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Rodríguez M, Cuervo L, Prado‐Alonso L, González‐Moreno MS, Olano C, Méndez C. The role of Streptomyces to achieve the United Nations sustainable development goals. Burning questions in searching for new compounds. Microb Biotechnol 2024; 17:e14541. [PMID: 39096299 PMCID: PMC11297445 DOI: 10.1111/1751-7915.14541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 07/08/2024] [Indexed: 08/05/2024] Open
Affiliation(s)
- Miriam Rodríguez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A)Universidad de OviedoOviedoSpain
- Instituto de Investigación Sanitaria de Asturias (ISPA)OviedoSpain
| | - Lorena Cuervo
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A)Universidad de OviedoOviedoSpain
- Instituto de Investigación Sanitaria de Asturias (ISPA)OviedoSpain
| | - Laura Prado‐Alonso
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A)Universidad de OviedoOviedoSpain
- Instituto de Investigación Sanitaria de Asturias (ISPA)OviedoSpain
| | - María Soledad González‐Moreno
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A)Universidad de OviedoOviedoSpain
- Instituto de Investigación Sanitaria de Asturias (ISPA)OviedoSpain
| | - Carlos Olano
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A)Universidad de OviedoOviedoSpain
- Instituto de Investigación Sanitaria de Asturias (ISPA)OviedoSpain
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A)Universidad de OviedoOviedoSpain
- Instituto de Investigación Sanitaria de Asturias (ISPA)OviedoSpain
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Cuervo L, Méndez C, Salas JA, Olano C, Malmierca MG. Volatile communication in Actinobacteria: a language for secondary metabolism regulation. Microb Cell Fact 2024; 23:181. [PMID: 38890640 PMCID: PMC11186294 DOI: 10.1186/s12934-024-02456-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 06/08/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Volatile compounds are key elements in the interaction and communication between organisms at both interspecific and intraspecific levels. In complex bacterial communities, the emission of these fast-acting chemical messengers allows an exchange of information even at a certain distance that can cause different types of responses in the receiving organisms. The changes in secondary metabolism as a consequence of this interaction arouse great interest in the field of searching for bioactive compounds since they can be used as a tool to activate silenced metabolic pathways. Regarding the great metabolic potential that the Actinobacteria group presents in the production of compounds with attractive properties, we evaluated the reply the emitted volatile compounds can generate in other individuals of the same group. RESULTS We recently reported that volatile compounds released by different streptomycete species trigger the modulation of biosynthetic gene clusters in Streptomyces spp. which finally leads to the activation/repression of the production of secondary metabolites in the recipient strains. Here we present the application of this rationale in a broader bacterial community to evaluate volatiles as signaling effectors that drive the activation of biosynthesis of bioactive compounds in other members of the Actinobacteria group. Using cocultures of different actinobacteria (where only the volatile compounds reach the recipient strain) we were able to modify the bacterial secondary metabolism that drives overproduction (e.g., granaticins, actiphenol, chromomycins) and/or de novo production (e.g., collismycins, skyllamycins, cosmomycins) of compounds belonging to different chemical species that present important biological activities. CONCLUSIONS This work shows how the secondary metabolism of different Actinobacteria species can vary significantly when exposed in co-culture to the volatile compounds of other phylum-shared bacteria, these effects being variable depending on strains and culture media. This approach can be applied to the field of new drug discovery to increase the battery of bioactive compounds produced by bacteria that can potentially be used in treatments for humans and animals.
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Affiliation(s)
- Lorena Cuervo
- Department Functional Biology, University of Oviedo, 33006, Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006, Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33006, Oviedo, Spain
| | - Carmen Méndez
- Department Functional Biology, University of Oviedo, 33006, Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006, Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33006, Oviedo, Spain
| | - José A Salas
- Department Functional Biology, University of Oviedo, 33006, Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006, Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33006, Oviedo, Spain
| | - Carlos Olano
- Department Functional Biology, University of Oviedo, 33006, Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006, Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33006, Oviedo, Spain
| | - Mónica G Malmierca
- Department Functional Biology, University of Oviedo, 33006, Oviedo, Spain.
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006, Oviedo, Spain.
- Health Research Institute of Asturias (ISPA), 33006, Oviedo, Spain.
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Olano C, Rodríguez M. Actinomycetes Associated with Arthropods as a Source of New Bioactive Compounds. Curr Issues Mol Biol 2024; 46:3822-3838. [PMID: 38785506 PMCID: PMC11119530 DOI: 10.3390/cimb46050238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/20/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Antimicrobial resistance is one of the main global threats to human health in the 21st century due to the rapid appearance of bacterial resistance and the lack of novel bioactive compounds. Natural products, especially from Actinomycetes, remain the best source to refill the drug industry pipeline. Different strategies have been pursued to increase the chances of discovering new molecules, such as studying underexplored environments like arthropod symbionts, which represent a relevant reservoir for active metabolites. This review summarizes recent research on the identification of bioactive molecules produced by Actinomycetes associated with arthropods' microbiome. The metabolites have been categorized based on their structural properties and host, highlighting that multidisciplinary approaches will be the key to fully understanding this complex relationship.
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Affiliation(s)
- Carlos Olano
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain;
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Miriam Rodríguez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain;
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
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4
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García-Gutiérrez C, Pérez-Victoria I, Montero I, Fernández-De la Hoz J, Malmierca MG, Martín J, Salas JA, Olano C, Reyes F, Méndez C. Unearthing a Cryptic Biosynthetic Gene Cluster for the Piperazic Acid-Bearing Depsipeptide Diperamycin in the Ant-Dweller Streptomyces sp. CS113. Int J Mol Sci 2024; 25:2347. [PMID: 38397022 PMCID: PMC10888640 DOI: 10.3390/ijms25042347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Piperazic acid is a cyclic nonproteinogenic amino acid that contains a hydrazine N-N bond formed by a piperazate synthase (KtzT-like). This amino acid, found in bioactive natural products synthesized by non-ribosomal peptide synthetases (NRPSs), confers conformational constraint to peptides, an important feature for their biological activities. Genome mining of Streptomyces strains has been revealed as a strategy to identify biosynthetic gene clusters (BGCs) for potentially active compounds. Moreover, the isolation of new strains from underexplored habitats or associated with other organisms has allowed to uncover new BGCs for unknown compounds. The in-house "Carlos Sialer (CS)" strain collection consists of seventy-one Streptomyces strains isolated from the cuticle of leaf-cutting ants of the tribe Attini. Genomes from twelve of these strains have been sequenced and mined using bioinformatics tools, highlighting their potential to encode secondary metabolites. In this work, we have screened in silico those genomes, using KtzT as a hook to identify BGCs encoding piperazic acid-containing compounds. This resulted in uncovering the new BGC dpn in Streptomyces sp. CS113, which encodes the biosynthesis of the hybrid polyketide-depsipeptide diperamycin. Analysis of the diperamycin polyketide synthase (PKS) and NRPS reveals their functional similarity to those from the aurantimycin A biosynthetic pathway. Experimental proof linking the dpn BGC to its encoded compound was achieved by determining the growth conditions for the expression of the cluster and by inactivating the NRPS encoding gene dpnS2 and the piperazate synthase gene dpnZ. The identity of diperamycin was confirmed by High-Resolution Mass Spectrometry (HRMS) and Nuclear Magnetic Resonance (NMR) and by analysis of the domain composition of modules from the DpnP PKS and DpnS NRPS. The identification of the dpn BGC expands the number of BGCs that have been confirmed to encode the relatively scarcely represented BGCs for depsipeptides of the azinothricin family of compounds and will facilitate the generation of new-to-nature analogues by combinatorial biosynthesis.
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Affiliation(s)
- Coral García-Gutiérrez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain; (C.G.-G.); (I.M.); (J.F.-D.l.H.); (M.G.M.); (J.A.S.); (C.O.)
- Instituto de Investigación Sanitaria de Asturias (ISPA), 33011 Oviedo, Spain
| | - Ignacio Pérez-Victoria
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, 18016 Granada, Spain; (I.P.-V.); (J.M.); (F.R.)
| | - Ignacio Montero
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain; (C.G.-G.); (I.M.); (J.F.-D.l.H.); (M.G.M.); (J.A.S.); (C.O.)
- Instituto de Investigación Sanitaria de Asturias (ISPA), 33011 Oviedo, Spain
| | - Jorge Fernández-De la Hoz
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain; (C.G.-G.); (I.M.); (J.F.-D.l.H.); (M.G.M.); (J.A.S.); (C.O.)
| | - Mónica G. Malmierca
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain; (C.G.-G.); (I.M.); (J.F.-D.l.H.); (M.G.M.); (J.A.S.); (C.O.)
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, 18016 Granada, Spain; (I.P.-V.); (J.M.); (F.R.)
| | - José A. Salas
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain; (C.G.-G.); (I.M.); (J.F.-D.l.H.); (M.G.M.); (J.A.S.); (C.O.)
- Instituto de Investigación Sanitaria de Asturias (ISPA), 33011 Oviedo, Spain
| | - Carlos Olano
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain; (C.G.-G.); (I.M.); (J.F.-D.l.H.); (M.G.M.); (J.A.S.); (C.O.)
- Instituto de Investigación Sanitaria de Asturias (ISPA), 33011 Oviedo, Spain
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, 18016 Granada, Spain; (I.P.-V.); (J.M.); (F.R.)
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain; (C.G.-G.); (I.M.); (J.F.-D.l.H.); (M.G.M.); (J.A.S.); (C.O.)
- Instituto de Investigación Sanitaria de Asturias (ISPA), 33011 Oviedo, Spain
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Cuervo L, Álvarez-García S, Salas JA, Méndez C, Olano C, Malmierca MG. The Volatile Organic Compounds of Streptomyces spp.: An In-Depth Analysis of Their Antifungal Properties. Microorganisms 2023; 11:1820. [PMID: 37512992 PMCID: PMC10384482 DOI: 10.3390/microorganisms11071820] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
The study of volatile organic compounds (VOCs) has expanded because of the growing need to search for new bioactive compounds that could be used as therapeutic alternatives. These small molecules serve as signals to establish interactions with other nearby organisms in the environment. In this work, we evaluated the antifungal effect of VOCs produced by different Streptomyces spp. This study was performed using VOC chamber devices that allow for the free exchange of VOCs without physical contact between microorganisms or the diffusible compounds they produce. Antifungal activity was tested against Escovopsis weberi, a fungal pathogen that affects ant nest stability, and the results showed that Streptomyces spp. CS014, CS057, CS131, CS147, CS159, CS207, and CS227 inhibit or reduce the fungal growth with their emitted VOCs. A GS-MS analysis of volatiles produced and captured by activated charcoal suggested that these Streptomyces strains synthesize several antifungal VOCs, many of them produced because of the presence of E. weberi, with the accumulation of various VOCs determining the growth inhibition effect.
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Affiliation(s)
- Lorena Cuervo
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), Av. del Hospital Universitario, s/n, 33011 Oviedo, Spain
| | - Samuel Álvarez-García
- Plant Physiology Area, Engineering and Agricultural Sciences Department, Universidad de León, 24009 León, Spain
| | - José A Salas
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), Av. del Hospital Universitario, s/n, 33011 Oviedo, Spain
| | - Carmen Méndez
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), Av. del Hospital Universitario, s/n, 33011 Oviedo, Spain
| | - Carlos Olano
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), Av. del Hospital Universitario, s/n, 33011 Oviedo, Spain
| | - Mónica G Malmierca
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), Av. del Hospital Universitario, s/n, 33011 Oviedo, Spain
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Cuervo L, Malmierca MG, García-Salcedo R, Méndez C, Salas JA, Olano C, Ceniceros A. Co-Expression of Transcriptional Regulators and Housekeeping Genes in Streptomyces spp.: A Strategy to Optimize Metabolite Production. Microorganisms 2023; 11:1585. [PMID: 37375086 DOI: 10.3390/microorganisms11061585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
The search for novel bioactive compounds to overcome resistance to current therapeutics has become of utmost importance. Streptomyces spp. are one of the main sources of bioactive compounds currently used in medicine. In this work, five different global transcriptional regulators and five housekeeping genes, known to induce the activation or overproduction of secondary metabolites in Streptomyces coelicolor, were cloned in two separated constructs and expressed in 12 different strains of Streptomyces spp. from the in-house CS collection. These recombinant plasmids were also inserted into streptomycin and rifampicin resistant Streptomyces strains (mutations known to enhance secondary metabolism in Streptomyces). Different media with diverse carbon and nitrogen sources were selected to assess the strains' metabolite production. Cultures were then extracted with different organic solvents and analysed to search for changes in their production profiles. An overproduction of metabolites already known to be produced by the biosynthesis wild-type strains was observed such as germicidin by CS113, collismycins by CS149 and CS014, or colibrimycins by CS147. Additionally, the activation of some compounds such as alteramides in CS090a pSETxkBMRRH and CS065a pSETxkDCABA or inhibition of the biosynthesis of chromomycins in CS065a in pSETxkDCABA when grown in SM10 was demonstrated. Therefore, these genetic constructs are a relatively simple tool to manipulate Streptomyces metabolism and explore their wide secondary metabolites production potential.
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Affiliation(s)
- Lorena Cuervo
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A.), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - Mónica G Malmierca
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A.), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - Raúl García-Salcedo
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A.), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - Carmen Méndez
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A.), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - José A Salas
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A.), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - Carlos Olano
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A.), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - Ana Ceniceros
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A.), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
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Baranova AA, Alferova VA, Korshun VA, Tyurin AP. Modern Trends in Natural Antibiotic Discovery. Life (Basel) 2023; 13:life13051073. [PMID: 37240718 DOI: 10.3390/life13051073] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/10/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Natural scaffolds remain an important basis for drug development. Therefore, approaches to natural bioactive compound discovery attract significant attention. In this account, we summarize modern and emerging trends in the screening and identification of natural antibiotics. The methods are divided into three large groups: approaches based on microbiology, chemistry, and molecular biology. The scientific potential of the methods is illustrated with the most prominent and recent results.
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Affiliation(s)
- Anna A Baranova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Gause Institute of New Antibiotics, Bolshaya Pirogovskaya 11, 119021 Moscow, Russia
| | - Vera A Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Gause Institute of New Antibiotics, Bolshaya Pirogovskaya 11, 119021 Moscow, Russia
| | - Vladimir A Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Anton P Tyurin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
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Cuervo L, Méndez C, Salas JA, Olano C, Malmierca MG. Volatile Compounds in Actinomycete Communities: A New Tool for Biosynthetic Gene Cluster Activation, Cooperative Growth Promotion, and Drug Discovery. Cells 2022; 11:3510. [PMID: 36359906 PMCID: PMC9655753 DOI: 10.3390/cells11213510] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/30/2022] [Accepted: 11/01/2022] [Indexed: 07/30/2023] Open
Abstract
The increasing appearance of multiresistant pathogens, as well as emerging diseases, has highlighted the need for new strategies to discover natural compounds that can be used as therapeutic alternatives, especially in the genus Streptomyces, which is one of the largest producers of bioactive metabolites. In recent years, the study of volatile compounds (VOCs) has raised interest because of the variety of their biological properties in addition to their involvement in cell communication. In this work, we analyze the implications of VOCs as mediating molecules capable of inducing the activation of biosynthetic pathways of bioactive compounds in surrounding Actinomycetes. For this purpose, several strains of Streptomyces were co-cultured in chamber devices that allowed VOC exchange while avoiding physical contact. In several of those strains, secondary metabolism was activated by VOCs emitted by companion strains, resulting in increased antibiotic production and synthesis of new VOCs. This study shows a novel strategy to exploit the metabolic potential of Actinomycetes as well as emphasizes the importance of studying the interactions between different microorganisms sharing the same ecological niche.
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Affiliation(s)
- Lorena Cuervo
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - Carmen Méndez
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - José A. Salas
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - Carlos Olano
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - Mónica G. Malmierca
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
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Kanoh N. Naturally Occurring Polyene Macrolactams as Pluripotent Stem Molecules: Their Chemistry and Biology, and Efforts toward the Creation of Polyene Macrolactam-based Induced Pluripotent Small Molecules. J SYN ORG CHEM JPN 2022. [DOI: 10.5059/yukigoseikyokaishi.80.817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Naoki Kanoh
- School of Pharmacy and Pharmaceutical Sciences, and Institute of Medicinal Chemistry, Hoshi University
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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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11
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Colibrimycins, novel halogenated hybrid PKS-NRPS compounds produced by Streptomyces sp. CS147. Appl Environ Microbiol 2021; 88:e0183921. [PMID: 34669429 DOI: 10.1128/aem.01839-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The improvement on genome sequencing techniques has brought to light the biosynthetic potential of actinomycetes due to the high number of gene clusters they present compared to the number of known compounds. Genome mining is a recent strategy in the search for novel bioactive compounds, which involves the analysis of sequenced genomes to identify uncharacterized natural product biosynthetic gene clusters, many of which are cryptic or silent under laboratory conditions, and to develop experimental approaches to identify their products. Owing to the importance of halogenation in terms of structural diversity, bioavailability and bioactivity, searching for new halogenated bioactive compounds has become an interesting issue in the field of natural product discovery. Following this purpose, a screening for halogenase coding genes was performed on twelve Streptomyces strains isolated from fungus growing ants of the Attini tribe. Using the bioinformatics tools antiSMASH and BLAST, six halogenase coding genes were identified. Some of these genes were located within biosynthetic gene clusters (BGCs), which were studied by construction of several mutants for the identification of the putative halogenated compounds produced. The comparison of the metabolite production profile of wild type strains and their corresponding mutants by UPLC-UV and HPLC-MS allowed us the identification of a novel family of halogenated compounds in Streptomyces sp. CS147, designated as colibrimycins. Importance Genome mining has proven its usefulness in the search for novel bioactive compounds produced by microorganisms, and halogenases comprise an interesting starting point. In this work, we have identified a new halogenase coding gene, which led to the discovery of novel lipopetide NRPS/PKS-derived natural products, the colibrimycins, produced by Streptomyces sp. CS147, isolated from Attini ant niche. Some colibrimycins display an unusual α-ketoamide moiety in the peptide structure. Although its biosynthetic origin remains unknown, its presence might be related with a hypothetical inhibition of virus proteases and, together with the presence of the halogenase, it represents a feature to be incorporated in the arsenal of structural modifications available for combinatorial biosynthesis.
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Mingyar E, Mühling L, Kulik A, Winkler A, Wibberg D, Kalinowski J, Blin K, Weber T, Wohlleben W, Stegmann E. A Regulator Based "Semi-Targeted" Approach to Activate Silent Biosynthetic Gene Clusters. Int J Mol Sci 2021; 22:ijms22147567. [PMID: 34299187 PMCID: PMC8306873 DOI: 10.3390/ijms22147567] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 12/29/2022] Open
Abstract
By culturing microorganisms under standard laboratory conditions, most biosynthetic gene clusters (BGCs) are not expressed, and thus, the products are not produced. To explore this biosynthetic potential, we developed a novel "semi-targeted" approach focusing on activating "silent" BGCs by concurrently introducing a group of regulator genes into streptomycetes of the Tübingen strain collection. We constructed integrative plasmids containing two classes of regulatory genes under the control of the constitutive promoter ermE*p (cluster situated regulators (CSR) and Streptomyces antibiotic regulatory proteins (SARPs)). These plasmids were introduced into Streptomyces sp. TÜ17, Streptomyces sp. TÜ10 and Streptomyces sp. TÜ102. Introduction of the CSRs-plasmid into strain S. sp. TÜ17 activated the production of mayamycin A. By using the individual regulator genes, we proved that Aur1P, was responsible for the activation. In strain S. sp. TÜ102, the introduction of the SARP-plasmid triggered the production of a chartreusin-like compound. Insertion of the CSRs-plasmid into strain S. sp. TÜ10 resulted in activating the warkmycin-BGC. In both recombinants, activation of the BGCs was only possible through the simultaneous expression of aur1PR3 and griR in S. sp. TÜ102 and aur1P and pntR in of S. sp. TÜ10.
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Affiliation(s)
- Erik Mingyar
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Auf der Morgenstelle 28, 72076 Tübingen, Germany; (E.M.); (L.M.); (A.K.); (W.W.)
- German Center for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Lucas Mühling
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Auf der Morgenstelle 28, 72076 Tübingen, Germany; (E.M.); (L.M.); (A.K.); (W.W.)
| | - Andreas Kulik
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Auf der Morgenstelle 28, 72076 Tübingen, Germany; (E.M.); (L.M.); (A.K.); (W.W.)
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Anika Winkler
- Center for Biotechnology (CeBiTec), Universität Bielefeld, 33615 Bielefeld, Germany; (A.W.); (D.W.); (J.K.)
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Universität Bielefeld, 33615 Bielefeld, Germany; (A.W.); (D.W.); (J.K.)
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Universität Bielefeld, 33615 Bielefeld, Germany; (A.W.); (D.W.); (J.K.)
| | - Kai Blin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark; (K.B.); (T.W.)
| | - Tilmann Weber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark; (K.B.); (T.W.)
| | - Wolfgang Wohlleben
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Auf der Morgenstelle 28, 72076 Tübingen, Germany; (E.M.); (L.M.); (A.K.); (W.W.)
- German Center for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence EXC 2124—Controlling Microbes to Fight Infections, 72076 Tübingen, Germany
| | - Evi Stegmann
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Auf der Morgenstelle 28, 72076 Tübingen, Germany; (E.M.); (L.M.); (A.K.); (W.W.)
- German Center for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Cluster of Excellence EXC 2124—Controlling Microbes to Fight Infections, 72076 Tübingen, Germany
- Correspondence:
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Undabarrena A, Valencia R, Cumsille A, Zamora-Leiva L, Castro-Nallar E, Barona-Gomez F, Cámara B. Rhodococcus comparative genomics reveals a phylogenomic-dependent non-ribosomal peptide synthetase distribution: insights into biosynthetic gene cluster connection to an orphan metabolite. Microb Genom 2021; 7:000621. [PMID: 34241590 PMCID: PMC8477407 DOI: 10.1099/mgen.0.000621] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/04/2021] [Indexed: 01/14/2023] Open
Abstract
Natural products (NPs) are synthesized by biosynthetic gene clusters (BGCs), whose genes are involved in producing one or a family of chemically related metabolites. Advances in comparative genomics have been favourable for exploiting huge amounts of data and discovering previously unknown BGCs. Nonetheless, studying distribution patterns of novel BGCs and elucidating the biosynthesis of orphan metabolites remains a challenge. To fill this knowledge gap, our study developed a pipeline for high-quality comparative genomics for the actinomycete genus Rhodococcus , which is metabolically versatile, yet understudied in terms of NPs, leading to a total of 110 genomes, 1891 BGCs and 717 non-ribosomal peptide synthetases (NRPSs). Phylogenomic inferences showed four major clades retrieved from strains of several ecological habitats. BiG-SCAPE sequence similarity BGC networking revealed 44 unidentified gene cluster families (GCFs) for NRPS, which presented a phylogenomic-dependent evolution pattern, supporting the hypothesis of vertical gene transfer. As a proof of concept, we analysed in-depth one of our marine strains, Rhodococcus sp. H-CA8f, which revealed a unique BGC distribution within its phylogenomic clade, involved in producing a chloramphenicol-related compound. While this BGC is part of the most abundant and widely distributed NRPS GCF, corason analysis unveiled major differences regarding its genetic context, co-occurrence patterns and modularity. This BGC is composed of three sections, two well-conserved right/left arms flanking a very variable middle section, composed of nrps genes. The presence of two non-canonical domains in H-CA8f’s BGC may contribute to adding chemical diversity to this family of NPs. Liquid chromatography-high resolution MS and dereplication efforts retrieved a set of related orphan metabolites, the corynecins, which to our knowledge are reported here for the first time in Rhodococcus . Overall, our data provide insights to connect BGC uniqueness with orphan metabolites, by revealing key comparative genomic features supported by models of BGC distribution along phylogeny.
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Affiliation(s)
- Agustina Undabarrena
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química y Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso 2340000, Chile
| | - Ricardo Valencia
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química y Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso 2340000, Chile
- Present address: Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, King’s Buildings, Edinburgh, UK
| | - Andrés Cumsille
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química y Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso 2340000, Chile
| | - Leonardo Zamora-Leiva
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química y Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso 2340000, Chile
| | - Eduardo Castro-Nallar
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Francisco Barona-Gomez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav, Irapuato, Guanajuato, Mexico
| | - Beatriz Cámara
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química y Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso 2340000, Chile
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14
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Botas A, Eitel M, Schwarz PN, Buchmann A, Costales P, Núñez LE, Cortés J, Morís F, Krawiec M, Wolański M, Gust B, Rodriguez M, Fischer W, Jandeleit B, Zakrzewska‐Czerwińska J, Wohlleben W, Stegmann E, Koch P, Méndez C, Gross H. Genetic Engineering in Combination with Semi‐Synthesis Leads to a New Route for Gram‐Scale Production of the Immunosuppressive Natural Product Brasilicardin A. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Alma Botas
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias Universidad de Oviedo and Instituto de Investigación Sanitaria de Asturias (ISPA) c/ Julián Clavería s/n. 33006 Oviedo Spain
| | - Michael Eitel
- Department of Pharmaceutical Chemistry Institute of Pharmaceutical Sciences University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Paul N. Schwarz
- Department of Microbiology and Biotechnology Interfaculty Institute of Microbiology and Infection Medicine University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
| | - Anina Buchmann
- Department of Pharmaceutical Biology Institute of Pharmaceutical Sciences University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Paula Costales
- EntreChem S.L. Vivero Ciencias de la Salud c/ Colegio Santo Domingo de Guzmán, s/n 33011 Oviedo Spain
| | - Luz Elena Núñez
- EntreChem S.L. Vivero Ciencias de la Salud c/ Colegio Santo Domingo de Guzmán, s/n 33011 Oviedo Spain
| | - Jesús Cortés
- EntreChem S.L. Vivero Ciencias de la Salud c/ Colegio Santo Domingo de Guzmán, s/n 33011 Oviedo Spain
| | - Francisco Morís
- EntreChem S.L. Vivero Ciencias de la Salud c/ Colegio Santo Domingo de Guzmán, s/n 33011 Oviedo Spain
| | - Michał Krawiec
- Department of Molecular Microbiology Faculty of Biotechnology University of Wrocław ul. F. Joliot-Curie 14A 50-383 Wrocław Poland
| | - Marcin Wolański
- Department of Molecular Microbiology Faculty of Biotechnology University of Wrocław ul. F. Joliot-Curie 14A 50-383 Wrocław Poland
| | - Bertolt Gust
- Department of Pharmaceutical Biology Institute of Pharmaceutical Sciences University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Mirna Rodriguez
- Quadriga BioSciences, Inc. 339 S. San Antonio Road, Suite 2A Los Altos CA 94022 USA
| | - Wolf‐Nicolas Fischer
- Quadriga BioSciences, Inc. 339 S. San Antonio Road, Suite 2A Los Altos CA 94022 USA
| | - Bernd Jandeleit
- Quadriga BioSciences, Inc. 339 S. San Antonio Road, Suite 2A Los Altos CA 94022 USA
| | - Jolanta Zakrzewska‐Czerwińska
- Department of Molecular Microbiology Faculty of Biotechnology University of Wrocław ul. F. Joliot-Curie 14A 50-383 Wrocław Poland
| | - Wolfgang Wohlleben
- Department of Microbiology and Biotechnology Interfaculty Institute of Microbiology and Infection Medicine University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
| | - Evi Stegmann
- Department of Microbiology and Biotechnology Interfaculty Institute of Microbiology and Infection Medicine University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
| | - Pierre Koch
- Department of Pharmaceutical Chemistry Institute of Pharmaceutical Sciences University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias Universidad de Oviedo and Instituto de Investigación Sanitaria de Asturias (ISPA) c/ Julián Clavería s/n. 33006 Oviedo Spain
| | - Harald Gross
- Department of Pharmaceutical Biology Institute of Pharmaceutical Sciences University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
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15
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Botas A, Eitel M, Schwarz PN, Buchmann A, Costales P, Núñez LE, Cortés J, Morís F, Krawiec M, Wolański M, Gust B, Rodriguez M, Fischer W, Jandeleit B, Zakrzewska‐Czerwińska J, Wohlleben W, Stegmann E, Koch P, Méndez C, Gross H. Genetic Engineering in Combination with Semi-Synthesis Leads to a New Route for Gram-Scale Production of the Immunosuppressive Natural Product Brasilicardin A. Angew Chem Int Ed Engl 2021; 60:13536-13541. [PMID: 33768597 PMCID: PMC8251711 DOI: 10.1002/anie.202015852] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/28/2021] [Indexed: 01/01/2023]
Abstract
Brasilicardin A (1) consists of an unusual anti/syn/anti-perhydrophenanthrene skeleton with a carbohydrate side chain and an amino acid moiety. It exhibits potent immunosuppressive activity, yet its mode of action differs from standard drugs that are currently in use. Further pre-clinical evaluation of this promising, biologically active natural product is hampered by restricted access to the ready material, as its synthesis requires both a low-yielding fermentation process using a pathogenic organism and an elaborate, multi-step total synthesis. Our semi-synthetic approach included a) the heterologous expression of the brasilicardin A gene cluster in different non-pathogenic bacterial strains producing brasilicardin A aglycone (5) in excellent yield and b) the chemical transformation of the aglycone 5 into the trifluoroacetic acid salt of brasilicardin A (1 a) via a short and straightforward five-steps synthetic route. Additionally, we report the first preclinical data for brasilicardin A.
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Affiliation(s)
- Alma Botas
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de AsturiasUniversidad de Oviedo and Instituto de Investigación Sanitaria de Asturias (ISPA)c/ Julián Clavería s/n.33006OviedoSpain
| | - Michael Eitel
- Department of Pharmaceutical ChemistryInstitute of Pharmaceutical SciencesUniversity of TübingenAuf der Morgenstelle 872076TübingenGermany
| | - Paul N. Schwarz
- Department of Microbiology and BiotechnologyInterfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenAuf der Morgenstelle 2872076TübingenGermany
| | - Anina Buchmann
- Department of Pharmaceutical BiologyInstitute of Pharmaceutical SciencesUniversity of TübingenAuf der Morgenstelle 872076TübingenGermany
| | - Paula Costales
- EntreChem S.L.Vivero Ciencias de la Saludc/ Colegio Santo Domingo de Guzmán, s/n33011OviedoSpain
| | - Luz Elena Núñez
- EntreChem S.L.Vivero Ciencias de la Saludc/ Colegio Santo Domingo de Guzmán, s/n33011OviedoSpain
| | - Jesús Cortés
- EntreChem S.L.Vivero Ciencias de la Saludc/ Colegio Santo Domingo de Guzmán, s/n33011OviedoSpain
| | - Francisco Morís
- EntreChem S.L.Vivero Ciencias de la Saludc/ Colegio Santo Domingo de Guzmán, s/n33011OviedoSpain
| | - Michał Krawiec
- Department of Molecular MicrobiologyFaculty of BiotechnologyUniversity of Wrocławul. F. Joliot-Curie 14A50-383WrocławPoland
| | - Marcin Wolański
- Department of Molecular MicrobiologyFaculty of BiotechnologyUniversity of Wrocławul. F. Joliot-Curie 14A50-383WrocławPoland
| | - Bertolt Gust
- Department of Pharmaceutical BiologyInstitute of Pharmaceutical SciencesUniversity of TübingenAuf der Morgenstelle 872076TübingenGermany
| | - Mirna Rodriguez
- Quadriga BioSciences, Inc.339 S. San Antonio Road, Suite 2ALos AltosCA94022USA
| | | | - Bernd Jandeleit
- Quadriga BioSciences, Inc.339 S. San Antonio Road, Suite 2ALos AltosCA94022USA
| | - Jolanta Zakrzewska‐Czerwińska
- Department of Molecular MicrobiologyFaculty of BiotechnologyUniversity of Wrocławul. F. Joliot-Curie 14A50-383WrocławPoland
| | - Wolfgang Wohlleben
- Department of Microbiology and BiotechnologyInterfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenAuf der Morgenstelle 2872076TübingenGermany
| | - Evi Stegmann
- Department of Microbiology and BiotechnologyInterfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenAuf der Morgenstelle 2872076TübingenGermany
| | - Pierre Koch
- Department of Pharmaceutical ChemistryInstitute of Pharmaceutical SciencesUniversity of TübingenAuf der Morgenstelle 872076TübingenGermany
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de AsturiasUniversidad de Oviedo and Instituto de Investigación Sanitaria de Asturias (ISPA)c/ Julián Clavería s/n.33006OviedoSpain
| | - Harald Gross
- Department of Pharmaceutical BiologyInstitute of Pharmaceutical SciencesUniversity of TübingenAuf der Morgenstelle 872076TübingenGermany
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Alvarez R, de Lera AR. Natural polyenic macrolactams and polycyclic derivatives generated by transannular pericyclic reactions: optimized biogenesis challenging chemical synthesis. Nat Prod Rep 2020; 38:1136-1220. [PMID: 33283831 DOI: 10.1039/d0np00050g] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Covering from 1992 to the end of 2020-11-20.Genetically-encoded polyenic macrolactams, which are constructed by Nature using hybrid polyketide synthase/nonribosomal peptide synthase (PKSs/NRPSs) assembly lines, are part of the large collection of natural products isolated from bacteria. Activation of cryptic (i.e., silent) gene clusters in these microorganisms has more recently allowed to generate and eventually isolate additional members of the family. Having two unsaturated fragments separated by short saturated chains, the primary macrolactam is posited to undergo transannular reactions and further rearrangements thus leading to the generation of a structurally diverse collection of polycyclic (natural) products and oxidized derivatives. The review will cover the challenges that scientists face on the isolation of these unstable compounds from the cultures of the producing microorganisms, their structural characterization, biological activities, optimized biogenetic routes, as well as the skeletal rearrangements of the primary structures of the natural macrolactams derived from pericyclic reactions of the polyenic fragments. The efforts of the synthetic chemists to emulate Nature on the successful generation and structural confirmation of these natural products will also be reported.
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Affiliation(s)
- Rosana Alvarez
- Department of Organic Chemistry and Center for Biomedical Research (CINBIO), IBIV, Universidade de Vigo, 36310 Vigo, Spain.
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Matroodi S, Siitonen V, Baral B, Yamada K, Akhgari A, Metsä-Ketelä M. Genotyping-Guided Discovery of Persiamycin A From Sponge-Associated Halophilic Streptomonospora sp. PA3. Front Microbiol 2020; 11:1237. [PMID: 32582127 PMCID: PMC7296137 DOI: 10.3389/fmicb.2020.01237] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/14/2020] [Indexed: 12/16/2022] Open
Abstract
Microbial natural products have been a cornerstone of the pharmaceutical industry, but the supply of novel bioactive secondary metabolites has diminished due to extensive exploration of the most easily accessible sources, namely terrestrial Streptomyces species. The Persian Gulf is a unique habitat for marine sponges, which contain diverse communities of microorganisms including marine Actinobacteria. These exotic ecosystems may cradle rare actinomycetes with high potential to produce novel secondary metabolites. In this study, we harvested 12 different species of sponges from two locations in the Persian Gulf and isolated 45 symbiotic actinomycetes to assess their biodiversity and sponge-microbe relationships. The isolates were classified into Nocardiopsis (24 isolates), Streptomyces (17 isolates) and rare genera (4 isolates) by 16S rRNA sequencing. Antibiotic activity tests revealed that culture extracts from half of the isolates displayed growth inhibitory effects against seven pathogenic bacteria. Next, we identified five strains with the genetic potential to produce aromatic polyketides by genotyping ketosynthase genes responsible for synthesis of carbon scaffolds. The combined data led us to focus on Streptomonospora sp. PA3, since the genus has rarely been examined for its capacity to produce secondary metabolites. Analysis of culture extracts led to the discovery of a new bioactive aromatic polyketide denoted persiamycin A and 1-hydroxy-4-methoxy-2-naphthoic acid. The genome harbored seven gene clusters involved in secondary metabolism, including a tetracenomycin-type polyketide synthase pathway likely involved in persiamycin formation. The work demonstrates the use of multivariate data and underexplored ecological niches to guide the drug discovery process for antibiotics and anticancer agents.
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Affiliation(s)
- Soheila Matroodi
- Laboratory of Biotechnology, Department of Marine Biology, Faculty of Marine Science and Oceanography, Khorramshahr University of Marine Science and Technology, Khorramshahr, Iran
- Laboratory of Antibiotic Biosynthesis Engineering, Department of Biochemistry, University of Turku, Turku, Finland
| | - Vilja Siitonen
- Laboratory of Antibiotic Biosynthesis Engineering, Department of Biochemistry, University of Turku, Turku, Finland
| | - Bikash Baral
- Laboratory of Antibiotic Biosynthesis Engineering, Department of Biochemistry, University of Turku, Turku, Finland
| | - Keith Yamada
- Laboratory of Antibiotic Biosynthesis Engineering, Department of Biochemistry, University of Turku, Turku, Finland
| | - Amir Akhgari
- Laboratory of Antibiotic Biosynthesis Engineering, Department of Biochemistry, University of Turku, Turku, Finland
| | - Mikko Metsä-Ketelä
- Laboratory of Antibiotic Biosynthesis Engineering, Department of Biochemistry, University of Turku, Turku, Finland
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19
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Generation of incednine derivatives by mutasynthesis. J Antibiot (Tokyo) 2020; 73:794-797. [DOI: 10.1038/s41429-020-0329-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 04/19/2020] [Accepted: 05/14/2020] [Indexed: 11/09/2022]
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New Sipanmycin Analogues Generated by Combinatorial Biosynthesis and Mutasynthesis Approaches Relying on the Substrate Flexibility of Key Enzymes in the Biosynthetic Pathway. Appl Environ Microbiol 2020; 86:AEM.02453-19. [PMID: 31732573 DOI: 10.1128/aem.02453-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 11/08/2019] [Indexed: 12/12/2022] Open
Abstract
The appearance of new infectious diseases, the increase in multidrug-resistant bacteria, and the need for more effective chemotherapeutic agents have oriented the interests of researchers toward the search for metabolites with novel or improved bioactivities. Sipanmycins are disaccharyl glycosylated macrolactams that exert antibiotic and cytotoxic activities. By applying combinatorial biosynthesis and mutasynthesis approaches, we have generated eight new members of the sipanmycin family. The introduction of plasmids harboring genes responsible for the biosynthesis of several deoxysugars into sipanmycin-producing Streptomyces sp. strain CS149 led to the production of six derivatives with altered glycosylation patterns. After structural elucidation of these new metabolites, we conclude that some of these sugars are the result of the combination of the enzymatic machinery encoded by the introduced plasmids and the native enzymes of the d-sipanose biosynthetic pathway of the wild-type CS149 strain. In addition, two analogues of the parental compounds with a modified polyketide backbone were generated by a mutasynthesis approach, feeding cultures of a mutant strain defective in sipanmycin biosynthesis with 3-aminopentanoic acid. The generation of new sipanmycin analogues shown in this work relied on the substrate flexibility of key enzymes involved in sipanmycin biosynthesis, particularly the glycosyltransferase pair SipS9/SipS14 and enzymes SipL3, SipL1, SipL7, and SipL2, which are involved in the incorporation of the polyketide synthase starting unit.IMPORTANCE Combinatorial biosynthesis has proved its usefulness in generating derivatives of already known compounds with novel or improved pharmacological properties. Sipanmycins are a family of glycosylated macrolactams produced by Streptomyces sp. strain CS149, whose antiproliferative activity is dependent on the sugar moieties attached to the aglycone. In this work, we report the generation of several sipanmycin analogues with different deoxysugars, showing the high degree of flexibility exerted by the glycosyltransferase machinery with respect to the recognition of diverse nucleotide-activated sugars. In addition, modifications in the macrolactam ring were introduced by mutasynthesis approaches, indicating that the enzymes involved in incorporating the starter unit have a moderate ability to introduce different types of β-amino acids. In conclusion, we have proved the substrate flexibility of key enzymes involved in sipanmycin biosynthesis, especially the glycosyltransferases, which can be exploited in future experiments.
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Abstract
The Mycobacterium sp. BRS2A-AR2 is an endophyte of the mangrove plant Rhizophora racemosa G. Mey., which grows along the banks of the River Butre, in the Western Region of Ghana. Chemical profiling using 1H-NMR and HRESI-LC-MS of fermentation extracts produced by the strain led to the isolation of the new compound, α-d-Glucopyranosyl-(1→2)-[6-O-(l-tryptophanyl)-β-d–fructofuranoside] or simply tortomycoglycoside (1). Compound 1 is an aminoglycoside consisting of a tryptophan moiety esterified to a disaccharide made up of β-d-fructofuranose and α-d-glucopyranose sugars. The full structure of 1 was determined using UV, IR, 1D, 2D-NMR and HRESI-LC-MS data. When tested against Trypanosoma brucei subsp. brucei, the parasite responsible for Human African Trypanosomiasis in sub-Saharan Africa, 1 (IC50 11.25 µM) was just as effective as Coptis japonica (Thunb.) Makino. (IC50 8.20 µM). The extract of Coptis japonica (Thunb.) Makino. is routinely used as laboratory standard due to its powerful antitrypanosomal activity. It is possible that, compound 1 interferes with the normal uptake and metabolism of tryptophan in the T. brucei subsp. brucei parasite.
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Cooperative Involvement of Glycosyltransferases in the Transfer of Amino Sugars during the Biosynthesis of the Macrolactam Sipanmycin by Streptomyces sp. Strain CS149. Appl Environ Microbiol 2018; 84:AEM.01462-18. [PMID: 30006405 DOI: 10.1128/aem.01462-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 07/11/2018] [Indexed: 12/22/2022] Open
Abstract
Macrolactams comprise a family of natural compounds with important bioactivities, such as antibiotic, antifungal, and antiproliferative activities. Sipanmycins A and B are two novel members of this family, with two sugar moieties attached to the aglycon. In the related macrolactam vicenistatin, the sugar moiety has been proven to be essential for cytotoxicity. In this work, the gene cluster responsible for the biosynthesis of sipanmycins (sip cluster) in Streptomyces sp. strain CS149 is described and the steps involved in the glycosylation of the final compounds unraveled. Also, the cooperation of two different glycosyltransferases in each glycosylation step is demonstrated. Additionally, the essential role of SipO2 as an auxiliary protein in the incorporation of the second deoxy sugar is addressed. In light of the results obtained by the generation of mutant strains and in silico characterization of the sip cluster, a biosynthetic pathway for sipanmycins and the two deoxy sugars attached is proposed. Finally, the importance of the hydroxyl group at C-10 of the macrolactam ring and the sugar moieties for cytotoxicity and antibiotic activity of sipanmycins is shown.IMPORTANCE The rapid emergence of infectious diseases and multiresistant pathogens has increased the necessity for new bioactive compounds; thus, novel strategies have to be developed to find them. Actinomycetes isolated in symbiosis with insects have attracted attention in recent years as producers of metabolites with important bioactivities. Sipanmycins are glycosylated macrolactams produced by Streptomyces sp. CS149, isolated from leaf-cutting ants, and show potent cytotoxic activity. Here, we characterize the sip cluster and propose a biosynthetic pathway for sipanmycins. As far as we know, it is the first time that the cooperation between two different glycosyltransferases is demonstrated to be strictly necessary for the incorporation of the same sugar. Also, a third protein with homology to P450 monooxygenases, SipO2, is shown to be essential in the second glycosylation step, forming a complex with the glycosyltransferase pair SipS9-SipS14.
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(-)-Shikimic Acid as a Chiral Building Block for the Synthesis of New Cytotoxic 6-Aza-Analogues of Angucyclinones. Molecules 2018; 23:molecules23061422. [PMID: 29895756 PMCID: PMC6099682 DOI: 10.3390/molecules23061422] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 06/09/2018] [Accepted: 06/10/2018] [Indexed: 01/28/2023] Open
Abstract
We describe the syntheses of nine new angucyclinone 6-aza-analogues, achieved through a hetero Diels-Alder reaction between the shikimic acid derivative-azadiene 13, with different naphthoquinones. The cytotoxic activity of the new synthesized compounds and five angucyclinones, previously reported, was evaluated in vitro against three cancer cell lines: PC-3 (prostate cancer), HT-29 (colon cancer), MCF-7 (breast cancer), and one non-tumoral cell line, human colon epithelial cells (CCD841 CoN). Our results showed that most 6-azadiene derivatives exhibited significant cytotoxic activities, which was demonstrated by their IC50 values (less than 10 μM), especially for the most sensitive cells, PC-3 and HT-29. From a chemical point of view, depending on the protected group of ring A and the pattern of substitution on ring D, cytotoxicity elicited these compounds, in terms of their potency and selectivity. Therefore, according to these chemical features, the most promising agents for every cancer cell line were 7a, 17, and 19c for PC-3 cells; 7a, 17, and 20 for HT-29 cells, and 19a for MCF-7 cells.
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