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Schniete JK, Fernández-Martínez LT. Natural product discovery in soil actinomycetes: unlocking their potential within an ecological context. Curr Opin Microbiol 2024; 79:102487. [PMID: 38733791 DOI: 10.1016/j.mib.2024.102487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/23/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024]
Abstract
Natural products (NPs) produced by bacteria, particularly soil actinomycetes, often possess diverse bioactivities and play a crucial role in human health, agriculture, and biotechnology. Soil actinomycete genomes contain a vast number of predicted biosynthetic gene clusters (BGCs) yet to be exploited. Understanding the factors governing NP production in an ecological context and activating cryptic and silent BGCs in soil actinomycetes will provide researchers with a wealth of molecules with potential novel applications. Here, we highlight recent advances in NP discovery strategies employing ecology-inspired approaches and discuss the importance of understanding the environmental signals responsible for activation of NP production, particularly in a soil microbial community context, as well as the challenges that remain.
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Affiliation(s)
- Jana K Schniete
- Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany.
| | - Lorena T Fernández-Martínez
- School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK.
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2
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Schniete JK, Brüser T, Horn MA, Tschowri N. Specialized biopolymers: versatile tools for microbial resilience. Curr Opin Microbiol 2024; 77:102405. [PMID: 38070462 DOI: 10.1016/j.mib.2023.102405] [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: 08/22/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 02/12/2024]
Abstract
Bacteria produce a wide range of specialized biopolymers that can be classified into polysaccharides, polyamides, and polyesters and are considered to fulfill storage functions. In this review, we highlight recent developments in the field linking metabolism of biopolymers to stress and signaling physiology of the producers and demonstrating that biopolymers contribute to bacterial stress resistance and shape structure and composition of microenvironments. While specialized biopolymers are currently the focus of much attention in biotechnology as innovative and biodegradable materials, our understanding about the regulation and functions of these valuable compounds for the producers, microbial communities, and our environment is still very limited. Addressing open questions about signals, mechanisms, and functions in the area of biopolymers harbors potential for exciting discoveries with high relevance for biotechnology and fundamental research.
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Affiliation(s)
- Jana K Schniete
- Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany.
| | - Thomas Brüser
- Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Marcus A Horn
- Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Natalia Tschowri
- Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany
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3
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Tinning PW, Schniete JK, Scrimgeour R, Kölln LS, Rooney LM, Bushell TJ, McConnell G. A simple image processing pipeline to sharpen topology maps in multi-wavelength interference microscopy. Opt Lett 2023; 48:1092-1095. [PMID: 36857221 DOI: 10.1364/ol.478402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
Multi-wavelength standing wave (SW) microscopy and interference reflection microscopy (IRM) are powerful techniques that use optical interference to study topographical structure. However, the use of more than two wavelengths to image the complex cell surface results in complicated topographical maps, and it can be difficult to resolve the three-dimensional contours. We present a simple image processing method to reduce the thickness and spacing of antinodal fringes in multi-wavelength interference microscopy by up to a factor of two to produce clearer and more precise topographical maps of cellular structures. We first demonstrate this improvement using model non-biological specimens, and we subsequently demonstrate the benefit of our method for reducing the ambiguity of surface topography and revealing obscured features in live and fixed-cell specimens.
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4
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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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Abstract
Here, we characterize an uncommon set of telomeres from Streptomyces rimosus ATCC 10970, the parental strain of a lineage of one of the earliest-discovered antibiotic producers. Following the closure of its genome sequence, we compared unusual telomeres from this organism with the other five classes of replicon ends found amongst streptomycetes. Closed replicons of streptomycete chromosomes were organized with respect to their phylogeny and physical orientation, which demonstrated that different telomeres were not associated with particular clades and are likely shared amongst different strains by plasmid-driven horizontal gene transfer. Furthermore, we identified a ~50 kb origin island with conserved synteny that is located at the core of all streptomycete chromosomes and forms an axis around which symmetrical chromosome inversions can take place. Despite this chromosomal bilateral symmetry, a bias in parS sites to the right of oriC is maintained across the family Streptomycetaceae and suggests that the formation of ParB/parS nucleoprotein complexes on the right replichore is a conserved feature in streptomycetes. Consequently, our studies reveal novel features of linear bacterial replicons that, through their manipulation, may lead to improvements in growth and productivity of this important industrial group of bacteria.
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Affiliation(s)
- Lis Algora-Gallardo
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Jana K Schniete
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK.,Department of Biology, Edge Hill University, Ormskirk L39 4QP, UK
| | - David R Mark
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Iain S Hunter
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Paul R Herron
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
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6
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Zin NM, Ismail A, Mark DR, Westrop G, Schniete JK, Herron PR. Adaptation to Endophytic Lifestyle Through Genome Reduction by Kitasatospora sp. SUK42. Front Bioeng Biotechnol 2021; 9:740722. [PMID: 34712653 PMCID: PMC8545861 DOI: 10.3389/fbioe.2021.740722] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/20/2021] [Indexed: 01/02/2023] Open
Abstract
Endophytic actinobacteria offer great potential as a source of novel bioactive compounds. In order to investigate the potential for the production of secondary metabolites by endophytes, we recovered a filamentous microorgansism from the tree Antidesma neurocarpum Miq. After phenotypic analysis and whole genome sequencing we demonstrated that this organism, SUK42 was a member of the actinobacterial genus Kitasatospora. This strain has a small genome in comparison with other type strains of this genus and has lost metabolic pathways associated with Stress Response, Nitrogen Metabolism and Secondary Metabolism. Despite this SUK42 can grow well in a laboratory environment and encodes a core genome that is consistent with other members of the genus. Finally, in contrast to other members of Kitasatospora, SUK42 encodes saccharide secondary metabolite biosynthetic gene clusters, one of which with similarity to the acarviostatin cluster, the product of which displays α-amylase inhibitory activity. As extracts of the host plant demonstrate this inhibitory activity, it suggests that the potential medicinal properties of A. neurocarpum Miq might be provided by the endophytic partner and illustrate the potential for exploitation of endophytes for clinical or industrial uses.
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Affiliation(s)
- Noraziah M Zin
- School of Diagnostic and Applied Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Aishah Ismail
- School of Diagnostic and Applied Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - David R Mark
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Gareth Westrop
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Jana K Schniete
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Paul R Herron
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
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7
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Undabarrena A, Pereira CF, Kruasuwan W, Parra J, Sélem-Mojica N, Vind K, Schniete JK. Integrating perspectives in actinomycete research: an ActinoBase review of 2020-21. Microbiology (Reading) 2021; 167:001084. [PMID: 34515628 PMCID: PMC8549240 DOI: 10.1099/mic.0.001084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 05/10/2021] [Accepted: 07/26/2021] [Indexed: 12/12/2022]
Abstract
Last year ActinoBase, a Wiki-style initiative supported by the UK Microbiology Society, published a review highlighting the research of particular interest to the actinomycete community. Here, we present the second ActinoBase review showcasing selected reports published in 2020 and early 2021, integrating perspectives in the actinomycete field. Actinomycetes are well-known for their unsurpassed ability to produce specialised metabolites, of which many are used as therapeutic agents with antibacterial, antifungal, or immunosuppressive activities. Much research is carried out to understand the purpose of these metabolites in the environment, either within communities or in host interactions. Moreover, many efforts have been placed in developing computational tools to handle big data, simplify experimental design, and find new biosynthetic gene cluster prioritisation strategies. Alongside, synthetic biology has provided advances in tools to elucidate the biosynthesis of these metabolites. Additionally, there are still mysteries to be uncovered in understanding the fundamentals of filamentous actinomycetes' developmental cycle and regulation of their metabolism. This review focuses on research using integrative methodologies and approaches to understand the bigger picture of actinomycete biology, covering four research areas: i) technology and methodology; ii) specialised metabolites; iii) development and regulation; and iv) ecology and host interactions.
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Affiliation(s)
- Agustina Undabarrena
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso 2340000, Chile
| | - Camila F Pereira
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Worarat Kruasuwan
- Microbial Cell Factory Research Team, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Jonathan Parra
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, UK
| | - Nelly Sélem-Mojica
- Centro de Ciencias Matemáticas, Antigua Carretera a Pátzcuaro # 8701, Col. Ex Hacienda San José de la Huerta, Morelia C.P. 58089, Michoacán, México
| | - Kristiina Vind
- NAICONS Srl, Viale Ortles 22/4, 20139 Milan (MI), Italy
- Host-Microbe Interactomics Group, Wageningen University, De Elst 1 6708 WD, Wageningen, Netherlands
| | - Jana K. Schniete
- Biology, Edge Hill University, St Helens Road, Ormskirk, L39 4QP, UK
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Schniete JK, Tinning PW, Scrimgeour RC, Robb G, Kölln LS, Wesencraft K, Paul NR, Bushell TJ, McConnell G. An evaluation of multi-excitation-wavelength standing-wave fluorescence microscopy (TartanSW) to improve sampling density in studies of the cell membrane and cytoskeleton. Sci Rep 2021; 11:2903. [PMID: 33536463 PMCID: PMC7858599 DOI: 10.1038/s41598-020-78282-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 05/21/2020] [Accepted: 11/23/2020] [Indexed: 11/16/2022] Open
Abstract
Conventional standing-wave (SW) fluorescence microscopy uses a single wavelength to excite fluorescence from the specimen, which is normally placed in contact with a first surface reflector. The resulting excitation SW creates a pattern of illumination with anti-nodal maxima at multiple evenly-spaced planes perpendicular to the optical axis of the microscope. These maxima are approximately 90 nm thick and spaced 180 nm apart. Where the planes intersect fluorescent structures, emission occurs, but between the planes are non-illuminated regions which are not sampled for fluorescence. We evaluate a multi-excitation-wavelength SW fluorescence microscopy (which we call TartanSW) as a method for increasing the density of sampling by using SWs with different axial periodicities, to resolve more of the overall cell structure. The TartanSW method increased the sampling density from 50 to 98% over seven anti-nodal planes, with no notable change in axial or lateral resolution compared to single-excitation-wavelength SW microscopy. We demonstrate the method with images of the membrane and cytoskeleton of living and fixed cells.
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Affiliation(s)
- Jana K Schniete
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow East, Glasgow, G4 0NG, UK.
| | - Peter W Tinning
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow East, Glasgow, G4 0NG, UK
| | - Ross C Scrimgeour
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow East, Glasgow, G4 0NG, UK
| | - Gillian Robb
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow East, Glasgow, G4 0NG, UK
| | - Lisa S Kölln
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow East, Glasgow, G4 0NG, UK
| | - Katrina Wesencraft
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow East, Glasgow, G4 0NG, UK
| | - Nikki R Paul
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
| | - Trevor J Bushell
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Gail McConnell
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow East, Glasgow, G4 0NG, UK
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9
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Schniete JK, Selem-Mojica N, Birke AS, Cruz-Morales P, Hunter IS, Barona-Gomez F, Hoskisson PA. ActDES - a curated Actinobacterial Database for Evolutionary Studies. Microb Genom 2021; 7:mgen000498. [PMID: 33433310 PMCID: PMC8115908 DOI: 10.1099/mgen.0.000498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 05/28/2020] [Accepted: 12/06/2020] [Indexed: 12/25/2022] Open
Abstract
Actinobacteria is a large and diverse phylum of bacteria that contains medically and ecologically relevant organisms. Many members are valuable sources of bioactive natural products and chemical precursors that are exploited in the clinic and made using the enzyme pathways encoded in their complex genomes. Whilst the number of sequenced genomes has increased rapidly in the last 20 years, the large size, complexity and high G+C content of many actinobacterial genomes means that the sequences remain incomplete and consist of large numbers of contigs with poor annotation, which hinders large-scale comparative genomic and evolutionary studies. To enable greater understanding and exploitation of actinobacterial genomes, specialized genomic databases must be linked to high-quality genome sequences. Here, we provide a curated database of 612 high-quality actinobacterial genomes from 80 genera, chosen to represent a broad phylogenetic group with equivalent genome re-annotation. Utilizing this database will provide researchers with a framework for evolutionary and metabolic studies, to enable a foundation for genome and metabolic engineering, to facilitate discovery of novel bioactive therapeutics and studies on gene family evolution. This article contains data hosted by Microreact.
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Affiliation(s)
- Jana K. Schniete
- Biology Department, Edge Hill University, St Helens Road, Ormskirk, Lancashire L39 4QP, UK
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Nelly Selem-Mojica
- Evolution of Metabolic Diversity Laboratory, Langebio, Cinvestav-IPN, Libramiento Norte Carretera Leon Km 9.6, 36821 Irapuato, Guanajuato, México
| | - Anna S. Birke
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Pablo Cruz-Morales
- Evolution of Metabolic Diversity Laboratory, Langebio, Cinvestav-IPN, Libramiento Norte Carretera Leon Km 9.6, 36821 Irapuato, Guanajuato, México
| | - Iain S. Hunter
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Francisco Barona-Gomez
- Evolution of Metabolic Diversity Laboratory, Langebio, Cinvestav-IPN, Libramiento Norte Carretera Leon Km 9.6, 36821 Irapuato, Guanajuato, México
| | - Paul A. Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
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10
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Schniete JK, Reumerman R, Kerr L, Tucker NP, Hunter IS, Herron PR, Hoskisson PA. Differential transcription of expanded gene families in central carbon metabolism of Streptomyces coelicolor A3(2). Access Microbiol 2020; 2:acmi000122. [PMID: 32974587 PMCID: PMC7494193 DOI: 10.1099/acmi.0.000122] [Citation(s) in RCA: 4] [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] [Received: 11/23/2019] [Accepted: 02/21/2020] [Indexed: 11/18/2022] Open
Abstract
Background Streptomycete bacteria are prolific producers of specialized metabolites, many of which have clinically relevant bioactivity. A striking feature of their genomes is the expansion of gene families that encode the same enzymatic function. Genes that undergo expansion events, either by horizontal gene transfer or duplication, can have a range of fates: genes can be lost, or they can undergo neo-functionalization or sub-functionalization. To test whether expanded gene families in Streptomyces exhibit differential expression, an RNA-Seq approach was used to examine cultures of wild-type Streptomyces coelicolor grown with either glucose or tween as the sole carbon source. Results RNA-Seq analysis showed that two-thirds of genes within expanded gene families show transcriptional differences when strains were grown on tween compared to glucose. In addition, expression of specialized metabolite gene clusters (actinorhodin, isorenieratane, coelichelin and a cryptic NRPS) was also influenced by carbon source. Conclusions Expression of genes encoding the same enzymatic function had transcriptional differences when grown on different carbon sources. This transcriptional divergence enables partitioning to function under different physiological conditions. These approaches can inform metabolic engineering of industrial Streptomyces strains and may help develop cultivation conditions to activate the so-called silent biosynthetic gene clusters.
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Affiliation(s)
- Jana K Schniete
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK.,Biology Department, Edge Hill University, St Helens Road, Ormskirk, Lancashire, L39 4QP, UK
| | | | - Leena Kerr
- Institute of Earth and Life Sciences, School of Energy, Geoscience, Infrastructure and Society, Heriot-Watt University, Riccarton, Edinburgh, EH14 4AS, UK
| | - Nicholas P Tucker
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Iain S Hunter
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Paul R Herron
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
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Cortés-Albayay C, Dorador C, Schumann P, Schniete JK, Herron P, Andrews B, Asenjo J, Nouioui I. Streptomyces altiplanensis sp. nov., an alkalitolerant species isolated from Chilean Altiplano soil, and emended description of Streptomyces chryseus (Krasil'nikov et al. 1965) Pridham 1970. Int J Syst Evol Microbiol 2019; 69:2498-2505. [PMID: 31204968 DOI: 10.1099/ijsem.0.003525] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic approach was used for evaluating the taxonomic status of strain HST21T isolated from Salar de Huasco in the Atacama Desert. The results of 16S rRNA gene and multilocus sequence phylogenetic analyses assigned strain HST21T to the genus Streptomyceswith Streptomyces albidochromogenes DSM 41800Tand Streptomyces flavidovirens DSM 40150T as its nearest neighbours. Digital DNA-DNA hydridization (dDDH) and average nucleotide identity (ANI) values between the genome sequences of strain HST21T and S. albidochromogenes DSM 41800T (35.6 and 88.2 %) and S. flavidovirens DSM 40105T (47.2 and 88.8 %) were below the thresholds of 70 and 95-96 % for prokaryotic conspecific assignation. Phenotypic, chemotaxonomic and genetic results distinguished strain HST21T from its closest neighbours. Strain HST21T is characterized by the presence of ll-diaminopimelic acid in its peptidoglycan layer; glucose and ribose as whole cell sugars; diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylinositol, glycophospholipids, unknown lipids and phospholipids as polar lipids; and anteiso-C15 : 0 (21.6 %) and anteiso-C17 : 0 (20.5 %) as major fatty acids (>15 %). Based on these results, strain HST21T merits recognition as a novel species, for which the name Streptomyces altiplanensis sp. nov. is proposed. The type strain is HST21T=DSM 107267T=CECT 9647T. While analysing the phylogenies of strain HST21T, Streptomyces chryseus DSM 40420T and Streptomyces helvaticus DSM 40431T were found to have 100 % 16S rRNA gene sequence similarity with digital DNA-DNA hydridization (dDDH) and average nucleotide identity (ANI) values of 95.3 and 99.4 %, respectively. Therefore, S. helvaticus is considered as a later heterotypic synonym of S. chryseus and, consequently, we emend the description of S. chryseus.
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Affiliation(s)
- Carlos Cortés-Albayay
- School of Natural and Environmental Sciences, Newcastle University, Devonshire Building, Newcastle upon Tyne NE1 7RU, UK
- Centre for Biotechnology and Bioengineering, University of Chile, Beauchef 851, Santiago, Chile
| | - Cristina Dorador
- Laboratory of Microbial Complexity and Functional Ecology, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos & Centre for Biotechnology and Bioengineering, Universidad de Antofagasta, Chile
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany
| | - Jana K Schniete
- Department of Physics, University of Strathclyde, 107 Rottenrow, Glasgow G4 0NG, UK
| | - Paul Herron
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Barbara Andrews
- Centre for Biotechnology and Bioengineering, University of Chile, Beauchef 851, Santiago, Chile
| | - Juan Asenjo
- Centre for Biotechnology and Bioengineering, University of Chile, Beauchef 851, Santiago, Chile
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Devonshire Building, Newcastle upon Tyne NE1 7RU, UK
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Schniete JK, Cruz-Morales P, Selem-Mojica N, Fernández-Martínez LT, Hunter IS, Barona-Gómez F, Hoskisson PA. Expanding Primary Metabolism Helps Generate the Metabolic Robustness To Facilitate Antibiotic Biosynthesis in Streptomyces. mBio 2018; 9:e02283-17. [PMID: 29437921 PMCID: PMC5801464 DOI: 10.1128/mbio.02283-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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: 12/12/2017] [Accepted: 01/09/2018] [Indexed: 02/04/2023] Open
Abstract
The expansion of the genetic repertoire of an organism by gene duplication or horizontal gene transfer (HGT) can aid adaptation. Streptomyces bacteria are prolific producers of bioactive specialized metabolites that have adaptive functions in nature and have found extensive utility in human medicine. While the biosynthesis of these specialized metabolites is directed by dedicated biosynthetic gene clusters, little attention has been focused on how these organisms have evolved robustness in their genomes to facilitate the metabolic plasticity required to provide chemical precursors for biosynthesis during the complex metabolic transitions from vegetative growth to specialized metabolite production and sporulation. Here, we examine genetic redundancy in actinobacteria and show that specialized metabolite-producing bacterial families exhibit gene family expansion in primary metabolism. Focusing on a gene duplication event, we show that the two pyruvate kinases in the genome of Streptomyces coelicolor arose by an ancient duplication event and that each has evolved altered enzymatic kinetics, with Pyk1 having a 20-fold-higher kcat than Pyk2 (4,703 s-1 compared to 215 s-1, respectively), and yet both are constitutively expressed. The pyruvate kinase mutants were also found to be compromised in terms of fitness compared to wild-type Streptomyces These data suggest that expanding gene families can help maintain cell functionality during metabolic perturbation such as nutrient limitation and/or specialized metabolite production.IMPORTANCE The rise of antimicrobial-resistant infections has prompted a resurgence in interest in understanding the production of specialized metabolites, such as antibiotics, by Streptomyces The presence of multiple genes encoding the same enzymatic function is an aspect of Streptomyces biology that has received little attention; however, understanding how the metabolic expansion influences these organisms can help enhance production of clinically useful molecules. Here, we show that expanding the number of pyruvate kinases enables metabolic adaptation, increases strain fitness, and represents an excellent target for metabolic engineering of industrial specialized metabolite-producing bacteria and the activation of cryptic specialized metabolites.
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Affiliation(s)
- Jana K Schniete
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Pablo Cruz-Morales
- Evolution of Metabolic Diversity Laboratory, Langebio, Guanajuato, Mexico
| | - Nelly Selem-Mojica
- Evolution of Metabolic Diversity Laboratory, Langebio, Guanajuato, Mexico
| | | | - Iain S Hunter
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | | | - Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
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