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Abstract
Communication between and within communities of cells or independent organisms is a crucial prerequisite for species survival. In response to variations in the extracellular environment, the collective behavior of cell populations can be coordinated by regulating community-level gene expression. This mechanism is strongly conserved during evolution, being shared both by bacterial communities and central nervous system cells. Notably, cyclic dipeptides (CDPs) are molecules that are implicated in these quorum sensing behaviors in both settings. Bacteria coordinate their collective behavior by producing CDPs (quorum sensing inducers) that enhance the capacity of individual members of the community to detect these signals and thus amplify the community-level response. In this review, we highlight recent data indicating that strikingly similar molecular mechanisms control communications between glial and neuronal cells to maintain homeostasis in the central nervous system, with a specific focus on the role of the thyrotropin-releasing hormone—derived CDP cyclo(His-Pro) in the protection against neurotoxic insults.
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102
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Hagen R, Verhoeve VI, Gillespie JJ, Driscoll TP. Conjugative Transposons and Their Cargo Genes Vary across Natural Populations of Rickettsia buchneri Infecting the Tick Ixodes scapularis. Genome Biol Evol 2018; 10:3218-3229. [PMID: 30398619 PMCID: PMC6300072 DOI: 10.1093/gbe/evy247] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2018] [Indexed: 12/11/2022] Open
Abstract
Rickettsia buchneri (formerly Rickettsia endosymbiont of Ixodes scapularis, or REIS) is an obligate intracellular endoparasite of the black-legged tick, the primary vector of Lyme disease in North America. It is noteworthy among the rickettsiae for its relatively large genome (1.8 Mb) and extraordinary proliferation of mobile genetic elements (MGEs), which comprise nearly 35% of its genome. Previous analysis of the R. buchneri genome identified several integrative conjugative elements named Rickettsiales amplified genomic elements (RAGEs); the composition of these RAGEs suggests that continued genomic invasions by MGEs facilitated the proliferation of rickettsial genes related to an intracellular lifestyle. In this study, we compare the genomic diversity at RAGE loci among sequenced rickettsiae that infect three related Ixodes spp., including two strains of R. buchneri and Rickettsia endosymbiont of Ixodes pacificus strain Humboldt, as well as a closely related species R. tamurae infecting Amblyomma testudinarium ticks. We further develop a novel multiplex droplet digital PCR assay and use it to quantify copy number ratios of chromosomal R. buchneri RAGE-A and RAGE-B to the single-copy gene gltA within natural populations of I. scapularis. Our results reveal substantial diversity among R. buchneri at these loci, both within individual ticks as well as in the I. scapularis population at large, demonstrating that genomic rearrangement of MGEs is an active process in these intracellular bacteria.
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Affiliation(s)
| | | | - Joseph J Gillespie
- Department of Microbiology and Immunology, University of Maryland School of Medicine
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103
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Guzmán-Chávez F, Zwahlen RD, Bovenberg RAL, Driessen AJM. Engineering of the Filamentous Fungus Penicillium chrysogenum as Cell Factory for Natural Products. Front Microbiol 2018; 9:2768. [PMID: 30524395 PMCID: PMC6262359 DOI: 10.3389/fmicb.2018.02768] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/29/2018] [Indexed: 12/14/2022] Open
Abstract
Penicillium chrysogenum (renamed P. rubens) is the most studied member of a family of more than 350 Penicillium species that constitute the genus. Since the discovery of penicillin by Alexander Fleming, this filamentous fungus is used as a commercial β-lactam antibiotic producer. For several decades, P. chrysogenum was subjected to a classical strain improvement (CSI) program to increase penicillin titers. This resulted in a massive increase in the penicillin production capacity, paralleled by the silencing of several other biosynthetic gene clusters (BGCs), causing a reduction in the production of a broad range of BGC encoded natural products (NPs). Several approaches have been used to restore the ability of the penicillin production strains to synthetize the NPs lost during the CSI. Here, we summarize various re-activation mechanisms of BGCs, and how interference with regulation can be used as a strategy to activate or silence BGCs in filamentous fungi. To further emphasize the versatility of P. chrysogenum as a fungal production platform for NPs with potential commercial value, protein engineering of biosynthetic enzymes is discussed as a tool to develop de novo BGC pathways for new NPs.
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Affiliation(s)
- Fernando Guzmán-Chávez
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Reto D Zwahlen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Roel A L Bovenberg
- Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,DSM Biotechnology Centre, Delft, Netherlands
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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104
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Application of HPCCC Combined with Polymeric Resins and HPLC for the Separation of Cyclic Lipopeptides Muscotoxins A⁻C and Their Antimicrobial Activity. Molecules 2018; 23:molecules23102653. [PMID: 30332796 PMCID: PMC6222847 DOI: 10.3390/molecules23102653] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/02/2018] [Accepted: 10/10/2018] [Indexed: 11/17/2022] Open
Abstract
Muscotoxins are cyanobacterial cyclic lipopeptides with potential applications in biomedicine and biotechnology. In this study, Desmonostoc muscorum CCALA125 strain extracts were enriched by polymeric resin treatment, and subjected to HPCCC affording three cyclic lipopeptides (1–3), which were further repurified by semi-preparative HPLC, affording 1, 2, and 3, with a purity of 86%, 92%, and 90%, respectively. The chemical identities of 2–3 were determined as muscotoxins A and B, respectively, by comparison with previously reported ESI-HRMS/MS data, whereas 1 was determined as a novel muscotoxin variant (muscotoxin C) using NMR and ESI-HRMS/MS data. Owing to the high yield (50 mg), compound 2 was broadly screened for its antimicrobial potential exhibiting a strong antifungal activity against Alternaria alternata, Monographella cucumerina, and Aspergillus fumigatus, with minimum inhibitory concentration (MIC) values of 0.58, 2.34, and 2.34 µg/mL; respectively, and weak antibacterial activity against Bacillus subtilis with a MIC value of 37.5 µg/mL. Compounds 1 and 3 were tested only against the plant pathogenic fungus Sclerotinia sclerotiorum due to their low yield, displaying a moderate antifungal activity. The developed chromatographic method proved to be an efficient tool for obtaining muscotoxins with potent antifungal properties.
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105
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An Orphan MbtH-Like Protein Interacts with Multiple Nonribosomal Peptide Synthetases in Myxococcus xanthus DK1622. J Bacteriol 2018; 200:JB.00346-18. [PMID: 30126939 DOI: 10.1128/jb.00346-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 08/13/2018] [Indexed: 11/20/2022] Open
Abstract
One mechanism by which bacteria and fungi produce bioactive natural products is the use of nonribosomal peptide synthetases (NRPSs). Many NRPSs in bacteria require members of the MbtH-like protein (MLP) superfamily for their solubility or function. Although MLPs are known to interact with the adenylation domains of NRPSs, the role MLPs play in NRPS enzymology has yet to be elucidated. MLPs are nearly always encoded within the biosynthetic gene clusters (BGCs) that also code for the NRPSs that interact with the MLP. Here, we identify 50 orphan MLPs from diverse bacteria. An orphan MLP is one that is encoded by a gene that is not directly adjacent to genes predicted to be involved in nonribosomal peptide biosynthesis. We targeted the orphan MLP MXAN_3118 from Myxococcus xanthus DK1622 for characterization. The M. xanthus DK1622 genome contains 15 NRPS-encoding BGCs but only one MLP-encoding gene (MXAN_3118). We tested the hypothesis that MXAN_3118 interacts with one or more NRPS using a combination of in vivo and in vitro assays. We determined that MXAN_3118 interacts with at least seven NRPSs from distinct BGCs. We show that one of these BGCs codes for NRPS enzymology that likely produces a valine-rich natural product that inhibits the clumping of M. xanthus DK1622 in liquid culture. MXAN_3118 is the first MLP to be identified that naturally interacts with multiple NRPS systems in a single organism. The finding of an MLP that naturally interacts with multiple NRPS systems suggests it may be harnessed as a "universal" MLP for generating functional hybrid NRPSs.IMPORTANCE MbtH-like proteins (MLPs) are essential accessory proteins for the function of many nonribosomal peptide synthetases (NRPSs). We identified 50 MLPs from diverse bacteria that are coded by genes that are not located near any NRPS-encoding biosynthetic gene clusters (BGCs). We define these as orphan MLPs because their NRPS partner(s) is unknown. Investigations into the orphan MLP from Myxococcus xanthus DK1622 determined that it interacts with NRPSs from at least seven distinct BGCs. Support for these MLP-NRPS interactions came from the use of a bacterial two-hybrid assay and copurification of the MLP with various NRPSs. The flexibility of this MLP to naturally interact with multiple NRPSs led us to hypothesize that this MLP may be used as a "universal" MLP during the construction of functional hybrid NRPSs.
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106
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Guo H, Schmidt A, Stephan P, Raguž L, Braga D, Kaiser M, Dahse HM, Weigel C, Lackner G, Beemelmanns C. Precursor-Directed Diversification of Cyclic Tetrapeptidic Pseudoxylallemycins. Chembiochem 2018; 19:2307-2311. [DOI: 10.1002/cbic.201800503] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Indexed: 01/18/2023]
Affiliation(s)
- Huijuan Guo
- Leibniz Institute for Natural Product Research and Infection Biology; Hans Knöll Institute; Beutenbergstraße 11a 07745 Jena Germany
| | - Alexander Schmidt
- Leibniz Institute for Natural Product Research and Infection Biology; Hans Knöll Institute; Beutenbergstraße 11a 07745 Jena Germany
| | - Philipp Stephan
- Leibniz Institute for Natural Product Research and Infection Biology; Hans Knöll Institute; Beutenbergstraße 11a 07745 Jena Germany
| | - Luka Raguž
- Leibniz Institute for Natural Product Research and Infection Biology; Hans Knöll Institute; Beutenbergstraße 11a 07745 Jena Germany
| | - Daniel Braga
- Leibniz Institute for Natural Product Research and Infection Biology; Hans Knöll Institute; Beutenbergstraße 11a 07745 Jena Germany
- Friedrich-Schiller-Universität Jena; Junior Research Group Synthetic Microbiology at the Hans-Knöll-Institute; Adolf-Reichwein-Strasse 23 07745 Jena Germany
| | - Marcel Kaiser
- Parasite Chemotherapy Unit; Swiss Tropical and Public Health Institute; Socinstrasse 57 4002 Basel Switzerland
- Parasite Chemotherapy; University of Basel; Petersplatz 1 4003 Basel Switzerland
| | - Hans-Martin Dahse
- Leibniz Institute for Natural Product Research and Infection Biology; Hans Knöll Institute; Beutenbergstraße 11a 07745 Jena Germany
| | - Christiane Weigel
- Leibniz Institute for Natural Product Research and Infection Biology; Hans Knöll Institute; Beutenbergstraße 11a 07745 Jena Germany
| | - Gerald Lackner
- Leibniz Institute for Natural Product Research and Infection Biology; Hans Knöll Institute; Beutenbergstraße 11a 07745 Jena Germany
- Friedrich-Schiller-Universität Jena; Junior Research Group Synthetic Microbiology at the Hans-Knöll-Institute; Adolf-Reichwein-Strasse 23 07745 Jena Germany
| | - Christine Beemelmanns
- Leibniz Institute for Natural Product Research and Infection Biology; Hans Knöll Institute; Beutenbergstraße 11a 07745 Jena Germany
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107
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Kretsch AM, Morgan GL, Tyrrell J, Mevers E, Vallet-Gély I, Li B. Discovery of (Dihydro)pyrazine N-Oxides via Genome Mining in Pseudomonas. Org Lett 2018; 20:4791-4795. [PMID: 30073838 DOI: 10.1021/acs.orglett.8b01944] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Overexpression of the Pseudomonas virulence factor ( pvf) biosynthetic operon led to the identification of a family of pyrazine N-oxides (PNOs), including a novel dihydropyrazine N,N'-dioxide (dPNO) metabolite. The nonribosomal peptide synthetase responsible for production of (d)PNOs was characterized, and a biosynthetic pathway for (d)PNOs was proposed. This work highlights the unique chemistry catalyzed by pvf-encoded enzymes and sets the stage for bioactivity studies of the metabolites produced by the virulence pathway.
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Affiliation(s)
- Ashley M Kretsch
- Department of Chemistry , The University of North Carolina at Chapel Hill , 250 Bell Tower Road , Chapel Hill , North Carolina 27599 , United States
| | - Gina L Morgan
- Department of Chemistry , The University of North Carolina at Chapel Hill , 250 Bell Tower Road , Chapel Hill , North Carolina 27599 , United States
| | - Jillian Tyrrell
- Department of Chemistry , The University of North Carolina at Chapel Hill , 250 Bell Tower Road , Chapel Hill , North Carolina 27599 , United States
| | - Emily Mevers
- Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , 240 Longwood Avenue , Boston , Massachusetts 02115 , United States
| | - Isabelle Vallet-Gély
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS , Univ. Paris-Sud, Université Paris-Saclay , 91198 , Gif-sur-Yvette cedex , France
| | - Bo Li
- Department of Chemistry , The University of North Carolina at Chapel Hill , 250 Bell Tower Road , Chapel Hill , North Carolina 27599 , United States
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108
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Junk L, Kazmaier U. Total Synthesis of Keramamides A and L from a Common Precursor by Late-Stage Indole Synthesis and Configurational Revision. Angew Chem Int Ed Engl 2018; 57:11432-11435. [PMID: 30019808 DOI: 10.1002/anie.201806657] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Indexed: 01/27/2023]
Abstract
The marine natural products keramamide A and L, members of the class of anabaenopeptin-type peptides, were synthesized for the first time by a convergent and flexible route. The installation of the substituted tryptophan moieties was accomplished at the very end of the synthesis on the cyclic peptides, and thus enabled the synthesis of both natural products from one common precursor. The preparation of several epimers clearly indicates that the originally proposed relative configurations of both Keramamides A and L were not correct.
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Affiliation(s)
- Lukas Junk
- Institut für Organische Chemie, Universität des Saarlandes, Campus C4.2, 66123, Saarbrücken, Germany
| | - Uli Kazmaier
- Institut für Organische Chemie, Universität des Saarlandes, Campus C4.2, 66123, Saarbrücken, Germany
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109
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Junk L, Kazmaier U. Totalsynthese der Keramamide A und L aus einer gemeinsamen Vorstufe durch späte Indolsynthese und Revision ihrer Konfiguration. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806657] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Lukas Junk
- Institut für Organische Chemie; Universität des Saarlandes; Campus C4.2 66123 Saarbrücken Deutschland
| | - Uli Kazmaier
- Institut für Organische Chemie; Universität des Saarlandes; Campus C4.2 66123 Saarbrücken Deutschland
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110
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Zhang XS, Li J, Krautkramer KA, Badri M, Battaglia T, Borbet TC, Koh H, Ng S, Sibley RA, Li Y, Pathmasiri W, Jindal S, Shields-Cutler RR, Hillmann B, Al-Ghalith GA, Ruiz VE, Livanos A, van 't Wout AB, Nagalingam N, Rogers AB, Sumner SJ, Knights D, Denu JM, Li H, Ruggles KV, Bonneau R, Williamson RA, Rauch M, Blaser MJ. Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity. eLife 2018; 7:37816. [PMID: 30039798 PMCID: PMC6085123 DOI: 10.7554/elife.37816] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/12/2018] [Indexed: 12/18/2022] Open
Abstract
The early-life intestinal microbiota plays a key role in shaping host immune system development. We found that a single early-life antibiotic course (1PAT) accelerated type 1 diabetes (T1D) development in male NOD mice. The single course had deep and persistent effects on the intestinal microbiome, leading to altered cecal, hepatic, and serum metabolites. The exposure elicited sex-specific effects on chromatin states in the ileum and liver and perturbed ileal gene expression, altering normal maturational patterns. The global signature changes included specific genes controlling both innate and adaptive immunity. Microbiome analysis revealed four taxa each that potentially protect against or accelerate T1D onset, that were linked in a network model to specific differences in ileal gene expression. This simplified animal model reveals multiple potential pathways to understand pathogenesis by which early-life gut microbiome perturbations alter a global suite of intestinal responses, contributing to the accelerated and enhanced T1D development.
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Affiliation(s)
- Xue-Song Zhang
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Jackie Li
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Kimberly A Krautkramer
- Department of Biomolecular Chemistry, Wisconsin Institute for Discovery, University of Wisconsin School of Medicine and Public Health, Madison, United States
| | - Michelle Badri
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States.,Center for Data Science, New York University, New York, United States
| | - Thomas Battaglia
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Timothy C Borbet
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Hyunwook Koh
- Department of Population Health, New York University Langone Medical Center, New York, United States
| | - Sandy Ng
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Rachel A Sibley
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Yuanyuan Li
- Nutrition Research Institute, University of North Carolina at Chapel Hill School of Public Health, Kannapolis, United States
| | - Wimal Pathmasiri
- Nutrition Research Institute, University of North Carolina at Chapel Hill School of Public Health, Kannapolis, United States
| | - Shawn Jindal
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Robin R Shields-Cutler
- Computer Science and Engineering, BioTechnology Institute, University of Minnesota, St. Paul, United States
| | - Ben Hillmann
- Computer Science and Engineering, BioTechnology Institute, University of Minnesota, St. Paul, United States
| | - Gabriel A Al-Ghalith
- Computer Science and Engineering, BioTechnology Institute, University of Minnesota, St. Paul, United States
| | - Victoria E Ruiz
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Alexandra Livanos
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Angélique B van 't Wout
- Janssen Prevention Center London, Janssen Pharmaceutical Companies of Johnson and Johnson, London, United Kingdom
| | - Nabeetha Nagalingam
- Janssen Prevention Center London, Janssen Pharmaceutical Companies of Johnson and Johnson, London, United Kingdom
| | - Arlin B Rogers
- Department of Biomedical Sciences, Cummings School of Veterinary Medicine, Tufts University, North Grafton, United States
| | - Susan Jenkins Sumner
- Nutrition Research Institute, University of North Carolina at Chapel Hill School of Public Health, Kannapolis, United States
| | - Dan Knights
- Computer Science and Engineering, BioTechnology Institute, University of Minnesota, St. Paul, United States
| | - John M Denu
- Department of Biomolecular Chemistry, Wisconsin Institute for Discovery, University of Wisconsin School of Medicine and Public Health, Madison, United States
| | - Huilin Li
- Department of Population Health, New York University Langone Medical Center, New York, United States
| | - Kelly V Ruggles
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Richard Bonneau
- Center for Data Science, New York University, New York, United States
| | - R Anthony Williamson
- Janssen Prevention Center London, Janssen Pharmaceutical Companies of Johnson and Johnson, London, United Kingdom
| | - Marcus Rauch
- Janssen Prevention Center London, Janssen Pharmaceutical Companies of Johnson and Johnson, London, United Kingdom
| | - Martin J Blaser
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States.,Department of Microbiology, New York Uniersity Langone Medical Center, New York, United States
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111
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Wagner A, Norris S, Chatterjee P, Morris PF, Wildschutte H. Aquatic Pseudomonads Inhibit Oomycete Plant Pathogens of Glycine max. Front Microbiol 2018; 9:1007. [PMID: 29896163 PMCID: PMC5986895 DOI: 10.3389/fmicb.2018.01007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 04/30/2018] [Indexed: 11/17/2022] Open
Abstract
Seedling root rot of soybeans caused by the host-specific pathogen Phytophthora sojae, and a large number of Pythium species, is an economically important disease across the Midwest United States that negatively impacts soybean yields. Research on biocontrol strategies for crop pathogens has focused on compounds produced by microbes from soil, however, recent studies suggest that aquatic bacteria express distinct compounds that efficiently inhibit a wide range of pathogens. Based on these observations, we hypothesized that freshwater strains of pseudomonads might be producing novel antagonistic compounds that inhibit the growth of oomycetes. To test this prediction, we utilized a collection of 330 Pseudomonas strains isolated from soil and freshwater habitats, and determined their activity against a panel of five oomycetes: Phytophthora sojae, Pythium heterothalicum, Pythium irregulare, Pythium sylvaticum, and Pythium ultimum, all of which are pathogenic on soybeans. Among the bacterial strains, 118 exhibited antagonistic activity against at least one oomycete species, and 16 strains were inhibitory to all pathogens. Antagonistic activity toward oomycetes was significantly more common for aquatic isolates than for soil isolates. One water-derived strain, 06C 126, was predicted to express a siderophore and exhibited diverse antagonistic profiles when tested on nutrient rich and iron depleted media suggesting that more than one compound was produced that effectively inhibited oomycetes. These results support the concept that aquatic strains are an efficient source of compounds that inhibit pathogens. We outline a strategy to identify other strains that express unique compounds that may be useful biocontrol agents.
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Affiliation(s)
| | | | | | - Paul F. Morris
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States
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112
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Reimer JM, Haque AS, Tarry MJ, Schmeing TM. Piecing together nonribosomal peptide synthesis. Curr Opin Struct Biol 2018; 49:104-113. [DOI: 10.1016/j.sbi.2018.01.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 01/08/2018] [Accepted: 01/22/2018] [Indexed: 10/18/2022]
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113
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Jenul C, Sieber S, Daeppen C, Mathew A, Lardi M, Pessi G, Hoepfner D, Neuburger M, Linden A, Gademann K, Eberl L. Biosynthesis of fragin is controlled by a novel quorum sensing signal. Nat Commun 2018; 9:1297. [PMID: 29602945 PMCID: PMC5878181 DOI: 10.1038/s41467-018-03690-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 03/05/2018] [Indexed: 11/23/2022] Open
Abstract
Members of the diazeniumdiolate class of natural compounds show potential for drug development because of their antifungal, antibacterial, antiviral, and antitumor activities. Yet, their biosynthesis has remained elusive to date. Here, we identify a gene cluster directing the biosynthesis of the diazeniumdiolate compound fragin in Burkholderia cenocepacia H111. We provide evidence that fragin is a metallophore and that metal chelation is the molecular basis of its antifungal activity. A subset of the fragin biosynthetic genes is involved in the synthesis of a previously undescribed cell-to-cell signal molecule, valdiazen. RNA-Seq analyses reveal that valdiazen controls fragin biosynthesis and affects the expression of more than 100 genes. Homologs of the valdiazen biosynthesis genes are found in various bacteria, suggesting that valdiazen-like compounds may constitute a new class of signal molecules. We use structural information, in silico prediction of enzymatic functions and biochemical data to propose a biosynthesis route for fragin and valdiazen. Fragin is a diazeniumdiolate metabolite with antifungal activity, produced by some bacteria. Here, Jenul et al. show that metal chelation is the molecular basis of fragin’s antifungal activity, and that a gene cluster directing fragin biosynthesis is also involved in the synthesis of a signal molecule.
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Affiliation(s)
- Christian Jenul
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Simon Sieber
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland.,Department of Chemistry, University of Basel, 4056, Basel, Switzerland
| | - Christophe Daeppen
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland.,Department of Chemistry, University of Basel, 4056, Basel, Switzerland
| | - Anugraha Mathew
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Martina Lardi
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Dominic Hoepfner
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Markus Neuburger
- Department of Chemistry, University of Basel, 4056, Basel, Switzerland
| | - Anthony Linden
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Karl Gademann
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland.
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland.
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114
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Miley GP, Rote JC, Silverman RB, Kelleher NL, Thomson RJ. Total Synthesis of Tambromycin Enabled by Indole C-H Functionalization. Org Lett 2018; 20:2369-2373. [PMID: 29584440 DOI: 10.1021/acs.orglett.8b00700] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The total synthesis of tambromycin (1), a recently isolated tetrapeptide, is reported. This unusual natural product possesses a highly modified tryptophan-derived indole fragment fused to an α-methylserine-derived oxazoline ring, and a unique noncanonical amino acid residue named tambroline (11). A convergent synthesis of tambromycin was achieved by a 13-step route that leveraged recent developments in the field of C-H functionalization to prepare the complex indole fragment, as well as an efficient synthesis of tambroline that featured a diastereoselective amination of homoproline.
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115
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Soslau G. Circular RNA (circRNA) was an important bridge in the switch from the RNA world to the DNA world. J Theor Biol 2018; 447:32-40. [PMID: 29567323 DOI: 10.1016/j.jtbi.2018.03.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 03/10/2018] [Accepted: 03/14/2018] [Indexed: 12/01/2022]
Abstract
The concept that life on Earth began as an RNA world has been built upon extensive experimentation demonstrating that many of the building blocks required for living cells could be synthesized in the laboratory under conditions approximating our primordial world. Many of the building blocks for life have also been found in meteorites indicating that meteors may have been a source for these molecules, or more likely, that they represent the chemical library present in most/all bodies in the universe after the big bang. Perhaps the most important support for the concept comes from the fact that some RNA species possess catalytic activity, ribozymes, and that RNA could be reverse transcribe to DNA. The thrust of numerous papers on this topic has been to explore how the available molecules on Earth, at its birth, gave rise to life as we know it today. This paper focuses more on a reverse view of the topic. The "how" molecular building blocks were synthesized is not addressed nor how the "first" RNA molecules were synthesized. We can clearly speculate on the variable environmental conditions and chemistry available on Earth billions of years ago. However, we can never truly replicate the changing conditions or know the chemical composition of Earth at the beginning of time. We can, however, confirm that over millions, perhaps billions of years the basic building blocks for life accumulated sufficiently to initiate evolution to an RNA world followed by our RNA/DNA world. Here we are attempting to take the information from our current knowledge of biology and by inference and extrapolation work backward to hypothesize biological events in the march forward from RNA to DNA. It is proposed that the primordial replicating RNA cell, the ribocyte, evolved from liposomes encompassing required reactants and products for "life" and that ribonucleopeptide complexes formed membrane pores to support bidirectional ion and molecular transport to maintain biological functions and osmolarity. Circular RNA, circRNA, is proposed as a critical stable RNA molecule that served as the genetic precursor for the switch to DNA and the replication of circRNA by a rolling circle mechanism gave rise to the RNA complexity required for the genetic functions of the cell. The replicating ribocyte would have required protein synthesis as well as RNA replication and a model for non-coded and primordial coded protein synthesis is proposed. Finally, the switch from the RNA to the DNA world would have involved the synthesis of an RNA:DNA hybrid prior to the formation of dsDNA. If the hybrid was a circular molecule that ultimately yielded a circular dsDNA molecule, it could predict that the primordial DNA cell would evolve into a bacterial cell with a single circular chromosome. One would hope that continued speculation of the origin of life will spur new directions of research that may never fully answer the questions of the past but add to our ability to regulate potentially harmful biological events in the present and in the future.
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Affiliation(s)
- Gerald Soslau
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N 15th ST, Philadelphia, PA 19102, United States.
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116
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Ho YTC, Leng DJ, Ghiringhelli F, Wilkening I, Bushell DP, Kostner O, Riva E, Havemann J, Passarella D, Tosin M. Novel chemical probes for the investigation of nonribosomal peptide assembly. Chem Commun (Camb) 2018. [PMID: 28627528 DOI: 10.1039/c7cc02427d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Chemical probes were devised and evaluated for the capture of biosynthetic intermediates involved in the bio-assembly of the nonribosomal peptide echinomycin. Putative intermediate peptide species were isolated and characterised, providing fresh insights into pathway substrate flexibility and paving the way for novel chemoenzymatic approaches towards unnatural peptides.
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Affiliation(s)
- Y T Candace Ho
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK.
| | - Daniel J Leng
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK.
| | - Francesca Ghiringhelli
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK. and Department of Chemistry, Universita' degli Studi di Milano, Via Golgi, 19 20133 Milano, Italy
| | - Ina Wilkening
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK.
| | - Dexter P Bushell
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK.
| | - Otto Kostner
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK. and Institut für Organische Chemie, Universität Wien, Währinger Str., 38 1090 Wien, Austria
| | - Elena Riva
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK.
| | - Judith Havemann
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK.
| | - Daniele Passarella
- Department of Chemistry, Universita' degli Studi di Milano, Via Golgi, 19 20133 Milano, Italy
| | - Manuela Tosin
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK.
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117
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Cell-free synthetic biology for in vitro biosynthesis of pharmaceutical natural products. Synth Syst Biotechnol 2018; 3:83-89. [PMID: 29900420 PMCID: PMC5995452 DOI: 10.1016/j.synbio.2018.02.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 01/29/2018] [Accepted: 02/08/2018] [Indexed: 01/26/2023] Open
Abstract
Natural products with significant biological activities continuously act as rich sources for drug discovery and development. To harness the potential of these valuable compounds, robust methods need to be developed for their rapid and sustainable production. Cell-free biosynthesis of pharmaceutical natural products by in vitro reconstruction of the entire biosynthetic pathways represents one such solution. In this review, we focus on in vitro biosynthesis of two important classes of natural products, polyketides (PKs) and nonribosomal peptides (NRPs). First, we summarize purified enzyme-based systems for the biosynthesis of PKs, NRPs, and PK/NRP hybrids. Then, we introduce the cell-free protein synthesis (CFPS)-based technology for natural product production. With that, we discuss challenges and opportunities of cell-free synthetic biology for in vitro biosynthesis of natural products.
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118
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Perez CE, Park HB, Crawford JM. Functional Characterization of a Condensation Domain That Links Nonribosomal Peptide and Pteridine Biosynthetic Machineries in Photorhabdus luminescens. Biochemistry 2018; 57:354-361. [PMID: 29111689 DOI: 10.1021/acs.biochem.7b00863] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) produce a wide variety of biologically important small molecules. NRPSs can interface with other enzymes to form hybrid biosynthetic systems that expand the structural and functional diversity of their products. The pepteridines are metabolites encoded by an unprecedented pteridine-NRPS-type hybrid biosynthetic gene cluster in Photorhabdus luminescens, but how the distinct enzymatic systems interface to produce these molecules has not been examined at the biochemical level. By an unknown mechanism, the genetic locus can also affect the regulation of other enzymes involved in autoinducer and secondary metabolite biosynthesis. Here, through in vitro protein biochemical assays, we demonstrate that an atypical NRPS condensation (C) domain present in the pathway condenses acyl units derived from α-keto acids onto a free 5,6,7,8-tetrahydropterin core, producing the tertiary cis-amide-containing pepteridines. Solution studies of the chemically synthesized molecules led to the same amide regiochemistries that were observed in the natural products. The biochemical transformations mediated by the C domain destroy the radical scavenging activity of its redox active tetrahydropterin substrate. Secondary metabolite analyses revealed that the pepteridine locus affects select metabolic pathways associated with quorum sensing, antibiosis, and symbiosis. Taken together, the results suggest that the pathway likely regulates cellular redox and specialized metabolic pathways through engagement with the citric acid cycle.
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Affiliation(s)
- Corey E Perez
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States
| | - Hyun Bong Park
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States
| | - Jason M Crawford
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States.,Department of Microbial Pathogenesis, Yale School of Medicine , New Haven, Connecticut 06510, United States
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119
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Zhou M, Liu F, Yang X, Jin J, Dong X, Zeng KW, Liu D, Zhang Y, Ma M, Yang D. Bacillibactin and Bacillomycin Analogues with Cytotoxicities against Human Cancer Cell Lines from Marine Bacillus sp. PKU-MA00093 and PKU-MA00092. Mar Drugs 2018; 16:E22. [PMID: 29320403 PMCID: PMC5793070 DOI: 10.3390/md16010022] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 12/21/2017] [Accepted: 01/05/2018] [Indexed: 12/12/2022] Open
Abstract
Nonribosomal peptides from marine Bacillus strains have received considerable attention for their complex structures and potent bioactivities. In this study, we carried out PCR-based genome mining for potential nonribosomal peptides producers from our marine bacterial library. Twenty-one "positive" strains were screened out from 180 marine bacterial strains, and subsequent small-scale fermentation, HPLC and phylogenetic analysis afforded Bacillus sp. PKU-MA00092 and PKU-MA00093 as two candidates for large-scale fermentation and isolation. Ten nonribosomal peptides, including four bacillibactin analogues (1-4) and six bacillomycin D analogues (5-10) were discovered from Bacillus sp. PKU-MA00093 and PKU-MA00092, respectively. Compounds 1 and 2 are two new compounds and the ¹H NMR and 13C NMR data of compounds 7 and 9 is first provided. All compounds 1-10 were assayed for their cytotoxicities against human cancer cell lines HepG2 and MCF7, and the bacillomycin D analogues 7-10 showed moderate cytotoxicities with IC50 values from 2.9 ± 0.1 to 8.2 ± 0.2 µM. The discovery of 5-10 with different fatty acid moieties gave us the opportunity to reveal the structure-activity relationships of bacillomycin analogues against these human cancer cell lines. These results enrich the structural diversity and bioactivity properties of nonribosomal peptides from marine Bacillus strains.
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Affiliation(s)
- Mengjie Zhou
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Fawang Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Xiaoyan Yang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Jing Jin
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Xin Dong
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Ke-Wu Zeng
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Dong Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Yingtao Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Ming Ma
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Donghui Yang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
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120
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De novo design and engineering of non-ribosomal peptide synthetases. Nat Chem 2017; 10:275-281. [PMID: 29461518 DOI: 10.1038/nchem.2890] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 10/06/2017] [Indexed: 01/20/2023]
Abstract
Peptides derived from non-ribosomal peptide synthetases (NRPSs) represent an important class of pharmaceutically relevant drugs. Methods to generate novel non-ribosomal peptides or to modify peptide natural products in an easy and predictable way are therefore of great interest. However, although the overall modular structure of NRPSs suggests the possibility of adjusting domain specificity and selectivity, only a few examples have been reported and these usually show a severe drop in production titre. Here we report a new strategy for the modification of NRPSs that uses defined exchange units (XUs) and not modules as functional units. XUs are fused at specific positions that connect the condensation and adenylation domains and respect the original specificity of the downstream module to enable the production of the desired peptides. We also present the use of internal condensation domains as an alternative to other peptide-chain-releasing domains for the production of cyclic peptides.
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121
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Nunn PB, Codd GA. Metabolic solutions to the biosynthesis of some diaminomonocarboxylic acids in nature: Formation in cyanobacteria of the neurotoxins 3-N-methyl-2,3-diaminopropanoic acid (BMAA) and 2,4-diaminobutanoic acid (2,4-DAB). PHYTOCHEMISTRY 2017; 144:253-270. [PMID: 29059579 DOI: 10.1016/j.phytochem.2017.09.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 09/18/2017] [Accepted: 09/20/2017] [Indexed: 06/07/2023]
Abstract
The non-encoded diaminomonocarboxylic acids, 3-N-methyl-2,3-diaminopropanoic acid (syn: α-amino-β-methylaminopropionic acid, MeDAP; β-N-methylaminoalanine, BMAA) and 2,4-diaminobutanoic acid (2,4-DAB), are distributed widely in cyanobacterial species in free and bound forms. Both amino acids are neurotoxic in whole animal and cell-based bioassays. The biosynthetic pathway to 2,4-DAB is well documented in bacteria and in one higher plant species, but has not been confirmed in cyanobacteria. The biosynthetic pathway to BMAA is unknown. This review considers possible metabolic routes, by analogy with reactions used in other species, by which these amino acids might be biosynthesised by cyanobacteria, which are a widespread potential environmental source of these neurotoxins. Where possible, the gene expression that might be implicated in these biosyntheses is discussed.
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Affiliation(s)
- Peter B Nunn
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, PO1 2DT, UK.
| | - Geoffrey A Codd
- School of Life Sciences, University of Dundee, DD1 5EH, UK; School of Natural Sciences, University of Stirling, FK9 4LA, UK.
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122
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Agrawal S, Acharya D, Adholeya A, Barrow CJ, Deshmukh SK. Nonribosomal Peptides from Marine Microbes and Their Antimicrobial and Anticancer Potential. Front Pharmacol 2017; 8:828. [PMID: 29209209 PMCID: PMC5702503 DOI: 10.3389/fphar.2017.00828] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/31/2017] [Indexed: 11/13/2022] Open
Abstract
Marine environments are largely unexplored and can be a source of new molecules for the treatment of many diseases such as malaria, cancer, tuberculosis, HIV etc. The Marine environment is one of the untapped bioresource of getting pharmacologically active nonribosomal peptides (NRPs). Bioprospecting of marine microbes have achieved many remarkable milestones in pharmaceutics. Till date, more than 50% of drugs which are in clinical use belong to the nonribosomal peptide or mixed polyketide-nonribosomal peptide families of natural products isolated from marine bacteria, cyanobacteria and fungi. In recent years large numbers of nonribosomal have been discovered from marine microbes using multi-disciplinary approaches. The present review covers the NRPs discovered from marine microbes and their pharmacological potential along with role of genomics, proteomics and bioinformatics in discovery and development of nonribosomal peptides drugs.
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Affiliation(s)
- Shivankar Agrawal
- Biotechnology and Management of Bioresources Division, TERI-Deakin Nano Biotechnology Centre, Energy and Resources Institute, New Delhi, India.,Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, Australia
| | - Debabrata Acharya
- Biotechnology and Management of Bioresources Division, TERI-Deakin Nano Biotechnology Centre, Energy and Resources Institute, New Delhi, India
| | - Alok Adholeya
- Biotechnology and Management of Bioresources Division, TERI-Deakin Nano Biotechnology Centre, Energy and Resources Institute, New Delhi, India
| | - Colin J Barrow
- Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, Australia
| | - Sunil K Deshmukh
- Biotechnology and Management of Bioresources Division, TERI-Deakin Nano Biotechnology Centre, Energy and Resources Institute, New Delhi, India
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123
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Nonribosomal biosynthesis of backbone-modified peptides. Nat Chem 2017; 10:282-287. [DOI: 10.1038/nchem.2891] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 10/06/2017] [Indexed: 01/01/2023]
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124
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Mishra AK, Choi J, Choi SJ, Baek KH. Cyclodipeptides: An Overview of Their Biosynthesis and Biological Activity. Molecules 2017; 22:molecules22101796. [PMID: 29065531 PMCID: PMC6151668 DOI: 10.3390/molecules22101796] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 10/18/2017] [Accepted: 10/19/2017] [Indexed: 01/06/2023] Open
Abstract
Cyclodipeptides (CDP) represent a diverse family of small, highly stable, cyclic peptides that are produced as secondary functional metabolites or side products of protein metabolism by bacteria, fungi, and animals. They are widespread in nature, and exhibit a broad variety of biological and pharmacological activities. CDP synthases (CDPSs) and non-ribosomal peptide synthetases (NRPSs) catalyze the biosynthesis of the CDP core structure, which is further modified by tailoring enzymes often associated with CDP biosynthetic gene clusters. In this review, we provide a comprehensive summary of CDP biosynthetic pathways and modifying enzymes. We also discuss the biological properties of some known CDPs and their possible applications in metabolic engineering.
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Affiliation(s)
- Awdhesh Kumar Mishra
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea.
| | - Jaehyuk Choi
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea.
| | - Seong-Jin Choi
- Department of Biotechnology, Daegu Catholic University, Gyeongsan 38430, Korea.
| | - Kwang-Hyun Baek
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea.
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125
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Guntaka NS, Healy AR, Crawford JM, Herzon SB, Bruner SD. Structure and Functional Analysis of ClbQ, an Unusual Intermediate-Releasing Thioesterase from the Colibactin Biosynthetic Pathway. ACS Chem Biol 2017; 12:2598-2608. [PMID: 28846367 PMCID: PMC5830302 DOI: 10.1021/acschembio.7b00479] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Colibactin is a genotoxic hybrid nonribosomal peptide/polyketide secondary metabolite produced by various pathogenic and probiotic bacteria residing in the human gut. The presence of colibactin metabolites has been correlated to colorectal cancer formation in several studies. The specific function of many gene products in the colibactin gene cluster can be predicted. However, the role of ClbQ, a type II editing thioesterase, has not been established. The importance of ClbQ has been demonstrated by genetic deletions that abolish colibactin cytotoxic activity, and recent studies suggest an atypical role in releasing pathway intermediates from the assembly line. Here we report the 2.0 Å crystal structure and biochemical characterization of ClbQ. Our data reveal that ClbQ exhibits greater catalytic efficiency toward acyl-thioester substrates as compared to precolibactin intermediates and does not discriminate among carrier proteins. Cyclized pyridone-containing colibactins, which are off-pathway derivatives, are not viable substrates for ClbQ, while linear precursors are, supporting a role of ClbQ in facilitating the promiscuous off-loading of premature precolibactin metabolites and novel insights into colibactin biosynthesis.
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Affiliation(s)
- Naga Sandhya Guntaka
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Alan R. Healy
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, United States
| | - Jason M. Crawford
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, United States
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, United States
| | - Seth B. Herzon
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520, United States
| | - Steven D. Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
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126
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Cleto S, Lu TK. An Engineered Synthetic Pathway for Discovering Nonnatural Nonribosomal Peptides in Escherichia coli. mBio 2017; 8:e01474-17. [PMID: 29018120 PMCID: PMC5635690 DOI: 10.1128/mbio.01474-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 09/08/2017] [Indexed: 01/15/2023] Open
Abstract
Peptides that are synthesized independently of the ribosome in plants, fungi, and bacteria can have clinically relevant anticancer, antihemochromatosis, and antiviral activities, among many other. Despite their natural origin, discovering new natural products is challenging, and there is a need to expand the chemical diversity that is accessible. In this work, we created a novel, compressed synthetic pathway for the heterologous expression and diversification of nonribosomal peptides (NRPs) based on homologs of siderophore pathways from Escherichia coli and Vibrio cholerae To enhance the likelihood of successful molecule production, we established a selective pressure via the iron-chelating properties of siderophores. By supplementing cells containing our synthetic pathway with different precursors that are incorporated into the pathway independently of NRP enzymes, we generated over 20 predesigned, novel, and structurally diverse NRPs. This engineering approach, where phylogenetically related genes from different organisms are integrated and supplemented with novel precursors, should enable heterologous expression and molecular diversification of NRPs.IMPORTANCE Nonribosomal peptides (NRPs) constitute a source of bioactive molecules with potential therapeutic applications. However, discovering novel NRPs by rational engineering of biosynthetic pathways remains challenging. Here, we show that a synthetic compressed pathway in which we replaced biosynthetic genes with their ancestral homologs and orthologs enabled successful heterologous NRP expression. Polyamines added exogenously were incorporated into nascent NRPs, and molecular production was pressured by growing the host under conditions that make such NRPs beneficial for survival. This multilayered approach resulted in the assembly of over 20 distinct and novel molecules. We envision this strategy being used to enable the production of NRPs from heterologous pathways.
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Affiliation(s)
- Sara Cleto
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Timothy K Lu
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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127
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Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition. Proc Natl Acad Sci U S A 2017; 114:10420-10425. [PMID: 28893989 DOI: 10.1073/pnas.1703663114] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Posttranslational modification of ribosomally synthesized peptides provides an elegant means for the production of biologically active molecules known as RiPPs (ribosomally synthesized and posttranslationally modified peptides). Although the leader sequence of the precursor peptide is often required for turnover, the exact mode of recognition by the modifying enzymes remains unclear for many members of this class of natural products. Here, we have used X-ray crystallography and computational modeling to examine the role of the leader peptide in the biosynthesis of a homolog of streptide, a recently identified peptide natural product with an intramolecular lysine-tryptophan cross-link, which is installed by the radical S-adenosylmethionine (SAM) enzyme, StrB. We present crystal structures of SuiB, a close ortholog of StrB, in various forms, including apo SuiB, SAM-bound SuiB, and a complex of SuiB with SAM and its peptide substrate, SuiA. Although the N-terminal domain of SuiB adopts a typical RRE (RiPP recognition element) motif, which has been implicated in precursor peptide recognition, we observe binding of the leader peptide in the catalytic barrel rather than the N-terminal domain. Computational simulations support a mechanism in which the leader peptide guides posttranslational modification by positioning the cross-linking residues of the precursor peptide within the active site. Together the results shed light onto binding of the precursor peptide and the associated conformational changes needed for the formation of the unique carbon-carbon cross-link in the streptide family of natural products.
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128
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A strategy for the identification of patterns in the biosynthesis of nonribosomal peptides by Betaproteobacteria species. Sci Rep 2017; 7:10400. [PMID: 28871139 PMCID: PMC5583390 DOI: 10.1038/s41598-017-11314-w] [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: 03/17/2017] [Accepted: 08/22/2017] [Indexed: 11/17/2022] Open
Abstract
Nonribosomal peptides have an important pharmacological role due to their extensive biological properties. The singularities in the biosynthesis of these natural products allowed the development of genome-mining strategies which associate them to their original biosynthetic gene clusters. Generally, these compounds present complex architectures that make their identification difficult. Based on these evidences, genomes from species of the class Betaproteobacteria were studied with the purpose of finding biosynthetic similarities among them. These organisms were applied as templates due to their large number of biosynthetic gene clusters and the natural products isolated from them. The strategy for Rapid Identification of Nonribosomal Peptides Portions (RINPEP) proposed in this work was built by reorganizing the data obtained from antiSMASH and NCBI with a product-centered way. The verification steps of RINPEP comprehended the fragments of existent compounds and predictions obtained in silico with the purpose of finding common subunits expressed by different genomic sequences. The results of this strategy revealed patterns in a global overview of the biosynthesis of nonribosomal peptides by Betaproteobacteria.
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129
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Kittilä T, Kittel C, Tailhades J, Butz D, Schoppet M, Büttner A, Goode RJA, Schittenhelm RB, van Pee KH, Süssmuth RD, Wohlleben W, Cryle MJ, Stegmann E. Halogenation of glycopeptide antibiotics occurs at the amino acid level during non-ribosomal peptide synthesis. Chem Sci 2017; 8:5992-6004. [PMID: 28989629 PMCID: PMC5620994 DOI: 10.1039/c7sc00460e] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/20/2017] [Indexed: 12/30/2022] Open
Abstract
Halogenation plays a significant role in the activity of the glycopeptide antibiotics (GPAs), although up until now the timing and therefore exact substrate involved was unclear. Here, we present results combined from in vivo and in vitro studies that reveal the substrates for the halogenase enzymes from GPA biosynthesis as amino acid residues bound to peptidyl carrier protein (PCP)-domains from the non-ribosomal peptide synthetase machinery: no activity was detected upon either free amino acids or PCP-bound peptides. Furthermore, we show that the selectivity of GPA halogenase enzymes depends upon both the structure of the bound amino acid and the PCP domain, rather than being driven solely via the PCP domain. These studies provide the first detailed understanding of how halogenation is performed during GPA biosynthesis and highlight the importance and versatility of trans-acting enzymes that operate during peptide assembly by non-ribosomal peptide synthetases.
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Affiliation(s)
- Tiia Kittilä
- Department of Biomolecular Mechanisms , Max Planck Institute for Medical Research , Jahnstrasse 29 , 69120 Heidelberg , Germany
| | - Claudia Kittel
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen , Microbiology/Biotechnology , University of Tuebingen , Auf der Morgenstelle 28 , 72076 Tuebingen , Germany .
| | - Julien Tailhades
- EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia .
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia
| | - Diane Butz
- Institut für Chemie , Technische Universität Berlin , 10623 Berlin , Germany
| | - Melanie Schoppet
- Department of Biomolecular Mechanisms , Max Planck Institute for Medical Research , Jahnstrasse 29 , 69120 Heidelberg , Germany
- EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia .
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia
| | - Anita Büttner
- Allgemeine Biochemie , TU Dresden , 01062 Dresden , Germany
| | - Rob J A Goode
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia
- Monash Biomedical Proteomics Facility , Monash University , Clayton , Victoria 3800 , Australia
| | - Ralf B Schittenhelm
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia
- Monash Biomedical Proteomics Facility , Monash University , Clayton , Victoria 3800 , Australia
| | - Karl-Heinz van Pee
- Institut für Chemie , Technische Universität Berlin , 10623 Berlin , Germany
| | | | - Wolfgang Wohlleben
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen , Microbiology/Biotechnology , University of Tuebingen , Auf der Morgenstelle 28 , 72076 Tuebingen , Germany .
- German Centre for Infection Research (DZIF) , Partner Site Tuebingen , Tuebingen , Germany
| | - Max J Cryle
- Department of Biomolecular Mechanisms , Max Planck Institute for Medical Research , Jahnstrasse 29 , 69120 Heidelberg , Germany
- EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia .
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia
- ARC Centre of Excellence in Advanced Molecular Imaging , Monash University , Clayton , Victoria 3800 , Australia
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen , Microbiology/Biotechnology , University of Tuebingen , Auf der Morgenstelle 28 , 72076 Tuebingen , Germany .
- German Centre for Infection Research (DZIF) , Partner Site Tuebingen , Tuebingen , Germany
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130
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Scaglione A, Fullone MR, Montemiglio LC, Parisi G, Zamparelli C, Vallone B, Savino C, Grgurina I. Structure of the adenylation domain Thr1 involved in the biosynthesis of 4-chlorothreonine in Streptomyces sp. OH-5093-protein flexibility and molecular bases of substrate specificity. FEBS J 2017; 284:2981-2999. [PMID: 28704585 DOI: 10.1111/febs.14163] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 05/19/2017] [Accepted: 07/10/2017] [Indexed: 12/13/2022]
Abstract
We determined the crystal structure of Thr1, the self-standing adenylation domain involved in the nonribosomal-like biosynthesis of free 4-chlorothreonine in Streptomyces sp. OH-5093. Thr1 shows two monomers in the crystallographic asymmetric unit with different relative orientations of the C- and N-terminal subdomains both in the presence of substrates and in the unliganded form. Cocrystallization with substrates, adenosine 5'-triphosphate and l-threonine, yielded one monomer containing the two substrates and the other in complex with l-threonine adenylate, locked in a postadenylation state. Steady-state kinetics showed that Thr1 activates l-Thr and its stereoisomers, as well as d-Ala, l- and d-Ser, albeit with lower efficiency. Modeling of these substrates in the active site highlighted the molecular bases of substrate discrimination. This work provides the first crystal structure of a threonine-activating adenylation enzyme, a contribution to the studies on conformational rearrangement in adenylation domains and on substrate recognition in nonribosomal biosynthesis. DATABASE Structural data are available in the Protein Data Bank under the accession number 5N9W and 5N9X.
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Affiliation(s)
- Antonella Scaglione
- Department of Biochemical Sciences "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, Italy.,Institute of Molecular Biology and Pathology, CNR - National Research Council of Italy, Rome, Italy
| | - Maria Rosaria Fullone
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy
| | - Linda Celeste Montemiglio
- Department of Biochemical Sciences "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, Italy.,Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy
| | - Giacomo Parisi
- Department of Biochemical Sciences "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, Italy.,Institute of Molecular Biology and Pathology, CNR - National Research Council of Italy, Rome, Italy
| | - Carlotta Zamparelli
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy
| | - Beatrice Vallone
- Department of Biochemical Sciences "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, Italy.,Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, CNR - National Research Council of Italy, Rome, Italy
| | - Ingeborg Grgurina
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy
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131
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Timmermans ML, Paudel YP, Ross AC. Investigating the Biosynthesis of Natural Products from Marine Proteobacteria: A Survey of Molecules and Strategies. Mar Drugs 2017; 15:E235. [PMID: 28762997 PMCID: PMC5577590 DOI: 10.3390/md15080235] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 07/21/2017] [Accepted: 07/24/2017] [Indexed: 02/07/2023] Open
Abstract
The phylum proteobacteria contains a wide array of Gram-negative marine bacteria. With recent advances in genomic sequencing, genome analysis, and analytical chemistry techniques, a whole host of information is being revealed about the primary and secondary metabolism of marine proteobacteria. This has led to the discovery of a growing number of medically relevant natural products, including novel leads for the treatment of multidrug-resistant Staphylococcus aureus (MRSA) and cancer. Of equal interest, marine proteobacteria produce natural products whose structure and biosynthetic mechanisms differ from those of their terrestrial and actinobacterial counterparts. Notable features of secondary metabolites produced by marine proteobacteria include halogenation, sulfur-containing heterocycles, non-ribosomal peptides, and polyketides with unusual biosynthetic logic. As advances are made in the technology associated with functional genomics, such as computational sequence analysis, targeted DNA manipulation, and heterologous expression, it has become easier to probe the mechanisms for natural product biosynthesis. This review will focus on genomics driven approaches to understanding the biosynthetic mechanisms for natural products produced by marine proteobacteria.
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Affiliation(s)
| | - Yagya P Paudel
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada.
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132
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Payne JAE, Schoppet M, Hansen MH, Cryle MJ. Diversity of nature's assembly lines - recent discoveries in non-ribosomal peptide synthesis. MOLECULAR BIOSYSTEMS 2017; 13:9-22. [PMID: 27853778 DOI: 10.1039/c6mb00675b] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The biosynthesis of complex natural products by non-ribosomal peptide synthetases (NRPSs) and the related polyketide synthases (PKSs) represents a major source of important bioactive compounds. These large, multi-domain machineries are able to produce a fascinating range of molecules due to the nature of their modular architectures, which allows natural products to be assembled and tailored in a modular, step-wise fashion. In recent years there has been significant progress in characterising the important domains and underlying mechanisms of non-ribosomal peptide synthesis. More significantly, several studies have uncovered important examples of novel activity in many NRPS domains. These discoveries not only greatly increase the structural diversity of the possible products of NRPS machineries but - possibly more importantly - they improve our understanding of what is a highly important, yet complex, biosynthetic apparatus. In this review, several recent examples of novel NRPS function will be introduced, which highlight the range of previously uncharacterised activities that have now been detected in the biosynthesis of important natural products by these mega-enzyme synthetases.
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Affiliation(s)
- Jennifer A E Payne
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia and The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.
| | - Melanie Schoppet
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia and The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.
| | | | - Max J Cryle
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia and The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.
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133
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Bloudoff K, Schmeing TM. Structural and functional aspects of the nonribosomal peptide synthetase condensation domain superfamily: discovery, dissection and diversity. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1587-1604. [PMID: 28526268 DOI: 10.1016/j.bbapap.2017.05.010] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 05/05/2017] [Accepted: 05/12/2017] [Indexed: 01/23/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) are incredible macromolecular machines that produce a wide range of biologically- and therapeutically-relevant molecules. During synthesis, peptide elongation is performed by the condensation (C) domain, as it catalyzes amide bond formation between the nascent peptide and the amino acid it adds to the chain. Since their discovery more than two decades ago, C domains have been subject to extensive biochemical, bioinformatic, mutagenic, and structural analyses. They are composed of two lobes, each with homology to chloramphenicol acetyltransferase, have two binding sites for their two peptidyl carrier protein-bound ligands, and have an active site with conserved motif HHxxxDG located between the two lobes. This review discusses some of the important insights into the structure, catalytic mechanism, specificity, and gatekeeping functions of C domains revealed since their discovery. In addition, C domains are the archetypal members of the C domain superfamily, which includes several other members that also function as NRPS domains. The other family members can replace the C domain in NRP synthesis, can work in concert with a C domain, or can fulfill diverse and novel functions. These domains include the epimerization (E) domain, the heterocyclization (Cy) domain, the ester-bond forming C domain, the fungal NRPS terminal C domain (CT), the β-lactam ring forming C domain, and the X domain. We also discuss structural and function insight into C, E, Cy, CT and X domains, to present a holistic overview of historical and current knowledge of the C domain superfamily. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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Affiliation(s)
- Kristjan Bloudoff
- Department of Biochemistry, McGill University, Montréal, QC H3G 0B1, Canada
| | - T Martin Schmeing
- Department of Biochemistry, McGill University, Montréal, QC H3G 0B1, Canada.
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134
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Biosynthesis of the antibiotic nonribosomal peptide penicillin in baker's yeast. Nat Commun 2017; 8:15202. [PMID: 28469278 PMCID: PMC5418595 DOI: 10.1038/ncomms15202] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 03/09/2017] [Indexed: 11/28/2022] Open
Abstract
Fungi are a valuable source of enzymatic diversity and therapeutic natural products including antibiotics. Here we engineer the baker's yeast Saccharomyces cerevisiae to produce and secrete the antibiotic penicillin, a beta-lactam nonribosomal peptide, by taking genes from a filamentous fungus and directing their efficient expression and subcellular localization. Using synthetic biology tools combined with long-read DNA sequencing, we optimize productivity by 50-fold to produce bioactive yields that allow spent S. cerevisiae growth media to have antibacterial action against Streptococcus bacteria. This work demonstrates that S. cerevisiae can be engineered to perform the complex biosynthesis of multicellular fungi, opening up the possibility of using yeast to accelerate rational engineering of nonribosomal peptide antibiotics. Filamentous fungi are a valuable source of natural therapeutic products such as antibiotics. Here the authors engineer monocellular S. cerevisiae to perform complex secondary metabolism typical of multicellular fungi in order to demonstrate biosynthesis and secretion of bioactive penicillin.
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135
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Metabolic role of lactobacilli in weight modification in humans and animals. Microb Pathog 2017; 106:182-194. [DOI: 10.1016/j.micpath.2016.03.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 03/11/2016] [Accepted: 03/22/2016] [Indexed: 02/07/2023]
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136
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Hill P, Heberlig GW, Boddy CN. Sampling Terrestrial Environments for Bacterial Polyketides. Molecules 2017; 22:E707. [PMID: 28468277 PMCID: PMC6154731 DOI: 10.3390/molecules22050707] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 04/14/2017] [Accepted: 04/18/2017] [Indexed: 12/17/2022] Open
Abstract
Bacterial polyketides are highly biologically active molecules that are frequently used as drugs, particularly as antibiotics and anticancer agents, thus the discovery of new polyketides is of major interest. Since the 1980s discovery of polyketides has slowed dramatically due in large part to the repeated rediscovery of known compounds. While recent scientific and technical advances have improved our ability to discover new polyketides, one key area has been under addressed, namely the distribution of polyketide-producing bacteria in the environment. Identifying environments where producing bacteria are abundant and diverse should improve our ability to discover (bioprospect) new polyketides. This review summarizes for the bioprospector the state-of-the-field in terrestrial microbial ecology. It provides insight into the scientific and technical challenges limiting the application of microbial ecology discoveries for bioprospecting and summarizes key developments in the field that will enable more effective bioprospecting. The major recent efforts by researchers to sample new environments for polyketide discovery is also reviewed and key emerging environments such as insect associated bacteria, desert soils, disease suppressive soils, and caves are highlighted. Finally strategies for taking and characterizing terrestrial samples to help maximize discovery efforts are proposed and the inclusion of non-actinomycetal bacteria in any terrestrial discovery strategy is recommended.
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Affiliation(s)
- Patrick Hill
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
| | - Graham W Heberlig
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
| | - Christopher N Boddy
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
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137
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Tarry MJ, Haque AS, Bui KH, Schmeing TM. X-Ray Crystallography and Electron Microscopy of Cross- and Multi-Module Nonribosomal Peptide Synthetase Proteins Reveal a Flexible Architecture. Structure 2017; 25:783-793.e4. [PMID: 28434915 DOI: 10.1016/j.str.2017.03.014] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/02/2017] [Accepted: 03/23/2017] [Indexed: 10/19/2022]
Abstract
Nonribosomal peptide synthetases (NRPS) are macromolecular machines that produce peptides with diverse activities. Structural information exists for domains, didomains, and even modules, but little is known about higher-order organization. We performed a multi-technique study on constructs from the dimodular NRPS DhbF. We determined a crystal structure of a cross-module construct including the adenylation (A) and peptidyl carrier protein (PCP) domains from module 1 and the condensation domain from module 2, complexed with an adenosine-vinylsulfonamide inhibitor and an MbtH-like protein (MLP). The action of the inhibitor and the role of the MLP were investigated using adenylation reactions and isothermal titration calorimetry. In the structure, the PCP and A domains adopt a novel conformation, and noncovalent, cross-module interactions are limited. We calculated envelopes of dimodular DhbF using negative-stain electron microscopy. The data show large conformational variability between modules. Together, our results suggest that NRPSs lack a uniform, rigid supermodular architecture.
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Affiliation(s)
- Michael J Tarry
- Department of Biochemistry, McGill University, Montréal, QC H3G 0B1, Canada
| | - Asfarul S Haque
- Department of Biochemistry, McGill University, Montréal, QC H3G 0B1, Canada
| | - Khanh Huy Bui
- Department of Anatomy and Cell Biology, McGill University, Montréal, QC H3A 0C7, Canada
| | - T Martin Schmeing
- Department of Biochemistry, McGill University, Montréal, QC H3G 0B1, Canada.
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138
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A proteasome inhibitor produced by Burkholderia pseudomallei modulates intracellular growth. Microb Pathog 2017; 107:175-180. [PMID: 28323151 DOI: 10.1016/j.micpath.2017.03.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 03/11/2017] [Accepted: 03/16/2017] [Indexed: 11/21/2022]
Abstract
The NRPS/PKS cluster encodes the enzymes necessary for glidobactin synthesis it is partially conserved in various members of the Burkholderia genus including B. pseudomallei. In this study we have shown that the insertional inactivation or deletion of glbC in this cluster in B. pseudomallei could reduce the ability of the bacterium to survive or grow in murine macrophages or in human neutrophils. Exogenously added proteasome inhibitors were able to chemically complement the mutation. The insertional inactivation or deletion of glbC increased virulence in an acute model of infection in Balb/c or C57BL/6 mice but virulence in a chronic model of infection was similar to that of the wild type. Our findings contrast with the previous finding that inactivation of the glb gene cluster in B. pseudomallei strain 1026b resulted in marked attenuation, and provides evidence of differential roles for some genes in virulence of different strains of B. pseudomallei.
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139
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Chemical Probes Allow Structural Insight into the Condensation Reaction of Nonribosomal Peptide Synthetases. Cell Chem Biol 2016; 23:331-9. [PMID: 26991102 DOI: 10.1016/j.chembiol.2016.02.012] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 02/03/2016] [Accepted: 02/19/2016] [Indexed: 01/24/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) synthesize a vast variety of small molecules, including antibiotics, antitumors, and immunosuppressants. The NRPS condensation (C) domain catalyzes amide bond formation, the central chemical step in nonribosomal peptide synthesis. The catalytic mechanism and substrate determinants of the reaction are under debate. We developed chemical probes to structurally study the NRPS condensation reaction. These substrate analogs become covalently tethered to a cysteine introduced near the active site, to mimic covalent substrate delivery by carrier domains. They are competent substrates in the condensation reaction and behave similarly to native substrates. Co-crystal structures show C domain-substrate interactions, and suggest that the catalytic histidine's principle role is to position the α-amino group for nucleophilic attack. Structural insight provided by these co-complexes also allowed us to alter the substrate specificity profile of the reaction with a single point mutation.
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140
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Cheel J, Urajová P, Hájek J, Hrouzek P, Kuzma M, Bouju E, Faure K, Kopecký J. Separation of cyclic lipopeptide puwainaphycins from cyanobacteria by countercurrent chromatography combined with polymeric resins and HPLC. Anal Bioanal Chem 2016; 409:917-930. [DOI: 10.1007/s00216-016-0066-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 09/28/2016] [Accepted: 10/28/2016] [Indexed: 11/30/2022]
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141
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Tobias NJ, Ahrendt T, Schell U, Miltenberger M, Hilbi H, Bode HB. Legionella shows a diverse secondary metabolism dependent on a broad spectrum Sfp-type phosphopantetheinyl transferase. PeerJ 2016; 4:e2720. [PMID: 27904811 PMCID: PMC5126622 DOI: 10.7717/peerj.2720] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/25/2016] [Indexed: 01/01/2023] Open
Abstract
Several members of the genus Legionella cause Legionnaires' disease, a potentially debilitating form of pneumonia. Studies frequently focus on the abundant number of virulence factors present in this genus. However, what is often overlooked is the role of secondary metabolites from Legionella. Following whole genome sequencing, we assembled and annotated the Legionella parisiensis DSM 19216 genome. Together with 14 other members of the Legionella, we performed comparative genomics and analysed the secondary metabolite potential of each strain. We found that Legionella contains a huge variety of biosynthetic gene clusters (BGCs) that are potentially making a significant number of novel natural products with undefined function. Surprisingly, only a single Sfp-like phosphopantetheinyl transferase is found in all Legionella strains analyzed that might be responsible for the activation of all carrier proteins in primary (fatty acid biosynthesis) and secondary metabolism (polyketide and non-ribosomal peptide synthesis). Using conserved active site motifs, we predict some novel compounds that are probably involved in cell-cell communication, differing to known communication systems. We identify several gene clusters, which may represent novel signaling mechanisms and demonstrate the natural product potential of Legionella.
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Affiliation(s)
- Nicholas J. Tobias
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe Universität, Frankfurt am Main, Germany
| | - Tilman Ahrendt
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe Universität, Frankfurt am Main, Germany
| | - Ursula Schell
- Max von Pettenkofer Institute, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Melissa Miltenberger
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe Universität, Frankfurt am Main, Germany
| | - Hubert Hilbi
- Max von Pettenkofer Institute, Ludwig-Maximilians-Universität München, Munich, Germany
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Helge B. Bode
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe Universität, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe Universität, Frankfurt am Main, Germany
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142
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Balhara M, Chaudhary R, Ruhil S, Singh B, Dahiya N, Parmar VS, Jaiwal PK, Chhillar AK. Siderophores; iron scavengers: the novel & promising targets for pathogen specific antifungal therapy. Expert Opin Ther Targets 2016; 20:1477-1489. [PMID: 27797604 DOI: 10.1080/14728222.2016.1254196] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION The recent emergence of resistance, toxicity paradigm and limited efficacy of conventional antifungal drugs necessitate the identification of de novo targets in fungal metabolism. One of the most critical physiological processes during in vivo pathogenesis is maintenance of iron homeostasis. The most life threatening opportunistic human fungal pathogens like Aspergillus, Candida and Cryptococcus exploit the siderophore mediated iron uptake mechanism either for survival, virulence, propagation or resistance to oxidative stress envisaged in vivo during infection. Areas covered: In this review, we will highlight the metabolic pathways; specifically siderophore biosynthesis, uptake and utilisation, triggered in the fungal pathogens in iron starving conditions and the various putative targets viable in these pathways to be recruited as novel therapeutic antidotes either via biosynthetic enzymes catalytic site inhibitors or as drug conjugates through trojan horse approach and further role in the development of fungal specific reliable diagnostic markers. Expert opinion: Siderophores are the weapons released by a pathogen to conquer the battle for iron acquisition. Hence, the fungal siderophore biosynthetic pathways along with their uptake and utilisation mechanisms represent an ideal target for pathogen specific, host friendly therapeutic strategy which would block the proliferation of parasite without causing any harm to the mammalian host.
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Affiliation(s)
- Meenakshi Balhara
- a Centre for Biotechnology , Maharshi Dayanand University , Rohtak , Haryana , India
| | - Renu Chaudhary
- a Centre for Biotechnology , Maharshi Dayanand University , Rohtak , Haryana , India
| | - Sonam Ruhil
- a Centre for Biotechnology , Maharshi Dayanand University , Rohtak , Haryana , India
| | - Bharat Singh
- a Centre for Biotechnology , Maharshi Dayanand University , Rohtak , Haryana , India
| | - Nisha Dahiya
- b Division of Epidemiology and Communicable Diseases , Indian Council of Medical Research , Delhi , India
| | - Virinder S Parmar
- c Bioorganic Laboratory, Department of Chemistry , University of Delhi , Delhi , India
| | - Pawan K Jaiwal
- a Centre for Biotechnology , Maharshi Dayanand University , Rohtak , Haryana , India
| | - Anil K Chhillar
- a Centre for Biotechnology , Maharshi Dayanand University , Rohtak , Haryana , India
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143
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Characterization and properties of biosurfactants produced by a newly isolated strain Bacillus methylotrophicus DCS1 and their applications in enhancing solubility of hydrocarbon. World J Microbiol Biotechnol 2016; 32:175. [DOI: 10.1007/s11274-016-2132-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 08/20/2016] [Indexed: 10/21/2022]
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144
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Blättner S, Das S, Paprotka K, Eilers U, Krischke M, Kretschmer D, Remmele CW, Dittrich M, Müller T, Schuelein-Voelk C, Hertlein T, Mueller MJ, Huettel B, Reinhardt R, Ohlsen K, Rudel T, Fraunholz MJ. Staphylococcus aureus Exploits a Non-ribosomal Cyclic Dipeptide to Modulate Survival within Epithelial Cells and Phagocytes. PLoS Pathog 2016; 12:e1005857. [PMID: 27632173 PMCID: PMC5025175 DOI: 10.1371/journal.ppat.1005857] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 08/10/2016] [Indexed: 12/21/2022] Open
Abstract
Community-acquired (CA) Staphylococcus aureus cause various diseases even in healthy individuals. Enhanced virulence of CA-strains is partly attributed to increased production of toxins such as phenol-soluble modulins (PSM). The pathogen is internalized efficiently by mammalian host cells and intracellular S. aureus has recently been shown to contribute to disease. Upon internalization, cytotoxic S. aureus strains can disrupt phagosomal membranes and kill host cells in a PSM-dependent manner. However, PSM are not sufficient for these processes. Here we screened for factors required for intracellular S. aureus virulence. We infected escape reporter host cells with strains from an established transposon mutant library and detected phagosomal escape rates using automated microscopy. We thereby, among other factors, identified a non-ribosomal peptide synthetase (NRPS) to be required for efficient phagosomal escape and intracellular survival of S. aureus as well as induction of host cell death. By genetic complementation as well as supplementation with the synthetic NRPS product, the cyclic dipeptide phevalin, wild-type phenotypes were restored. We further demonstrate that the NRPS is contributing to virulence in a mouse pneumonia model. Together, our data illustrate a hitherto unrecognized function of the S. aureus NRPS and its dipeptide product during S. aureus infection.
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Affiliation(s)
- Sebastian Blättner
- Biocenter, Chair of Microbiology, University of Würzburg, Würzburg, Germany
| | - Sudip Das
- Biocenter, Chair of Microbiology, University of Würzburg, Würzburg, Germany
| | - Kerstin Paprotka
- Biocenter, Chair of Microbiology, University of Würzburg, Würzburg, Germany
| | - Ursula Eilers
- Core Unit Functional Genomics, University of Würzburg, Würzburg, Germany
| | - Markus Krischke
- Biocenter, Chair of Pharmaceutical Biology, University of Würzburg, Würzburg, Germany
| | - Dorothee Kretschmer
- Department of Infection Biology, Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), University Tübingen, Tübingen, Germany
| | | | - Marcus Dittrich
- Biocenter, Chair of Bioinformatics, University of Würzburg, Würzburg, Germany
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Tobias Müller
- Biocenter, Chair of Bioinformatics, University of Würzburg, Würzburg, Germany
| | | | - Tobias Hertlein
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Martin J. Mueller
- Biocenter, Chair of Pharmaceutical Biology, University of Würzburg, Würzburg, Germany
| | | | | | - Knut Ohlsen
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Thomas Rudel
- Biocenter, Chair of Microbiology, University of Würzburg, Würzburg, Germany
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145
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Kittilä T, Mollo A, Charkoudian LK, Cryle MJ. New Structural Data Reveal the Motion of Carrier Proteins in Nonribosomal Peptide Synthesis. Angew Chem Int Ed Engl 2016; 55:9834-40. [PMID: 27435901 PMCID: PMC5113783 DOI: 10.1002/anie.201602614] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Indexed: 12/28/2022]
Abstract
The nonribosomal peptide synthetases (NRPSs) are one of the most promising resources for the production of new bioactive molecules. The mechanism of NRPS catalysis is based around sequential catalytic domains: these are organized into modules, where each module selects, modifies, and incorporates an amino acid into the growing peptide. The intermediates formed during NRPS catalysis are delivered between enzyme centers by peptidyl carrier protein (PCP) domains, which makes PCP interactions and movements crucial to NRPS mechanism. PCP movement has been linked to the domain alternation cycle of adenylation (A) domains, and recent complete NRPS module structures provide support for this hypothesis. However, it appears as though the A domain alternation alone is insufficient to account for the complete NRPS catalytic cycle and that the loaded state of the PCP must also play a role in choreographing catalysis in these complex and fascinating molecular machines.
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Affiliation(s)
- Tiia Kittilä
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Aurelio Mollo
- Department of Chemistry, Haverford College, Haverford, PA, 19041, USA
| | | | - Max J Cryle
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany. .,EMBL Australia, Monash University, Clayton, Victoria, 3800, Australia. .,The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia.
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146
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Kittilä T, Mollo A, Charkoudian LK, Cryle MJ. Neue Strukturdaten geben Einblick in die Bewegungen von Transportproteinen in der nicht-ribosomalen Peptidsynthese. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602614] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Tiia Kittilä
- Abteilung Biomolekulare Mechanismen; Max-Planck-Institut für Medizinische Forschung; Jahnstraße 29 69120 Heidelberg Deutschland
| | - Aurelio Mollo
- Department of Chemistry; Haverford College; Haverford PA 19041 USA
| | | | - Max J. Cryle
- Abteilung Biomolekulare Mechanismen; Max-Planck-Institut für Medizinische Forschung; Jahnstraße 29 69120 Heidelberg Deutschland
- EMBL Australia; Monash University; Clayton Victoria 3800 Australien
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging; Monash University; Clayton VIC 3800 Australien
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147
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Peschke M, Haslinger K, Brieke C, Reinstein J, Cryle MJ. Regulation of the P450 Oxygenation Cascade Involved in Glycopeptide Antibiotic Biosynthesis. J Am Chem Soc 2016; 138:6746-53. [DOI: 10.1021/jacs.6b00307] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Madeleine Peschke
- Department
of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Kristina Haslinger
- Department
of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Clara Brieke
- Department
of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Jochen Reinstein
- Department
of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Max J. Cryle
- Department
of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- EMBL
Australia, Monash University, Clayton, Victoria 3800, Australia
- The
Department of Biochemistry and Molecular Biology and ARC Centre of
Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
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148
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Kato H, Tsunematsu Y, Yamamoto T, Namiki T, Kishimoto S, Noguchi H, Watanabe K. New natural products isolated from Metarhizium robertsii ARSEF 23 by chemical screening and identification of the gene cluster through engineered biosynthesis in Aspergillus nidulans A1145. J Antibiot (Tokyo) 2016; 69:561-6. [DOI: 10.1038/ja.2016.54] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 04/05/2016] [Accepted: 04/21/2016] [Indexed: 11/09/2022]
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149
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Liu X, Jin Y, Cui Z, Nonaka K, Baba S, Funabashi M, Yang Z, Van Lanen SG. The Role of a Nonribosomal Peptide Synthetase in l-Lysine Lactamization During Capuramycin Biosynthesis. Chembiochem 2016; 17:804-10. [PMID: 26840634 PMCID: PMC4933962 DOI: 10.1002/cbic.201500701] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Indexed: 01/10/2023]
Abstract
Capuramycins are one of several known classes of natural products that contain an l-Lys-derived l-α-amino-ɛ-caprolactam (l-ACL) unit. The α-amino group of l-ACL in a capuramycin is linked to an unsaturated hexuronic acid component through an amide bond that was previously shown to originate by an ATP-independent enzymatic route. With the aid of a combined in vivo and in vitro approach, a predicted tridomain nonribosomal peptide synthetase CapU is functionally characterized here as the ATP-dependent amide-bond-forming catalyst responsible for the biosynthesis of the remaining amide bond present in l-ACL. The results are consistent with the adenylation domain of CapU as the essential catalytic component for l-Lys activation and thioesterification of the adjacent thiolation domain. However, in contrast to expectations, lactamization does not require any additional domains or proteins and is likely a nonenzymatic event. The results set the stage for examining whether a similar NRPS-mediated mechanism is employed in the biosynthesis of other l-ACL-containing natural products and, just as intriguingly, how spontaneous lactamization is avoided in the numerous NRPS-derived peptides that contain an unmodified l-Lys residue.
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Affiliation(s)
- Xiaodong Liu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536, USA
| | - Yuanyuan Jin
- Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medicinal Sciences & Peking Union Medical College, Beijing, China
| | - Zheng Cui
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536, USA
| | - Koichi Nonaka
- Biologics Technology Research Laboratories, Daiichi Sankyo, Co. Ltd., Gunma, 370-0503, Japan
| | - Satoshi Baba
- Biologics Technology Research Laboratories, Daiichi Sankyo, Co. Ltd., Gunma, 370-0503, Japan
| | - Masanori Funabashi
- Natural Product Research Group, Discovery Science and Technology Department, Daiichi Sankyo RD Novare Co. Ltd., Tokyo, 134-8630, Japan
| | - Zhaoyong Yang
- Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medicinal Sciences & Peking Union Medical College, Beijing, China
| | - Steven G Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536, USA.
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150
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Abstract
The emergence of next-generation sequencing has provided new opportunities in the discovery of new nonribosomal peptides (NRPs) and NRP synthethases (NRPSs). However, there remain challenges for the characterization of these megasynthases. While genetic methods in native hosts are critical in elucidation of the function of fungal NRPS, in vitro assays of intact heterologously expressed proteins provide deeper mechanistic insights in NRPS enzymology. Our previous work in the study of NRPS takes advantage of Saccharomyces cerevisiae strain BJ5464-npgA as a robust and versatile platform for characterization of fungal NRPSs. Here we describe the use of yeast recombination strategies in S. cerevisiae for cloning of the NRPS coding sequence in 2μ-based expression vector; the use of affinity chromatography for purification of NRPS from the total S. cerevisiae soluble protein fraction; and strategies for reconstitution of NRPSs activities in vitro.
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Affiliation(s)
- Ralph A Cacho
- Department of Chemical and Biomolecular Engineering, University of California, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA, 90095, USA
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA, 90095, USA.
- Department of Chemistry and Biochemistry, University of California, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA, 90095, USA.
- Department of Bioengineering, University of California, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA, 90095, USA.
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