1
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Wu Y, Peng X, Fan D, Han S, Yang X. Pathway reconstruction and metabolic engineering for the de novo and enhancing production of monacolin J in Pichia pastoris. Bioprocess Biosyst Eng 2024:10.1007/s00449-024-03069-2. [PMID: 39085651 DOI: 10.1007/s00449-024-03069-2] [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: 05/10/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024]
Abstract
The statin is the primary cholesterol-lowering drug. Monacolin J (MJ) is a key intermediate in the biosynthetic pathway of statin. It was obtained in industry by the alkaline hydrolysis of lovastatin. The hydrolysis process resulted in multiple by-products and expensive cost of wastewater treatment. In this work, we used Pichia pastoris as the host to produce the MJ. The biosynthesis pathway of MJ was built in P. pastoris. The stable recombinant strain MJ2 was obtained by the CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 genome-editing tool, and produced the MJ titer of 153.6 ± 2.4 mg/L. The metabolic engineering was utilized to enhance the production of MJ, and the fermentation condition was optimized. The MJ titer of 357.5 ± 5.0 mg/L was obtained from the recombinant strain MJ5-AZ with ATP-dependent citrate lyase (ACL), glucose-6-phosphate dehydrogenase (ZWF1) and four lovB genes, 132.7% higher than that from the original strain MJ2. The recombinant strain MJ5-AZ was cultured in a 7-L fermenter, and the MJ titer of 1493.0 ± 9.2 mg/L was achieved. The results suggested that increasing the gene dosage of rate-limiting step in the biosynthesis pathway of chemicals could improve the titer of production. It might be applicable to the production optimization of other polyketide metabolites.
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Affiliation(s)
- Yiping Wu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, Guangdong, People's Republic of China
| | - Xuefang Peng
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, Guangdong, People's Republic of China
| | - Dexun Fan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, Guangdong, People's Republic of China
| | - Shuangyan Han
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, Guangdong, People's Republic of China
| | - Xiaorong Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, Guangdong, People's Republic of China.
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2
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Glasser NR, Cui D, Risser DD, Okafor CD, Balskus EP. Accelerating the discovery of alkyl halide-derived natural products using halide depletion. Nat Chem 2024; 16:173-182. [PMID: 38216751 PMCID: PMC10849952 DOI: 10.1038/s41557-023-01390-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/30/2023] [Indexed: 01/14/2024]
Abstract
Even in the genomic era, microbial natural product discovery workflows can be laborious and limited in their ability to target molecules with specific structural features. Here we leverage an understanding of biosynthesis to develop a workflow that targets the discovery of alkyl halide-derived natural products by depleting halide anions, a key biosynthetic substrate for enzymatic halogenation, from microbial growth media. By comparing the metabolomes of bacterial cultures grown in halide-replete and deficient media, we rapidly discovered the nostochlorosides, the products of an orphan halogenase-encoding gene cluster from Nostoc punctiforme ATCC 29133. We further found that these products, a family of unusual chlorinated glycolipids featuring the rare sugar gulose, are polymerized via an unprecedented enzymatic etherification reaction. Together, our results highlight the power of leveraging an understanding of biosynthetic logic to streamline natural product discovery.
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Affiliation(s)
- Nathaniel R Glasser
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Dongtao Cui
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Douglas D Risser
- Department of Biology, University of the Pacific, Stockton, CA, USA
| | - C Denise Okafor
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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3
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Kouprina N, Larionov V. Transformation-associated recombination (TAR) cloning and its applications for gene function; genome architecture and evolution; biotechnology and biomedicine. Oncotarget 2023; 14:1009-1033. [PMID: 38147065 PMCID: PMC10750837 DOI: 10.18632/oncotarget.28546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 11/27/2023] [Indexed: 12/27/2023] Open
Abstract
Transformation-associated recombination (TAR) cloning represents a unique tool to selectively and efficiently recover a given chromosomal segment up to several hundred kb in length from complex genomes (such as animals and plants) and simple genomes (such as bacteria and viruses). The technique exploits a high level of homologous recombination in the yeast Sacharomyces cerevisiae. In this review, we summarize multiple applications of the pioneering TAR cloning technique, developed previously for complex genomes, for functional, evolutionary, and structural studies, and extended the modified TAR versions to isolate biosynthetic gene clusters (BGCs) from microbes, which are the major source of pharmacological agents and industrial compounds, and to engineer synthetic viruses with novel properties to design a new generation of vaccines. TAR cloning was adapted as a reliable method for the assembly of synthetic microbe genomes for fundamental research. In this review, we also discuss how the TAR cloning in combination with HAC (human artificial chromosome)- and CRISPR-based technologies may contribute to the future.
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Affiliation(s)
- Natalay Kouprina
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
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4
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Schmidt M, Lee N, Zhan C, Roberts JB, Nava AA, Keiser LS, Vilchez AA, Chen Y, Petzold CJ, Haushalter RW, Blank LM, Keasling JD. Maximizing Heterologous Expression of Engineered Type I Polyketide Synthases: Investigating Codon Optimization Strategies. ACS Synth Biol 2023; 12:3366-3380. [PMID: 37851920 PMCID: PMC10661030 DOI: 10.1021/acssynbio.3c00367] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Indexed: 10/20/2023]
Abstract
Type I polyketide synthases (T1PKSs) hold enormous potential as a rational production platform for the biosynthesis of specialty chemicals. However, despite great progress in this field, the heterologous expression of PKSs remains a major challenge. One of the first measures to improve heterologous gene expression can be codon optimization. Although controversial, choosing the wrong codon optimization strategy can have detrimental effects on the protein and product levels. In this study, we analyzed 11 different codon variants of an engineered T1PKS and investigated in a systematic approach their influence on heterologous expression in Corynebacterium glutamicum, Escherichia coli, and Pseudomonas putida. Our best performing codon variants exhibited a minimum 50-fold increase in PKS protein levels, which also enabled the production of an unnatural polyketide in each of these hosts. Furthermore, we developed a free online tool (https://basebuddy.lbl.gov) that offers transparent and highly customizable codon optimization with up-to-date codon usage tables. In this work, we not only highlight the significance of codon optimization but also establish the groundwork for the high-throughput assembly and characterization of PKS pathways in alternative hosts.
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Affiliation(s)
- Matthias Schmidt
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Institute
of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, 52062 Aachen, Germany
- California
Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
| | - Namil Lee
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
| | - Chunjun Zhan
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jacob B. Roberts
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint
Program in Bioengineering, University of
California, Berkeley, California 94720, United States
| | - Alberto A. Nava
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Leah S. Keiser
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Aaron A. Vilchez
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Yan Chen
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Christopher J. Petzold
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Robert W. Haushalter
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Lars M. Blank
- Institute
of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, 52062 Aachen, Germany
| | - Jay D. Keasling
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint
Program in Bioengineering, University of
California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Environmental
Genomics and Systems Biology Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Center
for Synthetic Biochemistry, Institute for
Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen 518071, China
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5
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Zhang Z, Yang S, Li Z, Wu Y, Tang J, Feng M, Chen S. High-titer production of staurosporine by heterologous expression and process optimization. Appl Microbiol Biotechnol 2023; 107:5701-5714. [PMID: 37480372 DOI: 10.1007/s00253-023-12661-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/15/2023] [Accepted: 06/21/2023] [Indexed: 07/24/2023]
Abstract
Staurosporine is the most well-known member of the indolocarbazole alkaloid family; it can induce apoptosis of many types of cells as a strong protein kinase inhibitor, and is used as an important lead compound for the synthesis of the antitumor drugs. However, the low fermentation level of the native producer remains the bottleneck of staurosporine production. Herein, integration of multi-copy biosynthetic gene cluster (BGC) in well characterized heterologous host and optimization of the fermentation process were performed to enable high-level production of staurosporine. First, the 22.5 kb staurosporine BGC was captured by CRISPR/Cas9-mediated TAR (transformation-associated recombination) from the native producer (145 mg/L), and then introduced into three heterologous hosts Streptomyces avermitilis (ATCC 31267), Streptomyces lividans TK24 and Streptomyces albus J1074 to evaluate the staurosporine production capacity. The highest yield was achieved in S. albus J1074 (750 mg/L), which was used for further production improvement. Next, we integrated two additional staurosporine BGCs into the chromosome of strain S-STA via two different attB sites (vwb and TG1), leading to a double increase in the production of staurosporine. And finally, optimization of fermentation process by controlling the pH and glucose feeding could improve the yield of staurosporine to 4568 mg/L, which was approximately 30-fold higher than that of the native producer. This is the highest yield ever reported, paving the way for the industrial production of staurosporine. KEYPOINTS: • Streptomyces albus J1074 was the most suitable heterologous host to express the biosynthetic gene cluster of staurosporine. • Amplification of the biosynthetic gene cluster had obvious effect on improving the production of staurosporine. • The highest yield of staurosporine was achieved to 4568 mg/L by stepwise increase strategy.
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Affiliation(s)
- Zhengyu Zhang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, 826 Zhangheng Road, Pudong, Shanghai, 201203, People's Republic of China
| | - Songbai Yang
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Pudong, Shanghai, 201203, People's Republic of China
| | - Zhenxin Li
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Pudong, Shanghai, 201203, People's Republic of China
| | - Yuanjie Wu
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Pudong, Shanghai, 201203, People's Republic of China
| | - Jiawei Tang
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Pudong, Shanghai, 201203, People's Republic of China
| | - Meiqing Feng
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, 826 Zhangheng Road, Pudong, Shanghai, 201203, People's Republic of China.
| | - Shaoxin Chen
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Pudong, Shanghai, 201203, People's Republic of China.
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6
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Gao Y, Birkelbach J, Fu C, Herrmann J, Irschik H, Morgenstern B, Hirschfelder K, Li R, Zhang Y, Jansen R, Müller R. The Disorazole Z Family of Highly Potent Anticancer Natural Products from Sorangium cellulosum: Structure, Bioactivity, Biosynthesis, and Heterologous Expression. Microbiol Spectr 2023; 11:e0073023. [PMID: 37318329 PMCID: PMC10434194 DOI: 10.1128/spectrum.00730-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/24/2023] [Indexed: 06/16/2023] Open
Abstract
Myxobacteria serve as a treasure trove of secondary metabolites. During our ongoing search for bioactive natural products, a novel subclass of disorazoles termed disorazole Z was discovered. Ten disorazole Z family members were purified from a large-scale fermentation of the myxobacterium Sorangium cellulosum So ce1875 and characterized by electrospray ionization-high-resolution mass spectrometry (ESI-HRMS), X-ray, nuclear magnetic resonance (NMR), and Mosher ester analysis. Disorazole Z compounds are characterized by the lack of one polyketide extension cycle, resulting in a shortened monomer in comparison to disorazole A, which finally forms a dimer in the bis-lactone core structure. In addition, an unprecedented modification of a geminal dimethyl group takes place to form a carboxylic acid methyl ester. The main component disorazole Z1 shows comparable activity in effectively killing cancer cells to disorazole A1 via binding to tubulin, which we show induces microtubule depolymerization, endoplasmic reticulum delocalization, and eventually apoptosis. The disorazole Z biosynthetic gene cluster (BGC) was identified and characterized from the alternative producer S. cellulosum So ce427 and compared to the known disorazole A BGC, followed by heterologous expression in the host Myxococcus xanthus DK1622. Pathway engineering by promoter substitution and gene deletion paves the way for detailed biosynthesis studies and efficient heterologous production of disorazole Z congeners. IMPORTANCE Microbial secondary metabolites are a prolific reservoir for the discovery of bioactive compounds, which prove to be privileged scaffolds for the development of new drugs such as antibacterial and small-molecule anticancer drugs. Consequently, the continuous discovery of novel bioactive natural products is of great importance for pharmaceutical research. Myxobacteria, especially Sorangium spp., which are known for their large genomes with yet-underexploited biosynthetic potential, are proficient producers of such secondary metabolites. From the fermentation broth of Sorangium cellulosum strain So ce1875, we isolated and characterized a family of natural products named disorazole Z, which showed potent anticancer activity. Further, we report on the biosynthesis and heterologous production of disorazole Z. These results can be stepping stones toward pharmaceutical development of the disorazole family of anticancer natural products for (pre)clinical studies.
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Affiliation(s)
- Yunsheng Gao
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Saarbrücken, Germany
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Helmholtz International Lab for Anti-Infectives, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Joy Birkelbach
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Saarbrücken, Germany
| | - Chengzhang Fu
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Saarbrücken, Germany
- Helmholtz International Lab for Anti-Infectives, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Jennifer Herrmann
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Saarbrücken, Germany
| | - Herbert Irschik
- Department of Microbial Drugs, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Bernd Morgenstern
- Department of Inorganic Chemistry, Saarland University, Saarbrücken, Germany
| | - Kerstin Hirschfelder
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Saarbrücken, Germany
| | - Ruijuan Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Rolf Jansen
- Department of Microbial Drugs, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Saarbrücken, Germany
- Helmholtz International Lab for Anti-Infectives, Helmholtz Center for Infection Research, Braunschweig, Germany
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7
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Peng J, Guo F, Liu S, Fang H, Xu Z, Wang T. Recent Advances and Future Prospects of Mycosporine-like Amino Acids. Molecules 2023; 28:5588. [PMID: 37513460 PMCID: PMC10384724 DOI: 10.3390/molecules28145588] [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: 06/06/2023] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Mycosporine-like amino acids (MAAs) are a class of water-soluble active substances produced by various aquatic organisms. However, due to the limitations of low accumulation of MAAs in organisms, the cumbersome extraction process, difficult identification, and high cost, MAAs have not yet been widely used in human life. Recently, there has been an emergence of heterologous synthesis for MAAs, making increasing yield the key to the quantification and application of MAAs. This review summarizes the latest research progress of MAAs, including: (1) introducing the biodistribution of MAAs and the content differences among different species to provide a reference for the selection of research subjects; (2) elaborating the species and molecular information of MAAs; (3) dissecting the synthesis mechanism and sorting out the synthesis pathways of various MAAs; (4) summarizing the methods of extraction and identification, summarizing the advantages and disadvantages, and providing a reference for the optimization of extraction protocols; (5) examining the heterologous synthesis method; and (6) summarizing the physiological functions of MAAs. This paper comprehensively updates the latest research status of MAAs and the various problems that need to be addressed, especially emphasizing the potential advantages of heterologous synthesis in the future production of MAAs.
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Affiliation(s)
- Jiahui Peng
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
| | - Fangyu Guo
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
| | - Sishi Liu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
| | - Haiyan Fang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
| | - Zhenshang Xu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
| | - Ting Wang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
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8
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Seo EY, Jung D, Epstein SS, Zhang W, Owen JS, Baba H, Yamamoto A, Harada M, Nakashimada Y, Kato S, Aoi Y, He S. A targeted liquid cultivation method for previously uncultured non-colony forming microbes. Front Microbiol 2023; 14:1194466. [PMID: 37362942 PMCID: PMC10288195 DOI: 10.3389/fmicb.2023.1194466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/10/2023] [Indexed: 06/28/2023] Open
Abstract
A large number of microbes are not able to form colonies using agar-plating methods, which is one of the reasons that cultivation based on solid media leaves the majority of microbial diversity in the environment inaccessible. We developed a new Non-Colony-Forming Liquid Cultivation method (NCFLC) that can selectively isolate non-colony-forming microbes that exclusively grow in liquid culture. The NCFLC method involves physically separating cells using dilution-to-extinction (DTE) cultivation and then selecting those that could not grow on a solid medium. The NCFLC was applied to marine samples from a coastal intertidal zone and soil samples from a forest area, and the results were compared with those from the standard direct plating method (SDP). The NCFLC yielded fastidious bacteria from marine samples such as Acidobacteriota, Epsilonproteobacteria, Oligoflexia, and Verrucomicrobiota. Furthermore, 62% of the isolated strains were potential new species, whereas only 10% were novel species from SDP. From soil samples, isolates belonging to Acidobacteriota and Armatimonadota (which are known as rare species among identified isolates) were exclusively isolated by NCFLC. Colony formation capabilities of isolates cultivated by NCFLC were tested using solid agar plates, among which approximately one-third of the isolates were non-colony-forming, approximately half-formed micro-colonies, and only a minority could form ordinary size colonies. This indicates that the majority of the strains cultivated by NCFLC were previously uncultured microbial species unavailable using the SDP method. The NCFCL method described here can serve as a new approach to accessing the hidden microbial dark matter.
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Affiliation(s)
- Eun-Young Seo
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
- Ningbo Institute of Marine Medicine, Peking University, Ningbo, China
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Japan
| | - Dawoon Jung
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
- Ningbo Institute of Marine Medicine, Peking University, Ningbo, China
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Japan
| | - Slava S. Epstein
- Department of Biology, Northeastern University, Boston, MA, United States
| | - Weiyan Zhang
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Jeffrey S. Owen
- Department of Environmental Science, Hankuk University of Foreign Studies, Yongin, Republic of Korea
| | - Hiroaki Baba
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
| | - Akina Yamamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
| | - Mifuyu Harada
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
| | - Yutaka Nakashimada
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
| | - Setsu Kato
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
| | - Yoshiteru Aoi
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
| | - Shan He
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
- Ningbo Institute of Marine Medicine, Peking University, Ningbo, China
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9
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The Potential Use of Fungal Co-Culture Strategy for Discovery of New Secondary Metabolites. Microorganisms 2023; 11:microorganisms11020464. [PMID: 36838429 PMCID: PMC9965835 DOI: 10.3390/microorganisms11020464] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
Fungi are an important and prolific source of secondary metabolites (SMs) with diverse chemical structures and a wide array of biological properties. In the past two decades, however, the number of new fungal SMs by traditional monoculture method had been greatly decreasing. Fortunately, a growing number of studies have shown that co-culture strategy is an effective approach to awakening silent SM biosynthetic gene clusters (BGCs) in fungal strains to produce cryptic SMs. To enrich our knowledge of this approach and better exploit fungal biosynthetic potential for new drug discovery, this review comprehensively summarizes all fungal co-culture methods and their derived new SMs as well as bioactivities on the basis of an extensive literature search and data analysis. Future perspective on fungal co-culture study, as well as its interaction mechanism, is supplied.
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10
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Liu J, Li SM. Genomics-Guided Efficient Identification of 2,5-Diketopiperazine Derivatives from Actinobacteria. Chembiochem 2023; 24:e202200502. [PMID: 36098493 PMCID: PMC10092475 DOI: 10.1002/cbic.202200502] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/12/2022] [Indexed: 02/04/2023]
Abstract
Secondary metabolites derived from microorganism constitute an important part of natural products. Mining of the microbial genomes revealed a large number of uncharacterized biosynthetic gene clusters, indicating their greater potential to synthetize specialized or secondary metabolites (SMs) than identified by classic fermentation and isolation approaches. Various bioinformatics tools have been developed to analyze and identify such gene clusters, thus accelerating significantly the mining process. Heterologous expression of an individual biosynthetic gene cluster has been proven as an efficient way to activate the genes and identify the encoded metabolites that cannot be detected under normal laboratory cultivation conditions. Herein, we describe a concept of genomics-guided approach by performing genome mining and heterologous expression to uncover novel CDPS-derived DKPs and functionally characterize novel tailoring enzymes embedded in the biosynthetic pathways. Recent works focused on the identification of the nucleobase-related and dimeric DKPs are also presented.
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Affiliation(s)
- Jing Liu
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037, Marburg, Germany.,Current address: Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037, Marburg, Germany
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11
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Taton A, Rohrer S, Diaz B, Reher R, Caraballo Rodriguez AM, Pierce ML, Dorrestein PC, Gerwick L, Gerwick WH, Golden JW. Heterologous Expression in Anabaena of the Columbamide Pathway from the Cyanobacterium Moorena bouillonii and Production of New Analogs. ACS Chem Biol 2022; 17:1910-1923. [DOI: 10.1021/acschembio.2c00347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Arnaud Taton
- School of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Sebastian Rohrer
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, California 92093, United States
| | - Brienna Diaz
- School of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Raphael Reher
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, California 92093, United States
- Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle (Saale) 06114, Germany
- Institute of Pharmaceutical Biology and Biotechnology, Philipps University of Marburg, Marburg 35037, Germany
| | | | - Marsha L. Pierce
- Department of Pharmacology, Midwestern University, Downers Grove, Illinois 60515, United States
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, California 92093, United States
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, California 92093, United States
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, California 92093, United States
| | - James W. Golden
- School of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
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12
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Recent Advances in the Heterologous Expression of Biosynthetic Gene Clusters for Marine Natural Products. Mar Drugs 2022; 20:md20060341. [PMID: 35736144 PMCID: PMC9225448 DOI: 10.3390/md20060341] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/11/2022] [Accepted: 05/20/2022] [Indexed: 12/29/2022] Open
Abstract
Marine natural products (MNPs) are an important source of biologically active metabolites, particularly for therapeutic agent development after terrestrial plants and nonmarine microorganisms. Sequencing technologies have revealed that the number of biosynthetic gene clusters (BGCs) in marine microorganisms and the marine environment is much higher than expected. Unfortunately, the majority of them are silent or only weakly expressed under traditional laboratory culture conditions. Furthermore, the large proportion of marine microorganisms are either uncultivable or cannot be genetically manipulated. Efficient heterologous expression systems can activate cryptic BGCs and increase target compound yield, allowing researchers to explore more unknown MNPs. When developing heterologous expression of MNPs, it is critical to consider heterologous host selection as well as genetic manipulations for BGCs. In this review, we summarize current progress on the heterologous expression of MNPs as a reference for future research.
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13
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Expression of Cyanobacterial Biosynthetic Gene Clusters in Escherichia coli. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2489:315-332. [PMID: 35524058 DOI: 10.1007/978-1-0716-2273-5_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Cyanobacteria represent an attractive source of natural bioactive compounds, ranging from sunscreens to cancer treatments. While many biosynthetic gene clusters (BGCs) that encode cyanobacterial natural products are known, the slow growth and lack of genetic tools in the native producers hampers their modification, characterization, and large-scale production. By engineering heterologous hosts for the expression of cyanobacterial BGCs, sufficient material can be produced for research or industry. Although several hosts have been evaluated for the expression of cyanobacterial natural products, this work details the process of expressing BGCs in Escherichia coli via promoter exchange.
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14
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Heterologous Expression and Biochemical Analysis Reveal a Schizokinen-Based Siderophore Pathway in Leptolyngbya (Cyanobacteria). Appl Environ Microbiol 2022; 88:e0237321. [PMID: 35285240 DOI: 10.1128/aem.02373-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Siderophores are low molecular weight iron-chelating molecules that many organisms secrete to scavenge ferric iron from the environment. While cyanobacteria inhabit a wide range of environments with poor iron availability, only two siderophore families have been characterized from this phylum. Herein, we sought to investigate siderophore production in the marine genus, Leptolyngbya. A 12 open reading frame (14.5 kb) putative nonribosomal peptide synthetase-independent siderophore biosynthesis gene cluster, identified in the genome of Leptolyngbya sp. PCC 7376, was cloned and heterologously expressed in Escherichia coli. Under iron-limiting conditions, expression strains harboring the first seven genes (lidA to lidF), produced a potent siderophore, which was subsequently identified via UPLC-MS/MS and NMR as schizokinen. The enzymes encoded by the remaining genes (lidG1 to lidG5) did not appear to be active in E. coli, therefore their function could not be determined. Bioinformatic analysis revealed gene clusters with high homology to lidA to lidF in phylogenetically and biogeographically diverse cyanobacteria, suggesting that schizokinen-based siderophore production is widespread in this phylum. Siderophore yields in E. coli expression strains were significantly higher than those achieved by Leptolyngbya, highlighting the potential of this platform for producing siderophores of industrial value. IMPORTANCE Iron availability limits the growth of many microorganisms, particularly those residing in high nutrient-low chlorophyll aquatic environments. Therefore, characterizing iron acquisition pathways in phytoplankton is essential for understanding nutrient cycling in our oceans. The results of this study suggest that Leptolyngbya sp. PCC 7376, and many other cyanobacteria, use schizokinen-based iron chelators (siderophores) to scavenge iron from the environment. We have shown that these pathways are amenable to heterologous expression in E. coli, which expands the limited arsenal of known cyanobacterial siderophores and is advantageous for the downstream overproduction of relevant siderophores of ecological and industrial value.
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15
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The Odilorhabdin Antibiotic Biosynthetic Cluster and Acetyltransferase Self-Resistance Locus Are Niche and Species Specific. mBio 2022; 13:e0282621. [PMID: 35012352 PMCID: PMC8749412 DOI: 10.1128/mbio.02826-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Antibiotic resistance is an increasing threat to human health. A direct link has been established between antimicrobial self-resistance determinants of antibiotic producers, environmental bacteria, and clinical pathogens. Natural odilorhabdins (ODLs) constitute a new family of 10-mer linear cationic peptide antibiotics inhibiting bacterial translation by binding to the 30S subunit of the ribosome. These bioactive secondary metabolites are produced by entomopathogenic bacterial symbiont Xenorhabdus (Morganellaceae), vectored by the soil-dwelling nematodes. ODL-producing Xenorhabdus nematophila symbionts have mechanisms of self-protection. In this study, we cloned the 44.5-kb odl biosynthetic gene cluster (odl-BGC) of the symbiont by recombineering and showed that the N-acetyltransferase-encoding gene, oatA, is responsible for ODL resistance. In vitro acetylation and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses showed that OatA targeted the side chain amino group of ODL rare amino acids, leading to a loss of translation inhibition and antibacterial properties. Functional, genomic, and phylogenetic analyses of oatA revealed an exclusive cis-link to the odilorhabdin BGC, found only in X. nematophila and a specific phylogenetic clade of Photorhabdus. This work highlights the coevolution of antibiotic production and self-resistance as ancient features of this unique tripartite complex of host-vector-symbiont interactions without odl-BGC dissemination by lateral gene transfer. IMPORTANCE Odilorhabdins (ODLs) constitute a novel antibiotic family with promising properties for treating problematic multidrug-resistant Gram-negative bacterial infections. ODLs are 10-mer linear cationic peptides inhibiting bacterial translation by binding to the small subunit of the ribosome. These natural peptides are produced by Xenorhabdus nematophila, a bacterial symbiont of entomopathogenic nematodes well known to produce large amounts of specialized secondary metabolites. Like other antimicrobial producers, ODL-producing Xenorhabdus nematophila has mechanisms of self-protection. In this study, we cloned the ODL-biosynthetic gene cluster of the symbiont by recombineering and showed that the N-acetyltransferase-encoding gene, oatA, is responsible for ODL resistance. In vitro acetylation and LC-MS/MS analyses showed that OatA targeted the side chain amino group of ODL rare amino acids, leading to a loss of translation inhibition and antibacterial properties. Functional, genomic, and phylogenetic analyses of oatA revealed the coevolution of antibiotic production and self-resistance as ancient feature of this particular niche in soil invertebrates without resistance dissemination.
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16
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Fidan O, Zhan J, Ren J. Engineered production of bioactive natural products from medicinal plants. WORLD JOURNAL OF TRADITIONAL CHINESE MEDICINE 2022. [DOI: 10.4103/wjtcm.wjtcm_66_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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17
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Fidan O, Zhan J, Ren J. Engineered production of bioactive natural products from medicinal plants. WORLD JOURNAL OF TRADITIONAL CHINESE MEDICINE 2022. [DOI: 10.4103/2311-8571.336839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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18
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Li H, Pan Y, Liu G. Multiplying the heterologous production of spinosad through tandem amplification of its biosynthetic gene cluster in Streptomyces coelicolor. Microb Biotechnol 2021; 15:1550-1560. [PMID: 34796664 PMCID: PMC9049625 DOI: 10.1111/1751-7915.13965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 10/21/2021] [Indexed: 12/14/2022] Open
Abstract
Heterologous expression of the biosynthetic gene cluster (BGC) is important for studying the microbial natural products (NPs), especially for those kept in silent or poorly expressed in their original strains. Here, we cloned the spinosad BGC through the Cas9-Assisted Targeting of Chromosome segments and amplified it to five copies through a ZouA-dependent DNA amplification system in Streptomyces coelicolor M1146. The resulting strain produced 1253.9 ± 78.2 μg l-1 of spinosad, which was about 224-fold compared with that of the parent strain carrying only one copy of the spinosad BGC. Moreover, we further increased spinosad to 1958.9 ± 73.5 μg l-1 by the dynamic regulation of intracellular triacylglycerol degradation. Our study indicates that tandem amplification of the targeted gene cluster is particularly suitable to enhance the heterologous production of valuable NPs with efficiency and simplicity.
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Affiliation(s)
- Hong Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuanyuan Pan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Gang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100864, China
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19
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Meng X, Fang Y, Ding M, Zhang Y, Jia K, Li Z, Collemare J, Liu W. Developing fungal heterologous expression platforms to explore and improve the production of natural products from fungal biodiversity. Biotechnol Adv 2021; 54:107866. [PMID: 34780934 DOI: 10.1016/j.biotechadv.2021.107866] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/04/2021] [Accepted: 11/05/2021] [Indexed: 12/14/2022]
Abstract
Natural products from fungi represent an important source of biologically active metabolites notably for therapeutic agent development. Genome sequencing revealed that the number of biosynthetic gene clusters (BGCs) in fungi is much larger than expected. Unfortunately, most of them are silent or barely expressed under laboratory culture conditions. Moreover, many fungi in nature are uncultivable or cannot be genetically manipulated, restricting the extraction and identification of bioactive metabolites from these species. Rapid exploration of the tremendous number of cryptic fungal BGCs necessitates the development of heterologous expression platforms, which will facilitate the efficient production of natural products in fungal cell factories. Host selection, BGC assembly methods, promoters used for heterologous gene expression, metabolic engineering strategies and compartmentalization of biosynthetic pathways are key aspects for consideration to develop such a microbial platform. In the present review, we summarize current progress on the above challenges to promote research effort in the relevant fields.
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Affiliation(s)
- Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Yu Fang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Mingyang Ding
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Yanyu Zhang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Kaili Jia
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Zhongye Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Jérôme Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China.
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20
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Heinrich S, Grote M, Sievers S, Kushnir S, Schulz F. Polyether Cyclization Cascade Alterations in Response to Monensin Polyketide Synthase Mutations. Chembiochem 2021; 23:e202100584. [PMID: 34729883 DOI: 10.1002/cbic.202100584] [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: 10/28/2021] [Indexed: 11/11/2022]
Abstract
The targeted manipulation of polyketide synthases has in recent years led to numerous new-to-nature polyketides. For type I polyketide synthases the response of post-polyketide synthases (PKS) processing enzymes onto the most frequently polyketide backbone manipulations is so far insufficiently studied. In particular, complex processes such as the polyether cyclisation in the biosynthesis of ionophores such as monensin pose interesting objects of research. We present here a study of the substrate promiscuity of the polyether cyclisation cascade enzymes in monensin biosynthesis in the conversion of redox derivatives of the nascent polyketide chain. LC-HRMS/MS2 -based studies revealed a remarkable flexibility of the post-PKS enzymes. They acted on derivatized polyketide backbones based on the three possible polyketide redox states within two different modules and gave rise to an altered polyether structure. One of these monensin derivatives was isolated and characterized by 2D-NMR spectroscopy, crystallography, and bioactivity studies.
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Affiliation(s)
- Sascha Heinrich
- Organic Chemistry I, Chemistry and Biochemistry of Natural Products, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Marius Grote
- Organic Chemistry I, Chemistry and Biochemistry of Natural Products, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Sonja Sievers
- Max PIanck Institute for molecular Physiology, COMAS - Compound Management and Screening Center, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Susanna Kushnir
- Organic Chemistry I, Chemistry and Biochemistry of Natural Products, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Frank Schulz
- Organic Chemistry I, Chemistry and Biochemistry of Natural Products, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
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21
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Pogorevc D, Müller R. Biotechnological production optimization of argyrins - a potent immunomodulatory natural product class. Microb Biotechnol 2021; 15:353-369. [PMID: 34724343 PMCID: PMC8719831 DOI: 10.1111/1751-7915.13959] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 12/13/2022] Open
Abstract
Argyrins represent a family of cyclic octapeptides exhibiting promising immunomodulatory activity via inhibiting mitochondrial protein synthesis, which leads to reduced IL-17 production by the T-helper 17 cells. Argyrins are formed by a non-ribosomal peptide synthetase (NRPS), originating from the myxobacterial producer strains Archangium gephyra Ar8082 and Cystobacter sp. SBCb004. In this work, a previously established heterologous production platform was employed to provide evidence of direct D-configured amino acid incorporation by the argyrin assembly line. An adenylation domain of the argyrin NRPS was characterized and shown to have a high preference for D-configured amino acids. Eight novel argyrin derivatives were generated via biosynthetic engineering of the heterologous production system. The system was also optimized to enable formation of methylated argyrin C and D derivatives with improved immunosuppressive activity compared with their unmethylated counterparts. Furthermore, the optimization of cultivation conditions allowed exclusive production of one major derivative at a time, drastically improving the purification process. Importantly, engineering of transcription and translation initiation resulted in a substantially improved production titre reaching 350-400 mg l-1 . The optimized system presented herein thus provides a versatile platform for production of this promising class of immunosuppressants at a scale that should provide sufficient supply for upcoming pre-clinical development.
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Affiliation(s)
- Domen Pogorevc
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrücken, 66123, Germany.,Department of Pharmacy, Saarland University, Saarbrücken, 66123, Germany.,DZIF - German Centre for Infection Research, Partnersite Hannover-Braunschweig, Braunschweig, Germany
| | - Rolf Müller
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrücken, 66123, Germany.,Department of Pharmacy, Saarland University, Saarbrücken, 66123, Germany.,DZIF - German Centre for Infection Research, Partnersite Hannover-Braunschweig, Braunschweig, Germany
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22
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23
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In vivo Characterization of the Inducible Promoter System of 3-hydroxypropionic Dehydrogenase in Pseudomonas denitrificans. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0291-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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24
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Kamdem RST, Ogbole O, Wafo P, Philip FU, Ali Z, Ntie-Kang F, Khan IA, Spiteller P. Rational engineering of specialized metabolites in bacteria and fungi. PHYSICAL SCIENCES REVIEWS 2021. [DOI: 10.1515/psr-2018-0170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Abstract
Bacteria and fungi have a high potential to produce compounds that display large structural change and diversity, thus displaying an extensive range of biological activities. Secondary metabolism or specialized metabolism is a term for pathways and small molecule products of metabolism that are not mandatory for the subsistence of the organism but improve and control their phenotype. Their interesting biological activities have occasioned their application in the fields of agriculture, food, and pharmaceuticals. Metabolic engineering is a powerful approach to improve access to these treasured molecules or to rationally engineer new ones. A thorough overview of engineering methods in secondary metabolism is presented, both in heterologous and epigenetic modification. Engineering methods to modify the structure of some secondary metabolite classes in their host are also intensively assessed.
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Affiliation(s)
- Ramsay Soup Teoua Kamdem
- Institut für Organische und Analytische Chemie , Universität Bremen , Leobener Strasse 7 (NW2C) , Bremen 28359 , Germany
- Department of Organic Chemistry, Higher Teachers’ Training College , University of Yaounde I. , P. O. Box 47 , Yaoundé , Cameroon
| | - Omonike Ogbole
- Department of Pharmacognosy , University of Ibadan , Ibadan , Nigeria
| | - Pascal Wafo
- Department of Organic Chemistry, Higher Teachers’ Training College , University of Yaounde I. , P. O. Box 47 , Yaoundé , Cameroon
| | - F. Uzor Philip
- Department of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmaceutical Sciences , University of Nigeria , Nsukka , 410001 Nigeria
| | - Zulfiqar Ali
- National Center for Natural Products Research , School of Pharmacy , University of Mississippi , MS 38677 , USA
| | - Fidele Ntie-Kang
- Chemistry Department , University of Buea , P. O. Box 63 , Buea , Cameroon
- Department of Pharmaceutical Chemistry , Martin-Luther-Universitat Halle-Wittenberg , Wolfgang-Langenbeck Str. 4 , Halle (Saale) 06120 , Germany
- Department of Informatics and Chemistry , University of Chemistry and Technology Prague , Technická 5 166 28 , Prague 6 Dejvice , Czech Republic
| | - Ikhlas A. Khan
- National Center for Natural Products Research , School of Pharmacy , University of Mississippi , MS 38677 , USA
| | - Peter Spiteller
- Institut für Organische und Analytische Chemie , Universität Bremen , Leobener Strasse 7 (NW2C) , Bremen 28359 , Germany
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25
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Jung D, Liu L, He S. Application of in situ cultivation in marine microbial resource mining. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:148-161. [PMID: 37073342 PMCID: PMC10077220 DOI: 10.1007/s42995-020-00063-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/28/2020] [Indexed: 05/03/2023]
Abstract
Microbial communities in marine habitats are regarded as underexplored reservoirs for discovering new natural products with potential application. However, only a few microbes in nature can be cultivated in the laboratory. This has led to the development of a variety of isolation and cultivation methods, and in situ cultivation is one of the most popular. Diverse in situ cultivation methods, with the same basic principle, have been applied to a variety of environmental samples. Compared with conventional approaches, these new methods are able to cultivate previously uncultured and phylogenetically novel microbes, many with biotechnological potential. This review introduces the various in situ cultivation methods for the isolation of previously uncultured microbial species and their potential for marine microbial resource mining. Furthermore, studies that investigated the key and previously unidentified mechanisms of growing uncultivated microorganisms by in situ cultivation, which will shed light on the understanding of microbial uncultivability, were also reviewed.
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Affiliation(s)
- Dawoon Jung
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315832 China
| | - Liwei Liu
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315832 China
| | - Shan He
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315832 China
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26
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Alam K, Hao J, Zhang Y, Li A. Synthetic biology-inspired strategies and tools for engineering of microbial natural product biosynthetic pathways. Biotechnol Adv 2021; 49:107759. [PMID: 33930523 DOI: 10.1016/j.biotechadv.2021.107759] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/28/2021] [Accepted: 04/23/2021] [Indexed: 02/08/2023]
Abstract
Microbial-derived natural products (NPs) and their derivative products are of great importance and used widely in many fields, especially in pharmaceutical industries. However, there is an immediate need to establish innovative approaches, strategies, and techniques to discover new NPs with novel or enhanced biological properties, due to the less productivity and higher cost on traditional drug discovery pipelines from natural bioresources. Revealing of untapped microbial cryptic biosynthetic gene clusters (BGCs) using DNA sequencing technology and bioinformatics tools makes genome mining possible for NP discovery from microorganisms. Meanwhile, new approaches and strategies in the area of synthetic biology offer great potentials for generation of new NPs by engineering or creating synthetic systems with improved and desired functions. Development of approaches, strategies and tools in synthetic biology can facilitate not only exploration and enhancement in supply, and also in the structural diversification of NPs. Here, we discussed recent advances in synthetic biology-inspired strategies, including bioinformatics and genetic engineering tools and approaches for identification, cloning, editing/refactoring of candidate biosynthetic pathways, construction of heterologous expression hosts, fitness optimization between target pathways and hosts and detection of NP production.
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Affiliation(s)
- Khorshed Alam
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
| | - Jinfang Hao
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR 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, PR China.
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Engineering Heterologous Hosts for the Enhanced Production of Non-ribosomal Peptides. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0080-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Lee N, Hwang S, Kim W, Lee Y, Kim JH, Cho S, Kim HU, Yoon YJ, Oh MK, Palsson BO, Cho BK. Systems and synthetic biology to elucidate secondary metabolite biosynthetic gene clusters encoded in Streptomyces genomes. Nat Prod Rep 2021; 38:1330-1361. [PMID: 33393961 DOI: 10.1039/d0np00071j] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: 2010 to 2020 Over the last few decades, Streptomyces have been extensively investigated for their ability to produce diverse bioactive secondary metabolites. Recent advances in Streptomyces research have been largely supported by improvements in high-throughput technology 'omics'. From genomics, numerous secondary metabolite biosynthetic gene clusters were predicted, increasing their genomic potential for novel bioactive compound discovery. Additional omics, including transcriptomics, translatomics, interactomics, proteomics and metabolomics, have been applied to obtain a system-level understanding spanning entire bioprocesses of Streptomyces, revealing highly interconnected and multi-layered regulatory networks for secondary metabolism. The comprehensive understanding derived from this systematic information accelerates the rational engineering of Streptomyces to enhance secondary metabolite production, integrated with the exploitation of the highly efficient 'Design-Build-Test-Learn' cycle in synthetic biology. In this review, we describe the current status of omics applications in Streptomyces research to better understand the organism and exploit its genetic potential for higher production of valuable secondary metabolites and novel secondary metabolite discovery.
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Affiliation(s)
- Namil Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Soonkyu Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Woori Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yongjae Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Ji Hun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yeo Joon Yoon
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
| | - Min-Kyu Oh
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea.
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA. and Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA and Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Lyngby, 2800, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea and Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Lyngby, 2800, Denmark
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Taton A, Ecker A, Diaz B, Moss NA, Anderson B, Reher R, Leão TF, Simkovsky R, Dorrestein PC, Gerwick L, Gerwick WH, Golden JW. Heterologous Expression of Cryptomaldamide in a Cyanobacterial Host. ACS Synth Biol 2020; 9:3364-3376. [PMID: 33180461 DOI: 10.1021/acssynbio.0c00431] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Filamentous marine cyanobacteria make a variety of bioactive molecules that are produced by polyketide synthases, nonribosomal peptide synthetases, and hybrid pathways that are encoded by large biosynthetic gene clusters. These cyanobacterial natural products represent potential drug leads; however, thorough pharmacological investigations have been impeded by the limited quantity of compound that is typically available from the native organisms. Additionally, investigations of the biosynthetic gene clusters and enzymatic pathways have been difficult due to the inability to conduct genetic manipulations in the native producers. Here we report a set of genetic tools for the heterologous expression of biosynthetic gene clusters in the cyanobacteria Synechococcus elongatus PCC 7942 and Anabaena (Nostoc) PCC 7120. To facilitate the transfer of gene clusters in both strains, we engineered a strain of Anabaena that contains S. elongatus homologous sequences for chromosomal recombination at a neutral site and devised a CRISPR-based strategy to efficiently obtain segregated double recombinant clones of Anabaena. These genetic tools were used to express the large 28.7 kb cryptomaldamide biosynthetic gene cluster from the marine cyanobacterium Moorena (Moorea) producens JHB in both model strains. S. elongatus did not produce cryptomaldamide; however, high-titer production of cryptomaldamide was obtained in Anabaena. The methods developed in this study will facilitate the heterologous expression of biosynthetic gene clusters isolated from marine cyanobacteria and complex metagenomic samples.
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Heterologous biosynthesis as a platform for producing new generation natural products. Curr Opin Biotechnol 2020; 66:123-130. [DOI: 10.1016/j.copbio.2020.06.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/27/2020] [Accepted: 06/30/2020] [Indexed: 12/18/2022]
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Qi R, Swayambhu G, Bruno M, Zhang G, Pfeifer BA. Consolidated plasmid Design for Stabilized Heterologous Production of the complex natural product Siderophore Yersiniabactin. Biotechnol Prog 2020; 37:e3103. [PMID: 33190425 DOI: 10.1002/btpr.3103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 10/24/2020] [Accepted: 11/11/2020] [Indexed: 11/09/2022]
Abstract
Yersiniabactin (Ybt) is a hybrid polyketide-nonribosomal complex natural product also known as a siderophore for its iron chelation properties. The native producer of Ybt, Yersinia pestis, is a priority pathogen responsible for the plague in which the siderophore properties of Ybt are used to sequester iron and other metal species upon host infection. Alternatively, the high metal binding properties of Ybt enable a plethora of potentially valuable applications benefiting from metal remediation and/or recovery. For these applications, a surrogate production source is highly preferred relative to the pathogenic native host. In this work, we present a modification to the heterologous Escherichia coli production system established for Ybt biosynthesis. In particular, the multiple plasmids originally used to express the genetic pathway required for Ybt biosynthesis were consolidated to a single, copy-amplifiable plasmid. In so doing, plasmid stability was improved from ~30% to ≥80% while production values maintained at 20-30% of the original system, which resulted in titers of 0.5-3 mg/L from shake flask vessels.
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Affiliation(s)
- Ruiquan Qi
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, New York, USA
| | - Girish Swayambhu
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, New York, USA
| | - Michael Bruno
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, New York, USA
| | - Guojian Zhang
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, New York, USA.,Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, People's Republic of China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, People's Republic of China
| | - Blaine A Pfeifer
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, New York, USA.,Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, People's Republic of China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, People's Republic of China
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32
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An efficient genetic transformation system for Chinese medicine fungus Tolypocladium ophioglossoides. J Microbiol Methods 2020; 176:106032. [PMID: 32805368 DOI: 10.1016/j.mimet.2020.106032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 07/26/2020] [Accepted: 07/29/2020] [Indexed: 11/22/2022]
Abstract
Tolypocladium ophioglossoides is a rare and valuable fungus extensively used in Chinese medicine for relieving postmenopausal syndrome in women yet its bioactive molecules are unknown. To explore its molecular mechanisms, we have developed a reliable Agrobacterium-mediated transformation system using the selective marker: the chlorimuron ethyl-resistance gene sur. For this purpose, we firstly constructed a T-DNA binary vector system and then improved the transformation efficiency by optimizing conditional parameters including the Agrobacterium tumefaciens concentration, the conidia number of T. ophioglossoides, the co-culture time and the concentration of acetosyringone. Furthermore, we have knocked-out the ku70 gene,which is a key gene in non-homologous end joining (NHEJ) DNA repair pathway,and the effect of the length of the homologous arms (HA) on the genetic transformation efficacy was also examined, which increased by 60% when HA was about 3 kb in length. Our results suggest that the genetic transformation system is efficient and feasible for the truffle-parasite fungus T. ophioglossoides, which can further be used in large-scale experiments for characterization of genes of interest in future work.
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Sampaio de Oliveira KB, Leite ML, Rodrigues GR, Duque HM, da Costa RA, Cunha VA, de Loiola Costa LS, da Cunha NB, Franco OL, Dias SC. Strategies for recombinant production of antimicrobial peptides with pharmacological potential. Expert Rev Clin Pharmacol 2020; 13:367-390. [PMID: 32357080 DOI: 10.1080/17512433.2020.1764347] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
INTRODUCTION The need to develop new drugs for the control of pathogenic microorganisms has redoubled efforts to prospect for antimicrobial peptides (AMPs) from natural sources and to characterize its structure and function. These molecules present a broad spectrum of action against different microorganisms and frequently present promiscuous action, with anticancer and immunomodulatory activities. Furthermore, AMPs can be used as biopharmaceuticals in the treatment of hospital-acquired infections and other serious diseases with relevant social and economic impacts.Areas covered: The low yield and the therefore difficult extraction and purification process in AMPs are problems that limit their industrial application and scientific research. Thus, optimized heterologous expression systems were developed to significantly boost AMP yields, allow high efficiency in purification and structural optimization for the increase of therapeutic activity.Expert opinion: This review provides an update on recent developments in the recombinant production of ribosomal and non-ribosomal synthesis of AMPs and on strategies to increase the expression of genes encoding AMPs at the transcriptional and translational levels and regulation of the post-translational modifications. Moreover, there are detailed reports of AMPs that have already reached marketable status or are in the pipeline under advanced stages of preclinical testing.
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Affiliation(s)
- Kamila Botelho Sampaio de Oliveira
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Michel Lopes Leite
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Gisele Regina Rodrigues
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Harry Morales Duque
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Rosiane Andrade da Costa
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Victor Albuquerque Cunha
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Lorena Sousa de Loiola Costa
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Nicolau Brito da Cunha
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Octavio Luiz Franco
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil.,Universidade de Brasília, Pós-graduação em Patologia Molecular, Campus Darcy Ribeiro , Brasília, Brazil.,S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco , Campo Grande, Mato Grosso do Sul, Brazil
| | - Simoni Campos Dias
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil.,Universidade de Brasília, Pós-graduação em Biologia Animal, Campus Darcy Ribeiro , Brasília, Brazil
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Markina NM, Kotlobay AA, Tsarkova AS. Heterologous Metabolic Pathways: Strategies for Optimal Expression in Eukaryotic Hosts. Acta Naturae 2020; 12:28-39. [PMID: 32742725 PMCID: PMC7385092 DOI: 10.32607/actanaturae.10966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 04/29/2020] [Indexed: 11/20/2022] Open
Abstract
Heterologous pathways are linked series of biochemical reactions occurring in a host organism after the introduction of foreign genes. Incorporation of metabolic pathways into host organisms is a major strategy used to increase the production of valuable secondary metabolites. Unfortunately, simple introduction of the pathway genes into the heterologous host in most cases does not result in successful heterologous expression. Extensive modification of heterologous genes and the corresponding enzymes on many different levels is required to achieve high target metabolite production rates. This review summarizes the essential techniques used to create heterologous biochemical pathways, with a focus on the key challenges arising in the process and the major strategies for overcoming them.
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Affiliation(s)
- N. M. Markina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
- Planta LLC, Moscow, 121205 Russia
| | - A. A. Kotlobay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
| | - A. S. Tsarkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
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Tan B, Zhang Q, Zhu Y, Jin H, Zhang L, Chen S, Zhang C. Deciphering Biosynthetic Enzymes Leading to 4-Chloro-6-Methyl-5,7-Dihydroxyphenylglycine, a Non-Proteinogenic Amino Acid in Totopotensamides. ACS Chem Biol 2020; 15:766-773. [PMID: 32118401 DOI: 10.1021/acschembio.9b00997] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Totopotensamide A (TPM A, 1) is a polyketide-peptide glycoside featuring a nonproteinogenic amino acid 4-chloro-6-methyl-5,7-dihydroxyphenylglycine (ClMeDPG). The biosynthetic gene cluster (BGC) of totopotensamides (tot) was previously activated by manipulating transcription regulators in marine-derived Streptomyces pactum SCSIO 02999. Herein, we report the heterologous expression of the tot BGC in Streptomyces lividans TK64, and the production improvement of TPM A via in-frame deletion of two negative regulators totR5 and totR3. The formation of ClMeDPG was proposed to require six enzymes, including four enzymes TotC1C2C3C4 for 3,5-dihydroxyphenylglycine (DPG) biosynthesis and two modifying enzymes TotH (halogenase) and TotM (methyltransferase). Heterologous expression of the four-gene cassette totC1C2C3C4 led to production of 3,5-dihydroxyphenylglyoxylate (DPGX). The aminotransferase TotC4 was biochemically characterized to convert DPGX to S-DPG. Inactivation of totH led to a mutant accumulated a deschloro derivative TPM H1, and the ΔtotHi/ΔtotMi double mutant afforded two deschloro-desmethyl products TPMs HM1 and HM2. A hydrolysis experiment demonstrated that the DPG moiety in TPM HM2 was S-DPG, consistent with that of the TotC4 enzymatic product. These results confirmed that TotH and TotM were responsible for ClMeDPG biosynthesis. Bioinformatics analysis indicated that both TotH and TotM might act on thiolation domain-tethered substrates. This study provided evidence for deciphering enzymes leading to ClMeDPG in TPM A, and unambiguously determined its absolute configuration as S.
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Affiliation(s)
- Bin Tan
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of the Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Qingbo Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Yiguang Zhu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Hongbo Jin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of the Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Liping Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Siqiang Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of the Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Changsheng Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
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Salwan R, Sharma V. Molecular and biotechnological aspects of secondary metabolites in actinobacteria. Microbiol Res 2020; 231:126374. [DOI: 10.1016/j.micres.2019.126374] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/10/2019] [Accepted: 11/11/2019] [Indexed: 12/21/2022]
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Mózsik L, Büttel Z, Bovenberg RAL, Driessen AJM, Nygård Y. Synthetic control devices for gene regulation in Penicillium chrysogenum. Microb Cell Fact 2019; 18:203. [PMID: 31739777 PMCID: PMC6859608 DOI: 10.1186/s12934-019-1253-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 11/10/2019] [Indexed: 12/01/2022] Open
Abstract
Background Orthogonal, synthetic control devices were developed for Penicillium chrysogenum, a model filamentous fungus and industrially relevant cell factory. In the synthetic transcription factor, the QF DNA-binding domain of the transcription factor of the quinic acid gene cluster of Neurospora crassa is fused to the VP16 activation domain. This synthetic transcription factor controls the expression of genes under a synthetic promoter containing quinic acid upstream activating sequence (QUAS) elements, where it binds. A gene cluster may demand an expression tuned individually for each gene, which is a great advantage provided by this system. Results The control devices were characterized with respect to three of their main components: expression of the synthetic transcription factors, upstream activating sequences, and the affinity of the DNA binding domain of the transcription factor to the upstream activating domain. This resulted in synthetic expression devices, with an expression ranging from hardly detectable to a level similar to that of highest expressed native genes. The versatility of the control device was demonstrated by fluorescent reporters and its application was confirmed by synthetically controlling the production of penicillin. Conclusions The characterization of the control devices in microbioreactors, proved to give excellent indications for how the devices function in production strains and conditions. We anticipate that these well-characterized and robustly performing control devices can be widely applied for the production of secondary metabolites and other compounds in filamentous fungi.![]()
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Affiliation(s)
- László Mózsik
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Zsófia Büttel
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Roel A L Bovenberg
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands.,Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Yvonne Nygård
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands. .,DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands. .,Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden.
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Ke J, Yoshikuni Y. Multi-chassis engineering for heterologous production of microbial natural products. Curr Opin Biotechnol 2019; 62:88-97. [PMID: 31639618 DOI: 10.1016/j.copbio.2019.09.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/30/2019] [Accepted: 09/09/2019] [Indexed: 12/11/2022]
Abstract
Microbial genomes encode numerous biosynthetic gene clusters (BGCs) that may produce natural products with diverse applications in medicine, agriculture, the environment, and materials science. With the advent of genome sequencing and bioinformatics, heterologous expression of BGCs is of increasing interest in bioactive natural product (NP) discovery. However, this approach has had limited success because expression of BGCs relies heavily on the physiology of just a few commonly available host chassis. Expanding and diversifying the chassis portfolio for heterologous BGC expression may greatly increase the chances for successful NP production. In this review, we first discuss genetic and genome engineering technologies used to clone, modify, and transform BGCs into multiple strains and to engineer chassis strains. We then highlight studies that employed the multi-chassis approach successfully to optimize NP production, discover previously uncharacterized NPs, and better understand BGC function.
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Affiliation(s)
- Jing Ke
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA 94598, USA
| | - Yasuo Yoshikuni
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA 94598, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, IL 61801, USA; Global Institution for Collaborative Research and Education, Hokkaido University, Hokkaido, 060-8589, Japan.
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Robertsen HL, Musiol-Kroll EM. Actinomycete-Derived Polyketides as a Source of Antibiotics and Lead Structures for the Development of New Antimicrobial Drugs. Antibiotics (Basel) 2019; 8:E157. [PMID: 31547063 PMCID: PMC6963833 DOI: 10.3390/antibiotics8040157] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/08/2019] [Accepted: 09/10/2019] [Indexed: 01/15/2023] Open
Abstract
Actinomycetes are remarkable producers of compounds essential for human and veterinary medicine as well as for agriculture. The genomes of those microorganisms possess several sets of genes (biosynthetic gene cluster (BGC)) encoding pathways for the production of the valuable secondary metabolites. A significant proportion of the identified BGCs in actinomycetes encode pathways for the biosynthesis of polyketide compounds, nonribosomal peptides, or hybrid products resulting from the combination of both polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). The potency of these molecules, in terms of bioactivity, was recognized in the 1940s, and started the "Golden Age" of antimicrobial drug discovery. Since then, several valuable polyketide drugs, such as erythromycin A, tylosin, monensin A, rifamycin, tetracyclines, amphotericin B, and many others were isolated from actinomycetes. This review covers the most relevant actinomycetes-derived polyketide drugs with antimicrobial activity, including anti-fungal agents. We provide an overview of the source of the compounds, structure of the molecules, the biosynthetic principle, bioactivity and mechanisms of action, and the current stage of development. This review emphasizes the importance of actinomycetes-derived antimicrobial polyketides and should serve as a "lexicon", not only to scientists from the Natural Products field, but also to clinicians and others interested in this topic.
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Affiliation(s)
- Helene L Robertsen
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
| | - Ewa M Musiol-Kroll
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
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Kouprina N, Larionov V. TAR Cloning: Perspectives for Functional Genomics, Biomedicine, and Biotechnology. Mol Ther Methods Clin Dev 2019; 14:16-26. [PMID: 31276008 PMCID: PMC6586605 DOI: 10.1016/j.omtm.2019.05.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Completion of the human genome sequence and recent advances in engineering technologies have enabled an unprecedented level of understanding of DNA variations and their contribution to human diseases and cellular functions. However, in some cases, long-read sequencing technologies do not allow determination of the genomic region carrying a specific mutation (e.g., a mutation located in large segmental duplications). Transformation-associated recombination (TAR) cloning allows selective, most accurate, efficient, and rapid isolation of a given genomic fragment or a full-length gene from simple and complex genomes. Moreover, this method is the only way to simultaneously isolate the same genomic region from multiple individuals. As such, TAR technology is currently in a leading position to create a library of the individual genes that comprise the human genome and physically characterize the sites of chromosomal alterations (copy number variations [CNVs], inversions, translocations) in the human population, associated with the predisposition to different diseases, including cancer. It is our belief that such a library and analysis of the human genome will be of great importance to the growing field of gene therapy, new drug design methods, and genomic research. In this review, we detail the motivation for TAR cloning for human genome studies, biotechnology, and biomedicine, discuss the recent progress of some TAR-based projects, and describe how TAR technology in combination with HAC (human artificial chromosome)-based and CRISPR-based technologies may contribute in the future.
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Affiliation(s)
- Natalay Kouprina
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
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Vassaux A, Meunier L, Vandenbol M, Baurain D, Fickers P, Jacques P, Leclère V. Nonribosomal peptides in fungal cell factories: from genome mining to optimized heterologous production. Biotechnol Adv 2019; 37:107449. [PMID: 31518630 DOI: 10.1016/j.biotechadv.2019.107449] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 12/15/2022]
Abstract
Fungi are notoriously prolific producers of secondary metabolites including nonribosomal peptides (NRPs). The structural complexity of NRPs grants them interesting activities such as antibiotic, anti-cancer, and anti-inflammatory properties. The discovery of these compounds with attractive activities can be achieved by using two approaches: either by screening samples originating from various environments for their biological activities, or by identifying the related clusters in genomic sequences thanks to bioinformatics tools. This genome mining approach has grown tremendously due to recent advances in genome sequencing, which have provided an incredible amount of genomic data from hundreds of microbial species. Regarding fungal organisms, the genomic data have revealed the presence of an unexpected number of putative NRP-related gene clusters. This highlights fungi as a goldmine for the discovery of putative novel bioactive compounds. Recent development of NRP dedicated bioinformatics tools have increased the capacity to identify these gene clusters and to deduce NRPs structures, speeding-up the screening process for novel metabolites discovery. Unfortunately, the newly identified compound is frequently not or poorly produced by native producers due to a lack of expression of the related genes cluster. A frequently employed strategy to increase production rates consists in transferring the related biosynthetic pathway in heterologous hosts. This review aims to provide a comprehensive overview about the topic of NRPs discovery, from gene cluster identification by genome mining to the heterologous production in fungal hosts. The main computational tools and methods for genome mining are herein presented with an emphasis on the particularities of the fungal systems. The different steps of the reconstitution of NRP biosynthetic pathway in heterologous fungal cell factories will be discussed, as well as the key factors to consider for maximizing productivity. Several examples will be developed to illustrate the potential of heterologous production to both discover uncharacterized novel compounds predicted in silico by genome mining, and to enhance the productivity of interesting bio-active natural products.
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Affiliation(s)
- Antoine Vassaux
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium; Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, F-59000 Lille, France
| | - Loïc Meunier
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium; InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liege, Boulevard du Rectorat 27, B-4000 Liège, Belgium
| | - Micheline Vandenbol
- TERRA Teaching and Research Centre, Microbiologie et Génomique, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Denis Baurain
- InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liege, Boulevard du Rectorat 27, B-4000 Liège, Belgium
| | - Patrick Fickers
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Philippe Jacques
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Valérie Leclère
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, F-59000 Lille, France.
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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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Grozdev L, Kaiser J, Berensmeier S. One-Step Purification of Microbially Produced Hydrophobic Terpenes via Process Chromatography. Front Bioeng Biotechnol 2019; 7:185. [PMID: 31417900 PMCID: PMC6681792 DOI: 10.3389/fbioe.2019.00185] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/15/2019] [Indexed: 12/31/2022] Open
Abstract
Novel and existing terpenes are already being produced by genetically modified microorganisms, leading to new process challenges for the isolation and purification of these terpenes. Here, eight different chromatographic resins were characterized for the packed bed adsorption of the model terpene β-caryophyllene, showing their applicability on an Escherichia coli fermentation mixture. The polystyrenic Rensa® RP (Ø 50 μm) shows the highest affinity, with a maximum capacity of >100 g L-1 and the best efficiency, with a height equivalent of a theoretical plate (HETP) of 0.022 cm. With this material, an optimized adsorption-based purification of β-caryophyllene from a fermentation mixture was developed, with the green solvent ethanol for desorption. A final yield of >80% and a purity of >99% were reached after only one process step with a total productivity of 0.83 g h-1 L-1. The product solution was loaded with a volume ratio (feed to column) of >500 and the adapted gradient elution yielded a 40 times higher concentration of β-caryophyllene. The adsorption-based chromatography represents therefore a serious alternative to the liquid-liquid extraction and achieves desired purities without the utilization of hazardous solvents.
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Affiliation(s)
| | | | - Sonja Berensmeier
- Bioseparation Engineering Group, Department of Mechanical Engineering, Technical University of Munich, Garching, Germany
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A novel unhairing enzyme produced by heterologous expression of keratinase gene (kerT) in Bacillus subtilis. World J Microbiol Biotechnol 2019; 35:122. [DOI: 10.1007/s11274-019-2701-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 07/22/2019] [Indexed: 01/24/2023]
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Pogorevc D, Panter F, Schillinger C, Jansen R, Wenzel SC, Müller R. Production optimization and biosynthesis revision of corallopyronin A, a potent anti-filarial antibiotic. Metab Eng 2019; 55:201-211. [PMID: 31340171 DOI: 10.1016/j.ymben.2019.07.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 07/16/2019] [Accepted: 07/20/2019] [Indexed: 10/26/2022]
Abstract
Corallopyronins (COR) are α-pyrone antibiotics from myxobacteria representing highly promising lead structures for the development of antibacterial therapeutic agents. Their ability to inhibit RNA polymerase through interaction with the "switch region", a novel target, distant from binding sites of previously characterized RNA polymerase inhibitors (e.g. rifampicin), makes them particularly promising as antibiotic candidates. Corallopyronin A is currently also investigated as a lead compound for the treatment of lymphatic filariasis because of its superb activity against the nematode symbiont Wolbachia. As total synthesis is not a valid production option biotechnological optimization of compound supply is of utmost importance to further develop this highly potent compound class. Here we describe decisive improvements of the previously reported heterologous COR production and engineering platform yielding production of ~100 mg/L COR A. Furthermore, we provide a revised model of COR biosynthesis shedding light on the function of several biosynthetic proteins, including an unusual ECH-like enzyme providing dehydration functionality in trans and an uncharacterized protein conferring COR self-resistance in the myxobacterial heterologous host Myxococcus xanthus DK1622. We also report two new COR derivatives, COR D and oxyCOR A discovered in genetically engineered strains.
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Affiliation(s)
- Domen Pogorevc
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) / Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany
| | - Fabian Panter
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) / Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany
| | - Carolina Schillinger
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) / Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
| | - Rolf Jansen
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Silke C Wenzel
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) / Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) / Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany.
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Lei X, Fan Q, Huang T, Liu H, Zhao G, Ding X. Efficient circular gene knockout system for Burkholderiales strain DSM 7029 and Mycobacterium smegmatis mc2 155. Acta Biochim Biophys Sin (Shanghai) 2019; 51:697-706. [PMID: 31187113 DOI: 10.1093/abbs/gmz054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Indexed: 11/14/2022] Open
Abstract
Multiple gene knockouts are often employed in studies of microbial physiology and genetics. However, the selective markers that confer antibiotic resistance are generally limited, so it is necessary to remove these resistance genes before the next round of using, which is time consuming and labor intensive. Here, we created a universal circular gene knockout system for both the gram-negative bacterial Burkholderiales strain DSM 7029 and the gram-positive bacterial Mycobacterium smegmatis mc2 155, by combining the homologous recombination with multiple serine integrase-meditated site-specific recombination systems. In this system, a resistance gene and an integrase gene were constructed within the two attachment sites corresponding to a second, different integrase to form a cassette for gene disruption, which could be easily removed by the second integrase during the subsequent round of gene knockout. The sacB gene was also employed for negative selection. As the integrase-mediated deletion of the resistance/integrase gene cassette was highly efficient and concurrent with the following knockout round, the cyclic use of three cassettes could achieve multiple gene knockout in a sequential manner. Following the modularity concept in synthetic biology, common components of the knockout plasmids were retained as BioBricks, accelerating the knockout plasmids construction process. The circular gene knockout system can also be used for multiple gene insertions and applied to other microorganisms.
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Affiliation(s)
- Xiaolai Lei
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Qiuxia Fan
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Tian Huang
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Haiyun Liu
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Guoping Zhao
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
- Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Center, Shanghai, China
| | - Xiaoming Ding
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China
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Wang X, Yin S, Bai J, Liu Y, Fan K, Wang H, Yuan F, Zhao B, Li Z, Wang W. Heterologous production of chlortetracycline in an industrial grade Streptomyces rimosus host. Appl Microbiol Biotechnol 2019; 103:6645-6655. [PMID: 31240365 DOI: 10.1007/s00253-019-09970-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/28/2019] [Accepted: 06/05/2019] [Indexed: 01/06/2023]
Abstract
High-yielding industrial Streptomyces producer is usually obtained by multiple rounds of random mutagenesis and screening. These strains have great potential to be developed as the versatile chassis for the discovery and titer improvement of desired heterologous products. Here, the industrial strain Streptomyces rimosus 461, which is a high producer of oxytetracycline, has been engineered as a robust host for heterologous expression of chlortetracycline (CTC) biosynthetic gene cluster. First, the industrial chassis strain SR0 was constructed by deleting the whole oxytetracycline gene cluster of S. rimosus 461. Then, the biosynthetic gene cluster ctc of Streptomyces aureofaciens ATCC 10762 was integrated into the chromosome of SR0. With an additional constitutively expressed cluster-situated activator gene ctcB, the CTC titer of the engineering strain SRC1 immediately reached 1.51 g/L in shaking flask. Then, the CTC titers were upgraded to 2.15 and 3.27 g/L, respectively, in the engineering strains SRC2 and SRC3 with the enhanced ctcB expression. Further, two cluster-situated resistance genes were co-overexpressed with ctcB. The resultant strain produced CTC up to 3.80 g/L in shaking flask fermentation, which represents 38 times increase in comparison with that of the original producer. Overall, SR0 presented in this study have great potential to be used for heterologous production of tetracyclines and other type II polyketides.
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Affiliation(s)
- Xuefeng Wang
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China.,Hebei Shengxue Dacheng Pharmaceutical Co., Ltd., Shijiazhuang, 051430, Hebei, People's Republic of China
| | - Shouliang Yin
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, People's Republic of China
| | - Jing Bai
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China
| | - Yang Liu
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, People's Republic of China
| | - Keqiang Fan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Huizhuan Wang
- Hebei Shengxue Dacheng Pharmaceutical Co., Ltd., Shijiazhuang, 051430, Hebei, People's Republic of China
| | - Fang Yuan
- Hebei Shengxue Dacheng Pharmaceutical Co., Ltd., Shijiazhuang, 051430, Hebei, People's Republic of China
| | - Baohua Zhao
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China.
| | - Zilong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, People's Republic of China.
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, People's Republic of China.
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Shao M, Ma J, Li Q, Ju J. Identification of the Anti-Infective Aborycin Biosynthetic Gene Cluster from Deep-Sea-Derived Streptomyces sp. SCSIO ZS0098 Enables Production in a Heterologous Host. Mar Drugs 2019; 17:md17020127. [PMID: 30795576 PMCID: PMC6409603 DOI: 10.3390/md17020127] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 02/15/2019] [Accepted: 02/17/2019] [Indexed: 11/21/2022] Open
Abstract
Aborycin is a ribosomally synthesized member of the type I lasso peptide natural products. In the present study, aborycin was isolated and identified from the deep-sea-derived microbe Streptomyces sp. SCSIO ZS0098. The aborycin biosynthetic gene cluster (abo) was identified on the basis of genome sequence analyses and then heterologously expressed in Streptomyces coelicolor M1152 to effectively produce aborycin. Aborycin generated in this fashion exhibited moderate antibacterial activity against 13 Staphylococcus aureus strains from various sources with minimum inhibitory concentrations MICs = 8.0~128 µg/mL, against Enterococcus faecalis ATCC 29212 with an MIC = 8.0 µg/mL, and against Bacillus thuringiensis with MIC = 2.0 µg/mL. Additionally, aborycin displayed potent antibacterial activity (MIC = 0.5 µg/mL) against the poultry pathogen Enterococcus gallinarum 5F52C. The reported abo cluster clearly has the potential to provide a means of expanding the repertoire of anti-infective type I lasso peptides.
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Affiliation(s)
- Mingwei Shao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 110039, China.
| | - Juying Ma
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 110039, China.
| | - Qinglian Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 110039, China.
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 110039, China.
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50
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Huo L, Hug JJ, Fu C, Bian X, Zhang Y, Müller R. Heterologous expression of bacterial natural product biosynthetic pathways. Nat Prod Rep 2019. [DOI: 10.1039/c8np00091c [epub ahead of print]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The review highlights the 2013–2018 literature on the heterologous expression of bacterial natural product biosynthetic pathways and emphasises new techniques, heterologous hosts, and novel chemistry.
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Affiliation(s)
- Liujie Huo
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Joachim J. Hug
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
| | - Chengzhang Fu
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
| | - Xiaoying Bian
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Youming Zhang
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Rolf Müller
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
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