determination of antibiotic effects. Here, we use a modular method to construct an arrayed library of chromosomally integrated CRISPRi strains targeting the essential genes of the model bacterium Escherichia coli. This library enables targeted studies of essential gene depletions and high-throughput determination of antibiotic targets and facilitates studies targeting the outer membrane, an essential component that serves as the major barrier to antibiotics.
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Affiliation(s)
- Melanie R. Silvis
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, USA
| | - Manohary Rajendram
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Handuo Shi
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Hendrik Osadnik
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, USA
| | - Andrew N. Gray
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, USA
| | - Spencer Cesar
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Jason M. Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Cameron C. Hearne
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, USA
| | - Parth Kumar
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, USA
| | - Horia Todor
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Carol A. Gross
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, USA
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9
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MdaB and NfrA, two novel reductases important in the survival and persistence of the major enteropathogen Campylobacter jejuni. J Bacteriol 2021; 204:e0042121. [PMID: 34606373 PMCID: PMC8765430 DOI: 10.1128/jb.00421-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The paralogues RrpA and RrpB, which are members of the MarR family of DNA binding proteins, are important for the survival of the global bacterial foodborne pathogen Campylobacter jejuni under redox stress. We report that RrpA is a positive regulator of mdaB, encoding a flavin-dependent quinone reductase that contributes to the protection from redox stress mediated by structurally diverse quinones, while RrpB negatively regulates the expression of cj1555c (renamed nfrA for NADPH-flavin reductase A), encoding a flavin reductase. NfrA reduces riboflavin at a greater rate than its derivatives, suggesting that exogenous free flavins are the natural substrate. MdaB and NfrA both prefer NADPH as an electron donor. Cysteine substitution and posttranslational modification analyses indicated that RrpA and RrpB employ a cysteine-based redox switch. Complete genome sequence analyses revealed that mdaB is frequently found in Campylobacter and related Helicobacter spp., while nfrA is predominant in C. jejuni strains. Quinones and flavins are redox cycling agents secreted by a wide range of cell types that can form damaging superoxide by one-electron reactions. We propose a model for stress adaptation where MdaB and NfrA facilitate a two-electron reduction mechanism to the less toxic hydroquinones, thus aiding survival and persistence of this major pathogen. IMPORTANCE Changes in cellular redox potential result in alteration in the oxidation state of intracellular metabolites and enzymes; consequently, cells make adjustments that favor growth and survival. The work we present here answers some of the many questions that have remained elusive over the years of investigation into the enigmatic microaerophile bacterium Campylobacter jejuni. We employed molecular approaches to understand the regulation mechanisms and functional analyses to reveal the roles of two novel quinone and flavin reductases; both serve as major pools of cellular redox-active molecules. This work extends our knowledge on bacterial redox sensing mechanisms and the significance of hemostasis.
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10
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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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11
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An rfuABCD-like operon and its relationship to riboflavin utilization and mammalian. Infect Immun 2021; 89:e0030721. [PMID: 34310888 DOI: 10.1128/iai.00307-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Riboflavin is an essential micronutrient, but its transport and utilization has remained largely understudied among pathogenic spirochetes. Here we show that Borrelia burgdorferi, the zoonotic spirochete that causes Lyme disease, is able to import riboflavin via products of its rfuABCD-like operon as well as synthesize flavin mononucleotide and flavin adenine dinucleotide despite lacking canonical genes for their synthesis. Additionally, a mutant deficient in the rfuABCD-like operon is resistant to the antimicrobial effect of roseoflavin, a natural riboflavin analog, and is attenuated in a murine model of Lyme borreliosis. Our combined results indicate that not only are riboflavin and the maintenance of flavin pools essential for B. burgdorferi growth, but that flavin utilization and its downstream products (e.g., flavoproteins) may play a more prominent role in B. burgdorferi pathogenesis than previously appreciated.
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12
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Schneider C, Mack M. A second riboflavin import system is present in flavinogenic Streptomyces davaonensis and supports roseoflavin biosynthesis. Mol Microbiol 2021; 116:470-482. [PMID: 33829573 DOI: 10.1111/mmi.14726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 12/01/2022]
Abstract
The antibiotic roseoflavin is produced by Streptomyces davaonensis in the stationary phase of growth. To support biosynthesis of the secondary metabolite roseoflavin, S. davaonensis underwent several genetic adaptations with regard to metabolism of the roseoflavin precursor and primary metabolite riboflavin. In addition to 17 riboflavin biosynthesis genes at different chromosomal locations, S. davaonensis contains the riboflavin transporter gene ribM being part of the riboflavin biosynthetic operon ribE1MAB5H. Deletion of this operon generated riboflavin auxotrophic S. davaonensis strains. The finding that S. davaonensis ΔribE1MAB5H was able to grow in a culture medium containing low levels of riboflavin indicated that in addition to RibM, a second riboflavin transporter is present in this bacterium. The S. davaonensis genes ribXY (former rosXY) represented candidate genes for such a second riboflavin transport system and the results of our experiments now show that RibXY from S. davaonensis is a highly efficient riboflavin importer but not a roseoflavin importer.
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Affiliation(s)
- Carmen Schneider
- Institute for Technical Microbiology, Department of Biotechnology, Mannheim University of Applied Sciences, Mannheim, Germany
| | - Matthias Mack
- Institute for Technical Microbiology, Department of Biotechnology, Mannheim University of Applied Sciences, Mannheim, Germany
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13
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Zhou LF, Wu J, Li S, Li Q, Jin LP, Yin CP, Zhang YL. Antibacterial Potential of Termite-Associated Streptomyces spp. ACS OMEGA 2021; 6:4329-4334. [PMID: 33623843 PMCID: PMC7893633 DOI: 10.1021/acsomega.0c05580] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
Twenty-one strains of termite-associated actinomycetes were tested for their activities against three bacteria. The results showed that nine strains showed bacteriostatic activities against at least one tested bacterium, and the actinomycete YH01, which was isolated from the body surface of the queen of Odontotermes formosanus, had potent antibacterial activity. The YH01 was further identified as Streptomyces davaonensis. Two metabolites roseoflavin (1) and 8-methylamino-8-demethyl-d-riboflavin (2) were isolated and purified from S. davaonensis YH01. Their structures were determined by NMR, MS, and the related literature. The metabolite 1 showed strong inhibition activities against Bacillus subtilis (MIC = 1.56 μg/mL) and Staphylococcus aureus (MIC = 3.125 μg/mL), which were comparable to referenced gentamycin sulfate, with MIC values of 1.56 and 1.56 μg/mL, respectively. Furthermore, the anti-MRSA potential of compound 1 was determined against nine kinds of MRSA strains, with inhibition zones in the ranges of 12.7-19.7 mm under a concentration of 15 μg/6 mm discs and 18.3-22.7 mm under a concentration of 30 μg/6 mm discs. However, metabolite 1 had no inhibitory effect on Gram-negative bacteria. These results suggested that roseoflavin produced by YH01 holds promise for use against Gram-positive bacteria, especially to MRSA.
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Affiliation(s)
- Ling-Feng Zhou
- College
of Life Sciences, Anhui Agricultural University, Hefei 230036, People’s Republic of China
| | - Jun Wu
- College
of Life Sciences, Anhui Agricultural University, Hefei 230036, People’s Republic of China
| | - Shuai Li
- College
of Chemistry and Life Sciences, Zhejiang
Normal University, Jinhua 321004, People’s Republic
of China
| | - Qi Li
- Zhejiang
Jinhua Guangfu Hospital, Jinhua 321004, People’s Republic
of China
| | - Li-Ping Jin
- College
of Chemistry and Life Sciences, Zhejiang
Normal University, Jinhua 321004, People’s Republic
of China
| | - Cai-Ping Yin
- College
of Life Sciences, Anhui Agricultural University, Hefei 230036, People’s Republic of China
| | - Ying-Lao Zhang
- College
of Life Sciences, Anhui Agricultural University, Hefei 230036, People’s Republic of China
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14
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Molecular insights into the mechanism of substrate binding and catalysis of bifunctional FAD synthetase from Staphylococcus aureus. Biochimie 2021; 182:217-227. [PMID: 33516756 DOI: 10.1016/j.biochi.2021.01.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/05/2021] [Accepted: 01/19/2021] [Indexed: 11/24/2022]
Abstract
Flavin adenine dinucleotide synthetase (FADS), a bifunctional prokaryotic enzyme, is involved in the synthesis of two vital cofactors, flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). Here, we investigated the biochemical characteristics of FADS from Staphylococcus aureus (Sa), a pathogenic bacteria causing food-borne diseases. The SaFADS possesses riboflavin kinase (RFK) and FMN adenylyltransferase (FMNAT) activities that transforms riboflavin to FMN and FMN to FAD, respectively. The FMNAT domain also exhibits reversible FAD pyrophosphorylase activity (FADpp). Further, we show that the FMNAT and FADpp activities are dependent on the reducing environment. Mutations of the conserved K289 and F290 residues present on the RFK domain affect the kinetic parameters of both the RFK and FMNAT domains. Additionally, the molecular dynamics analysis of apo and riboflavin: ATP: Mg2+ ternary complex of SaFADS shows that F290 is involved in stabilizing the active site geometry to hold the enzyme-substrate complex. In addition, the deletion of the αh2 helix that acts as a connecting linker between the FMNAT and RFK domains showed substantial loss of their activities. The helix deletion could have affected the flap motion of L2c, L4c, β4n and L3n present in the close proximity resulting in the distortion of the active site geometry. In conclusion, our study has characterized the RFK and FMNAT activities of SaFADS and shown the importance of conserved K289 and F290 in RFK activity. As FADSs are potential drug targets, understanding their mechanism of action might help in discovering species-specific antibacterial drugs.
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15
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Structural basis for antibiotic action of the B 1 antivitamin 2'-methoxy-thiamine. Nat Chem Biol 2020; 16:1237-1245. [PMID: 32839604 DOI: 10.1038/s41589-020-0628-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 07/17/2020] [Indexed: 02/07/2023]
Abstract
The natural antivitamin 2'-methoxy-thiamine (MTh) is implicated in the suppression of microbial growth. However, its mode of action and enzyme-selective inhibition mechanism have remained elusive. Intriguingly, MTh inhibits some thiamine diphosphate (ThDP) enzymes, while being coenzymatically active in others. Here we report the strong inhibition of Escherichia coli transketolase activity by MTh and unravel its mode of action and the structural basis thereof. The unique 2'-methoxy group of MTh diphosphate (MThDP) clashes with a canonical glutamate required for cofactor activation in ThDP-dependent enzymes. This glutamate is forced into a stable, anticatalytic low-barrier hydrogen bond with a neighboring glutamate, disrupting cofactor activation. Molecular dynamics simulations of transketolases and other ThDP enzymes identify active-site flexibility and the topology of the cofactor-binding locale as key determinants for enzyme-selective inhibition. Human enzymes either retain enzymatic activity with MThDP or preferentially bind authentic ThDP over MThDP, while core bacterial metabolic enzymes are inhibited, demonstrating therapeutic potential.
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16
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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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17
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Kißling L, Schneider C, Seibel K, Dorjjugder N, Busche T, Kalinowski J, Mack M. The roseoflavin producer
Streptomyces davaonensis
has a high catalytic capacity and specific genetic adaptations with regard to the biosynthesis of riboflavin. Environ Microbiol 2020; 22:3248-3265. [DOI: 10.1111/1462-2920.15066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/06/2020] [Accepted: 05/10/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Lena Kißling
- Institute for Technical Microbiology, Department of Biotechnology Mannheim University of Applied Sciences Mannheim 68163 Germany
| | - Carmen Schneider
- Institute for Technical Microbiology, Department of Biotechnology Mannheim University of Applied Sciences Mannheim 68163 Germany
| | - Katharina Seibel
- Institute for Technical Microbiology, Department of Biotechnology Mannheim University of Applied Sciences Mannheim 68163 Germany
| | - Nasanjargal Dorjjugder
- Institute for Technical Microbiology, Department of Biotechnology Mannheim University of Applied Sciences Mannheim 68163 Germany
| | - Tobias Busche
- Center for Biotechnology Bielefeld University Bielefeld 33594 Germany
| | - Jörn Kalinowski
- Center for Biotechnology Bielefeld University Bielefeld 33594 Germany
| | - Matthias Mack
- Institute for Technical Microbiology, Department of Biotechnology Mannheim University of Applied Sciences Mannheim 68163 Germany
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18
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Feyza Özgen F, Runda ME, Burek BO, Wied P, Bloh JZ, Kourist R, Schmidt S. Artifizielle Lichtsammelkomplexe ermöglichen Rieske‐Oxygenase‐ katalysierte Hydroxylierungen in nicht‐photosynthetischen Zellen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- F. Feyza Özgen
- Institute für Molekulare Biotechnologie Technische Universität Graz Petersgasse 14/1 8010 Graz Österreich
| | - Michael E. Runda
- Institute für Molekulare Biotechnologie Technische Universität Graz Petersgasse 14/1 8010 Graz Österreich
| | - Bastien O. Burek
- DECHEMA-Forschungsinstitut Theodor-Heuss-Allee 25 60486 Frankfurt am Main Deutschland
| | - Peter Wied
- Institute für Molekulare Biotechnologie Technische Universität Graz Petersgasse 14/1 8010 Graz Österreich
| | - Jonathan Z. Bloh
- DECHEMA-Forschungsinstitut Theodor-Heuss-Allee 25 60486 Frankfurt am Main Deutschland
| | - Robert Kourist
- Institute für Molekulare Biotechnologie Technische Universität Graz Petersgasse 14/1 8010 Graz Österreich
| | - Sandy Schmidt
- Institute für Molekulare Biotechnologie Technische Universität Graz Petersgasse 14/1 8010 Graz Österreich
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19
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Feyza Özgen F, Runda ME, Burek BO, Wied P, Bloh JZ, Kourist R, Schmidt S. Artificial Light-Harvesting Complexes Enable Rieske Oxygenase Catalyzed Hydroxylations in Non-Photosynthetic cells. Angew Chem Int Ed Engl 2020; 59:3982-3987. [PMID: 31850622 PMCID: PMC7065155 DOI: 10.1002/anie.201914519] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Indexed: 01/27/2023]
Abstract
In this study, we coupled a well-established whole-cell system based on E. coli via light-harvesting complexes to Rieske oxygenase (RO)-catalyzed hydroxylations in vivo. Although these enzymes represent very promising biocatalysts, their practical applicability is hampered by their dependency on NAD(P)H as well as their multicomponent nature and intrinsic instability in cell-free systems. In order to explore the boundaries of E. coli as chassis for artificial photosynthesis, and due to the reported instability of ROs, we used these challenging enzymes as a model system. The light-driven approach relies on light-harvesting complexes such as eosin Y, 5(6)-carboxyeosin, and rose bengal and sacrificial electron donors (EDTA, MOPS, and MES) that were easily taken up by the cells. The obtained product formations of up to 1.3 g L-1 and rates of up to 1.6 mm h-1 demonstrate that this is a comparable approach to typical whole-cell transformations in E. coli. The applicability of this photocatalytic synthesis has been demonstrated and represents the first example of a photoinduced RO system.
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Affiliation(s)
- F. Feyza Özgen
- Institute of Molecular BiotechnologyGraz University of TechnologyPetersgasse 14/18010GrazAustria
| | - Michael E. Runda
- Institute of Molecular BiotechnologyGraz University of TechnologyPetersgasse 14/18010GrazAustria
| | - Bastien O. Burek
- DECHEMA-ForschungsinstitutTheodor-Heuss-Allee 2560486Frankfurt am MainGermany
| | - Peter Wied
- Institute of Molecular BiotechnologyGraz University of TechnologyPetersgasse 14/18010GrazAustria
| | - Jonathan Z. Bloh
- DECHEMA-ForschungsinstitutTheodor-Heuss-Allee 2560486Frankfurt am MainGermany
| | - Robert Kourist
- Institute of Molecular BiotechnologyGraz University of TechnologyPetersgasse 14/18010GrazAustria
| | - Sandy Schmidt
- Institute of Molecular BiotechnologyGraz University of TechnologyPetersgasse 14/18010GrazAustria
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20
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Bourdeaux F, Ludwig P, Paithankar K, Sander B, Essen LO, Grininger M, Mack M. Comparative biochemical and structural analysis of the flavin-binding dodecins from Streptomyces davaonensis and Streptomyces coelicolor reveals striking differences with regard to multimerization. MICROBIOLOGY-SGM 2020; 165:1095-1106. [PMID: 31339487 DOI: 10.1099/mic.0.000835] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Dodecins are small flavin-binding proteins that are widespread amongst haloarchaeal and bacterial species. Haloarchaeal dodecins predominantly bind riboflavin, while bacterial dodecins have been reported to bind riboflavin-5'-phosphate, also called flavin mononucleotide (FMN), and the FMN derivative, flavin adenine dinucleotide (FAD). Dodecins form dodecameric complexes and represent buffer systems for cytoplasmic flavins. In this study, dodecins of the bacteria Streptomyces davaonensis (SdDod) and Streptomyces coelicolor (ScDod) were investigated. Both dodecins showed an unprecedented low affinity for riboflavin, FMN and FAD when compared to other bacterial dodecins. Significant binding of FMN and FAD occurred at relatively low temperatures and under acidic conditions. X-ray diffraction analyses of SdDod and ScDod revealed that the structures of both Streptomyces dodecins are highly similar, which explains their similar binding properties for FMN and FAD. In contrast, SdDod and ScDod showed very different properties with regard to the stability of their dodecameric complexes. Site-directed mutagenesis experiments revealed that a specific salt bridge (D10-K62) is responsible for this difference in stability.
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Affiliation(s)
- Florian Bourdeaux
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Petra Ludwig
- Institute for Technical Microbiology, Faculty for Biotechnology, Mannheim University of Applied Sciences, 68163 Mannheim, Germany
| | - Karthik Paithankar
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Bodo Sander
- Unit for Structural Biology, Department of Chemistry and Biology, Philipps University Marburg, 35032 Marburg, Germany
| | - Lars-Oliver Essen
- Unit for Structural Biology, Department of Chemistry and Biology, Philipps University Marburg, 35032 Marburg, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Matthias Mack
- Institute for Technical Microbiology, Faculty for Biotechnology, Mannheim University of Applied Sciences, 68163 Mannheim, Germany
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21
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Rodionova IA, Heidari Tajabadi F, Zhang Z, Rodionov DA, Saier MH. A Riboflavin Transporter in Bdellovibrio exovorous JSS. J Mol Microbiol Biotechnol 2019; 29:27-34. [PMID: 31509826 DOI: 10.1159/000501354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/05/2019] [Indexed: 12/12/2022] Open
Abstract
The ImpX transporters of the drug/metabolite transporter superfamily were first proposed to transport riboflavin (RF; vitamin B2) based on findings of a cis-regulatory RNA element responding to flavin mononucleotide (an FMN riboswitch). Bdellovibrio exovorous JSS has a homolog belonging to this superfamily. It has 10 TMSs and shows 30% identity to the previously characterized ImpX transporter from Fusobacterium nucleatum. However, the ImpX homolog is not regulated by an FMN-riboswitch. In order to test the putative function of the ImpX homolog from B. exovorous (BexImpX), we cloned and heterologously expressed its gene. We used functional complementation, growth inhibition experiments, direct uptake experiments and inhibition studies, suggesting a high degree of specificity for RF uptake. The EC50 for growth with RF was estimated to be in the range 0.5-1 µM, estimated from the half-maximal RF concentration supporting the growth of a RF auxotrophic Escherichia coli strain, but the Khalf for RF uptake was 20 µM. Transport experiments suggested that the energy source is the proton motive force but that NaCl stimulates uptake. Thus, members of the ImpX family members are capable of RF uptake, not only in RF prototrophic species such as F. nucleatum, but also in the B2 auxotrophic species, B. exovorous.
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Affiliation(s)
- Irina A Rodionova
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, San Diego, California, USA
| | - Fereshteh Heidari Tajabadi
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, San Diego, California, USA.,Department of Plant Protection, University of Tehran, Tehran, Iran
| | - Zhongge Zhang
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, San Diego, California, USA
| | - Dmitry A Rodionov
- Sanford Burnham Prebys Medical Research Institute, San Diego, California, USA
| | - Milton H Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, San Diego, California, USA,
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22
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Mora-Lugo R, Stegmüller J, Mack M. Metabolic engineering of roseoflavin-overproducing microorganisms. Microb Cell Fact 2019; 18:146. [PMID: 31451111 PMCID: PMC6709556 DOI: 10.1186/s12934-019-1181-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/30/2019] [Indexed: 12/20/2022] Open
Abstract
Background Roseoflavin, a promising broad-spectrum antibiotic, is naturally produced by the bacteria Streptomyces davaonensis and Streptomyces cinnabarinus. The key enzymes responsible for roseoflavin biosynthesis and the corresponding genes were recently identified. In this study we aimed to enhance roseoflavin production in S. davaonensis and to synthesize roseoflavin in the heterologous hosts Bacillus subtilis and Corynebacterium glutamicum by (over)expression of the roseoflavin biosynthesis genes. Results While expression of the roseoflavin biosynthesis genes from S. davaonensis was not observed in recombinant strains of B. subtilis, overexpression was successful in C. glutamicum and S. davaonensis. Under the culture conditions tested, a maximum of 1.6 ± 0.2 µM (ca. 0.7 mg/l) and 34.9 ± 5.2 µM (ca. 14 mg/l) roseoflavin was produced with recombinant strains of C. glutamicum and S. davaonensis, respectively. In S. davaonensis the roseoflavin yield was increased by 78%. Conclusions The results of this study provide a sound basis for the development of an economical roseoflavin production process. Electronic supplementary material The online version of this article (10.1186/s12934-019-1181-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rodrigo Mora-Lugo
- Institute for Technical Microbiology, Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163, Mannheim, Germany
| | - Julian Stegmüller
- Institute for Technical Microbiology, Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163, Mannheim, Germany
| | - Matthias Mack
- Institute for Technical Microbiology, Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163, Mannheim, Germany.
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23
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Disney MD. Targeting RNA with Small Molecules To Capture Opportunities at the Intersection of Chemistry, Biology, and Medicine. J Am Chem Soc 2019; 141:6776-6790. [PMID: 30896935 DOI: 10.1021/jacs.8b13419] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The biology of healthy and disease-affected cells is often mediated by RNA structures, desirable targets for small molecule chemical probes and lead medicines. Although structured regions are found throughout the transcriptome, some even with demonstrated functionality, human RNAs are considered recalcitrant to small molecule targeting. However, targeting structured regions with small molecules provides an important alternative to oligonucleotides that target sequence. In this Perspective, we describe challenges and progress in developing small molecules interacting with RNA (SMIRNAs) to capture their significant opportunities at the intersection of chemistry, biology, and medicine. Key to establishing a new paradigm in chemical biology and medicine is the development of methods to obtain, preferably by design, bioactive compounds that modulate RNA targets and companion methods that validate their direct effects in cells and pre-clinical models. While difficult, demonstration of direct target engagement in the complex cellular milieu, along with methods to establish modes of action, is required to push this field forward. We also describe frameworks for accelerated advancements in this burgeoning area, their implications, key new technologies for development of SMIRNAs, and milestones that have led to broader acceptance of RNA as a small molecule druggable target.
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Affiliation(s)
- Matthew D Disney
- Department of Chemistry , The Scripps Research Institute , Jupiter , Florida 33458 , United States
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24
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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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25
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Lakemeyer M, Zhao W, Mandl FA, Hammann P, Sieber SA. Thinking Outside the Box-Novel Antibacterials To Tackle the Resistance Crisis. Angew Chem Int Ed Engl 2018; 57:14440-14475. [PMID: 29939462 DOI: 10.1002/anie.201804971] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Indexed: 12/13/2022]
Abstract
The public view on antibiotics as reliable medicines changed when reports about "resistant superbugs" appeared in the news. While reasons for this resistance development are easily spotted, solutions for re-establishing effective antibiotics are still in their infancy. This Review encompasses several aspects of the antibiotic development pipeline from very early strategies to mature drugs. An interdisciplinary overview is given of methods suitable for mining novel antibiotics and strategies discussed to unravel their modes of action. Select examples of antibiotics recently identified by using these platforms not only illustrate the efficiency of these measures, but also highlight promising clinical candidates with therapeutic potential. Furthermore, the concept of molecules that disarm pathogens by addressing gatekeepers of virulence will be covered. The Review concludes with an evaluation of antibacterials currently in clinical development. Overall, this Review aims to connect select innovative antimicrobial approaches to stimulate interdisciplinary partnerships between chemists from academia and industry.
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Affiliation(s)
- Markus Lakemeyer
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Weining Zhao
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Franziska A Mandl
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Peter Hammann
- R&D Therapeutic Area Infectious Diseases, Sanofi-Aventis (Deutschland) GmbH, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Stephan A Sieber
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
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26
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Lakemeyer M, Zhao W, Mandl FA, Hammann P, Sieber SA. Über bisherige Denkweisen hinaus - neue Wirkstoffe zur Überwindung der Antibiotika-Krise. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804971] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Markus Lakemeyer
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Weining Zhao
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Franziska A. Mandl
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Peter Hammann
- R&D Therapeutic Area Infectious Diseases; Sanofi-Aventis (Deutschland) GmbH; Industriepark Höchst 65926 Frankfurt am Main Deutschland
| | - Stephan A. Sieber
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
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Kapoor I, Nair SK. Structure-Guided Analyses of a Key Enzyme Involved in the Biosynthesis of an Antivitamin. Biochemistry 2018; 57:5282-5288. [PMID: 30125480 DOI: 10.1021/acs.biochem.8b00576] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
RosB catalyzes the formation of 8-aminoriboflavin 5'-phosphate (AFP), the key intermediate in roseoflavin biosynthesis, from the metabolic precursors riboflavin 5'-phosphate (RP, also known as FMN) and glutamate. The conversion of the aromatic methyl group at position 8 in RP into the aromatic amine in AFP occurs via two intermediates, namely, the aldehyde 8-formyl-RP and the acid 8-carboxy-RP. To gain insights into the mechanism for this chemically challenging transformation, we utilized a structure-based approach to identify active site variants of RosB that stall the reaction at various points along the reaction coordinate. Crystal structures of individual variants in complex with different reaction intermediates, identified via mass spectroscopic analysis, illuminate conformational changes that occur at the active site during multistep conversion. These studies provide a plausible route for the progression of the reaction and a molecular rationale for the mechanism of this unusual biocatalyst.
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Strong increase in the autofluorescence of cells signals struggle for survival. Sci Rep 2018; 8:12088. [PMID: 30108248 PMCID: PMC6092379 DOI: 10.1038/s41598-018-30623-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 08/03/2018] [Indexed: 01/13/2023] Open
Abstract
Prokaryotic and eukaryotic cells exhibit an intrinsic natural fluorescence due to the presence of fluorescent cellular structural components and metabolites. Therefore, cellular autofluorescence (AF) is expected to vary with the metabolic states of cells. We examined how exposure to the different stressors changes the AF of Escherichia coli cells. We observed that bactericidal treatments increased green cellular AF, and that de novo protein synthesis was required for the observed AF increase. Excitation and emission spectra and increased expression of the genes from the flavin biosynthesis pathway, strongly suggested that flavins are major contributors to the increased AF. An increased expression of genes encoding diverse flavoproteins which are involved in energy production and ROS detoxification, indicates a cellular strategy to cope with severe stresses. An observed increase in AF under stress is an evolutionary conserved phenomenon as it occurs not only in cells from different bacterial species, but also in yeast and human cells.
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29
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Rizvi NF, Howe JA, Nahvi A, Klein DJ, Fischmann TO, Kim HY, McCoy MA, Walker SS, Hruza A, Richards MP, Chamberlin C, Saradjian P, Butko MT, Mercado G, Burchard J, Strickland C, Dandliker PJ, Smith GF, Nickbarg EB. Discovery of Selective RNA-Binding Small Molecules by Affinity-Selection Mass Spectrometry. ACS Chem Biol 2018; 13:820-831. [PMID: 29412640 DOI: 10.1021/acschembio.7b01013] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Recent advances in understanding the relevance of noncoding RNA (ncRNA) to disease have increased interest in drugging ncRNA with small molecules. The recent discovery of ribocil, a structurally distinct synthetic mimic of the natural ligand of the flavin mononucleotide (FMN) riboswitch, has revealed the potential chemical diversity of small molecules that target ncRNA. Affinity-selection mass spectrometry (AS-MS) is theoretically applicable to high-throughput screening (HTS) of small molecules binding to ncRNA. Here, we report the first application of the Automated Ligand Detection System (ALIS), an indirect AS-MS technique, for the selective detection of small molecule-ncRNA interactions, high-throughput screening against large unbiased small-molecule libraries, and identification and characterization of novel compounds (structurally distinct from both FMN and ribocil) that target the FMN riboswitch. Crystal structures reveal that different compounds induce various conformations of the FMN riboswitch, leading to different activity profiles. Our findings validate the ALIS platform for HTS screening for RNA-binding small molecules and further demonstrate that ncRNA can be broadly targeted by chemically diverse yet selective small molecules as therapeutics.
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Affiliation(s)
- Noreen F. Rizvi
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - John A. Howe
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Ali Nahvi
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Daniel J. Klein
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | | | - Hai-Young Kim
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Mark A. McCoy
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Scott S. Walker
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Alan Hruza
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | | | - Chad Chamberlin
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Peter Saradjian
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | | | - Gabriel Mercado
- Biodesy, Inc., South San Francisco, California 94080, United States
| | - Julja Burchard
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | | | | | - Graham F. Smith
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
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30
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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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31
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Michelson K, Sanford RA, Valocchi AJ, Werth CJ. Nanowires of Geobacter sulfurreducens Require Redox Cofactors to Reduce Metals in Pore Spaces Too Small for Cell Passage. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:11660-11668. [PMID: 28929755 DOI: 10.1021/acs.est.7b02531] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Members of the Geobacteraceae family are ubiquitous metal reducers that utilize conductive "nanowires" to reduce Mn(IV) and Fe(III) oxides in anaerobic sediments. However, it is not currently known if and to what extent the Mn(IV) and Fe(III) oxides in soil grains and low permeability sediments that are sequestered in pore spaces too small for cell passage can be reduced by long-range extracellular electron transport via Geobacter nanowires, and what mechanisms control this reduction. We developed a microfluidic reactor that physically separates Geobacter sulfurreducens from the Mn(IV) mineral birnessite by a 1.4 μm thick wall containing <200 nm pores. Using optical microscopy and Raman spectroscopy, we show that birnessite can be reduced up to 15 μm away from cell bodies, similar to the reported length of Geobacter nanowires. Reduction across the nanoporous wall required reducing conditions, provided by Escherichia coli, and an exogenous supply of riboflavin. Our results discount electron shuttling by dissolved flavins, and instead support their role as bound redox cofactors in electron transport from nanowires to metal oxides. We also show that upon addition of a soluble electron shuttle (i.e., AQDS), reduction extends beyond the reported nanowire length up to 40 μm into a layer of birnessite.
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Affiliation(s)
- Kyle Michelson
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign , 205 North Mathews Avenue, Urbana, Illinois 61801, United States
- Department of Civil, Architectural, and Environmental Engineering, University of Texas at Austin , 301 E. Dean Keeton Street, Austin, Texas 78712, United States
| | - Robert A Sanford
- Department of Geology, University of Illinois at Urbana-Champaign , 1301 West Green Street, Urbana, Illinois 61801, United States
| | - Albert J Valocchi
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign , 205 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Charles J Werth
- Department of Civil, Architectural, and Environmental Engineering, University of Texas at Austin , 301 E. Dean Keeton Street, Austin, Texas 78712, United States
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32
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Ignatov D, Johansson J. RNA-mediated signal perception in pathogenic bacteria. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28792118 DOI: 10.1002/wrna.1429] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/11/2017] [Accepted: 05/11/2017] [Indexed: 11/09/2022]
Abstract
Bacterial pathogens encounter several different environments during an infection, many of them possibly being detrimental. In order to sense its surroundings and adjust the gene expression accordingly, different regulatory schemes are undertaken. With these, the bacterium appropriately can differentiate between various environmental cues to express the correct virulence factor at the appropriate time and place. An attractive regulator device is RNA, which has an outstanding ability to alter its structure in response to external stimuli, such as metabolite concentration or alterations in temperature, to control its downstream gene expression. This review will describe the function of riboswitches and thermometers, with a particular emphasis on regulatory RNAs being important for bacterial pathogenicity. WIREs RNA 2017, 8:e1429. doi: 10.1002/wrna.1429 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Dmitriy Ignatov
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden.,Department of Molecular Biology, Umeå University, Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Jörgen Johansson
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden.,Department of Molecular Biology, Umeå University, Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
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33
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Sebastián M, Lira-Navarrete E, Serrano A, Marcuello C, Velázquez-Campoy A, Lostao A, Hurtado-Guerrero R, Medina M, Martínez-Júlvez M. The FAD synthetase from the human pathogen Streptococcus pneumoniae: a bifunctional enzyme exhibiting activity-dependent redox requirements. Sci Rep 2017; 7:7609. [PMID: 28790457 PMCID: PMC5548840 DOI: 10.1038/s41598-017-07716-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/28/2017] [Indexed: 11/12/2022] Open
Abstract
Prokaryotic bifunctional FAD synthetases (FADSs) catalyze the biosynthesis of FMN and FAD, whereas in eukaryotes two enzymes are required for the same purpose. FMN and FAD are key cofactors to maintain the flavoproteome homeostasis in all type of organisms. Here we shed light to the properties of the hitherto unstudied bacterial FADS from the human pathogen Streptococcus pneumoniae (SpnFADS). As other members of the family, SpnFADS catalyzes the three typical activities of prokaryotic FADSs: riboflavin kinase (RFK), ATP:FMN:adenylyltransferase (FMNAT), and FAD pyrophosphorylase (FADpp). However, several SpnFADS biophysical properties differ from those of other family members. In particular; i) the RFK activity is not inhibited by the riboflavin (RF) substrate, ii) the FMNAT and FADSpp activities require flavin substrates in the reduced state, iii) binding of adenine nucleotide ligands is required for the binding of flavinic substrates/products and iv) the monomer is the preferred state. Collectively, our results add interesting mechanistic differences among the few prokaryotic bifunctional FADSs already characterized, which might reflect the adaptation of the enzyme to relatively different environments. In a health point of view, differences among FADS family members provide us with a framework to design selective compounds targeting these enzymes for the treatment of diverse infectious diseases.
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Affiliation(s)
- María Sebastián
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) and GBsC-CSIC and BIFI-CSIC Joint Units, Universidad de Zaragoza, Zaragoza, Spain
| | - Erandi Lira-Navarrete
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) and GBsC-CSIC and BIFI-CSIC Joint Units, Universidad de Zaragoza, Zaragoza, Spain.,Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Ana Serrano
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) and GBsC-CSIC and BIFI-CSIC Joint Units, Universidad de Zaragoza, Zaragoza, Spain.,Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040, Madrid, Spain
| | - Carlos Marcuello
- Laboratorio de Microscopías Avanzadas (LMA), Instituto de Nanociencia de Aragón (INA), and Fundación INA, Universidad de Zaragoza, Zaragoza, Spain.,Univ Reims, Lab Rech Nanosci, EA4682, F-51100 Reims and INRA, FARE Lab, F-51100, Reims, France
| | - Adrián Velázquez-Campoy
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) and GBsC-CSIC and BIFI-CSIC Joint Units, Universidad de Zaragoza, Zaragoza, Spain.,Fundación ARAID, Diputación General de Aragón, Aragón, Spain.,Aragon Institute for Health Research (IIS Aragon), Zaragoza, 50009, Spain
| | - Anabel Lostao
- Laboratorio de Microscopías Avanzadas (LMA), Instituto de Nanociencia de Aragón (INA), and Fundación INA, Universidad de Zaragoza, Zaragoza, Spain.,Fundación ARAID, Diputación General de Aragón, Aragón, Spain
| | - Ramón Hurtado-Guerrero
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) and GBsC-CSIC and BIFI-CSIC Joint Units, Universidad de Zaragoza, Zaragoza, Spain.,Fundación ARAID, Diputación General de Aragón, Aragón, Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain. .,Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) and GBsC-CSIC and BIFI-CSIC Joint Units, Universidad de Zaragoza, Zaragoza, Spain.
| | - Marta Martínez-Júlvez
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain. .,Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) and GBsC-CSIC and BIFI-CSIC Joint Units, Universidad de Zaragoza, Zaragoza, Spain.
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Dual-Targeting Small-Molecule Inhibitors of the Staphylococcus aureus FMN Riboswitch Disrupt Riboflavin Homeostasis in an Infectious Setting. Cell Chem Biol 2017; 24:576-588.e6. [PMID: 28434876 DOI: 10.1016/j.chembiol.2017.03.014] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 02/03/2017] [Accepted: 03/23/2017] [Indexed: 11/22/2022]
Abstract
Riboswitches are bacterial-specific, broadly conserved, non-coding RNA structural elements that control gene expression of numerous metabolic pathways and transport functions essential for cell growth. As such, riboswitch inhibitors represent a new class of potential antibacterial agents. Recently, we identified ribocil-C, a highly selective inhibitor of the flavin mononucleotide (FMN) riboswitch that controls expression of de novo riboflavin (RF, vitamin B2) biosynthesis in Escherichia coli. Here, we provide a mechanistic characterization of the antibacterial effects of ribocil-C as well as of roseoflavin (RoF), an antimetabolite analog of RF, among medically significant Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA) and Enterococcus faecalis. We provide genetic, biophysical, computational, biochemical, and pharmacological evidence that ribocil-C and RoF specifically inhibit dual FMN riboswitches, separately controlling RF biosynthesis and uptake processes essential for MRSA growth and pathogenesis. Such a dual-targeting mechanism is specifically required to develop broad-spectrum Gram-positive antibacterial agents targeting RF metabolism.
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The superfamily keeps growing: Identification in trypanosomatids of RibJ, the first riboflavin transporter family in protists. PLoS Negl Trop Dis 2017; 11:e0005513. [PMID: 28406895 PMCID: PMC5404878 DOI: 10.1371/journal.pntd.0005513] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 04/25/2017] [Accepted: 03/21/2017] [Indexed: 01/07/2023] Open
Abstract
Background Trypanosomatid parasites represent a major health issue affecting hundreds of million people worldwide, with clinical treatments that are partially effective and/or very toxic. They are responsible for serious human and plant diseases including Trypanosoma cruzi (Chagas disease), Trypanosoma brucei (Sleeping sickness), Leishmania spp. (Leishmaniasis), and Phytomonas spp. (phytoparasites). Both, animals and trypanosomatids lack the biosynthetic riboflavin (vitamin B2) pathway, the vital precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) cofactors. While metazoans obtain riboflavin from the diet through RFVT/SLC52 transporters, the riboflavin transport mechanisms in trypanosomatids still remain unknown. Methodology/Principal findings Here, we show that riboflavin is imported with high affinity in Trypanosoma cruzi, Trypanosoma brucei, Leishmania (Leishmania) mexicana, Crithidia fasciculata and Phytomonas Jma using radiolabeled riboflavin transport assays. The vitamin is incorporated through a saturable carrier-mediated process. Effective competitive uptake occurs with riboflavin analogs roseoflavin, lumiflavin and lumichrome, and co-factor derivatives FMN and FAD. Moreover, important biological processes evaluated in T. cruzi (i.e. proliferation, metacyclogenesis and amastigote replication) are dependent on riboflavin availability. In addition, the riboflavin competitive analogs were found to interfere with parasite physiology on riboflavin-dependent processes. By means of bioinformatics analyses we identified a novel family of riboflavin transporters (RibJ) in trypanosomatids. Two RibJ members, TcRibJ and TbRibJ from T. cruzi and T. brucei respectively, were functionally characterized using homologous and/or heterologous expression systems. Conclusions/Significance The RibJ family represents the first riboflavin transporters found in protists and the third eukaryotic family known to date. The essentiality of riboflavin for trypanosomatids, and the structural/biochemical differences that RFVT/SLC52 and RibJ present, make the riboflavin transporter -and its downstream metabolism- a potential trypanocidal drug target. In this work, we show that riboflavin plays a key role in the trypanosomatid life cycles and describe a novel family of riboflavin transporters (RibJ) with uptake function. Despite the vital importance of riboflavin for all living cells, RibJ are the first transporters described in protists. We functionally characterized the T. cruzi and T. brucei RibJ members and the effect of riboflavin analogs on parasite physiology. The structural and biochemical differences presented between human transporters and RibJ members make riboflavin transport and downstream metabolism, attractive and potential trypanosomatid targets.
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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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Howe JA, Xiao L, Fischmann TO, Wang H, Tang H, Villafania A, Zhang R, Barbieri CM, Roemer T. Atomic resolution mechanistic studies of ribocil: A highly selective unnatural ligand mimic of the E. coli FMN riboswitch. RNA Biol 2016; 13:946-954. [PMID: 27485612 PMCID: PMC5056776 DOI: 10.1080/15476286.2016.1216304] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Bacterial riboswitches are non-coding RNA structural elements that direct gene expression in numerous metabolic pathways. The key regulatory roles of riboswitches, and the urgent need for new classes of antibiotics to treat multi-drug resistant bacteria, has led to efforts to develop small-molecules that mimic natural riboswitch ligands to inhibit metabolic pathways and bacterial growth. Recently, we reported the results of a phenotypic screen targeting the riboflavin biosynthesis pathway in the Gram-negative bacteria Escherichia coli that led to the identification of ribocil, a small molecule inhibitor of the flavin mononucleotide (FMN) riboswitch controlling expression of this biosynthetic pathway. Although ribocil is structurally distinct from FMN, ribocil functions as a potent and highly selective synthetic mimic of the natural ligand to repress riboswitch-mediated ribB gene expression and inhibit bacterial growth both in vitro and in vivo. Herein, we expand our analysis of ribocil; including mode of binding in the FMN binding pocket of the riboswitch, mechanisms of resistance and structure-activity relationship guided efforts to generate more potent analogs.
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Affiliation(s)
- John A Howe
- a Merck Research Laboratories , Kenilworth , NJ , USA
| | - Li Xiao
- a Merck Research Laboratories , Kenilworth , NJ , USA
| | | | - Hao Wang
- a Merck Research Laboratories , Kenilworth , NJ , USA
| | - Haifeng Tang
- a Merck Research Laboratories , Kenilworth , NJ , USA
| | | | - Rumin Zhang
- a Merck Research Laboratories , Kenilworth , NJ , USA
| | | | - Terry Roemer
- a Merck Research Laboratories , Kenilworth , NJ , USA
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Jhulki I, Chanani PK, Abdelwahed SH, Begley TP. A Remarkable Oxidative Cascade That Replaces the Riboflavin C8 Methyl with an Amino Group during Roseoflavin Biosynthesis. J Am Chem Soc 2016; 138:8324-7. [PMID: 27331868 PMCID: PMC5610575 DOI: 10.1021/jacs.6b02469] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Roseoflavin is a naturally occurring riboflavin analogue with antibiotic properties. It is biosynthesized from riboflavin in a reaction involving replacement of the C8 methyl with a dimethylamino group. Herein we report the identification of a flavin-dependent enzyme that converts flavin mononucleotide (FMN) and glutamate to 8-amino-FMN via the intermediacy of 8-formyl-FMN. A mechanistic proposal for this remarkable transformation is proposed.
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Affiliation(s)
- Isita Jhulki
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
| | - Prem K. Chanani
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
| | - Sameh H. Abdelwahed
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
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Schwarz J, Konjik V, Jankowitsch F, Sandhoff R, Mack M. Identifizierung des Schlüsselenzyms der Roseoflavinbiosynthese. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600581] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Julia Schwarz
- Fakultät für Biotechnologie Institut für Technische Mikrobiologie Hochschule Mannheim Paul-Wittsack-Straße 10 68163 Mannheim Deutschland
| | - Valentino Konjik
- Fakultät für Biotechnologie Institut für Technische Mikrobiologie Hochschule Mannheim Paul-Wittsack-Straße 10 68163 Mannheim Deutschland
| | - Frank Jankowitsch
- Fakultät für Biotechnologie Institut für Technische Mikrobiologie Hochschule Mannheim Paul-Wittsack-Straße 10 68163 Mannheim Deutschland
| | - Roger Sandhoff
- Pathobiochemie der Lipide im Deutschen Krebsforschungszentrum Heidelberg Deutschland
| | - Matthias Mack
- Fakultät für Biotechnologie Institut für Technische Mikrobiologie Hochschule Mannheim Paul-Wittsack-Straße 10 68163 Mannheim Deutschland
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Schwarz J, Konjik V, Jankowitsch F, Sandhoff R, Mack M. Identification of the Key Enzyme of Roseoflavin Biosynthesis. Angew Chem Int Ed Engl 2016; 55:6103-6. [DOI: 10.1002/anie.201600581] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 03/07/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Julia Schwarz
- Fakultät für Biotechnologie Institut für Technische Mikrobiologie Hochschule Mannheim Paul-Wittsack-Strasse 10 68163 Mannheim Germany
| | - Valentino Konjik
- Fakultät für Biotechnologie Institut für Technische Mikrobiologie Hochschule Mannheim Paul-Wittsack-Strasse 10 68163 Mannheim Germany
| | - Frank Jankowitsch
- Fakultät für Biotechnologie Institut für Technische Mikrobiologie Hochschule Mannheim Paul-Wittsack-Strasse 10 68163 Mannheim Germany
| | - Roger Sandhoff
- Pathobiochemie der Lipide im Deutschen Krebsforschungszentrum (DKFZ) Heidelberg Germany
| | - Matthias Mack
- Fakultät für Biotechnologie Institut für Technische Mikrobiologie Hochschule Mannheim Paul-Wittsack-Strasse 10 68163 Mannheim Germany
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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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Quehl P, Hollender J, Schüürmann J, Brossette T, Maas R, Jose J. Co-expression of active human cytochrome P450 1A2 and cytochrome P450 reductase on the cell surface of Escherichia coli. Microb Cell Fact 2016; 15:26. [PMID: 26838175 PMCID: PMC4736170 DOI: 10.1186/s12934-016-0427-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 01/19/2016] [Indexed: 11/23/2022] Open
Abstract
Background Human cytochrome P450 (CYP) enzymes mediate the first step in the breakdown of most drugs and are strongly involved in drug–drug interactions, drug clearance and activation of prodrugs. Their biocatalytic behavior is a key parameter during drug development which requires preparative synthesis of CYP related drug metabolites. However, recombinant expression of CYP enzymes is a challenging bottleneck for drug metabolite biosynthesis. Therefore, we developed a novel approach by displaying human cytochrome P450 1A2 (CYP1A2) and cytochrome P450 reductase (CPR) on the surface of Escherichia coli. Results To present human CYP1A2 and CPR on the surface, we employed autodisplay. Both enzymes were displayed on the surface which was demonstrated by protease and antibody accessibility tests. CPR activity was first confirmed with the protein substrate cytochrome c. Cells co-expressing CYP1A2 and CPR were capable of catalyzing the conversion of the known CYP1A2 substrates 7-ethoxyresorufin, phenacetin and the artificial substrate luciferin-MultiCYP, which would not have been possible without interaction of both enzymes. Biocatalytic activity was strongly influenced by the composition of the growth medium. Addition of 5-aminolevulinic acid was necessary to obtain a fully active whole cell biocatalyst and was superior to the addition of heme. Conclusion We demonstrated that CYP1A2 and CPR can be co-expressed catalytically active on the cell surface of E. coli. It is a promising step towards pharmaceutical applications such as the synthesis of drug metabolites. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0427-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paul Quehl
- Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, 48149, Münster, Germany.
| | - Joel Hollender
- Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, 48149, Münster, Germany. .,Autodisplay Biotech GmbH, Merowingerplatz 1a, 40225, Düsseldorf, Germany.
| | - Jan Schüürmann
- Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, 48149, Münster, Germany.
| | - Tatjana Brossette
- Autodisplay Biotech GmbH, Merowingerplatz 1a, 40225, Düsseldorf, Germany.
| | - Ruth Maas
- Autodisplay Biotech GmbH, Merowingerplatz 1a, 40225, Düsseldorf, Germany.
| | - Joachim Jose
- Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, 48149, Münster, Germany.
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Howe JA, Wang H, Fischmann TO, Balibar CJ, Xiao L, Galgoci AM, Malinverni JC, Mayhood T, Villafania A, Nahvi A, Murgolo N, Barbieri CM, Mann PA, Carr D, Xia E, Zuck P, Riley D, Painter RE, Walker SS, Sherborne B, de Jesus R, Pan W, Plotkin MA, Wu J, Rindgen D, Cummings J, Garlisi CG, Zhang R, Sheth PR, Gill CJ, Tang H, Roemer T. Selective small-molecule inhibition of an RNA structural element. Nature 2015; 526:672-7. [PMID: 26416753 DOI: 10.1038/nature15542] [Citation(s) in RCA: 276] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 09/04/2015] [Indexed: 02/06/2023]
Abstract
Riboswitches are non-coding RNA structures located in messenger RNAs that bind endogenous ligands, such as a specific metabolite or ion, to regulate gene expression. As such, riboswitches serve as a novel, yet largely unexploited, class of emerging drug targets. Demonstrating this potential, however, has proven difficult and is restricted to structurally similar antimetabolites and semi-synthetic analogues of their cognate ligand, thus greatly restricting the chemical space and selectivity sought for such inhibitors. Here we report the discovery and characterization of ribocil, a highly selective chemical modulator of bacterial riboflavin riboswitches, which was identified in a phenotypic screen and acts as a structurally distinct synthetic mimic of the natural ligand, flavin mononucleotide, to repress riboswitch-mediated ribB gene expression and inhibit bacterial cell growth. Our findings indicate that non-coding RNA structural elements may be more broadly targeted by synthetic small molecules than previously expected.
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Affiliation(s)
- John A Howe
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | - Hao Wang
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | | | - Carl J Balibar
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | - Li Xiao
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | | | | | - Todd Mayhood
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | | | - Ali Nahvi
- Merck Research Laboratories, West Point, Pennsylvania 19486, USA
| | | | | | - Paul A Mann
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | - Donna Carr
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | - Ellen Xia
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | - Paul Zuck
- Merck Research Laboratories, North Wales, Pennsylvania 19454, USA
| | - Dan Riley
- Merck Research Laboratories, North Wales, Pennsylvania 19454, USA
| | | | - Scott S Walker
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | - Brad Sherborne
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | | | - Weidong Pan
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | | | - Jin Wu
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | - Diane Rindgen
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | - John Cummings
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | | | - Rumin Zhang
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | - Payal R Sheth
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | - Charles J Gill
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | - Haifeng Tang
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | - Terry Roemer
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
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Novel riboswitch-binding flavin analog that protects mice against Clostridium difficile infection without inhibiting cecal flora. Antimicrob Agents Chemother 2015; 59:5736-46. [PMID: 26169403 DOI: 10.1128/aac.01282-15] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/03/2015] [Indexed: 01/08/2023] Open
Abstract
Novel mechanisms of action and new chemical scaffolds are needed to rejuvenate antibacterial drug discovery, and riboswitch regulators of bacterial gene expression are a promising class of targets for the discovery of new leads. Herein, we report the characterization of 5-(3-(4-fluorophenyl)butyl)-7,8-dimethylpyrido[3,4-b]quinoxaline-1,3(2H,5H)-dione (5FDQD)-an analog of riboflavin that was designed to bind riboswitches that naturally recognize the essential coenzyme flavin mononucleotide (FMN) and regulate FMN and riboflavin homeostasis. In vitro, 5FDQD and FMN bind to and trigger the function of an FMN riboswitch with equipotent activity. MIC and time-kill studies demonstrated that 5FDQD has potent and rapidly bactericidal activity against Clostridium difficile. In C57BL/6 mice, 5FDQD completely prevented the onset of lethal antibiotic-induced C. difficile infection (CDI). Against a panel of bacteria representative of healthy bowel flora, the antibacterial selectivity of 5FDQD was superior to currently marketed CDI therapeutics, with very little activity against representative strains from the Bacteroides, Lactobacillus, Bifidobacterium, Actinomyces, and Prevotella genera. Accordingly, a single oral dose of 5FDQD caused less alteration of culturable cecal flora in mice than the comparators. Collectively, these data suggest that 5FDQD or closely related analogs could potentially provide a high rate of CDI cure with a low likelihood of infection recurrence. Future studies will seek to assess the role of FMN riboswitch binding to the mechanism of 5FDQD antibacterial action. In aggregate, our results indicate that riboswitch-binding antibacterial compounds can be discovered and optimized to exhibit activity profiles that merit preclinical and clinical development as potential antibacterial therapeutic agents.
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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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Pedrolli DB, Jankowitsch F, Schwarz J, Langer S, Nakanishi S, Mack M. Natural riboflavin analogs. Methods Mol Biol 2014; 1146:41-63. [PMID: 24764087 DOI: 10.1007/978-1-4939-0452-5_3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Riboflavin analogs have a good potential to serve as basic structures for the development of novel anti-infectives. Riboflavin analogs have multiple cellular targets, since riboflavin (as a precursor to flavin cofactors) is active at more than one site in the cell. As a result, the frequency of developing resistance to antimicrobials based on riboflavin analogs is expected to be significantly lower. The only known natural riboflavin analog with antibiotic function is roseoflavin from the bacterium Streptomyces davawensis. This antibiotic negatively affects flavoenzymes and FMN riboswitches. Another roseoflavin producer, Streptomyces cinnabarinus, was recently identified. Possibly, flavin analogs with antibiotic activity are more widespread than anticipated. The same could be true for flavin analogs yet to be discovered, which could constitute tools for cellular chemistry, thus allowing a further extension of the catalytic spectrum of flavoenzymes.
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Affiliation(s)
- Danielle Biscaro Pedrolli
- Institute for Technical Microbiology, Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163, Mannheim, Germany
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