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Baukova A, Bogun A, Sushkova S, Minkina T, Mandzhieva S, Alliluev I, Jatav HS, Kalinitchenko V, Rajput VD, Delegan Y. New Insights into Pseudomonas spp.-Produced Antibiotics: Genetic Regulation of Biosynthesis and Implementation in Biotechnology. Antibiotics (Basel) 2024; 13:597. [PMID: 39061279 PMCID: PMC11273644 DOI: 10.3390/antibiotics13070597] [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: 05/23/2024] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024] Open
Abstract
Pseudomonas bacteria are renowned for their remarkable capacity to synthesize antibiotics, namely mupirocin, gluconic acid, pyrrolnitrin, and 2,4-diacetylphloroglucinol (DAPG). While these substances are extensively employed in agricultural biotechnology to safeguard plants against harmful bacteria and fungi, their potential for human medicine and healthcare remains highly promising for common science. However, the challenge of obtaining stable producers that yield higher quantities of these antibiotics continues to be a pertinent concern in modern biotechnology. Although the interest in antibiotics of Pseudomonas bacteria has persisted over the past century, many uncertainties still surround the regulation of the biosynthetic pathways of these compounds. Thus, the present review comprehensively studies the genetic organization and regulation of the biosynthesis of these antibiotics and provides a comprehensive summary of the genetic organization of antibiotic biosynthesis pathways in pseudomonas strains, appealing to both molecular biologists and biotechnologists. In addition, attention is also paid to the application of antibiotics in plant protection.
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Affiliation(s)
- Alexandra Baukova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (A.B.); (A.B.)
- Pushchino Branch of Federal State Budgetary Educational Institution of Higher Education “Russian Biotechnology University (ROSBIOTECH)”, 142290 Pushchino, Moscow Region, Russia
| | - Alexander Bogun
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (A.B.); (A.B.)
| | - Svetlana Sushkova
- Academy of Biology and Biotechnology behalf D.I. Ivanovskyi, Southern Federal University, 344006 Rostov-on-Don, Russia; (S.S.); (T.M.); (S.M.); (I.A.); (V.D.R.)
| | - Tatiana Minkina
- Academy of Biology and Biotechnology behalf D.I. Ivanovskyi, Southern Federal University, 344006 Rostov-on-Don, Russia; (S.S.); (T.M.); (S.M.); (I.A.); (V.D.R.)
| | - Saglara Mandzhieva
- Academy of Biology and Biotechnology behalf D.I. Ivanovskyi, Southern Federal University, 344006 Rostov-on-Don, Russia; (S.S.); (T.M.); (S.M.); (I.A.); (V.D.R.)
| | - Ilya Alliluev
- Academy of Biology and Biotechnology behalf D.I. Ivanovskyi, Southern Federal University, 344006 Rostov-on-Don, Russia; (S.S.); (T.M.); (S.M.); (I.A.); (V.D.R.)
| | - Hanuman Singh Jatav
- Soil Science & Agricultural Chemistry, S.K.N. Agriculture University-Jobner, Jaipur 303329, Rajasthan, India;
| | - Valery Kalinitchenko
- Institute of Fertility of Soils of South Russia, 346493 Persianovka, Rostov Region, Russia;
- All-Russian Research Institute for Phytopathology of the Russian Academy of Sciences, Institute St., 5, 143050 Big Vyazyomy, Moscow Region, Russia
| | - Vishnu D. Rajput
- Academy of Biology and Biotechnology behalf D.I. Ivanovskyi, Southern Federal University, 344006 Rostov-on-Don, Russia; (S.S.); (T.M.); (S.M.); (I.A.); (V.D.R.)
| | - Yanina Delegan
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (A.B.); (A.B.)
- Academy of Biology and Biotechnology behalf D.I. Ivanovskyi, Southern Federal University, 344006 Rostov-on-Don, Russia; (S.S.); (T.M.); (S.M.); (I.A.); (V.D.R.)
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2
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Kudo K, Nishimura T, Izumikawa M, Kozone I, Hashimoto J, Fujie M, Suenaga H, Ikeda H, Satoh N, Shin-Ya K. Capability of a large bacterial artificial chromosome clone harboring multiple biosynthetic gene clusters for the production of diverse compounds. J Antibiot (Tokyo) 2024; 77:288-298. [PMID: 38438499 DOI: 10.1038/s41429-024-00711-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/02/2024] [Accepted: 02/12/2024] [Indexed: 03/06/2024]
Abstract
The biosynthetic gene clusters (BGCs) for the macrocyclic lactone-based polyketide compounds are extremely large-sized because the polyketide synthases that generate the polyketide chains of the basic backbone are of very high molecular weight. In developing a heterologous expression system for the large BGCs amenable to the production of such natural products, we selected concanamycin as an appropriate target. We obtained a bacterial artificial chromosome (BAC) clone with a 211-kb insert harboring the entire BGC responsible for the biosynthesis of concanamycin. Heterologous expression of this clone in a host strain, Streptomyces avermitilis SUKA32, permitted the production of concanamycin, as well as that of two additional aromatic polyketides. Structural elucidation identified these additional products as ent-gephyromycin and a novel compound that was designated JBIR-157. We describe herein sequencing and expression studies performed on these BGCs, demonstrating the utility of large BAC clones for the heterologous expression of cryptic or near-silent loci.
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Affiliation(s)
- Kei Kudo
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Takehiro Nishimura
- Technology Research Association for Next Generation Natural Products Chemistry, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
- Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo, 105-8512, Japan
| | - Miho Izumikawa
- Japan Biological Informatics Consortium (JBIC), 2-4-32 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Ikuko Kozone
- Japan Biological Informatics Consortium (JBIC), 2-4-32 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium (JBIC), 2-4-32 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Manabu Fujie
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Hikaru Suenaga
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
- Technology Research Association for Next Generation Natural Products Chemistry, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Nori Satoh
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Kazuo Shin-Ya
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
- Technology Research Association for Next Generation Natural Products Chemistry, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
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3
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Schlimpert S, Elliot MA. The Best of Both Worlds-Streptomyces coelicolor and Streptomyces venezuelae as Model Species for Studying Antibiotic Production and Bacterial Multicellular Development. J Bacteriol 2023; 205:e0015323. [PMID: 37347176 PMCID: PMC10367585 DOI: 10.1128/jb.00153-23] [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] [Indexed: 06/23/2023] Open
Abstract
Streptomyces bacteria have been studied for more than 80 years thanks to their ability to produce an incredible array of antibiotics and other specialized metabolites and their unusual fungal-like development. Their antibiotic production capabilities have ensured continual interest from both academic and industrial sectors, while their developmental life cycle has provided investigators with unique opportunities to address fundamental questions relating to bacterial multicellular growth. Much of our understanding of the biology and metabolism of these fascinating bacteria, and many of the tools we use to manipulate these organisms, have stemmed from investigations using the model species Streptomyces coelicolor and Streptomyces venezuelae. Here, we explore the pioneering work in S. coelicolor that established foundational genetic principles relating to specialized metabolism and development, alongside the genomic and cell biology developments that led to the emergence of S. venezuelae as a new model system. We highlight key discoveries that have stemmed from studies of these two systems and discuss opportunities for future investigations that leverage the power and understanding provided by S. coelicolor and S. venezuelae.
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Affiliation(s)
- Susan Schlimpert
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Marie A. Elliot
- Department of Biology and M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
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4
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Sun L, Zhu H, Zhang L, Zhu Y, Ratnasekera D, Zhang C, Zhang Q. Aromatic Polyketides from the Mangrove-Derived Streptomyces sp. SCSIO 40069. JOURNAL OF NATURAL PRODUCTS 2023; 86:979-985. [PMID: 36921263 DOI: 10.1021/acs.jnatprod.2c01169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A chemical investigation of Streptomyces sp. SCSIO 40069 resulted in the isolation of a series of aromatic polyketides with rare skeletons, including five new compounds RM18c-RM18g (1-5) and three known ones (6-8). Their structures and absolute configurations were determined by diverse methods, including HRMS and NMR spectra, chemical reaction, Snatzke's method, quantum mechanical-nuclear magnetic resonance (QM-NMR), and X-ray crystallographic analysis. Compounds 1, 2, 4b, and 8 displayed moderate or weak antibacterial activities.
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Affiliation(s)
- Lili Sun
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanning Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya, 572000, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya, 572000, China
| | - Disna Ratnasekera
- Department of Agricultural Biology, Faculty of Agriculture, University of Ruhuna, Matara 81000, Sri Lanka
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya, 572000, China
| | - Qingbo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya, 572000, China
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5
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Enzymology of assembly line synthesis by modular polyketide synthases. Nat Chem Biol 2023; 19:401-415. [PMID: 36914860 DOI: 10.1038/s41589-023-01277-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/31/2023] [Indexed: 03/16/2023]
Abstract
Modular polyketide synthases (PKSs) run catalytic reactions over dozens of steps in a highly orchestrated manner. To accomplish this synthetic feat, they form megadalton multienzyme complexes that are among the most intricate proteins on earth. Polyketide products are of elaborate chemistry with molecular weights of usually several hundred daltons and include clinically important drugs such as erythromycin (antibiotic), rapamycin (immunosuppressant) and epothilone (anticancer drug). The term 'modular' refers to a hierarchical structuring of modules and domains within an overall assembly line arrangement, in which PKS organization is colinearly translated into the polyketide structure. New structural information obtained during the past few years provides substantial direct insight into the orchestration of catalytic events within a PKS module and leads to plausible models for synthetic progress along assembly lines. In light of these structural insights, the PKS engineering field is poised to enter a new era of engineering.
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6
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Xu H, Zhang W, Zhou Y, Yue Z, Yan T, Zhang Y, Liu Y, Hong Y, Liu S, Zhu F, Tao L. Systematic Description of the Content Variation of Natural Products (NPs): To Prompt the Yield of High-Value NPs and the Discovery of New Therapeutics. J Chem Inf Model 2023; 63:1615-1625. [PMID: 36795011 DOI: 10.1021/acs.jcim.2c01459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Natural products (NPs) have long been associated with human production and play a key role in the survival of species. Significant variations in NP content may severely affect the "return on investment" of NP-based industries and render ecological systems vulnerable. Thus, it is crucial to construct a platform that relates variations in NP content to their corresponding mechanisms. In this study, a publicly accessible online platform, NPcVar (http://npcvar.idrblab.net/), was developed, which systematically described the variations of NP contents and their corresponding mechanisms. The platform comprises 2201 NPs and 694 biological resources, including plants, bacteria, and fungi, curated using 126 diverse factors with 26,425 records. Each record contains information about the species, NP, and factors involved, as well as NP content data, parts of the plant that produce NPs, the location of the experiment, and reference information. All factors were manually curated and categorized into 42 classes which belong to four mechanisms (molecular regulation, species factor, environmental condition, and combined factor). Additionally, the cross-links of species and NP to well-established databases and the visualization of NP content under various experimental conditions were provided. In conclusion, NPcVar is a valuable resource for understanding the relationship between species, factors, and NP contents and is anticipated to serve as a promising tool for improving the yield of high-value NPs and facilitating the development of new therapeutics.
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Affiliation(s)
- Hongquan Xu
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Wei Zhang
- The Second Affiliated Hospital, Zhejiang University School of Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Innovation Institute for Affiliated Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Ying Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University, Hangzhou 310000, China
| | - Zixuan Yue
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Tianci Yan
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Yuanyuan Zhang
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Yuhong Liu
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Yanfeng Hong
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Shuiping Liu
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Feng Zhu
- The Second Affiliated Hospital, Zhejiang University School of Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Innovation Institute for Affiliated Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Lin Tao
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
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7
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Cox RJ. Curiouser and curiouser: progress in understanding the programming of iterative highly-reducing polyketide synthases. Nat Prod Rep 2023; 40:9-27. [PMID: 35543313 DOI: 10.1039/d2np00007e] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Covering: 1996-2022Investigations over the last 2 decades have begun to reveal how fungal iterative highly-reducing polyketide synthases are programmed. Both in vitro and in vivo experiments have revealed the interplay of intrinsic and extrinsic selectivity of the component catalytic domains of these systems. Structural biology has begun to provide high resolution structures of hr-PKS that can be used as the basis for their engineering and reprogramming, but progress to-date remains rudimentary. However, significant opportunities exist for translating the current level of understanding into the ability to rationally re-engineer these highly efficient systems for the production of important biologically active compounds through biotechnology.
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Affiliation(s)
- Russell J Cox
- Institute for Organic Chemistry and BMWZ, Leibniz University of Hannover, Schneiderberg 38, 30167, Hannover, Germany.
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8
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Iqbal S, Begum F, Rabaan AA, Aljeldah M, Al Shammari BR, Alawfi A, Alshengeti A, Sulaiman T, Khan A. Classification and Multifaceted Potential of Secondary Metabolites Produced by Bacillus subtilis Group: A Comprehensive Review. Molecules 2023; 28:molecules28030927. [PMID: 36770594 PMCID: PMC9919246 DOI: 10.3390/molecules28030927] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/31/2022] [Accepted: 01/04/2023] [Indexed: 01/19/2023] Open
Abstract
Despite their remarkable biosynthetic potential, Bacillus subtilis have been widely overlooked. However, their capability to withstand harsh conditions (extreme temperature, Ultraviolet (UV) and γ-radiation, and dehydration) and the promiscuous metabolites they synthesize have created increased commercial interest in them as a therapeutic agent, a food preservative, and a plant-pathogen control agent. Nevertheless, the commercial-scale availability of these metabolites is constrained due to challenges in their accessibility via synthesis and low fermentation yields. In the context of this rising in interest, we comprehensively visualized the antimicrobial peptides produced by B. subtilis and highlighted their prospective applications in various industries. Moreover, we proposed and classified these metabolites produced by the B. subtilis group based on their biosynthetic pathways and chemical structures. The biosynthetic pathway, bioactivity, and chemical structure are discussed in detail for each class. We believe that this review will spark a renewed interest in the often disregarded B. subtilis and its remarkable biosynthetic capabilities.
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Affiliation(s)
- Sajid Iqbal
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
- Correspondence: or
| | - Farida Begum
- Department of Biochemistry, Abdul Wali Khan University Mardan (AWKUM), Mardan 23200, Pakistan
| | - Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Mohammed Aljeldah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi Arabia
| | - Basim R. Al Shammari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi Arabia
| | - Abdulsalam Alawfi
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah 41491, Saudi Arabia
| | - Amer Alshengeti
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah 41491, Saudi Arabia
- Department of Infection Prevention and Control, Prince Mohammad Bin Abdulaziz Hospital, National Guard Health Affairs, Al-Madinah 41491, Saudi Arabia
| | - Tarek Sulaiman
- Infectious Diseases Section, Medical Specialties Department, King Fahad Medical City, Riyadh 12231, Saudi Arabia
| | - Alam Khan
- Department of Life Sciences, Abasyn University Islamabad Campus, Islamabad 44000, Pakistan
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9
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Rebets Y, Kormanec J, Lutzhetskyy A, Bernaerts K, Anné J. Cloning and Expression of Metagenomic DNA in Streptomyces lividans and Its Subsequent Fermentation for Optimized Production. Methods Mol Biol 2023; 2555:213-260. [PMID: 36306090 DOI: 10.1007/978-1-0716-2795-2_16] [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] [Indexed: 06/16/2023]
Abstract
The choice of an expression system for the metagenomic DNA of interest is of vital importance for the detection of any particular gene or gene cluster. Most of the screens to date have used the Gram-negative bacterium Escherichia coli as a host for metagenomic gene libraries. However, the use of E. coli introduces a potential host bias since only 40% of the enzymatic activities may be readily recovered by random cloning in E. coli. To recover some of the remaining 60%, alternative cloning hosts such as Streptomyces spp. have been used. Streptomycetes are high-GC Gram-positive bacteria belonging to the Actinomycetales and they have been studied extensively for more than 25 years as an alternative expression system. They are extremely well suited for the expression of DNA from other actinomycetes and genomes of high GC content. Furthermore, due to its high innate, extracellular secretion capacity, Streptomyces can be a better system than E. coli for the production of many extracellular proteins. In this article, an overview is given about the materials and methods for growth and successful expression and secretion of heterologous proteins from diverse origin using Streptomyces lividans as a host. More in detail, an overview is given about the protocols of transformation, type of plasmids used and of vectors useful for integration of DNA into the host chromosome, and accompanying cloning strategies. In addition, various control elements for gene expression including synthetic promoters are discussed, and methods to compare their strength are described. Stable and efficient marker-less integration of the gene of interest under the control of the promoter of choice into S. lividans chromosome via homologous recombination using pAMR23A-based system will be explained. Finally, a basic protocol for bench-top bioreactor experiments which can form the start in the production process optimization and up-scaling will be provided.
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Affiliation(s)
| | - Jan Kormanec
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Andriy Lutzhetskyy
- Department of Pharmaceutical Biotechnology, University of Saarland, Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), University of Saarland, Saarbrücken, Germany
| | - Kristel Bernaerts
- Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety Division, KU Leuven, Leuven, Belgium
| | - Jozef Anné
- Department of Microbiology, Immunology and Transplantation, lab. Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium.
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10
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Wang R, Nguyen J, Hecht J, Schwartz N, Brown KV, Ponomareva LV, Niemczura M, van Dissel D, van Wezel GP, Thorson JS, Metsä-Ketelä M, Shaaban KA, Nybo SE. A BioBricks Metabolic Engineering Platform for the Biosynthesis of Anthracyclinones in Streptomyces coelicolor. ACS Synth Biol 2022; 11:4193-4209. [PMID: 36378506 PMCID: PMC9764417 DOI: 10.1021/acssynbio.2c00498] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Actinomycetes produce a variety of clinically indispensable molecules, such as antineoplastic anthracyclines. However, the actinomycetes are hindered in their further development as genetically engineered hosts for the synthesis of new anthracycline analogues due to their slow growth kinetics associated with their mycelial life cycle and the lack of a comprehensive genetic toolbox for combinatorial biosynthesis. In this report, we tackled both issues via the development of the BIOPOLYMER (BIOBricks POLYketide Metabolic EngineeRing) toolbox: a comprehensive synthetic biology toolbox consisting of engineered strains, promoters, vectors, and biosynthetic genes for the synthesis of anthracyclinones. An improved derivative of the production host Streptomyces coelicolor M1152 was created by deleting the matAB gene cluster that specifies extracellular poly-β-1,6-N-acetylglucosamine (PNAG). This resulted in a loss of mycelial aggregation, with improved biomass accumulation and anthracyclinone production. We then leveraged BIOPOLYMER to engineer four distinct anthracyclinone pathways, identifying optimal combinations of promoters, genes, and vectors to produce aklavinone, 9-epi-aklavinone, auramycinone, and nogalamycinone at titers between 15-20 mg/L. Optimization of nogalamycinone production strains resulted in titers of 103 mg/L. We structurally characterized six anthracyclinone products from fermentations, including new compounds 9,10-seco-7-deoxy-nogalamycinone and 4-O-β-d-glucosyl-nogalamycinone. Lastly, we tested the antiproliferative activity of the anthracyclinones in a mammalian cancer cell viability assay, in which nogalamycinone, auramycinone, and aklavinone exhibited moderate cytotoxicity against several cancer cell lines. We envision that BIOPOLYMER will serve as a foundational platform technology for the synthesis of designer anthracycline analogues.
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Affiliation(s)
- Rongbin Wang
- Department
of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Jennifer Nguyen
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Jacob Hecht
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Nora Schwartz
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Katelyn V. Brown
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Larissa V. Ponomareva
- §Center for Pharmaceutical
Research and Innovation, ∥Department of Pharmaceutical Sciences,
College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Magdalena Niemczura
- Department
of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Dino van Dissel
- Institute
of Biology, Leiden University, Sylviusweg 72, 2333
BE Leiden, The Netherlands,Department
of Biotechnology and Nanomedicine, SINTEF
AS, P.O. Box 4760 Torgarden, NO-7465 Trondheim, Norway
| | - Gilles P. van Wezel
- Institute
of Biology, Leiden University, Sylviusweg 72, 2333
BE Leiden, The Netherlands
| | - Jon S. Thorson
- §Center for Pharmaceutical
Research and Innovation, ∥Department of Pharmaceutical Sciences,
College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Mikko Metsä-Ketelä
- Department
of Life Technologies, University of Turku, FIN-20014 Turku, Finland,
| | - Khaled A. Shaaban
- §Center for Pharmaceutical
Research and Innovation, ∥Department of Pharmaceutical Sciences,
College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States,
| | - S. Eric Nybo
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States,
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11
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Mehta T, Meena M, Nagda A. Bioactive compounds of Curvularia species as a source of various biological activities and biotechnological applications. Front Microbiol 2022; 13:1069095. [PMID: 36569099 PMCID: PMC9777749 DOI: 10.3389/fmicb.2022.1069095] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
Many filamentous fungi are known to produce several secondary metabolites or bioactive compounds during their growth and reproduction with sort of various biological activities. Genus Curvularia (Pleosporaceae) is a dematiaceous filamentous fungus that exhibits a facultative pathogenic and endophytic lifestyle. It contains ~213 species among which Curvularia lunata, C. geniculata, C. clavata, C. pallescens, and C. andropogonis are well-known. Among them, C. lunata is a major pathogenic species of various economical important crops especially cereals of tropical regions while other species like C. geniculata is of endophytic nature with numerous bioactive compounds. Curvularia species contain several diverse groups of secondary metabolites including alkaloids, terpenes, polyketides, and quinones. Which possess various biological activities including anti-cancer, anti-inflammatory, anti-microbial, anti-oxidant, and phytotoxicity. Several genes and gene factors are involved to carry and regulate the expression of these activities which are influenced by environmental signals. Some species of Curvularia also show negative impacts on humans and animals. Apart from their negative effects, there are some beneficial implications like production of enzymes of industrial value, bioherbicides, and source of nanoparticles is reported. Many researchers are working on these aspects all over the world but there is no review in literature which provides significant understanding about these all aspects. Thus, this review will provide significant information about secondary metabolic diversity, their biological activities and biotechnological implications of Curvularia species.
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12
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The Rare Actinobacterium Crossiella sp. Is a Potential Source of New Bioactive Compounds with Activity against Bacteria and Fungi. Microorganisms 2022; 10:microorganisms10081575. [PMID: 36013993 PMCID: PMC9415966 DOI: 10.3390/microorganisms10081575] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/30/2022] [Accepted: 08/03/2022] [Indexed: 11/29/2022] Open
Abstract
Antimicrobial resistance has become a global problem in recent decades. A gradual reduction in drug discoveries has led to the current antimicrobial resistance crisis. Caves and other subsurface environments are underexplored thus far, and they represent indispensable ecological niches that could offer new molecules of interest to medicine and biotechnology. We explored Spanish show caves to test the bioactivity of the bacteria dwelling in the walls and ceilings, as well as airborne bacteria. We reported the isolation of two strains of the genus Crossiella, likely representing a new species, isolated from Altamira Cave, Spain. In vitro and in silico analyses showed the inhibition of pathogenic Gram-positive and Gram-negative bacteria, and fungi, as well as the taxonomical distance of both strains from their closest relative, Crossiella cryophila. The presence of an exclusive combination of gene clusters involved in the synthesis of lanthipeptides, lasso peptides, nonribosomal peptides and polyketides indicates that species of this genus could represent a source of new compounds. Overall, there is promising evidence for antimicrobial discovery in subterranean environments, which increases the possibility of identifying new bioactive molecules.
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13
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Li X, Li X, Zhang QY, Lv P, Jia Y, Wei D. Cofactor-free ActVA-Orf6 monooxygenase catalysis via proton-coupled electron transfer: A QM/MM study. Org Biomol Chem 2022; 20:5525-5534. [DOI: 10.1039/d2ob00848c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Uncovering the comprehensive catalytic mechanism for the activation of triplet O2 through metal-free and cofactor-free oxidases and oxygenases remains one of the most challenging questions in the area of enzymatic...
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14
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Klaus M, Rossini E, Linden A, Paithankar KS, Zeug M, Ignatova Z, Urlaub H, Khosla C, Köfinger J, Hummer G, Grininger M. Solution Structure and Conformational Flexibility of a Polyketide Synthase Module. JACS AU 2021; 1:2162-2171. [PMID: 34977887 PMCID: PMC8717363 DOI: 10.1021/jacsau.1c00043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Indexed: 05/28/2023]
Abstract
Polyketide synthases (PKSs) are versatile C-C bond-forming enzymes that are broadly distributed in bacteria and fungi. The polyketide compound family includes many clinically useful drugs such as the antibiotic erythromycin, the antineoplastic epothilone, and the cholesterol-lowering lovastatin. Harnessing PKSs for custom compound synthesis remains an open challenge, largely because of the lack of knowledge about key structural properties. Particularly, the domains-well characterized on their own-are poorly understood in their arrangement, conformational dynamics, and interplay in the intricate quaternary structure of modular PKSs. Here, we characterize module 2 from the 6-deoxyerythronolide B synthase by small-angle X-ray scattering and cross-linking mass spectrometry with coarse-grained structural modeling. The results of this hybrid approach shed light on the solution structure of a cis-AT type PKS module as well as its inherent conformational dynamics. Supported by a directed evolution approach, we also find that acyl carrier protein (ACP)-mediated substrate shuttling appears to be steered by a nonspecific electrostatic interaction network.
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Affiliation(s)
- Maja Klaus
- Institute
of Organic Chemistry and Chemical Biology, Buchmann Institute for
Molecular Life Sciences, Goethe University
Frankfurt, Max-von-Laue Strasse 15, Frankfurt am Main 60438, Germany
| | - Emanuele Rossini
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue
Strasse 3, Frankfurt am Main 60438, Germany
| | - Andreas Linden
- Max
Planck Institute for Biophysical Chemistry, Am Fassberg 11, Goettingen 37077, Germany
- Institute
for Clinical Chemistry, University Medical
Center Göttingen, Robert Koch Strasse 40, Goettingen 37075, Germany
| | - Karthik S. Paithankar
- Institute
of Organic Chemistry and Chemical Biology, Buchmann Institute for
Molecular Life Sciences, Goethe University
Frankfurt, Max-von-Laue Strasse 15, Frankfurt am Main 60438, Germany
| | - Matthias Zeug
- Institute
of Organic Chemistry and Chemical Biology, Buchmann Institute for
Molecular Life Sciences, Goethe University
Frankfurt, Max-von-Laue Strasse 15, Frankfurt am Main 60438, Germany
| | - Zoya Ignatova
- Institute
for Biochemistry and Molecular Biology, University of Hamburg, Notkestrasse 85, Hamburg 22607, Germany
| | - Henning Urlaub
- Max
Planck Institute for Biophysical Chemistry, Am Fassberg 11, Goettingen 37077, Germany
- Institute
for Clinical Chemistry, University Medical
Center Göttingen, Robert Koch Strasse 40, Goettingen 37075, Germany
| | - Chaitan Khosla
- Department
of Chemistry, Stanford ChEM-H, Department of Chemical Engineering Stanford University, Stanford, California 94305, United States
| | - Jürgen Köfinger
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue
Strasse 3, Frankfurt am Main 60438, Germany
| | - Gerhard Hummer
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue
Strasse 3, Frankfurt am Main 60438, Germany
- Institute
of Biophysics, Goethe University Frankfurt, Max-von-Laue Strasse 1, Frankfurt am Main 60438, Germany
| | - Martin Grininger
- Institute
of Organic Chemistry and Chemical Biology, Buchmann Institute for
Molecular Life Sciences, Goethe University
Frankfurt, Max-von-Laue Strasse 15, Frankfurt am Main 60438, Germany
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15
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An Z, Tao H, Wang Y, Xia B, Zou Y, Fu S, Fang F, Sun X, Huang R, Xia Y, Deng Z, Liu R, Liu T. Increasing the heterologous production of spinosad in Streptomyces albus J1074 by regulating biosynthesis of its polyketide skeleton. Synth Syst Biotechnol 2021; 6:292-301. [PMID: 34584996 PMCID: PMC8453208 DOI: 10.1016/j.synbio.2021.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 08/27/2021] [Accepted: 09/13/2021] [Indexed: 11/18/2022] Open
Abstract
Spinosyns are natural broad-spectrum biological insecticides with a double glycosylated polyketide structure that are produced by aerobic fermentation of the actinomycete, Saccharopolyspora spinosa. However, their large-scale overproduction is hindered by poorly understood bottlenecks in optimizing the original strain, and poor adaptability of the heterologous strain to the production of spinosyn. In this study, we genetically engineered heterologous spinosyn-producer Streptomyces albus J1074 and optimized the fermentation to improve the production of spinosad (spinosyn A and spinosyn D) based on our previous work. We systematically investigated the result of overexpressing polyketide synthase genes (spnA, B, C, D, E) using a constitutive promoter on the spinosad titer in S. albus J1074. The supply of polyketide synthase precursors was then increased to further improve spinosad production. Finally, increasing or replacing the carbon source of the culture medium resulted in a final spinosad titer of ∼70 mg/L, which is the highest titer of spinosad achieved in heterologous Streptomyces species. This research provides useful strategies for efficient heterologous production of natural products.
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Key Words
- 2-[2-hydroxy-1,1-bis(hydroxymethyl)ethyl)amino]ethanesulfonic acid, (TES)
- HPLC-high resolution mass spectrometer, (HPLC-HRMS)
- Heterologous production
- Luria−Bertani, (LB)
- Polyketide
- Polyketide synthase
- Spinosad
- Spinosyn
- Streptomyces
- acetyl-CoA carboxylase, (ACC)
- acetyl-CoA synthetase, (AcsA)
- biosynthetic gene cluster, (BGC)
- high-performance liquid chromatography, (HPLC)
- limit of detection, (LoD)
- overlap extension-polymerase chain reaction, (OE-PCR)
- polyketide synthase, (PKS)
- propionyl-CoA carboxylase, (PCC)
- soya flour mannitol, (SFM)
- β and ε subunits of Acc, (AccBE)
- β and ε subunits of PCC, (PccBE)
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Affiliation(s)
- Ziheng An
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Hui Tao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Yong Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Bingqing Xia
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Yang Zou
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Shuai Fu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Fang Fang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Xiao Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Renqiong Huang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Yao Xia
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Ran Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, PR China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
- Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan, 430075, PR China
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16
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Jiang C, Zhou H, Sun H, He R, Song C, Cui T, Luan J, Fu J, Zhang Y, Jiao N, Wang H. Establishing an efficient salinomycin biosynthetic pathway in three heterologous Streptomyces hosts by constructing a 106-kb multioperon artificial gene cluster. Biotechnol Bioeng 2021; 118:4668-4677. [PMID: 34436784 DOI: 10.1002/bit.27928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/06/2021] [Accepted: 08/19/2021] [Indexed: 11/09/2022]
Abstract
Salinomycin is a promising anticancer drug for chemotherapy. A highly productive biosynthetic gene cluster will facilitate the creation of analogs with improved therapeutic activity and reduced side effects. In this study, we engineered an artificial 106-kb salinomycin gene cluster and achieved efficient heterologous expression in three hosts: Streptomyces coelicolor CH999, S. lividans K4-114, and S. albus J1074. The six-operon artificial gene cluster consists of 25 genes from the native gene cluster organized into five operons and five fatty acid β-oxidation genes into one operon. All operons are driven by strong constitutive promoters. For K4-114 and J1074 harboring the artificial gene cluster, salinomycin production in shake flask cultures was 14.3 mg L-1 and 19.3 mg L-1 , respectively. The production was 1.3-fold and 1.7-fold higher, respectively, than that of the native producer S. albus DSM41398. K4-114 and J1074 harboring the native gene cluster produced an undetectable amount of salinomycin and 0.5 mg L-1 , respectively. CH999 harboring the artificial gene cluster produced 10.3 mg L-1 of salinomycin, which was 92% of the production by DSM41398. The efficient heterologous expression system based on the 106-kb multioperon artificial gene cluster established in this study will facilitate structural diversification of salinomycin, which is valuable for drug development and structure-activity studies.
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Affiliation(s)
- Chanjuan Jiang
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong, China.,State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Haibo Zhou
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Hongluan Sun
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Ruoting He
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Chaoyi Song
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Tianqi Cui
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Ji Luan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Jun Fu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Nianzhi Jiao
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong, China
| | - Hailong Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
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17
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Sharma V, Kaur R, Salwan R. Streptomyces: host for refactoring of diverse bioactive secondary metabolites. 3 Biotech 2021; 11:340. [PMID: 34221811 DOI: 10.1007/s13205-021-02872-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/31/2021] [Indexed: 12/22/2022] Open
Abstract
Microbial secondary metabolites are intensively explored due to their demands in pharmaceutical, agricultural and food industries. Streptomyces are one of the largest sources of secondary metabolites having diverse applications. In particular, the abundance of secondary metabolites encoding biosynthetic gene clusters and presence of wobble position in Streptomyces strains make it potential candidate as a native or heterologous host for secondary metabolite production including several cryptic gene clusters expression. Here, we have discussed the developments in Streptomyces strains genome mining, its exploration as a suitable host and application of synthetic biology for refactoring genetic systems for developing chassis for enhanced as well as novel secondary metabolites with reduced genome and cleaned background.
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Affiliation(s)
- Vivek Sharma
- University Centre for Research and Development, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
| | - Randhir Kaur
- University Centre for Research and Development, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
| | - Richa Salwan
- College of Horticulture and Forestry, Dr YS Parmar University of Horticulture and Forestry, Neri, Hamirpur, Himachal Pradesh 177001 India
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18
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Cai X, Taguchi T, Wang H, Yuki M, Tanaka M, Gong K, Xu J, Zhao Y, Ichinose K, Li A. Identification of a C-Glycosyltransferase Involved in Medermycin Biosynthesis. ACS Chem Biol 2021; 16:1059-1069. [PMID: 34080843 DOI: 10.1021/acschembio.1c00227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
C-Glycosylation in the biosynthesis of bioactive natural products is quite unique, which has not been studied well. Medermycin, as an antitumor agent in the family of pyranonaphthoquinone antibiotics, is featured with unique C-glycosylation. Here, a new C-glycosyltransferase (C-GT) Med-8 was identified to be essential for the biosynthesis of medermycin, as the first example of C-GT to recognize a rare deoxyaminosugar (angolosamine). med-8 and six genes (med-14, -15, -16, -17, -18, and -20 located in the medermycin biosynthetic gene cluster) predicted for the biosynthesis of angolosamine were proved to be functional and sufficient for C-glycosylation. A C-glycosylation cassette composed of these seven genes could convert a proposed substrate into a C-glycosylated product. In conclusion, these genes involved in the C-glycosylation of medermycin were functionally identified and biosynthetically engineered, and they provided the possibility of producing new C-glycosylated compounds.
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Affiliation(s)
- Xiaofeng Cai
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- The College of Life Sciences, Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, Central China Normal University, Wuhan 430079, China
- School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Takaaki Taguchi
- Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo 202-8585, Japan
| | - Huili Wang
- The College of Life Sciences, Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, Central China Normal University, Wuhan 430079, China
| | - Megumi Yuki
- Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo 202-8585, Japan
| | - Megumi Tanaka
- Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo 202-8585, Japan
| | - Kai Gong
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Jinghua Xu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yiming Zhao
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Koji Ichinose
- Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo 202-8585, Japan
| | - Aiying Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- The College of Life Sciences, Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, Central China Normal University, Wuhan 430079, China
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19
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Cai X, Li C, Ichinose K, Jiang Y, Liu M, Wang H, Gong C, Li L, Wan J, Zhao Y, Yang Q, Li A. A single-domain small protein Med-ORF10 regulates the production of antitumour agent medermycin in Streptomyces. Microb Biotechnol 2021; 14:1918-1930. [PMID: 34139068 PMCID: PMC8449675 DOI: 10.1111/1751-7915.13834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/19/2021] [Accepted: 05/03/2021] [Indexed: 11/28/2022] Open
Abstract
Med-ORF10, a single-domain protein with unknown function encoded by a gene located in a gene cluster responsible for the biosynthesis of a novel antitumour antibiotic medermycin, shares high homology to a group of small proteins widely distributed in many aromatic polyketide antibiotic pathways. This group of proteins contain a nuclear transport factor-2 (NTF-2) domain and appear to undergo an evolutionary divergence in their functions. Gene knockout and interspecies complementation suggested that Med-ORF10 plays a regulatory role in medermycin biosynthetic pathway. Overexpression of med-ORF10 in its wild-type strain led to significant increase of medermycin production. It was also shown by qRT-PCR and Western blot that Med-ORF10 controls the expression of genes encoding tailoring enzymes involved in medermycin biosynthesis. Transcriptome analysis and qRT-PCR revealed that Med-ORF10 has pleiotropic effects on more targets. However, there is no similar conserved domain available in Med-ORF10 compared to those of mechanistically known regulatory proteins; meanwhile, no direct interaction between Med-ORF10 and its target promoter DNA was detected via gel shift assay. All these studies suggest that Med-ORF10 regulates medermycin biosynthesis probably via an indirect mode.
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Affiliation(s)
- Xiaofeng Cai
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.,The College of Life Sciences, Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, China.,School of Pharmacy, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Caiyun Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Koji Ichinose
- Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo, 202-8585, Japan
| | - Yali Jiang
- The College of Life Sciences, Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, China
| | - Ming Liu
- The College of Life Sciences, Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, China
| | - Huili Wang
- The College of Life Sciences, Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, China
| | - Caixia Gong
- The College of Life Sciences, Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, China
| | - Le Li
- The College of Life Sciences, Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, China
| | - Juan Wan
- The College of Life Sciences, Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, China
| | - Yiming Zhao
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Qing Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Songhu Road 2005, Shanghai, 200438, China
| | - Aiying Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.,The College of Life Sciences, Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, China
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20
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Cinar B, Demir Z, Tunca S. Heterologous expression of 8-demethyl-tetracenomycin (8-dmtc) affected Streptomyces coelicolor life cycle. Braz J Microbiol 2021; 52:1107-1118. [PMID: 33876406 DOI: 10.1007/s42770-021-00499-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 04/08/2021] [Indexed: 10/21/2022] Open
Abstract
Heterologous hosts are highly important to detect the expression of biosynthetic gene clusters that are cryptic or poorly expressed in their natural hosts. To investigate whether actinorhodin-overproducer Streptomyces coelicolor ∆ppk mutant strain could be a possible prototype as a heterologous expression host, a cosmid containing most of the elm gene cluster of Streptomyces olivaceus Tü2353 was integrated into chromosomes of both S. coelicolor A3(2) and ∆ppk strains. Interestingly, it was found that the production of tetracyclic polyketide 8-demethyl-tetracenomycin (8-DMTC) by recombinant strains caused significant changes in the morphology of cells. All the pellets and clumps were disentangled and mycelia were fragmented in the recombinant strains. Moreover, they produce neither pigmented antibiotics nor agarase and did not sporulate. By eliminating the elm biosynthesis genes from the cosmid, we showed that the morphological properties of recombinants were caused by the production of 8-DMTC. Extracellular application of 8-DMTC on S. coelicolor wild-type cells caused a similar phenotype with the 8-DMTC-producing recombinant strains. The results of this study may contribute to the understanding of the effect of 8-DMTC in Streptomyces since the morphological changes that we have observed have not been reported before. It is also valuable in that it provides useful information about the use of Streptomyces as hosts for the heterologous expression of 8-DMTC.
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Affiliation(s)
- Buse Cinar
- Molecular Biology and Genetics Department, Faculty of Science, Gebze Technical University, 41400 Gebze, Kocaeli, Turkey.,Institute of Microbiology, Leibniz University Hannover, D-30419, Hannover, Germany
| | - Zeynep Demir
- Molecular Biology and Genetics Department, Faculty of Science, Gebze Technical University, 41400 Gebze, Kocaeli, Turkey
| | - Sedef Tunca
- Molecular Biology and Genetics Department, Faculty of Science, Gebze Technical University, 41400 Gebze, Kocaeli, Turkey.
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21
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Stegemann F, Grininger M. Transacylation Kinetics in Fatty Acid and Polyketide Synthases and its Sensitivity to Point Mutations**. ChemCatChem 2021. [DOI: 10.1002/cctc.202002077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Franziska Stegemann
- Institute of Organic Chemistry and Chemical Biology Buchmann Institute for Molecular Life Sciences Goethe University Frankfurt Max-von-Laue-Str. 15 60438 Frankfurt am Main Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology Buchmann Institute for Molecular Life Sciences Goethe University Frankfurt Max-von-Laue-Str. 15 60438 Frankfurt am Main Germany
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22
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Rana B, Bhattacharyya M, Patni B, Arya M, Joshi GK. The Realm of Microbial Pigments in the Food Color Market. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.603892] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Colors are added to food items to make them more attractive and appealing. Food colorants therefore, have an impressive market due to the requirements of food industries. A variety of synthetic coloring agents approved as food additives are available and being used in different types of food prepared or manufactured worldwide. However, there is a growing concern that the use of synthetic colors may exert a negative impact on human health and environment in the long run. The natural pigments obtained from animals, plants, and microorganisms are a promising alternative to synthetic food colorants. Compared to animal and plant sources, microorganisms offer many advantages such as no seasonal impact on the quality and quantity of the pigment, ease of handling and genetic manipulation, amenability to large scale production with little or no impact on biodiversity etc. Among the microorganisms algae, fungi and bacteria are being used to produce pigments as food colorants. This review describes the types of microbial food pigments in use, their benefits, production strategies, and associated challenges.
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23
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Zhu X, Siitonen V, Melançon III CE, Metsä-Ketelä M. Biosynthesis of Diverse Type II Polyketide Core Structures in Streptomyces coelicolor M1152. ACS Synth Biol 2021; 10:243-251. [PMID: 33471506 DOI: 10.1021/acssynbio.0c00482] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Synthetic biology-based approaches have been employed to generate advanced natural product (NP) pathway intermediates to overcome obstacles in NP drug discovery and production. Type II polyketides (PK-IIs) comprise a major subclass of NPs that provide attractive structures for antimicrobial and anticancer drug development. Herein, we have assembled five biosynthetic pathways using a generalized operon design strategy in Streptomyces coelicolor M1152 to allow comparative analysis of metabolite production in an improved heterologous host. The work resulted in production of four distinct PK-II core structures, namely benzoisochromanequinone, angucycline, tetracenomycin, and pentangular compounds, which serve as precursors to diverse pharmaceutically important NPs. Our bottom-up design strategy provided evidence that the biosynthetic pathway of BE-7585A proceeds via an angucycline core structure, instead of rearrangement of an anthracycline aglycone, and led to the discovery of a novel 26-carbon pentangular polyketide. The synthetic biology platform presented here provides an opportunity for further controlled production of diverse PK-IIs in a heterologous host.
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Affiliation(s)
- Xuechen Zhu
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131-0001, United States
| | - Vilja Siitonen
- Department of Biochemistry, University of Turku, Turku, FIN-20014, Finland
| | - Charles E. Melançon III
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131-0001, United States
| | - Mikko Metsä-Ketelä
- Department of Biochemistry, University of Turku, Turku, FIN-20014, Finland
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24
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Guo R, Chen Y, Borgard H, Jijiwa M, Nasu M, He M, Deng Y. The Function and Mechanism of Lipid Molecules and Their Roles in The Diagnosis and Prognosis of Breast Cancer. Molecules 2020; 25:E4864. [PMID: 33096860 PMCID: PMC7588012 DOI: 10.3390/molecules25204864] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/18/2020] [Accepted: 10/19/2020] [Indexed: 12/12/2022] Open
Abstract
Lipids are essential components of cell structure and play important roles in signal transduction between cells and body metabolism. With the continuous development and innovation of lipidomics technology, many studies have shown that the relationship between lipids and cancer is steadily increasing, involving cancer occurrence, proliferation, migration, and apoptosis. Breast cancer has seriously affected the safety and quality of life of human beings worldwide and has become a significant public health problem in modern society, with an especially high incidence among women. Therefore, the issue has inspired scientific researchers to study the link between lipids and breast cancer. This article reviews the research progress of lipidomics, the biological characteristics of lipid molecules, and the relationship between some lipids and cancer drug resistance. Furthermore, this work summarizes the lipid molecules related to breast cancer diagnosis and prognosis, and then it clarifies their impact on the occurrence and development of breast cancer The discussion revolves around the current research hotspot long-chain non-coding RNAs (lncRNAs), summarizes and explains their impact on tumor lipid metabolism, and provides more scientific basis for future cancer research studies.
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Affiliation(s)
- Rui Guo
- School of Public Health, Guangxi Medical University, 22 Shuangyong Rd, Qingxiu District, Nanning 530021, China;
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, 651 Ilalo Street, Honolulu, HI 96813, USA; (Y.C.); (H.B.); (M.J.); (M.N.)
| | - Yu Chen
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, 651 Ilalo Street, Honolulu, HI 96813, USA; (Y.C.); (H.B.); (M.J.); (M.N.)
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa,1955 East West Road, Agricultural Sciences, Honolulu, HI 96822, USA
| | - Heather Borgard
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, 651 Ilalo Street, Honolulu, HI 96813, USA; (Y.C.); (H.B.); (M.J.); (M.N.)
| | - Mayumi Jijiwa
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, 651 Ilalo Street, Honolulu, HI 96813, USA; (Y.C.); (H.B.); (M.J.); (M.N.)
| | - Masaki Nasu
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, 651 Ilalo Street, Honolulu, HI 96813, USA; (Y.C.); (H.B.); (M.J.); (M.N.)
| | - Min He
- School of Public Health, Guangxi Medical University, 22 Shuangyong Rd, Qingxiu District, Nanning 530021, China;
| | - Youping Deng
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, 651 Ilalo Street, Honolulu, HI 96813, USA; (Y.C.); (H.B.); (M.J.); (M.N.)
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25
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Molecular Basis for Polyketide Ketoreductase-Substrate Interactions. Int J Mol Sci 2020; 21:ijms21207562. [PMID: 33066287 PMCID: PMC7588967 DOI: 10.3390/ijms21207562] [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: 09/25/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 11/16/2022] Open
Abstract
Polyketides are a large class of structurally and functionally diverse natural products with important bioactivities. Many polyketides are synthesized by reducing type II polyketide synthases (PKSs), containing transiently interacting standalone enzymes. During synthesis, ketoreductase (KR) catalyzes regiospecific carbonyl to hydroxyl reduction, determining the product outcome, yet little is known about what drives specific KR-substrate interactions. In this study, computational approaches were used to explore KR-substrate interactions based on previously solved apo and mimic cocrystal structures. We found five key factors guiding KR-substrate binding. First, two major substrate binding motifs were identified. Second, substrate length is the key determinant of substrate binding position. Third, two key residues in chain length specificity were confirmed. Fourth, phosphorylation of substrates is critical for binding. Finally, packing/hydrophobic effects primarily determine the binding stability. The molecular bases revealed here will help further engineering of type II PKSs and directed biosynthesis of new polyketides.
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26
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Raps FC, Fäseke VC, Häussinger D, Sparr C. Catalyst‐Controlled Transannular Polyketide Cyclization Cascades: Selective Folding of Macrocyclic Polyketides. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Felix C. Raps
- Department of Chemistry University of Basel St. Johanns-Ring 19 4056 Basel Switzerland
| | - Vincent C. Fäseke
- Department of Chemistry University of Basel St. Johanns-Ring 19 4056 Basel Switzerland
| | - Daniel Häussinger
- Department of Chemistry University of Basel St. Johanns-Ring 19 4056 Basel Switzerland
| | - Christof Sparr
- Department of Chemistry University of Basel St. Johanns-Ring 19 4056 Basel Switzerland
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27
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Raps FC, Fäseke VC, Häussinger D, Sparr C. Catalyst‐Controlled Transannular Polyketide Cyclization Cascades: Selective Folding of Macrocyclic Polyketides. Angew Chem Int Ed Engl 2020; 59:18390-18394. [DOI: 10.1002/anie.202005733] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Felix C. Raps
- Department of Chemistry University of Basel St. Johanns-Ring 19 4056 Basel Switzerland
| | - Vincent C. Fäseke
- Department of Chemistry University of Basel St. Johanns-Ring 19 4056 Basel Switzerland
| | - Daniel Häussinger
- Department of Chemistry University of Basel St. Johanns-Ring 19 4056 Basel Switzerland
| | - Christof Sparr
- Department of Chemistry University of Basel St. Johanns-Ring 19 4056 Basel Switzerland
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28
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Wang J, Zhang R, Chen X, Sun X, Yan Y, Shen X, Yuan Q. Biosynthesis of aromatic polyketides in microorganisms using type II polyketide synthases. Microb Cell Fact 2020; 19:110. [PMID: 32448179 PMCID: PMC7247197 DOI: 10.1186/s12934-020-01367-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/15/2020] [Indexed: 12/13/2022] Open
Abstract
Aromatic polyketides have attractive biological activities and pharmacological properties. Different from other polyketides, aromatic polyketides are characterized by their polycyclic aromatic structure. The biosynthesis of aromatic polyketides is usually accomplished by the type II polyketide synthases (PKSs), which produce highly diverse polyketide chains by sequential condensation of the starter units with extender units, followed by reduction, cyclization, aromatization and tailoring reactions. Recently, significant progress has been made in characterization and engineering of type II PKSs to produce novel products and improve product titers. In this review, we briefly summarize the architectural organizations and genetic contributions of PKS genes to provide insight into the biosynthetic process. We then review the most recent progress in engineered biosynthesis of aromatic polyketides, with emphasis on generating novel molecular structures. We also discuss the current challenges and future perspectives in the rational engineering of type II PKSs for large scale production of aromatic polyketides.
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Affiliation(s)
- Jia Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China
| | - Ruihua Zhang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, University of Georgia, Athens, GA, 30602, USA
| | - Xin Chen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, University of Georgia, Athens, GA, 30602, USA
| | - Xiaolin Shen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China.
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China.
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29
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Zabala D, Song L, Dashti Y, Challis GL, Salas JA, Méndez C. Heterologous reconstitution of the biosynthesis pathway for 4-demethyl-premithramycinone, the aglycon of antitumor polyketide mithramycin. Microb Cell Fact 2020; 19:111. [PMID: 32448325 PMCID: PMC7247220 DOI: 10.1186/s12934-020-01368-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/15/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Mithramycin is an anti-tumor compound of the aureolic acid family produced by Streptomyces argillaceus. Its biosynthesis gene cluster has been cloned and characterized, and several new analogs with improved pharmacological properties have been generated through combinatorial biosynthesis. To further study these compounds as potential new anticancer drugs requires their production yields to be improved significantly. The biosynthesis of mithramycin proceeds through the formation of the key intermediate 4-demethyl-premithramycinone. Extensive studies have characterized the biosynthesis pathway from this intermediate to mithramycin. However, the biosynthesis pathway for 4-demethyl-premithramycinone remains unclear. RESULTS Expression of cosmid cosAR7, containing a set of mithramycin biosynthesis genes, in Streptomyces albus resulted in the production of 4-demethyl-premithramycinone, delimiting genes required for its biosynthesis. Inactivation of mtmL, encoding an ATP-dependent acyl-CoA ligase, led to the accumulation of the tricyclic intermediate 2-hydroxy-nogalonic acid, proving its essential role in the formation of the fourth ring of 4-demethyl-premithramycinone. Expression of different sets of mithramycin biosynthesis genes as cassettes in S. albus and analysis of the resulting metabolites, allowed the reconstitution of the biosynthesis pathway for 4-demethyl-premithramycinone, assigning gene functions and establishing the order of biosynthetic steps. CONCLUSIONS We established the biosynthesis pathway for 4-demethyl-premithramycinone, and identified the minimal set of genes required for its assembly. We propose that the biosynthesis starts with the formation of a linear decaketide by the minimal polyketide synthase MtmPKS. Then, the cyclase/aromatase MtmQ catalyzes the cyclization of the first ring (C7-C12), followed by formation of the second and third rings (C5-C14; C3-C16) catalyzed by the cyclase MtmY. Formation of the fourth ring (C1-C18) requires MtmL and MtmX. Finally, further oxygenation and reduction is catalyzed by MtmOII and MtmTI/MtmTII respectively, to generate the final stable tetracyclic intermediate 4-demethyl-premithramycinone. Understanding the biosynthesis of this compound affords enhanced possibilities to generate new mithramycin analogs and improve their production titers for bioactivity investigation.
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Affiliation(s)
- Daniel Zabala
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), University of Oviedo, Oviedo, Spain
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Lijiang Song
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Yousef Dashti
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Gregory L Challis
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, CV4 7AL, UK
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - José A Salas
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), University of Oviedo, Oviedo, Spain
- Instituto de Investigación Sanitaria de Asturias (ISPA), Oviedo, Spain
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), University of Oviedo, Oviedo, Spain.
- Instituto de Investigación Sanitaria de Asturias (ISPA), Oviedo, Spain.
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30
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Liu AJ, Xie KB, Liu YY, Sui SY, Chen RD, Chen DW, Liu JM, Yang L, Dai JG. Biosynthesis of polyketides by two type III polyketide synthases from Aloe barbadensis. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2020; 22:434-443. [PMID: 31791147 DOI: 10.1080/10286020.2019.1674287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/25/2019] [Accepted: 09/25/2019] [Indexed: 06/10/2023]
Abstract
Various bioactive polyketides have been found in Aloe barbadensis. However, the polyketide synthases (PKSs), which participate in biosynthesis of polyketides in A. barbadensis remain unknown. In this study, two type III PKSs (AbPKS1 and AbPKS2) were identified from A. barbadensis. AbPKS1 and AbPKS2 were able to utilize malonyl-CoA to yield heptaketides (TW93a and aloesone) and octaketides (SEK4 and SEK4b), respectively. AbPKS1 also exhibited catalytic promiscuity in recognizing CoA thioesters of aromatics to produce unusual polyketides. What Is more, a whole cell biocatalysis system with the capability of producing 26.4 mg/L of SEK4/SEK4b and 2.1 mg/L of aloesone was successfully established.
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Affiliation(s)
- Ai-Jing Liu
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Ke-Bo Xie
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs; NHC Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Yu-Yu Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs; NHC Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Song-Yang Sui
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Ri-Dao Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs; NHC Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Da-Wei Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs; NHC Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Ji-Mei Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs; NHC Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Lin Yang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Jun-Gui Dai
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs; NHC Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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31
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Bacteria as genetically programmable producers of bioactive natural products. Nat Rev Chem 2020; 4:172-193. [PMID: 37128046 DOI: 10.1038/s41570-020-0176-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2020] [Indexed: 12/17/2022]
Abstract
Next to plants, bacteria account for most of the biomass on Earth. They are found everywhere, although certain species thrive only in specific ecological niches. These microorganisms biosynthesize a plethora of both primary and secondary metabolites, defined, respectively, as those required for the growth and maintenance of cellular functions and those not required for survival but offering a selective advantage for the producer under certain conditions. As a result, bacterial fermentation has long been used to manufacture valuable natural products of nutritional, agrochemical and pharmaceutical interest. The interactions of secondary metabolites with their biological targets have been optimized by millions of years of evolution and they are, thus, considered to be privileged chemical structures, not only for drug discovery. During the last two decades, functional genomics has allowed for an in-depth understanding of the underlying biosynthetic logic of secondary metabolites. This has, in turn, paved the way for the unprecedented use of bacteria as programmable biochemical workhorses. In this Review, we discuss the multifaceted use of bacteria as biological factories in diverse applications and highlight recent advances in targeted genetic engineering of bacteria for the production of valuable bioactive compounds. Emphasis is on current advances to access nature's abundance of natural products.
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32
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Jakočiūnas T, Klitgaard AK, Kontou EE, Nielsen JB, Thomsen E, Romero-Suarez D, Blin K, Petzold CJ, Gin JW, Tong Y, Gotfredsen CH, Charusanti P, Frandsen RJN, Weber T, Lee SY, Jensen MK, Keasling JD. Programmable polyketide biosynthesis platform for production of aromatic compounds in yeast. Synth Syst Biotechnol 2020; 5:11-18. [PMID: 32021916 PMCID: PMC6992897 DOI: 10.1016/j.synbio.2020.01.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 01/13/2020] [Indexed: 12/14/2022] Open
Abstract
To accelerate the shift to bio-based production and overcome complicated functional implementation of natural and artificial biosynthetic pathways to industry relevant organisms, development of new, versatile, bio-based production platforms is required. Here we present a novel yeast-based platform for biosynthesis of bacterial aromatic polyketides. The platform is based on a synthetic polyketide synthase system enabling a first demonstration of bacterial aromatic polyketide biosynthesis in a eukaryotic host.
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Affiliation(s)
- Tadas Jakočiūnas
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Andreas K Klitgaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Eftychia Eva Kontou
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Julie Bang Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Emil Thomsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - David Romero-Suarez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | | | - Yaojun Tong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Pep Charusanti
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Rasmus J N Frandsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Sang Yup Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.,Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Michael K Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jay D Keasling
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.,Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Chemical and Biomolecular Engineering & Department of Bioengineering University of California, Berkeley, CA, USA.,Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
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33
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Ahmed Y, Rebets Y, Estévez MR, Zapp J, Myronovskyi M, Luzhetskyy A. Engineering of Streptomyces lividans for heterologous expression of secondary metabolite gene clusters. Microb Cell Fact 2020; 19:5. [PMID: 31918711 PMCID: PMC6950998 DOI: 10.1186/s12934-020-1277-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 01/02/2020] [Indexed: 12/04/2022] Open
Abstract
Background Heterologous expression of secondary metabolite gene clusters is used to achieve increased production of desired compounds, activate cryptic gene clusters, manipulate clusters from genetically unamenable strains, obtain natural products from uncultivable species, create new unnatural pathways, etc. Several Streptomyces species are genetically engineered for use as hosts for heterologous expression of gene clusters. S. lividans TK24 is one of the most studied and genetically tractable actinobacteria, which remain untapped. It was therefore important to generate S. lividans chassis strains with clean metabolic backgrounds. Results In this study, we generated a set of S. lividans chassis strains by deleting endogenous gene clusters and introducing additional φC31 attB loci for site-specific integration of foreign DNA. In addition to the simplified metabolic background, the engineered S. lividans strains had better growth characteristics than the parental strain in liquid production medium. The utility of the developed strains was validated by expressing four secondary metabolite gene clusters responsible for the production of different classes of natural products. Engineered strains were found to be superior to the parental strain in production of heterologous natural products. Furthermore, S. lividans-based strains were better producers of amino acid-based natural products than other tested common hosts. Expression of a Streptomyces albus subsp. chlorinus NRRL B-24108 genomic library in the modified S. lividans ΔYA9 and S. albus Del14 strains resulted in the production of 7 potentially new compounds, only one of which was produced in both strains. Conclusion The constructed S. lividans-based strains are a great complement to the panel of heterologous hosts for actinobacterial secondary metabolite gene expression. The expansion of the number of such engineered strains will contribute to an increased success rate in isolation of new natural products originating from the expression of genomic and metagenomic libraries, thus raising the chance to obtain novel biologically active compounds.
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Affiliation(s)
- Yousra Ahmed
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Yuriy Rebets
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | | | - Josef Zapp
- Pharmazeutische Biologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Maksym Myronovskyi
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Andriy Luzhetskyy
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany. .,Helmholtz-Institut für Pharmazeutische Forschung Saarland, Saarbrücken, Germany.
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Musiol-Kroll EM, Tocchetti A, Sosio M, Stegmann E. Challenges and advances in genetic manipulation of filamentous actinomycetes - the remarkable producers of specialized metabolites. Nat Prod Rep 2019; 36:1351-1369. [PMID: 31517370 DOI: 10.1039/c9np00029a] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: up to February 2019Actinomycetes are Gram positive bacteria of the phylum Actinobacteria. These organisms are one of the most important sources of structurally diverse, clinically used antibiotics and other valuable bioactive products, as well as biotechnologically relevant enzymes. Most strains were discovered by their ability to produce a given molecule and were often poorly characterized, physiologically and genetically. The development of genetic methods for Streptomyces and related filamentous actinomycetes has led to the successful manipulation of antibiotic biosynthesis to attain structural modification of microbial metabolites that would have been inaccessible by chemical means and improved production yields. Moreover, genome mining reveals that actinomycete genomes contain multiple biosynthetic gene clusters (BGCs), however only a few of them are expressed under standard laboratory conditions, leading to the production of the respective compound(s). Thus, to access and activate the so-called "silent" BGCs, to improve their biosynthetic potential and to discover novel natural products methodologies for genetic manipulation are required. Although different methods have been applied for many actinomycete strains, genetic engineering is still remaining very challenging for some "underexplored" and poorly characterized actinomycetes. This review summarizes the strategies developed to overcome the obstacles to genetic manipulation of actinomycetes and allowing thereby rational genetic engineering of this industrially relevant group of microorganisms. At the end of this review we give some tips to researchers with limited or no previous experience in genetic manipulation of actinomycetes. The article covers the most relevant literature published until February 2019.
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Affiliation(s)
- Ewa M Musiol-Kroll
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, Auf der Morgenstelle 28, Tübingen, 72076, Germany.
| | | | | | - Evi Stegmann
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, Auf der Morgenstelle 28, Tübingen, 72076, Germany.
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Myronovskyi M, Luzhetskyy A. Heterologous production of small molecules in the optimized Streptomyces hosts. Nat Prod Rep 2019; 36:1281-1294. [PMID: 31453623 DOI: 10.1039/c9np00023b] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Time span of literature covered: 2010-2018The genome mining of streptomycetes has revealed their great biosynthetic potential to produce novel natural products. One of the most promising exploitation routes of this biosynthetic potential is the refactoring and heterologous expression of corresponding biosynthetic gene clusters in a panel of specifically selected and optimized chassis strains. This article will review selected recent reports on heterologous production of natural products in streptomycetes. In the first part, the importance of heterologous production for drug discovery will be discussed. In the second part, the review will discuss recently developed genetic control elements (such as promoters, ribosome binding sites, terminators) and their application to achieve successful heterologous expression of biosynthetic gene clusters. Finally, the most widely used Streptomyces hosts for heterologous expression of biosynthetic gene clusters will be compared in detail. The article will be of interest to natural product chemists, molecular biologists, pharmacists and all individuals working in the natural products drug discovery field.
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Affiliation(s)
| | - Andriy Luzhetskyy
- Saarland University, Department Pharmacy, Saarbrücken, Germany and Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany.
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36
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Highlights of Streptomyces genetics. Heredity (Edinb) 2019; 123:23-32. [PMID: 31189905 DOI: 10.1038/s41437-019-0196-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/06/2019] [Accepted: 02/06/2019] [Indexed: 02/06/2023] Open
Abstract
Sixty years ago, the actinomycetes, which include members of the genus Streptomyces, with their bacterial cellular dimensions but a mycelial growth habit like fungi, were generally regarded as a possible intermediate group, and virtually nothing was known about their genetics. We now know that they are bacteria, but with many original features. Their genome is linear with a unique mode of replication, not circular like those of nearly all other bacteria. They transfer their chromosome from donor to recipient by a conjugation mechanism, but this is radically different from the E. coli paradigm. They have twice as many genes as a typical rod-shaped bacterium like Escherichia coli or Bacillus subtilis, and the genome typically carries 20 or more gene clusters encoding the biosynthesis of antibiotics and other specialised metabolites, only a small proportion of which are expressed under typical laboratory screening conditions. This means that there is a vast number of potentially valuable compounds to be discovered when these 'sleeping' genes are activated. Streptomyces genetics has revolutionised natural product chemistry by facilitating the analysis of novel biosynthetic steps and has led to the ability to engineer novel biosynthetic pathways and hence 'unnatural natural products', with potential to generate lead compounds for use in the struggle to combat the rise of antimicrobial resistance.
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Sen T, Barrow CJ, Deshmukh SK. Microbial Pigments in the Food Industry-Challenges and the Way Forward. Front Nutr 2019; 6:7. [PMID: 30891448 PMCID: PMC6411662 DOI: 10.3389/fnut.2019.00007] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 01/17/2019] [Indexed: 11/30/2022] Open
Abstract
Developing new colors for the food industry is challenging, as colorants need to be compatible with a food flavors, safety, and nutritional value, and which ultimately have a minimal impact on the price of the product. In addition, food colorants should preferably be natural rather than synthetic compounds. Micro-organisms already produce industrially useful natural colorants such as carotenoids and anthocyanins. Microbial food colorants can be produced at scale at relatively low costs. This review highlights the significance of color in the food industry, why there is a need to shift to natural food colors compared to synthetic ones and how using microbial pigments as food colorants, instead of colors from other natural sources, is a preferable option. We also summarize the microbial derived food colorants currently used and discuss their classification based on their chemical structure. Finally, we discuss the challenges faced by the use and development of food grade microbial pigments and how to deal with these challenges, using advanced techniques including metabolic engineering and nanotechnology.
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Affiliation(s)
- Tanuka Sen
- TERI-Deakin Nano Biotechnology Centre, The Energy and Resources Institute, New Delhi, India
| | - Colin J Barrow
- Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin University, Burwood, VIC, Australia
| | - Sunil Kumar Deshmukh
- TERI-Deakin Nano Biotechnology Centre, The Energy and Resources Institute, New Delhi, India
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Song C, Luan J, Cui Q, Duan Q, Li Z, Gao Y, Li R, Li A, Shen Y, Li Y, Stewart AF, Zhang Y, Fu J, Wang H. Enhanced Heterologous Spinosad Production from a 79-kb Synthetic Multioperon Assembly. ACS Synth Biol 2019; 8:137-147. [PMID: 30590919 DOI: 10.1021/acssynbio.8b00402] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Refactoring biosynthetic pathways for enhanced secondary metabolite production is a central challenge for synthetic biology. Here we applied advanced DNA assembly methods and a uniform overexpression logic using constitutive promoters to achieve efficient heterologous production of the complex insecticidal macrolide spinosad. We constructed a 79-kb artificial gene cluster in which 23 biosynthetic genes were grouped into 7 operons, each with a strong constitutive promoter. Compared with the original gene cluster, the artificial gene cluster resulted in a 328-fold enhanced spinosad production in Streptomyces albus J1074. To achieve this goal, we applied the ExoCET DNA assembly method to build a plasmid from 13 GC-rich fragments with high efficiency in one step. Together with our previous direct cloning and recombineering tools, we present new synthetic biology options for refactoring large gene clusters for diverse applications.
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Affiliation(s)
- Chaoyi Song
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Ji Luan
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Qingwen Cui
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Qiuyue Duan
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Zhen Li
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Yunsheng Gao
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Ruijuan Li
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Aiying Li
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Yuemao Shen
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Yuezhong Li
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - A. Francis Stewart
- Genomics, Biotechnology Center, Technische Universität Dresden, Tatzberg 47-51, Dresden 01307, Germany
- GenArc GmbH, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Youming Zhang
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Jun Fu
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Hailong Wang
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
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Abstract
This review highlights the protein–protein interactions between type II post-PKS tailoring enzymes with an emphasis on gilvocarcin and mithramycin.
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Affiliation(s)
- Redding Gober
- Department of Pharmaceutical Sciences
- College of Pharmacy
- University of Kentucky
- Lexington
- USA
| | - Ryan Wheeler
- Department of Pharmaceutical Sciences
- College of Pharmacy
- University of Kentucky
- Lexington
- USA
| | - Jürgen Rohr
- Department of Pharmaceutical Sciences
- College of Pharmacy
- University of Kentucky
- Lexington
- USA
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Nepal KK, Wang G. Streptomycetes: Surrogate hosts for the genetic manipulation of biosynthetic gene clusters and production of natural products. Biotechnol Adv 2019; 37:1-20. [PMID: 30312648 PMCID: PMC6343487 DOI: 10.1016/j.biotechadv.2018.10.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/04/2018] [Accepted: 10/05/2018] [Indexed: 12/23/2022]
Abstract
Due to the worldwide prevalence of multidrug-resistant pathogens and high incidence of diseases such as cancer, there is an urgent need for the discovery and development of new drugs. Nearly half of the FDA-approved drugs are derived from natural products that are produced by living organisms, mainly bacteria, fungi, and plants. Commercial development is often limited by the low yield of the desired compounds expressed by the native producers. In addition, recent advances in whole genome sequencing and bioinformatics have revealed an abundance of cryptic biosynthetic gene clusters within microbial genomes. Genetic manipulation of clusters in the native host is commonly used to awaken poorly expressed or silent gene clusters, however, the lack of feasible genetic manipulation systems in many strains often hinders our ability to engineer the native producers. The transfer of gene clusters into heterologous hosts for expression of partial or entire biosynthetic pathways is an approach that can be used to overcome this limitation. Heterologous expression also facilitates the chimeric fusion of different biosynthetic pathways, leading to the generation of "unnatural" natural products. The genus Streptomyces is especially known to be a prolific source of drugs/antibiotics, its members are often used as heterologous expression hosts. In this review, we summarize recent applications of Streptomyces species, S. coelicolor, S. lividans, S. albus, S. venezuelae and S. avermitilis, as heterologous expression systems.
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Affiliation(s)
- Keshav K Nepal
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 U.S. 1 North, Fort Pierce, FL 34946, USA
| | - Guojun Wang
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 U.S. 1 North, Fort Pierce, FL 34946, USA.
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Shih PM. Towards a sustainable bio-based economy: Redirecting primary metabolism to new products with plant synthetic biology. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:84-91. [PMID: 29907312 PMCID: PMC6005202 DOI: 10.1016/j.plantsci.2018.03.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 02/28/2018] [Accepted: 03/10/2018] [Indexed: 05/23/2023]
Abstract
Humans have domesticated many plant species as indispensable sources of food, materials, and medicines. The dawning era of synthetic biology represents a means to further refine, redesign, and engineer crops to meet various societal and industrial needs. Current and future endeavors will utilize plants as the foundation of a bio-based economy through the photosynthetic production of carbohydrate feedstocks for the microbial fermentation of biofuels and bioproducts, with the end goal of decreasing our dependence on petrochemicals. As our technological capabilities improve, metabolic engineering efforts may expand the utility of plants beyond sugar feedstocks through the direct production of target compounds, including pharmaceuticals, renewable fuels, and commodity chemicals. However, relatively little work has been done to fully realize the potential in redirecting central carbon metabolism in plants for the engineering of novel bioproducts. Although our ability to rationally engineer and manipulate plant metabolism is in its infancy, I highlight some of the opportunities and challenges in applying synthetic biology towards engineering plant primary metabolism.
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Affiliation(s)
- Patrick M Shih
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA, 94608, United States; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Rd, Berkeley, CA, 94720, United States; Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, United States.
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Musiol-Kroll EM, Wohlleben W. Acyltransferases as Tools for Polyketide Synthase Engineering. Antibiotics (Basel) 2018; 7:antibiotics7030062. [PMID: 30022008 PMCID: PMC6164871 DOI: 10.3390/antibiotics7030062] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 07/14/2018] [Accepted: 07/16/2018] [Indexed: 12/16/2022] Open
Abstract
Polyketides belong to the most valuable natural products, including diverse bioactive compounds, such as antibiotics, anticancer drugs, antifungal agents, immunosuppressants and others. Their structures are assembled by polyketide synthases (PKSs). Modular PKSs are composed of modules, which involve sets of domains catalysing the stepwise polyketide biosynthesis. The acyltransferase (AT) domains and their “partners”, the acyl carrier proteins (ACPs), thereby play an essential role. The AT loads the building blocks onto the “substrate acceptor”, the ACP. Thus, the AT dictates which building blocks are incorporated into the polyketide structure. The precursor- and occasionally the ACP-specificity of the ATs differ across the polyketide pathways and therefore, the ATs contribute to the structural diversity within this group of complex natural products. Those features make the AT enzymes one of the most promising tools for manipulation of polyketide assembly lines and generation of new polyketide compounds. However, the AT-based PKS engineering is still not straightforward and thus, rational design of functional PKSs requires detailed understanding of the complex machineries. This review summarizes the attempts of PKS engineering by exploiting the AT attributes for the modification of polyketide structures. The article includes 253 references and covers the most relevant literature published until May 2018.
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Affiliation(s)
- Ewa Maria Musiol-Kroll
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
| | - Wolfgang Wohlleben
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
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Tsai SC(S. The Structural Enzymology of Iterative Aromatic Polyketide Synthases: A Critical Comparison with Fatty Acid Synthases. Annu Rev Biochem 2018; 87:503-531. [DOI: 10.1146/annurev-biochem-063011-164509] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Polyketides are a large family of structurally complex natural products including compounds with important bioactivities. Polyketides are biosynthesized by polyketide synthases (PKSs), multienzyme complexes derived evolutionarily from fatty acid synthases (FASs). The focus of this review is to critically compare the properties of FASs with iterative aromatic PKSs, including type II PKSs and fungal type I nonreducing PKSs whose chemical logic is distinct from that of modular PKSs. This review focuses on structural and enzymological studies that reveal both similarities and striking differences between FASs and aromatic PKSs. The potential application of FAS and aromatic PKS structures for bioengineering future drugs and biofuels is highlighted.
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Affiliation(s)
- Shiou-Chuan (Sheryl) Tsai
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
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Sun L, Zeng J, Cui P, Wang W, Yu D, Zhan J. Manipulation of two regulatory genes for efficient production of chromomycins in Streptomyces reseiscleroticus. J Biol Eng 2018; 12:9. [PMID: 29977332 PMCID: PMC5992853 DOI: 10.1186/s13036-018-0103-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 05/30/2018] [Indexed: 11/23/2022] Open
Abstract
Background Regulatory genes play critical roles in natural product biosynthetic pathways. Chromomycins are promising anticancer natural products from actinomycetes. This study is aimed to create an efficient strain for production of these molecules by manipulating the regulatory genes. Results A putative but silent chromomycin biosynthetic gene cluster was discovered in Streptomyces reseiscleroticus. Heterologous expression of the ketosynthase, chain length factor, and acyl carrier protein in Streptomyces lividans confirmed that they are responsible for the assembly of a decaketide. Two regulatory genes are present in this gene cluster, including SARP-type activator SrcmRI and PadR-like repressor SrcmRII. Either overexpression of SrcmRI or disruption of SrcmRII turned on the biosynthetic pathway of chromomycins. The production titers of chromomycin A3/A2 in R5 agar in these two strains reached 8.9 ± 1.2/13.2 ± 1.6 and 49.3 ± 4.3/53.3 ± 3.6 mg/L, respectively. An engineered strain was then constructed with both SrcmRII disruption and SrcmRI overexpression, which produced chromomycins A3 and A2 in R5 agar at 69.4 ± 7.6 and 81.7 ± 7.2 mg/L, respectively. Optimization of the culture conditions further increased the titers of chromomycins A3 and A2 respectively to 145.1 ± 15.3 and 158.3 ± 15.4 mg/L in liquid fermentation. Conclusions This work revealed the synergistic effect of manipulation of pathway repressor and activator genes in the engineering of a natural product biosynthetic pathway. The resulting engineered strain showed the highest production titers of chromomycins by a strain of Streptomyces, providing an efficient way to produce these pharmaceutically valuable molecules. Electronic supplementary material The online version of this article (10.1186/s13036-018-0103-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lei Sun
- 1Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT 84322-4105 USA
| | - Jia Zeng
- 1Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT 84322-4105 USA
| | - Peiwu Cui
- 2TCM and Ethnomedicine Innovation & Development Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, Hunan 410208 China
| | - Wei Wang
- 2TCM and Ethnomedicine Innovation & Development Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, Hunan 410208 China
| | - Dayu Yu
- Hangzhou Viablife Biotech Co., Ltd., 1 Jingyi Road, Yuhang District, Hangzhou, Zhejiang 311113 China
| | - Jixun Zhan
- 1Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT 84322-4105 USA.,2TCM and Ethnomedicine Innovation & Development Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, Hunan 410208 China
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Andersen-Ranberg J, Kongstad KT, Nafisi M, Staerk D, Okkels FT, Mortensen UH, Lindberg Møller B, Frandsen RJN, Kannangara R. Synthesis of C-Glucosylated Octaketide Anthraquinones in Nicotiana benthamiana by Using a Multispecies-Based Biosynthetic Pathway. Chembiochem 2017; 18:1893-1897. [PMID: 28719729 DOI: 10.1002/cbic.201700331] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Indexed: 12/27/2022]
Abstract
Carminic acid is a C-glucosylated octaketide anthraquinone and the main constituent of the natural dye carmine (E120), possessing unique coloring, stability, and solubility properties. Despite being used since ancient times, longstanding efforts to elucidate its route of biosynthesis have been unsuccessful. Herein, a novel combination of enzymes derived from a plant (Aloe arborescens, Aa), a bacterium (Streptomyces sp. R1128, St), and an insect (Dactylopius coccus, Dc) that allows for the biosynthesis of the C-glucosylated anthraquinone, dcII, a precursor for carminic acid, is reported. The pathway, which consists of AaOKS, StZhuI, StZhuJ, and DcUGT2, presents an alternative biosynthetic approach for the production of polyketides by using a type III polyketide synthase (PKS) and tailoring enzymes originating from a type II PKS system. The current study showcases the power of using transient expression in Nicotiana benthamiana for efficient and rapid identification of functional biosynthetic pathways, including both soluble and membrane-bound enzymes.
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Affiliation(s)
- Johan Andersen-Ranberg
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
- Present address: Department of Plant Microbial Biology, University of California Berkeley, 441 Koshland Hall, Berkeley, CA, 94720-3102, USA
| | - Kenneth Thermann Kongstad
- Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Majse Nafisi
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
- Chr. Hansen A/S, Bøge Alle 10-12, 2970, Hørsholm, Denmark
| | - Dan Staerk
- Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Finn Thyge Okkels
- Chr. Hansen A/S, Bøge Alle 10-12, 2970, Hørsholm, Denmark
- Present address: ActaBio ApS, Kongemarken 11, 4000, Roskilde, Denmark
| | - Uffe Hasbro Mortensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221 and 223, 2800, Kongens Lyngby, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Rasmus John Normand Frandsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221 and 223, 2800, Kongens Lyngby, Denmark
| | - Rubini Kannangara
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
- Chr. Hansen A/S, Bøge Alle 10-12, 2970, Hørsholm, Denmark
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Liang C, Hu R, Ramelot TA, Kennedy MA, Li X, Yang Y, Zhu J, Liu M. Chemical shift assignments of polyketide cyclase_like protein CGL2373 from Corynebacterium glutamicum. BIOMOLECULAR NMR ASSIGNMENTS 2017; 11:289-292. [PMID: 28825188 DOI: 10.1007/s12104-017-9765-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 08/10/2017] [Indexed: 06/07/2023]
Abstract
Protein CGL2373 from Corynebacterium glutamicum, which is 155 amino acids long and 17.7 kDa, is a member of the polyketide_cyc2 family. As a potential polyketide cyclase, it may play an important role in the biosynthesis of aromatic polyketides that are the source of many bioactive molecules. Here we report the complete 1H, 13C and 15N chemical shift assignments of CGL2373, which lays a foundation for further structural and functional research.
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Affiliation(s)
- Chunjie Liang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rui Hu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Theresa A Ramelot
- Department of Chemistry and Biochemistry, and the Northeast Structural Genomics Consortium, Miami University, Oxford, OH, 45056, USA
| | - Michael A Kennedy
- Department of Chemistry and Biochemistry, and the Northeast Structural Genomics Consortium, Miami University, Oxford, OH, 45056, USA
| | - Xuegang Li
- College of Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China.
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Narsing Rao MP, Xiao M, Li WJ. Fungal and Bacterial Pigments: Secondary Metabolites with Wide Applications. Front Microbiol 2017; 8:1113. [PMID: 28690593 PMCID: PMC5479939 DOI: 10.3389/fmicb.2017.01113] [Citation(s) in RCA: 173] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 05/31/2017] [Indexed: 12/21/2022] Open
Abstract
The demand for natural colors is increasing day by day due to harmful effects of some synthetic dyes. Bacterial and fungal pigments provide a readily available alternative source of naturally derived pigments. In contrast to other natural pigments, they have enormous advantages including rapid growth, easy processing, and independence of weather conditions. Apart from colorant, bacterial and fungal pigments possess many biological properties such as antioxidant, antimicrobial and anticancer activity. This review outlines different types of pigments. It lists some bacterial and fungal pigments and current bacterial and fungal pigment status and challenges. It also focuses on possible fungal and bacterial pigment applications.
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Affiliation(s)
- Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen UniversityGuangzhou, China
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen UniversityGuangzhou, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen UniversityGuangzhou, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of SciencesÛrúmqi, China
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48
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Tan GY, Deng K, Liu X, Tao H, Chang Y, Chen J, Chen K, Sheng Z, Deng Z, Liu T. Heterologous Biosynthesis of Spinosad: An Omics-Guided Large Polyketide Synthase Gene Cluster Reconstitution in Streptomyces. ACS Synth Biol 2017; 6:995-1005. [PMID: 28264562 DOI: 10.1021/acssynbio.6b00330] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the advent of the genomics era, heterologous gene expression has been used extensively as a means of accessing natural products (NPs) from environmental DNA samples. However, the heterologous production of NPs often has very low efficiency or is unable to produce targeted NPs. Moreover, due to the complicated transcriptional and metabolic regulation of NP biosynthesis in native producers, especially in the cases of genome mining, it is also difficult to rationally and systematically engineer synthetic pathways to improved NPs biosynthetic efficiency. In this study, various strategies ranging from heterologous production of a NP to subsequent application of omics-guided synthetic modules optimization for efficient biosynthesis of NPs with complex structure have been developed. Heterologous production of spinosyn in Streptomyces spp. has been demonstrated as an example of the application of these approaches. Combined with the targeted omics approach, several rate-limiting steps of spinosyn heterologous production in Streptomyces spp. have been revealed. Subsequent engineering work overcame three of selected rate-limiting steps, and the production of spinosad was increased step by step and finally reached 1460 μg/L, which is about 1000-fold higher than the original strain S. albus J1074 (C4I6-M). These results indicated that the omics platform developed in this work was a powerful tool for guiding the rational refactoring of heterologous biosynthetic pathway in Streptomyces host. Additionally, this work lays the foundation for further studies aimed at the more efficient production of spinosyn in a heterologous host. And the strategy developed in this study is expected to become readily adaptable to highly efficient heterologous production of other NPs with complex structure.
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Affiliation(s)
- Gao-Yi Tan
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- State
Key Laboratory of Bioreactor Engineering, School of Bioengineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Kunhua Deng
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- Hubei
Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Xinhua Liu
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- Hubei
Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Hui Tao
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- Hubei
Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Yingying Chang
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- Hubei
Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Jia Chen
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- Hubei
Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Kai Chen
- Shenyang Research Institute of Chemical Industry Ltd., Co., SINOCHEM Group, Shengyang 110021, China
| | - Zhi Sheng
- Shenyang Research Institute of Chemical Industry Ltd., Co., SINOCHEM Group, Shengyang 110021, China
| | - Zixin Deng
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- Hubei
Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Tiangang Liu
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- Hubei
Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
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49
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Taguchi T, Awakawa T, Nishihara Y, Kawamura M, Ohnishi Y, Ichinose K. Bifunctionality of ActIV as a Cyclase-Thioesterase Revealed by in Vitro Reconstitution of Actinorhodin Biosynthesis in Streptomyces coelicolor A3(2). Chembiochem 2017; 18:316-323. [PMID: 27897367 DOI: 10.1002/cbic.201600589] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Indexed: 11/11/2022]
Abstract
Type II polyketide synthases iteratively generate a nascent polyketide thioester of the acyl carrier protein (ACP); this is structurally modified to produce an ACP-free intermediate towards the final metabolite. However, the timing of ACP off-loading is not well defined because of the lack of an apparent thioesterase (TE) among relevant biosynthetic enzymes. Here, ActIV, which had been assigned as a second ring cyclase (CYC) in actinorhodin (ACT) biosynthesis, was shown to possess TE activity in vitro with a model substrate, anthraquinone-2-carboxylic acid-N-acetylcysteamine. In order to investigate its function further, the ACT biosynthetic pathway in Streptomyces coelicolor A3(2) was reconstituted in vitro in a stepwise fashion up to (S)-DNPA, and the product of ActIV reaction was characterized as an ACP-free bicyclic intermediate. These findings indicate that ActIV is a bifunctional CYC-TE and provide clear evidence for the release timing of the intermediate from the ACP anchor.
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Affiliation(s)
- Takaaki Taguchi
- Research Institute of Pharmaceutical Sciences, Musashino University, Shinmachi, Nishitokyo-shi, Tokyo, 202-8585, Japan
| | - Takayoshi Awakawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.,Present address: Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yukitaka Nishihara
- Research Institute of Pharmaceutical Sciences, Musashino University, Shinmachi, Nishitokyo-shi, Tokyo, 202-8585, Japan
| | - Michiho Kawamura
- Research Institute of Pharmaceutical Sciences, Musashino University, Shinmachi, Nishitokyo-shi, Tokyo, 202-8585, Japan
| | - Yasuo Ohnishi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Koji Ichinose
- Research Institute of Pharmaceutical Sciences, Musashino University, Shinmachi, Nishitokyo-shi, Tokyo, 202-8585, Japan
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50
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Tan GY, Liu T. Rational synthetic pathway refactoring of natural products biosynthesis in actinobacteria. Metab Eng 2017; 39:228-236. [DOI: 10.1016/j.ymben.2016.12.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 10/31/2016] [Accepted: 12/05/2016] [Indexed: 11/28/2022]
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