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Narh Mensah DL, Wingfield BD, Coetzee MPA. Two distinct non-ribosomal peptide synthetase-independent siderophore synthetase gene clusters identified in Armillaria and other species in the Physalacriaceae. G3 (BETHESDA, MD.) 2023; 13:jkad205. [PMID: 37843963 PMCID: PMC10700112 DOI: 10.1093/g3journal/jkad205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/28/2023] [Indexed: 10/18/2023]
Abstract
Siderophores are important for ferric iron solubilization, sequestration, transportation, and storage, especially under iron-limiting conditions such as aerobic conditions at high pH. Siderophores are mainly produced by non-ribosomal peptide synthetase-dependent siderophore pathway, non-ribosomal peptide synthetase-independent siderophore synthetase pathway, or the hybrid non-ribosomal peptide synthetases/non-ribosomal peptide synthetases-independent siderophore pathway. Outcompeting or inhibition of plant pathogens, alteration of host defense mechanisms, and alteration of plant-fungal interactions have been associated with fungal siderophores. To understand these mechanisms in fungi, studies have been conducted on siderophore biosynthesis by ascomycetes with limited focus on the basidiomycetes. Armillaria includes several species that are pathogens of woody plants and trees important to agriculture, horticulture, and forestry. The aim of this study was to investigate the presence of non-ribosomal peptide synthetases-independent siderophore synthetase gene cluster(s) in genomes of Armillaria species using a comparative genomics approach. Iron-dependent growth and siderophore biosynthesis in strains of selected Armillaria spp. were also evaluated in vitro. Two distinct non-ribosomal peptide synthetases-independent siderophore synthetase gene clusters were identified in all the genomes. All non-ribosomal peptide synthetases-independent siderophore synthetase genes identified putatively encode Type A' non-ribosomal peptide synthetases-independent siderophore synthetases, most of which have IucA_IucC and FhuF-like transporter domains at their N- and C-terminals, respectively. The effect of iron on culture growth varied among the strains studied. Bioassays using the CAS assay on selected Armillaria spp. revealed in vitro siderophore biosynthesis by all strains irrespective of added FeCl3 concentration. This study highlights some of the tools that Armillaria species allocate to iron homeostasis. The information generated from this study may in future aid in developing molecular based methods to control these phytopathogens.
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Affiliation(s)
- Deborah L Narh Mensah
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa
- CSIR—Food Research Institute, Microbiology and Mushroom Research Division, P. O. Box, M20, Accra, Ghana
| | - Brenda D Wingfield
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa
| | - Martin P A Coetzee
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa
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2
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Kontou EE, Walter A, Alka O, Pfeuffer J, Sachsenberg T, Mohite OS, Nuhamunada M, Kohlbacher O, Weber T. UmetaFlow: an untargeted metabolomics workflow for high-throughput data processing and analysis. J Cheminform 2023; 15:52. [PMID: 37173725 PMCID: PMC10176759 DOI: 10.1186/s13321-023-00724-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Metabolomics experiments generate highly complex datasets, which are time and work-intensive, sometimes even error-prone if inspected manually. Therefore, new methods for automated, fast, reproducible, and accurate data processing and dereplication are required. Here, we present UmetaFlow, a computational workflow for untargeted metabolomics that combines algorithms for data pre-processing, spectral matching, molecular formula and structural predictions, and an integration to the GNPS workflows Feature-Based Molecular Networking and Ion Identity Molecular Networking for downstream analysis. UmetaFlow is implemented as a Snakemake workflow, making it easy to use, scalable, and reproducible. For more interactive computing, visualization, as well as development, the workflow is also implemented in Jupyter notebooks using the Python programming language and a set of Python bindings to the OpenMS algorithms (pyOpenMS). Finally, UmetaFlow is also offered as a web-based Graphical User Interface for parameter optimization and processing of smaller-sized datasets. UmetaFlow was validated with in-house LC-MS/MS datasets of actinomycetes producing known secondary metabolites, as well as commercial standards, and it detected all expected features and accurately annotated 76% of the molecular formulas and 65% of the structures. As a more generic validation, the publicly available MTBLS733 and MTBLS736 datasets were used for benchmarking, and UmetaFlow detected more than 90% of all ground truth features and performed exceptionally well in quantification and discriminating marker selection. We anticipate that UmetaFlow will provide a useful platform for the interpretation of large metabolomics datasets.
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Affiliation(s)
- Eftychia E Kontou
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, 2800, Kgs. Lyngby, Denmark
| | - Axel Walter
- Applied Bioinformatics, Department of Computer Science, Eberhard Karls University Tübingen, Sand 14, 72076, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Oliver Alka
- Applied Bioinformatics, Department of Computer Science, Eberhard Karls University Tübingen, Sand 14, 72076, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Julianus Pfeuffer
- Visual and Data-Centric Computing, Zuse Institute Berlin, Takustr. 7, 14195, Berlin, Germany
- Algorithmic Bioinformatics, Freie Universität Berlin, Takustr. 9, 14195, Berlin, Germany
| | - Timo Sachsenberg
- Applied Bioinformatics, Department of Computer Science, Eberhard Karls University Tübingen, Sand 14, 72076, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Omkar S Mohite
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, 2800, Kgs. Lyngby, Denmark
| | - Matin Nuhamunada
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, 2800, Kgs. Lyngby, Denmark
| | - Oliver Kohlbacher
- Applied Bioinformatics, Department of Computer Science, Eberhard Karls University Tübingen, Sand 14, 72076, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
- Translational Bioinformatics, University Hospital Tübingen, Schaffhausenstr. 77, 72072, Tübingen, Germany
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, 2800, Kgs. Lyngby, Denmark.
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3
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Borba MP, Witusk JP, Cunha DM, de Lima-Morales D, Martins AF, Van Der Sand S. Whole-genome sequencing-based characterization of Streptomyces sp. 6(4): focus on natural product. Access Microbiol 2023; 5:000466.v3. [PMID: 37091737 PMCID: PMC10118248 DOI: 10.1099/acmi.0.000466.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/23/2022] [Indexed: 03/06/2023] Open
Abstract
We have sequenced the whole genome of
Streptomyces
sp. 6(4) isolated from tomato roots that presents antifungal activity against phytopathogenic fungi, mainly Bipolaris sorokiniana. The genome has almost 7 Mb and 3368 hypothetical proteins that were analysed and characterized in Uniprot with the emphasis on biological compounds. Multilocus sequence typing (MLST) analyses were performed in an effort to characterize and identify this isolate, resulting in a new sequence type (ST), classified as ST64. Phenetic and phylogenetic trees were constructed to investigate
Streptomyces
sp. 6(4) evolution and sequence similarity, and the isolate is a strain closer to
Streptomyces prasinus
and
Streptomyces viridosporus
. It is known that the genus
Streptomyces
possess huge metabolic capacity with the presence of cryptic genes. These genes are usually present in clusters, which are responsible for the production of diverse natural products, mainly antibiotics. In addition, 6(4) showed 11 biosynthetic gene clusters through antiSMASH, including 3 polyketide synthase (PKS) and non-ribosomal peptide synthase (NRPS) type clusters.
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Affiliation(s)
- Marcela Proença Borba
- Programa de Pós-graduação em Microbiologia Agrícola e do Ambiente, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - João Paulo Witusk
- Programa de Pós-graduação em Microbiologia Agrícola e do Ambiente, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Débora Marchesan Cunha
- Programa de Pós-graduação em Microbiologia Agrícola e do Ambiente, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Daiana de Lima-Morales
- Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
- Núcleo de Bioinformática do Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Andreza Francisco Martins
- Programa de Pós-graduação em Microbiologia Agrícola e do Ambiente, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Sueli Van Der Sand
- Programa de Pós-graduação em Microbiologia Agrícola e do Ambiente, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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4
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Jiang W, Sun J, Gao H, Tang Y, Wang C, Jiang Y, Zhang W, Xin F, Jiang M. Carotenoids production and genome analysis of a novel carotenoid producing Rhodococcus aetherivorans N1. Enzyme Microb Technol 2023; 164:110190. [PMID: 36603321 DOI: 10.1016/j.enzmictec.2022.110190] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022]
Abstract
Carotenoids are a series of natural pigments with unique structure and physiological functions. In this study, a novel Rhodococcus aetherivorans strain N1 was discovered, which can produce 6.4 mg/g carotenoids including β-carotene, zeaxanthin and isorenieratene from glucose. Moreover, strain N1 can directly produce 3.0 mg/g carotenoids from the undetoxified straw hydrolysate, representing the highest carotenoids production from the undetoxified lignocellulosic hydrolysate. The crude carotenoid extracts of strain N1 showed efficient free radical scavenging activity and stability. Strain N1 has complete methylerythritol 4-phosphate (MEP) pathway and related genes for carotenoid synthesis, especially the rare aromatic carotenoid of isorenieratene. Genomic comparison between strain N1 and other carotenoid producing Rhodococcus sp. strains showed the conservatism and universality of carotenoids synthesis gene. These results proved that R. aetherivorans strain N1 can serve as a promising producer for the industrialization of carotenoid production.
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Affiliation(s)
- Wankui Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Jingxiang Sun
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Haiyan Gao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Yunhan Tang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Chao Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China.
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China
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5
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Narh Mensah DL, Wingfield BD, Coetzee MPA. Nonribosomal peptide synthetase gene clusters and characteristics of predicted NRPS-dependent siderophore synthetases in Armillaria and other species in the Physalacriaceae. Curr Genet 2023; 69:7-24. [PMID: 36369495 DOI: 10.1007/s00294-022-01256-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 11/13/2022]
Abstract
Fungal secondary metabolites are often pathogenicity or virulence factors synthesized by genes contained in secondary metabolite gene clusters (SMGCs). Nonribosomal polypeptide synthetase (NRPS) clusters are SMGCs which produce peptides such as siderophores, the high affinity ferric iron chelating compounds required for iron uptake under aerobic conditions. Armillaria spp. are mostly facultative necrotrophs of woody plants. NRPS-dependent siderophore synthetase (NDSS) clusters of Armillaria spp. and selected Physalacriaceae were investigated using a comparative genomics approach. Siderophore biosynthesis by strains of selected Armillaria spp. was evaluated using CAS and split-CAS assays. At least one NRPS cluster and other clusters were detected in the genomes studied. No correlation was observed between the number and types of SMGCs and reported pathogenicity of the species studied. The genomes contained one NDSS cluster each. All NDSSs were multi-modular with the domain architecture (ATC)3(TC)2. NDSS clusters of the Armillaria spp. showed a high degree of microsynteny. In the genomes of Desarmillaria spp. and Guyanagaster necrorhizus, NDSS clusters were more syntenic with NDSS clusters of Armillaria spp. than to those of the other Physalacriaceae species studied. Three A-domain orthologous groups were identified in the NDSSs, and atypical Stachelhaus codes were predicted for the A3 orthologous group. In vitro biosynthesis of mainly hydroxamate and some catecholate siderophores was observed. Hence, Armillaria spp. generally contain one highly conserved, NDSS cluster although some interspecific variations in the products of these clusters is expected. Results from this study lays the groundwork for future studies to elucidate the molecular biology of fungal phyto-pathogenicity.
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Affiliation(s)
- Deborah L Narh Mensah
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.,Council for Scientific and Industrial Research-Food Research Institute (CSIR-FRI), P. O. Box M20, Accra, Ghana
| | - Brenda D Wingfield
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Martin P A Coetzee
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.
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6
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Steven R, Humaira Z, Natanael Y, Dwivany FM, Trinugroho JP, Dwijayanti A, Kristianti T, Tallei TE, Emran TB, Jeon H, Alhumaydhi FA, Radjasa OK, Kim B. Marine Microbial-Derived Resource Exploration: Uncovering the Hidden Potential of Marine Carotenoids. Mar Drugs 2022; 20:352. [PMID: 35736155 PMCID: PMC9229179 DOI: 10.3390/md20060352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/13/2022] [Accepted: 05/18/2022] [Indexed: 12/04/2022] Open
Abstract
Microbes in marine ecosystems are known to produce secondary metabolites. One of which are carotenoids, which have numerous industrial applications, hence their demand will continue to grow. This review highlights the recent research on natural carotenoids produced by marine microorganisms. We discuss the most recent screening approaches for discovering carotenoids, using in vitro methods such as culture-dependent and culture-independent screening, as well as in silico methods, using secondary metabolite Biosynthetic Gene Clusters (smBGCs), which involves the use of various rule-based and machine-learning-based bioinformatics tools. Following that, various carotenoids are addressed, along with their biological activities and metabolic processes involved in carotenoids biosynthesis. Finally, we cover the application of carotenoids in health and pharmaceutical industries, current carotenoids production system, and potential use of synthetic biology in carotenoids production.
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Affiliation(s)
- Ray Steven
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung 40132, Indonesia; (R.S.); (Z.H.); (Y.N.)
| | - Zalfa Humaira
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung 40132, Indonesia; (R.S.); (Z.H.); (Y.N.)
| | - Yosua Natanael
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung 40132, Indonesia; (R.S.); (Z.H.); (Y.N.)
| | - Fenny M. Dwivany
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung 40132, Indonesia; (R.S.); (Z.H.); (Y.N.)
| | - Joko P. Trinugroho
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW72AZ, UK;
| | - Ari Dwijayanti
- CNRS@CREATE Ltd., 1 Create Way, #08-01 Create Tower, Singapore 138602, Singapore;
| | | | - Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia;
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh;
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh
| | - Heewon Jeon
- Department of Pathology, College of Korean Medicine, Kyung Hee University, 1-5 Hoegidong, Seoul 02447, Korea;
| | - Fahad A. Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 52571, Saudi Arabia;
| | - Ocky Karna Radjasa
- Oceanography Research Center, The Earth Sciences and Maritime Research Organization, National Research and Innovation Agency, North Jakarta 14430, Indonesia
| | - Bonglee Kim
- Department of Pathology, College of Korean Medicine, Kyung Hee University, 1-5 Hoegidong, Seoul 02447, Korea;
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7
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Baltz RH. Genome mining for drug discovery: progress at the front end. J Ind Microbiol Biotechnol 2021; 48:6324007. [PMID: 34279640 PMCID: PMC8788784 DOI: 10.1093/jimb/kuab044] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 07/11/2021] [Indexed: 12/12/2022]
Abstract
Microbial genome mining for drug discovery and development has been accelerating in recent years, driven by technical advancements in genome sequencing, bioinformatics, metabolomics/metabologenomics, and synthetic biology. Microbial genome mining is a multistep process that starts with the sequencing of microbes that encode multiple secondary metabolites and identifying new and novel secondary metabolite biosynthetic gene clusters (BGCs) to pursue. The initial steps in the process are critical for the overall success, and they encompass the most innovative new technologies to revitalize natural product discovery. As microbial genome mining has matured in recent years, unvalidated conjectures about what microbes to pursue, how to identify legitimate secondary metabolite BGCs, and how to sequence DNA to satisfactory levels of completion have been identified. The solutions to correct the misconceptions around these topics are beginning to be implemented.
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Affiliation(s)
- Richard H Baltz
- CognoGen Biotechnology Consulting, 7757 Uliva Way, Sarasota, FL 34238, USA
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8
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A Multidisciplinary Approach to Unraveling the Natural Product Biosynthetic Potential of a Streptomyces Strain Collection Isolated from Leaf-Cutting Ants. Microorganisms 2021; 9:microorganisms9112225. [PMID: 34835350 PMCID: PMC8621525 DOI: 10.3390/microorganisms9112225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/22/2021] [Accepted: 10/23/2021] [Indexed: 12/27/2022] Open
Abstract
The rapid emergence of bacterial resistance to antibiotics has urged the need to find novel bioactive compounds against resistant microorganisms. For that purpose, different strategies are being followed, one of them being exploring secondary metabolite production in microorganisms from uncommon sources. In this work, we have analyzed the genome of 12 Streptomyces sp. strains of the CS collection isolated from the surface of leaf-cutting ants of the Attini tribe and compared them to four Streptomyces model species and Pseudonocardia sp. Ae150A_Ps1, which shares the ecological niche with those of the CS collection. We used a combination of phylogenetics, bioinformatics and dereplication analysis to study the biosynthetic potential of our strains. 51.5% of the biosynthetic gene clusters (BGCs) predicted by antiSMASH were unknown and over half of them were strain-specific, making this strain collection an interesting source of putative novel compounds.
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9
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Terra L, Ratcliffe N, Castro HC, Vicente ACP, Dyson P. Biotechnological Potential of Streptomyces Siderophores as New Antibiotics. Curr Med Chem 2021; 28:1407-1421. [PMID: 32389112 DOI: 10.2174/0929867327666200510235512] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 02/29/2020] [Accepted: 03/23/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Siderophores are small-molecule iron-chelators produced by microorganisms and plants growing mostly under low iron conditions. Siderophores allow iron capture and transport through cell membranes into the cytoplasm, where iron is released for use in biological processes. These bacterial iron uptake systems can be used for antibiotic conjugation or as targets for killing pathogenic bacteria. Siderophores have been explored recently because of their potential applications in environmental and therapeutic research. They are present in Streptomyces, Grampositive bacteria that are an important source for discovering new siderophores. OBJECTIVE This review summarizes siderophore molecules produced by the genus Streptomyces emphasizing their potential as biotechnological producers and also illustrating genomic tools for discovering siderophores useful for treating bacterial infections. METHODS The literature search was performed using PUBMED and MEDLINE databases with keywords siderophore, secondary metabolites, Trojan horse strategy, sideromycin and Streptomyces. The literature research focused on bibliographic databases including all siderophores identified in the genus Streptomyces. In addition, reference genomes of Streptomyces from GenBank were used to identify siderophore biosynthetic gene clusters by using the antiSMASH platform. RESULTS This review has highlighted some of the many siderophore molecules produced by Streptomyces, illustrating the diversity of their chemical structures and a wide spectrum of bioactivities against pathogenic bacteria. Furthermore, the possibility of using siderophores conjugated with antibiotics could be an alternative to overcome bacterial resistance to drugs and could improve their therapeutic efficacy. CONCLUSION This review confirms the importance of Streptomyces as a rich source of siderophores, and underlines their potential as antibacterial agents.
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Affiliation(s)
- Luciana Terra
- Programa de Pos-Graduacao em Ciencias e Biotecnologia, Instituto de Biologia, UFF, Brazil
| | - Norman Ratcliffe
- Programa de Pos-Graduacao em Ciencias e Biotecnologia, Instituto de Biologia, UFF, Brazil
| | - Helena Carla Castro
- Programa de Pos-Graduacao em Ciencias e Biotecnologia, Instituto de Biologia, UFF, Brazil
| | | | - Paul Dyson
- Institute of Life Science, Swansea University Medical School, Singleton Park, Swansea SA2 8PP, United Kingdom
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10
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Polishchuk LV, Lukyanchuk VV. General Trends in the Organization and Localization of crt-Clusters in Streptomyces Genomes. CYTOL GENET+ 2021. [DOI: 10.3103/s0095452721020122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Baltz RH. Genome mining for drug discovery: cyclic lipopeptides related to daptomycin. J Ind Microbiol Biotechnol 2021; 48:6178872. [PMID: 33739403 PMCID: PMC9113097 DOI: 10.1093/jimb/kuab020] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 11/17/2020] [Indexed: 11/25/2022]
Abstract
The cyclic lipopeptide antibiotics structurally related to daptomycin were first reported in the 1950s. Several have common lipopeptide initiation, elongation, and termination mechanisms. Initiation requires the use of a fatty acyl-AMP ligase (FAAL), a free-standing acyl carrier protein (ACP), and a specialized condensation (CIII) domain on the first NRPS elongation module to couple the long chain fatty acid to the first amino acid. Termination is carried out by a dimodular NRPS that contains a terminal thioesterase (Te) domain (CAT-CATTe). Lipopeptide BGCs also encode ABC transporters, apparently for export and resistance. The use of this mechanism of initiation, elongation, and termination, coupled with molecular target-agnostic resistance, has provided a unique basis for robust natural and experimental combinatorial biosynthesis to generate a large variety of structurally related compounds, some with altered or different antibacterial mechanisms of action. The FAAL, ACP, and dimodular NRPS genes were used as molecular beacons to identify phylogenetically related BGCs by BLASTp analysis of finished and draft genome sequences. These and other molecular beacons have identified: (i) known, but previously unsequenced lipopeptide BGCs in draft genomes; (ii) a new daptomycin family BGC in a draft genome of Streptomyces sedi; and (iii) novel lipopeptide BGCs in the finished genome of Streptomyces ambofaciens and the draft genome of Streptomyces zhaozhouensis.
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Affiliation(s)
- Richard H Baltz
- CognoGen Biotechnology Consulting, 7757 Uliva Way, Sarasota, FL 34238, USA
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12
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Soldatou S, Eldjárn GH, Ramsay A, van der Hooft JJJ, Hughes AH, Rogers S, Duncan KR. Comparative Metabologenomics Analysis of Polar Actinomycetes. Mar Drugs 2021; 19:103. [PMID: 33578887 PMCID: PMC7916644 DOI: 10.3390/md19020103] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 12/16/2022] Open
Abstract
Biosynthetic and chemical datasets are the two major pillars for microbial drug discovery in the omics era. Despite the advancement of analysis tools and platforms for multi-strain metabolomics and genomics, linking these information sources remains a considerable bottleneck in strain prioritisation and natural product discovery. In this study, molecular networking of the 100 metabolite extracts derived from applying the OSMAC approach to 25 Polar bacterial strains, showed growth media specificity and potential chemical novelty was suggested. Moreover, the metabolite extracts were screened for antibacterial activity and promising selective bioactivity against drug-persistent pathogens such as Klebsiella pneumoniae and Acinetobacter baumannii was observed. Genome sequencing data were combined with metabolomics experiments in the recently developed computational approach, NPLinker, which was used to link BGC and molecular features to prioritise strains for further investigation based on biosynthetic and chemical information. Herein, we putatively identified the known metabolites ectoine and chrloramphenicol which, through NPLinker, were linked to their associated BGCs. The metabologenomics approach followed in this study can potentially be applied to any large microbial datasets for accelerating the discovery of new (bioactive) specialised metabolites.
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Affiliation(s)
- Sylvia Soldatou
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK; (S.S.); (A.H.H.)
| | | | - Andrew Ramsay
- School of Computing Science, University of Glasgow, Glasgow G12 8RZ, UK; (G.H.E.); (A.R.); (S.R.)
| | | | - Alison H. Hughes
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK; (S.S.); (A.H.H.)
| | - Simon Rogers
- School of Computing Science, University of Glasgow, Glasgow G12 8RZ, UK; (G.H.E.); (A.R.); (S.R.)
| | - Katherine R. Duncan
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK; (S.S.); (A.H.H.)
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13
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Chanadech S, Ruen-Ngam D, Intaraudom C, Pittayakhajonwut P, Chongruchiroj S, Pratuangdejkul J, Thawai C. Isolation of manumycin-type derivatives and genome characterization of a marine Streptomyces sp. C1-2. Res Microbiol 2021; 172:103812. [PMID: 33497762 DOI: 10.1016/j.resmic.2021.103812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 01/04/2021] [Accepted: 01/15/2021] [Indexed: 11/18/2022]
Abstract
A marine actinomycete strain C1-2 was taxonomically characterized as the genus Streptomyces, based on whole-genome sequence analysis. The highest average nucleotide identity (ANI) value (98.96%) and digital DNA-DNA hybridization (DDH) value (90.4%) were observed between Streptomyces sp. C1-2 and Streptomyces griseoaurantiacus. Thus, Streptomyces sp. C1-2 could be identified as S. griseoaurantiacus. Genome analysis revealed that Streptomyces sp. C1-2 contained 22 biosynthetic gene clusters (BGCs) for secondary metabolites, where among them, 54% have low similarities with known BGCs. The chemical investigation led to the isolation of three new manumycin-type derivatives and two known analog antibiotics named SW-B and cornifronin B. All compounds showed antioxidant activity with the half-maximal inhibitory concentration (IC50) values in a range of 50.82 ± 0.8-112.04 ± 1.0 μg/mL with no cytotoxicity against Vero cells. This is the first report of the antioxidant property of manumycin-type derivatives. Moreover, two known compounds exhibited antifungal activity against Phytophthora capsici, Fusarium oxysporum f. sp. cucumerinum, and Magnaporthe grisea, with the minimum inhibitory concentration (MIC) values in a range of 125-500 μg/mL.
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Affiliation(s)
- Sakkarn Chanadech
- Department of Biology, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - Duangkamol Ruen-Ngam
- Rattanakosin College for Sustainable Energy and Environment (RCSEE), Rajamangala University of Technology Rattanakosin, Nakhon Pathom, 73170, Thailand
| | - Chakapong Intaraudom
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phaholyothin Road, Klong Luang, Pathum Thani, 12120, Thailand
| | - Pattama Pittayakhajonwut
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phaholyothin Road, Klong Luang, Pathum Thani, 12120, Thailand
| | - Sumet Chongruchiroj
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Phayathai, Bangkok 10400, Thailand
| | - Jaturong Pratuangdejkul
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Phayathai, Bangkok 10400, Thailand
| | - Chitti Thawai
- Department of Biology, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand; Actinobacterial Research Unit, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand.
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14
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Draft Genome Sequence of Terrestrial Streptomyces sp. Strain VITNK9, Isolated from Vellore, Tamil Nadu, India, Exhibiting Antagonistic Activity against Fish Pathogens. Microbiol Resour Announc 2021; 10:10/1/e01282-20. [PMID: 33414310 PMCID: PMC8407733 DOI: 10.1128/mra.01282-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the draft genome sequence of Streptomyces sp. strain VITNK9, isolated from a soil sample collected in Vellore District (12.9165°N, 79.1325°E), Tamil Nadu, India, with an assembly size of 7,920,076 bp and 72.7% GC content.
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15
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Liang L, Haltli B, Marchbank DH, Fischer M, Kirby CW, Correa H, Clark TN, Gray CA, Kerr RG. Discovery of an Isothiazolinone-Containing Antitubercular Natural Product Levesquamide. J Org Chem 2020; 85:6450-6462. [PMID: 32363877 DOI: 10.1021/acs.joc.0c00339] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Antitubercular agent levesquamide is a new polyketide-nonribosomal peptide (PK-NRP) hybrid marine natural product isolated from Streptomyces sp. RKND-216. The structure contains a rare isothiazolinone moiety which has only been reported in collismycin SN. Structure elucidation by NMR spectroscopy was a significant challenge due to a deficiency of protons in this aromatic moiety. Therefore, the genome of Streptomyces sp. RKND-216 was sequenced to identify the levesquamide biosynthetic gene cluster (BGC). Analysis of the BGC provided structural insights and guided stable-isotope labeling experiments, which led to the assignment of the fused pyridine-isothiazolinone moiety. The BGC and the labeling experiments provide further insights into the biosynthetic origin of isothiazolinones. Levesquamide exhibited antimicrobial activity in the microplate alamarBlue assay (MABA) and low oxygen recovery assay (LORA) against Mycobacterium tuberculosis H37Rv with minimum inhibitory concentration (MIC) values of 9.65 and 22.28 μM, respectively. Similar activity was exhibited against rifampicin- and isoniazid-resistant M. tuberculosis strains with MIC values of 9.46 and 9.90 μM, respectively. This result suggests levesquamide has a different mode of action against M. tuberculosis compared to the two first-line antitubercular drugs rifampicin and isoniazid. Furthermore, levesquamide shows no cytotoxicity against the Vero cell line, suggesting it may have a useful therapeutic window.
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Affiliation(s)
| | - Bradley Haltli
- Nautilus Biosciences Croda, 550 University Avenue, Regis and Joan Duffy Research Centre, Charlottetown, PE C1A 4P3, Canada
| | - Douglas H Marchbank
- Nautilus Biosciences Croda, 550 University Avenue, Regis and Joan Duffy Research Centre, Charlottetown, PE C1A 4P3, Canada
| | - Maike Fischer
- Charlottetown Research & Development Centre, Agriculture and Agri-Food Canada, 440 University Avenue, Charlottetown, PE C1A 4N6, Canada
| | - Christopher W Kirby
- Charlottetown Research & Development Centre, Agriculture and Agri-Food Canada, 440 University Avenue, Charlottetown, PE C1A 4N6, Canada
| | - Hebelin Correa
- Nautilus Biosciences Croda, 550 University Avenue, Regis and Joan Duffy Research Centre, Charlottetown, PE C1A 4P3, Canada
| | - Trevor N Clark
- Department of Chemistry, University of New Brunswick, 30 Dineen Drive, Fredericton, NB E3B 5A3, Canada
| | - Christopher A Gray
- Department of Chemistry, University of New Brunswick, 30 Dineen Drive, Fredericton, NB E3B 5A3, Canada.,Department of Biological Sciences, University of New Brunswick, 100 Tucker Park Road, Saint John, NB E2L 4L5, Canada
| | - Russell G Kerr
- Nautilus Biosciences Croda, 550 University Avenue, Regis and Joan Duffy Research Centre, Charlottetown, PE C1A 4P3, Canada
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Strub C, Dieye CAT, Nguyen PA, Constancias F, Durand N, Guendouz S, Pratlong M, Fontana A, Schorr-Galindo S. Transcriptomes of the interaction between Fusarium verticillioides and a Streptomyces strain reveal the fungal defense strategy under the pressure of a potential biocontrol agent. Fungal Biol 2019; 125:78-88. [PMID: 33518208 DOI: 10.1016/j.funbio.2019.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/31/2019] [Accepted: 11/12/2019] [Indexed: 12/17/2022]
Abstract
The actinobacteria Streptomyces sp. AV05 appears to be a potential biocontrol agent (BCA) against mycotoxigenic fungi. It was found to significantly inhibit F. verticillioides growth and mycotoxin production during their co-cultivation. F. verticillioides growth was durably affected while the decrease of the toxin production levels was reversible, suggesting different BCA actions. The study of both transcriptomes brought useful information on the microbial interaction. RNA-seq data indicated that the dual interaction modified genetic expression of both microorganisms as 18.5 % of the genes were differentially expressed for the fungus against 3.8 % for the actinobacteria. Fungal differentially expressed genes (DEGs) were equally up and down regulated while bacterial ones were mainly upregulated. We especially focused the analysis of DEGs on fungal defense reaction to bacterial attack. For example, if this potential BCA implements a strategy of antibiosis with the over expression of 'siderophore-interacting protein' linked to the production of bacteriocins, the fungus in a state of stress is able to adapt its metabolism by up-regulation of amidase. It could correspond to the induction of resistance gene clusters and suggest a detoxification process. Moreover fumonisins-related pathway appears underexpressed in the presence of Streptomyces that explain the reduction of fumonisin accumulation observed.
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Affiliation(s)
- C Strub
- Qualisud, Univ Montpellier, CIRAD, Montpellier SupAgro, Univ d'Avignon, Univ de La Réunion, Montpellier, France
| | - C A T Dieye
- Qualisud, Univ Montpellier, CIRAD, Montpellier SupAgro, Univ d'Avignon, Univ de La Réunion, Montpellier, France
| | - P A Nguyen
- Qualisud, Univ Montpellier, CIRAD, Montpellier SupAgro, Univ d'Avignon, Univ de La Réunion, Montpellier, France
| | - F Constancias
- Qualisud, Univ Montpellier, CIRAD, Montpellier SupAgro, Univ d'Avignon, Univ de La Réunion, Montpellier, France; CIRAD, UMR Qualisud, F-34398, Montpellier, France
| | - N Durand
- Qualisud, Univ Montpellier, CIRAD, Montpellier SupAgro, Univ d'Avignon, Univ de La Réunion, Montpellier, France; CIRAD, UMR Qualisud, F-34398, Montpellier, France
| | - S Guendouz
- MGX, Biocampus Montpellier, CNRS, INSERM, Univ Montpellier, Montpellier, France
| | - M Pratlong
- MGX, Biocampus Montpellier, CNRS, INSERM, Univ Montpellier, Montpellier, France
| | - A Fontana
- Qualisud, Univ Montpellier, CIRAD, Montpellier SupAgro, Univ d'Avignon, Univ de La Réunion, Montpellier, France
| | - S Schorr-Galindo
- Qualisud, Univ Montpellier, CIRAD, Montpellier SupAgro, Univ d'Avignon, Univ de La Réunion, Montpellier, France.
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17
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Highly efficient DSB-free base editing for streptomycetes with CRISPR-BEST. Proc Natl Acad Sci U S A 2019; 116:20366-20375. [PMID: 31548381 PMCID: PMC6789908 DOI: 10.1073/pnas.1913493116] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Although CRISPR-Cas9 tools dramatically simplified the genetic manipulation of actinomycetes, significant concerns of genome instability caused by the DNA double-strand breaks (DSBs) and common off-target effects remain. To address these concerns, we developed CRISPR-BEST, a DSB-free and high-fidelity single-nucleotide–resolution base editing system for streptomycetes and validated its use by determining editing properties and genome-wide off-target effects. Furthermore, our CRISPR-BEST toolkit supports Csy4-based multiplexing to target multiple genes of interest in parallel. We believe that our CRISPR-BEST approach is a significant improvement over existing genetic manipulation methods to engineer streptomycetes, especially for those strains that cannot be genome-edited using normal DSB-based genome editing systems, such as CRISPR-Cas9. Streptomycetes serve as major producers of various pharmacologically and industrially important natural products. Although CRISPR-Cas9 systems have been developed for more robust genetic manipulations, concerns of genome instability caused by the DNA double-strand breaks (DSBs) and the toxicity of Cas9 remain. To overcome these limitations, here we report development of the DSB-free, single-nucleotide–resolution genome editing system CRISPR-BEST (CRISPR-Base Editing SysTem), which comprises a cytidine (CRISPR-cBEST) and an adenosine (CRISPR-aBEST) deaminase-based base editor. Specifically targeted by an sgRNA, CRISPR-cBEST can efficiently convert a C:G base pair to a T:A base pair and CRISPR-aBEST can convert an A:T base pair to a G:C base pair within a window of approximately 7 and 6 nucleotides, respectively. CRISPR-BEST was validated and successfully used in different Streptomyces species. Particularly in nonmodel actinomycete Streptomyces collinus Tü365, CRISPR-cBEST efficiently inactivated the 2 copies of kirN gene that are in the duplicated kirromycin biosynthetic pathways simultaneously by STOP codon introduction. Generating such a knockout mutant repeatedly failed using the conventional DSB-based CRISPR-Cas9. An unbiased, genome-wide off-target evaluation indicates the high fidelity and applicability of CRISPR-BEST. Furthermore, the system supports multiplexed editing with a single plasmid by providing a Csy4-based sgRNA processing machinery. To simplify the protospacer identification process, we also updated the CRISPy-web (https://crispy.secondarymetabolites.org), and now it allows designing sgRNAs specifically for CRISPR-BEST applications.
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18
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Biochemical Characteristics of Microbial Enzymes and Their Significance from Industrial Perspectives. Mol Biotechnol 2019; 61:579-601. [DOI: 10.1007/s12033-019-00187-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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19
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Natural product drug discovery in the genomic era: realities, conjectures, misconceptions, and opportunities. ACTA ACUST UNITED AC 2019; 46:281-299. [DOI: 10.1007/s10295-018-2115-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/20/2018] [Indexed: 12/21/2022]
Abstract
Abstract
Natural product discovery from microorganisms provided important sources for antibiotics, anti-cancer agents, immune-modulators, anthelminthic agents, and insecticides during a span of 50 years starting in the 1940s, then became less productive because of rediscovery issues, low throughput, and lack of relevant new technologies to unveil less abundant or not easily detected drug-like natural products. In the early 2000s, it was observed from genome sequencing that Streptomyces species encode about ten times as many secondary metabolites as predicted from known secondary metabolomes. This gave rise to a new discovery approach—microbial genome mining. As the cost of genome sequencing dropped, the numbers of sequenced bacteria, fungi and archaea expanded dramatically, and bioinformatic methods were developed to rapidly scan whole genomes for the numbers, types, and novelty of secondary metabolite biosynthetic gene clusters. This methodology enabled the identification of microbial taxa gifted for the biosynthesis of drug-like secondary metabolites. As genome sequencing technology progressed, the realities relevant to drug discovery have emerged, the conjectures and misconceptions have been clarified, and opportunities to reinvigorate microbial drug discovery have crystallized. This perspective addresses these critical issues for drug discovery.
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Draft Genome Sequence of the Novonestmycin-Producing Strain Streptomyces sp. Z26, Isolated from Potato Rhizosphere in Morocco. Microbiol Resour Announc 2019; 8:MRA01514-18. [PMID: 30637404 PMCID: PMC6318375 DOI: 10.1128/mra.01514-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 11/26/2018] [Indexed: 11/20/2022] Open
Abstract
Streptomyces sp. strain Z26 exhibited antifungal activity and turned out to be a producer of the secondary metabolites novonestmycin A and B. The 6.5-Mb draft genome gives insight into the complete secondary metabolite production capacity and builds the basis to find and locate the biosynthetic gene cluster encoding the novonestmycins. Streptomyces sp. strain Z26 exhibited antifungal activity and turned out to be a producer of the secondary metabolites novonestmycin A and B. The 6.5-Mb draft genome gives insight into the complete secondary metabolite production capacity and builds the basis to find and locate the biosynthetic gene cluster encoding the novonestmycins.
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21
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Draft Genome Sequence of the Xanthocidin-Producing Strain Streptomyces sp. AcE210, Isolated from a Root Nodule of Alnus glutinosa (L.). Microbiol Resour Announc 2018; 7:MRA01190-18. [PMID: 30533708 PMCID: PMC6256639 DOI: 10.1128/mra.01190-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 09/24/2018] [Indexed: 01/12/2023] Open
Abstract
Streptomyces sp. strain AcE210 exhibited antibacterial activity toward Gram-positive microorganisms and turned out to be a rare producer of the specialized metabolite xanthocidin. Streptomyces sp. strain AcE210 exhibited antibacterial activity toward Gram-positive microorganisms and turned out to be a rare producer of the specialized metabolite xanthocidin. The 10.6-Mb draft genome sequence gives insight into the complete specialized metabolite production capacity and builds the basis to find and locate the biosynthetic gene cluster of xanthocidin.
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22
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Musiol-Kroll EM, Wohlleben W. Acyltransferases as Tools for Polyketide Synthase Engineering. Antibiotics (Basel) 2018; 7:antibiotics7030062. [PMID: 30022008 PMCID: PMC6164871 DOI: 10.3390/antibiotics7030062] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 07/14/2018] [Accepted: 07/16/2018] [Indexed: 12/16/2022] Open
Abstract
Polyketides belong to the most valuable natural products, including diverse bioactive compounds, such as antibiotics, anticancer drugs, antifungal agents, immunosuppressants and others. Their structures are assembled by polyketide synthases (PKSs). Modular PKSs are composed of modules, which involve sets of domains catalysing the stepwise polyketide biosynthesis. The acyltransferase (AT) domains and their “partners”, the acyl carrier proteins (ACPs), thereby play an essential role. The AT loads the building blocks onto the “substrate acceptor”, the ACP. Thus, the AT dictates which building blocks are incorporated into the polyketide structure. The precursor- and occasionally the ACP-specificity of the ATs differ across the polyketide pathways and therefore, the ATs contribute to the structural diversity within this group of complex natural products. Those features make the AT enzymes one of the most promising tools for manipulation of polyketide assembly lines and generation of new polyketide compounds. However, the AT-based PKS engineering is still not straightforward and thus, rational design of functional PKSs requires detailed understanding of the complex machineries. This review summarizes the attempts of PKS engineering by exploiting the AT attributes for the modification of polyketide structures. The article includes 253 references and covers the most relevant literature published until May 2018.
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Affiliation(s)
- Ewa Maria Musiol-Kroll
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
| | - Wolfgang Wohlleben
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
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23
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Becerril A, Álvarez S, Braña AF, Rico S, Díaz M, Santamaría RI, Salas JA, Méndez C. Uncovering production of specialized metabolites by Streptomyces argillaceus: Activation of cryptic biosynthesis gene clusters using nutritional and genetic approaches. PLoS One 2018; 13:e0198145. [PMID: 29795673 PMCID: PMC5993118 DOI: 10.1371/journal.pone.0198145] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/14/2018] [Indexed: 11/22/2022] Open
Abstract
Sequencing of Streptomyces genomes has revealed they harbor a high number of biosynthesis gene cluster (BGC), which uncovered their enormous potentiality to encode specialized metabolites. However, these metabolites are not usually produced under standard laboratory conditions. In this manuscript we report the activation of BGCs for antimycins, carotenoids, germicidins and desferrioxamine compounds in Streptomyces argillaceus, and the identification of the encoded compounds. This was achieved by following different strategies, including changing the growth conditions, heterologous expression of the cluster and inactivating the adpAa or overexpressing the abrC3 global regulatory genes. In addition, three new carotenoid compounds have been identified.
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Affiliation(s)
- Adriana Becerril
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, Oviedo, Spain
- Instituto de Investigación Sanitaria de Asturias (ISPA), Oviedo, Spain
| | - Susana Álvarez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, Oviedo, Spain
| | - Alfredo F. Braña
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, Oviedo, Spain
- Instituto de Investigación Sanitaria de Asturias (ISPA), Oviedo, Spain
| | - Sergio Rico
- Departamento de Microbiología y Genética, Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, Salamanca, Spain
| | - Margarita Díaz
- Departamento de Microbiología y Genética, Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, Salamanca, Spain
| | - Ramón I. Santamaría
- Departamento de Microbiología y Genética, Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, Salamanca, Spain
| | - José A. Salas
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, Oviedo, Spain
- Instituto de Investigación Sanitaria de Asturias (ISPA), Oviedo, Spain
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, Oviedo, Spain
- Instituto de Investigación Sanitaria de Asturias (ISPA), Oviedo, Spain
- * E-mail:
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24
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Palazzotto E, Weber T. Omics and multi-omics approaches to study the biosynthesis of secondary metabolites in microorganisms. Curr Opin Microbiol 2018; 45:109-116. [PMID: 29656009 DOI: 10.1016/j.mib.2018.03.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 03/28/2018] [Accepted: 03/30/2018] [Indexed: 10/17/2022]
Abstract
Natural products produced by microorganisms represent the main source of bioactive molecules. The development of high-throughput (omics) techniques have importantly contributed to the renaissance of new antibiotic discovery increasing our understanding of complex mechanisms controlling the expression of biosynthetic gene clusters (BGCs) encoding secondary metabolites. In this context this review highlights recent progress in the use and integration of 'omics' approaches with focuses on genomics, transcriptomics, proteomics metabolomics meta-omics and combined omics as powerful strategy to discover new antibiotics.
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Affiliation(s)
- Emilia Palazzotto
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs., Lyngby, Denmark
| | - Tilmann Weber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs., Lyngby, Denmark.
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25
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Charousová I, Medo J, Hleba L, Javoreková S. Streptomyces globosus DK15 and Streptomyces ederensis ST13 as new producers of factumycin and tetrangomycin antibiotics. Braz J Microbiol 2018; 49:816-822. [PMID: 29705162 PMCID: PMC6175699 DOI: 10.1016/j.bjm.2017.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 11/17/2017] [Accepted: 12/13/2017] [Indexed: 12/08/2022] Open
Abstract
Fifty seven soil-borne actinomycete strains were assessed for the antibiotic production. Two of the most active isolates, designed as Streptomyces ST-13 and DK-15 exhibited a broad range of antimicrobial activity and therefore they were selected for HPLC fractionation against the most suppressed bacteria Staphylococcus aureus (ST-13) and Chromobacterium violaceum (DK-15). LC/MS analysis of extracts showed the presence of polyketides factumycin (DK15) and tetrangomycin (ST13). The taxonomic position of the antibiotic-producing actinomycetes was determined using a polyphasic approach. Phenotypic characterization and 16S rRNA gene sequence analysis of the isolates matched those described for members of the genus Streptomyces. DK-15 strain exhibited the highest 16S rRNA gene sequence similarity to Streptomyces globosus DSM-40815 (T) and Streptomyces toxytricini DSM-40178 (T) and ST-13 strain to Streptomyces ederensis DSM-40741 (T) and Streptomyces phaeochromogenes DSM-40073 (T). For the proper identification, MALDI-TOF/MS profile of whole-cell proteins led to the identification of S. globosus DK-15 (accession number: KX527570) and S. ederensis ST13 (accession number: KX527568). To our knowledge, there is no report about the production of these antibiotics by S.globosus and S. ederensis, thus isolates DK15 and ST13 identified as S. globosus DK-15 and S.ederensis ST-13 can be considered as new sources of these unique antibacterial metabolites.
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Affiliation(s)
- Ivana Charousová
- Slovak University of Agriculture in Nitra, Faculty of Biotechnology and Food Sciences, Department of Microbiology, Tr. A. Hlinku 2, 949 76, Nitra, Slovak Republic.
| | - Juraj Medo
- Slovak University of Agriculture in Nitra, Faculty of Biotechnology and Food Sciences, Department of Microbiology, Tr. A. Hlinku 2, 949 76, Nitra, Slovak Republic
| | - Lukáš Hleba
- Slovak University of Agriculture in Nitra, Faculty of Biotechnology and Food Sciences, Department of Microbiology, Tr. A. Hlinku 2, 949 76, Nitra, Slovak Republic
| | - Soňa Javoreková
- Slovak University of Agriculture in Nitra, Faculty of Biotechnology and Food Sciences, Department of Microbiology, Tr. A. Hlinku 2, 949 76, Nitra, Slovak Republic
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Undabarrena A, Ugalde JA, Seeger M, Cámara B. -Genomic data mining of the marine actinobacteria Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis. PeerJ 2017; 5:e2912. [PMID: 28229018 PMCID: PMC5312570 DOI: 10.7717/peerj.2912] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/14/2016] [Indexed: 12/25/2022] Open
Abstract
Streptomyces sp. H-KF8 is an actinobacterial strain isolated from marine sediments of a Chilean Patagonian fjord. Morphological characterization together with antibacterial activity was assessed in various culture media, revealing a carbon-source dependent activity mainly against Gram-positive bacteria (S. aureus and L. monocytogenes). Genome mining of this antibacterial-producing bacterium revealed the presence of 26 biosynthetic gene clusters (BGCs) for secondary metabolites, where among them, 81% have low similarities with known BGCs. In addition, a genomic search in Streptomyces sp. H-KF8 unveiled the presence of a wide variety of genetic determinants related to heavy metal resistance (49 genes), oxidative stress (69 genes) and antibiotic resistance (97 genes). This study revealed that the marine-derived Streptomyces sp. H-KF8 bacterium has the capability to tolerate a diverse set of heavy metals such as copper, cobalt, mercury, chromate and nickel; as well as the highly toxic tellurite, a feature first time described for Streptomyces. In addition, Streptomyces sp. H-KF8 possesses a major resistance towards oxidative stress, in comparison to the soil reference strain Streptomyces violaceoruber A3(2). Moreover, Streptomyces sp. H-KF8 showed resistance to 88% of the antibiotics tested, indicating overall, a strong response to several abiotic stressors. The combination of these biological traits confirms the metabolic versatility of Streptomyces sp. H-KF8, a genetically well-prepared microorganism with the ability to confront the dynamics of the fjord-unique marine environment.
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Affiliation(s)
- Agustina Undabarrena
- Departmento de Química & Centro de Biotecnología, Universidad Técnica Federico Santa María , Valparaiso , Chile
| | - Juan A Ugalde
- Centro de Genética y Genómica, Facultad de Medicina Clinica Alemana, Universidad del Desarrollo , Santiago , Chile
| | - Michael Seeger
- Departmento de Química & Centro de Biotecnología, Universidad Técnica Federico Santa María , Valparaiso , Chile
| | - Beatriz Cámara
- Departmento de Química & Centro de Biotecnología, Universidad Técnica Federico Santa María , Valparaiso , Chile
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27
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Molecular beacons to identify gifted microbes for genome mining. J Antibiot (Tokyo) 2017; 70:639-646. [DOI: 10.1038/ja.2017.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/12/2016] [Accepted: 12/26/2016] [Indexed: 12/19/2022]
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Gifted microbes for genome mining and natural product discovery. J Ind Microbiol Biotechnol 2016; 44:573-588. [PMID: 27520548 DOI: 10.1007/s10295-016-1815-x] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 07/30/2016] [Indexed: 10/21/2022]
Abstract
Actinomycetes are historically important sources for secondary metabolites (SMs) with applications in human medicine, animal health, and plant crop protection. It is now clear that actinomycetes and other microorganisms with large genomes have the capacity to produce many more SMs than was anticipated from standard fermentation studies. Indeed ~90 % of SM gene clusters (SMGCs) predicted from genome sequencing are cryptic under conventional fermentation and analytical analyses. Previous studies have suggested that among the actinomycetes with large genomes, some have the coding capacity to produce many more SMs than others, and that strains with the largest genomes tend to be the most gifted. These contentions have been evaluated more quantitatively by antiSMASH 3.0 analyses of microbial genomes, and the results indicate that many actinomycetes with large genomes are gifted for SM production, encoding 20-50 SMGCs, and devoting 0.8-3.0 Mb of coding capacity to SM production. Several Proteobacteria and Firmacutes with large genomes encode 20-30 SMGCs and devote 0.8-1.3 Mb of DNA to SM production, whereas cultured bacteria and archaea with small genomes devote insignificant coding capacity to SM production. Fully sequenced genomes of uncultured bacteria and archaea have small genomes nearly devoid of SMGCs.
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Ziemert N, Alanjary M, Weber T. The evolution of genome mining in microbes - a review. Nat Prod Rep 2016; 33:988-1005. [PMID: 27272205 DOI: 10.1039/c6np00025h] [Citation(s) in RCA: 411] [Impact Index Per Article: 51.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Covering: 2006 to 2016The computational mining of genomes has become an important part in the discovery of novel natural products as drug leads. Thousands of bacterial genome sequences are publically available these days containing an even larger number and diversity of secondary metabolite gene clusters that await linkage to their encoded natural products. With the development of high-throughput sequencing methods and the wealth of DNA data available, a variety of genome mining methods and tools have been developed to guide discovery and characterisation of these compounds. This article reviews the development of these computational approaches during the last decade and shows how the revolution of next generation sequencing methods has led to an evolution of various genome mining approaches, techniques and tools. After a short introduction and brief overview of important milestones, this article will focus on the different approaches of mining genomes for secondary metabolites, from detecting biosynthetic genes to resistance based methods and "evo-mining" strategies including a short evaluation of the impact of the development of genome mining methods and tools on the field of natural products and microbial ecology.
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Affiliation(s)
- Nadine Ziemert
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbiology and Biotechnology, University of Tuebingen, Germany.
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Iftime D, Jasyk M, Kulik A, Imhoff JF, Stegmann E, Wohlleben W, Süssmuth RD, Weber T. Streptocollin, a Type IV Lanthipeptide Produced by Streptomyces collinus Tü 365. Chembiochem 2015; 16:2615-23. [PMID: 26437689 DOI: 10.1002/cbic.201500377] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Indexed: 11/10/2022]
Abstract
Lanthipeptides are ribosomally synthesized and post-translationally modified microbial secondary metabolites. Here, we report the identification and isolation of streptocollin from Streptomyces collinus Tü 365, a new member of class IV lanthipeptides. Insertion of the constitutive ermE* promoter upstream of the lanthipeptide synthetase gene stcL resulted in peptide production. The streptocollin gene cluster was heterologously expressed in S. coelicolor M1146 and M1152 with 3.5- and 5.5-fold increased yields, respectively. The structure and ring topology of streptocollin were determined by high resolution MS/MS analysis. Streptocollin contains four macrocyclic rings, with one lanthionine and three methyllanthionine residues. To the best of our knowledge, this is the first report on the isolation of a class IV lanthipeptide in preparative amounts, and on the successful heterologous expression of a class IV lanthipeptide gene cluster.
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Affiliation(s)
- Dumitrita Iftime
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen, Mikrobiologie/Biotechnologie, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Martin Jasyk
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623, Berlin, Germany
| | - Andreas Kulik
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen, Mikrobiologie/Biotechnologie, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Johannes F Imhoff
- GEOMAR, Helmholtz-Zentrum für Ozeanforschung Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany
| | - Evi Stegmann
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen, Mikrobiologie/Biotechnologie, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany.,Deutsches Zentrum für Infektionsforschung, Partner Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Wolfgang Wohlleben
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen, Mikrobiologie/Biotechnologie, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany.,Deutsches Zentrum für Infektionsforschung, Partner Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Roderich D Süssmuth
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623, Berlin, Germany
| | - Tilmann Weber
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen, Mikrobiologie/Biotechnologie, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany. .,Deutsches Zentrum für Infektionsforschung, Partner Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany. .,The Novo Nordisk foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, 2970, Hørsholm, Denmark.
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