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Magar RT, Pham VTT, Poudel PB, Bridget AF, Sohng JK. A new peucemycin derivative and impacts of peuR and bldA on peucemycin biosynthesis in Streptomyces peucetius. Appl Microbiol Biotechnol 2024; 108:107. [PMID: 38217253 PMCID: PMC10786969 DOI: 10.1007/s00253-023-12923-4] [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: 07/23/2023] [Revised: 10/05/2023] [Accepted: 10/30/2023] [Indexed: 01/15/2024]
Abstract
Streptomyces peucetius ATCC 27952 is known to produce a variety of secondary metabolites, including two important antitumor anthracyclines: daunorubicin and doxorubicin. Identification of peucemycin and 25-hydroxy peucemycin (peucemycin A), as well as their biosynthetic pathway, has expanded its biosynthetic potential. In this study, we isolated a new peucemycin derivative and identified it as 19-hydroxy peucemycin (peucemycin B). Its antibacterial activity was lower than those of peucemycin and peucemycin A. On the other hand, this newly identified peucemycin derivative had higher anticancer activity than the other two compounds for MKN45, NCI-H1650, and MDA-MB-231 cancer cell lines with IC50 values of 76.97 µM, 99.68 µM, and 135.2 µM, respectively. Peucemycin biosynthetic gene cluster revealed the presence of a SARP regulator named PeuR whose role was unknown. The presence of the TTA codon in the peuR and the absence of global regulator BldA in S. peucetius reduced its ability to regulate the peucemycin biosynthetic gene cluster. Hence, different mutants harboring these genes were prepared. S. peucetius bldA25 harboring bldA produced 1.75 times and 1.77 times more peucemycin A (11.8 mg/L) and peucemycin B (21.2 mg/L), respectively, than the wild type. On the other hand, S. peucetius R25 harboring peuR produced 1.86 and 1.79 times more peucemycin A (12.5 mg/L) and peucemycin B (21.5 mg/L), respectively, than the wild type. Finally, strain S. peucetius bldAR25 carrying bldA and peuR produced roughly 3.52 and 2.63 times more peucemycin A (23.8 mg/L) and peucemycin B (31.5 mg/L), respectively, than the wild type. KEY POINTS: • This study identifies a new peucemycin derivative, 19-hydroxy peucemycin (peucemycin B). • The SARP regulator (PeuR) acts as a positive regulator of the peucemycin biosynthetic gene cluster. • The overexpression of peuR and heterologous expression of bldA increase the production of peucemycin derivatives.
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Affiliation(s)
- Rubin Thapa Magar
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, 31460, Chungnam, Korea
| | - Van Thuy Thi Pham
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, 31460, Chungnam, Korea
| | - Purna Bahadur Poudel
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, 31460, Chungnam, Korea
| | - Adzemye Fovennso Bridget
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, 31460, Chungnam, Korea
| | - Jae Kyung Sohng
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, 31460, Chungnam, Korea.
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, 31460, Chungnam, Korea.
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Rodriguez-Sanchez AC, Gónzalez-Salazar LA, Rodriguez-Orduña L, Cumsille Á, Undabarrena A, Camara B, Sélem-Mojica N, Licona-Cassani C. Phylogenetic classification of natural product biosynthetic gene clusters based on regulatory mechanisms. Front Microbiol 2023; 14:1290473. [PMID: 38029100 PMCID: PMC10663231 DOI: 10.3389/fmicb.2023.1290473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
The natural products (NPs) biosynthetic gene clusters (BGCs) represent the adapting biochemical toolkit for microorganisms to thrive different microenvironments. Despite their high diversity, particularly at the genomic level, detecting them in a shake-flask is challenging and remains the primary obstacle limiting our access to valuable chemicals. Studying the molecular mechanisms that regulate BGC expression is crucial to design of artificial conditions that derive on their expression. Here, we propose a phylogenetic analysis of regulatory elements linked to biosynthesis gene clusters, to classify BGCs to regulatory mechanisms based on protein domain information. We utilized Hidden Markov Models from the Pfam database to retrieve regulatory elements, such as histidine kinases and transcription factors, from BGCs in the MIBiG database, focusing on actinobacterial strains from three distinct environments: oligotrophic basins, rainforests, and marine environments. Despite the environmental variations, our isolated microorganisms share similar regulatory mechanisms, suggesting the potential to activate new BGCs using activators known to affect previously characterized BGCs.
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Affiliation(s)
| | - Luz A. Gónzalez-Salazar
- Centro de Biotecnologia FEMSA, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Monterrey, Mexico
| | - Lorena Rodriguez-Orduña
- Centro de Biotecnologia FEMSA, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Monterrey, Mexico
| | - Ándres Cumsille
- Centro de Biotecnología Daniel Alkalay, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Agustina Undabarrena
- Centro de Biotecnología Daniel Alkalay, Universidad Técnica Federico Santa María, Valparaíso, Chile
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Beatriz Camara
- Centro de Biotecnología Daniel Alkalay, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | | | - Cuauhtemoc Licona-Cassani
- Centro de Biotecnologia FEMSA, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Monterrey, Mexico
- Integrative Biology Unit, The Institute for Obesity Research, Tecnológico de Monterrey, Monterrey, Mexico
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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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Krysenko S, Wohlleben W. Polyamine and Ethanolamine Metabolism in Bacteria as an Important Component of Nitrogen Assimilation for Survival and Pathogenicity. Med Sci (Basel) 2022; 10:40. [PMID: 35997332 PMCID: PMC9397018 DOI: 10.3390/medsci10030040] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
Nitrogen is an essential element required for bacterial growth. It serves as a building block for the biosynthesis of macromolecules and provides precursors for secondary metabolites. Bacteria have developed the ability to use various nitrogen sources and possess two enzyme systems for nitrogen assimilation involving glutamine synthetase/glutamate synthase and glutamate dehydrogenase. Microorganisms living in habitats with changeable availability of nutrients have developed strategies to survive under nitrogen limitation. One adaptation is the ability to acquire nitrogen from alternative sources including the polyamines putrescine, cadaverine, spermidine and spermine, as well as the monoamine ethanolamine. Bacterial polyamine and monoamine metabolism is not only important under low nitrogen availability, but it is also required to survive under high concentrations of these compounds. Such conditions can occur in diverse habitats such as soil, plant tissues and human cells. Strategies of pathogenic and non-pathogenic bacteria to survive in the presence of poly- and monoamines offer the possibility to combat pathogens by using their capability to metabolize polyamines as an antibiotic drug target. This work aims to summarize the knowledge on poly- and monoamine metabolism in bacteria and its role in nitrogen metabolism.
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Affiliation(s)
- Sergii Krysenko
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Department of Microbiology and Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany;
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, 72076 Tübingen, Germany
| | - Wolfgang Wohlleben
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Department of Microbiology and Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany;
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, 72076 Tübingen, Germany
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Rang J, Xia Z, Shuai L, Cao L, Liu Y, Li X, Xie J, Li Y, Hu S, Xie Q, Xia L. A TetR family transcriptional regulator, SP_2854 can affect the butenyl-spinosyn biosynthesis by regulating glucose metabolism in Saccharopolyspora pogona. Microb Cell Fact 2022; 21:83. [PMID: 35568948 PMCID: PMC9107242 DOI: 10.1186/s12934-022-01808-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/27/2022] [Indexed: 11/10/2022] Open
Abstract
Background Butenyl-spinosyn produced by Saccharopolyspora pogona exhibits strong insecticidal activity and a broad pesticidal spectrum. Currently, important functional genes involve in butenyl-spinosyn biosynthesis remain unknown, which leads to difficulty in efficiently understanding its regulatory mechanism, and improving its production by metabolic engineering. Results Here, we identified a TetR family transcriptional regulator, SP_2854, that can positively regulate butenyl-spinosyn biosynthesis and affect strain growth, glucose consumption, and mycelial morphology in S. pogona. Using targeted metabolomic analyses, we found that SP_2854 overexpression enhanced glucose metabolism, while SP_2854 deletion had the opposite effect. To decipher the overproduction mechanism in detail, comparative proteomic analysis was carried out in the SP-2854 overexpressing mutant and the original strain, and we found that SP_2854 overexpression promoted the expression of proteins involved in glucose metabolism. Conclusion Our findings suggest that SP_2854 can affect strain growth and development and butenyl-spinosyn biosynthesis in S. pogona by controlling glucose metabolism. The strategy reported here will be valuable in paving the way for genetic engineering of regulatory elements in actinomycetes to improve important natural products production. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01808-2.
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Affiliation(s)
- Jie Rang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China.,Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (MOE of China), National & Local Joint Engineering Laboratory for New Petro-Chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China
| | - Ziyuan Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Ling Shuai
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Li Cao
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yang Liu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Xiaomin Li
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Jiao Xie
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yunlong Li
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Shengbiao Hu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Qingji Xie
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (MOE of China), National & Local Joint Engineering Laboratory for New Petro-Chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China.
| | - Liqiu Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China.
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Li C, Wang J, Lin H, Zhang Y, Ma Z, Bechthold A, Yu X. Protein X0P338, a GntR-type pleiotropic regulator for morphological differentiation and secondary metabolites production in Streptomyces diastatochromogenes 1628. J Basic Microbiol 2022; 62:788-800. [PMID: 35485240 DOI: 10.1002/jobm.202200086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 04/08/2022] [Accepted: 04/15/2022] [Indexed: 11/07/2022]
Abstract
The nucleoside antibiotic, toyocamycin (TM) exhibits excellent potent activity against several phytopathogenic fungi. Despite of its importance, little is known about key factors regulating TM biosynthesis and morphological differentiation in S. diastatochromogenes 1628. Based on proteomics data obtained from the analysis between wild-type (WT) S. diastatochromogenes 1628 strain and mutant strain 1628-T62 having a low-yield of TM, we observed that the differentially expressed protein, X0P338, which was proposed to be a regulator of the GntR-family, exhibited a higher expression level in S. diastatochromogenes 1628. Therefore, in this study, to explore whether protein X0P338 was involved in morphological differentiation and biosynthesis of secondary metabolites, especially TM, the gene called the gntR sd -encoding protein X0P338 was cloned and over-expressed in WT strain 1628 and mutant strain 1628-T62, respectively. The results indicated that the over-expression of gntR sd enhanced TM production in both strain 1628 (120.6 mg/L vs. 306.6 mg/L) and strain 1628-T62 (15.6 mg/L vs. 258.9 mg/L). Besides, the over-expression of gntR sd had positive and negative effects on morphological differentiation in strain 1628 and strain 1628-T62, respectively. The results also showed opposite effects on tetraene macrolide production during the over-expression of gntR sd in strain 1628 and strain 1628-T62. Moreover, transcription levels of genes involved in morphological differentiation and secondary metabolites production were affected by the over-expression of gntR sd gene, both in strain 1628 and strain 1628-T62. These results confirm that X0P338 as a GntR-type pleiotropic regulator that regulates the morphological differentiation and biosynthesis of secondary metabolites, and especially has a positive effect on TM biosynthesis. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Chouqiang Li
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang Province, 310018, China
| | - Juan Wang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang Province, 310018, China
| | - Hengyi Lin
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang Province, 310018, China
| | - Yongyong Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang Province, 310018, China
| | | | - Andreas Bechthold
- University of Freiburg, Institute for Pharmaceutical Sciences, Pharmaceutical Biology and Biotechnology, Freiburg, Germany
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Global Chromosome Topology and the Two-Component Systems in Concerted Manner Regulate Transcription in Streptomyces. mSystems 2021; 6:e0114221. [PMID: 34783581 PMCID: PMC8594442 DOI: 10.1128/msystems.01142-21] [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] [Indexed: 11/25/2022] Open
Abstract
Bacterial gene expression is controlled at multiple levels, with chromosome supercoiling being one of the most global regulators. Global DNA supercoiling is maintained by the orchestrated action of topoisomerases. In Streptomyces, mycelial soil bacteria with a complex life cycle, topoisomerase I depletion led to elevated chromosome supercoiling, changed expression of a significant fraction of genes, delayed growth, and blocked sporulation. To identify supercoiling-induced sporulation regulators, we searched for Streptomyces coelicolor transposon mutants that were able to restore sporulation despite high chromosome supercoiling. We established that transposon insertion in genes encoding a novel two-component system named SatKR reversed the sporulation blockage resulting from topoisomerase I depletion. Transposition in satKR abolished the transcriptional induction of the genes within the so-called supercoiling-hypersensitive cluster (SHC). Moreover, we found that activated SatR also induced the same set of SHC genes under normal supercoiling conditions. We determined that the expression of genes in this region impacted S. coelicolor growth and sporulation. Interestingly, among the associated products is another two-component system (SitKR), indicating the potential for cascading regulatory effects driven by the SatKR and SitKR two-component systems. Thus, we demonstrated the concerted activity of chromosome supercoiling and a hierarchical two-component signaling system that impacts gene activity governing Streptomyces growth and sporulation. IMPORTANCEStreptomyces microbes, soil bacteria with complex life cycle, are the producers of a broad range of biologically active compounds (e.g., antibiotics). Streptomyces bacteria respond to various environmental signals using a complex transcriptional regulation mechanism. Understanding regulation of their gene expression is crucial for Streptomyces application as industrial organisms. Here, on the basis of the results of extensive transcriptomics analyses, we describe the concerted gene regulation by global DNA supercoiling and novel two-component system. Our data indicate that regulated genes encode growth and sporulation regulators. Thus, we demonstrate that Streptomyces bacteria link the global regulatory strategies to adjust life cycle to unfavorable conditions.
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Transcriptional regulation of congocidine (netropsin) biosynthesis and resistance. Appl Environ Microbiol 2021; 87:e0138021. [PMID: 34586912 DOI: 10.1128/aem.01380-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The production of specialized metabolites by Streptomyces bacteria is usually temporally regulated. This regulation is complex and frequently involves both global and pathway-specific mechanisms. Streptomyces ambofaciens ATCC23877 produces several specialized metabolites, including spiramycins, stambomycins, kinamycins and congocidine. The production of the first three molecules has been shown to be controlled by one or several cluster-situated transcriptional regulators. However, nothing is known regarding the regulation of congocidine biosynthesis. Congocidine (netropsin) belongs to the family of pyrrolamide metabolites, which also includes distamycin and anthelvencins. Most pyrrolamides bind into the minor groove of DNA, specifically in A/T-rich regions, which gives them numerous biological activities, such as antimicrobial and antitumoral activities. We previously reported the characterization of the pyrrolamide biosynthetic gene clusters of congocidine (cgc) in S. ambofaciens ATCC23877, distamycin (dst) in Streptomyces netropsis DSM40846 and anthelvencins (ant) in Streptomyces venezuelae ATCC14583. The three gene clusters contain a gene encoding a putative transcriptional regulator, cgc1, dst1 and ant1 respectively. Cgc1, Dst1 and Ant1 present a high percentage of amino acid sequence similarity. We demonstrate here that Cgc1, an atypical orphan response regulator, activates the transcription of all cgc genes in the stationary phase of S. ambofaciens growth. We also show that the cgc cluster is constituted of eight main transcriptional units. Finally, we show that congocidine induces the expression of the transcriptional regulator Cgc1 and of the operon containing the resistance genes (cgc20 and cgc21, coding for an ABC transporter), and propose a model for the transcriptional regulation of the cgc gene cluster. Importance Understanding the mechanisms of regulation of specialized metabolite production can have important implications both at the level of specialized metabolism study (expression of silent gene clusters) and the biotechnological level (increase of the production of a metabolite of interest). We report here a study on the regulation of the biosynthesis of a metabolite from the pyrrolamide family, congocidine. We show that congocidine biosynthesis and resistance is controlled by Cgc1, a cluster-situated regulator. As the gene clusters directing the biosynthesis of the pyrrolamides distamycin and anthelvencin encode a homolog of Cgc1, our findings may be relevant for the biosynthesis of other pyrrolamides. In addition, our results reveal a new type of feed-forward induction mechanism, in which congocidine induces its own biosynthesis through the induction of the transcription of cgc1.
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Wang S, Lu F, Yang Z, Li Z, Tian Y. Combining Ribosomal Engineering with Heterologous Expression of a Regulatory Gene to Improve Milbemycin Production in Streptomyces
milbemycinicus A2079. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821030133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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López-Agudelo VA, Gómez-Ríos D, Ramirez-Malule H. Clavulanic Acid Production by Streptomyces clavuligerus: Insights from Systems Biology, Strain Engineering, and Downstream Processing. Antibiotics (Basel) 2021; 10:84. [PMID: 33477401 PMCID: PMC7830376 DOI: 10.3390/antibiotics10010084] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 12/16/2022] Open
Abstract
Clavulanic acid (CA) is an irreversible β-lactamase enzyme inhibitor with a weak antibacterial activity produced by Streptomyces clavuligerus (S. clavuligerus). CA is typically co-formulated with broad-spectrum β‑lactam antibiotics such as amoxicillin, conferring them high potential to treat diseases caused by bacteria that possess β‑lactam resistance. The clinical importance of CA and the complexity of the production process motivate improvements from an interdisciplinary standpoint by integrating metabolic engineering strategies and knowledge on metabolic and regulatory events through systems biology and multi-omics approaches. In the large-scale bioprocessing, optimization of culture conditions, bioreactor design, agitation regime, as well as advances in CA separation and purification are required to improve the cost structure associated to CA production. This review presents the recent insights in CA production by S. clavuligerus, emphasizing on systems biology approaches, strain engineering, and downstream processing.
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Affiliation(s)
| | - David Gómez-Ríos
- Grupo de Investigación en Simulación, Diseño, Control y Optimización de Procesos (SIDCOP), Departamento de Ingeniería Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín 050010, Colombia;
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Xu F, Liang Y, Ren J, Wang S, Zhan J. Discovery of a novel analogue of FR901533 and the corresponding biosynthetic gene cluster from Streptosporangium roseum No. 79089. Appl Microbiol Biotechnol 2020; 104:7131-7142. [DOI: 10.1007/s00253-020-10765-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/22/2020] [Accepted: 06/30/2020] [Indexed: 11/29/2022]
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Makitrynskyy R, Tsypik O, Nuzzo D, Paululat T, Zechel DL, Bechthold A. Secondary nucleotide messenger c-di-GMP exerts a global control on natural product biosynthesis in streptomycetes. Nucleic Acids Res 2020; 48:1583-1598. [PMID: 31956908 PMCID: PMC7026642 DOI: 10.1093/nar/gkz1220] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 12/17/2019] [Accepted: 01/16/2020] [Indexed: 11/13/2022] Open
Abstract
Cyclic dimeric 3'-5' guanosine monophosphate, c-di-GMP, is a ubiquitous second messenger controlling diverse cellular processes in bacteria. In streptomycetes, c-di-GMP plays a crucial role in a complex morphological differentiation by modulating an activity of the pleiotropic regulator BldD. Here we report that c-di-GMP plays a key role in regulating secondary metabolite production in streptomycetes by altering the expression levels of bldD. Deletion of cdgB encoding a diguanylate cyclase in Streptomycesghanaensis reduced c-di-GMP levels and the production of the peptidoglycan glycosyltransferase inhibitor moenomycin A. In contrast to the cdgB mutant, inactivation of rmdB, encoding a phosphodiesterase for the c-di-GMP hydrolysis, positively correlated with the c-di-GMP and moenomycin A accumulation. Deletion of bldD adversely affected the synthesis of secondary metabolites in S. ghanaensis, including the production of moenomycin A. The bldD-deficient phenotype is partly mediated by an increase in expression of the pleiotropic regulatory gene wblA. Genetic and biochemical analyses demonstrate that a complex of c-di-GMP and BldD effectively represses transcription of wblA, thus preventing sporogenesis and sustaining antibiotic synthesis. These results show that manipulation of the expression of genes controlling c-di-GMP pool has the potential to improve antibiotic production as well as activate the expression of silent gene clusters.
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Affiliation(s)
- Roman Makitrynskyy
- Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs University, Freiburg 79104, Germany
| | - Olga Tsypik
- Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs University, Freiburg 79104, Germany
| | - Desirèe Nuzzo
- Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs University, Freiburg 79104, Germany
| | - Thomas Paululat
- Organic Chemistry, University of Siegen, Siegen 57068, Germany
| | - David L Zechel
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Andreas Bechthold
- Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs University, Freiburg 79104, Germany
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13
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Robertsen HL, Musiol-Kroll EM. Actinomycete-Derived Polyketides as a Source of Antibiotics and Lead Structures for the Development of New Antimicrobial Drugs. Antibiotics (Basel) 2019; 8:E157. [PMID: 31547063 PMCID: PMC6963833 DOI: 10.3390/antibiotics8040157] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/08/2019] [Accepted: 09/10/2019] [Indexed: 01/15/2023] Open
Abstract
Actinomycetes are remarkable producers of compounds essential for human and veterinary medicine as well as for agriculture. The genomes of those microorganisms possess several sets of genes (biosynthetic gene cluster (BGC)) encoding pathways for the production of the valuable secondary metabolites. A significant proportion of the identified BGCs in actinomycetes encode pathways for the biosynthesis of polyketide compounds, nonribosomal peptides, or hybrid products resulting from the combination of both polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). The potency of these molecules, in terms of bioactivity, was recognized in the 1940s, and started the "Golden Age" of antimicrobial drug discovery. Since then, several valuable polyketide drugs, such as erythromycin A, tylosin, monensin A, rifamycin, tetracyclines, amphotericin B, and many others were isolated from actinomycetes. This review covers the most relevant actinomycetes-derived polyketide drugs with antimicrobial activity, including anti-fungal agents. We provide an overview of the source of the compounds, structure of the molecules, the biosynthetic principle, bioactivity and mechanisms of action, and the current stage of development. This review emphasizes the importance of actinomycetes-derived antimicrobial polyketides and should serve as a "lexicon", not only to scientists from the Natural Products field, but also to clinicians and others interested in this topic.
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Affiliation(s)
- Helene L Robertsen
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
| | - Ewa M Musiol-Kroll
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
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14
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Szafran MJ, Strzałka A, Jakimowicz D. A highly processive actinobacterial topoisomerase I - thoughts on Streptomyces' demand for an enzyme with a unique C-terminal domain. MICROBIOLOGY-SGM 2019; 166:120-128. [PMID: 31390324 PMCID: PMC7398561 DOI: 10.1099/mic.0.000841] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Topoisomerase I (TopA) is an essential enzyme that is required to remove excess negative supercoils from chromosomal DNA. Actinobacteria encode unusual TopA homologues with a unique C-terminal domain that contains lysine repeats and confers high enzyme processivity. Interestingly, the longest stretch of lysine repeats was identified in TopA from Streptomyces, environmental bacteria that undergo complex differentiation and produce a plethora of secondary metabolites. In this review, we aim to discuss potential advantages of the lysine repeats in Streptomyces TopA. We speculate that the chromosome organization, transcriptional regulation and lifestyle of these species demand a highly processive but also fine-tuneable relaxase. We hypothesize that the unique TopA provides flexible control of chromosomal topology and globally regulates gene expression.
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Affiliation(s)
- Marcin J Szafran
- Laboratory of Molecular Microbiology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Agnieszka Strzałka
- Laboratory of Molecular Microbiology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Dagmara Jakimowicz
- Laboratory of Molecular Microbiology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
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15
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Yin H, Wang W, Fan K, Li Z. Regulatory perspective of antibiotic biosynthesis in Streptomyces. SCIENCE CHINA-LIFE SCIENCES 2019; 62:698-700. [PMID: 30931496 DOI: 10.1007/s11427-019-9497-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 12/26/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Hanzhi Yin
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,School of Life Science, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Keqiang Fan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zilong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
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16
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Ward AL, Reddyvari P, Borisova R, Shilabin AG, Lampson BC. An inhibitory compound produced by a soil isolate of Rhodococcus has strong activity against the veterinary pathogen R. equi. PLoS One 2018; 13:e0209275. [PMID: 30592730 PMCID: PMC6310278 DOI: 10.1371/journal.pone.0209275] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 12/03/2018] [Indexed: 01/22/2023] Open
Abstract
Complete genome sequencing of dozens of strains of the soil bacterium Rhodococcus has revealed the presence of many cryptic biosynthetic gene clusters, presumably dedicated to the production of small molecules. This has sparked a renewed interest in this underexplored member of the Actinobacteria as a potential source of new bioactive compounds. Reported here is the discovery of a potent inhibitory molecule produced by a newly isolated strain of Rhodococcus, strain MTM3W5.2. This small inhibitory molecule shows strong activity against all Rhodococcus species tested, including the veterinary pathogen R. equi, and some closely related genera. It is not active against other Gram positive or Gram negative bacteria. A screen of random transposon mutants identified a gene required to produce this inhibitory compound. This gene is a large multi-domain, type I polyketide synthase that is part of a very large multi-gene biosynthetic gene cluster in the chromosome of strain MTM3W5.2. The high resolution mass spectrum of a major chromatogram peak from a broth culture extract of MTM3W5.2 shows the presence of a compound at m/z 911.5490 atomic mass units. This compound is not detected in the culture extracts from a non-producing mutant strain of MTM3W5.2. A large gene cluster containing at least 14 different type I polyketide synthase genes is proposed to be required to synthesize this antibiotic-like compound.
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Affiliation(s)
- Amber L. Ward
- Department of Health Sciences, East Tennessee State University, Johnson City, TN, United States of America
| | - Pushpavathi Reddyvari
- Department of Chemistry, East Tennessee State University, Johnson City, TN, United States of America
| | - Ralitsa Borisova
- Department of Health Sciences, East Tennessee State University, Johnson City, TN, United States of America
| | - Abbas G. Shilabin
- Department of Chemistry, East Tennessee State University, Johnson City, TN, United States of America
| | - Bert C. Lampson
- Department of Health Sciences, East Tennessee State University, Johnson City, TN, United States of America
- * E-mail:
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17
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Lu W, Alanzi AR, Abugrain ME, Ito T, Mahmud T. Global and pathway-specific transcriptional regulations of pactamycin biosynthesis in Streptomyces pactum. Appl Microbiol Biotechnol 2018; 102:10589-10601. [PMID: 30276712 DOI: 10.1007/s00253-018-9375-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/28/2018] [Accepted: 09/05/2018] [Indexed: 11/26/2022]
Abstract
Pactamycin, a structurally unique aminocyclitol natural product isolated from Streptomyces pactum, has potent antibacterial, antitumor, and anti-protozoa activities. However, its production yields under currently used culture conditions are generally low. To understand how pactamycin biosynthesis is regulated and explore the possibility of improving pactamycin production in S. pactum, we investigated the transcription regulations of pactamycin biosynthesis. In vivo inactivation of two putative pathway-specific regulatory genes, ptmE and ptmF, resulted in mutant strains that are not able to produce pactamycin. Genetic complementation using a cassette containing ptmE and ptmF integrated into the S. pactum chromosome rescued the production of pactamycin. Transcriptional analysis of the ΔptmE and ΔptmF strains suggests that both genes control the expression of the whole pactamycin biosynthetic gene cluster. However, attempts to overexpress these regulatory genes by introducing a second copy of the genes in S. pactum did not improve the production yield of pactamycin. We discovered that pactamycin biosynthesis is sensitive to phosphate regulation. Concentration of inorganic phosphate higher than 2 mM abolished both the transcription of the biosynthetic genes and the production of the antibiotic. Draft genome sequencing of S. pactum and bioinformatics studies revealed the existence of global regulatory genes, e.g., genes that encode a two-component PhoR-PhoP system, which are commonly involved in secondary metabolism. Inactivation of phoP did not show any significant effect to pactamycin production. However, in the phoP::aac(3)IV mutant, pactamycin biosynthesis is not affected by external inorganic phosphate concentration.
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Affiliation(s)
- Wanli Lu
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331-3507, USA
| | - Abdullah R Alanzi
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331-3507, USA
| | - Mostafa E Abugrain
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331-3507, USA
| | - Takuya Ito
- Faculty of Pharmacy, Osaka-Ohtani University, 3-11-1 Nisikiorikita, Tondabayashi, Osaka, 584-8540, Japan
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331-3507, USA.
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