1
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Pei X, Lei Y, Zhang H. Transcriptional regulators of secondary metabolite biosynthesis in Streptomyces. World J Microbiol Biotechnol 2024; 40:156. [PMID: 38587708 DOI: 10.1007/s11274-024-03968-2] [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: 02/14/2024] [Accepted: 03/25/2024] [Indexed: 04/09/2024]
Abstract
In the post-genome era, great progress has been made in metabolic engineering using recombinant DNA technology to enhance the production of high-value products by Streptomyces. With the development of microbial genome sequencing techniques and bioinformatic tools, a growing number of secondary metabolite (SM) biosynthetic gene clusters in Streptomyces and their biosynthetic logics have been uncovered and elucidated. In order to increase our knowledge about transcriptional regulators in SM of Streptomyces, this review firstly makes a comprehensive summary of the characterized factors involved in enhancing SM production and awakening SM biosynthesis. Future perspectives on transcriptional regulator engineering for new SM biosynthesis by Streptomyces are also provided.
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Affiliation(s)
- Xinwei Pei
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yunyun Lei
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Huawei Zhang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China.
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2
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Augustijn HE, Roseboom AM, Medema MH, van Wezel GP. Harnessing regulatory networks in Actinobacteria for natural product discovery. J Ind Microbiol Biotechnol 2024; 51:kuae011. [PMID: 38569653 PMCID: PMC10996143 DOI: 10.1093/jimb/kuae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/02/2024] [Indexed: 04/05/2024]
Abstract
Microbes typically live in complex habitats where they need to rapidly adapt to continuously changing growth conditions. To do so, they produce an astonishing array of natural products with diverse structures and functions. Actinobacteria stand out for their prolific production of bioactive molecules, including antibiotics, anticancer agents, antifungals, and immunosuppressants. Attention has been directed especially towards the identification of the compounds they produce and the mining of the large diversity of biosynthetic gene clusters (BGCs) in their genomes. However, the current return on investment in random screening for bioactive compounds is low, while it is hard to predict which of the millions of BGCs should be prioritized. Moreover, many of the BGCs for yet undiscovered natural products are silent or cryptic under laboratory growth conditions. To identify ways to prioritize and activate these BGCs, knowledge regarding the way their expression is controlled is crucial. Intricate regulatory networks control global gene expression in Actinobacteria, governed by a staggering number of up to 1000 transcription factors per strain. This review highlights recent advances in experimental and computational methods for characterizing and predicting transcription factor binding sites and their applications to guide natural product discovery. We propose that regulation-guided genome mining approaches will open new avenues toward eliciting the expression of BGCs, as well as prioritizing subsets of BGCs for expression using synthetic biology approaches. ONE-SENTENCE SUMMARY This review provides insights into advances in experimental and computational methods aimed at predicting transcription factor binding sites and their applications to guide natural product discovery.
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Affiliation(s)
- Hannah E Augustijn
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Anna M Roseboom
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
- Netherlands Institute for Ecology (NIOO-KNAW), Wageningen, The Netherlands
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3
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Karimian S, Farahmandzad N, Mohammadipanah F. Manipulation and epigenetic control of silent biosynthetic pathways in actinobacteria. World J Microbiol Biotechnol 2024; 40:65. [PMID: 38191749 DOI: 10.1007/s11274-023-03861-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 11/29/2023] [Indexed: 01/10/2024]
Abstract
Most biosynthetic gene clusters (BGCs) of Actinobacteria are either silent or expressed less than the detectable level. The non-genetic approaches including biological interactions, chemical agents, and physical stresses that can be used to awaken silenced pathways are compared in this paper. These non-genetic induction strategies often need screening approaches, including one strain many compounds (OSMAC), reporter-guided mutant selection, and high throughput elicitor screening (HiTES) have been developed. Different types of genetic manipulations applied in the induction of cryptic BGCs of Actinobacteria can be categorized as genome-wide pleiotropic and targeted approaches like manipulation of global regulatory systems, modulation of regulatory genes, ribosome and engineering of RNA polymerase or phosphopantheteine transferases. Targeted approaches including genome editing by CRISPR, mutation in transcription factors and modification of BGCs promoters, inactivation of the highly expressed biosynthetic pathways, deleting the suppressors or awakening the activators, heterologous expression, or refactoring of gene clusters can be applied for activation of pathways which are predicted to synthesize new bioactive structures in genome mining studies of Acinobacteria. In this review, the challenges and advantages of employing these approaches in induction of Actinobacteria BGCs are discussed. Further, novel natural products needed as drug for pharmaceutical industry or as biofertilizers in agricultural industry can be discovered even from known species of Actinobactera by the innovative approaches of metabolite biosynthesis elicitation.
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Affiliation(s)
- Sanaz Karimian
- Department of Biotechnology, Faculty of Biological Science, Alzahra University, Tehran, Iran
| | - Navid Farahmandzad
- Department of Biosystems Engineering, Auburn university, Auburn, AL 36849, USA
- Pharmaceutical Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, 14155-6455, Iran
| | - Fatemeh Mohammadipanah
- Pharmaceutical Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, 14155-6455, Iran.
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4
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Tay DWP, Tan LL, Heng E, Zulkarnain N, Ching KC, Wibowo M, Chin EJ, Tan ZYQ, Leong CY, Ng VWP, Yang LK, Seow DCS, Lim YW, Koh W, Koduru L, Kanagasundaram Y, Ng SB, Lim YH, Wong FT. Exploring a general multi-pronged activation strategy for natural product discovery in Actinomycetes. Commun Biol 2024; 7:50. [PMID: 38184720 PMCID: PMC10771470 DOI: 10.1038/s42003-023-05648-7] [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: 08/16/2023] [Accepted: 11/29/2023] [Indexed: 01/08/2024] Open
Abstract
Natural products possess significant therapeutic potential but remain underutilized despite advances in genomics and bioinformatics. While there are approaches to activate and upregulate natural product biosynthesis in both native and heterologous microbial strains, a comprehensive strategy to elicit production of natural products as well as a generalizable and efficient method to interrogate diverse native strains collection, remains lacking. Here, we explore a flexible and robust integrase-mediated multi-pronged activation approach to reliably perturb and globally trigger antibiotics production in actinobacteria. Across 54 actinobacterial strains, our approach yielded 124 distinct activator-strain combinations which consistently outperform wild type. Our approach expands accessible metabolite space by nearly two-fold and increases selected metabolite yields by up to >200-fold, enabling discovery of Gram-negative bioactivity in tetramic acid analogs. We envision these findings as a gateway towards a more streamlined, accelerated, and scalable strategy to unlock the full potential of Nature's chemical repertoire.
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Grants
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- C211917006 Agency for Science, Technology and Research (A*STAR)
- C233017006 Agency for Science, Technology and Research (A*STAR)
- C211917003 Agency for Science, Technology and Research (A*STAR)
- C211917006 Agency for Science, Technology and Research (A*STAR)
- C233017006 Agency for Science, Technology and Research (A*STAR)
- C211917006 Agency for Science, Technology and Research (A*STAR)
- National Research Foundation Singapore (National Research Foundation-Prime Minister’s office, Republic of Singapore)
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Affiliation(s)
- Dillon W P Tay
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore
| | - Lee Ling Tan
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore
| | - Elena Heng
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore
| | - Nadiah Zulkarnain
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore
| | - Kuan Chieh Ching
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Mario Wibowo
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Elaine Jinfeng Chin
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Zann Yi Qi Tan
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Chung Yan Leong
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Veronica Wee Pin Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Lay Kien Yang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Deborah C S Seow
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Yi Wee Lim
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore
| | - Winston Koh
- Bioinformatics Institute (BII), Agency of Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Republic of Singapore
| | - Lokanand Koduru
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore
| | - Yoganathan Kanagasundaram
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Yee Hwee Lim
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore.
- Synthetic Biology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, Singapore, 117597, Republic of Singapore.
| | - Fong Tian Wong
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore.
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore.
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5
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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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6
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Krol E, Werel L, Essen LO, Becker A. Structural and functional diversity of bacterial cyclic nucleotide perception by CRP proteins. MICROLIFE 2023; 4:uqad024. [PMID: 37223727 PMCID: PMC10187061 DOI: 10.1093/femsml/uqad024] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/07/2023] [Accepted: 04/28/2023] [Indexed: 05/25/2023]
Abstract
Cyclic AMP (cAMP) is a ubiquitous second messenger synthesized by most living organisms. In bacteria, it plays highly diverse roles in metabolism, host colonization, motility, and many other processes important for optimal fitness. The main route of cAMP perception is through transcription factors from the diverse and versatile CRP-FNR protein superfamily. Since the discovery of the very first CRP protein CAP in Escherichia coli more than four decades ago, its homologs have been characterized in both closely related and distant bacterial species. The cAMP-mediated gene activation for carbon catabolism by a CRP protein in the absence of glucose seems to be restricted to E. coli and its close relatives. In other phyla, the regulatory targets are more diverse. In addition to cAMP, cGMP has recently been identified as a ligand of certain CRP proteins. In a CRP dimer, each of the two cyclic nucleotide molecules makes contacts with both protein subunits and effectuates a conformational change that favors DNA binding. Here, we summarize the current knowledge on structural and physiological aspects of E. coli CAP compared with other cAMP- and cGMP-activated transcription factors, and point to emerging trends in metabolic regulation related to lysine modification and membrane association of CRP proteins.
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Affiliation(s)
- Elizaveta Krol
- Department of Biology, Philipps-Universität Marburg, Karl-von-Frisch-Straße 8, 35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35043 Marburg, Germany
| | - Laura Werel
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Lars Oliver Essen
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Anke Becker
- Corresponding author. Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35043 Marburg. E-mail:
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7
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Xu X, Zhang F, Zhou L, Chang Y, Che Q, Zhu T, Li D, Zhang G. Overexpression of Global Regulator SCrp Leads to the Discovery of New Angucyclines in Streptomyces sp. XS-16. Mar Drugs 2023; 21:md21040240. [PMID: 37103379 PMCID: PMC10146017 DOI: 10.3390/md21040240] [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: 02/25/2023] [Revised: 04/12/2023] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
Six angucyclines including three unreported compounds (1-3) were isolated from Streptomyces sp. XS-16 by overexpressing the native global regulator of SCrp (cyclic AMP receptor). The structures were characterized based on nuclear magnetic resonance (NMR) and spectrometry analysis and assisted by electronic circular dichroism (ECD) calculations. All compounds were tested for their antitumor and antimicrobial activities, and compound 1 showed different inhibitory activities against various tumor cell lines with IC50 values ranging from 0.32 to 5.33 μM.
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Affiliation(s)
- Xiao Xu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Falei Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Luning Zhou
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yimin Chang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Qian Che
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Tianjiao Zhu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Guojian Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Marine Biomedical Research Institute of Qingdao, Qingdao 266101, China
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8
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Schulz S, Sletta H, Fløgstad Degnes K, Krysenko S, Williams A, Olsen SM, Vernstad K, Mitulski A, Wohlleben W. Optimization of FK-506 production in Streptomyces tsukubaensis by modulation of Crp-mediated regulation. Appl Microbiol Biotechnol 2023; 107:2871-2886. [PMID: 36949330 PMCID: PMC10033298 DOI: 10.1007/s00253-023-12473-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/24/2023]
Abstract
FK-506 is a potent immunosuppressive macrocyclic polyketide with growing pharmaceutical interest, produced by Streptomyces tsukubaensis. However, due to low levels synthesized by the wild-type strain, biotechnological production of FK-506 is rather limited. Optimization strategies to enhance the productivity of S. tsukubaensis by means of genetic engineering have been established. In this work primarily global regulatory aspects with respect to the FK-506 biosynthesis have been investigated with the focus on the global Crp (cAMP receptor protein) regulator. In expression analyses and protein-DNA interaction studies, the role of Crp during FK-506 biosynthesis was elucidated. Overexpression of Crp resulted in two-fold enhancement of FK-506 production in S. tsukubaensis under laboratory conditions. Further optimizations using fermentors proved that the strategy described in this study can be transferred to industrial scale, presenting a new approach for biotechnological FK-506 production. KEY POINTS: • The role of the global Crp (cAMP receptor protein) regulator for FK-506 biosynthesis in S. tsukubaensis was demonstrated • Crp overexpression in S. tsukubaensis was applied as an optimization strategy to enhance FK-506 and FK-520 production resulting in two-fold yield increase.
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Affiliation(s)
- Susann Schulz
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
- Novartis AG, Stein, Switzerland
| | - Håvard Sletta
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Richard Birkelands vei 3, Trondheim, Norway.
| | - Kristin Fløgstad Degnes
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Richard Birkelands vei 3, Trondheim, Norway
| | - Sergii Krysenko
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
- Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
- Valent BioSciences, 1910 Innovation Wy Suite 100, Libertyville, IL, 60048, USA
| | - Alicia Williams
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Silje Malene Olsen
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Richard Birkelands vei 3, Trondheim, Norway
| | - Kai Vernstad
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Sem Sælands veg 2a, Trondheim, Norway
| | - Agnieszka Mitulski
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
- Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Wolfgang Wohlleben
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany.
- Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany.
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9
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Vladimirov M, Zhang RX, Mak S, Nodwell JR, Davidson AR. A contractile injection system is required for developmentally regulated cell death in Streptomyces coelicolor. Nat Commun 2023; 14:1469. [PMID: 36927736 PMCID: PMC10020575 DOI: 10.1038/s41467-023-37087-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
Diverse bacterial species produce extracellular contractile injection systems (eCISs). Although closely related to contractile phage tails, eCISs can inject toxic proteins into eukaryotic cells. Thus, these systems are commonly viewed as cytotoxic defense mechanisms that are not central to other aspects of bacterial biology. Here, we provide evidence that eCISs appear to participate in the complex developmental process of the bacterium Streptomyces coelicolor. In particular, we show that S. coelicolor produces eCIS particles during its normal growth cycle, and that strains lacking functional eCIS particles exhibit pronounced alterations in their developmental program. Furthermore, eCIS-deficient mutants display reduced levels of cell death and altered morphology during growth in liquid media. Our results suggest that the main role of eCISs in S. coelicolor is to modulate the developmental switch that leads to aerial hyphae formation and sporulation, rather than to attack other species.
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Affiliation(s)
- Maria Vladimirov
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Ruo Xi Zhang
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Stefanie Mak
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Justin R Nodwell
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Alan R Davidson
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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10
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Clara L, David C, Laila S, Virginie R, Marie-Joelle V. Comparative Proteomic Analysis of Transcriptional and Regulatory Proteins Abundances in S. lividans and S. coelicolor Suggests a Link between Various Stresses and Antibiotic Production. Int J Mol Sci 2022; 23:ijms232314792. [PMID: 36499130 PMCID: PMC9739823 DOI: 10.3390/ijms232314792] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/29/2022] Open
Abstract
Streptomyces coelicolor and Streptomyces lividans constitute model strains to study the regulation of antibiotics biosynthesis in Streptomyces species since these closely related strains possess the same pathways directing the biosynthesis of various antibiotics but only S. coelicolor produces them. To get a better understanding of the origin of the contrasted abilities of these strains to produce bioactive specialized metabolites, these strains were grown in conditions of phosphate limitation or proficiency and a comparative analysis of their transcriptional/regulatory proteins was carried out. The abundance of the vast majority of the 355 proteins detected greatly differed between these two strains and responded differently to phosphate availability. This study confirmed, consistently with previous studies, that S. coelicolor suffers from nitrogen stress. This stress likely triggers the degradation of the nitrogen-rich peptidoglycan cell wall in order to recycle nitrogen present in its constituents, resulting in cell wall stress. When an altered cell wall is unable to fulfill its osmo-protective function, the bacteria also suffer from osmotic stress. This study thus revealed that these three stresses are intimately linked in S. coelicolor. The aggravation of these stresses leading to an increase of antibiotic biosynthesis, the connection between these stresses, and antibiotic production are discussed.
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Affiliation(s)
- Lejeune Clara
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, Group “Energetic Metabolism of Streptomyces”, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Cornu David
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, Group “Energetic Metabolism of Streptomyces”, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Sago Laila
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, Group “Energetic Metabolism of Streptomyces”, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Redeker Virginie
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, Group “Energetic Metabolism of Streptomyces”, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
- Laboratory of Neurodegenerative Diseases, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA) and Centre National de la Recherche Scientifique (CNRS), Molecular Imaging Center (MIRCen), Institut François Jacob, Université Paris-Saclay, 92260 Fontenay-aux-Roses, France
| | - Virolle Marie-Joelle
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, Group “Energetic Metabolism of Streptomyces”, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
- Correspondence:
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11
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Abstract
Streptomycetes are highly metabolically gifted bacteria with the abilities to produce bioproducts that have profound economic and societal importance. These bioproducts are produced by metabolic pathways including those for the biosynthesis of secondary metabolites and catabolism of plant biomass constituents. Advancements in genome sequencing technologies have revealed a wealth of untapped metabolic potential from Streptomyces genomes. Here, we report the largest Streptomyces pangenome generated by using 205 complete genomes. Metabolic potentials of the pangenome and individual genomes were analyzed, revealing degrees of conservation of individual metabolic pathways and strains potentially suitable for metabolic engineering. Of them, Streptomyces bingchenggensis was identified as a potent degrader of plant biomass. Polyketide, non-ribosomal peptide, and gamma-butyrolactone biosynthetic enzymes are primarily strain specific while ectoine and some terpene biosynthetic pathways are highly conserved. A large number of transcription factors associated with secondary metabolism are strain-specific while those controlling basic biological processes are highly conserved. Although the majority of genes involved in morphological development are highly conserved, there are strain-specific varieties which may contribute to fine tuning the timing of cellular differentiation. Overall, these results provide insights into the metabolic potential, regulation and physiology of streptomycetes, which will facilitate further exploitation of these important bacteria.
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12
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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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13
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A butenolide signaling system synergized with biosynthetic gene modules led to effective activation and enhancement of silent oviedomycin production in Streptomyces. Metab Eng 2022; 72:289-296. [DOI: 10.1016/j.ymben.2022.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 03/11/2022] [Accepted: 04/13/2022] [Indexed: 11/16/2022]
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14
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Zambri MP, Williams MA, Elliot MA. How Streptomyces thrive: Advancing our understanding of classical development and uncovering new behaviors. Adv Microb Physiol 2022; 80:203-236. [PMID: 35489792 DOI: 10.1016/bs.ampbs.2022.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Streptomyces are soil- and marine-dwelling microbes that need to survive dramatic fluctuations in nutrient levels and environmental conditions. Here, we explore the advances made in understanding how Streptomyces bacteria can thrive in their natural environments. We examine their classical developmental cycle, and the intricate regulatory cascades that govern it. We discuss alternative growth strategies and behaviors, like the rapid expansion and colonization properties associated with exploratory growth, the release of membrane vesicles and S-cells from hyphal tips, and the acquisition of exogenous DNA along the lateral walls. We further investigate Streptomyces interactions with other organisms through the release of volatile compounds that impact nutrient levels, microbial growth, and insect behavior. Finally, we explore the increasingly diverse strategies employed by Streptomyces species in escaping and thwarting phage infections.
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Affiliation(s)
- Matthew P Zambri
- Department of Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Michelle A Williams
- Department of Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Marie A Elliot
- Department of Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
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15
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Pepler MA, Zhang X, Elliot MA. Inducing Global Expression of Actinobacterial Biosynthetic Gene Clusters. Methods Mol Biol 2022; 2489:157-171. [PMID: 35524050 DOI: 10.1007/978-1-0716-2273-5_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Bacteria produce an impressive array of bioactive specialized metabolites, with Streptomyces (and the actinobacteria more generally) being unusually diverse and prolific producers. However, the biosynthetic potential of these organisms has yet to be fully explored, as many of the biosynthetic gene clusters that direct the synthesis of these natural products are transcriptionally silent under laboratory growth conditions. Here, we describe strategies that can be employed to broadly stimulate the expression of biosynthetic gene clusters in Streptomyces and their relatives, follow the transcription of these genes, and assess the antimicrobial activity of the resulting molecules.
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Affiliation(s)
- Meghan A Pepler
- Department of Biology and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Xiafei Zhang
- Department of Biology and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Marie A Elliot
- Department of Biology and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
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16
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Rodríguez-Valverde D, León-Montes N, Soria-Bustos J, Martínez-Cruz J, González-Ugalde R, Rivera-Gutiérrez S, González-y-Merchand JA, Rosales-Reyes R, García-Morales L, Hirakawa H, Fox JG, Girón JA, De la Cruz MA, Ares MA. cAMP Receptor Protein Positively Regulates the Expression of Genes Involved in the Biosynthesis of Klebsiella oxytoca Tilivalline Cytotoxin. Front Microbiol 2021; 12:743594. [PMID: 34659176 PMCID: PMC8515920 DOI: 10.3389/fmicb.2021.743594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 08/31/2021] [Indexed: 01/09/2023] Open
Abstract
Klebsiella oxytoca is a resident of the human gut. However, certain K. oxytoca toxigenic strains exist that secrete the nonribosomal peptide tilivalline (TV) cytotoxin. TV is a pyrrolobenzodiazepine that causes antibiotic-associated hemorrhagic colitis (AAHC). The biosynthesis of TV is driven by enzymes encoded by the aroX and NRPS operons. In this study, we determined the effect of environmental signals such as carbon sources, osmolarity, and divalent cations on the transcription of both TV biosynthetic operons. Gene expression was enhanced when bacteria were cultivated in tryptone lactose broth. Glucose, high osmolarity, and depletion of calcium and magnesium diminished gene expression, whereas glycerol increased transcription of both TV biosynthetic operons. The cAMP receptor protein (CRP) is a major transcriptional regulator in bacteria that plays a key role in metabolic regulation. To investigate the role of CRP on the cytotoxicity of K. oxytoca, we compared levels of expression of TV biosynthetic operons and synthesis of TV in wild-type strain MIT 09-7231 and a Δcrp isogenic mutant. In summary, we found that CRP directly activates the transcription of the aroX and NRPS operons and that the absence of CRP reduced cytotoxicity of K. oxytoca on HeLa cells, due to a significant reduction in TV production. This study highlights the importance of the CRP protein in the regulation of virulence genes in enteric bacteria and broadens our knowledge on the regulatory mechanisms of the TV cytotoxin.
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Affiliation(s)
- Diana Rodríguez-Valverde
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Nancy León-Montes
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Jorge Soria-Bustos
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Jessica Martínez-Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Ricardo González-Ugalde
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Sandra Rivera-Gutiérrez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Jorge A. González-y-Merchand
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Roberto Rosales-Reyes
- Unidad de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Lázaro García-Morales
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Hidetada Hirakawa
- Department of Bacteriology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - James G. Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Jorge A. Girón
- Centro de Detección Biomolecular, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Miguel A. De la Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Miguel A. Ares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
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17
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Interplay between Nucleoid-Associated Proteins and Transcription Factors in Controlling Specialized Metabolism in Streptomyces. mBio 2021; 12:e0107721. [PMID: 34311581 PMCID: PMC8406272 DOI: 10.1128/mbio.01077-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Lsr2 is a small nucleoid-associated protein found throughout the actinobacteria. Lsr2 functions similarly to the well-studied H-NS, in that it preferentially binds AT-rich sequences and represses gene expression. In Streptomyces venezuelae, Lsr2 represses the expression of many specialized metabolic clusters, including the chloramphenicol antibiotic biosynthetic gene cluster, and deleting lsr2 leads to significant upregulation of chloramphenicol cluster expression. We show here that Lsr2 likely exerts its repressive effects on the chloramphenicol cluster by polymerizing along the chromosome and by bridging sites within and adjacent to the chloramphenicol cluster. CmlR is a known activator of the chloramphenicol cluster, but expression of its associated gene is not upregulated in an lsr2 mutant strain. We demonstrate that CmlR is essential for chloramphenicol production, and further reveal that CmlR functions to “countersilence” Lsr2’s repressive effects by recruiting RNA polymerase and enhancing transcription, with RNA polymerase effectively clearing bound Lsr2 from the chloramphenicol cluster DNA. Our results provide insight into the interplay between opposing regulatory proteins that govern antibiotic production in S. venezuelae, which could be exploited to maximize the production of bioactive natural products in other systems.
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18
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Kim JH, Lee N, Hwang S, Kim W, Lee Y, Cho S, Palsson BO, Cho BK. Discovery of novel secondary metabolites encoded in actinomycete genomes through coculture. J Ind Microbiol Biotechnol 2021; 48:6119915. [PMID: 33825906 PMCID: PMC9113425 DOI: 10.1093/jimb/kuaa001] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/02/2020] [Indexed: 01/23/2023]
Abstract
Actinomycetes are a rich source of bioactive natural products important for novel drug leads. Recent genome mining approaches have revealed an enormous number of secondary metabolite biosynthetic gene clusters (smBGCs) in actinomycetes. However, under standard laboratory culture conditions, many smBGCs are silent or cryptic. To activate these dormant smBGCs, several approaches, including culture-based or genetic engineering-based strategies, have been developed. Above all, coculture is a promising approach to induce novel secondary metabolite production from actinomycetes by mimicking an ecological habitat where cryptic smBGCs may be activated. In this review, we introduce coculture studies that aim to expand the chemical diversity of actinomycetes, by categorizing the cases by the type of coculture partner. Furthermore, we discuss the current challenges that need to be overcome to support the elicitation of novel bioactive compounds from actinomycetes.
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Affiliation(s)
- Ji Hun Kim
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Namil Lee
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Soonkyu Hwang
- 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
| | - 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
| | - Bernhard O 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, 2800 Lyngby, 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
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19
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Wu J, Chen D, Wu J, Chu X, Yang Y, Fang L, Zhang W. Comparative Transcriptome Analysis Demonstrates the Positive Effect of the Cyclic AMP Receptor Protein Crp on Daptomycin Biosynthesis in Streptomyces roseosporus. Front Bioeng Biotechnol 2021; 9:618029. [PMID: 34150723 PMCID: PMC8212052 DOI: 10.3389/fbioe.2021.618029] [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: 10/16/2020] [Accepted: 04/23/2021] [Indexed: 11/21/2022] Open
Abstract
Daptomycin, which is produced by Streptomyces roseosporus, has been characterized as a novel cyclic lipopeptide antibiotic that is effective against Gram-positive bacteria. The biosynthesis of daptomycin is regulated by various factors. In the present study, we demonstrated that the cyclic AMP receptor protein (Crp) plays an important role in producing daptomycin in the S. roseosporus industrial strain. We found that daptomycin production from the crp deletion strain decreased drastically, whereas production from the crp overexpression strain increased by 22.1%. Transcriptome and qPCR analyses showed that some genes related to the daptomycin biosynthetic gene cluster (dpt) and the pleiotropic regulator (adpA) were significantly upregulated. RNA-seq also shows Crp to be a multifunctional regulator that modulates primary metabolism and enhances precursor flux to secondary metabolite biosynthesis. These results provide guidance for the development and improvement of potential natural products.
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Affiliation(s)
- Jiequn Wu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Danqing Chen
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Jinrong Wu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Xiaohe Chu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Yongmei Yang
- Hangzhou Zhongmei Huadong Pharmaceutical Co., Ltd., Hangzhou, China
| | - Lina Fang
- Hangzhou Zhongmei Huadong Pharmaceutical Co., Ltd., Hangzhou, China
| | - Wei Zhang
- Hangzhou Zhongmei Huadong Pharmaceutical Co., Ltd., Hangzhou, China
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20
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Krysenko S, Matthews A, Busche T, Bera A, Wohlleben W. Poly- and Monoamine Metabolism in Streptomyces coelicolor: The New Role of Glutamine Synthetase-Like Enzymes in the Survival under Environmental Stress. Microb Physiol 2021; 31:233-247. [PMID: 34044403 DOI: 10.1159/000516644] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 04/17/2021] [Indexed: 11/19/2022]
Abstract
Soil bacteria from the genus Streptomyces, phylum Actinobacteria, feature a complex metabolism and diverse adaptations to environmental stress. These characteristics are consequences of variable nutrition availability in the soil and allow survival under changing nitrogen conditions. Streptomyces coelicolor is a model organism for Actinobacteria and is able to use nitrogen from a variety of sources including unusual compounds originating from the decomposition of dead plant and animal material, such as polyamines or monoamines (like ethanolamine). Assimilation of nitrogen from these sources in S. coelicolor remains largely unstudied. Using microbiological, biochemical and in silico approaches, it was recently possible to postulate polyamine and monoamine (ethanolamine) utilization pathways in S. coelicolor. Glutamine synthetase-like enzymes (GS-like) play a central role in these pathways. Extensive studies have revealed that these enzymes are able to detoxify polyamines or monoamines and allow the survival of S. coelicolor in soil containing an excess of these compounds. On the other hand, at low concentrations, polyamines and monoamines can be utilized as nitrogen and carbon sources. It has been demonstrated that the first step in poly-/monoamine assimilation is catalyzed by GlnA3 (a γ-glutamylpolyamine synthetase) and GlnA4 (a γ-glutamylethanolamide synthetase), respectively. First insights into the regulation of polyamine and ethanolamine metabolism have revealed that the expression of the glnA3 and the glnA4 gene are controlled on the transcriptional level.
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Affiliation(s)
- Sergii Krysenko
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Arne Matthews
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Agnieszka Bera
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Wolfgang Wohlleben
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
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21
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Szafran MJ, Jakimowicz D, Elliot MA. Compaction and control-the role of chromosome-organizing proteins in Streptomyces. FEMS Microbiol Rev 2021; 44:725-739. [PMID: 32658291 DOI: 10.1093/femsre/fuaa028] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/09/2020] [Indexed: 12/17/2022] Open
Abstract
Chromosomes are dynamic entities, whose organization and structure depend on the concerted activity of DNA-binding proteins and DNA-processing enzymes. In bacteria, chromosome replication, segregation, compaction and transcription are all occurring simultaneously, and to ensure that these processes are appropriately coordinated, all bacteria employ a mix of well-conserved and species-specific proteins. Unusually, Streptomyces bacteria have large, linear chromosomes and life cycle stages that include multigenomic filamentous hyphae and unigenomic spores. Moreover, their prolific secondary metabolism yields a wealth of bioactive natural products. These different life cycle stages are associated with profound changes in nucleoid structure and chromosome compaction, and require distinct repertoires of architectural-and regulatory-proteins. To date, chromosome organization is best understood during Streptomyces sporulation, when chromosome segregation and condensation are most evident, and these processes are coordinated with synchronous rounds of cell division. Advances are, however, now being made in understanding how chromosome organization is achieved in multigenomic hyphal compartments, in defining the functional and regulatory interplay between different architectural elements, and in appreciating the transcriptional control exerted by these 'structural' proteins.
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Affiliation(s)
- Marcin J Szafran
- Laboratory of Molecular Microbiology, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Dagmara Jakimowicz
- Laboratory of Molecular Microbiology, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Marie A Elliot
- Department of Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada
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22
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Yushchuk O, Ostash I, Mösker E, Vlasiuk I, Deneka M, Rückert C, Busche T, Fedorenko V, Kalinowski J, Süssmuth RD, Ostash B. Eliciting the silent lucensomycin biosynthetic pathway in Streptomyces cyanogenus S136 via manipulation of the global regulatory gene adpA. Sci Rep 2021; 11:3507. [PMID: 33568768 PMCID: PMC7875965 DOI: 10.1038/s41598-021-82934-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/25/2021] [Indexed: 12/14/2022] Open
Abstract
Actinobacteria are among the most prolific sources of medically and agriculturally important compounds, derived from their biosynthetic gene clusters (BGCs) for specialized (secondary) pathways of metabolism. Genomics witnesses that the majority of actinobacterial BGCs are silent, most likely due to their low or zero transcription. Much effort is put into the search for approaches towards activation of silent BGCs, as this is believed to revitalize the discovery of novel natural products. We hypothesized that the global transcriptional factor AdpA, due to its highly degenerate operator sequence, could be used to upregulate the expression of silent BGCs. Using Streptomyces cyanogenus S136 as a test case, we showed that plasmids expressing either full-length adpA or its DNA-binding domain led to significant changes in the metabolome. These were evident as changes in the accumulation of colored compounds, bioactivity, as well as the emergence of a new pattern of secondary metabolites as revealed by HPLC-ESI-mass spectrometry. We further focused on the most abundant secondary metabolite and identified it as the polyene antibiotic lucensomycin. Finally, we uncovered the entire gene cluster for lucensomycin biosynthesis (lcm), that remained elusive for five decades until now, and outlined an evidence-based scenario for its adpA-mediated activation.
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Affiliation(s)
- Oleksandr Yushchuk
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Rm. 102, Lviv, 79005, Ukraine
| | - Iryna Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Rm. 102, Lviv, 79005, Ukraine
| | - Eva Mösker
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany
| | - Iryna Vlasiuk
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Rm. 102, Lviv, 79005, Ukraine
| | - Maksym Deneka
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Rm. 102, Lviv, 79005, Ukraine
| | - Christian Rückert
- Technology Platform Genomics, CeBiTec, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Tobias Busche
- Technology Platform Genomics, CeBiTec, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Rm. 102, Lviv, 79005, Ukraine
| | - Jörn Kalinowski
- Technology Platform Genomics, CeBiTec, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Roderich D Süssmuth
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany.
| | - Bohdan Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Rm. 102, Lviv, 79005, Ukraine.
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Liu W, Chen Y, Zhou X, Liu J, Zhu J, Wang S, Liu C, Sun D. The Cyclic AMP Receptor Protein, Crp, Is Required for the Decolorization of Acid Yellow 36 in Shewanella putrefaciens CN32. Front Microbiol 2020; 11:596372. [PMID: 33362744 PMCID: PMC7755654 DOI: 10.3389/fmicb.2020.596372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/15/2020] [Indexed: 01/20/2023] Open
Abstract
Shewanella shows good application potentials in the decolorization and detoxification of azo dye wastewater. However, the molecular mechanism of decolorization is still lacking. In this study, it was found that Shewanella putrefaciens CN32 exhibited good decolorization ability to various azo dyes, and a global regulatory protein cAMP receptor protein (Crp) was identified to be required for the decolorization of acid yellow 36 (AY) by constructing a transposon mutant library. Then, the molecular mechanism of AY decolorization regulated by Crp was further investigated. RT-qPCR and electrophoretic mobility shift assay (EMSA) results showed that Crp was able to directly bind to the promoter region of the cymA gene and promote its expression. Riboflavin acting as an electron shuttle could accelerate the AY decolorization efficiency of S. putrefaciens CN32 wild-type (WT) but did not show a promoting effect to Δcrp mutant and ΔcymA mutant, further confirming that Crp promotes the decolorization through regulating electron transport chains. Moreover, the mutant with cymA overexpression could slightly enhance the AY decolorization efficiency compared with the WT strain. In addition, it was found that MtrA, MtrB, and MtrC partially contribute to the electron transfer from CymA to dye molecules, and other main electron transport chains need to be identified in future experiments. This study revealed the molecular mechanism of a global regulator Crp regulating the decolorization of azo dye, which is helpful in understanding the relationship between the decolorization and other metabolic processes in S. putrefaciens CN32.
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Affiliation(s)
- Weijie Liu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Ying Chen
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Xuge Zhou
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Jiawen Liu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Jingrong Zhu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Shiwei Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, China
| | - Cong Liu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Di Sun
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
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24
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Nitta K, Carratore FD, Breitling R, Takano E, Putri SP, Fukusaki E. Multi-Omics Analysis of the Effect of cAMP on Actinorhodin Production in Streptomyces coelicolor. Front Bioeng Biotechnol 2020; 8:595552. [PMID: 33251203 PMCID: PMC7674942 DOI: 10.3389/fbioe.2020.595552] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/08/2020] [Indexed: 12/16/2022] Open
Abstract
Cyclic adenosine monophosphate (cAMP) has been known to play an important role in regulating morphological development and antibiotic production in Streptomyces coelicolor. However, the functional connection between cAMP levels and antibiotic production and the mechanism by which cAMP regulates antibiotic production remain unclear. In this study, metabolomics- and transcriptomics-based multi-omics analysis was applied to S. coelicolor strains that either produce the secondary metabolite actinorhodin (Act) or lack most secondary metabolite biosynthesis pathways including Act. Comparative multi-omics analysis of the two strains revealed that intracellular and extracellular cAMP abundance was strongly correlated with actinorhodin production. Notably, supplementation of cAMP improved cell growth and antibiotic production. Further multi-omics analysis of cAMP-supplemented S. coelicolor cultures showed an increase of guanine and the expression level of purine metabolism genes. Based on this phenomenon, supplementation with 7-methylguanine, a competitive inhibitor of reactions utilizing guanine, with or without additional cAMP supplementation, was performed. This experiment revealed that the reactions inhibited by 7-methylguanine are mediating the positive effect on growth and antibiotic production, which may occur downstream of cAMP supplementation.
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Affiliation(s)
- Katsuaki Nitta
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Francesco Del Carratore
- Department of Chemistry, Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Rainer Breitling
- Department of Chemistry, Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Eriko Takano
- Department of Chemistry, Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Sastia P Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
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25
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A Hierarchical Network of Four Regulatory Genes Controlling Production of the Polyene Antibiotic Candicidin in Streptomyces sp. Strain FR-008. Appl Environ Microbiol 2020; 86:AEM.00055-20. [PMID: 32086301 DOI: 10.1128/aem.00055-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 02/18/2020] [Indexed: 11/20/2022] Open
Abstract
The four regulatory genes fscR1 to fscR4 in Streptomyces sp. strain FR-008 form a genetic arrangement that is widely distributed in macrolide-producing bacteria. Our previous work has demonstrated that fscR1 and fscR4 are critical for production of the polyene antibiotic candicidin. In this study, we further characterized the roles of the other two regulatory genes, fscR2 and fscR3, focusing on the relationship between these four regulatory genes. Disruption of a single or multiple regulatory genes did not affect bacterial growth, but transcription of genes in the candicidin biosynthetic gene cluster decreased, and candicidin production was abolished, indicating a critical role for each of the four regulatory genes, including fscR2 and fscR3, in candicidin biosynthesis. We found that fscR1 to fscR4, although differentially expressed throughout the growth phase, displayed similar temporal expression patterns, with an abrupt increase in the early exponential phase, coincident with initial detection of antibiotic production in the same phase. Our data suggest that the four regulatory genes fscR1 to fscR4 have various degrees of control over structural genes in the biosynthetic cluster under the conditions examined. Extensive transcriptional analysis indicated that complex regulation exists between these four regulatory genes, forming a regulatory network, with fscR1 and fscR4 functioning at a lower level. Comprehensive cross-complementation analysis indicates that functional complementation is restricted among the four regulators and unidirectional, with fscR1 complementing the loss of fscR3 or -4 and fscR4 complementing loss of fscR2 Our study provides more insights into the roles of, and the regulatory network formed by, these four regulatory genes controlling production of an important pharmaceutical compound.IMPORTANCE The regulation of antibiotic biosynthesis by Streptomyces species is complex, especially for biosynthetic gene clusters with multiple regulatory genes. The biosynthetic gene cluster for the polyene antibiotic candicidin contains four consecutive regulatory genes, which encode regulatory proteins from different families and which form a subcluster within the larger biosynthetic gene cluster in Streptomyces sp. FR-008. Syntenic arrangements of these regulatory genes are widely distributed in polyene gene clusters, such as the amphotericin and nystatin gene clusters, suggesting a conserved regulatory mechanism controlling production of these clinically important medicines. However, the relationships between these multiple regulatory genes are unknown. In this study, we determined that each of these four regulatory genes is critical for candicidin production. Additionally, using transcriptional analyses, bioassays, high-performance liquid chromatography (HPLC) analysis, and genetic cross-complementation, we showed that FscR1 to FscR4 comprise a hierarchical regulatory network that controls candicidin production and is likely representative of how expression of other polyene biosynthetic gene clusters is controlled.
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26
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Kim J, Kwon YS, Bae DW, Kwak YS. Proteomic Reference Map and Comparative Analysis between Streptomyces griseus S4-7 and wbiE2 Transcription Factor-Mutant Strain. THE PLANT PATHOLOGY JOURNAL 2020; 36:185-191. [PMID: 32296298 PMCID: PMC7143519 DOI: 10.5423/ppj.nt.02.2020.0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/06/2020] [Accepted: 03/08/2020] [Indexed: 06/11/2023]
Abstract
Streptomyces griseus S4-7, a well-characterized keystone taxon among strawberry microbial communities, shows exceptional disease-preventing ability. The whole-genome sequence, functional genes, and bioactive secondary metabolites of the strain have been described in previous studies. However, proteomics studies of not only the S4-7 strain, but also the Streptomyces genus as a whole, remain limited to date. Therefore, in the present study, we created a proteomics reference map for S. griseus S4-7. Additionally, analysis of differentially expressed proteins was performed against a wblE2 mutant, which was deficient in spore chain development and did not express an antifungal activity-regulatory transcription factor. We believe that our data provide a foundation for further in-depth studies of functional keystone taxa of the phytobiome and elucidation of the mechanisms underlying plant-microbe interactions, es-pecially those involving the Streptomyces genus.
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Affiliation(s)
- Jisu Kim
- Department of Plant Medicine, Gyeongsang National University, Jinju 52828, Korea
| | - Young Sang Kwon
- Environmental Chemistry Research Center, Korea Institute of Toxicology, Jinju 52834, Korea
| | - Dong-Won Bae
- Center for Research Facilities, Gyeongsang National University, Jinju 52828, Korea
| | - Youn-Sig Kwak
- Department of Plant Medicine, Gyeongsang National University, Jinju 52828, Korea
- Division of Applied Life Science (BK21Plus) and RILS, Gyeongsang National University, Jinju 52828, Korea
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27
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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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28
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Regulatory Patterns of Crp on Monensin Biosynthesis in Streptomyces cinnamonensis. Microorganisms 2020; 8:microorganisms8020271. [PMID: 32079344 PMCID: PMC7074812 DOI: 10.3390/microorganisms8020271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/12/2020] [Accepted: 02/15/2020] [Indexed: 01/03/2023] Open
Abstract
Monensin, produced by Streptomyces cinnamonensis, is a polyether ionophore antibiotic widely used as a coccidiostat and a growth-promoting agent in agricultural industry. In this study, cyclic AMP receptor protein (Crp), the global transcription factor for regulation of monensin biosynthesis, was deciphered. The overexpression and antisense RNA silencing of crp revealed that Crp plays a positive role in monensin biosynthesis. RNA sequencing analysis indicated that Crp exhibited extensive regulatory effects on genes involved in both primary metabolic pathways and the monensin biosynthetic gene cluster (mon). The primary metabolic genes, including acs, pckA, accB, acdH, atoB, mutB, epi and ccr, which are pivotal in the biosynthesis of monensin precursors malonyl-CoA, methylmalonyl-CoA and ethylmalonyl-CoA, are transcriptionally upregulated by Crp. Furthermore, Crp upregulates the expression of most mon genes, including all PKS genes (monAI to monAVIII), tailoring genes (monBI-monBII-monCI, monD and monAX) and a pathway-specific regulatory gene (monRI). Enhanced precursor supply and the upregulated expression of mon cluser by Crp would allow the higher production of monensin in S. cinnamonensis. This study gives a more comprehensive understanding of the global regulator Crp and extends the knowledge of Crp regulatory mechanism in Streptomyces.
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29
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Latoscha A, Wörmann ME, Tschowri N. Nucleotide second messengers in Streptomyces. MICROBIOLOGY-SGM 2020; 165:1153-1165. [PMID: 31535967 DOI: 10.1099/mic.0.000846] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Antibiotic producing Streptomyces sense and respond to environmental signals by using nucleotide second messengers, including (p)ppGpp, cAMP, c-di-GMP and c-di-AMP. As summarized in this review, these molecules are important message carriers that coordinate the complex Streptomyces morphological transition from filamentous growth to sporulation along with the secondary metabolite production. Here, we provide an overview of the enzymes that make and break these second messengers and suggest candidates for (p)ppGpp and cAMP enzymes to be studied. We highlight the target molecules that bind these signalling molecules and elaborate individual functions that they control in the context of Streptomyces development. Finally, we discuss open questions in the field, which may guide future studies in this exciting research area.
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Affiliation(s)
- Andreas Latoscha
- Department of Biology / Microbiology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Mirka E Wörmann
- Department of Biology / Microbiology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Natalia Tschowri
- Department of Biology / Microbiology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
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30
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Martín JF, Liras P. The Balance Metabolism Safety Net: Integration of Stress Signals by Interacting Transcriptional Factors in Streptomyces and Related Actinobacteria. Front Microbiol 2020; 10:3120. [PMID: 32038560 PMCID: PMC6988585 DOI: 10.3389/fmicb.2019.03120] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 12/24/2019] [Indexed: 12/19/2022] Open
Abstract
Soil dwelling Streptomyces species are faced with large variations in carbon or nitrogen sources, phosphate, oxygen, iron, sulfur, and other nutrients. These drastic changes in key nutrients result in an unbalanced metabolism that have undesirable consequences for growth, cell differentiation, reproduction, and secondary metabolites biosynthesis. In the last decades evidence has accumulated indicating that mechanisms to correct metabolic unbalances in Streptomyces species take place at the transcriptional level, mediated by different transcriptional factors. For example, the master regulator PhoP and the large SARP-type regulator AfsR bind to overlapping sequences in the afsS promoter and, therefore, compete in the integration of signals of phosphate starvation and S-adenosylmethionine (SAM) concentrations. The cross-talk between phosphate control of metabolism, mediated by the PhoR-PhoP system, and the pleiotropic orphan nitrogen regulator GlnR, is very interesting; PhoP represses GlnR and other nitrogen metabolism genes. The mechanisms of control by GlnR of several promoters of ATP binding cassettes (ABC) sugar transporters and carbon metabolism are highly elaborated. Another important cross-talk that governs nitrogen metabolism involves the competition between GlnR and the transcriptional factor MtrA. GlnR and MtrA exert opposite effects on expression of nitrogen metabolism genes. MtrA, under nitrogen rich conditions, represses expression of nitrogen assimilation and regulatory genes, including GlnR, and competes with GlnR for the GlnR binding sites. Strikingly, these sites also bind to PhoP. Novel examples of interacting transcriptional factors, discovered recently, are discussed to provide a broad view of this interactions. Altogether, these findings indicate that cross-talks between the major transcriptional factors protect the cell metabolic balance. A detailed analysis of the transcriptional factors binding sequences suggests that the transcriptional factors interact with specific regions, either by overlapping the recognition sequence of other factors or by binding to adjacent sites in those regions. Additional interactions on the regulatory backbone are provided by sigma factors, highly phosphorylated nucleotides, cyclic dinucleotides, and small ligands that interact with cognate receptor proteins and with TetR-type transcriptional regulators. We propose to define the signal integration DNA regions (so called integrator sites) that assemble responses to different stress, nutritional or environmental signals. These integrator sites constitute nodes recognized by two, three, or more transcriptional factors to compensate the unbalances produced by metabolic stresses. This interplay mechanism acts as a safety net to prevent major damage to the metabolism under extreme nutritional and environmental conditions.
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Affiliation(s)
- Juan F Martín
- Área de Microbiología, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Paloma Liras
- Área de Microbiología, Departamento de Biología Molecular, Universidad de León, León, Spain
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31
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Xia H, Zhan X, Mao XM, Li YQ. The regulatory cascades of antibiotic production in Streptomyces. World J Microbiol Biotechnol 2020; 36:13. [PMID: 31897764 DOI: 10.1007/s11274-019-2789-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 12/18/2019] [Indexed: 01/27/2023]
Abstract
Streptomyces is famous for its capability to produce the most abundant antibiotics in all kingdoms. All Streptomyces antibiotics are natural products, whose biosynthesis from the so-called gene clusters are elaborately regulated by pyramidal transcriptional regulatory cascades. In the past decades, scientists have striven to unveil the regulatory mechanisms involved in antibiotic production in Streptomyces. Here we mainly focus on three aspects of the regulation on antibiotic production. 1. The onset of antibiotic production triggered by hormones and their coupled receptors as regulators; 2. The cascades of global and pathway-specific regulators governing antibiotic production; 3. The feedback regulation of antibiotics and/or intermediates on the gene cluster expression for their coordinated production. This review will summarize how the antibiotic production is stringently regulated in Streptomyces based on the signaling, and lay a theoretical foundation for improvement of antibiotic production and potentially drug discovery.
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Affiliation(s)
- Haiyang Xia
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, 318000, China
| | - Xinqiao Zhan
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, 318000, China
| | - Xu-Ming Mao
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, 318000, China. .,Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, 310058, China.
| | - Yong-Quan Li
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, 318000, China. .,Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, 310058, China.
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32
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Construction and application of a "superplasmid" for enhanced production of antibiotics. Appl Microbiol Biotechnol 2019; 104:1647-1660. [PMID: 31853567 DOI: 10.1007/s00253-019-10283-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 11/20/2019] [Accepted: 11/26/2019] [Indexed: 10/25/2022]
Abstract
More than two-third of known antibiotics are produced by actinomycetes of the genus Streptomyces. Unfortunately, the production rate from Streptomyces natural antibiotic is extremely slow and thus cannot satisfy industrial demand. In this study, the production of antibiotics by Streptomyces is enhanced by a "superplasmid" which including global regulatory factors afsR, cyclic adenosine receptor protein (CRP), RNA polymerase beta subunits (rpoB) with point mutation and acetyl coenzyme A carboxylase gene (accA2BE), these elements are controlled by the PermE* promoter and then transfer into Streptomyces coelicolor M145, Streptomyces mutabilis TRM45540, Streptomyces hygroscopicus XM201, and Streptomyces hygroscopicus ATCC29253 by conjugation to generate exconjugants. NMR, HPLC, and LC-MS analyses revealed that the superplasmid led to the overproduction of actinorhodin (101.90%), undecylprodigiosin (181.60%) in S. coelicolor M145:: pLQ003, of rapamycin (110%), hygrocin A (163.4%) in S. hygroscopicus ATCC29253:: pLQ003, and of actinomycin D (11.78%) in S. mutabilis TRM45540:: pLQ003, and also to the downregulation of geldanamycin in S. hygroscopicus XM201, but we found that mutant strains in mutant strains of S. hygroscopicus XM201 with regulatory factors inserted showed several peaks that were not found in wild-type strains. The results of the present work indicated that the regulator net working in Streptomyces was not uniform, the superplasmid we constructed possibly caused this overproduction and downregulation in different Streptomyces.
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33
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Zhang X, Hindra, Elliot MA. Unlocking the trove of metabolic treasures: activating silent biosynthetic gene clusters in bacteria and fungi. Curr Opin Microbiol 2019; 51:9-15. [DOI: 10.1016/j.mib.2019.03.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/22/2019] [Accepted: 03/08/2019] [Indexed: 12/25/2022]
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34
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Multi-level regulation of coelimycin synthesis in Streptomyces coelicolor A3(2). Appl Microbiol Biotechnol 2019; 103:6423-6434. [PMID: 31250060 PMCID: PMC6667686 DOI: 10.1007/s00253-019-09975-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/06/2019] [Accepted: 06/12/2019] [Indexed: 11/03/2022]
Abstract
Despite being a yellow pigment visible to the human eye, coelimycin (CPK) remained to be an undiscovered secondary metabolite for over 50 years of Streptomyces research. Although the function of this polyketide is still unclear, we now know that its "cryptic" nature is attributed to a very complex and precise mechanism of cpk gene cluster regulation in the model actinomycete S. coelicolor A3(2). It responds to the stringent culture density and timing of the transition phase by the quorum-sensing butanolide system and to the specific nutrient availability/uptake signals mediated by the global (pleiotropic) regulators; many of which are two-component signal transduction systems. The final effectors of this regulation cascade are predicted to be two cluster-situated Streptomyces antibiotic regulatory proteins (SARPs) putatively activating the expression of type I polyketide synthase (PKS I) genes. After its synthesis, unstable, colorless antibiotic coelimycin A reacts with specific compounds in the medium losing its antibacterial properties and giving rise to yellow coelimycins P1 and P2. Here we review the current knowledge on coelimycin synthesis regulation in Streptomyces coelicolor A3(2). We focus on the regulatory feedback loop which interconnects the butanolide system with other cpk cluster-situated regulators. We also present the effects exerted on cpk genes expression by the global, pleiotropic regulators, and the regulatory connections between cpk and other biosynthetic gene clusters.
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Gehrke EJ, Zhang X, Pimentel-Elardo SM, Johnson AR, Rees CA, Jones SE, Hindra, Gehrke SS, Turvey S, Boursalie S, Hill JE, Carlson EE, Nodwell JR, Elliot MA. Silencing cryptic specialized metabolism in Streptomyces by the nucleoid-associated protein Lsr2. eLife 2019; 8:47691. [PMID: 31215866 PMCID: PMC6584129 DOI: 10.7554/elife.47691] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 06/04/2019] [Indexed: 12/17/2022] Open
Abstract
Lsr2 is a nucleoid-associated protein conserved throughout the actinobacteria, including the antibiotic-producing Streptomyces. Streptomyces species encode paralogous Lsr2 proteins (Lsr2 and Lsr2-like, or LsrL), and we show here that of the two, Lsr2 has greater functional significance. We found that Lsr2 binds AT-rich sequences throughout the chromosome, and broadly represses gene expression. Strikingly, specialized metabolic clusters were over-represented amongst its targets, and the cryptic nature of many of these clusters appears to stem from Lsr2-mediated repression. Manipulating Lsr2 activity in model species and uncharacterized isolates resulted in the production of new metabolites not seen in wild type strains. Our results suggest that the transcriptional silencing of biosynthetic clusters by Lsr2 may protect Streptomyces from the inappropriate expression of specialized metabolites, and provide global control over Streptomyces’ arsenal of signaling and antagonistic compounds.
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Affiliation(s)
- Emma J Gehrke
- Department of Biology, McMaster University, Hamilton, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
| | - Xiafei Zhang
- Department of Biology, McMaster University, Hamilton, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
| | | | - Andrew R Johnson
- Department of Chemistry, Indiana University, Bloomington, United States
| | - Christiaan A Rees
- Geisel School of Medicine and Thayer School of Engineering, Dartmouth College, Hanover, United States
| | - Stephanie E Jones
- Department of Biology, McMaster University, Hamilton, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
| | - Hindra
- Department of Biology, McMaster University, Hamilton, Canada
| | - Sebastian S Gehrke
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Sonya Turvey
- Department of Biology, McMaster University, Hamilton, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
| | - Suzanne Boursalie
- Department of Biology, McMaster University, Hamilton, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
| | - Jane E Hill
- Geisel School of Medicine and Thayer School of Engineering, Dartmouth College, Hanover, United States
| | - Erin E Carlson
- Department of Chemistry, Indiana University, Bloomington, United States.,Department of Chemistry, University of Minnesota, Minneapolis, United States
| | - Justin R Nodwell
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Marie A Elliot
- Department of Biology, McMaster University, Hamilton, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
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36
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McLean TC, Wilkinson B, Hutchings MI, Devine R. Dissolution of the Disparate: Co-ordinate Regulation in Antibiotic Biosynthesis. Antibiotics (Basel) 2019; 8:E83. [PMID: 31216724 PMCID: PMC6627628 DOI: 10.3390/antibiotics8020083] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/10/2019] [Accepted: 06/14/2019] [Indexed: 12/25/2022] Open
Abstract
Discovering new antibiotics is vital to combat the growing threat of antimicrobial resistance. Most currently used antibiotics originate from the natural products of actinomycete bacteria, particularly Streptomyces species, that were discovered over 60 years ago. However, genome sequencing has revealed that most antibiotic-producing microorganisms encode many more natural products than previously thought. Biosynthesis of these natural products is tightly regulated by global and cluster situated regulators (CSRs), most of which respond to unknown environmental stimuli, and this likely explains why many biosynthetic gene clusters (BGCs) are not expressed under laboratory conditions. One approach towards novel natural product discovery is to awaken these cryptic BGCs by re-wiring the regulatory control mechanism(s). Most CSRs bind intergenic regions of DNA in their own BGC to control compound biosynthesis, but some CSRs can control the biosynthesis of multiple natural products by binding to several different BGCs. These cross-cluster regulators present an opportunity for natural product discovery, as the expression of multiple BGCs can be affected through the manipulation of a single regulator. This review describes examples of these different mechanisms, including specific examples of cross-cluster regulation, and assesses the impact that this knowledge may have on the discovery of novel natural products.
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Affiliation(s)
- Thomas C McLean
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Matthew I Hutchings
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
| | - Rebecca Devine
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
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van der Heul HU, Bilyk BL, McDowall KJ, Seipke RF, van Wezel GP. Regulation of antibiotic production in Actinobacteria: new perspectives from the post-genomic era. Nat Prod Rep 2019; 35:575-604. [PMID: 29721572 DOI: 10.1039/c8np00012c] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: 2000 to 2018 The antimicrobial activity of many of their natural products has brought prominence to the Streptomycetaceae, a family of Gram-positive bacteria that inhabit both soil and aquatic sediments. In the natural environment, antimicrobial compounds are likely to limit the growth of competitors, thereby offering a selective advantage to the producer, in particular when nutrients become limited and the developmental programme leading to spores commences. The study of the control of this secondary metabolism continues to offer insights into its integration with a complex lifecycle that takes multiple cues from the environment and primary metabolism. Such information can then be harnessed to devise laboratory screening conditions to discover compounds with new or improved clinical value. Here we provide an update of the review we published in NPR in 2011. Besides providing the essential background, we focus on recent developments in our understanding of the underlying regulatory networks, ecological triggers of natural product biosynthesis, contributions from comparative genomics and approaches to awaken the biosynthesis of otherwise silent or cryptic natural products. In addition, we highlight recent discoveries on the control of antibiotic production in other Actinobacteria, which have gained considerable attention since the start of the genomics revolution. New technologies that have the potential to produce a step change in our understanding of the regulation of secondary metabolism are also described.
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38
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Mycobacteria and their sweet proteins: An overview of protein glycosylation and lipoglycosylation in M. tuberculosis. Tuberculosis (Edinb) 2019; 115:1-13. [PMID: 30948163 DOI: 10.1016/j.tube.2019.01.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 01/10/2019] [Accepted: 01/13/2019] [Indexed: 12/16/2022]
Abstract
Post-translational modifications represent a key aspect of enzyme and protein regulation and function. Post-translational modifications are involved in signaling and response to stress, adaptation to changing environments, regulation of toxic and damaged proteins, proteins localization and host-pathogen interactions. Glycosylation in Mycobacterium tuberculosis (Mtb), is a post-translational modification often found in conjunction with acylation in mycobacterial proteins. Since the discovery of glycosylated proteins in the early 1980's, important advances in our understanding of the mechanisms of protein glycosylation have been made. The number of known glycosylated substrates in Mtb has grown through the years, yet many questions remain. This review will explore the current knowledge on protein glycosylation in Mtb, causative agent of Tuberculosis and number one infectious killer in the world. The mechanism and significance of this post-translational modification, as well as maturation, export and acylation of glycosylated proteins will be reviewed. We expect to provide the reader with an overall view of protein glycosylation in Mtb, as well as the significance of this post-translational modification to the physiology and host-pathogen interactions of this important pathogen. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD011081 and 10.6019/PXD011081.
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Streptomyces: implications and interactions in plant growth promotion. Appl Microbiol Biotechnol 2018; 103:1179-1188. [PMID: 30594952 PMCID: PMC6394478 DOI: 10.1007/s00253-018-09577-y] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 12/10/2018] [Accepted: 12/11/2018] [Indexed: 12/25/2022]
Abstract
With the impending increase of the world population by 2050, more activities have been directed toward the improvement of crop yield and a safe environment. The need for chemical-free agricultural practices is becoming eminent due to the effects of these chemicals on the environment and human health. Actinomycetes constitute a significant percentage of the soil microbial community. The Streptomyces genus, which is the most abundant and arguably the most important actinomycetes, is a good source of bioactive compounds, antibiotics, and extracellular enzymes. These genera have shown over time great potential in improving the future of agriculture. This review highlights and buttresses the agricultural importance of Streptomyces through its biocontrol and plant growth-promoting activities. These activities are highlighted and discussed in this review. Some biocontrol products from this genus are already being marketed while work is still ongoing on this productive genus. Compared to more focus on its biocontrol ability, less work has been done on it as a biofertilizer until recently. This genus is as efficient as a biofertilizer as it is as a biocontrol.
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Current strategies to induce secondary metabolites from microbial biosynthetic cryptic gene clusters. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1351-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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41
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Daniel-Ivad M, Pimentel-Elardo S, Nodwell JR. Control of Specialized Metabolism by Signaling and Transcriptional Regulation: Opportunities for New Platforms for Drug Discovery? Annu Rev Microbiol 2018; 72:25-48. [PMID: 29799791 DOI: 10.1146/annurev-micro-022618-042458] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Specialized metabolites are bacterially produced small molecules that have an extraordinary diversity of important biological activities. They are useful as biochemical probes of living systems, and they have been adapted for use as drugs for human afflictions ranging from infectious diseases to cancer. The biosynthetic genes for these molecules are controlled by a dense network of regulatory mechanisms: Cell-cell signaling and nutrient sensing are conspicuous features of this network. While many components of these mechanisms have been identified, important questions about their biological roles remain shrouded in mystery. In addition to identifying new molecules and solving their mechanisms of action (a central preoccupation in this field), we suggest that addressing questions of quorum sensing versus diffusion sensing and identifying the dominant nutritional and environmental cues for specialized metabolism are important directions for research.
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Affiliation(s)
- M Daniel-Ivad
- Department of Biochemistry, University of Toronto, Ontario M5G 1M1, Canada;
| | - S Pimentel-Elardo
- Department of Biochemistry, University of Toronto, Ontario M5G 1M1, Canada;
| | - J R Nodwell
- Department of Biochemistry, University of Toronto, Ontario M5G 1M1, Canada;
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Kallifidas D, Jiang G, Ding Y, Luesch H. Rational engineering of Streptomyces albus J1074 for the overexpression of secondary metabolite gene clusters. Microb Cell Fact 2018; 17:25. [PMID: 29454348 PMCID: PMC5816538 DOI: 10.1186/s12934-018-0874-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 02/09/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genome sequencing revealed that Streptomyces sp. can dedicate up to ~ 10% of their genomes for the biosynthesis of bioactive secondary metabolites. However, the majority of these biosynthetic gene clusters are only weakly expressed or not at all. Indeed, the biosynthesis of natural products is highly regulated through integrating multiple nutritional and environmental signals perceived by pleiotropic and pathway-specific transcriptional regulators. Although pathway-specific refactoring has been a proved, productive approach for the activation of individual gene clusters, the construction of a global super host strain by targeting pleiotropic-specific genes for the expression of multiple diverse gene clusters is an attractive approach. RESULTS Streptomyces albus J1074 is a gifted heterologous host. To further improve its secondary metabolite expression capability, we rationally engineered the host by targeting genes affecting NADPH availability, precursor flux, cell growth and biosynthetic gene transcriptional activation. These studies led to the activation of the native paulomycin pathway in engineered S. albus strains and importantly the upregulated expression of the heterologous actinorhodin gene cluster. CONCLUSIONS Rational engineering of Streptomyces albus J1074 yielded a series of mutants with improved capabilities for native and heterologous expression of secondary metabolite gene clusters.
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Affiliation(s)
- Dimitris Kallifidas
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610 USA
- Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610 USA
| | - Guangde Jiang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610 USA
- Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610 USA
| | - Yousong Ding
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610 USA
- Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610 USA
| | - Hendrik Luesch
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610 USA
- Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610 USA
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New Kid on the Block: LmbU Expands the Repertoire of Specialized Metabolic Regulators in Streptomyces. J Bacteriol 2017; 200:JB.00559-17. [PMID: 29084856 DOI: 10.1128/jb.00559-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptomyces has an extensive natural product repertoire, including most of the naturally derived antibiotics. Understanding the control of natural product biosynthesis is central to antibiotic discovery and production optimization. Here, Hou et al. (J. Bacteriol. 200:00447-17, 2018, https://doi.org/10.1128/JB.00447-17) report the identification and characterization of a novel regulator-LmbU-that functions primarily as an activator of lincomycin production in Streptomyces lincolnensis Importantly, members of this new regulator family are associated with natural product biosynthetic clusters throughout the streptomycetes and their actinomycete relatives.
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44
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Čihák M, Kameník Z, Šmídová K, Bergman N, Benada O, Kofroňová O, Petříčková K, Bobek J. Secondary Metabolites Produced during the Germination of Streptomyces coelicolor. Front Microbiol 2017; 8:2495. [PMID: 29326665 PMCID: PMC5733532 DOI: 10.3389/fmicb.2017.02495] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/30/2017] [Indexed: 11/16/2022] Open
Abstract
Spore awakening is a series of actions that starts with purely physical processes and continues via the launching of gene expression and metabolic activities, eventually achieving a vegetative phase of growth. In spore-forming microorganisms, the germination process is controlled by intra- and inter-species communication. However, in the Streptomyces clade, which is capable of developing a plethora of valuable compounds, the chemical signals produced during germination have not been systematically studied before. Our previously published data revealed that several secondary metabolite biosynthetic genes are expressed during germination. Therefore, we focus here on the secondary metabolite production during this developmental stage. Using high-performance liquid chromatography-mass spectrometry, we found that the sesquiterpenoid antibiotic albaflavenone, the polyketide germicidin A, and chalcone are produced during germination of the model streptomycete, S. coelicolor. Interestingly, the last two compounds revealed an inhibitory effect on the germination process. The secondary metabolites originating from the early stage of microbial growth may coordinate the development of the producer (quorum sensing) and/or play a role in competitive microflora repression (quorum quenching) in their nature environments.
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Affiliation(s)
- Matouš Čihák
- First Faculty of Medicine, Institute of Immunology and Microbiology, Charles University, Prague, Czechia
| | - Zdeněk Kameník
- Institute of Microbiology, The Czech Academy of Sciences, Prague, Czechia
| | - Klára Šmídová
- First Faculty of Medicine, Institute of Immunology and Microbiology, Charles University, Prague, Czechia.,Institute of Microbiology, The Czech Academy of Sciences, Prague, Czechia
| | - Natalie Bergman
- Chemistry Department, Faculty of Science, J. E. Purkinje University, Ústí nad Labem, Czechia
| | - Oldřich Benada
- Institute of Microbiology, The Czech Academy of Sciences, Prague, Czechia.,Chemistry Department, Faculty of Science, J. E. Purkinje University, Ústí nad Labem, Czechia
| | - Olga Kofroňová
- Institute of Microbiology, The Czech Academy of Sciences, Prague, Czechia
| | - Kateřina Petříčková
- First Faculty of Medicine, Institute of Immunology and Microbiology, Charles University, Prague, Czechia
| | - Jan Bobek
- First Faculty of Medicine, Institute of Immunology and Microbiology, Charles University, Prague, Czechia.,Institute of Microbiology, The Czech Academy of Sciences, Prague, Czechia.,Chemistry Department, Faculty of Science, J. E. Purkinje University, Ústí nad Labem, Czechia
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45
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Mak S, Nodwell JR. Actinorhodin is a redox-active antibiotic with a complex mode of action against Gram-positive cells. Mol Microbiol 2017; 106:597-613. [PMID: 28906045 DOI: 10.1111/mmi.13837] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2017] [Indexed: 11/29/2022]
Abstract
Actinorhodin is a blue-pigmented, redox-active secondary metabolite that is produced by the bacterium Streptomyces coelicolor. Although actinorhodin has been used as a model compound for studying secondary metabolism, its biological activity is not well understood. Indeed, redox-active antibiotics in general have not been widely investigated at the mechanistic level. In this work, we have conducted a comprehensive chemical genetic investigation of actinorhodin's antibacterial effect on target organisms. We find that actinorhodin is a potent, bacteriostatic, pH-responsive antibiotic. Cells activate at least three stress responses in the presence of actinorhodin, including those responsible for managing oxidative damage, protein damage and selected forms of DNA damage. We find that mutations in the Staphylococcus aureus walRKHI operon can confer low-level resistance to actinorhodin, indicating possible targeting of the cell envelope. Our study indicates a complex mechanism of action, involving multiple molecular targets, that is distinct from other antibiotics.
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Affiliation(s)
- Stefanie Mak
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Justin R Nodwell
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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46
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Ordóñez-Robles M, Santos-Beneit F, Albillos SM, Liras P, Martín JF, Rodríguez-García A. Streptomyces tsukubaensis as a new model for carbon repression: transcriptomic response to tacrolimus repressing carbon sources. Appl Microbiol Biotechnol 2017; 101:8181-8195. [PMID: 28983826 DOI: 10.1007/s00253-017-8545-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 09/16/2017] [Accepted: 09/18/2017] [Indexed: 11/26/2022]
Abstract
In this work, we identified glucose and glycerol as tacrolimus repressing carbon sources in the important species Streptomyces tsukubaensis. A genome-wide analysis of the transcriptomic response to glucose and glycerol additions was performed using microarray technology. The transcriptional time series obtained allowed us to compare the transcriptomic profiling of S. tsukubaensis growing under tacrolimus producing and non-producing conditions. The analysis revealed important and different metabolic changes after the additions and a lack of transcriptional activation of the fkb cluster. In addition, we detected important differences in the transcriptional response to glucose between S. tsukubaensis and the model species Streptomyces coelicolor. A number of genes encoding key players of morphological and biochemical differentiation were strongly and permanently downregulated by the carbon sources. Finally, we identified several genes showing transcriptional profiles highly correlated to that of the tacrolimus biosynthetic pathway regulator FkbN that might be potential candidates for the improvement of tacrolimus production.
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Affiliation(s)
- María Ordóñez-Robles
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071, León, Spain
- Instituto de Biotecnología de León, INBIOTEC, Avda. Real no. 1, 24006, León, Spain
| | - Fernando Santos-Beneit
- Instituto de Biotecnología de León, INBIOTEC, Avda. Real no. 1, 24006, León, Spain
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Silvia M Albillos
- Instituto de Biotecnología de León, INBIOTEC, Avda. Real no. 1, 24006, León, Spain
- Departamento de Biotecnología y Ciencia de los Alimentos, Facultad de Ciencias, Universidad de Burgos, 09001, Burgos, Spain
| | - Paloma Liras
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071, León, Spain
- Instituto de Biotecnología de León, INBIOTEC, Avda. Real no. 1, 24006, León, Spain
| | - Juan F Martín
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071, León, Spain
- Instituto de Biotecnología de León, INBIOTEC, Avda. Real no. 1, 24006, León, Spain
| | - Antonio Rodríguez-García
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071, León, Spain.
- Instituto de Biotecnología de León, INBIOTEC, Avda. Real no. 1, 24006, León, Spain.
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47
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Ceniceros A, Dijkhuizen L, Petrusma M, Medema MH. Genome-based exploration of the specialized metabolic capacities of the genus Rhodococcus. BMC Genomics 2017; 18:593. [PMID: 28793878 PMCID: PMC5550956 DOI: 10.1186/s12864-017-3966-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/27/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Bacteria of the genus Rhodococcus are well known for their ability to degrade a large range of organic compounds. Some rhodococci are free-living, saprophytic bacteria; others are animal and plant pathogens. Recently, several studies have shown that their genomes encode putative pathways for the synthesis of a large number of specialized metabolites that are likely to be involved in microbe-microbe and host-microbe interactions. To systematically explore the specialized metabolic potential of this genus, we here performed a comprehensive analysis of the biosynthetic coding capacity across publicly available rhododoccal genomes, and compared these with those of several Mycobacterium strains as well as that of their mutual close relative Amycolicicoccus subflavus. RESULTS Comparative genomic analysis shows that most predicted biosynthetic gene cluster families in these strains are clade-specific and lack any homology with gene clusters encoding the production of known natural products. Interestingly, many of these clusters appear to encode the biosynthesis of lipopeptides, which may play key roles in the diverse environments were rhodococci thrive, by acting as biosurfactants, pathogenicity factors or antimicrobials. We also identified several gene cluster families that are universally shared among all three genera, which therefore may have a more 'primary' role in their physiology. Inactivation of these clusters by mutagenesis might help to generate weaker strains that can be used as live vaccines. CONCLUSIONS The genus Rhodococcus thus provides an interesting target for natural product discovery, in view of its large and mostly uncharacterized biosynthetic repertoire, its relatively fast growth and the availability of effective genetic tools for its genomic modification.
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Affiliation(s)
- Ana Ceniceros
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
| | - Lubbert Dijkhuizen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands.
| | - Mirjan Petrusma
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands.
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48
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Romero-Rodríguez A, Rocha D, Ruiz-Villafán B, Guzmán-Trampe S, Maldonado-Carmona N, Vázquez-Hernández M, Zelarayán A, Rodríguez-Sanoja R, Sánchez S. Carbon catabolite regulation in Streptomyces: new insights and lessons learned. World J Microbiol Biotechnol 2017; 33:162. [PMID: 28770367 DOI: 10.1007/s11274-017-2328-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 07/30/2017] [Indexed: 11/25/2022]
Abstract
One of the most significant control mechanisms of the physiological processes in the genus Streptomyces is carbon catabolite repression (CCR). This mechanism controls the expression of genes involved in the uptake and utilization of alternative carbon sources in Streptomyces and is mostly independent of the phosphoenolpyruvate phosphotransferase system (PTS). CCR also affects morphological differentiation and the synthesis of secondary metabolites, although not all secondary metabolite genes are equally sensitive to the control by the carbon source. Even when the outcome effect of CCR in bacteria is the same, their essential mechanisms can be rather different. Although usually, glucose elicits this phenomenon, other rapidly metabolized carbon sources can also cause CCR. Multiple efforts have been put through to the understanding of the mechanism of CCR in this genus. However, a reasonable mechanism to explain the nature of this process in Streptomyces does not yet exist. Several examples of primary and secondary metabolites subject to CCR will be examined in this review. Additionally, recent advances in the metabolites and protein factors involved in the Streptomyces CCR, as well as their mechanisms will be described and discussed in this review.
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Affiliation(s)
- Alba Romero-Rodríguez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior de Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Diana Rocha
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior de Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Beatriz Ruiz-Villafán
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior de Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Silvia Guzmán-Trampe
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior de Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Nidia Maldonado-Carmona
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior de Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Melissa Vázquez-Hernández
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior de Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Augusto Zelarayán
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior de Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Romina Rodríguez-Sanoja
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior de Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior de Ciudad Universitaria, Mexico City, 04510, Mexico.
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Lu F, Hou Y, Zhang H, Chu Y, Xia H, Tian Y. Regulatory genes and their roles for improvement of antibiotic biosynthesis in Streptomyces. 3 Biotech 2017; 7:250. [PMID: 28718097 DOI: 10.1007/s13205-017-0875-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/07/2017] [Indexed: 01/23/2023] Open
Abstract
The numerous secondary metabolites in Streptomyces spp. are crucial for various applications. For example, cephamycin C is used as an antibiotic, and avermectin is used as an insecticide. Specifically, antibiotic yield is closely related to many factors, such as the external environment, nutrition (including nitrogen and carbon sources), biosynthetic efficiency and the regulatory mechanisms in producing strains. There are various types of regulatory genes that work in different ways, such as pleiotropic (or global) regulatory genes, cluster-situated regulators, which are also called pathway-specific regulatory genes, and many other regulators. The study of regulatory genes that influence antibiotic biosynthesis in Streptomyces spp. not only provides a theoretical basis for antibiotic biosynthesis in Streptomyces but also helps to increase the yield of antibiotics via molecular manipulation of these regulatory genes. Currently, more and more emphasis is being placed on the regulatory genes of antibiotic biosynthetic gene clusters in Streptomyces spp., and many studies on these genes have been performed to improve the yield of antibiotics in Streptomyces. This paper lists many antibiotic biosynthesis regulatory genes in Streptomyces spp. and focuses on frequently investigated regulatory genes that are involved in pathway-specific regulation and pleiotropic regulation and their applications in genetic engineering.
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50
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Vetsigian K. Diverse modes of eco-evolutionary dynamics in communities of antibiotic-producing microorganisms. Nat Ecol Evol 2017. [DOI: 10.1038/s41559-017-0189] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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