1
|
Krishna KV, Ulhas RS, Malaviya A. Bioactive compounds from Cordyceps and their therapeutic potential. Crit Rev Biotechnol 2024; 44:753-773. [PMID: 37518188 DOI: 10.1080/07388551.2023.2231139] [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: 01/27/2023] [Revised: 04/23/2023] [Accepted: 05/11/2023] [Indexed: 08/01/2023]
Abstract
The Clavicipitaceae family's largest and most diverse genus is Cordyceps. They are most abundant and diverse in humid temperate and tropical forests and have a wide distribution in: Europe, North America, and East and Southeast Asian countries, particularly: Bhutan, China, Japan, Nepal, Korea, Thailand, Vietnam, Tibet, and the Himalayan region of India, and Sikkim. It is a well-known parasitic fungus that feeds on insects and other arthropods belonging to 10 different orders. Over 200 bioactive metabolites, that include: nucleotides and nucleosides, polysaccharides, proteins, polypeptides, amino acids, sterols, and fatty acids, among others have been extracted from Cordyceps spp. demonstrating the phytochemical richness of this genus. These components have been associated with a variety of pharmacological effects, including: anti-microbial, anti-apoptotic, anti-cancer, anti-inflammatory, antioxidant, and immunomodulatory activities. In this paper, the bioactivity of various classes of metabolites produced by Cordyceps spp., and their therapeutic properties have been reviewed in an attempt to update the existing literature. Furthermore, one of its nucleoside and a key bioactive compound, cordycepin has been critically elaborated with regard to its biosynthesis pathway and the recently proposed protector-protégé mechanism as well as various biological and pharmacological effects, such as: suppression of purine and nucleic acid biosynthesis, induction of apoptosis, and cell cycle regulation with their mechanism of action. This review provides current knowledge on the bioactive potential of Cordyceps spp.
Collapse
Affiliation(s)
- Kondapalli Vamsi Krishna
- Applied and Industrial Biotechnology Laboratory, Christ (Deemed-to-be University), Bangalore, Karnataka, India
| | - Rutwick Surya Ulhas
- Institute of Biochemistry and Biophysics, Faculty of Life Sciences, University of Jena (Friedrich-Schiller-Universität Jena), Jena, Germany
| | - Alok Malaviya
- Applied and Industrial Biotechnology Laboratory, Christ (Deemed-to-be University), Bangalore, Karnataka, India
- Division of Life Sciences, Gyeongsang National University, Gyeongsangnam-do, South Korea
- QuaLife Biotech Pvt Ltd, Bangalore, India
| |
Collapse
|
2
|
Motter J, Benckendorff CMM, Westarp S, Sunde-Brown P, Neubauer P, Kurreck A, Miller GJ. Purine nucleoside antibiotics: recent synthetic advances harnessing chemistry and biology. Nat Prod Rep 2024; 41:873-884. [PMID: 38197414 PMCID: PMC11188666 DOI: 10.1039/d3np00051f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Indexed: 01/11/2024]
Abstract
Covering: 2019 to 2023Nucleoside analogues represent one of the most important classes of small molecule pharmaceuticals and their therapeutic development is successfully established within oncology and for the treatment of viral infections. However, there are currently no nucleoside analogues in clinical use for the management of bacterial infections. Despite this, a significant number of clinically recognised nucleoside analogues are known to possess some antibiotic activity, thereby establishing a potential source for new therapeutic discovery in this area. Furthermore, given the rise in antibiotic resistance, the discovery of new clinical candidates remains an urgent global priority and natural product-derived nucleoside analogues may also present a rich source of discovery space for new modalities. This Highlight, covering work published from 2019 to 2023, presents a current perspective surrounding the synthesis of natural purine nucleoside antibiotics. By amalgamating recent efforts from synthetic chemistry with advances in biosynthetic understanding and the use of recombinant enzymes, prospects towards different structural classes of purines are detailed.
Collapse
Affiliation(s)
- Jonas Motter
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, D-13355, Berlin, Germany
| | - Caecilie M M Benckendorff
- School of Chemical and Physical Sciences and Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, UK.
| | - Sarah Westarp
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, D-13355, Berlin, Germany
- BioNukleo GmbH, Ackerstraße 76, 13355 Berlin, Germany.
| | - Peter Sunde-Brown
- School of Chemical and Physical Sciences and Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, UK.
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, D-13355, Berlin, Germany
| | - Anke Kurreck
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, D-13355, Berlin, Germany
- BioNukleo GmbH, Ackerstraße 76, 13355 Berlin, Germany.
| | - Gavin J Miller
- School of Chemical and Physical Sciences and Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, UK.
| |
Collapse
|
3
|
Sang M, Feng P, Chi LP, Zhang W. The biosynthetic logic and enzymatic machinery of approved fungi-derived pharmaceuticals and agricultural biopesticides. Nat Prod Rep 2024; 41:565-603. [PMID: 37990930 DOI: 10.1039/d3np00040k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Covering: 2000 to 2023The kingdom Fungi has become a remarkably valuable source of structurally complex natural products (NPs) with diverse bioactivities. Since the revolutionary discovery and application of the antibiotic penicillin from Penicillium, a number of fungi-derived NPs have been developed and approved into pharmaceuticals and pesticide agents using traditional "activity-guided" approaches. Although emerging genome mining algorithms and surrogate expression hosts have brought revolutionary approaches to NP discovery, the time and costs involved in developing these into new drugs can still be prohibitively high. Therefore, it is essential to maximize the utility of existing drugs by rational design and systematic production of new chemical structures based on these drugs by synthetic biology. To this purpose, there have been great advances in characterizing the diversified biosynthetic gene clusters associated with the well-known drugs and in understanding the biosynthesis logic mechanisms and enzymatic transformation processes involved in their production. We describe advances made in the heterogeneous reconstruction of complex NP scaffolds using fungal polyketide synthases (PKSs), non-ribosomal peptide synthetases (NRPSs), PKS/NRPS hybrids, terpenoids, and indole alkaloids and also discuss mechanistic insights into metabolic engineering, pathway reprogramming, and cell factory development. Moreover, we suggest pathways for expanding access to the fungal chemical repertoire by biosynthesis of representative family members via common platform intermediates and through the rational manipulation of natural biosynthetic machineries for drug discovery.
Collapse
Affiliation(s)
- Moli Sang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Peiyuan Feng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Lu-Ping Chi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Wei Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, China
| |
Collapse
|
4
|
Zhang SY, Fu GN, Du LH, Lin H, Zhang AY, Xie HJ, Sheng ZK, Xue MM, Yan BL, Liu Y, Ruan ZX, Pan BL, Zhou TY, Luo XP. Continuous flow biocatalysis: synthesis of purine nucleoside esters catalyzed by lipase TL IM from Thermomyces lanuginosus. RSC Adv 2024; 14:10953-10961. [PMID: 38577433 PMCID: PMC10993233 DOI: 10.1039/d4ra00097h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/05/2024] [Indexed: 04/06/2024] Open
Abstract
Purine nucleoside ester is one of the derivatives of purine nucleoside, which has antiviral and anticancer activities. In this work, a continuous flow synthesis of purine nucleoside esters catalyzed by lipase TL IM from Thermomyces lanuginosus was successfully achieved. Various parameters including solvent, reaction temperature, reaction time/flow rate and substrate ratio were investigated. The best yields were obtained with a continuous flow microreactor for 35 min at 50 °C with the substrate ratio of 1 : 5 (nucleosides to vinyl esters) in the solvent of tert-amyl alcohol. 12 products were efficiently synthesized with yields of 78-93%. Here we reported for the first time the use of lipase TL IM from Thermomyces lanuginosus in the synthesis of purine nucleoside esters. The significant advantages of this methodology are a green solvent and mild conditions, a simple work-up procedure and the highly reusable biocatalyst. This research provides a new technique for rapid synthesis of anticancer and antiviral nucleoside drugs and is helpful for further screening of drug activity.
Collapse
Affiliation(s)
- Shi-Yi Zhang
- College of Pharmaceutical Science, ZheJiang University of Technology Hangzhou 310014 China +86-189-690-693-99
| | - Guo-Neng Fu
- College of Pharmaceutical Science, ZheJiang University of Technology Hangzhou 310014 China +86-189-690-693-99
| | - Li-Hua Du
- College of Pharmaceutical Science, ZheJiang University of Technology Hangzhou 310014 China +86-189-690-693-99
| | - Hang Lin
- College of Pharmaceutical Science, ZheJiang University of Technology Hangzhou 310014 China +86-189-690-693-99
| | - Ao-Ying Zhang
- College of Pharmaceutical Science, ZheJiang University of Technology Hangzhou 310014 China +86-189-690-693-99
| | - Han-Jia Xie
- College of Pharmaceutical Science, ZheJiang University of Technology Hangzhou 310014 China +86-189-690-693-99
| | - Zhi-Kai Sheng
- College of Pharmaceutical Science, ZheJiang University of Technology Hangzhou 310014 China +86-189-690-693-99
| | - Miao-Miao Xue
- College of Pharmaceutical Science, ZheJiang University of Technology Hangzhou 310014 China +86-189-690-693-99
| | - Bing-Lin Yan
- College of Pharmaceutical Science, ZheJiang University of Technology Hangzhou 310014 China +86-189-690-693-99
| | - Yi Liu
- College of Pharmaceutical Science, ZheJiang University of Technology Hangzhou 310014 China +86-189-690-693-99
| | - Zhi-Xuan Ruan
- College of Pharmaceutical Science, ZheJiang University of Technology Hangzhou 310014 China +86-189-690-693-99
| | - Bing-Le Pan
- College of Pharmaceutical Science, ZheJiang University of Technology Hangzhou 310014 China +86-189-690-693-99
| | - Tong-Yao Zhou
- College of Pharmaceutical Science, ZheJiang University of Technology Hangzhou 310014 China +86-189-690-693-99
| | - Xi-Ping Luo
- Zhejiang Provincial Key Laboratory of Chemical Utilization of Forestry Biomass, Zhejiang A&F University Hangzhou 311300 China
| |
Collapse
|
5
|
Raethong N, Thananusak R, Cheawchanlertfa P, Prabhakaran P, Rattanaporn K, Laoteng K, Koffas M, Vongsangnak W. Functional genomics and systems biology of Cordyceps species for biotechnological applications. Curr Opin Biotechnol 2023; 81:102939. [PMID: 37075529 DOI: 10.1016/j.copbio.2023.102939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 04/21/2023]
Abstract
The use of Cordyceps species for the manufacture of natural products has been established; however, the tremendous advances observed in recent years in genetic engineering and molecular biology have revolutionized the optimization of Cordyceps as cell factories and drastically expanded the biotechnological potential of these fungi. Here, we present a review of systems and synthetic biology studies of Cordyceps and their implications for fungal biology and industrial applications. We summarize the current status of synthetic biology for enhancing targeted metabolites in Cordyceps species, such as cordycepin, adenosine, polysaccharide, and pentostatin. Progress in the systems and synthetic biology of Cordyceps provides a strategy for comprehensively comprehensive controlling efficient cell factories of natural bioproducts and novel synthetic biology toolbox for targeted engineering.
Collapse
Affiliation(s)
- Nachon Raethong
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Institute of Nutrition, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Roypim Thananusak
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Pattsarun Cheawchanlertfa
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Pranesha Prabhakaran
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Kittipong Rattanaporn
- Fermentation Technology Research Center (FTRC), Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand
| | - Kobkul Laoteng
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology BIOTEC, National Science and Technology Development Agency NSTDA, Pathum Thani 12120, Thailand
| | - Mattheos Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand.
| |
Collapse
|
6
|
Duan X, Yang H, Wang C, Liu H, Lu X, Tian Y. Microbial synthesis of cordycepin, current systems and future perspectives. Trends Food Sci Technol 2023. [DOI: 10.1016/j.tifs.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
7
|
Zhai G, Gong R, Lin Y, Zhang M, Li J, Deng Z, Sun J, Chen W, Zhang Z. Structural Insight into the Catalytic Mechanism of Non-Heme Iron Halogenase AdaV in 2′-Chloropentostatin Biosynthesis. ACS Catal 2022. [DOI: 10.1021/acscatal.2c04608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guoqing Zhai
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Rong Gong
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Yaxin Lin
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Meng Zhang
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Jiahui Li
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Zixin Deng
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Jiazhong Sun
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Wenqing Chen
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Abichem Biotech Joint Center for Pharmaceutical Innovation, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Zhengyu Zhang
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| |
Collapse
|
8
|
Pentostatin Biosynthesis Pathway Elucidation and Its Application. FERMENTATION 2022. [DOI: 10.3390/fermentation8090459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Pentostatin (PNT), a nucleoside antibiotic with a 1,3-diazo ring structure, is distributed in several actinomycetes and fungi species. Its special structure makes PNT possess a wide spectrum of biological and pharmacological properties, such as antibacterial, antitrypanosomal, anticancer, antiviral, herbicidal, insecticidal, and immunomodulatory effects. Because of the promising adenosine deaminase inhibitory activity of PNT, its extensive application in the clinical treatment of malignant tumors has been extensively studied. However, the fermentation level of microbial-derived PNT is low and cannot meet medical needs. Because the biosynthesis pathway of PNT is obscure, only high-yield mutant screening and optimization of medium components and fermentation processes have been conducted for enhancing its production. Recently, the biosynthesis pathways of PNT in actinomycetes and fungi hosts have been revealed successively, and the large-scale production of PNT by systematic metabolic engineering will become an inevitable trend. Therefore, this review covers all aspects of PNT research, in which major advances in understanding the resource microorganisms, mechanism of action, and biosynthesis pathway of PNT were achieved and diverse clinical applications of PNT were emphasized, and it will lay the foundation for commercial transformation and industrial technology of PNT based on systematic metabolic engineering.
Collapse
|
9
|
Enhancement of cordycepin production from Cordyceps militaris culture by epigenetic modification. Biotechnol Lett 2022; 44:581-593. [PMID: 35262812 DOI: 10.1007/s10529-022-03241-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 02/25/2022] [Indexed: 11/02/2022]
Abstract
Cordycepin (3'-deoxyadenosine) is a nucleoside analogue and biosynthesised by Cordyceps militaris, an entomopathogenic fungus. In this study, an epigenetic modifier was applied to static liquid cultures to enhance cordycepin production. C. militaris was cultured in a static liquid culture, and valproic acid (VPA), a histone deacetylase (HDAC) inhibitor, was supplemented in order to modifying the epigenetic status. Gene regulatory network was explored to understand the molecular mechanisms underlying cordycepin production. 50 micromolar of VPA enhanced cordycepin production by 41.187% via the upregulation of 5'-nucleotidase, adenylate kinase, phosphorybosyltransferase, Cns1, Cns2, Cnsa3, and Cns4 of C. militaris for at least 2 days after VPA treatment. The maximum production of cordycepin was 2,835.32 ± 34.35 mg/L in 400 mL-working volume. A scaled-up culture was established with a working volume of 10 L, which led to the slight decrease of cordycepin production. This might due to multifactorial effects, for instance limited aeration and an uneven dispersion of nutrients in the culture system. This scaled-up culture was still needed further optimization. The modification of epigenetic status by VPA significantly enhanced cordycepin production by altering key gene regulatory network of C. militaris. The strategy established in this study might be applicable to other microorganism culture in order to improving the production of bioactive compounds. This work aimed to enhance the production of cordycepin by modifying the epigenetic status of C. militaris, in which subsequently altered gene regulatory network of cordycepin biosynthesis pathway. The weekly supplementation of valproic acid (VPA), a histone deacetylase (HDAC) inhibitor, significantly improve cordycepin production over 40%, compared to the untreated control, and the gene regulatory network of C. militaris was also adapted.
Collapse
|
10
|
Favipiravir Inhibits Hepatitis A Virus Infection in Human Hepatocytes. Int J Mol Sci 2022; 23:ijms23052631. [PMID: 35269774 PMCID: PMC8910232 DOI: 10.3390/ijms23052631] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 02/06/2023] Open
Abstract
Hepatitis A virus (HAV) is a causative agent of acute hepatitis and can occasionally induce acute liver failure. However, specific potent anti-HAV drug is not available on the market currently. Thus, we investigated several novel therapeutic drugs through a drug repositioning approach, targeting ribonucleic acid (RNA)-dependent RNA polymerase and RNA-dependent deoxyribonucleic acid polymerase. In the present study, we examined the anti-HAV activity of 18 drugs by measuring the HAV subgenomic replicon and HAV HA11-1299 genotype IIIA replication in human hepatoma cell lines, using a reporter assay and real-time reverse transcription polymerase chain reaction, respectively. Mutagenesis of the HAV 5’ untranslated region was also examined by next-generation sequencing. These specific parameters were explored because lethal mutagenesis has emerged as a novel potential therapeutic approach to treat RNA virus infections. Favipiravir inhibited HAV replication in both Huh7 and PLC/PRF/5 cells, although ribavirin inhibited HAV replication in only Huh7 cells. Next-generation sequencing demonstrated that favipiravir could introduce nucleotide mutations into the HAV genome more than ribavirin. In conclusion, favipiravir could introduce nucleotide mutations into the HAV genome and work as an antiviral against HAV infection. Provided that further in vivo experiments confirm its efficacy, favipiravir would be useful for the treatment of severe HAV infection.
Collapse
|
11
|
Lv G, Zhu Y, Cheng X, Cao Y, Zeng B, Liu X, He B. Transcriptomic Responses of Cordyceps militaris to Salt Treatment During Cordycepins Production. Front Nutr 2022; 8:793795. [PMID: 35004818 PMCID: PMC8733472 DOI: 10.3389/fnut.2021.793795] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Cordycepin is a major bioactive compound found in Cordyceps militaris (C. militaris) that exhibits a broad spectrum of biological activities. Hence, it is potentially a bioactive ingredient of pharmaceutical and cosmetic products. However, overexploitation and low productivity of natural C. militaris is a barrier to commercialization, which leads to insufficient supply to meet its existing market demands. In this study, a preliminary study of distinct concentrations of salt treatments toward C. militaris was conducted. Although the growth of C. militaris was inhibited by different salt treatments, the cordycepin production increased significantly accompanied by the increment of salt concentration. Among them, the content of cordycepin in the 7% salt-treated group was five-fold higher than that of the control group. Further transcriptome analysis of samples with four salt concentrations, coupled with Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, several differentially expressed genes (DEGs) were found. Finally, dynamic changes of the expression patterns of four genes involved in the cordycepin biosynthesis pathway were observed by the quantitative real-time PCR. Taken together, our study provides a global transcriptome characterization of the salt treatment adaptation process in C. militaris and facilitates the construction of industrial strains with a high cordycepin production and salt tolerance.
Collapse
Affiliation(s)
- Gongbo Lv
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-innovation Center for in-vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Yue Zhu
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-innovation Center for in-vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Xiaojie Cheng
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Yan Cao
- Information Institute of Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Bin Zeng
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-innovation Center for in-vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China.,College of Pharmacy, Shenzhen Technology University, Shenzhen, China
| | - Xinping Liu
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-innovation Center for in-vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Bin He
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-innovation Center for in-vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| |
Collapse
|
12
|
Biology and applications of co-produced, synergistic antimicrobials from environmental bacteria. Nat Microbiol 2021; 6:1118-1128. [PMID: 34446927 DOI: 10.1038/s41564-021-00952-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 07/21/2021] [Indexed: 02/07/2023]
Abstract
Environmental bacteria, such as Streptomyces spp., produce specialized metabolites that are potent antibiotics and therapeutics. Selected specialized antimicrobials are co-produced and function together synergistically. Co-produced antimicrobials comprise multiple chemical classes and are produced by a wide variety of bacteria in different environmental niches, suggesting that their combined functions are ecologically important. Here, we highlight the exquisite mechanisms that underlie the simultaneous production and functional synergy of 16 sets of co-produced antimicrobials. To date, antibiotic and antifungal discovery has focused mainly on single molecules, but we propose that methods to target co-produced antimicrobials could widen the scope and applications of discovery programs.
Collapse
|
13
|
Zhao M, Zhang H, Lou T, Zhao K, Wang S. [Simultaneous determination of pentostatin and 2'-amino-2'-deoxyadenosine in fermentation broth by high performance liquid chromatography-tandem mass spectrometry]. Se Pu 2021; 39:744-749. [PMID: 34227372 PMCID: PMC9404223 DOI: 10.3724/sp.j.1123.2020.09018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
建立了高效液相色谱-串联质谱(HPLC-MS/MS)同时测定发酵液中喷司他丁和2'-氨基-2'-脱氧腺苷含量的方法。发酵液经高速离心、水溶液稀释、微孔过滤后进行HPLC-MS/MS分析测定。选用Waters Atlantis® T3色谱柱(100 mm×2.1 mm, 5 μm)及其保护柱(5 mm×2.1 mm, 5 μm)进行分离,选择10 mmol/L甲酸铵(含0.1%甲酸)-甲醇(含0.02%甲酸)溶液为流动相进行梯度洗脱,流速为0.3 mL/min,柱温为25 ℃,进样量为10 μL。在电喷雾电离、正离子模式下收集数据,对目标化合物进行定性定量分析。喷司他丁定量离子对为m/z 269.17>153.20,碰撞能为11 V, 2'-氨基-2'-脱氧腺苷定量离子对为m/z 267.00>136.10,碰撞能为18 V。采用外标法对喷司他丁和2'-氨基-2'-脱氧腺苷定量分析。结果表明,喷司他丁和2'-氨基-2'-脱氧腺苷在1.0~250 μg/L范围内呈现出良好的线性关系,相关系数(R2)为0.9969~0.9996,相对标准偏差(RSD)为6.51%~8.35%(n=8)。在发酵液样品中进行加标水平为1.0、5.0和25 μg/L的添加回收试验(n=6),喷司他丁的回收率为97.94%~104.46%, RSD为3.74%~4.88%; 2'-氨基-2'-脱氧腺苷回收率为89.96%~107.21%, RSD为4.81%~13.29%。喷司他丁和2'-氨基-2'-脱氧腺苷的检出限为0.003~0.060 μg/L,定量限为0.010~0.200 μg/L。该文系统性地建立了基于HPLC-MS/MS测定发酵液中喷司他丁和2'-氨基-2'-脱氧腺苷的方法,在实际样品检测中,操作简便,准确度高,灵敏快速,有效克服了基质效应对目标化合物的影响,改善了目标化合物的峰形和稳定性,为从微生物发酵液中检测喷司他丁和2'-氨基-2'-脱氧腺苷提供了方法学基础和借鉴。
Collapse
Affiliation(s)
- Minmin Zhao
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Hongyu Zhang
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Tingting Lou
- Animal, Plant and Foodstuffs Inspection Center of Tianjin Customs, Tianjin 300461, China
| | - Kongxiang Zhao
- Animal, Plant and Foodstuffs Inspection Center of Tianjin Customs, Tianjin 300461, China
| | - Suying Wang
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| |
Collapse
|
14
|
Gong R, Yu L, Qin Y, Price NPJ, He X, Deng Z, Chen W. Harnessing synthetic biology-based strategies for engineered biosynthesis of nucleoside natural products in actinobacteria. Biotechnol Adv 2020; 46:107673. [PMID: 33276073 DOI: 10.1016/j.biotechadv.2020.107673] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/29/2020] [Accepted: 11/25/2020] [Indexed: 01/01/2023]
Abstract
Antibiotic resistance poses an increasing threat to global health, and it is urgent to reverse the present trend by accelerating development of new natural product derived drugs. Nucleoside antibiotics, a valuable family of promising natural products with remarkable structural features and diverse biological activities, have played significant roles in healthcare and for plant protection. Understanding the biosynthesis of these intricate molecules has provided a foundation for bioengineering the microbial cell factory towards yield enhancement and structural diversification. In this review, we summarize the recent progresses in employing synthetic biology-based strategies to improve the production of target nucleoside antibiotics. Moreover, we delineate the advances on rationally accessing the chemical diversities of natural nucleoside antibiotics.
Collapse
Affiliation(s)
- Rong Gong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Le Yu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Yini Qin
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Neil P J Price
- US Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | - Xinyi He
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Wenqing Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.
| |
Collapse
|
15
|
Characterization of the coformycin biosynthetic gene cluster in Streptomyces kaniharaensis. Proc Natl Acad Sci U S A 2020; 117:10265-10270. [PMID: 32350138 DOI: 10.1073/pnas.2000111117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Coformycin and pentostatin are structurally related N-nucleoside inhibitors of adenosine deaminase characterized by an unusual 1,3-diazepine nucleobase. Herein, the cof gene cluster responsible for coformycin biosynthesis is identified. Reconstitution of the coformycin biosynthetic pathway in vitro demonstrates that it overlaps significantly with the early stages of l-histidine biosynthesis. Committed entry into the coformycin pathway takes place via conversion of a shared branch point intermediate to 8-ketocoformycin-[Formula: see text]-monophosphate catalyzed by CofB, which is a homolog of succinylaminoimidazolecarboxamide ribotide (SAICAR) synthetase. This reaction appears to proceed via a Dieckmann cyclization and a retro-aldol elimination, releasing ammonia and D-erythronate-4-phosphate as coproducts. Completion of coformycin biosynthesis involves reduction and dephosphorylation of the CofB product, with the former reaction being catalyzed by the NADPH-dependent dehydrogenase CofA. CofB also shows activation by adenosine triphosphate (ATP) despite the reaction requiring neither a phosphorylated nor an adenylated intermediate. This may serve to help regulate metabolic partitioning between the l-histidine and coformycin pathways.
Collapse
|
16
|
Daley SK, Cordell GA. Homopurine Alkaloids: A Brief Overview. Nat Prod Commun 2020. [DOI: 10.1177/1934578x20917787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The isolation, structure elucidation, synthesis, biological properties, and biosynthesis of the homopurine alkaloids are reviewed, with an emphasis on the “victim-guardian” relationships between co-occurring alkaloids.
Collapse
Affiliation(s)
| | - Geoffrey A. Cordell
- Natural Products Inc., Evanston, IL, USA
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| |
Collapse
|
17
|
Zhao C, Yan S, Li Q, Zhu H, Zhong Z, Ye Y, Deng Z, Zhang Y. An Fe 2+ - and α-Ketoglutarate-Dependent Halogenase Acts on Nucleotide Substrates. Angew Chem Int Ed Engl 2020; 59:9478-9484. [PMID: 32160364 DOI: 10.1002/anie.201914994] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 02/04/2020] [Indexed: 11/08/2022]
Abstract
While halogenated nucleosides are used as common anticancer and antiviral drugs, naturally occurring halogenated nucleosides are rare. Adechlorin (ade) is a 2'-chloro nucleoside natural product first identified from Actinomadura sp. ATCC 39365. However, the installation of chlorine in the ade biosynthetic pathway remains elusive. Reported herein is a Fe2+ -α-ketoglutarate halogenase AdeV that can install a chlorine atom at the C2' position of 2'-deoxyadenosine monophosphate to afford 2'-chloro-2'-deoxyadenosine monophosphate. Furthermore, 2',3'-dideoxyadenosine-5'-monophosphate and 2'-deoxyinosine-5'-monophosphate can also be converted, albeit 20-fold and 2-fold, respectively, less efficiently relative to the conversion of 2'-deoxyadenosine monophosphate. AdeV represents the first example of a Fe2+ -α-ketoglutarate-dependent halogenase that converts nucleotides into chlorinated analogues.
Collapse
Affiliation(s)
- Chunhua Zhao
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Shan Yan
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Qin Li
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hucheng Zhu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Zhiyu Zhong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, P. R. China
| | - Ying Ye
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, P. R. China
| | - Yonghui Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| |
Collapse
|
18
|
Zhao C, Yan S, Li Q, Zhu H, Zhong Z, Ye Y, Deng Z, Zhang Y. An Fe
2+
‐ and α‐Ketoglutarate‐Dependent Halogenase Acts on Nucleotide Substrates. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914994] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Chunhua Zhao
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource EvaluationSchool of PharmacyTongji Medical CollegeHuazhong University of Science and Technology Wuhan 430030 China
| | - Shan Yan
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource EvaluationSchool of PharmacyTongji Medical CollegeHuazhong University of Science and Technology Wuhan 430030 China
| | - Qin Li
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource EvaluationSchool of PharmacyTongji Medical CollegeHuazhong University of Science and Technology Wuhan 430030 China
| | - Hucheng Zhu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource EvaluationSchool of PharmacyTongji Medical CollegeHuazhong University of Science and Technology Wuhan 430030 China
| | - Zhiyu Zhong
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of EducationSchool of Pharmaceutical SciencesWuhan University Wuhan 430071 P. R. China
| | - Ying Ye
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource EvaluationSchool of PharmacyTongji Medical CollegeHuazhong University of Science and Technology Wuhan 430030 China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of EducationSchool of Pharmaceutical SciencesWuhan University Wuhan 430071 P. R. China
| | - Yonghui Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource EvaluationSchool of PharmacyTongji Medical CollegeHuazhong University of Science and Technology Wuhan 430030 China
| |
Collapse
|
19
|
Comparative Investigation into Formycin A and Pyrazofurin A Biosynthesis Reveals Branch Pathways for the Construction of C-Nucleoside Scaffolds. Appl Environ Microbiol 2020; 86:AEM.01971-19. [PMID: 31676476 DOI: 10.1128/aem.01971-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/25/2019] [Indexed: 12/23/2022] Open
Abstract
Formycin A (FOR-A) and pyrazofurin A (PRF-A) are purine-related C-nucleoside antibiotics in which ribose and a pyrazole-derived base are linked by a C-glycosidic bond. However, the logic underlying the biosynthesis of these molecules has remained largely unexplored. Here, we report the discovery of the pathways for FOR-A and PRF-A biosynthesis from diverse actinobacteria and propose that their biosynthesis is likely initiated by a lysine N 6-monooxygenase. Moreover, we show that forT and prfT (involved in FOR-A and PRF-A biosynthesis, respectively) mutants are correspondingly capable of accumulating the unexpected pyrazole-related intermediates 4-amino-3,5-dicarboxypyrazole and 3,5-dicarboxy-4-oxo-4,5-dihydropyrazole. We also decipher the enzymatic mechanism of ForT/PrfT for C-glycosidic bond formation in FOR-A/PRF-A biosynthesis. To our knowledge, ForT/PrfT represents an example of β-RFA-P (β-ribofuranosyl-aminobenzene 5'-phosphate) synthase-like enzymes governing C-nucleoside scaffold construction in natural product biosynthesis. These data establish a foundation for combinatorial biosynthesis of related purine nucleoside antibiotics and also open the way for target-directed genome mining of PRF-A/FOR-A-related antibiotics.IMPORTANCE FOR-A and PRF-A are C-nucleoside antibiotics known for their unusual chemical structures and remarkable biological activities. Deciphering the enzymatic mechanism for the construction of a C-nucleoside scaffold during FOR-A/PRF-A biosynthesis will not only expand the biochemical repertoire for novel enzymatic reactions but also permit target-oriented genome mining of FOR-A/PRF-A-related C-nucleoside antibiotics. Moreover, the availability of FOR-A/PRF-A biosynthetic gene clusters will pave the way for the rational generation of designer FOR-A/PRF-A derivatives with enhanced/selective bioactivity via synthetic biology strategies.
Collapse
|
20
|
Ji Z, Nie Q, Yin Y, Zhang M, Pan H, Hou X, Tang G. Activation and Characterization of Cryptic Gene Cluster: Two Series of Aromatic Polyketides Biosynthesized by Divergent Pathways. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Zhen‐Yu Ji
- State Key Laboratory of Bioorganic and Natural Products ChemistryCenter for Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesChinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
| | - Qiu‐Yue Nie
- State Key Laboratory of Bioorganic and Natural Products ChemistryCenter for Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesChinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
| | - Yue Yin
- State Key Laboratory of Bioorganic and Natural Products ChemistryCenter for Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesChinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
| | - Mei Zhang
- State Key Laboratory of Bioorganic and Natural Products ChemistryCenter for Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesChinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
| | - Hai‐Xue Pan
- State Key Laboratory of Bioorganic and Natural Products ChemistryCenter for Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesChinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
| | - Xian‐Feng Hou
- State Key Laboratory of Bioorganic and Natural Products ChemistryCenter for Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesChinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
| | - Gong‐Li Tang
- State Key Laboratory of Bioorganic and Natural Products ChemistryCenter for Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesChinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
| |
Collapse
|
21
|
Ren D, Wang S, Ko Y, Geng Y, Ogasawara Y, Liu H. Identification of the
C
‐Glycoside Synthases during Biosynthesis of the Pyrazole‐
C
‐Nucleosides Formycin and Pyrazofurin. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Daan Ren
- Department of Chemistry and Division of Chemical Biology and Medicinal Chemistry College of Pharmacy University of Texas at Austin Austin TX 78712 USA
| | - Shao‐An Wang
- Department of Chemistry and Division of Chemical Biology and Medicinal Chemistry College of Pharmacy University of Texas at Austin Austin TX 78712 USA
| | - Yeonjin Ko
- Department of Chemistry and Division of Chemical Biology and Medicinal Chemistry College of Pharmacy University of Texas at Austin Austin TX 78712 USA
| | - Yujie Geng
- Department of Chemistry and Division of Chemical Biology and Medicinal Chemistry College of Pharmacy University of Texas at Austin Austin TX 78712 USA
| | - Yasushi Ogasawara
- Department of Chemistry and Division of Chemical Biology and Medicinal Chemistry College of Pharmacy University of Texas at Austin Austin TX 78712 USA
- Current address: Graduate School of Engineering Sapporo Hokkaido 060-8628 Japan
| | - Hung‐wen Liu
- Department of Chemistry and Division of Chemical Biology and Medicinal Chemistry College of Pharmacy University of Texas at Austin Austin TX 78712 USA
| |
Collapse
|
22
|
Ren D, Wang SA, Ko Y, Geng Y, Ogasawara Y, Liu HW. Identification of the C-Glycoside Synthases during Biosynthesis of the Pyrazole-C-Nucleosides Formycin and Pyrazofurin. Angew Chem Int Ed Engl 2019; 58:16512-16516. [PMID: 31518483 PMCID: PMC6911263 DOI: 10.1002/anie.201910356] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Indexed: 12/18/2022]
Abstract
C-Nucleosides are characterized by a C-C rather than a C-N linkage between the heterocyclic base and the ribofuranose ring. While the biosynthesis of pseudouridine-C-nucleosides has been studied, less is known about the pyrazole-C-nucleosides such as the formycins and pyrazofurin. Herein, genome screening of Streptomyces candidus NRRL 3601 led to the discovery of the pyrazofurin biosynthetic gene cluster pyf. In vitro characterization of gene product PyfQ demonstrated that it is able to catalyze formation of the C-glycoside carboxyhydroxypyrazole ribonucleotide (CHPR) from 4-hydroxy-1H-pyrazole-3,5-dicarboxylic acid and phosphoribosyl pyrophosphate (PRPP). Similarly, ForT, the PyfQ homologue in the formycin pathway, can catalyze the coupling of 4-amino-1H-pyrazole-3,5-dicarboxylic acid and PRPP to form carboxyaminopyrazole ribonucleotide. Finally, PyfP and PyfT are shown to catalyze amidation of CHPR to pyrazofurin 5'-phosphate thereby establishing the latter stages of both pyrazofurin and formycin biosynthesis.
Collapse
Affiliation(s)
| | | | - Yeonjin Ko
- Department of Chemistry and Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712 (USA)
| | - Yujie Geng
- Department of Chemistry and Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712 (USA)
| | | | - Hung-wen Liu
- Department of Chemistry and Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712 (USA)
| |
Collapse
|
23
|
AbuSara NF, Piercey BM, Moore MA, Shaikh AA, Nothias LF, Srivastava SK, Cruz-Morales P, Dorrestein PC, Barona-Gómez F, Tahlan K. Comparative Genomics and Metabolomics Analyses of Clavulanic Acid-Producing Streptomyces Species Provides Insight Into Specialized Metabolism. Front Microbiol 2019; 10:2550. [PMID: 31787949 PMCID: PMC6856088 DOI: 10.3389/fmicb.2019.02550] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 10/22/2019] [Indexed: 01/13/2023] Open
Abstract
Clavulanic acid is a bacterial specialized metabolite, which inhibits certain serine β-lactamases, enzymes that inactivate β-lactam antibiotics to confer resistance. Due to this activity, clavulanic acid is widely used in combination with penicillin and cephalosporin (β-lactam) antibiotics to treat infections caused by β-lactamase-producing bacteria. Clavulanic acid is industrially produced by fermenting Streptomyces clavuligerus, as large-scale chemical synthesis is not commercially feasible. Other than S. clavuligerus, Streptomyces jumonjinensis and Streptomyces katsurahamanus also produce clavulanic acid along with cephamycin C, but information regarding their genome sequences is not available. In addition, the Streptomyces contain many biosynthetic gene clusters thought to be "cryptic," as the specialized metabolites produced by them are not known. Therefore, we sequenced the genomes of S. jumonjinensis and S. katsurahamanus, and examined their metabolomes using untargeted mass spectrometry along with S. clavuligerus for comparison. We analyzed the biosynthetic gene cluster content of the three species to correlate their biosynthetic capacities, by matching them with the specialized metabolites detected in the current study. It was recently reported that S. clavuligerus can produce the plant-associated metabolite naringenin, and we describe more examples of such specialized metabolites in extracts from the three Streptomyces species. Detailed comparisons of the biosynthetic gene clusters involved in clavulanic acid (and cephamycin C) production were also performed, and based on our analyses, we propose the core set of genes responsible for producing this medicinally important metabolite.
Collapse
Affiliation(s)
- Nader F. AbuSara
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Brandon M. Piercey
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Marcus A. Moore
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Arshad Ali Shaikh
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Louis-Félix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
| | | | - Pablo Cruz-Morales
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Mexico
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Francisco Barona-Gómez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Mexico
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
| |
Collapse
|
24
|
Ji ZY, Nie QY, Yin Y, Zhang M, Pan HX, Hou XF, Tang GL. Activation and Characterization of Cryptic Gene Cluster: Two Series of Aromatic Polyketides Biosynthesized by Divergent Pathways. Angew Chem Int Ed Engl 2019; 58:18046-18054. [PMID: 31553109 DOI: 10.1002/anie.201910882] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Indexed: 12/15/2022]
Abstract
One biosynthetic gene cluster (BGC) usually governs the biosynthesis of a series of compounds exhibiting either the same or similar molecular scaffolds. Reported here is a multiplex activation strategy to awaken a cryptic BGC associated with tetracycline polyketides, resulting in the discovery of compounds having different core structures. By constitutively expressing a positive regulator gene in tandem mode, a single BGC directed the biosynthesis of eight aromatic polyketides with two types of frameworks, two pentacyclic isomers and six glycosylated tetracyclines. The proposed biosynthetic pathway, based on systematic gene inactivation and identification of intermediates, employs two sets of tailoring enzymes with a branching point from the same intermediate. These findings not only provide new insights into the role of tailoring enzymes in the diversification of polyketides, but also highlight a reliable strategy for genome mining of natural products.
Collapse
Affiliation(s)
- Zhen-Yu Ji
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Qiu-Yue Nie
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Yue Yin
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Mei Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Hai-Xue Pan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Xian-Feng Hou
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Gong-Li Tang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| |
Collapse
|
25
|
Therapeutic Potential and Biological Applications of Cordycepin and Metabolic Mechanisms in Cordycepin-Producing Fungi. Molecules 2019; 24:molecules24122231. [PMID: 31207985 PMCID: PMC6632035 DOI: 10.3390/molecules24122231] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 06/03/2019] [Accepted: 06/06/2019] [Indexed: 12/11/2022] Open
Abstract
Cordycepin (3′-deoxyadenosine), a cytotoxic nucleoside analogue found in Cordyceps militaris, has attracted much attention due to its therapeutic potential and biological value. Cordycepin interacts with multiple medicinal targets associated with cancer, tumor, inflammation, oxidant, polyadenylation of mRNA, etc. The investigation of the medicinal drug actions supports the discovery of novel targets and the development of new drugs to enhance the therapeutic potency and reduce toxicity. Cordycepin may be of great value owing to its medicinal potential as an external drug, such as in cosmeceutical, traumatic, antalgic and muscle strain applications. In addition, the biological application of cordycepin, for example, as a ligand, has been used to uncover molecular structures. Notably, studies that investigated the metabolic mechanisms of cordycepin-producing fungi have yielded significant information related to the biosynthesis of high levels of cordycepin. Here, we summarized the medicinal targets, biological applications, cytotoxicity, delivery carriers, stability, and pros/cons of cordycepin in clinical applications, as well as described the metabolic mechanisms of cordycepin in cordycepin-producing fungi. We posit that new approaches, including single-cell analysis, have the potential to enhance medicinal potency and unravel all facets of metabolic mechanisms of cordycepin in Cordyceps militaris.
Collapse
|
26
|
Wang SA, Ko Y, Zeng J, Geng Y, Ren D, Ogasawara Y, Irani S, Zhang Y, Liu HW. Identification of the Formycin A Biosynthetic Gene Cluster from Streptomyces kaniharaensis Illustrates the Interplay between Biological Pyrazolopyrimidine Formation and de Novo Purine Biosynthesis. J Am Chem Soc 2019; 141:6127-6131. [PMID: 30942582 DOI: 10.1021/jacs.9b00241] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Formycin A is a potent purine nucleoside antibiotic with a C-glycosidic linkage between the ribosyl moiety and the pyrazolopyrimidine base. Herein, a cosmid is identified from the Streptomyces kaniharaensis genome library that contains the for gene cluster responsible for the biosynthesis of formycin. Subsequent gene deletion experiments and in vitro characterization of the forBCH gene products established their catalytic functions in formycin biosynthesis. Results also demonstrated that PurH from de novo purine biosynthesis plays a key role in pyrazolopyrimidine formation during biosynthesis of formycin A. The participation of PurH in both pathways represents a good example of how primary and secondary metabolism are interlinked.
Collapse
|
27
|
Enrichment of cordycepin for cosmeceutical applications: culture systems and strategies. Appl Microbiol Biotechnol 2019; 103:1681-1691. [DOI: 10.1007/s00253-019-09623-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/03/2019] [Accepted: 01/04/2019] [Indexed: 12/17/2022]
|
28
|
Coordinated Biosynthesis of the Purine Nucleoside Antibiotics Aristeromycin and Coformycin in Actinomycetes. Appl Environ Microbiol 2018; 84:AEM.01860-18. [PMID: 30217843 DOI: 10.1128/aem.01860-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 09/04/2018] [Indexed: 02/05/2023] Open
Abstract
Purine nucleoside antibiotic pairs, concomitantly produced by a single strain, are an important group of microbial natural products. Here, we report a target-directed genome mining approach to elucidate the biosynthesis of the purine nucleoside antibiotic pair aristeromycin (ARM) and coformycin (COF) in Micromonospora haikouensis DSM 45626 (a new producer for ARM and COF) and Streptomyces citricolor NBRC 13005 (a new COF producer). We also provide biochemical data that MacI and MacT function as unusual phosphorylases, catalyzing an irreversible reaction for the tailoring assembly of neplanocin A (NEP-A) and ARM. Moreover, we demonstrate that MacQ is shown to be an adenosine-specific deaminase, likely relieving the potential "excess adenosine" for producing cells. Finally, we report that MacR, an annotated IMP dehydrogenase, is actually an NADPH-dependent GMP reductase, which potentially plays a salvage role for the efficient supply of the precursor pool. Hence, these findings illustrate a fine-tuned pathway for the biosynthesis of ARM and also open the way for the rational search for purine antibiotic pairs.IMPORTANCE ARM and COF are well known for their prominent biological activities and unusual chemical structures; however, the logic of their biosynthesis has long been poorly understood. Actually, the new insights into the ARM and COF pathway will not only enrich the biochemical repertoire for interesting enzymatic reactions but may also lay a solid foundation for the combinatorial biosynthesis of this group of antibiotics via a target-directed genome mining strategy.
Collapse
|
29
|
Liu Y, Gong R, Liu X, Zhang P, Zhang Q, Cai YS, Deng Z, Winkler M, Wu J, Chen W. Discovery and characterization of the tubercidin biosynthetic pathway from Streptomyces tubercidicus NBRC 13090. Microb Cell Fact 2018; 17:131. [PMID: 30153835 PMCID: PMC6112128 DOI: 10.1186/s12934-018-0978-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 08/14/2018] [Indexed: 11/30/2022] Open
Abstract
Background Tubercidin (TBN), an adenosine analog with potent antimycobacteria and antitumor bioactivities, highlights an intriguing structure, in which a 7-deazapurine core is linked to the ribose moiety by an N-glycosidic bond. However, the molecular logic underlying the biosynthesis of this antibiotic has remained poorly understood. Results Here, we report the discovery and characterization of the TBN biosynthetic pathway from Streptomyces tubercidicus NBRC 13090 via reconstitution of its production in a heterologous host. We demonstrated that TubE specifically utilizes phosphoribosylpyrophosphate and 7-carboxy-7-deazaguanine for the precise construction of the deazapurine nucleoside scaffold. Moreover, we provided biochemical evidence that TubD functions as an NADPH-dependent reductase, catalyzing irreversible reductive deamination. Finally, we verified that TubG acts as a Nudix hydrolase, preferring Co2+ for the maintenance of maximal activity, and is responsible for the tailoring hydrolysis step leading to TBN. Conclusions These findings lay a foundation for the rational generation of TBN analogs through synthetic biology strategy, and also open the way for the target-directed search of TBN-related antibiotics. Electronic supplementary material The online version of this article (10.1186/s12934-018-0978-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yan Liu
- State Key Laboratory of Virology, and College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Rong Gong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Xiaoqin Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Peichao Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Qi Zhang
- State Key Laboratory of Virology, and College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - You-Sheng Cai
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Margit Winkler
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria
| | - Jianguo Wu
- State Key Laboratory of Virology, and College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Wenqing Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.
| |
Collapse
|
30
|
Fungal Cordycepin Biosynthesis Is Coupled with the Production of the Safeguard Molecule Pentostatin. Cell Chem Biol 2017; 24:1479-1489.e4. [DOI: 10.1016/j.chembiol.2017.09.001] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 05/05/2017] [Accepted: 09/01/2017] [Indexed: 12/31/2022]
|
31
|
Biosynthesis of 2'-Chloropentostatin and 2'-Amino-2'-Deoxyadenosine Highlights a Single Gene Cluster Responsible for Two Independent Pathways in Actinomadura sp. Strain ATCC 39365. Appl Environ Microbiol 2017; 83:AEM.00078-17. [PMID: 28258148 DOI: 10.1128/aem.00078-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 02/26/2017] [Indexed: 01/30/2023] Open
Abstract
2'-Chloropentostatin (2'-Cl PTN, 2'-chloro-2'-deoxycoformycin) and 2'-amino-2'-deoxyadenosine (2'-amino dA) are two adenosine-derived nucleoside antibiotics coproduced by Actinomadura sp. strain ATCC 39365. 2'-Cl PTN is a potent adenosine deaminase (ADA) inhibitor featuring an intriguing 1,3-diazepine ring, as well as a chlorination at C-2' of ribose, and 2'-amino dA is an adenosine analog showing bioactivity against RNA-type virus infection. However, the biosynthetic logic of them has remained poorly understood. Here, we report the identification of a single gene cluster (ada) essential for the biosynthesis of 2'-Cl PTN and 2'-amino dA. Further systematic genetic investigations suggest that 2'-Cl PTN and 2'-amino dA are biosynthesized by independent pathways. Moreover, we provide evidence that a predicted cation/H+ antiporter, AdaE, is involved in the chlorination step during 2'-Cl PTN biosynthesis. Notably, we demonstrate that 2'-amino dA biosynthesis is initiated by a Nudix hydrolase, AdaJ, catalyzing the hydrolysis of ATP. Finally, we reveal that the host ADA (designated ADA1), capable of converting adenosine/2'-amino dA to inosine/2'-amino dI, is not very sensitive to the powerful ADA inhibitor pentostatin. These findings provide a basis for the further rational pathway engineering of 2'-Cl PTN and 2'-amino dA production.IMPORTANCE 2'-Cl PTN/PTN and 2'-amino dA have captivated the great interests of scientists, owing to their unusual chemical structures and remarkable bioactivities. However, the precise logic for their biosynthesis has been elusive for decades. Actually, the identification and elucidation of their biosynthetic pathways not only enrich the biochemical repertoire of novel enzymatic reactions but may also lay solid foundations for the pathway engineering and combinatorial biosynthesis of this family of purine nucleoside antibiotics to generate novel hybrid analogs with improved features.
Collapse
|