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Boruta T, Antecka A. Co-cultivation of filamentous microorganisms in the presence of aluminum oxide microparticles. Appl Microbiol Biotechnol 2022; 106:5459-5477. [PMID: 35906994 PMCID: PMC9418094 DOI: 10.1007/s00253-022-12087-7] [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: 06/24/2022] [Revised: 06/24/2022] [Accepted: 07/19/2022] [Indexed: 11/22/2022]
Abstract
In the present work, the approaches of submerged co-cultivation and microparticle-enhanced cultivation (MPEC) were combined and evaluated over the course of three case studies. The filamentous fungus Aspergillus terreus was co-cultivated with Penicillium rubens, Streptomyces rimosus, or Cerrena unicolor in shake flasks with or without the addition of aluminum oxide microparticles. The influence of microparticles on the production of lovastatin, penicillin G, oxytetracycline, and laccase in co-cultures was compared with the effects recorded for the corresponding monocultures. In addition, the quantitative analyses of morphological parameters, sugars consumption, and by-products formation were performed. The study demonstrated that the influence of microparticles on the production of a given molecule in mono- and co-culture may differ considerably, e.g., the biosynthesis of oxytetracycline was shown to be inhibited due to the presence of aluminum oxide in "A. terreus vs. S. rimosus" co-cultivation variants but not in S. rimosus monocultures. The differences were also observed regarding the morphological characteristics, e.g., the microparticles-induced changes of projected area in the co-cultures and the corresponding monocultures were not always comparable. In addition, the study showed the importance of medium composition on the outcomes of MPEC, as exemplified by lovastatin production in A. terreus monocultures. Finally, the co-cultures of A. terreus with a white-rot fungus C. unicolor were described here for the first time. KEY POINTS: • Aluminum oxide affects secondary metabolites production in submerged co-cultures. • Mono- and co-cultures are differently impacted by the addition of aluminum oxide. • Effect of aluminum oxide on metabolites production depends on medium composition.
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Affiliation(s)
- Tomasz Boruta
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, ul. Wolczanska 213, 93-005, Lodz, Poland.
| | - Anna Antecka
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, ul. Wolczanska 213, 93-005, Lodz, Poland
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2
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Araújo RG, Zavala NR, Castillo-Zacarías C, Barocio ME, Hidalgo-Vázquez E, Parra-Arroyo L, Rodríguez-Hernández JA, Martínez-Prado MA, Sosa-Hernández JE, Martínez-Ruiz M, Chen WN, Barceló D, Iqbal HM, Parra-Saldívar R. Recent Advances in Prodigiosin as a Bioactive Compound in Nanocomposite Applications. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27154982. [PMID: 35956931 PMCID: PMC9370345 DOI: 10.3390/molecules27154982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/23/2022] [Accepted: 07/28/2022] [Indexed: 12/02/2022]
Abstract
Bionanocomposites based on natural bioactive entities have gained importance due to their abundance; renewable and environmentally benign nature; and outstanding properties with applied perspective. Additionally, their formulation with biological molecules with antimicrobial, antioxidant, and anticancer activities has been produced nowadays. The present review details the state of the art and the importance of this pyrrolic compound produced by microorganisms, with interest towards Serratia marcescens, including production strategies at a laboratory level and scale-up to bioreactors. Promising results of its biological activity have been reported to date, and the advances and applications in bionanocomposites are the most recent strategy to potentiate and to obtain new carriers for the transport and controlled release of prodigiosin. Prodigiosin, a bioactive secondary metabolite, produced by Serratia marcescens, is an effective proapoptotic agent against bacterial and fungal strains as well as cancer cell lines. Furthermore, this molecule presents antioxidant activity, which makes it ideal for treating wounds and promoting the general improvement of the immune system. Likewise, some of the characteristics of prodigiosin, such as hydrophobicity, limit its use for medical and biotechnological applications; however, this can be overcome by using it as a component of a bionanocomposite. This review focuses on the chemistry and the structure of the bionanocomposites currently developed using biorenewable resources. Moreover, the work illuminates recent developments in pyrrole-based bionanocomposites, with special insight to its application in the medical area.
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Affiliation(s)
- Rafael G. Araújo
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing Monterrey, Monterrey 64849, Mexico
| | - Natalia Rodríguez Zavala
- Chemical & Biochemical Engineering Department, Tecnológico Nacional de México-Instituto Tecnológico de Durango (TecNM-ITD), Blvd. Felipe Pescador 1830 Ote. Durango, Durango 34080, Mexico
| | - Carlos Castillo-Zacarías
- Universidad Autónoma de Nuevo León, Facultad de Ingeniería Civil, Departamento de Ingeniería Ambiental, Ciudad Universitaria S/N, San Nicolás de los Garza 66455, Mexico
| | - Mario E. Barocio
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | | | - Lizeth Parra-Arroyo
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | | | - María Adriana Martínez-Prado
- Chemical & Biochemical Engineering Department, Tecnológico Nacional de México-Instituto Tecnológico de Durango (TecNM-ITD), Blvd. Felipe Pescador 1830 Ote. Durango, Durango 34080, Mexico
| | - Juan Eduardo Sosa-Hernández
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing Monterrey, Monterrey 64849, Mexico
| | - Manuel Martínez-Ruiz
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing Monterrey, Monterrey 64849, Mexico
| | - Wei Ning Chen
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637457, Singapore
| | - Damià Barceló
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, 08034 Barcelona, Spain
- Catalan Institute for Water Research (ICRA-CERCA), Parc Científic i Tecnològic de la Universitat de Girona, Edifici H2O, 17003 Girona, Spain
- Sustainability Cluster, School of Engineering, UPES, Dehradun 248007, India
| | - Hafiz M.N. Iqbal
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing Monterrey, Monterrey 64849, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
- Correspondence: (H.M.N.I.); (R.P.-S.)
| | - Roberto Parra-Saldívar
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing Monterrey, Monterrey 64849, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
- Correspondence: (H.M.N.I.); (R.P.-S.)
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3
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Boruta T. A bioprocess perspective on the production of secondary metabolites by Streptomyces in submerged co-cultures. World J Microbiol Biotechnol 2021; 37:171. [PMID: 34490503 PMCID: PMC8421279 DOI: 10.1007/s11274-021-03141-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/31/2021] [Indexed: 12/17/2022]
Abstract
Filamentous microorganisms are potent sources of bioactive secondary metabolites, the molecules formed in response to complex environmental signals. The chemical diversity encoded in microbial genomes is only partially revealed by following the standard microbiological approaches. Mimicking the natural stimuli through laboratory co-cultivation is one of the most effective methods of awakening the formation of high-value metabolic products. Whereas the biosynthetic outcomes of co-cultures are reviewed extensively, the bioprocess aspects of such efforts are often overlooked. The aim of the present review is to discuss the submerged co-cultivation strategies used for triggering and enhancing secondary metabolites production in Streptomyces, a heavily investigated bacterial genus exhibiting an impressive repertoire of secondary metabolites, including a vast array of antibiotics. The previously published studies on influencing the biosynthetic capabilities of Streptomyces through co-cultivation are comparatively analyzed in the bioprocess perspective, mainly with the focus on the approaches of co-culture initiation, the experimental setup, the design of experimental controls and the ways of influencing the outcomes of co-cultivation processes. These topics are discussed in the general context of secondary metabolites production in submerged microbial co-cultures by referring to the Streptomyces-related studies as illustrative examples.
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Affiliation(s)
- Tomasz Boruta
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, ul. Wolczanska 213, 90-924, Lodz, Poland.
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4
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Rational engineering strategies for achieving high-yield, high-quality and high-stability of natural product production in actinomycetes. Metab Eng 2021; 67:198-215. [PMID: 34166765 DOI: 10.1016/j.ymben.2021.06.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/30/2021] [Accepted: 06/19/2021] [Indexed: 12/11/2022]
Abstract
Actinomycetes are recognized as excellent producers of microbial natural products, which have a wide range of applications, especially in medicine, agriculture and stockbreeding. The three main indexes of industrialization (titer, purity and stability) must be taken into overall consideration in the manufacturing process of natural products. Over the past decades, synthetic biology techniques have expedited the development of industrially competitive strains with excellent performances. Here, we summarize various rational engineering strategies for upgrading the performance of industrial actinomycetes, which include enhancing the yield of natural products, eliminating the by-products and improving the genetic stability of engineered strains. Furthermore, the current challenges and future perspectives for optimizing the industrial strains more systematically through combinatorial engineering strategies are also discussed.
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Bikash B, Vilja S, Mitchell L, Keith Y, Mikael I, Mikko MK, Jarmo N. Differential regulation of undecylprodigiosin biosynthesis in the yeast-scavenging Streptomyces strain MBK6. FEMS Microbiol Lett 2021; 368:6244240. [PMID: 33881506 PMCID: PMC8102152 DOI: 10.1093/femsle/fnab044] [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: 09/25/2020] [Accepted: 04/19/2021] [Indexed: 12/22/2022] Open
Abstract
Streptomyces are efficient chemists with a capacity to generate diverse and potent chemical scaffolds. The secondary metabolism of these soil-dwelling prokaryotes is stimulated upon interaction with other microbes in their complex ecosystem. We observed such an interaction when a Streptomyces isolate was cultivated in a media supplemented with dead yeast cells. Whole-genome analysis revealed that Streptomyces sp. MBK6 harbors the red cluster that is cryptic under normal environmental conditions. An interactive culture of MBK6 with dead yeast triggered the production of the red pigments metacycloprodigiosin and undecylprodigiosin. Streptomyces sp. MBK6 scavenges dead-yeast cells and preferentially grows in aggregates of sequestered yeasts within its mycelial network. We identified that the activation depends on the cluster-situated regulator, mbkZ, which may act as a cross-regulator. Cloning of this master regulator mbkZ in S. coelicolor with a constitutive promoter and promoter-deprived conditions generated different production levels of the red pigments. These surprising results were further validated by DNA–protein binding assays. The presence of the red cluster in Streptomyces sp. MBK6 provides a vivid example of horizontal gene transfer of an entire metabolic pathway followed by differential adaptation to a new environment through mutations in the receiver domain of the key regulatory protein MbkZ.
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Affiliation(s)
- Baral Bikash
- Department of Biotechnology, University of Turku, FIN-20014 Turku, Finland
| | - Siitonen Vilja
- Department of Biotechnology, University of Turku, FIN-20014 Turku, Finland
| | - Laughlin Mitchell
- Department of Biotechnology, University of Turku, FIN-20014 Turku, Finland
| | - Yamada Keith
- Department of Biotechnology, University of Turku, FIN-20014 Turku, Finland
| | - Ilomäki Mikael
- Department of Biotechnology, University of Turku, FIN-20014 Turku, Finland
| | - Metsä-Ketelä Mikko
- Department of Biotechnology, University of Turku, FIN-20014 Turku, Finland
| | - Niemi Jarmo
- Department of Biotechnology, University of Turku, FIN-20014 Turku, Finland
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Setiyono E, Adhiwibawa MA, Indrawati R, Prihastyanti MNU, Shioi Y, Brotosudarmo THP. An Indonesian Marine Bacterium, Pseudoalteromonas rubra, Produces Antimicrobial Prodiginine Pigments. ACS OMEGA 2020; 5:4626-4635. [PMID: 32175509 PMCID: PMC7066656 DOI: 10.1021/acsomega.9b04322] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/14/2020] [Indexed: 05/19/2023]
Abstract
Red pigmented marine bacteria, Pseudoalteromonas rubra strains PS1 and SB14, were isolated from two sampling locations in different ecosystems on Alor Island, Indonesia, and cultured in the laboratory. We analyzed the 16S rRNA gene sequences and examined the pigment composition and found that both strains produced cycloprodigiosin (3), prodigiosin (4), and 2-methyl-3-hexyl-prodiginine (5) as major compounds. In addition, we detected three minor compounds: prodigiosin derivatives 2-methyl-3-propyl prodiginine (1), 2-methyl-3-butyl prodiginine (2), and 2-methyl-3-heptyl-prodiginine (6). To our knowledge, this is the first report that P. rubra synthesizes not only prodigiosin and cycloprodigiosin but also four prodigiosin derivatives that differ in the length of the alkyl chain. The antimicrobial activity of cycloprodigiosin, prodigiosin, and 2-methyl-3-hexyl-prodiginine was examined by a disk-diffusion test against Escherichia coli, Staphylococcus aureus, Salmonella typhi, and Candida albicans. We found that, at a concentration of 20 μg/mL, cycloprodigiosin showed the greatest inhibition (25.1 ± 0.55 mm) against S. aureus.
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Affiliation(s)
- Edi Setiyono
- Ma Chung Research Center
for Photosynthetic Pigments (MRCPP) and Department of Chemistry, Universitas Ma Chung, Villa Puncak Tidar N01, Malang 65151, Jawa Timur, Indonesia
| | - Marcelinus Alfasisurya
Setya Adhiwibawa
- Ma Chung Research Center
for Photosynthetic Pigments (MRCPP) and Department of Chemistry, Universitas Ma Chung, Villa Puncak Tidar N01, Malang 65151, Jawa Timur, Indonesia
| | - Renny Indrawati
- Ma Chung Research Center
for Photosynthetic Pigments (MRCPP) and Department of Chemistry, Universitas Ma Chung, Villa Puncak Tidar N01, Malang 65151, Jawa Timur, Indonesia
| | - Monika Nur Utami Prihastyanti
- Ma Chung Research Center
for Photosynthetic Pigments (MRCPP) and Department of Chemistry, Universitas Ma Chung, Villa Puncak Tidar N01, Malang 65151, Jawa Timur, Indonesia
| | - Yuzo Shioi
- Ma Chung Research Center
for Photosynthetic Pigments (MRCPP) and Department of Chemistry, Universitas Ma Chung, Villa Puncak Tidar N01, Malang 65151, Jawa Timur, Indonesia
| | - Tatas Hardo Panintingjati Brotosudarmo
- Ma Chung Research Center
for Photosynthetic Pigments (MRCPP) and Department of Chemistry, Universitas Ma Chung, Villa Puncak Tidar N01, Malang 65151, Jawa Timur, Indonesia
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7
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Lee N, Kim W, Chung J, Lee Y, Cho S, Jang KS, Kim SC, Palsson B, Cho BK. Iron competition triggers antibiotic biosynthesis in Streptomyces coelicolor during coculture with Myxococcus xanthus. ISME JOURNAL 2020; 14:1111-1124. [PMID: 31992858 PMCID: PMC7174319 DOI: 10.1038/s41396-020-0594-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 01/09/2020] [Accepted: 01/17/2020] [Indexed: 01/09/2023]
Abstract
Microbial coculture to mimic the ecological habitat has been suggested as an approach to elucidate the effect of microbial interaction on secondary metabolite biosynthesis of Streptomyces. However, because of chemical complexity during coculture, underlying mechanisms are largely unknown. Here, we found that iron competition triggered antibiotic biosynthesis in Streptomyces coelicolor during coculture with Myxococcus xanthus. During coculture, M. xanthus enhanced the production of a siderophore, myxochelin, leading M. xanthus to dominate iron scavenging and S. coelicolor to experience iron-restricted conditions. This chemical competition, but not physical contact, activated the actinorhodin biosynthetic gene cluster and the branched-chain amino acid degradation pathway which imply the potential to produce precursors, along with activation of a novel actinorhodin export system. Furthermore, we found that iron restriction increased the expression of 21 secondary metabolite biosynthetic gene clusters (smBGCs) in other Streptomyces species. These findings suggested that the availability for key ions stimulates specific smBGCs, which had the potential to enhance secondary metabolite biosynthesis in Streptomyces.
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Affiliation(s)
- Namil Lee
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Woori Kim
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Jinkyoo Chung
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Yongjae Lee
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Kyoung-Soon Jang
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea.,Division of Bio-Analytical Science, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Sun Chang Kim
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,Intelligent Synthetic Biology Center, Daejeon, 34141, Republic of Korea
| | - Bernhard Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, 2800, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea. .,Intelligent Synthetic Biology Center, Daejeon, 34141, Republic of Korea. .,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, 2800, Denmark.
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8
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Martín JF, Liras P. Harnessing microbiota interactions to produce bioactive metabolites: communication signals and receptor proteins. Curr Opin Pharmacol 2019; 48:8-16. [PMID: 30933876 DOI: 10.1016/j.coph.2019.02.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/23/2019] [Accepted: 02/27/2019] [Indexed: 11/30/2022]
Abstract
Numerous microbial communities live in soil, aquatic habitats, plants, and animal bodies. Microbial genome sequences have revealed that thousands of biosynthetic gene clusters (BGCs) are present in different bacteria and filamentous fungi. Many of these BGCs are not expressed in pure cultures in the laboratory. However, a large part of these silent clusters is expressed in nature when complex microbial populations are studied. The encoding specialized metabolites are frequently produced at very low concentrations but still they serve as communication signals that produce important biochemical and differentiation effects on other microorganisms of the consortium. Many specialized metabolites acting as communication signals have been identified, including autoinducers, intergeneric, and interkingdom cues. These signals trigger expression of silent BGCs in other microorganisms, thus providing new compounds with interesting biological and pharmacological activities. Examples of interactions between different bacteria or between bacteria and fungi are described here. Finally, the relevance of the human microbiota and the production in vivo of specialized metabolites of medical interest is discussed.
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Affiliation(s)
- Juan F Martín
- Department of Molecular Biology, Section Microbiology, University of León, 24071 León, Spain.
| | - Paloma Liras
- Department of Molecular Biology, Section Microbiology, University of León, 24071 León, Spain
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9
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Tenconi E, Traxler MF, Hoebreck C, van Wezel GP, Rigali S. Production of Prodiginines Is Part of a Programmed Cell Death Process in Streptomyces coelicolor. Front Microbiol 2018; 9:1742. [PMID: 30127771 PMCID: PMC6087738 DOI: 10.3389/fmicb.2018.01742] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 07/12/2018] [Indexed: 12/24/2022] Open
Abstract
Actinobacteria are prolific producers of antitumor antibiotics with antiproliferative activity, but why these bacteria synthetize metabolites with this bioactivity has so far remained a mystery. In this work we raised the hypothesis that under certain circumstances, production of antiproliferative agents could be part of a genetically programmed death of the producing organism. While programmed cell death (PCD) has been well documented when Streptomyces species switch from vegetative (nutrition) to aerial (reproduction) growth, lethal determinants are yet to be discovered. Using DNA-damaging prodiginines of Streptomyces coelicolor as model system, we revealed that, under certain conditions, their biosynthesis is always triggered in the dying zone of the mycelial network prior to morphological differentiation, right after an initial round of cell death. The programmed massive death round of the vegetative mycelium is absent in a prodiginine non-producer (ΔredD strain), and mutant complementation restored both prodiginine production and cell death. The redD null mutant of S. coelicolor also showed increased DNA, RNA, and proteins synthesis when most of the mycelium of the wild-type strain was dead when prodiginines accumulated. Moreover, addition of the prodiginine synthesis inhibitors also resulted in enhanced accumulation of viable filaments. Overall, our data enable us to propose a model where the time-space production of prodiginines is programmed to be triggered by the perception of dead cells, and their biosynthesis further amplifies the PCD process. As prodiginine production coincides with the moment S. coelicolor undergoes morphogenesis, the production of these lethal compounds might be used to eradicate the obsolete part of the population in order to provide nutrients for development of the survivors. Hence, next to weapons in competition between organisms or signals in inter- and intra-species communications, we propose a third role for antibiotics (in the literal meaning of the word ‘against life’) i.e., elements involved in self-toxicity in order to control cell proliferation, and/or for PCD associated with developmental processes.
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Affiliation(s)
- Elodie Tenconi
- InBioS - Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, Liège, Belgium
| | - Matthew F Traxler
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Charline Hoebreck
- InBioS - Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, Liège, Belgium
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Sébastien Rigali
- InBioS - Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, Liège, Belgium
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Abstract
Covering: 2010 up to 2017Life on Earth is characterized by a remarkable abundance of symbiotic and highly refined relationships among life forms. Defined as any kind of close, long-term association between two organisms, symbioses can be mutualistic, commensalistic or parasitic. Historically speaking, selective pressures have shaped symbioses in which one organism (typically a bacterium or fungus) generates bioactive small molecules that impact the host (and possibly other symbionts); the symbiosis is driven fundamentally by the genetic machineries available to the small molecule producer. The human microbiome is now integral to the most recent chapter in animal-microbe symbiosis studies and plant-microbe symbioses have significantly advanced our understanding of natural products biosynthesis; this also is the case for studies of fungal-microbe symbioses. However, much less is known about microbe-microbe systems involving interspecies interactions. Microbe-derived small molecules (i.e. antibiotics and quorum sensing molecules, etc.) have been shown to regulate transcription in microbes within the same environmental niche, suggesting interspecies interactions whereas, intraspecies interactions, such as those that exploit autoinducing small molecules, also modulate gene expression based on environmental cues. We, and others, contend that symbioses provide almost unlimited opportunities for the discovery of new bioactive compounds whose activities and applications have been evolutionarily optimized. Particularly intriguing is the possibility that environmental effectors can guide laboratory expression of secondary metabolites from "orphan", or silent, biosynthetic gene clusters (BGCs). Notably, many of the studies summarized here result from advances in "omics" technologies and highlight how symbioses have given rise to new anti-bacterial and antifungal natural products now being discovered.
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Affiliation(s)
- Navid Adnani
- University of Wisconsin Madison, School of Pharmacy, Div. of Pharmaceutical Sciences, 777 Highland Ave., Madison, WI 53705-2222, USA.
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11
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Sharma R, Jamwal V, Singh VP, Wazir P, Awasthi P, Singh D, Vishwakarma RA, Gandhi SG, Chaubey A. Revelation and cloning of valinomycin synthetase genes in Streptomyces lavendulae ACR-DA1 and their expression analysis under different fermentation and elicitation conditions. J Biotechnol 2017; 253:40-47. [PMID: 28528783 DOI: 10.1016/j.jbiotec.2017.05.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 05/02/2017] [Accepted: 05/08/2017] [Indexed: 11/26/2022]
Abstract
Streptomyces species are amongst the most exploited microorganisms due to their ability to produce a plethora of secondary metabolites with bioactive potential, including several well known drugs. They are endowed with immense unexplored potential and substantial efforts are required for their isolation as well as characterization for their bioactive potential. Unexplored niches and extreme environments are host to diverse microbial species. In this study, we report Streptomyces lavendulae ACR-DA1, isolated from extreme cold deserts of the North Western Himalayas, which produces a macrolactone antibiotic, valinomycin. Valinomycin is a K+ ionophoric non-ribosomal cyclodepsipeptide with a broad range of bioactivities including antibacterial, antifungal, antiviral and cytotoxic/anticancer activities. Production of valinomycin by the strain S. lavendulae ACR-DA1 was studied under different fermentation conditions like fermentation medium, temperature and addition of biosynthetic precursors. Synthetic medium at 10°C in the presence of precursors i.e. valine and pyruvate showed enhanced valinomycin production. In order to assess the impact of various elicitors, expression of the two genes viz. vlm1 and vlm2 that encode components of heterodimeric valinomycin synthetase, was analyzed using RT-PCR and correlated with quantity of valinomycin using LC-MS/MS. Annelid, bacterial and yeast elicitors increased valinomycin production whereas addition of fungal and plant elicitors down regulated the biosynthetic genes and reduced valinomycin production. This study is also the first report of valinomycin biosynthesis by Streptomyces lavendulae.
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Affiliation(s)
- Richa Sharma
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu,180001, India; Academy of Scientific & Innovative Research, New Delhi, 110001, India
| | - Vijaylakshmi Jamwal
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu,180001, India
| | - Varun P Singh
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu,180001, India
| | - Priya Wazir
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu,180001, India
| | - Praveen Awasthi
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu,180001, India
| | - Deepika Singh
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu,180001, India; Academy of Scientific & Innovative Research, New Delhi, 110001, India
| | - Ram A Vishwakarma
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu,180001, India; Academy of Scientific & Innovative Research, New Delhi, 110001, India
| | - Sumit G Gandhi
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu,180001, India; Academy of Scientific & Innovative Research, New Delhi, 110001, India.
| | - Asha Chaubey
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu,180001, India; Academy of Scientific & Innovative Research, New Delhi, 110001, India.
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12
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Mavituna F, Luti KJK, Gu L. In Search of the E. coli Compounds that Change the Antibiotic Production Pattern of Streptomyces coelicolor During Inter-species Interaction. Enzyme Microb Technol 2016; 90:45-52. [DOI: 10.1016/j.enzmictec.2016.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 03/04/2016] [Accepted: 03/13/2016] [Indexed: 02/04/2023]
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13
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Asamizu S, Ozaki T, Teramoto K, Satoh K, Onaka H. Killing of Mycolic Acid-Containing Bacteria Aborted Induction of Antibiotic Production by Streptomyces in Combined-Culture. PLoS One 2015; 10:e0142372. [PMID: 26544713 PMCID: PMC4636228 DOI: 10.1371/journal.pone.0142372] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/21/2015] [Indexed: 02/02/2023] Open
Abstract
Co-culture of Streptomyces with mycolic acid-containing bacteria (MACB), which we termed “combined-culture,” alters the secondary metabolism pattern in Streptomyces and has been a useful method for the discovery of bioactive natural products. In the course of our investigation to identify the inducing factor(s) of MACB, we previously observed that production of pigments in Streptomyces lividans was not induced by factors such as culture extracts or mycolic acids. Although dynamic changes occurred in culture conditions because of MACB, the activation of pigment production by S. lividans was observed in a limited area where both colonies were in direct contact. This suggested that direct attachment of cells is a requirement and that components on the MACB cell membrane may play an important role in the response by S. lividans. Here we examined whether this response was influenced by dead MACB that possess intact mycolic acids assembled on the outer cell membrane. Formaldehyde fixation and γ-irradiation were used to prepare dead cells that retain their shape and mycolic acids of three MACB species: Tsukamurella pulmonis, Rhodococcus erythropolis, and Rhodococcus opacus. Culturing tests verified that S. lividans does not respond to the intact dead cells of three MACB. Observation of combined-culture by scanning electron microscopy (SEM) indicated that adhesion of live MACB to S. lividans mycelia were a significant interaction that resulted in formation of co-aggregation. In contrast, in the SEM analysis, dead cells were not observed to adhere. Therefore, direct attachment by live MACB cells is proposed as one of the possible factors that causes Streptomyces to alter its specialized metabolism in combined-culture.
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Affiliation(s)
- Shumpei Asamizu
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
- * E-mail: (SA); (HO)
| | - Taro Ozaki
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Kanae Teramoto
- Advanced Technology Department, JEOL Ltd., Akishima, Tokyo, Japan
| | - Katsuya Satoh
- Ion Beam Mutagenesis Research Group, Biotechnology and Medical Application Division, Quantum Beam Science Center, Japan Atomic Energy Agency, Takasaki, Gunma, Japan
| | - Hiroyasu Onaka
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
- * E-mail: (SA); (HO)
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14
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Abdelmohsen UR, Grkovic T, Balasubramanian S, Kamel MS, Quinn RJ, Hentschel U. Elicitation of secondary metabolism in actinomycetes. Biotechnol Adv 2015; 33:798-811. [PMID: 26087412 DOI: 10.1016/j.biotechadv.2015.06.003] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 05/29/2015] [Accepted: 06/09/2015] [Indexed: 10/23/2022]
Abstract
Genomic sequence data have revealed the presence of a large fraction of putatively silent biosynthetic gene clusters in the genomes of actinomycetes that encode for secondary metabolites, which are not detected under standard fermentation conditions. This review focuses on the effects of biological (co-cultivation), chemical, as well as molecular elicitation on secondary metabolism in actinomycetes. Our review covers the literature until June 2014 and exemplifies the diversity of natural products that have been recovered by such approaches from the phylum Actinobacteria.
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Affiliation(s)
- Usama Ramadan Abdelmohsen
- Department of Botany II, Julius-von-Sachs-Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, 97082 Würzburg, Germany; Department of Pharmacognosy, Faculty of Pharmacy, Minia University, 61519 Minia, Egypt.
| | - Tanja Grkovic
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Srikkanth Balasubramanian
- Department of Botany II, Julius-von-Sachs-Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, 97082 Würzburg, Germany
| | - Mohamed Salah Kamel
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, 61519 Minia, Egypt
| | - Ronald J Quinn
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Ute Hentschel
- Department of Botany II, Julius-von-Sachs-Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, 97082 Würzburg, Germany
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15
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Goodwin CR, Covington BC, Derewacz DK, McNees CR, Wikswo JP, McLean JA, Bachmann BO. Structuring Microbial Metabolic Responses to Multiplexed Stimuli via Self-Organizing Metabolomics Maps. ACTA ACUST UNITED AC 2015; 22:661-70. [PMID: 25937311 DOI: 10.1016/j.chembiol.2015.03.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 03/26/2015] [Accepted: 03/30/2015] [Indexed: 11/19/2022]
Abstract
Secondary metabolite biosynthesis in microorganisms responds to discrete chemical and biological stimuli; however, untargeted identification of these responses presents a significant challenge. Herein we apply multiplexed stimuli to Streptomyces coelicolor and collect the resulting response metabolomes via ion mobility-mass spectrometric analysis. Self-organizing map (SOM) analytics adapted for metabolomic data demonstrate efficient characterization of the subsets of primary and secondary metabolites that respond similarly across stimuli. Over 60% of all metabolic features inventoried from responses are either not observed under control conditions or produced at greater than 2-fold increase in abundance in response to at least one of the multiplexing conditions, reflecting how metabolites encode phenotypic changes in an organism responding to multiplexed challenges. Using abundance as an additional filter, each of 16 known S. coelicolor secondary metabolites is prioritized via SOM and observed at increased levels (1.2- to 22-fold compared with unperturbed) in response to one or more challenge conditions.
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Affiliation(s)
- Cody R Goodwin
- Department of Chemistry, Vanderbilt University, 7300 Stevenson Center, Nashville, TN 37235, USA; Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, 6301 Stevenson Center, Nashville, TN 37235, USA; Center for Innovative Technology, Vanderbilt University, 5401 Stevenson Center, Nashville, TN 37235, USA
| | - Brett C Covington
- Department of Chemistry, Vanderbilt University, 7300 Stevenson Center, Nashville, TN 37235, USA
| | - Dagmara K Derewacz
- Department of Chemistry, Vanderbilt University, 7300 Stevenson Center, Nashville, TN 37235, USA
| | - C Ruth McNees
- Department of Chemistry, Vanderbilt University, 7300 Stevenson Center, Nashville, TN 37235, USA
| | - John P Wikswo
- Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, 6301 Stevenson Center, Nashville, TN 37235, USA; Department of Biomedical Engineering, Department of Molecular Physiology and Biophysics, and Department of Physics and Astronomy, Vanderbilt University, 6301 Stevenson Center, Nashville, TN 37235, USA
| | - John A McLean
- Department of Chemistry, Vanderbilt University, 7300 Stevenson Center, Nashville, TN 37235, USA; Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, 6301 Stevenson Center, Nashville, TN 37235, USA; Vanderbilt Institute of Chemical Biology, Vanderbilt University, 7300 Stevenson Center, Nashville, TN 37235, USA; Center for Innovative Technology, Vanderbilt University, 5401 Stevenson Center, Nashville, TN 37235, USA.
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, 7300 Stevenson Center, Nashville, TN 37235, USA; Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, 6301 Stevenson Center, Nashville, TN 37235, USA; Vanderbilt Institute of Chemical Biology, Vanderbilt University, 7300 Stevenson Center, Nashville, TN 37235, USA.
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16
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Stankovic N, Senerovic L, Ilic-Tomic T, Vasiljevic B, Nikodinovic-Runic J. Properties and applications of undecylprodigiosin and other bacterial prodigiosins. Appl Microbiol Biotechnol 2014; 98:3841-58. [PMID: 24562326 DOI: 10.1007/s00253-014-5590-1] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 02/03/2014] [Accepted: 02/03/2014] [Indexed: 10/25/2022]
Abstract
The growing demand to fulfill the needs of present-day medicine in terms of novel effective molecules has lead to reexamining some of the old and known bacterial secondary metabolites. Bacterial prodigiosins (prodiginines) have a long history of being re markable multipurpose compounds, best examined for their anticancer and antimalarial activities. Production of prodigiosin in the most common producer strain Serratia marcescens has been described in great detail. However, few reports have discussed the ecophysiological roles of these molecules in the producing strains, as well as their antibiotic and UV-protective properties. This review describes recent advances in the production process, biosynthesis, properties, and applications of bacterial prodigiosins. Special emphasis is put on undecylprodigiosin which has generally been a less studied member of the prodigiosin family. In addition, it has been suggested that proteins involved in undecylprodigiosin synthesis, RedG and RedH, could be a useful addition to the biocatalytic toolbox being able to mediate regio- and stereoselective oxidative cyclization. Judging by the number of recent references (216 for the 2007-2013 period), it has become clear that undecylprodigiosin and other bacterial prodigiosins still hold surprises in terms of valuable properties and applicative potential to medical and other industrial fields and that they still deserve continuing research curiosity.
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Affiliation(s)
- Nada Stankovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, P.O. Box 23, 11000, Belgrade, Serbia
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Schäberle TF, Orland A, König GM. Enhanced production of undecylprodigiosin in Streptomyces coelicolor by co-cultivation with the corallopyronin A-producing myxobacterium, Corallococcus coralloides. Biotechnol Lett 2013; 36:641-8. [PMID: 24249103 DOI: 10.1007/s10529-013-1406-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 10/30/2013] [Indexed: 12/11/2022]
Abstract
Prolific producers of natural products like streptomycetes and myxobacteria live in complex natural frameworks consisting of many microorganisms. Presumably intricate physiological and metabolic regulatory networks have evolved to enable the organisms to respond to intra- and interspecies interactions, e.g. biosynthesis of specific natural products is up-regulated due to competitors in the surrounding area. The soil-dwelling bacterium, Streptomyces coelicolor, produces the biologically-active compound, undecylprodigiosin (Red). Co-incubation with the corallopyronin A-producer, Corallococcus coralloides, was performed to explore the hypothesis that Red production can be enhanced by a myxobacterial competitor. Co-cultivation resulted in earlier onset and increased production of Red (60-fold increase of the intra-cellular concentration). Using different Corallococcus-derived extracts for elicitation, revealed that water-soluble factors triggered the enhanced production of Red which shows antimicrobial, immunosuppressive and anticancer properties.
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Affiliation(s)
- Till F Schäberle
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany,
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18
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Interspecies interactions stimulate diversification of the Streptomyces coelicolor secreted metabolome. mBio 2013; 4:mBio.00459-13. [PMID: 23963177 PMCID: PMC3747584 DOI: 10.1128/mbio.00459-13] [Citation(s) in RCA: 254] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Soils host diverse microbial communities that include filamentous actinobacteria (actinomycetes). These bacteria have been a rich source of useful metabolites, including antimicrobials, antifungals, anticancer agents, siderophores, and immunosuppressants. While humans have long exploited these compounds for therapeutic purposes, the role these natural products may play in mediating interactions between actinomycetes has been difficult to ascertain. As an initial step toward understanding these chemical interactions at a systems level, we employed the emerging techniques of nanospray desorption electrospray ionization (NanoDESI) and matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) imaging mass spectrometry to gain a global chemical view of the model bacterium Streptomyces coelicolor interacting with five other actinomycetes. In each interaction, the majority of secreted compounds associated with S. coelicolor colonies were unique, suggesting an idiosyncratic response from S. coelicolor. Spectral networking revealed a family of unknown compounds produced by S. coelicolor during several interactions. These compounds constitute an extended suite of at least 12 different desferrioxamines with acyl side chains of various lengths; their production was triggered by siderophores made by neighboring strains. Taken together, these results illustrate that chemical interactions between actinomycete bacteria exhibit high complexity and specificity and can drive differential secondary metabolite production. Actinomycetes, filamentous actinobacteria from the soil, are the deepest natural source of useful medicinal compounds, including antibiotics, antifungals, and anticancer agents. There is great interest in developing new strategies that increase the diversity of metabolites secreted by actinomycetes in the laboratory. Here we used several metabolomic approaches to examine the chemicals made by these bacteria when grown in pairwise coculture. We found that these interspecies interactions stimulated production of numerous chemical compounds that were not made when they grew alone. Among these compounds were at least 12 different versions of a molecule called desferrioxamine, a siderophore used by the bacteria to gather iron. Many other compounds of unknown identity were also observed, and the pattern of compound production varied greatly among the interaction sets. These findings suggest that chemical interactions between actinomycetes are surprisingly complex and that coculture may be a promising strategy for finding new molecules from actinomycetes.
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