1
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Parra J, Beaton A, Seipke RF, Wilkinson B, Hutchings MI, Duncan KR. Antibiotics from rare actinomycetes, beyond the genus Streptomyces. Curr Opin Microbiol 2023; 76:102385. [PMID: 37804816 DOI: 10.1016/j.mib.2023.102385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 10/09/2023]
Abstract
Throughout the golden age of antibiotic discovery, Streptomyces have been unsurpassed for their ability to produce bioactive metabolites. Yet, this success has been hampered by rediscovery. As we enter a new stage of biodiscovery, omics data and existing scientific repositories can enable informed choices on the biodiversity that may yield novel antibiotics. Here, we focus on the chemical potential of rare actinomycetes, defined as bacteria within the order Actinomycetales, but not belonging to the genus Streptomyces. They are named as such due to their less-frequent isolation under standard laboratory practices, yet there is increasing evidence to suggest these biologically diverse genera harbour considerable biosynthetic and chemical diversity. In this review, we focus on examples of successful isolation and genera that have been the focus of more concentrated biodiscovery efforts, we survey the representation of rare actinomycete taxa, compared with Streptomyces, across natural product data repositories in addition to its biosynthetic potential. This is followed by an overview of clinically useful drugs produced by rare actinomycetes and considerations for future biodiscovery efforts. There is much to learn about these underexplored taxa, and mounting evidence suggests that they are a fruitful avenue for the discovery of novel antimicrobials.
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Affiliation(s)
- Jonathan Parra
- Instituto de Investigaciones Farmacéuticas (INIFAR), Facultad de Farmacia, Universidad de Costa Rica, San José 11501-2060, Costa Rica; Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José 1174-1200, Costa Rica
| | - Ainsley Beaton
- John Innes Centre, Department of Molecular Microbiology, Norwich Research Park, Norwich NR4 7UH, UK
| | - Ryan F Seipke
- University of Leeds, Faculty of Biological Sciences, Astbury Centre for Structural Molecular Biology, Leeds LS2 9JT, UK
| | - Barrie Wilkinson
- John Innes Centre, Department of Molecular Microbiology, Norwich Research Park, Norwich NR4 7UH, UK
| | - Matthew I Hutchings
- John Innes Centre, Department of Molecular Microbiology, Norwich Research Park, Norwich NR4 7UH, UK
| | - Katherine R Duncan
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, 141 Cathedral Street, Glasgow G4 0RE, UK.
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2
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Abstract
SurE is a standalone peptide cyclase essential for the production of surugamide antibiotics. Although SurE catalyses the cyclisation of varied nonribosomal peptides in vivo, its substrate specificity is poorly understood. To address this issue, an on-resin SurE cyclisation assay was developed and in combination with SNAC thioesters and kinetic measurements was used to define the chemical space of the N-terminal substrate residue. The N-terminal substrate specificity of the SurE peptide cyclase was elucidated using a combination of on-resin biomemtic substrates and conventional SNAC thioesters.![]()
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Affiliation(s)
- Asif Fazal
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK. .,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
| | - Jake Wheeler
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
| | - Michael E Webb
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
| | - Ryan F Seipke
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK. .,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
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3
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Feeney MA, Newitt JT, Addington E, Algora-Gallardo L, Allan C, Balis L, Birke AS, Castaño-Espriu L, Charkoudian LK, Devine R, Gayrard D, Hamilton J, Hennrich O, Hoskisson PA, Keith-Baker M, Klein JG, Kruasuwan W, Mark DR, Mast Y, McHugh RE, McLean TC, Mohit E, Munnoch JT, Murray J, Noble K, Otani H, Parra J, Pereira CF, Perry L, Pintor-Escobar L, Pritchard L, Prudence SMM, Russell AH, Schniete JK, Seipke RF, Sélem-Mojica N, Undabarrena A, Vind K, van Wezel GP, Wilkinson B, Worsley SF, Duncan KR, Fernández-Martínez LT, Hutchings MI. ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria. Microb Genom 2022; 8. [PMID: 35775972 PMCID: PMC9455695 DOI: 10.1099/mgen.0.000824] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Actinobacteria is an ancient phylum of Gram-positive bacteria with a characteristic high GC content to their DNA. The ActinoBase Wiki is focused on the filamentous actinobacteria, such as Streptomyces species, and the techniques and growth conditions used to study them. These organisms are studied because of their complex developmental life cycles and diverse specialised metabolism which produces many of the antibiotics currently used in the clinic. ActinoBase is a community effort that provides valuable and freely accessible resources, including protocols and practical information about filamentous actinobacteria. It is aimed at enabling knowledge exchange between members of the international research community working with these fascinating bacteria. ActinoBase is an anchor platform that underpins worldwide efforts to understand the ecology, biology and metabolic potential of these organisms. There are two key differences that set ActinoBase apart from other Wiki-based platforms: [1] ActinoBase is specifically aimed at researchers working on filamentous actinobacteria and is tailored to help users overcome challenges working with these bacteria and [2] it provides a freely accessible resource with global networking opportunities for researchers with a broad range of experience in this field.
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Affiliation(s)
- Morgan Anne Feeney
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Jake Terry Newitt
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Emily Addington
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Lis Algora-Gallardo
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Craig Allan
- Swansea University Institute of Life Science, College of Medicine, Swansea, Wales, UK
| | - Lucas Balis
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Anna S Birke
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Laia Castaño-Espriu
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | | | - Rebecca Devine
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Damien Gayrard
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Jacob Hamilton
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Oliver Hennrich
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Paul A Hoskisson
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Molly Keith-Baker
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | | | - Worarat Kruasuwan
- Division of Bioinformatics and Data Management for Research, Research Group and Research Network Division, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - David R Mark
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Yvonne Mast
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Rebecca E McHugh
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Thomas C McLean
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Elmira Mohit
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - John T Munnoch
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Jordan Murray
- Department of Physics, SUPA, University of Strathclyde, Glasgow, G4 0NG, UK
| | - Katie Noble
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Hiroshi Otani
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA 94720, USA
| | - Jonathan Parra
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Camila F Pereira
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Louisa Perry
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | | | - Leighton Pritchard
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Samuel M M Prudence
- School of Biological and Behavioral Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | | | - Jana K Schniete
- Biology Department, Edge Hill University, St Helens Road, Ormskirk, L39 4QP, UK
| | - Ryan F Seipke
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Nelly Sélem-Mojica
- Universidad Nacional Autónoma de México, Centro de Ciencias Matemáticas, en Morelia, Michoacán, Mexico
| | - Agustina Undabarrena
- Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Valparaíso, 2340000, Chile
| | - Kristiina Vind
- Host-Microbe Interactomics Group, Wageningen University, 6708 WD Wageningen, The Netherlands
| | - Gilles P van Wezel
- Microbial Biotechnology, Institute of Biology, Leiden University, Rapenburg, The Netherlands
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Katherine R Duncan
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | | | - Matthew I Hutchings
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
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4
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Abstract
New lipopeptide antibiotics provide hope in the fight against multidrug-resistant bacteria.
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Affiliation(s)
- Ryan F Seipke
- Faculty of Biological Sciences, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
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5
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Fazal A, Hemsworth GR, Webb ME, Seipke RF. A Standalone β-Ketoreductase Acts Concomitantly with Biosynthesis of the Antimycin Scaffold. ACS Chem Biol 2021; 16:1152-1158. [PMID: 34151573 DOI: 10.1021/acschembio.1c00229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Antimycins are anticancer compounds produced by a hybrid nonribosomal peptide synthetase/polyketide synthase (NRPS/PKS) pathway. The biosynthesis of these compounds is well characterized, with the exception of the standalone β-ketoreductase enzyme AntM that is proposed to catalyze the reduction of the C8 carbonyl of the antimycin scaffold. Inactivation of antM and structural characterization suggested that rather than functioning as a post-PKS tailoring enzyme, AntM acts upon the terminal biosynthetic intermediate while it is tethered to the PKS acyl carrier protein. Mutational analysis identified two amino acid residues (Tyr185 and Phe223) that are proposed to serve as checkpoints controlling substrate access to the AntM active site. Aromatic checkpoint residues are conserved in uncharacterized standalone β-ketoreductases, indicating that they may also act concomitantly with synthesis of the scaffold. These data provide novel mechanistic insights into the functionality of standalone β-ketoreductases and will enable their reprogramming for combinatorial biosynthesis.
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Affiliation(s)
- Asif Fazal
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
- School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Glyn R. Hemsworth
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Michael E. Webb
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
- School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Ryan F. Seipke
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
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6
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Fazal A, Thankachan D, Harris E, Seipke RF. A chromatogram-simplified Streptomyces albus host for heterologous production of natural products. Antonie Van Leeuwenhoek 2020; 113:511-520. [PMID: 31781915 PMCID: PMC7089911 DOI: 10.1007/s10482-019-01360-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/14/2019] [Indexed: 12/16/2022]
Abstract
Cloning natural product biosynthetic gene clusters from cultured or uncultured sources and their subsequent expression by genetically tractable heterologous hosts is an essential strategy for the elucidation and characterisation of novel microbial natural products. The availability of suitable expression hosts is a critical aspect of this workflow. In this work, we mutagenised five endogenous biosynthetic gene clusters from Streptomyces albus S4, which reduced the complexity of chemical extracts generated from the strain and eliminated antifungal and antibacterial bioactivity. We showed that the resulting quintuple mutant can express foreign biosynthetic gene clusters by heterologously producing actinorhodin, cinnamycin and prunustatin. We envisage that our strain will be a useful addition to the growing suite of heterologous expression hosts available for exploring microbial secondary metabolism.
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Affiliation(s)
- Asif Fazal
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Divya Thankachan
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Ellie Harris
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Ryan F Seipke
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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7
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Thankachan D, Fazal A, Francis D, Song L, Webb ME, Seipke RF. A trans-Acting Cyclase Offloading Strategy for Nonribosomal Peptide Synthetases. ACS Chem Biol 2019; 14:845-849. [PMID: 30925045 DOI: 10.1021/acschembio.9b00095] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The terminal step in the biosynthesis of nonribosomal peptides is the hydrolytic release and, frequently, macrocyclization of an aminoacyl-S-thioester by an embedded thioesterase. The surugamide biosynthetic pathway is composed of two nonribosomal peptide synthetase (NRPS) assembly lines in which one produces surugamide A, which is a cyclic octapeptide, and the other produces surugamide F, a linear decapeptide. The terminal module of each system lacks an embedded thioesterase, which led us to question how the peptides are released from the assembly line (and cyclized in the case of surugamide A). We characterized a cyclase belonging to the β-lactamase superfamily in vivo, established that it is a trans-acting release factor for both compounds, and verified this functionality in vitro with a thioester mimic of linear surugamide A. Using bioinformatics, we estimate that ∼11% of filamentous Actinobacteria harbor an NRPS system lacking an embedded thioesterase and instead employ a trans-acting cyclase. This study improves the paradigmatic understanding of how nonribosomal peptides are released from the terminal peptidyl carrier protein and adds a new dimension to the synthetic biology toolkit.
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Affiliation(s)
| | | | | | - Lijiang Song
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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8
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van der Heul HU, Bilyk BL, McDowall KJ, Seipke RF, van Wezel GP. Regulation of antibiotic production in Actinobacteria: new perspectives from the post-genomic era. Nat Prod Rep 2019; 35:575-604. [PMID: 29721572 DOI: 10.1039/c8np00012c] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: 2000 to 2018 The antimicrobial activity of many of their natural products has brought prominence to the Streptomycetaceae, a family of Gram-positive bacteria that inhabit both soil and aquatic sediments. In the natural environment, antimicrobial compounds are likely to limit the growth of competitors, thereby offering a selective advantage to the producer, in particular when nutrients become limited and the developmental programme leading to spores commences. The study of the control of this secondary metabolism continues to offer insights into its integration with a complex lifecycle that takes multiple cues from the environment and primary metabolism. Such information can then be harnessed to devise laboratory screening conditions to discover compounds with new or improved clinical value. Here we provide an update of the review we published in NPR in 2011. Besides providing the essential background, we focus on recent developments in our understanding of the underlying regulatory networks, ecological triggers of natural product biosynthesis, contributions from comparative genomics and approaches to awaken the biosynthesis of otherwise silent or cryptic natural products. In addition, we highlight recent discoveries on the control of antibiotic production in other Actinobacteria, which have gained considerable attention since the start of the genomics revolution. New technologies that have the potential to produce a step change in our understanding of the regulation of secondary metabolism are also described.
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9
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Som NF, Heine D, Holmes NA, Munnoch JT, Knowles F, Chandra G, Seipke RF, Hoskisson PA, Wilkinson B, Hutchings MI. The MtrAB-LpqB two component system links development with secondary metabolite production in Streptomyces species and can be manipulated to switch on silent secondary metabolite clusters. Access Microbiol 2019. [DOI: 10.1099/acmi.ac2019.po0054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
| | | | | | - John T. Munnoch
- 3Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, United Kingdom
| | | | | | - Ryan F. Seipke
- 6The Astbury Centre for Structural Molecular Biology, Leeds, United Kingdom
| | - Paul A. Hoskisson
- 7Strat Strathclyde Institute of Pharmacy and Biomedical Scienceshclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, United Kingdom
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10
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Abstract
Antimycins are a family of natural products possessing outstanding biological activities and unique structures, which have intrigued chemists for over a half century. Of particular interest are the ring-expanded antimycins that show promising anticancer potential and whose biosynthesis remains uncharacterized. Specifically, neoantimycin and its analogs have been shown to be effective regulators of the oncogenic proteins GRP78/BiP and K-Ras. The neoantimycin structural skeleton is built on a 15-membered tetralactone ring containing one methyl, one hydroxy, one benzyl, and three alkyl moieties, as well as an amide linkage to a conserved 3-formamidosalicylic acid moiety. Although the biosynthetic gene cluster for neoantimycins was recently identified, the enzymatic logic that governs the synthesis of neoantimycins has not yet been revealed. In this work, the neoantimycin gene cluster is identified, and an updated sequence and annotation is provided delineating a nonribosomal peptide synthetase/polyketide synthase (NRPS/PKS) hybrid scaffold. Using cosmid expression and CRISPR/Cas-based genome editing, several heterologous expression strains for neoantimycin production are constructed in two separate Streptomyces species. A combination of in vivo and in vitro analysis is further used to completely characterize the biosynthesis of neoantimycins including the megasynthases and trans-acting domains. This work establishes a set of highly tractable hosts for producing and engineering neoantimycins and their C11 oxidized analogs, paving the way for neoantimycin-based drug discovery and development.
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Affiliation(s)
| | | | | | | | | | - Wenjun Zhang
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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11
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Holmes NA, Devine R, Qin Z, Seipke RF, Wilkinson B, Hutchings MI. Complete genome sequence of Streptomyces formicae KY5, the formicamycin producer. J Biotechnol 2018; 265:116-118. [PMID: 29191667 DOI: 10.1016/j.jbiotec.2017.11.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/17/2017] [Accepted: 11/25/2017] [Indexed: 11/24/2022]
Abstract
Here we report the complete genome of the new species Streptomyces formicae KY5 isolated from Tetraponera fungus growing ants. S. formicae was sequenced using the PacBio and 454 platforms to generate a single linear chromosome with terminal inverted repeats. Illumina MiSeq sequencing was used to correct base changes resulting from the high error rate associated with PacBio. The genome is 9.6 Mbps, has a GC content of 71.38% and contains 8162 protein coding sequences. Predictive analysis shows this strain encodes at least 45 gene clusters for the biosynthesis of secondary metabolites, including a type 2 polyketide synthase encoding cluster for the antibacterial formicamycins. Streptomyces formicae KY5 is a new, taxonomically distinct Streptomyces species and this complete genome sequence provides an important marker in the genus of Streptomyces.
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Affiliation(s)
- Neil A Holmes
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom.
| | - Rebecca Devine
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Zhiwei Qin
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Ryan F Seipke
- School of Molecular and Cellular Biology, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Matthew I Hutchings
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
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12
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Abstract
Streptomyces species and other Actinobacteria are ubiquitous in diverse environments worldwide and are the source of, or inspiration for, the majority of antibiotics. The genomic era has enhanced biosynthetic understanding of these valuable chemical entities and has also provided a window into the diversity and distribution of natural product biosynthetic gene clusters. Antimycin is an inhibitor of mitochondrial cytochrome c reductase and more recently was shown to inhibit Bcl-2/Bcl-XL-related anti-apoptotic proteins commonly overproduced by cancerous cells. Here we identify 73 putative antimycin biosynthetic gene clusters (BGCs) in publicly available genome sequences of Actinobacteria and classify them based on the presence or absence of cluster-situated genes antP and antQ, which encode a kynureninase and a phosphopantetheinyl transferase (PPTase), respectively. The majority of BGCs possess either both antP and antQ (L-form) or neither (S-form), while a minority of them lack either antP or antQ (IQ- or IP-form, respectively). We also evaluate the biogeographical distribution and phylogenetic relationships of antimycin producers and BGCs. We show that antimycin BGCs occur on five of the seven continents and are frequently isolated from plants and other higher organisms. We also provide evidence for two distinct phylogenetic clades of antimycin producers and gene clusters, which delineate S-form from L- and I-form BGCs. Finally, our findings suggest that the ancestral antimycin producer harboured an L-form gene cluster which was primarily propagated by vertical transmission and subsequently diversified into S-, IQ- and IP-form biosynthetic pathways.
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Affiliation(s)
- Rebecca Joynt
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Ryan F Seipke
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
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13
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Som NF, Heine D, Holmes N, Knowles F, Chandra G, Seipke RF, Hoskisson PA, Wilkinson B, Hutchings MI. The MtrAB two-component system controls antibiotic production in Streptomyces coelicolor A3(2). Microbiology (Reading) 2017; 163:1415-1419. [PMID: 28884676 PMCID: PMC5845573 DOI: 10.1099/mic.0.000524] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/15/2017] [Indexed: 12/24/2022]
Abstract
MtrAB is a highly conserved two-component system implicated in the regulation of cell division in the Actinobacteria. It coordinates DNA replication with cell division in the unicellular Mycobacterium tuberculosis and links antibiotic production to sporulation in the filamentous Streptomyces venezuelae. Chloramphenicol biosynthesis is directly regulated by MtrA in S. venezuelae and deletion of mtrB constitutively activates MtrA and results in constitutive over-production of chloramphenicol. Here we report that in Streptomyces coelicolor, MtrA binds to sites upstream of developmental genes and the genes encoding ActII-1, ActII-4 and RedZ, which are cluster-situated regulators of the antibiotics actinorhodin (Act) and undecylprodigiosin (Red). Consistent with this, deletion of mtrB switches on the production of Act, Red and streptorubin B, a product of the Red pathway. Thus, we propose that MtrA is a key regulator that links antibiotic production to development and can be used to upregulate antibiotic production in distantly related streptomycetes.
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Affiliation(s)
- Nicolle F. Som
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Daniel Heine
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Neil Holmes
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Felicity Knowles
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ryan F. Seipke
- School of Molecular and Cellular Biology, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Paul A. Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161, Cathedral Street, Glasgow, G4 0RE, UK
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Matthew I. Hutchings
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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14
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Som NF, Heine D, Holmes NA, Munnoch JT, Chandra G, Seipke RF, Hoskisson PA, Wilkinson B, Hutchings MI. The Conserved Actinobacterial Two-Component System MtrAB Coordinates Chloramphenicol Production with Sporulation in Streptomyces venezuelae NRRL B-65442. Front Microbiol 2017; 8:1145. [PMID: 28702006 PMCID: PMC5487470 DOI: 10.3389/fmicb.2017.01145] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 06/06/2017] [Indexed: 12/30/2022] Open
Abstract
Streptomyces bacteria make numerous secondary metabolites, including half of all known antibiotics. Production of antibiotics is usually coordinated with the onset of sporulation but the cross regulation of these processes is not fully understood. This is important because most Streptomyces antibiotics are produced at low levels or not at all under laboratory conditions and this makes large scale production of these compounds very challenging. Here, we characterize the highly conserved actinobacterial two-component system MtrAB in the model organism Streptomyces venezuelae and provide evidence that it coordinates production of the antibiotic chloramphenicol with sporulation. MtrAB are known to coordinate DNA replication and cell division in Mycobacterium tuberculosis where TB-MtrA is essential for viability but MtrB is dispensable. We deleted mtrB in S. venezuelae and this resulted in a global shift in the metabolome, including constitutive, higher-level production of chloramphenicol. We found that chloramphenicol is detectable in the wild-type strain, but only at very low levels and only after it has sporulated. ChIP-seq showed that MtrA binds upstream of DNA replication and cell division genes and genes required for chloramphenicol production. dnaA, dnaN, oriC, and wblE (whiB1) are DNA binding targets for MtrA in both M. tuberculosis and S. venezuelae. Intriguingly, over-expression of TB-MtrA and gain of function TB- and Sv-MtrA proteins in S. venezuelae also switched on higher-level production of chloramphenicol. Given the conservation of MtrAB, these constructs might be useful tools for manipulating antibiotic production in other filamentous actinomycetes.
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Affiliation(s)
- Nicolle F. Som
- School of Biological Sciences, University of East AngliaNorwich, United Kingdom
| | - Daniel Heine
- Department of Molecular Microbiology, John Innes CentreNorwich, United Kingdom
| | - Neil A. Holmes
- School of Biological Sciences, University of East AngliaNorwich, United Kingdom
| | - John T. Munnoch
- School of Biological Sciences, University of East AngliaNorwich, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes CentreNorwich, United Kingdom
| | - Ryan F. Seipke
- School of Biological Sciences, University of East AngliaNorwich, United Kingdom
- School of Molecular and Cellular Biology, Astbury Centre for Structural Molecular Biology, University of LeedsLeeds, United Kingdom
| | - Paul A. Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of StrathclydeGlasgow, United Kingdom
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes CentreNorwich, United Kingdom
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15
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Qin Z, Munnoch JT, Devine R, Holmes NA, Seipke RF, Wilkinson KA, Wilkinson B, Hutchings MI. Formicamycins, antibacterial polyketides produced by Streptomyces formicae isolated from African Tetraponera plant-ants. Chem Sci 2017; 8:3218-3227. [PMID: 28507698 PMCID: PMC5414599 DOI: 10.1039/c6sc04265a] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 02/09/2017] [Indexed: 12/03/2022] Open
Abstract
We report a new Streptomyces species named S. formicae that was isolated from the African fungus-growing plant-ant Tetraponera penzigi and show that it produces novel pentacyclic polyketides that are active against MRSA and VRE. The chemical scaffold of these compounds, which we have called the formicamycins, is similar to the fasamycins identified from the heterologous expression of clones isolated from environmental DNA, but has significant differences that allow the scaffold to be decorated with up to four halogen atoms. We report the structures and bioactivities of 16 new molecules and show, using CRISPR/Cas9 genome editing, that biosynthesis of these compounds is encoded by a single type 2 polyketide synthase biosynthetic gene cluster in the S. formicae genome. Our work has identified the first antibiotic from the Tetraponera system and highlights the benefits of exploring unusual ecological niches for new actinomycete strains and novel natural products.
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Affiliation(s)
- Zhiwei Qin
- Department of Molecular Microbiology , John Innes Centre , Norwich Research Park , Norwich , NR4 7UH , UK .
| | - John T Munnoch
- School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
| | - Rebecca Devine
- School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
| | - Neil A Holmes
- School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
| | - Ryan F Seipke
- School of Molecular and Cellular Biology , Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds , LS2 9JT , UK
| | - Karl A Wilkinson
- Scientific Research Computing Unit , Department of Chemistry , University of Cape Town , Rondebosch 7701 , Cape Town , South Africa
| | - Barrie Wilkinson
- Department of Molecular Microbiology , John Innes Centre , Norwich Research Park , Norwich , NR4 7UH , UK .
| | - Matthew I Hutchings
- School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
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16
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Medema MH, Kottmann R, Yilmaz P, Cummings M, Biggins JB, Blin K, de Bruijn I, Chooi YH, Claesen J, Coates RC, Cruz-Morales P, Duddela S, Düsterhus S, Edwards DJ, Fewer DP, Garg N, Geiger C, Gomez-Escribano JP, Greule A, Hadjithomas M, Haines AS, Helfrich EJN, Hillwig ML, Ishida K, Jones AC, Jones CS, Jungmann K, Kegler C, Kim HU, Kötter P, Krug D, Masschelein J, Melnik AV, Mantovani SM, Monroe EA, Moore M, Moss N, Nützmann HW, Pan G, Pati A, Petras D, Reen FJ, Rosconi F, Rui Z, Tian Z, Tobias NJ, Tsunematsu Y, Wiemann P, Wyckoff E, Yan X, Yim G, Yu F, Xie Y, Aigle B, Apel AK, Balibar CJ, Balskus EP, Barona-Gómez F, Bechthold A, Bode HB, Borriss R, Brady SF, Brakhage AA, Caffrey P, Cheng YQ, Clardy J, Cox RJ, De Mot R, Donadio S, Donia MS, van der Donk WA, Dorrestein PC, Doyle S, Driessen AJM, Ehling-Schulz M, Entian KD, Fischbach MA, Gerwick L, Gerwick WH, Gross H, Gust B, Hertweck C, Höfte M, Jensen SE, Ju J, Katz L, Kaysser L, Klassen JL, Keller NP, Kormanec J, Kuipers OP, Kuzuyama T, Kyrpides NC, Kwon HJ, Lautru S, Lavigne R, Lee CY, Linquan B, Liu X, Liu W, Luzhetskyy A, Mahmud T, Mast Y, Méndez C, Metsä-Ketelä M, Micklefield J, Mitchell DA, Moore BS, Moreira LM, Müller R, Neilan BA, Nett M, Nielsen J, O’Gara F, Oikawa H, Osbourn A, Osburne MS, Ostash B, Payne SM, Pernodet JL, Petricek M, Piel J, Ploux O, Raaijmakers JM, Salas JA, Schmitt EK, Scott B, Seipke RF, Shen B, Sherman DH, Sivonen K, Smanski MJ, Sosio M, Stegmann E, Süssmuth RD, Tahlan K, Thomas CM, Tang Y, Truman AW, Viaud M, Walton JD, Walsh CT, Weber T, van Wezel GP, Wilkinson B, Willey JM, Wohlleben W, Wright GD, Ziemert N, Zhang C, Zotchev SB, Breitling R, Takano E, Glöckner FO. Minimum Information about a Biosynthetic Gene cluster. Nat Chem Biol 2015; 11:625-31. [PMID: 26284661 PMCID: PMC5714517 DOI: 10.1038/nchembio.1890] [Citation(s) in RCA: 544] [Impact Index Per Article: 60.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Marnix H Medema
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Renzo Kottmann
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Pelin Yilmaz
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Matthew Cummings
- Manchester Centre for Synthetic Biology ofFine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - John B Biggins
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
| | - Kai Blin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Irene de Bruijn
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Wageningen, the Netherlands
| | - Yit Heng Chooi
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California, USA,Departmentof Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, USA,School of Chemistry and Biochemistry, University of Western Australia, Perth, Western Australia, Australia
| | - Jan Claesen
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA,California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, USA
| | - R Cameron Coates
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA
| | - Pablo Cruz-Morales
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Irapuato, Guanajuato, México
| | - Srikanth Duddela
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Stephanie Düsterhus
- Institute for Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Daniel J Edwards
- Department of Chemistry and Biochemistry, California State University, Chico, California, USA
| | - David P Fewer
- Microbiology and Biotechnology Division, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Neha Garg
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Christoph Geiger
- Institute for Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | | | - Anja Greule
- Department of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Michalis Hadjithomas
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA
| | | | - Eric J N Helfrich
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Matthew L Hillwig
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Keishi Ishida
- Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Adam C Jones
- Gordon and Betty Moore Foundation, Palo Alto, California, USA
| | - Carla S Jones
- Sustainable Studies Program, Roosevelt University Chicago, Illinois, USA
| | - Katrin Jungmann
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Carsten Kegler
- Merck Stiftungsprofessur für Molekular Biotechnologie, Goethe Universität Frankfurt, Fachbereich Biowissenschaften, Frankfurt, Germany
| | - Hyun Uk Kim
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark,BioInformatics Research Center, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Peter Kötter
- Institute for Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Daniel Krug
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Joleen Masschelein
- Laboratory of Gene Technology, KU Leuven, Heverlee, Belgium,Laboratory of Food Microbiology, KU Leuven, Heverlee, Belgium
| | - Alexey V Melnik
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Simone M Mantovani
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Emily A Monroe
- Department of Biology, William Paterson University, Wayne, New Jersey, USA
| | - Marcus Moore
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Nathan Moss
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Hans-Wilhelm Nützmann
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Guohui Pan
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, USA
| | - Amrita Pati
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA
| | - Daniel Petras
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - F Jerry Reen
- BIOMERIT Research Centre, School of Microbiology, University College Cork–National University of Ireland, Cork, Ireland
| | - Federico Rosconi
- Departamento de Bioquímica y Genómica Microbianas, IBCE, Montevideo, Uruguay
| | - Zhe Rui
- Energy Biosciences Institute, University of California Berkeley, Berkeley, California, USA,Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California, USA
| | - Zhenhua Tian
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Nicholas J Tobias
- Merck Stiftungsprofessur für Molekular Biotechnologie, Goethe Universität Frankfurt, Fachbereich Biowissenschaften, Frankfurt, Germany
| | - Yuta Tsunematsu
- Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany,Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Philipp Wiemann
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Elizabeth Wyckoff
- Department of Molecular Biosciences, The University of Texas, Austin, Texas, USA,Institute for Cellular and Molecular Biology, The University of Texas, Austin, Texas, USA
| | - Xiaohui Yan
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, USA
| | - Grace Yim
- Department of Biochemistry and Biomedical Sciences, The M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Fengan Yu
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA,Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA,Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA,Department of Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Yunchang Xie
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Bertrand Aigle
- Dynamique des Génomes et Adaptation Microbienne, Université de Lorraine and Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche (UMR) 1128, Vandoeuvre-lès-Nancy, France
| | - Alexander K Apel
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany,German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Carl J Balibar
- Infectious Disease Research, Merck Research Laboratories, Kenilworth, New Jersey, USA
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Francisco Barona-Gómez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Irapuato, Guanajuato, México
| | - Andreas Bechthold
- Department of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Helge B Bode
- Merck Stiftungsprofessur für Molekular Biotechnologie, Goethe Universität Frankfurt, Fachbereich Biowissenschaften, Frankfurt, Germany,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt, Frankfurt, Germany
| | - Rainer Borriss
- Fachbereich Phytomedizin, Albrecht Thaer Institut, Humboldt Universität Berlin, Berlin, Germany
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
| | - Axel A Brakhage
- Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Patrick Caffrey
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Yi-Qiang Cheng
- UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Russell J Cox
- Institut für Organische Chemie, Leibniz Universität Hannover, Hannover, Germany,School of Chemistry, University of Bristol, Bristol, UK
| | - René De Mot
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, University of Leuven, Heverlee, Belgium
| | | | - Mohamed S Donia
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Wilfred A van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana-Champaign, Illinois, USA,Howard Hughes Medical Institute, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA,Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, California, USA
| | - Sean Doyle
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Monika Ehling-Schulz
- Functional Microbiology, Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Karl-Dieter Entian
- Institute for Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Michael A Fischbach
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA,California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - William H Gerwick
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Harald Gross
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany,German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Bertolt Gust
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany,German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany,Friedrich Schiller University, Jena, Germany
| | - Monica Höfte
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Susan E Jensen
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Jianhua Ju
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Leonard Katz
- Synthetic Biology Engineering Research Center (SynBERC), University of California Emeryville, Emeryville, California, USA
| | - Leonard Kaysser
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany,German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Jonathan L Klassen
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, Wisconsin, USA,Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Jan Kormanec
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Tomohisa Kuzuyama
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Nikos C Kyrpides
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA,Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hyung-Jin Kwon
- Division of Bioscience and Bioinformatics, Myongji University, Yongin-si, Gyeonggi-Do, South Korea
| | - Sylvie Lautru
- Institute of Integrative Biology of the Cell (I2BC), Commissariat à l’Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris Sud, Orsay, France
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Heverlee, Belgium
| | - Chia Y Lee
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Bai Linquan
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China,School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinyu Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Andriy Luzhetskyy
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Yvonne Mast
- Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Faculty of Science, University of Tübingen, Tübingen, Germany
| | - Carmen Méndez
- Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain,Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, Oviedo, Spain
| | | | | | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana-Champaign, Illinois, USA
| | - Bradley S Moore
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Leonilde M Moreira
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Brett A Neilan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Markus Nett
- Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Jens Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark,Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Fergal O’Gara
- BIOMERIT Research Centre, School of Microbiology, University College Cork–National University of Ireland, Cork, Ireland,Curtin University, School of Biomedical Sciences, Perth, Western Australia, Australia
| | - Hideaki Oikawa
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo, Japan
| | - Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Marcia S Osburne
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Bohdan Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - Shelley M Payne
- Department of Molecular Biosciences, The University of Texas, Austin, Texas, USA,Institute for Cellular and Molecular Biology, The University of Texas, Austin, Texas, USA
| | - Jean-Luc Pernodet
- Institute of Integrative Biology of the Cell (I2BC), Commissariat à l’Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris Sud, Orsay, France
| | - Miroslav Petricek
- Institute of Microbiology, Academy of Sciences of the Czech Republic (ASCR), Prague, Czech Republic
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Olivier Ploux
- Laboratoire Interdisciplinaire des Energies de Demain (LIED), UMR 8236 CNRS, Université Paris Diderot, Paris, France
| | - Jos M Raaijmakers
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Wageningen, the Netherlands
| | - José A Salas
- Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain
| | - Esther K Schmitt
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland
| | - Barry Scott
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Ryan F Seipke
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, USA,Molecular Therapeutics and Natural Products Library Initiative, The Scripps Research Institute, Jupiter, Florida, USA
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA,Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA,Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA,Department of Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kaarina Sivonen
- Microbiology and Biotechnology Division, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Michael J Smanski
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota–Twin Cities, Saint Paul, Minnesota, USA,BioTechnology Institute, University of Minnesota–Twin Cities, Saint Paul, Minnesota, USA
| | | | - Evi Stegmann
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany,Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Faculty of Science, University of Tübingen, Tübingen, Germany
| | | | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | | | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California, USA,Departmentof Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, USA
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Muriel Viaud
- Unité BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA), Grignon, France
| | - Jonathan D Walton
- Department of Energy Great Lakes Bioenergy Research Center and Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
| | - Christopher T Walsh
- Chemistry, Engineering & Medicine for Human Health (ChEM-H) Institute, Stanford University, Stanford, California, USA
| | - Tilmann Weber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Joanne M Willey
- Hofstra North Shore–Long Island Jewish School of Medicine, Hempstead, New York, USA
| | - Wolfgang Wohlleben
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany,Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Faculty of Science, University of Tübingen, Tübingen, Germany
| | - Gerard D Wright
- Department of Biochemistry and Biomedical Sciences, The M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Nadine Ziemert
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany,Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Faculty of Science, University of Tübingen, Tübingen, Germany
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Sergey B Zotchev
- Department of Biotechnology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Rainer Breitling
- Manchester Centre for Synthetic Biology ofFine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Eriko Takano
- Manchester Centre for Synthetic Biology ofFine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Frank Oliver Glöckner
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany,Jacobs University Bremen gGmbH, Bremen, Germany
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17
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Liu J, Zhu X, Seipke RF, Zhang W. Biosynthesis of antimycins with a reconstituted 3-formamidosalicylate pharmacophore in Escherichia coli. ACS Synth Biol 2015; 4:559-65. [PMID: 25275920 DOI: 10.1021/sb5003136] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Antimycins are a family of natural products generated from a hybrid nonribosomal peptide synthetase (NRPS)-polyketide synthase (PKS) assembly line. Although they possess an array of useful biological activities, their structural complexity makes chemical synthesis challenging, and their biosynthesis has thus far been dependent on slow-growing source organisms. Here, we reconstituted the biosynthesis of antimycins in Escherichia coli, a versatile host that is robust and easy to manipulate genetically. Along with Streptomyces genetic studies, the heterologous expression of different combinations of ant genes enabled us to systematically confirm the functions of the modification enzymes, AntHIJKL and AntO, in the biosynthesis of the 3-formamidosalicylate pharmacophore of antimycins. Our E. coli-based antimycin production system can not only be used to engineer the increased production of these bioactive compounds, but it also paves the way for the facile generation of novel and diverse antimycin analogues through combinatorial biosynthesis.
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Affiliation(s)
| | | | - Ryan F. Seipke
- School
of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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18
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Abstract
Streptomyces spp. are robust producers of medicinally-, industrially- and agriculturally-important small molecules. Increased resistance to antibacterial agents and the lack of new antibiotics in the pipeline have led to a renaissance in natural product discovery. This endeavor has benefited from inexpensive high quality DNA sequencing technology, which has generated more than 140 genome sequences for taxonomic type strains and environmental Streptomyces spp. isolates. Many of the sequenced streptomycetes belong to the same species. For instance, Streptomyces albus has been isolated from diverse environmental niches and seven strains have been sequenced, consequently this species has been sequenced more than any other streptomycete, allowing valuable analyses of strain-level diversity in secondary metabolism. Bioinformatics analyses identified a total of 48 unique biosynthetic gene clusters harboured by Streptomyces albus strains. Eighteen of these gene clusters specify the core secondary metabolome of the species. Fourteen of the gene clusters are contained by one or more strain and are considered auxiliary, while 16 of the gene clusters encode the production of putative strain-specific secondary metabolites. Analysis of Streptomyces albus strains suggests that each strain of a Streptomyces species likely harbours at least one strain-specific biosynthetic gene cluster. Importantly, this implies that deep sequencing of a species will not exhaust gene cluster diversity and will continue to yield novelty.
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Affiliation(s)
- Ryan F. Seipke
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
- * E-mail:
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19
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20
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Seipke RF, Patrick E, Hutchings MI. Regulation of antimycin biosynthesis by the orphan ECF RNA polymerase sigma factor σ (AntA.). PeerJ 2014; 2:e253. [PMID: 24688837 PMCID: PMC3933326 DOI: 10.7717/peerj.253] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 01/07/2014] [Indexed: 12/03/2022] Open
Abstract
Antimycins are an extended family of depsipeptides that are made by filamentous actinomycete bacteria and were first isolated more than 60 years ago. Recently, antimycins have attracted renewed interest because of their activities against the anti-apoptotic machineries inside human cells which could make them promising anti-cancer compounds. The biosynthetic pathway for antimycins was recently characterised but very little is known about the organisation and regulation of the antimycin (ant) gene cluster. Here we report that the ant gene cluster in Streptomyces albus is organized into four transcriptional units; the antBA, antCDE, antGF and antHIJKLMNO operons. Unusually for secondary metabolite clusters, the antG and antH promoters are regulated by an extracytoplasmic function (ECF) RNA polymerase sigma factor named σAntA which represents a new sub-family of ECF σ factors that is only found in antimycin producing strains. We show that σAntA controls production of the unusual precursor 3-aminosalicylate which is absolutely required for the production of antimycins. σAntA is highly conserved in antimycin producing strains and the −10 and −35 elements at the σAntA regulated antG and antH promoters are also highly conserved suggesting a common mechanism of regulation. We also demonstrate that altering the C-terminal Ala-Ala residues found in all σAntA proteins to Asp-Asp increases expression of the antFG and antGHIJKLMNO operons and we speculate that this Ala-Ala motif may be a signal for the protease ClpXP.
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Affiliation(s)
- Ryan F Seipke
- School of Biological Sciences, University of East Anglia , Norwich Research Park , Norwich , United Kingdom
| | - Elaine Patrick
- School of Biological Sciences, University of East Anglia , Norwich Research Park , Norwich , United Kingdom
| | - Matthew I Hutchings
- School of Biological Sciences, University of East Anglia , Norwich Research Park , Norwich , United Kingdom
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21
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Gao H, Grüschow S, Barke J, Seipke RF, Hill LM, Orivel J, Yu DW, Hutchings M, Goss RJM. Filipins: the first antifungal “weed killers” identified from bacteria isolated from the trap-ant. RSC Adv 2014. [DOI: 10.1039/c4ra09875g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Allomerus ants cultivate fungus to fabricate their insect traps. Speculation is that the ants employ actinomycetes to help achieve fungal monoculture. From an associated actinomycete we identify the first antifungal compounds and encoding genes.
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Affiliation(s)
- Hong Gao
- School of Chemistry
- University of St. Andrews
- St. Andrews, UK KY16 9ST
- School of Chemistry
- University of East Anglia
| | - Sabine Grüschow
- School of Chemistry
- University of St. Andrews
- St. Andrews, UK KY16 9ST
- School of Chemistry
- University of East Anglia
| | - Jörg Barke
- School of Biological Sciences
- University of East Anglia
- Norwich, UK NR4 7TJ
| | - Ryan F. Seipke
- School of Biological Sciences
- University of East Anglia
- Norwich, UK NR4 7TJ
| | | | - Jérôme Orivel
- CNRS
- UMR Ecologie des Forêts de Guyane
- Campus Agronomique
- 97379 Kourou Cedex, France
| | - Douglas W. Yu
- School of Biological Sciences
- University of East Anglia
- Norwich, UK NR4 7TJ
- State Key Laboratory of Genetic Resources and Evolution
- Kunming Institute of Zoology
| | - Matthew Hutchings
- School of Biological Sciences
- University of East Anglia
- Norwich, UK NR4 7TJ
| | - Rebecca J. M. Goss
- School of Chemistry
- University of St. Andrews
- St. Andrews, UK KY16 9ST
- School of Chemistry
- University of East Anglia
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22
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Abstract
Antimycins (>40 members) were discovered nearly 65 years ago but the discovery of the gene cluster encoding antimycin biosynthesis in 2011 has facilitated rapid progress in understanding the unusual biosynthetic pathway. Antimycin A is widely used as a piscicide in the catfish farming industry and also has potent killing activity against insects, nematodes and fungi. The mode of action of antimycins is to inhibit cytochrome c reductase in the electron transport chain and halt respiration. However, more recently, antimycin A has attracted attention as a potent and selective inhibitor of the mitochondrial anti-apoptotic proteins Bcl-2 and Bcl-xL. Remarkably, this inhibition is independent of the main mode of action of antimycins such that an artificial derivative named 2-methoxyantimycin A inhibits Bcl-xL but does not inhibit respiration. The Bcl-2/Bcl-xL family of proteins are over-produced in cancer cells that are resistant to apoptosis-inducing chemotherapy agents, so antimycins have great potential as anticancer drugs used in combination with existing chemotherapeutics. Here we review what is known about antimycins, the regulation of the ant gene cluster and the unusual biosynthetic pathway.
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Affiliation(s)
- Ryan F Seipke
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom ; School of Molecular and Cellular Biology, Garstang Buildling, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Matthew I Hutchings
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
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23
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Seipke RF, Barke J, Heavens D, Yu DW, Hutchings MI. Analysis of the bacterial communities associated with two ant-plant symbioses. Microbiologyopen 2013; 2:276-83. [PMID: 23417898 PMCID: PMC3633351 DOI: 10.1002/mbo3.73] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 01/07/2013] [Accepted: 01/08/2013] [Indexed: 02/01/2023] Open
Abstract
Insect fungiculture is practiced by ants, termites, beetles, and gall midges and it has been suggested to be widespread among plant–ants. Some of the insects engaged in fungiculture, including attine ants and bark beetles, are known to use symbiotic antibiotic-producing actinobacteria to protect themselves and their fungal cultivars against infection. In this study, we analyze the bacterial communities on the cuticles of the plant–ant genera Allomerus and Tetraponera using deep sequencing of 16S rRNA. Allomerus ants cultivate fungus as a building material to strengthen traps for prey, while Tetraponera ants cultivate fungus as a food source. We report that Allomerus and Tetraponera microbiomes contain >75% Proteobacteria and remarkably the bacterial phyla that dominate their cuticular microbiomes are very similar despite their geographic separation (South America and Africa, respectively). Notably, antibiotic-producing actinomycete bacteria represent a tiny fraction of the cuticular microbiomes of both Allomerus and Tetraponera spp. and instead they are dominated by γ-proteobacteria Erwinia and Serratia spp. Both these phyla are known to contain antibiotic-producing species which might therefore play a protective role in these ant–plant systems.
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Affiliation(s)
- Ryan F Seipke
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom.
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24
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Clark LC, Seipke RF, Prieto P, Willemse J, van Wezel GP, Hutchings MI, Hoskisson PA. Mammalian cell entry genes in Streptomyces may provide clues to the evolution of bacterial virulence. Sci Rep 2013; 3:1109. [PMID: 23346366 PMCID: PMC3552289 DOI: 10.1038/srep01109] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 12/06/2012] [Indexed: 11/09/2022] Open
Abstract
Understanding the evolution of virulence is key to appreciating the role specific loci play in pathogenicity. Streptomyces species are generally non-pathogenic soil saprophytes, yet within their genome we can find homologues of virulence loci. One example of this is the mammalian cell entry (mce) locus, which has been characterised in Mycobacterium tuberculosis. To investigate the role in Streptomyces we deleted the mce locus and studied its impact on cell survival, morphology and interaction with other soil organisms. Disruption of the mce cluster resulted in virulence towards amoebae (Acanthamoeba polyphaga) and reduced colonization of plant (Arabidopsis) models, indicating these genes may play an important role in Streptomyces survival in the environment. Our data suggest that loss of mce in Streptomyces spp. may have profound effects on survival in a competitive soil environment, and provides insight in to the evolution and selection of these genes as virulence factors in related pathogenic organisms.
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Affiliation(s)
- Laura C Clark
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, Glasgow, UK
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25
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Seipke RF, Kaltenpoth M, Hutchings MI. Streptomycesas symbionts: an emerging and widespread theme? FEMS Microbiol Rev 2012; 36:862-76. [DOI: 10.1111/j.1574-6976.2011.00313.x] [Citation(s) in RCA: 277] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 10/20/2011] [Indexed: 12/24/2022] Open
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26
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Abstract
We describe methods used to isolate and identify antifungal compounds from actinomycete strains associated with the leaf-cutter ant Acromyrmex octospinosus. These ants use antibiotics produced by symbiotic actinomycete bacteria to protect themselves and their fungal cultivar against bacterial and fungal infections. The fungal cultivar serves as the sole food source for the ant colony, which can number up to tens of thousands of individuals. We describe how we isolate bacteria from leaf-cutter ants collected in Trinidad and analyze the antifungal compounds made by two of these strains (Pseudonocardia and Streptomyces spp.), using a combination of genome analysis, mutagenesis, and chemical isolation. These methods should be generalizable to a wide variety of insect-symbiont situations. Although more time consuming than traditional activity-guided fractionation methods, this approach provides a powerful technique for unlocking the complete biosynthetic potential of individual strains and for avoiding the problems of rediscovery of known compounds. We describe the discovery of a novel nystatin compound, named nystatin P1, and identification of the biosynthetic pathway for antimycins, compounds that were first described more than 60 years ago. We also report that disruption of two known antifungal pathways in a single Streptomyces strain has revealed a third, and likely novel, antifungal plus four more pathways with unknown products. This validates our approach, which clearly has the potential to identify numerous new compounds, even from well-characterized actinomycete strains.
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Affiliation(s)
- Ryan F Seipke
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
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27
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Moore JM, Bradshaw E, Seipke RF, Hutchings MI, McArthur M. Use and discovery of chemical elicitors that stimulate biosynthetic gene clusters in Streptomyces bacteria. Methods Enzymol 2012; 517:367-85. [PMID: 23084948 DOI: 10.1016/b978-0-12-404634-4.00018-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Secondary metabolite production from Streptomyces bacteria is primarily controlled at the level of transcription. Under normal laboratory conditions, the majority of the biosynthetic pathways of Streptomyces coelicolor are transcriptionally silent. These are often referred to as "cryptic" pathways and it is thought that they may encode the biosynthesis of yet unseen natural products with novel structures that may be valuable leads for therapeutics and as bioactive compounds. Sequencing of microbial genomes has supported the notion that cryptic pathways are widely distributed and likely to be a source of new chemical diversity. Hence, techniques that can reverse the silencing will be valuable for natural product screening as well as giving access to interesting new biology. We have focused on the identification of chemical elicitors capable of inducing expression of secondary metabolic gene clusters and to do so have drawn a parallel with fungal biology where inhibitors of histone acetylation change chromatin structure to derepress biosynthetic pathways. Similarly, we find that the same chemicals can also modify the expression of pathways in S. coelicolor and other Streptomyces spp. They variously act to increase expression from known pathways as well as inducing cryptic pathways. We hypothesize that nucleoid structure may be playing an analogous role to fungal chromatin structure in controlling transcriptional programs. Further, we speculate that microbial natural product collections could themselves be a rich source of new histone deacetylase inhibitors that have many applications in human health, such as anticancer therapeutics, beyond their traditional use as antimicrobials.
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Affiliation(s)
- Jane M Moore
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
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28
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Seipke RF, Barke J, Brearley C, Hill L, Yu DW, Goss RJM, Hutchings MI. A single Streptomyces symbiont makes multiple antifungals to support the fungus farming ant Acromyrmex octospinosus. PLoS One 2011; 6:e22028. [PMID: 21857911 PMCID: PMC3153929 DOI: 10.1371/journal.pone.0022028] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 06/13/2011] [Indexed: 11/18/2022] Open
Abstract
Attine ants are dependent on a cultivated fungus for food and use antibiotics produced by symbiotic Actinobacteria as weedkillers in their fungus gardens. Actinobacterial species belonging to the genera Pseudonocardia, Streptomyces and Amycolatopsis have been isolated from attine ant nests and shown to confer protection against a range of microfungal weeds. In previous work on the higher attine Acromyrmex octospinosus we isolated a Streptomyces strain that produces candicidin, consistent with another report that attine ants use Streptomyces-produced candicidin in their fungiculture. Here we report the genome analysis of this Streptomyces strain and identify multiple antibiotic biosynthetic pathways. We demonstrate, using gene disruptions and mass spectrometry, that this single strain has the capacity to make candicidin and multiple antimycin compounds. Although antimycins have been known for >60 years we report the sequence of the biosynthetic gene cluster for the first time. Crucially, disrupting the candicidin and antimycin gene clusters in the same strain had no effect on bioactivity against a co-evolved nest pathogen called Escovopsis that has been identified in ∼30% of attine ant nests. Since the Streptomyces strain has strong bioactivity against Escovopsis we conclude that it must make additional antifungal(s) to inhibit Escovopsis. However, candicidin and antimycins likely offer protection against other microfungal weeds that infect the attine fungal gardens. Thus, we propose that the selection of this biosynthetically prolific strain from the natural environment provides A. octospinosus with broad spectrum activity against Escovopsis and other microfungal weeds.
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Affiliation(s)
- Ryan F. Seipke
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
- * E-mail: (RFS); (MIH)
| | - Jörg Barke
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Charles Brearley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Lionel Hill
- Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Douglas W. Yu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
- State Key Laboratory of Genetic Resources, and Evolution, Ecology, Conservation, and Environment Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Rebecca J. M. Goss
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Matthew I. Hutchings
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
- * E-mail: (RFS); (MIH)
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29
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Barke J, Seipke RF, Yu DW, Hutchings MI. A mutualistic microbiome: How do fungus-growing ants select their antibiotic-producing bacteria? Commun Integr Biol 2011; 4:41-3. [PMID: 21509175 DOI: 10.4161/cib.4.1.13552] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Accepted: 09/06/2010] [Indexed: 11/19/2022] Open
Abstract
We recently published a paper titled "A mixed community of actinomycetes produce multiple antibiotics for the fungus farming ant Acromyrmex octospinosus" showing that attine ants use multidrug therapy to maintain their fungal cultivars. This paper tested two theories that have been put forward to explain how attine ants establish mutualism with actinomycete symbionts: environmental acquisition versus co-evolution. We found good evidence for environmental acquisition, in agreement with other recent studies. We also found evidence that supports (but does not prove) co-evolution. Here we place the environmental acquisition and co-evolution arguments within the framework of general mutualism theory and discuss how this system provides insights into the mechanisms that assemble microbiomes. We conclude by discussing future directions for research into the attine ant-actinomycete mutualism.
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Affiliation(s)
- Jörg Barke
- School of Biological Sciences; University of East Anglia; Norwich, Norwich Research Park UK
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30
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Seipke RF, Song L, Bicz J, Laskaris P, Yaxley AM, Challis GL, Loria R. The plant pathogen Streptomyces scabies 87-22 has a functional pyochelin biosynthetic pathway that is regulated by TetR- and AfsR-family proteins. Microbiology (Reading) 2011; 157:2681-2693. [PMID: 21757492 DOI: 10.1099/mic.0.047977-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Siderophores are high-affinity iron-chelating compounds produced by bacteria for iron uptake that can act as important virulence determinants for both plant and animal pathogens. Genome sequencing of the plant pathogen Streptomyces scabies 87-22 revealed the presence of a putative pyochelin biosynthetic gene cluster (PBGC). Liquid chromatography (LC)-MS analyses of culture supernatants of S. scabies mutants, in which expression of the cluster is upregulated and which lack a key biosynthetic gene from the cluster, indicated that pyochelin is a product of the PBGC. LC-MS comparisons with authentic standards on a homochiral stationary phase confirmed that pyochelin and not enantio-pyochelin (ent-pyochelin) is produced by S. scabies. Transcription of the S. scabies PBGC occurs via ~19 kb and ~3 kb operons and transcription of the ~19 kb operon is regulated by TetR- and AfsR-family proteins encoded by the cluster. This is the first report, to our knowledge, of pyochelin production by a Gram-positive bacterium; interestingly regulation of pyochelin production is distinct from characterized PBGCs in Gram-negative bacteria. Though pyochelin-mediated iron acquisition by Pseudomonas aeruginosa is important for virulence, in planta bioassays failed to demonstrate that pyochelin production by S. scabies is required for development of disease symptoms on excised potato tuber tissue or radish seedlings.
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Affiliation(s)
- Ryan F Seipke
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Lijiang Song
- Department of Chemistry, University of Warwick, Coventry, UK
| | - Joanna Bicz
- Department of Chemistry, University of Warwick, Coventry, UK
| | - Paris Laskaris
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Alice M Yaxley
- Department of Biological Sciences, University of Warwick, Coventry, UK
| | | | - Rosemary Loria
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
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31
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Seipke RF, Barke J, Ruiz-Gonzalez MX, Orivel J, Yu DW, Hutchings MI. Fungus-growing Allomerus ants are associated with antibiotic-producing actinobacteria. Antonie Van Leeuwenhoek 2011; 101:443-7. [PMID: 21748399 DOI: 10.1007/s10482-011-9621-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 07/02/2011] [Indexed: 11/26/2022]
Abstract
Fungus-growing attine ants use natural-product antibiotics produced by mutualist actinobacteria as 'weedkillers' in their fungal gardens. Here we report for the first time that fungus-growing Allomerus ants, which lie outside the tribe Attini, are associated with antifungal-producing actinobacteria, which offer them protection against non-cultivar fungi isolated from their ant-plants.
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Affiliation(s)
- Ryan F Seipke
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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32
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Barke J, Seipke RF, Grüschow S, Heavens D, Drou N, Bibb MJ, Goss RJM, Yu DW, Hutchings MI. A mixed community of actinomycetes produce multiple antibiotics for the fungus farming ant Acromyrmex octospinosus. BMC Biol 2010; 8:109. [PMID: 20796277 PMCID: PMC2942817 DOI: 10.1186/1741-7007-8-109] [Citation(s) in RCA: 163] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Accepted: 08/26/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Attine ants live in an intensely studied tripartite mutualism with the fungus Leucoagaricus gongylophorus, which provides food to the ants, and with antibiotic-producing actinomycete bacteria. One hypothesis suggests that bacteria from the genus Pseudonocardia are the sole, co-evolved mutualists of attine ants and are transmitted vertically by the queens. A recent study identified a Pseudonocardia-produced antifungal, named dentigerumycin, associated with the lower attine Apterostigma dentigerum consistent with the idea that co-evolved Pseudonocardia make novel antibiotics. An alternative possibility is that attine ants sample actinomycete bacteria from the soil, selecting and maintaining those species that make useful antibiotics. Consistent with this idea, a Streptomyces species associated with the higher attine Acromyrmex octospinosus was recently shown to produce the well-known antifungal candicidin. Candicidin production is widespread in environmental isolates of Streptomyces, so this could either be an environmental contaminant or evidence of recruitment of useful actinomycetes from the environment. It should be noted that the two possibilities for actinomycete acquisition are not necessarily mutually exclusive. RESULTS In order to test these possibilities we isolated bacteria from a geographically distinct population of A. octospinosus and identified a candicidin-producing Streptomyces species, which suggests that they are common mutualists of attine ants, most probably recruited from the environment. We also identified a Pseudonocardia species in the same ant colony that produces an unusual polyene antifungal, providing evidence for co-evolution of Pseudonocardia with A. octospinosus. CONCLUSIONS Our results show that a combination of co-evolution and environmental sampling results in the diversity of actinomycete symbionts and antibiotics associated with attine ants.
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Affiliation(s)
- Jörg Barke
- School of Biological Sciences, University of East Anglia, Norwich, Norwich Research Park, UK
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Bignell DRD, Seipke RF, Huguet-Tapia JC, Chambers AH, Parry RJ, Loria R. Streptomyces scabies 87-22 contains a coronafacic acid-like biosynthetic cluster that contributes to plant-microbe interactions. Mol Plant Microbe Interact 2010; 23:161-75. [PMID: 20064060 DOI: 10.1094/mpmi-23-2-0161] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Plant-pathogenic Streptomyces spp. cause scab disease on economically important root and tuber crops, the most important of which is potato. Key virulence determinants produced by these species include the cellulose synthesis inhibitor, thaxtomin A, and the secreted Nec1 protein that is required for colonization of the plant host. Recently, the genome sequence of Streptomyces scabies 87-22 was completed, and a biosynthetic cluster was identified that is predicted to synthesize a novel compound similar to coronafacic acid (CFA), a component of the virulence-associated coronatine phytotoxin produced by the plant-pathogenic bacterium Pseudomonas syringae. Southern analysis indicated that the cfa-like cluster in S. scabies 87-22 is likely conserved in other strains of S. scabies but is absent from two other pathogenic streptomycetes, S. turgidiscabies and S. acidiscabies. Transcriptional analyses demonstrated that the cluster is expressed during plant-microbe interactions and that expression requires a transcriptional regulator embedded in the cluster as well as the bldA tRNA. A knockout strain of the biosynthetic cluster displayed a reduced virulence phenotype on tobacco seedlings compared with the wild-type strain. Thus, the cfa-like biosynthetic cluster is a newly discovered locus in S. scabies that contributes to host-pathogen interactions.
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Affiliation(s)
- Dawn R D Bignell
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA.
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Abstract
The actinomycete Streptomyces scabies 87-22 is the causal agent of common scab, an economically important disease of potato and taproot crops. Sequencing of the S. scabies 87-22 genome revealed the presence of a gene with high homology to the gene encoding the alpha-tomatine-detoxifying enzyme tomatinase found in fungal tomato pathogens. The tomA gene from S. scabies 87-22 was cotranscribed with a putative family 1 glycosyl hydrolase gene, and purified TomA protein was active only on alpha-tomatine and not potato glycoalkaloids or xylans. Tomatinase-null mutants were more sensitive to alpha-tomatine than the wild-type strain in a disk diffusion assay. Interestingly, tomatine affected only aerial mycelium and not vegetative mycelium, suggesting that the target(s) of alpha-tomatine is not present during vegetative growth. Severities of disease for tomato seedlings affected by S. scabies 87-22 wild-type and DeltatomA1 strains were indistinguishable, suggesting that tomatinase is not important in pathogenicity on tomato plants. However, conservation of tomA on a pathogenicity island in S. acidiscabies and S. turgidiscabies suggests a role in plant-microbe interaction.
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Affiliation(s)
- Ryan F Seipke
- Department of Plant Pathology, Cornell University, 334 Plant Science Building, Ithaca, NY 14853, USA
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