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Xie H, Su YT, Bu QT, Li YP, Zhao QW, Du YL, Li YQ. Stepwise increase of fidaxomicin in an engineered heterologous host Streptomyces albus through multi-level metabolic engineering. Synth Syst Biotechnol 2024; 9:766-774. [PMID: 39021363 PMCID: PMC11253128 DOI: 10.1016/j.synbio.2024.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/28/2024] [Accepted: 06/12/2024] [Indexed: 07/20/2024] Open
Abstract
The anti-Clostridium difficile infection (CDI) drug fidaxomicin is a natural polyketide metabolite mainly produced by Micromonosporaceae, such as Actinoplanes deccanensis, Dactylosporangium aurantiacum, and Micromonospora echinospora. In the present study, we employed a stepwise strategy by combining heterologous expression, chassis construction, promoter engineering, activator and transporters overexpression, and optimization of fermentation media for high-level production of fidaxomicin. The maximum yield of 384 mg/L fidaxomicin was achieved with engineered Streptomyces albus D7-VHb in 5 L-tank bioreactor, and it was approximately 15-fold higher than the native strain Actinoplanes deccanensis YP-1 with higher strain stability and growth rate. This study developed an enhanced chassis strain, and for the first time, achieved the heterologous synthesis of fidaxomicin through a combinatorial metabolic engineering strategy.
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Affiliation(s)
- Huang Xie
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Yi-Ting Su
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Qing-Ting Bu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Yue-Ping Li
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Qing-Wei Zhao
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yi-Ling Du
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Yong-Quan Li
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
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2
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He F, Liu X, Tang M, Wang H, Wu Y, Liang S. CRISETR: an efficient technology for multiplexed refactoring of biosynthetic gene clusters. Nucleic Acids Res 2024; 52:11378-11393. [PMID: 39271125 DOI: 10.1093/nar/gkae781] [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: 04/01/2024] [Revised: 08/16/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024] Open
Abstract
The efficient refactoring of natural product biosynthetic gene clusters (BGCs) for activating silent BGCs is a central challenge for the discovery of new bioactive natural products. Herein, we have developed a simple and robust CRISETR (CRISPR/Cas9 and RecET-mediated Refactoring) technique, combining clustered regulatory interspaced short palindromic repeats (CRISPR)/Cas9 and RecET, for the multiplexed refactoring of natural product BGCs. By this approach, natural product BGCs can be refactored through the synergistic interaction between RecET-mediated efficient homologous recombination and the CRISPR/Cas9 system. We first performed a proof-of-concept validation of the ability of CRISETR, and CRISETR can achieve simultaneous replacement of four promoter sites and marker-free replacement of single promoter site in natural product BGCs. Subsequently, we applied CRISETR to the promoter engineering of the 74-kb daptomycin BGC containing a large number of direct repeat sequences for enhancing the heterologous production of daptomycin. We used combinatorial design to build multiple refactored daptomycin BGCs with diverse combinations of promoters different in transcriptional strengths, and the yield of daptomycin was improved 20.4-fold in heterologous host Streptomyces coelicolor A3(2). In general, CRISETR exhibits enhanced tolerance to repetitive sequences within gene clusters, enabling efficient refactoring of diverse and complex BGCs, which would greatly accelerate discovery of novel bioactive metabolites present in microorganism.
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Affiliation(s)
- Fuqiang He
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P.R. China
| | - Xinpeng Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P.R. China
| | - Min Tang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P.R. China
| | - Haiyi Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P.R. China
| | - Yun Wu
- Department of Cell Biology, College of Life Science, Sichuan Normal University, Chengdu, Sichuan, 610101, P.R. China
| | - Shufang Liang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P.R. China
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3
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Wang L, Hu J, Li K, Zhao Y, Zhu M. Advancements in gene editing technologies for probiotic-enabled disease therapy. iScience 2024; 27:110791. [PMID: 39286511 PMCID: PMC11403445 DOI: 10.1016/j.isci.2024.110791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024] Open
Abstract
Probiotics typically refer to microorganisms that have been identified for their health benefits, and they are added to foods or supplements to promote the health of the host. A growing number of probiotic strains have been identified lately and developed into valuable regulatory pharmaceuticals for nutritional and medical applications. Gene editing technologies play a crucial role in addressing the need for safe and therapeutic probiotics in disease treatment. These technologies offer valuable assistance in comprehending the underlying mechanisms of probiotic bioactivity and in the development of advanced probiotics. This review aims to offer a comprehensive overview of gene editing technologies applied in the engineering of both traditional and next-generation probiotics. It further explores the potential for on-demand production of customized products derived from enhanced probiotics, with a particular emphasis on the future of gene editing in the development of live biotherapeutics.
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Affiliation(s)
- Lixuan Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Hu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kun Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Motao Zhu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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4
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Svendsen PB, Henriksen NNSE, Jarmusch SA, Andersen AJC, Smith K, Selsmark MW, Zhang SD, Schostag MD, Gram L. Co-existence of two antibiotic-producing marine bacteria: Pseudoalteromonas piscicida reduce gene expression and production of the antibacterial compound, tropodithietic acid, in Phaeobacter sp. Appl Environ Microbiol 2024; 90:e0058824. [PMID: 39136490 PMCID: PMC11409694 DOI: 10.1128/aem.00588-24] [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: 03/26/2024] [Accepted: 07/16/2024] [Indexed: 09/19/2024] Open
Abstract
Many bacteria co-exist and produce antibiotics, yet we know little about how they cope and occupy the same niche. The purpose of the present study was to determine if and how two potent antibiotic-producing marine bacteria influence the secondary metabolome of each other. We established an agar- and broth-based system allowing co-existence of a Phaeobacter species and Pseudoalteromonas piscicida that, respectively, produce tropodithietic acid (TDA) and bromoalterochromides (BACs). Co-culturing of Phaeobacter sp. strain A36a-5a on Marine Agar with P. piscicida strain B39bio caused a reduction of TDA production in the Phaeobacter colony. We constructed a transcriptional gene reporter fusion in the tdaC gene in the TDA biosynthetic pathway in Phaeobacter and demonstrated that the reduction of TDA by P. piscicida was due to the suppression of the TDA biosynthesis. A stable liquid co-cultivation system was developed, and the expression of tdaC in Phaeobacter was reduced eightfold lower (per cell) in the co-culture compared to the monoculture. Mass spectrometry imaging of co-cultured colonies revealed a reduction of TDA and indicated that BACs diffused into the Phaeobacter colony. BACs were purified from Pseudoalteromonas; however, when added as pure compounds or a mixture they did not influence TDA production. In co-culture, the metabolome was dominated by Pseudoalteromonas features indicating that production of other Phaeobacter compounds besides TDA was reduced. In conclusion, co-existence of two antibiotic-producing bacteria may be allowed by one causing reduction in the antagonistic potential of the other. The reduction (here of TDA) was not caused by degradation but by a yet uncharacterized mechanism allowing Pseudoalteromonas to reduce expression of the TDA biosynthetic pathway.IMPORTANCEThe drug potential of antimicrobial secondary metabolites has been the main driver of research into these compounds. However, in recent years, their natural role in microbial systems and microbiomes has become important to determine the assembly and development of microbiomes. Herein, we demonstrate that two potent antibiotic-producing bacteria can co-exist, and one mechanism allowing the co-existence is the specific reduction of antibiotic production in one bacterium by the other. Understanding the molecular mechanisms in complex interactions provides insights for applied uses, such as when developing TDA-producing bacteria for use as biocontrol in aquaculture.
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Affiliation(s)
- Peter Bing Svendsen
- Department of Biotechnology and Biomedicine, Center for Microbial Secondary Metabolites, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Nathalie N. S. E. Henriksen
- Department of Biotechnology and Biomedicine, Center for Microbial Secondary Metabolites, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Scott A. Jarmusch
- Department of Biotechnology and Biomedicine, Center for Microbial Secondary Metabolites, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Aaron J. C. Andersen
- Department of Biotechnology and Biomedicine, Center for Microbial Secondary Metabolites, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Kirsty Smith
- Department of Biotechnology and Biomedicine, Center for Microbial Secondary Metabolites, Technical University of Denmark, Kgs. Lyngby, Denmark
- Department of Chemistry, University of Aberdeen, King’s College, Aberdeen, United Kingdom
| | - Marcus Weichel Selsmark
- Department of Biotechnology and Biomedicine, Center for Microbial Secondary Metabolites, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Sheng-Da Zhang
- Department of Biotechnology and Biomedicine, Center for Microbial Secondary Metabolites, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Morten D. Schostag
- Department of Biotechnology and Biomedicine, Center for Microbial Secondary Metabolites, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Center for Microbial Secondary Metabolites, Technical University of Denmark, Kgs. Lyngby, Denmark
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Zheng Y, Zhang Y, Li X, Liu L. Proof of ssDNA degraded from dsDNA for ET recombination. Biochem Biophys Rep 2024; 39:101750. [PMID: 39035021 PMCID: PMC11257833 DOI: 10.1016/j.bbrep.2024.101750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 06/04/2024] [Indexed: 07/23/2024] Open
Abstract
The widely used ET recombination requires an ssDNA product degraded by Rac phage protein E588 from dsDNA for strand invasion. However, proof of the ssDNA product is still elusive. The study provided three levels of proof sequentially. The probable ssDNAs degraded by E588 from the fluorescent plus-, minus-, or double-stranded dsDNA pET28a-xylanase exhibited a half fluorescence intensity of the corresponding dsDNAs, equivalent to the E588 degradation nucleotides half that of the total nucleotides degraded from the corresponding dsDNA. The ssDNA product degraded by E588 from the fluorescent minus-stranded dsDNA was confirmed by gradient gel-electrophoresis and two nuclease degradation reactions. Degraded by E588 from the dsDNA pET28a-xylanase that had a phosphorothioated plus-stranded 5'-terminus, the plus-stranded ssDNA product was separated via gel electrophoresis and recovered via a DNAclean kit. The recovered ssDNA product was proven to have intact 5'- and 3'-ends by DNA sequencing analysis. This study provides a solid foundation for the mechanism of ssDNA invasion.
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Affiliation(s)
- Yuanxia Zheng
- Life Science College, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yi Zhang
- Life Science College, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xuegang Li
- Life Science College, Henan Agricultural University, Zhengzhou, 450046, China
| | - Liangwei Liu
- Life Science College, Henan Agricultural University, Zhengzhou, 450046, China
- The Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, Zhengzhou, 450046, 218 Pingan Road, China
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6
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Cui D, Li S, Yin B, Li C, Zhang L, Li Z, Huang J. Rapid Rescue of Goose Astrovirus Genome via Red/ET Assembly. FOOD AND ENVIRONMENTAL VIROLOGY 2024; 16:297-306. [PMID: 38582780 DOI: 10.1007/s12560-024-09593-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 02/28/2024] [Indexed: 04/08/2024]
Abstract
The host-specific infection of Avian Astrovirus (AAstVs) has posed significant challenges to the poultry industry, resulting in substantial economic losses. However, few reports exist on the functional consequences of genome diversity, cross-species infectivity and mechanisms governing virus replication of AAstVs, making it difficult to develop measures to control astrovirus transmission. Reverse genetics technique can be used to study the function of viruses at the molecular level, as well as investigating pathogenic mechanisms and guide vaccine development and disease treatment. Herein, the reverse genetics technique of goose astrovirus GAstV/JS2019 strain was developed based on use of a reconstructed vector including CMV promotor, hammerhead ribozyme (HamRz), hepatitis delta virus ribozyme (HdvRz), and SV40 tail, then the cloned viral genome fragments were connected using Red/ET recombineering. The recombinant rGAstV-JS2019 was readily rescued by transfected the infectious clone plasmid into LMH cells. Importantly, the rescued rGAstV/JS2019 exhibited similar growth kinetics comparable to those of the parental GAstV/JS2019 isolate in cultured cells. Our research results provide an alternative and more effective reverse genetic tool for a detailed understanding of viral replication, pathogenic mechanisms, and molecular mechanisms of evolution.
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Affiliation(s)
- Daqing Cui
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Shujun Li
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Boxuan Yin
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Changyan Li
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Lilin Zhang
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Zexing Li
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China.
| | - Jinhai Huang
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China.
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Yan P, Wang G, Huang M, Liu Z, Dai C, Hu B, Gu M, Deng Z, Liu R, Wang X, Liu T. Combinatorial Biosynthesis Creates a Novel Aglycone Polyether with High Potency and Low Side Effects Against Bladder Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2404668. [PMID: 38935027 PMCID: PMC11348059 DOI: 10.1002/advs.202404668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/11/2024] [Indexed: 06/28/2024]
Abstract
Polyethers play a crucial role in the development of anticancer drugs. To enhance the anticancer efficacy and reduce the toxicity of these compounds, thereby advancing their application in cancer treatment, herein, guided by the structure-activity relationships of aglycone polyethers, novel aglycone polyethers are rationally redesigned with potentially improved efficacy and reduced toxicity against tumors. To realize the biosynthesis of the novel aglycone polyethers, the gene clusters and the post-polyketide synthase tailoring pathways for aglycone polyethers endusamycin and lenoremycin are identified and subjected to combinatorial biosynthesis studies, resulting in the creation of a novel aglycone polyether termed End-16, which demonstrates significant potential for treating bladder cancer (BLCA). End-16 demonstrates the ability to suppress the proliferation, migration, invasion, and cellular protrusions formation of BLCA cells, as well as induce cell cycle arrest in the G1 phase in vitro. Notably, End-16 exhibits superior inhibitory activity and fewer side effects against BLCA compared to the frontline anti-BLCA drug cisplatin in vivo, thereby warranting further preclinical studies. This study highlights the significant potential of integrating combinatorial biosynthesis strategies with rational design to create unnatural products with enhanced pharmacological properties.
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Affiliation(s)
- Pan Yan
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Gang Wang
- Department of UrologyZhongnan Hospital of Wuhan UniversityWuhan430071China
- Department of Biological RepositoriesHuman Genetic Resource Preservation Center of Hubei ProvinceZhongnan Hospital of Wuhan UniversityWuhan430071China
- Medical Research InstituteFrontier Science Center of Immunology and MetabolismWuhan UniversityWuhan430071China
| | - Minjian Huang
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
- Wuhan Hesheng Technology Co., LtdWuhan430074China
| | - Zhen Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Chong Dai
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Ben Hu
- Precision Cancer Diagnostic CenterZhongnan Hospital of Wuhan UniversityWuhan430071China
| | - Meijia Gu
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Zixin Deng
- State Key Laboratory of Microbial MetabolismSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
| | - Ran Liu
- State Key Laboratory of Microbial MetabolismSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
- Key Laboratory of Quantitative Synthetic BiologyShenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen518055China
| | - Xinghuan Wang
- Department of UrologyZhongnan Hospital of Wuhan UniversityWuhan430071China
- Department of Biological RepositoriesHuman Genetic Resource Preservation Center of Hubei ProvinceZhongnan Hospital of Wuhan UniversityWuhan430071China
- Medical Research InstituteFrontier Science Center of Immunology and MetabolismWuhan UniversityWuhan430071China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
- Wuhan Hesheng Technology Co., LtdWuhan430074China
- State Key Laboratory of Microbial MetabolismSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
- Department of UrologyZhongnan Hospital of Wuhan UniversitySchool of Pharmaceutical SciencesWuhan UniversityWuhan430071China
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8
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Shen L, Wang Y, Liu C, Alateng W, Wang Y, Zeeck A, Wang W, Zhang P, Wei Y, Cai X. Genome-Driven Discovery of Antiviral Atralabdans A-C from the Soil-Dwelling Streptomyces atratus. JOURNAL OF NATURAL PRODUCTS 2024; 87:1735-1745. [PMID: 38976838 DOI: 10.1021/acs.jnatprod.4c00225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Heterologous expression of an atr terpenoid gene cluster derived from Streptomyces atratus Gö66 in S. albus J1074 led to the discovery of three novel labdane diterpenoids featuring an unprecedented 6/6/5-fused tricyclic skeleton, designated as atralabdans A-C (1-3), along with a known compound, labdanmycin A. Compounds 1-3 were identified through extensive spectroscopic analysis, including NMR calculations with DP4+ probability analysis, and a comparative assessment of experimental and theoretical electronic circular dichroism (ECD) spectra. A plausible biosynthetic pathway for these compounds was proposed. Compounds 1-3 exhibited inhibitory activity against the human neurotropic coxsackievirus B3 (CVB3); 1 was the most potent, surpassing the positive control ribavirin with a higher therapeutic index.
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Affiliation(s)
- Ling Shen
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Yanyan Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Chengxin Liu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Wula Alateng
- Sino-German Biomedical Center, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, People's Republic of China
| | - Yuxin Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Axel Zeeck
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Göttingen 37073, Germany
| | - Weiguang Wang
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, Ministry of Education, Yunnan Minzu University, Kunming 650031, People's Republic of China
| | - Peng 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, People's Republic of China
| | - Yanhong Wei
- Sino-German Biomedical Center, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, People's Republic of China
| | - Xiaofeng Cai
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
- State Key Laboratory of Dao-di Herbs, Beijing 100700, People's Republic of China
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9
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Guo Y, Cai G, Li H, Lin Z, Shi S, Jin J, Liu Z. A CRISPR-Cas9-Mediated Large-Fragment Assembly Method for Cloning Genomes and Biosynthetic Gene Cluster. Microorganisms 2024; 12:1462. [PMID: 39065230 PMCID: PMC11279360 DOI: 10.3390/microorganisms12071462] [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: 06/25/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
The ability to clone large DNA fragments from genomes is valuable for both basic and applied research, such as the construction of synthetic genomes, and the expression of biosynthetic gene clusters (BGCs) for natural product discovery. Here, we report a fast and efficient platform for the direct capture of genome DNAs, by combining CRISPR and Gibson assembly. We demonstrate this method with the ability of cloning large DNA fragments ranging from 30 to 77 kb from various host genomes, achieving a near 100% cloning fidelity for DNA fragments below 50 kb. We next demonstrate this method by the cloning of a 40 kb fragment from Streptomyces ceruleus A3(2), which is rich in BGCs for natural products; and used this method cloning the 40 kb fengycin synthetic gene cluster from B. subtilis 168, encoding for a class of peptides with bioactivity. This method provides efficient and simple opportunities for assembling large DNA constructs from distant sources.
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Affiliation(s)
| | | | | | | | | | - Jin Jin
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China (S.S.)
| | - Zihe Liu
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China (S.S.)
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10
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Luan J, Song C, Liu Y, He R, Guo R, Cui Q, Jiang C, Li X, Hao K, Stewart AF, Fu J, Zhang Y, Wang H. Seamless site-directed mutagenesis in complex cloned DNA sequences using the RedEx method. Nat Protoc 2024:10.1038/s41596-024-01016-9. [PMID: 39009664 DOI: 10.1038/s41596-024-01016-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 05/01/2024] [Indexed: 07/17/2024]
Abstract
Seamless site-directed mutagenesis is an important technique for studying protein functions, tuning enzyme catalytic activities and modifying genetic elements in multiple rounds because it can insert, delete or substitute nucleotides, DNA segments or even entire genes at the target site without introducing any unwanted change. To facilitate seamless site-directed mutagenesis in large plasmids and bacterial artificial chromosomes (BACs) with repetitive sequences, we recently developed the RedEx strategy. Compared with previous methods, our approach achieves the recovery of correct recombinants with high accuracy by circumventing unwanted recombination between repetitive sequences. RedEx readily yields more than 80% accuracy in seamless DNA insertion and deletion in large multimodular polyketide synthase gene clusters, which are among the most difficult targets due to the large number of repetitive DNA sequences in modules encoding almost identical enzymes. Here we present the RedEx method by describing in detail the seamless site-directed mutagenesis in a BAC vector. Overall, the process includes three parts: (1) insertion of the RedEx cassette containing the desired mutation together with selection-counterselection markers flanked by unique restriction sites and 20-bp overlapping sequences into the target site by recombineering, (2) removal of the selection-counterselection markers in the BAC by restriction digestion and (3) circularization of the linear BAC by exonuclease-mediated in vitro DNA annealing. This protocol can be performed within 3 weeks and will enable researchers with DNA cloning experience to master seamless site-directed mutagenesis to accelerate their research.
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Affiliation(s)
- Ji Luan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Chaoyi Song
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Yan Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Ruoting He
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Ruofei Guo
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Qingwen Cui
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Chanjuan Jiang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Xiaochen Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Kexin Hao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - A Francis Stewart
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Jun Fu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Hailong Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China.
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11
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Ji CH, Je HW, Kim H, Kang HS. Promoter engineering of natural product biosynthetic gene clusters in actinomycetes: concepts and applications. Nat Prod Rep 2024; 41:672-699. [PMID: 38259139 DOI: 10.1039/d3np00049d] [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: 01/24/2024]
Abstract
Covering 2011 to 2022Low titers of natural products in laboratory culture or fermentation conditions have been one of the challenging issues in natural products research. Many natural product biosynthetic gene clusters (BGCs) are also transcriptionally silent in laboratory culture conditions, making it challenging to characterize the structures and activities of their metabolites. Promoter engineering offers a potential solution to this problem by providing tools for transcriptional activation or optimization of biosynthetic genes. In this review, we summarize the 10 years of progress in promoter engineering approaches in natural products research focusing on the most metabolically talented group of bacteria actinomycetes.
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Affiliation(s)
- Chang-Hun Ji
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea.
| | - Hyun-Woo Je
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea.
| | - Hiyoung Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea.
| | - Hahk-Soo Kang
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea.
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12
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Yu G, Duan Q, Cui T, Jiang C, Li X, Li Y, Fu J, Zhang Y, Wang H, Luan J. Development of a bacterial gene transcription activating strategy based on transcriptional activator positive feedback. J Adv Res 2023:S2090-1232(23)00400-9. [PMID: 38123018 DOI: 10.1016/j.jare.2023.12.015] [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: 10/01/2023] [Revised: 11/26/2023] [Accepted: 12/16/2023] [Indexed: 12/23/2023] Open
Abstract
INTRODUCTION Transcription of biological nitrogen fixation (nif) genes is activated by the NifA protein which recognizes specific activating sequences upstream of σ54-dependent nif promoters. The large quantities of nitrogenase which can make up 20% of the total proteins in the cell indicates high transcription activating efficiency of NifA and high transcription level of nifHDK nitrogenase genes. OBJECTIVES Development of an efficient gene transcription activating strategy in bacteria based on positive transcription regulatory proteins and their regulating DNA sequences. METHODS We designed a highly efficient gene transcription activating strategy in which the nifA gene was placed directly downstream of its regulating sequences. The NifA protein binds its regulating sequences and stimulates transcription of itself and downstream genes. Overexpressed NifA causes transcription activation by positive reinforcement. RESULTS When this gene transcription activating strategy was used to overexpress NifA in Pseudomonas stutzeri DSM4166 containing the nif gene cluster, the nitrogenase activity was increased by 368 folds which was 16 times higher than that obtained by nifA driven by the strongest endogenous constitutive promoter. When this strategy was used to activate transcription of exogenous biosynthetic genes for the plant auxin indole-3-acetic acid and the antitumor alkaloid pigment prodigiosin in DSM4166, both of them resulted in better performance than the strongest endogenous constitutive promoter and the highest reported productions in heterologous hosts to date. Finally, we demonstrated the universality of this strategy using the positive transcriptional regulator of the psp operon, PspF, in E. coli and the pathway-specific positive transcription regulator of the polyene antibiotic salinomycin biosynthesis, SlnR, in Streptomyces albus. CONCLUSION Many positive transcription regulatory proteins and their regulating DNA sequences have been identified in bacteria. The gene transcription activating strategy developed in this study will have broad applications in molecular biology and biotechnology.
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Affiliation(s)
- Guangle Yu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, 266237, Qingdao, Shandong, China
| | - Qiuyue Duan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, 266237, Qingdao, Shandong, China
| | - Tianqi Cui
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, 266237, Qingdao, Shandong, China
| | - Chanjuan Jiang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, 266237, Qingdao, Shandong, China
| | - Xiaochen Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, 266237, Qingdao, Shandong, China
| | - Yutong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, 266237, Qingdao, Shandong, China
| | - Jun Fu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, 266237, Qingdao, Shandong, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, 266237, Qingdao, Shandong, China
| | - Hailong Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, 266237, Qingdao, Shandong, China.
| | - Ji Luan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, 266237, Qingdao, Shandong, China.
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Wen Y, Kong J, Shen Y, He J, Shao G, Feng K, Xie Q, Zhang X. Construction and immune evaluation of the recombinant duck adenovirus type 3 delivering capsid protein VP1 of the type 1 duck hepatitis virus. Poult Sci 2023; 102:103117. [PMID: 37852056 PMCID: PMC10591007 DOI: 10.1016/j.psj.2023.103117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 10/20/2023] Open
Abstract
Adenovirus serves as an excellent viral vector and is employed in vector vaccine research. Duck hepatitis A virus type 1 (DHAV1) and duck adenovirus type 3 (DAdV3) cause significant economic losses in the Chinese duck industry. In this study, we found an excellent exogenous gene insertion site in DAdV3 genome of CH-GD-12-2014 strain, within 3 intergenic regions (IGR). Subsequently, we generated a recombinant duck adenovirus named rDAdV3-VP1-188, which exhibits excellent replication characteristics and immunogenicity of DAdV3 and DHAV1. Animal experiments showed that rDAdV3-VP1-188 can provide 100% protection against the DAdV3 and 80% protection against DHAV1. These results showed that rDAdV3-VP1-188 could induce protection against DAdV3 and DHAV1 in ducks, thus indicating the feasibility of DAdV3 as a vector for the development of avian vector vaccines. These insights contribute to the further development of DAdV3 vectors and other adenovirus vectors.
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Affiliation(s)
- Yongsen Wen
- Heyuan Branch, Guangdong Laboratory of Lingnan Modern Agricultural Science and technology, College of Animal Science and Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong AiHealth Biotechnology Co., Ltd., Qingyuan 511899, PR China
| | - Jie Kong
- Heyuan Branch, Guangdong Laboratory of Lingnan Modern Agricultural Science and technology, College of Animal Science and Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, PR China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, PR China; Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou 510642, Guangdong, PR China; Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yong Shen
- Heyuan Branch, Guangdong Laboratory of Lingnan Modern Agricultural Science and technology, College of Animal Science and Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, PR China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, PR China; Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou 510642, Guangdong, PR China; Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jiahui He
- Heyuan Branch, Guangdong Laboratory of Lingnan Modern Agricultural Science and technology, College of Animal Science and Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, PR China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, PR China; Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou 510642, Guangdong, PR China; Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Guanming Shao
- Heyuan Branch, Guangdong Laboratory of Lingnan Modern Agricultural Science and technology, College of Animal Science and Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, PR China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, PR China; Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou 510642, Guangdong, PR China; Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Keyu Feng
- Heyuan Branch, Guangdong Laboratory of Lingnan Modern Agricultural Science and technology, College of Animal Science and Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, PR China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, PR China; Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou 510642, Guangdong, PR China; Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Qingmei Xie
- Heyuan Branch, Guangdong Laboratory of Lingnan Modern Agricultural Science and technology, College of Animal Science and Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, PR China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, PR China; Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou 510642, Guangdong, PR China; Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xinheng Zhang
- Heyuan Branch, Guangdong Laboratory of Lingnan Modern Agricultural Science and technology, College of Animal Science and Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, PR China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, PR China; Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou 510642, Guangdong, PR China; Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.
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14
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Bai X, Chen H, Ren X, Zhong L, Wang X, Ji X, Zhang Y, Wang Y, Bian X. Heterologous Biosynthesis of Complex Bacterial Natural Products in Burkholderia gladioli. ACS Synth Biol 2023; 12:3072-3081. [PMID: 37708405 DOI: 10.1021/acssynbio.3c00389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Bacterial natural products (NPs) are an indispensable source of drugs and biopesticides. Heterologous expression is an essential method for discovering bacterial NPs and the efficient biosynthesis of valuable NPs, but the chassis for Gram-negative bacterial NPs remains inadequate. In this study, we built a Burkholderiales mutant Burkholderia gladioli Δgbn::attB by introducing an integrated site (attB) to inactivate the native gladiolin (gbn) biosynthetic gene cluster, which stabilizes large foreign gene clusters and reduces the native metabolite profile. The growth and successful heterologous production of high-value NPs such as phylogenetically close Burkholderiales-derived antitumor polyketides (PKs) rhizoxins, phylogenetically distant Gammaproteobacteria-derived anti-MRSA (methicillin-resistant Staphylococcus aureus) antibiotics WAP-8294As, and Deltaproteobacteria-derived antitumor PKs disorazols demonstrate that this strain is a potential chassis for Gram-negative bacterial NPs. We further improved the yields of WAP-8294As through promoter insertions and precursor pathway overexpression based on heterologous expression in this strain. This study provides a robust bacterial chassis for genome mining, efficient production, and molecular engineering of bacterial NPs.
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Affiliation(s)
- Xianping Bai
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Hanna Chen
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xiangmei Ren
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Lin Zhong
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xingyan Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xiaoqi Ji
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Yan Wang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266100, China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
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15
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Chen H, Bai X, Sun T, Wang X, Zhang Y, Bian X, Zhou H. The Genomic-Driven Discovery of Glutarimide-Containing Derivatives from Burkholderia gladioli. Molecules 2023; 28:6937. [PMID: 37836780 PMCID: PMC10574677 DOI: 10.3390/molecules28196937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/20/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Glutarimide-containing polyketides exhibiting potent antitumor and antimicrobial activities were encoded via conserved module blocks in various strains that favor the genomic mining of these family compounds. The bioinformatic analysis of the genome of Burkholderia gladioli ATCC 10248 showed a silent trans-AT PKS biosynthetic gene cluster (BGC) on chromosome 2 (Chr2C8), which was predicted to produce new glutarimide-containing derivatives. Then, the silent polyketide synthase gene cluster was successfully activated via in situ promoter insertion and heterologous expression. As a result, seven glutarimide-containing analogs, including five new ones, gladiofungins D-H (3-7), and two known gladiofungin A/gladiostatin (1) and 2 (named gladiofungin C), were isolated from the fermentation of the activated mutant. Their structures were elucidated through the analysis of HR-ESI-MS and NMR spectroscopy. The structural diversities of gladiofungins may be due to the degradation of the butenolide group in gladiofungin A (1) during the fermentation and extraction process. Bioactivity screening showed that 2 and 4 had moderate anti-inflammatory activities. Thus, genome mining combined with promoter engineering and heterologous expression were proved to be effective strategies for the pathway-specific activation of the silent BGCs for the directional discovery of new natural products.
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Affiliation(s)
- Hanna Chen
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (H.C.); (X.B.); (T.S.); (X.W.)
- School of Medicine, Linyi University, Shuangling Road, Linyi 276000, China
| | - Xianping Bai
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (H.C.); (X.B.); (T.S.); (X.W.)
| | - Tao Sun
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (H.C.); (X.B.); (T.S.); (X.W.)
| | - Xingyan Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (H.C.); (X.B.); (T.S.); (X.W.)
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (H.C.); (X.B.); (T.S.); (X.W.)
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (H.C.); (X.B.); (T.S.); (X.W.)
| | - Haibo Zhou
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (H.C.); (X.B.); (T.S.); (X.W.)
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16
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Li LF, Wu QX, Wu H, Li Y, Peng Q, Han RH, Zhang DH, Yu WD, Xu R, Wang J, Fan Z, Hou SY. Complete Genome Sequence of Streptomyces sp. HP-A2021, a Promising Bacterium for Natural Product Discovery. Biochem Genet 2023; 61:2042-2055. [PMID: 36929358 DOI: 10.1007/s10528-023-10350-8] [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: 04/19/2022] [Accepted: 02/15/2023] [Indexed: 03/18/2023]
Abstract
Streptomyces are one of the most prolific sources of bioactive and structurally diverse secondary metabolites for natural product drug discovery. Genome sequencing and bioinformatics analysis revealed that the genomes of Streptomyces harbor a wealth of cryptic secondary metabolite biosynthetic gene clusters that could encode novel compounds. In this work, a genome mining approach was employed to investigate the biosynthetic potential of Streptomyces sp. HP-A2021, isolated from rhizosphere soil of Ginkgo biloba L. The complete genome of HP-A2021 was sequenced and contained the 9,607,552 base pair linear chromosome with a GC content of 71.07%. The annotation results revealed the presence of 8534 CDSs, 76 tRNA genes, and 18 rRNA genes in HP-A2021. The highest dDDH and ANI values based on genome sequences between HP-A2021 and the most closely related type strain, Streptomyces coeruleorubidus JCM 4359, were 64.2% and 92.41%, respectively. In total, 33 secondary metabolite biosynthetic gene clusters with an average length of 105,594 bp were identified, including the putative thiotetroamide, alkylresorcinol, coelichelin, and geosmin. The antibacterial activity assay confirmed that the crude extracts of HP-A2021 showed potent antimicrobial activity against human pathogenic bacteria. Our study demonstrated that Streptomyces sp. HP-A2021 will propose a potential use in biotechnological and novel bioactive secondary metabolite biosynthetic applications.
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Affiliation(s)
- Lan-Fang Li
- College of Pharmacy, Heze University, Heze, 274015, People's Republic of China
| | - Qing-Xuan Wu
- College of Pharmacy, Heze University, Heze, 274015, People's Republic of China
| | - Hao Wu
- College of Pharmacy, Heze University, Heze, 274015, People's Republic of China
| | - Yao Li
- College of Pharmacy, Heze University, Heze, 274015, People's Republic of China
| | - Qian Peng
- College of Pharmacy, Heze University, Heze, 274015, People's Republic of China
| | - Ren-Hao Han
- College of Pharmacy, Heze University, Heze, 274015, People's Republic of China
| | - Da-Hu Zhang
- Shandong Bigtree Dreyfus Special Meals Food Co., Ltd, Heze, 274015, People's Republic of China
| | - Wei-Dong Yu
- Shandong Bigtree Dreyfus Special Meals Food Co., Ltd, Heze, 274015, People's Republic of China
| | - Rui Xu
- College of Pharmacy, Heze University, Heze, 274015, People's Republic of China
| | - Juan Wang
- College of Pharmacy, Heze University, Heze, 274015, People's Republic of China.
- Heze Key Laboratory of Targeting Antitumor Natural Compounds, Heze, 274015, People's Republic of China.
| | - Zhaobin Fan
- College of Pharmacy, Heze University, Heze, 274015, People's Republic of China.
| | - Shao-Yang Hou
- College of Pharmacy, Heze University, Heze, 274015, People's Republic of China.
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Zeng X, Wang S, Liang M, Wang W, Jiang Y, Xu F, Liu L, Yan H, Tong Y, Zhang L, Tan GY. An in vitro CRISPR-Cas12a-mediated protocol for direct cloning of large DNA fragments. STAR Protoc 2023; 4:102435. [PMID: 37432853 PMCID: PMC10362190 DOI: 10.1016/j.xpro.2023.102435] [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: 03/18/2023] [Revised: 05/08/2023] [Accepted: 06/13/2023] [Indexed: 07/13/2023] Open
Abstract
Large biosynthetic gene cluster (BGC) cloning is important for discovering natural product-based drugs and remains challenging in high GC content microorganisms (e.g., Actinobacteria). Here, we present an in vitro CRISPR-Cas12a-mediated protocol for direct cloning of large DNA fragments. We describe steps for crRNA design and preparation, genomic DNA isolation, and CRISPR-Cas12a cleavage and capture plasmid construction and linearization. We then detail target BGC and plasmid DNA ligation and transformation and screening for positive clones. For complete details on the use and execution of this protocol, please refer to Liang et al.1.
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Affiliation(s)
- Xiaoqian Zeng
- State Key Laboratory of Bioreactor Engineering, and School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Shuliu Wang
- State Key Laboratory of Bioreactor Engineering, and School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Mindong Liang
- State Key Laboratory of Bioreactor Engineering, and School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yue Jiang
- State Key Laboratory of Bioreactor Engineering, and School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Fei Xu
- Institute of Pharmaceutical Biotechnology and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Leshi Liu
- State Key Laboratory of Bioreactor Engineering, and School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Hao Yan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yaojun Tong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, and School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Gao-Yi Tan
- State Key Laboratory of Bioreactor Engineering, and School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China.
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Zheng W, Xia Y, Wang X, Gao S, Zhou D, Ravichandran V, Jiang C, Tu Q, Yin Y, Zhang Y, Fu J, Li R, Yin J. Precise genome engineering in Pseudomonas using phage-encoded homologous recombination and the Cascade-Cas3 system. Nat Protoc 2023; 18:2642-2670. [PMID: 37626246 DOI: 10.1038/s41596-023-00856-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 05/11/2023] [Indexed: 08/27/2023]
Abstract
A lack of generic and effective genetic manipulation methods for Pseudomonas has restricted fundamental research and utilization of this genus for biotechnology applications. Phage-encoded homologous recombination (PEHR) is an efficient tool for bacterial genome engineering. This PEHR system is based on a lambda Red-like operon (BAS) from Pseudomonas aeruginosa phage Ab31 and a Rac bacteriophage RecET-like operon (Rec-TEPsy) from P. syringae pv. syringae B728a and also contains exogenous elements, including the RecBCD inhibitor (Redγ or Pluγ) or single-stranded DNA-binding protein (SSB), that were added to enhance the PEHR recombineering efficiency. To solve the problem of false positives in Pseudomonas editing with the PEHR system, the processive enzyme Cas3 with a minimal Type I-C Cascade-based system was combined with PEHR. This protocol describes the utilization of a Pseudomonas-specific PEHR-Cas3 system that was designed to universally and proficiently modify the genomes of Pseudomonas species. The pipeline uses standardized cassettes combined with the concerted use of SacB counterselection and Cre site-specific recombinase for markerless or seamless genome modification, in association with vectors that possess the selectively replicating template R6K to minimize recombineering background. Compared with the traditional allelic exchange editing method, the PEHR-Cas3 system does not need to construct suicide plasmids carrying long homologous arms, thus simplifying the experimental procedure and shortening the traceless editing period. Compared with general editing systems based on phage recombinases, the PEHR-Cas3 system can effectively improve the screening efficiency of mutants using the cutting ability of Cas3 protein. The entire procedure requires ~12 days.
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Affiliation(s)
- Wentao Zheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yandong Xia
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Sciences, Hunan Normal University, Changsha, China
- College of Life Science and Technology, Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-wood Forest Cultivation and Conservation of Ministry of Education, Central South University of Forestry and Technology, Changsha, China
| | - Xue Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Shiqing Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Diao Zhou
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Sciences, Hunan Normal University, Changsha, China
| | | | - Chanjuan Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qiang Tu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yulong Yin
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jun Fu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
| | - Ruijuan Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
| | - Jia Yin
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Sciences, Hunan Normal University, Changsha, China.
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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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Duan Y, Niu W, Pang L, Mu DS, Du ZJ, Zhang Y, Bian X, Zhong G. Leader peptide removal in lasso peptide biosynthesis based on penultimate isoleucine residue. Front Microbiol 2023; 14:1181125. [PMID: 37497541 PMCID: PMC10368454 DOI: 10.3389/fmicb.2023.1181125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/19/2023] [Indexed: 07/28/2023] Open
Abstract
Lasso peptides are ribosomally synthesized peptides that undergo post-translational modifications including leader peptide removal by B (or the segregated B1 and B2) proteins and core peptide macrolactamization by C proteins to form a unique lariat topology. A conserved threonine residue at the penultimate position of leader peptide is hitherto found in lasso peptide precursors and shown to be a critical recognition element for effective enzymatic processing. We identified a lasso peptide biosynthetic gene cluster (bsf) from Bradymonas sediminis FA350, a Gram-negative and facultatively prey-dependent bacterium that belongs to a novel bacterial order Bradymonadales in the class Deltaproteobacteria. The kinase BsfK specifically catalyzes the phosphorylation of the precursor peptide BsfA on the Ser3 residue. BsfB1 performs dual functions to accelerate the post-translational phosphorylation and assist BsfB2 in leader peptide removal. Most importantly, the penultimate residue of leader peptide is an isoleucine rather than the conserved threonine and this isoleucine has a marked impact on the phosphorylation of Ser3 as well as leader peptide removal, implying that BsfB1 and BsfB2 exhibit a new substrate selectivity for leader peptide binding and excision. This is the first experimentally validated penultimate isoleucine residue in a lasso peptide precursor to our knowledge. In silico analysis reveals that the leader peptide Ile/Val(-2) residue is rare but not uncommon in phosphorylated lasso peptides, as this residue is also discovered in Acidobacteriaceae and Sphingomonadales in addition to Bradymonadales.
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Affiliation(s)
- Yuwei Duan
- Helmholtz International Laboratory for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Weijing Niu
- Helmholtz International Laboratory for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Linlin Pang
- Helmholtz International Laboratory for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Da-Shuai Mu
- Helmholtz International Laboratory for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Marine College, Shandong University, Weihai, China
| | - Zong-Jun Du
- Helmholtz International Laboratory for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Marine College, Shandong University, Weihai, China
| | - Youming Zhang
- Helmholtz International Laboratory for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology and Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiaoying Bian
- Helmholtz International Laboratory for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Guannan Zhong
- Helmholtz International Laboratory for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Suzhou Research Institute of Shandong University, Suzhou, China
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21
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Wang X, Zhou N, Wang B. Bacterial synthetic biology: tools for novel drug discovery. Expert Opin Drug Discov 2023; 18:1087-1097. [PMID: 37482696 DOI: 10.1080/17460441.2023.2239704] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/19/2023] [Indexed: 07/25/2023]
Abstract
INTRODUCTION Bacterial synthetic biology has provided powerful tools to revolutionize the drug discovery process. These tools can be harnessed to generate bacterial novel pharmaceutical compounds with enhanced bioactivity and selectivity or to create genetically modified microorganisms as living drugs. AREAS COVERED This review provides a current overview of the state-of-the-art in bacterial synthetic biology tools for novel drug discovery. The authors discuss the application of these tools including bioinformatic tools, CRISPR tools, engineered bacterial transcriptional regulators, and synthetic biosensors for novel drug discovery. Additionally, the authors present the recent progress on reprogramming bacteriophages as living drugs to fight against antibiotic-resistant pathogens. EXPERT OPINION The field of using bacterial synthetic biology tools for drug discovery is rapidly advancing. However, challenges remain in developing reliable and robust methods to engineer bacteria. Further advancements in synthetic biology hold promise to speed up drug discovery, facilitating the development of novel therapeutics against various diseases.
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Affiliation(s)
- Xiyan Wang
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Nan Zhou
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Baojun Wang
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
- Research Center of Biological Computation, Zhejiang Laboratory, Hangzhou, China
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22
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Wu G, Zhou J, Zheng J, Abdalmegeed D, Tian J, Wang M, Sun S, Sedjoah RCAA, Shao Y, Sun S, Xin Z. Construction of lipopeptide mono-producing Bacillus strains and comparison of their antimicrobial activity. FOOD BIOSCI 2023; 53:102813. [DOI: 10.1016/j.fbio.2023.102813] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
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23
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Yu G, Li X, Duan Q, Fu J, Zhang Y, Wang H, Luan J. Systematic identification of endogenous strong constitutive promoters from the diazotrophic rhizosphere bacterium Pseudomonas stutzeri DSM4166 to improve its nitrogenase activity. Microb Cell Fact 2023; 22:91. [PMID: 37138314 PMCID: PMC10155442 DOI: 10.1186/s12934-023-02085-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/09/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND Biological nitrogen fixation converting atmospheric dinitrogen to ammonia is an important way to provide nitrogen for plants. Pseudomonas stutzeri DSM4166 is a diazotrophic Gram-negative bacterium isolated from the rhizosphere of cereal Sorghum nutans. Endogenous constitutive promoters are important for engineering of the nitrogen fixation pathway, however, they have not been systematically characterized in DSM4166. RESULTS Twenty-six candidate promoters were identified from DSM4166 by RNA-seq analysis. These 26 promoters were cloned and characterized using the firefly luciferase gene. The strengths of nineteen promoters varied from 100 to 959% of the strength of the gentamicin resistance gene promoter. The strongest P12445 promoter was used to overexpress the biological nitrogen fixation pathway-specific positive regulator gene nifA. The transcription level of nitrogen fixation genes in DSM4166 were significantly increased and the nitrogenase activity was enhanced by 4.1 folds determined by the acetylene reduction method. The nifA overexpressed strain produced 359.1 µM of extracellular ammonium which was 25.6 times higher than that produced by the wild-type strain. CONCLUSIONS The endogenous strong constitutive promoters identified in this study will facilitate development of DSM4166 as a microbial cell factory for nitrogen fixation and production of other useful compounds.
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Affiliation(s)
- Guangle Yu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, Shandong, 266237, China
| | - Xiaochen Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, Shandong, 266237, China
| | - Qiuyue Duan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, Shandong, 266237, China
| | - Jun Fu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, Shandong, 266237, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, Shandong, 266237, China
| | - Hailong Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, Shandong, 266237, China
| | - Ji Luan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, Shandong, 266237, China.
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Wei B, Du AQ, Ying TT, Hu GA, Zhou ZY, Yu WC, He J, Yu YL, Wang H, Xu XW. Secondary Metabolic Potential of Kutzneria. JOURNAL OF NATURAL PRODUCTS 2023; 86:1120-1127. [PMID: 36912649 DOI: 10.1021/acs.jnatprod.3c00007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Kutzneria is a rare genus of Actinobacteria that harbors a variety of secondary metabolite gene clusters and produces several interesting types of bioactive secondary metabolites. Recent efforts have partially elucidated the biosynthetic pathways of some of these bioactive natural products, suggesting the diversity and specificity of secondary metabolism within this genus. Here, we summarized the chemical structures, biosynthetic pathways, and key metabolic enzymes of the secondary metabolites isolated from Kutzneria strains. In-depth comparative genomic analysis of all six available high-quality Kutzneria genomes revealed that the majority (77%) of the biosynthetic gene cluster families of Kutzneria were untapped and identified homologues of key metabolic enzymes in the putative gene clusters, including cytochrome P450s, halogenases, and flavin-dependent N-hydroxylases. The present study suggests that Kutzneria exhibits great potential to synthesize novel secondary metabolites, encodes a variety of valuable metabolic enzymes, and also provides valuable information for the targeted discovery and biosynthesis of novel natural products from Kutzneria.
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Affiliation(s)
- Bin Wei
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou 310014, China
| | - Ao-Qi Du
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou 310014, China
| | - Ti-Ti Ying
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou 310014, China
| | - Gang-Ao Hu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou 310014, China
| | - Zhen-Yi Zhou
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wen-Chao Yu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jing He
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yan-Lei Yu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou 310014, China
| | - Hong Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China
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Duan J, Zhao Q, Wang Y, Chi Z, Li W, Wang X, Liu S, Bi S. The dCache Domain of the Chemoreceptor Tlp1 in Campylobacter jejuni Binds and Triggers Chemotaxis toward Formate. mBio 2023:e0356422. [PMID: 37052512 DOI: 10.1128/mbio.03564-22] [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: 04/14/2023] Open
Abstract
Chemotaxis is an important virulence factor in some enteric pathogens, and it is involved in the pathogenesis and colonization of the host. However, there is limited knowledge regarding the environmental signals that promote chemotactic behavior and the sensing of these signals by chemoreceptors. To date, there is no information on the ligand molecule that directly binds to and is sensed by Campylobacter jejuni Tlp1, which is a chemoreceptor with a dCache-type ligand-binding domain (LBD). dCache (double Calcium channels and chemotaxis receptor) is the largest group of sensory domains in bacteria, but the dCache-type chemoreceptor that directly binds to formate has not yet been discovered. In this study, formate was identified as a direct-binding ligand of C. jejuni Tlp1 with high sensing specificity. We used the strategy of constructing a functional hybrid receptor of C. jejuni Tlp1 and the Escherichia coli chemoreceptor Tar to screen for the potential ligand of Tlp1, with the binding of formate to Tlp1-LBD being verified using isothermal titration calorimetry. Molecular docking and experimental analyses indicated that formate binds to the membrane-proximal pocket of the dCache subdomain. Chemotaxis assays demonstrated that formate elicits robust attractant responses of the C. jejuni strain NCTC 11168, specifically via Tlp1. The chemoattraction effect of formate via Tlp1 promoted the growth of C. jejuni, especially when competing with Tlp1- or CheY-knockout strains. Our study reveals the molecular mechanisms by which C. jejuni mediates chemotaxis toward formate, and, to our knowledge, is the first report on the high-specificity binding of the dCache-type chemoreceptor to formate as well as the physiological role of chemotaxis toward formate. IMPORTANCE Chemotaxis is important for Campylobacter jejuni to colonize favorable niches in the gastrointestinal tract of its host. However, there is still a lack of knowledge about the ligand molecules for C. jejuni chemoreceptors. The dCache-type chemoreceptor, namely, Tlp1, is the most conserved chemoreceptor in C. jejuni strains; however, the direct-binding ligand(s) triggering chemotaxis has not yet been discovered. In the present study, we found that the ligand that binds directly to Tlp1-LBD with high specificity is formate. C. jejuni exhibits robust chemoattraction toward formate, primarily via Tlp1. Tlp1 is the first reported dCache-type chemoreceptor that specifically binds formate and triggers strong chemotaxis. We further demonstrated that the formate-mediated promotion of C. jejuni growth is correlated with Tlp1-mediated chemotaxis toward formate. Our work provides important insights into the mechanism and physiological function of chemotaxis toward formate and will facilitate further investigations into the involvement of microbial chemotaxis in pathogen-host interactions.
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Affiliation(s)
- Jingjing Duan
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
| | - Qi Zhao
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
| | - Yuxin Wang
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
| | - Zhe Chi
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Wei Li
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, China
| | - Xue Wang
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
| | - Shuangjiang Liu
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuangyu Bi
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
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Duan H, Wang F, Zhang C, Dong Y, Li H, Xiao F, Li W. Elucidation of the Late Steps during Hexacosalactone A Biosynthesis in Streptomyces samsunensis OUCT16-12. Appl Environ Microbiol 2023; 89:e0195822. [PMID: 36847553 PMCID: PMC10057877 DOI: 10.1128/aem.01958-22] [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: 11/20/2022] [Accepted: 02/02/2023] [Indexed: 03/01/2023] Open
Abstract
Hexacosalactone A (1) is a polyene macrolide compound featuring a 2-amino-3-hydroxycyclopent-2-enone (C5N)-fumaryl moiety. While compound 1 has been proposed to be assembled via a type I modular polyketide synthase (PKS) system, most of the putative biosynthetic steps lack experimental evidence. In this study, we elucidated the post-PKS tailoring steps of compound 1 through in vivo gene inactivation and in vitro biochemical assays. We demonstrated that the amide synthetase HexB and O-methyltransferase HexF are responsible for the installations of the C5N moiety and the methyl group at 15-OH of compound 1, respectively; two new hexacosalactone analogs, named hexacosalactones B (4) and C (5), were purified and structurally characterized, followed by anti-multidrug resistance (anti-MDR) bacterial assays, revealing that the C5N ring and the methyl group are necessary for the antibacterial bioactivities. Through database mining of C5N-forming proteins HexABC, six uncharacterized biosynthetic gene clusters (BGCs), putatively encoding compounds with different types of backbones, were identified, providing potentials to discover novel bioactive compounds with C5N moiety. IMPORTANCE In this study, we elucidate the post-PKS tailoring steps during the biosynthesis of compound 1 and demonstrate that both C5N and 15-OMe groups are critical for the antibacterial activities of compound 1, paving the way for generation of hexacosalactone derivatives via synthetic biology strategy. In addition, mining of HexABC homologs from the GenBank database revealed their wide distribution across the bacterial world, facilitating the discovery of other bioactive natural products with C5N moiety.
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Affiliation(s)
- He Duan
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Fang Wang
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Chuchu Zhang
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Yujing Dong
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Huayue Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Fei Xiao
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Wenli Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Luan J, Ju J, Li X, Wang X, Tan Y, Xia G. Functional identification of moss PpGATA1 provides insights into the evolution of LLM-domain B-GATA transcription factors in plants. Gene 2023; 855:147103. [PMID: 36513191 DOI: 10.1016/j.gene.2022.147103] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/28/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
B-GATA transcription factors with the LLM domain (LLM-domain B-GATAs) play important roles in developmental processes and environmental responses in flowering plants. Their characterization can therefore provide insights into the structural and functional evolution of functional gene families. Phylogenetic and sequence analysis suggests that LLM-domain B-GATAs evolved from ancestral GATA transcription factors before the divergence of chlorophyte algae and Streptophyta. We compared the function of PpGATA1, a LLM-domain B-GATA gene in moss Physcomitrium patens, with Arabidopsis thaliana counterparts and showed that, in P. patens, PpGATA1 controls growth and greening in haploid gametophytes, while in transgenic Arabidopsis it affects germination, leaf development, flowering time, greening and light responses in diploid sporophytes. These PpGATA1 functions are similar to those of Arabidopsis counterparts, AtGNC, AtGNL and AtGATA17. PpGATA1 was able to complement the role of GNC and GNL in a gnc gnl double mutant, and the LLM domains of PpGATA1 and GNC behaved similarly. The functions of LLM-domain B-GATAs regulating hypocotyl elongation and cotyledon epinasty in flowering plants pre-exist before the divergence of mosses and the lineage leading to flowering plants. This study sheds light on adaption of PpGATA1 and its homologs to new developmental designs during the evolution.
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Affiliation(s)
- Ji Luan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong 266237, China; The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China.
| | - Jianfang Ju
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Xiaochen Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong 266237, China
| | - Xiuling Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong 266237, China
| | - Yufei Tan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong 266237, China
| | - Guangmin Xia
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China.
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Li X, Guo R, Luan J, Fu J, Zhang Y, Wang H. Improving spinosad production by tuning expressions of the forosamine methyltransferase and the forosaminyl transferase to reduce undesired less active byproducts in the heterologous host Streptomyces albus J1074. Microb Cell Fact 2023; 22:15. [PMID: 36658647 PMCID: PMC9854174 DOI: 10.1186/s12934-023-02023-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/12/2023] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Spinosad is a macrolide insecticide with the tetracyclic lactone backbone to which forosamine and tri-O-methylrhamnose are attached. Both the sugar moieties are essential for its insecticidal activity. In biosynthesis of spinosad, the amino group of forosamine is dimethylated by SpnS and then transferred onto the lactone backbone by SpnP. Because the spinosad native producer is difficult to genetically manipulate, we previously changed promoters, ribosome binding sites and start codons of 23 spinosad biosynthetic genes to construct an artificial gene cluster which resulted in a 328-fold yield improvement in the heterologous host Streptomyces albus J1074 compared with the native gene cluster. However, in fermentation of J1074 with the artificial gene cluster, the N-monodesmethyl spinosad with lower insecticidal activity was always produced with the same titer as spinosad. RESULTS By tuning expression of SpnS with an inducible promotor, we found that the undesired less active byproduct N-monodesmethyl spinosad was produced when SpnS was expressed at low level. Although N-monodesmethyl spinosad can be almost fully eliminated with high SpnS expression level, the titer of desired product spinosad was only increased by less than 38%. When the forosaminyl transferase SpnP was further overexpressed together with SpnS, the titer of spinosad was improved by 5.3 folds and the content of N-desmethyl derivatives was decreased by ~ 90%. CONCLUSION N-monodesmethyl spinosad was produced due to unbalanced expression of spnS and upstream biosynthetic genes in the refactored artificial gene cluster. The accumulated N-desmethyl forosamine was transferred onto the lactone backbone by SpnP. This study suggested that balanced expression of biosynthetic genes should be considered in the refactoring strategy to avoid accumulation of undesired intermediates or analogues which may affect optimal production of desired compounds.
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Affiliation(s)
- Xiaochen Li
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University–Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, 266237 Shandong China
| | - Ruofei Guo
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University–Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, 266237 Shandong China
| | - Ji Luan
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University–Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, 266237 Shandong China
| | - Jun Fu
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University–Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, 266237 Shandong China
| | - Youming Zhang
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University–Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, 266237 Shandong China
| | - Hailong Wang
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University–Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, 266237 Shandong China
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Baral B, Matroodi S, Siitonen V, Thapa K, Akhgari A, Yamada K, Nuutila A, Metsä-Ketelä M. Co-factor independent oxidases ncnN and actVA-3 are involved in the dimerization of benzoisochromanequinone antibiotics in naphthocyclinone and actinorhodin biosynthesis. FEMS Microbiol Lett 2023; 370:fnad123. [PMID: 37989784 PMCID: PMC10697411 DOI: 10.1093/femsle/fnad123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/19/2023] [Accepted: 11/20/2023] [Indexed: 11/23/2023] Open
Abstract
Streptomyces produce complex bioactive secondary metabolites with remarkable chemical diversity. Benzoisochromanequinone polyketides actinorhodin and naphthocyclinone are formed through dimerization of half-molecules via single or double carbon-carbon bonds, respectively. Here we sequenced the genome of S. arenae DSM40737 to identify the naphthocyclinone gene cluster and established heterologous production in S. albus J1074 by utilizing direct cluster capture techniques. Comparative sequence analysis uncovered ncnN and ncnM gene products as putative enzymes responsible for dimerization. Inactivation of ncnN that is homologous to atypical co-factor independent oxidases resulted in the accumulation of fogacin, which is likely a reduced shunt product of the true substrate for naphthocyclinone dimerization. In agreement, inactivation of the homologous actVA-3 in S. coelicolor M145 also led to significantly reduced production of actinorhodin. Previous work has identified the NAD(P)H-dependent reductase ActVA-4 as the key enzyme in actinorhodin dimerization, but surprisingly inactivation of the homologous ncnM did not abolish naphthocyclinone formation and the mutation may have been complemented by an endogenous gene product. Our data suggests that dimerization of benzoisochromanequinone polyketides require two-component reductase-oxidase systems.
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Affiliation(s)
- Bikash Baral
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Soheila Matroodi
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
- Laboratory of Biotechnology, Department of Marine Biology, Faculty of Marine Science and Oceanography, University of Marine Science and Technology, 64199-34619 Khorramshahr, Iran
| | - Vilja Siitonen
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Keshav Thapa
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Amir Akhgari
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Keith Yamada
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Aleksi Nuutila
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Mikko Metsä-Ketelä
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
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Gong K, Wang M, Duan Q, Li G, Yong D, Ren C, Li Y, Zhang Q, Wang Z, Sun T, Zhang H, Tu Q, Wu C, Fu J, Li A, Song C, Zhang Y, Li R. High-yield production of FK228 and new derivatives in a Burkholderia chassis. Metab Eng 2023; 75:131-142. [PMID: 36528227 DOI: 10.1016/j.ymben.2022.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/30/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
FK228 (romidepsin) is the only natural histone deacetylases (HDACs) inhibitor approved by FDA to treat cutaneous and peripheral T-cell lymphoma. However, the limited supply and severe cardiotoxicity of FK228 underscore the importance to develop an effective synthetic biology platform for the manufacturing and fine-tuning of this drug lead. In this work, we constructed a Burkholderia chassis for the high-yield production of FK228-family (unnatural) natural products. By virtue of the optimized Burkholderia-specific recombineering system, the biosynthetic gene cluster (BGC) encoding the FK228-like skeleton thailandepsins (tdp) in Burkholderia thailandensis E264 was replaced with an attB integration site to afford the basal chassis KOGC1. The tdp BGC directly captured from E264 was hybridized with the FK228-encoding BGC (dep) using the versatile Red/ET technology. The hybrid BGC (tdp-dep) was integrated into the attB site of KOGC1, resulting in the heterologous expression of FK228. Remarkably, the titer reached 581 mg/L, which is 30-fold higher than that of native producer Chromobacterium violaceum No. 968. This success encouraged us to further engineer the NRPS modules 4 or 6 of hybrid tdp-dep BGC by domain units swapping strategy, and eight new FK228 derivatives (1-8) varying in the composition of amino acids were generated. Especially, the titers of 2 and 3 in KOGC1 were up to 985 mg/L and 453 mg/L, respectively. 2 and 3 displayed stronger cytotoxic activity than FK228. All in all, this work established a robust platform to produce FK228 and its new derivatives in sufficient quantities for anticancer drug development.
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Affiliation(s)
- Kai Gong
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Maoqin Wang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Qiong Duan
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Gang Li
- Department of Natural Medicinal Chemistry and Pharmacognosy, Qingdao University, Qingdao, Shandong, China
| | - Daojing Yong
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Cailing Ren
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Yue Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Qijun Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Zongjie Wang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Tao Sun
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Huanyun Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Qiang Tu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China; Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Changsheng Wu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Jun Fu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Aiying Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Chaoyi Song
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China.
| | - Youming Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China; Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Ruijuan Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China.
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Abstract
The technology of recombineering, in vivo genetic engineering, was initially developed in Escherichia coli and uses bacteriophage-encoded homologous recombination proteins to efficiently recombine DNA at short homologies (35 to 50 nt). Because the technology is homology driven, genomic DNA can be modified precisely and independently of restriction site location. Recombineering uses linear DNA substrates that are introduced into the cell by electroporation; these can be PCR products, synthetic double-strand DNA (dsDNA), or single-strand DNA (ssDNA). Here we describe the applications, challenges, and factors affecting ssDNA and dsDNA recombineering in a variety of non-model bacteria, both Gram-negative and -positive, and recent breakthroughs in the field. We list different microbes in which the widely used phage λ Red and Rac RecET recombination systems have been used for in vivo genetic engineering. New homologous ssDNA and dsDNA recombineering systems isolated from non-model bacteria are also described. The Basic Protocol outlines a method for ssDNA recombineering in the non-model species of Shewanella. The Alternate Protocol describes the use of CRISPR/Cas as a counter-selection system in conjunction with recombineering to enhance recovery of recombinants. We provide additional background information, pertinent considerations for experimental design, and parameters critical for success. The design of ssDNA oligonucleotides (oligos) and various internet-based tools for oligo selection from genome sequences are also described, as is the use of oligo-mediated recombination. This simple form of genome editing uses only ssDNA oligo(s) and does not require an exogenous recombination system. The information presented here should help researchers identify a recombineering system suitable for their microbe(s) of interest. If no system has been characterized for a specific microbe, researchers can find guidance in developing a recombineering system from scratch. We provide a flowchart of decision-making paths for strategically applying annealase-dependent or oligo-mediated recombination in non-model and undomesticated bacteria. © 2022 Wiley Periodicals LLC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA. Basic Protocol: ssDNA recombineering in Shewanella species Alternate Protocol: ssDNA recombineering coupled to CRISPR/Cas9 in Shewanella species.
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Affiliation(s)
- Anna Corts
- Cultivarium, 490 Arsenal Way, Ste 110, Watertown, Massachusetts 02472
| | - Lynn C. Thomason
- Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland 21702
| | - Nina Costantino
- Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland 21702
| | - Donald L. Court
- Emeritus, Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland 21702
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Yong D, Li Y, Gong K, Yu Y, Zhao S, Duan Q, Ren C, Li A, Fu J, Ni J, Zhang Y, Li R. Biocontrol of strawberry gray mold caused by Botrytis cinerea with the termite associated Streptomyces sp. sdu1201 and actinomycin D. Front Microbiol 2022; 13:1051730. [PMID: 36406410 PMCID: PMC9674021 DOI: 10.3389/fmicb.2022.1051730] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022] Open
Abstract
Strawberry gray mold caused by Botrytis cinerea is one of the most severe diseases in pre- and post-harvest periods. Although fungicides have been an effective way to control this disease, they can cause serious “3R” problems (Resistance, Resurgence and Residue). In this study, Streptomyces sp. sdu1201 isolated from the hindgut of the fungus-growing termite Odontotermes formosanus revealed significant antifungal activity against B. cinerea. Four compounds (1–4) were isolated from Streptomyces sp. sdu1201 and further identified as actinomycins by the HRMS and 1D NMR data. Among them, actinomycin D had the strongest inhibitory activity against B. cinerea with the EC50 value of 7.65 μg mL−1. The control effect of actinomycin D on strawberry gray mold was also tested on fruits and leaves in vitro, and its control efficiency on leaves was 78.77% at 3 d. Moreover, actinomycin D can also inhibit the polarized growth of germ tubes of B. cinerea. Therefore, Streptomyces sp. sdu1201 and actinomycin D have great potential to gray mold as biocontrol agents.
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Affiliation(s)
- Daojing Yong
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Qingdao Zhongda Agritech Co., Ltd., Qingdao, China
| | - Yue Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Kai Gong
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yingying Yu
- Qingdao Zhongda Agritech Co., Ltd., Qingdao, China
| | - Shuai Zhao
- Qingdao Zhongda Agritech Co., Ltd., Qingdao, China
| | - Qiong Duan
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Cailing Ren
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Aiying Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jun Fu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jinfeng Ni
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- *Correspondence: Jinfeng Ni,
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Youming Zhang,
| | - Ruijuan Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Ruijuan Li,
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Wang H, He Y, Jian M, Fu X, Cheng Y, He Y, Fang J, Li L, Zhang D. Breaking the Bottleneck in Anticancer Drug Development: Efficient Utilization of Synthetic Biology. Molecules 2022; 27:7480. [PMID: 36364307 PMCID: PMC9656990 DOI: 10.3390/molecules27217480] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 08/13/2024] Open
Abstract
Natural products have multifarious bioactivities against bacteria, fungi, viruses, cancers and other diseases due to their diverse structures. Nearly 65% of anticancer drugs are natural products or their derivatives. Thus, natural products play significant roles in clinical cancer therapy. With the development of biosynthetic technologies, an increasing number of natural products have been discovered and developed as candidates for clinical cancer therapy. Here, we aim to summarize the anticancer natural products approved from 1950 to 2021 and discuss their molecular mechanisms. We also describe the available synthetic biology tools and highlight their applications in the development of natural products.
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Affiliation(s)
- Haibo Wang
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Yu He
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Meiling Jian
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Xingang Fu
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Yuheng Cheng
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Yujia He
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Jun Fang
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Lin Li
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Dan Zhang
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
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Li S, Chi LP, Li Z, Liu M, Liu R, Sang M, Zheng X, Du L, Zhang W, Li S. Discovery of venediols by activation of a silent type I polyketide biosynthetic gene cluster in Streptomyces venezuelae ATCC 15439. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.133072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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35
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Cui Y, Pei TT, Liang X, Li H, Zheng HY, Dong T. Heterologous Assembly of the Type VI Secretion System Empowers Laboratory Escherichia coli with Antimicrobial and Cell Penetration Capabilities. Appl Environ Microbiol 2022; 88:e0130522. [PMID: 36154120 PMCID: PMC9552605 DOI: 10.1128/aem.01305-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/02/2022] [Indexed: 11/20/2022] Open
Abstract
The synthetic biology toolbox has amassed a vast number of diverse functional modules, but protein translocation modules for cell penetration and cytosol-to-cytosol delivery remain relatively scarce. The type VI secretion system (T6SS), commonly found in many Gram-negative pathogens, functions as a contractile device to translocate protein toxins to prokaryotic and eukaryotic cells. Here, we have assembled the T6SS of Aeromonas dhakensis, an opportunistic waterborne pathogen, in the common laboratory strain Escherichia coli BL21(DE3). We constructed a series of plasmids (pT6S) carrying the T6SS structural and effector genes under native or tetracycline-inducible promoters, the latter for controlled expression. Using fluorescence microscopy and biochemical analyses, we demonstrate a functional T6SS in E. coli capable of secreting proteins directly into the cytosol of neighboring bacteria and outcompeting a number of drug-resistant pathogens. The heterologous assembly of T6SS not only confers the lab workhorse E. coli with the cytosol-to-cytosol protein delivery capability but also demonstrates the potential for harnessing the T6SS of various pathogens for general protein delivery and antibacterial applications. IMPORTANCE The T6SS is a powerful and versatile protein delivery system. However, the complexity of its macromolecular structure and gene regulation makes it not a trivial task to reconstitute the T6SSs of pathogens in a nonpathogenic host. In this study, we have assembled an inducible T6SS in E. coli BL21(DE3) and demonstrated its functions in protein delivery and antimicrobial activities. The engineered T6SS empowers E. coli to deliver protein cargos into a wide range of prokaryotic and eukaryotic cells.
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Affiliation(s)
- Yang Cui
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Tong-Tong Pei
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoye Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hao-Yu Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Tao Dong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
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Wei J, Chen B, Dong J, Wang X, Li Y, Liu Y, Guan W. Salinomycin biosynthesis reversely regulates the β-oxidation pathway in Streptomyces albus by carrying a 3-hydroxyacyl-CoA dehydrogenase gene in its biosynthetic gene cluster. Microb Biotechnol 2022; 15:2890-2904. [PMID: 36099515 PMCID: PMC9733648 DOI: 10.1111/1751-7915.14145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/31/2022] [Indexed: 12/14/2022] Open
Abstract
Streptomyces is well known for synthesis of many biologically active secondary metabolites, such as polyketides and non-ribosomal peptides. Understanding the coupling mechanisms of primary and secondary metabolism can help develop strategies to improve secondary metabolite production in Streptomyces. In this work, Streptomyces albus ZD11, an oil-preferring industrial Streptomyces strain, was proved to have a remarkable capability to generate abundant acyl-CoA precursors for salinomycin biosynthesis with the aid of its enhanced β-oxidation pathway. It was found that the salinomycin biosynthetic gene cluster contains a predicted 3-hydroxyacyl-CoA dehydrogenase (FadB3), which is the third enzyme of β-oxidation cycle. Deletion of fadB3 significantly reduced the production of salinomycin. A variety of experimental evidences showed that FadB3 was mainly involved in the β-oxidation pathway rather than ethylmalonyl-CoA biosynthesis and played a very important role in regulating the rate of β-oxidation in S. albus ZD11. Our findings elucidate an interesting coupling mechanism by which a PKS biosynthetic gene cluster could regulate the β-oxidation pathway by carrying β-oxidation genes, enabling Streptomyces to efficiently synthesize target polyketides and economically utilize environmental nutrients.
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Affiliation(s)
- Jiaxiu Wei
- The Fourth Affiliated HospitalZhejiang University School of MedicineHangzhouChina,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic EngineeringHangzhouChina
| | - Binbin Chen
- ZJU‐Hangzhou Global Scientific and Technological Innovation CenterHangzhouChina
| | - Jianxin Dong
- The Fourth Affiliated HospitalZhejiang University School of MedicineHangzhouChina,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic EngineeringHangzhouChina
| | - Xueyu Wang
- The Fourth Affiliated HospitalZhejiang University School of MedicineHangzhouChina,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic EngineeringHangzhouChina
| | - Yongquan Li
- The Fourth Affiliated HospitalZhejiang University School of MedicineHangzhouChina,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic EngineeringHangzhouChina
| | - Yingchun Liu
- Department of ChemistryZhejiang UniversityHangzhouChina
| | - Wenjun Guan
- The Fourth Affiliated HospitalZhejiang University School of MedicineHangzhouChina,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic EngineeringHangzhouChina
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Solonamides, a Group of Cyclodepsipeptides, Influence Motility in the Native Producer Photobacterium galatheae S2753. Appl Environ Microbiol 2022; 88:e0110522. [PMID: 36000852 PMCID: PMC9469707 DOI: 10.1128/aem.01105-22] [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
The marine bacterium Photobacterium galatheae S2753 produces a group of cyclodepsipeptides, called solonamides, which impede the virulence but not the survival of Staphylococcus aureus. In addition to their invaluable antivirulence activity, little is known about the biosynthesis and physiological function of solonamides in the native producer. This study generated a solonamide-deficient (Δsol) mutant by in-frame deletion of the sol gene, thereby identifying the core gene for solonamide biosynthesis. By annotation from antiSMASH, the biosynthetic pathway of solonamides in S2753 was also proposed. Mass spectrometry analysis of cell extracts found that deficiency of solonamide production influenced the production of a group of unknown compounds but otherwise did not alter the overall secondary metabolite profile. Physiological comparison between Δsol and wild-type S2753 demonstrated that growth dynamics and biofilm formation of both strains were similar; however, the Δsol mutant displayed reduced motility rings compared to the wild type. Reintroduction of sol restored solonamide production and motility to the mutant, indicating that solonamides influence the motility behavior of P. galatheae S2753. Proteomic analysis of the Δsol and wild-type strains found that eliminating solonamides influenced many cellular processes, including swimming-related proteins and proteins adjusting the cellular cyclic di-GMP concentration. In conclusion, our results revealed the biosynthetic pathway of solonamides and their ecological benefits to P. galatheae S2753 by enhancing motility, likely by altering the motile physiology. IMPORTANCE The broad range of bioactive potentials of cyclodepsipeptides makes these compounds invaluable in the pharmaceutical industry. Recently, a few novel cyclodepsipeptides have been discovered in marine Proteobacteria; however, their biosynthetic pathways remain to be revealed. Here, we demonstrated the biosynthetic genetic basis and pathway of the antivirulence compounds known as solonamides in P. galatheae S2753. This can pave the way for the biological overproduction of solonamides on an industrial scale. Moreover, the comparison of a solonamide-deficient mutant and wild-type S2753 demonstrated that solonamides stimulate the swimming behavior of S2753 and also influence a few key physiological processes of the native producers. These results evidenced that, in addition to their importance as novel drug candidates, these compounds play a pivotal role in the physiology of the producing microorganisms and potentially provide the native producer competitive benefits for their survival in nature.
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Lyu ZY, Bu QT, Fang JL, Zhu CY, Xu WF, Ma L, Gao WL, Chen XA, Li YQ. Improving the Yield and Quality of Daptomycin in Streptomyces roseosporus by Multilevel Metabolic Engineering. Front Microbiol 2022; 13:872397. [PMID: 35509317 PMCID: PMC9058172 DOI: 10.3389/fmicb.2022.872397] [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: 02/09/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
Daptomycin is a cyclic lipopeptide antibiotic with a significant antibacterial action against antibiotic-resistant Gram-positive bacteria. Despite numerous attempts to enhance daptomycin yield throughout the years, the production remains unsatisfactory. This study reports the application of multilevel metabolic engineering strategies in Streptomyces roseosporus to reconstruct high-quality daptomycin overproducing strain L2797-VHb, including precursor engineering (i.e., refactoring kynurenine pathway), regulatory pathway reconstruction (i.e., knocking out negative regulatory genes arpA and phaR), byproduct engineering (i.e., removing pigment), multicopy biosynthetic gene cluster (BGC), and fermentation process engineering (i.e., enhancing O2 supply). The daptomycin titer of L2797-VHb arrived at 113 mg/l with 565% higher comparing the starting strain L2790 (17 mg/l) in shake flasks and was further increased to 786 mg/l in 15 L fermenter. This multilevel metabolic engineering method not only effectively increases daptomycin production, but can also be applied to enhance antibiotic production in other industrial strains.
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Affiliation(s)
- Zhong-Yuan Lyu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, China
| | - Qing-Ting Bu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, China
| | - Jiao-Le Fang
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, China
| | - Chen-Yang Zhu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, China
| | - Wei-Feng Xu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, China
| | - Lie Ma
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, China
| | - Wen-Li Gao
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, China
| | - Xin-Ai Chen
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, China
| | - Yong-Quan Li
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, China
- *Correspondence: Yong-Quan Li,
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Pang Q, Ma S, Han H, Jin X, Liu X, Su T, Qi Q. Phage Enzyme-Assisted Direct In Vivo DNA Assembly in Multiple Microorganisms. ACS Synth Biol 2022; 11:1477-1487. [PMID: 35298132 DOI: 10.1021/acssynbio.1c00529] [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: 11/29/2022]
Abstract
The assembly of DNA fragments is extremely important for molecular biology. Increasing numbers of studies have focused on streamlining the laborious and costly protocols via in vivo DNA assembly. However, the existing methods were mainly developed for Escherichia coli or Saccharomyces cerevisiae, whereas there are few direct in vivo DNA assembly methods for other microorganisms. The use of shuttle vectors and tedious plasmid extraction and transformation procedures make DNA cloning in other microorganisms laborious and inefficient, especially for DNA library construction. In this study, we developed a "phage enzyme-assisted in vivo DNA assembly" (PEDA) method via combinatorial expression of T5 exonuclease and T4 DNA ligase. PEDA facilitated the in vivo assembly of DNA fragments with homologous sequences as short as 5 bp, and it is applicable to multiple microorganisms, such as Ralstonia eutropha, Pseudomonas putida, Lactobacillus plantarum, and Yarrowia lipolytica. The cloning efficiency of optimized PEDA is much higher than that of the existing in vivo DNA assembly methods and comparable to that of in vitro DNA assembly, making it extremely suitable for DNA library cloning. Collectively, PEDA will boost the application of in vivo DNA assembly in various microorganisms.
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Affiliation(s)
- Qingxiao Pang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People’s Republic of China
| | - Shuai Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People’s Republic of China
| | - Hao Han
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People’s Republic of China
| | - Xin Jin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People’s Republic of China
| | - Xiaoqin Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People’s Republic of China
| | - Tianyuan Su
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People’s Republic of China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People’s Republic of China
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Liang M, Liu L, Xu F, Zeng X, Wang R, Yang J, Wang W, Karthik L, Liu J, Yang Z, Zhu G, Wang S, Bai L, Tong Y, Liu X, Wu M, Zhang LX, Tan GY. Activating cryptic biosynthetic gene cluster through a CRISPR-Cas12a-mediated direct cloning approach. Nucleic Acids Res 2022; 50:3581-3592. [PMID: 35323947 PMCID: PMC8989516 DOI: 10.1093/nar/gkac181] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 03/05/2022] [Accepted: 03/10/2022] [Indexed: 11/12/2022] Open
Abstract
Direct cloning of biosynthetic gene clusters (BGCs) from microbial genomes facilitates natural product-based drug discovery. Here, by combining Cas12a and the advanced features of bacterial artificial chromosome library construction, we developed a fast yet efficient in vitro platform for directly capturing large BGCs, named CAT-FISHING (CRISPR/Cas12a-mediated fast direct biosynthetic gene cluster cloning). As demonstrations, several large BGCs from different actinomycetal genomic DNA samples were efficiently captured by CAT-FISHING, the largest of which was 145 kb with 75% GC content. Furthermore, the directly cloned, 110 kb long, cryptic polyketide encoding BGC from Micromonospora sp. 181 was then heterologously expressed in a Streptomyces chassis. It turned out to be a new macrolactam compound, marinolactam A, which showed promising anticancer activity. Our results indicate that CAT-FISHING is a powerful method for complicated BGC cloning, and we believe that it would be an important asset to the entire community of natural product-based drug discovery.
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Affiliation(s)
- Mindong Liang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Leshi Liu
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Fei Xu
- Institute of Pharmaceutical Biotechnology and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiaoqian Zeng
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Ruijun Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Jinling Yang
- Institute of Pharmaceutical Biotechnology and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Loganathan Karthik
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Jiakun Liu
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zhiheng Yang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Guoliang Zhu
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Shuliu Wang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yaojun Tong
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Li-Xin Zhang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Gao-Yi Tan
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
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Yang Y, Yu Q, Wang M, Zhao R, Liu H, Xun L, Xia Y. Escherichia coli BW25113 Competent Cells Prepared Using a Simple Chemical Method Have Unmatched Transformation and Cloning Efficiencies. Front Microbiol 2022; 13:838698. [PMID: 35401484 PMCID: PMC8989280 DOI: 10.3389/fmicb.2022.838698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 03/01/2022] [Indexed: 11/26/2022] Open
Abstract
Escherichia coli recA− strains are usually used for cloning to prevent insert instability via RecA-dependent recombination. Here, we report that E. coli BW25113 (recA+) competent cells prepared by using a previously reported transformation and storage solution (TSS) had 100-fold or higher transformation efficiency than the commonly used E. coli cloning strains, including XL1-Blue MRF’. The cloning success rates with E. coli BW25113 were 440 to 1,267-fold higher than those with E. coli XL1-Blue MRF’ when several inserts were assembled into four vectors by using a simple DNA assembly method. The difference was in part due to RecA, as the recA deletion in E. coli BW25113 reduced the transformation efficiency by 16 folds and cloning success rate by about 10 folds. However, the transformation efficiency and the cloning success rate of the recA deletion mutant of E. coli BW25113 are still 12- and >48-fold higher than those of E. coli XL1-Blue MRF’, which is a commonly used cloning strain. The cloned inserts with different lengths of homologous sequences were assembled into four vectors and transformed into E. coli BW25113, and they were stably maintained in BW25113. Thus, we recommend using E. coli BW25113 for efficient cloning and DNA assembly.
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Affiliation(s)
- Yuqing Yang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qiaoli Yu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Min Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Rui Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Huaiwei Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Luying Xun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
- *Correspondence: Luying Xun, Yongzhen Xia,
| | - Yongzhen Xia
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- *Correspondence: Luying Xun, Yongzhen Xia,
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The TelN/tos-assisted Precise Targeting of Chromosome Segments (TAPE). J Adv Res 2022; 41:169-177. [PMID: 36328746 PMCID: PMC9637730 DOI: 10.1016/j.jare.2022.01.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/12/2022] [Accepted: 01/29/2022] [Indexed: 01/04/2023] Open
Abstract
We first apply the TelN/tos system to target genomic segments in E. coli host. We successfully cloned the targeted bacterial DNA fragment up to 156 kb. The TAPE method takes no more than five days to directly obtain the large DNA sequence. The TAPE method has no preferences on genome sequence. The results showed a considerable improvement of cloning efficiency. The TAPE method provides a powerful tool to support the study on synthetic biology.
Introduction Performing genomic large segmentation experiments will promote the annotation of complex genomic functions and contribute to the synthesis of designed genomes. It is challenging to obtain and manipulate large or complex DNA sequences with high efficiency. Objectives This study aims to develop an effective method for direct cloning of target genome sequences from different species. Methods The TelN/tos system and a linear plasmid vector were first used to directly clone the large genomic segments in E. coli. For the in vitro cloning reaction, two telomeric sites were developed using TelN protelomerase at the end of the linear plasmid vector. The target DNA sequence can be easily hooked with the homology arms and maintained as a linear artificial chromosome with arbitrary restriction sites in a specific E. coli strain. Results Using the linear cloning strategy, we successfully cloned the bacterial DNA fragment of 156 kb, a yeast genomic fragment of 124 kb and mammalian mitochondrial fragment of 16 kb. The results showed a considerable improvement in cloning efficiency and demonstrated the important role of vector ratio in the cloning process. Conclusion Due to the high efficiency and stability, TAPE is an effective technique for DNA cloning and fundamental molecular biotechnology method in synthetic biology.
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Development of a new recombineering system for Agrobacterium species. Appl Environ Microbiol 2022; 88:e0249921. [PMID: 35044833 DOI: 10.1128/aem.02499-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Discovery of new and efficient genetic engineering technologies for Agrobacterium will broaden the capacity for fundamental research on this genus and for its utilization as a transgenic vehicle. In this study, we aim to develop an efficient recombineering system for Agrobacterium species. We examined isolates of Agrobacterium and the closely related genus Rhizobium to identify pairs of ET-like recombinases that would aid in the recombineering of Agrobacterium species. Four pairs of ET-like recombinases, named RecETh1h2h3h4AGROB6, RecETh1h2P3RHI597, RecETRHI145, and RecEThRHI483, were identified in Agrobacterium tumefaciens str. B6, Rhizobium leguminosarum bv. trifolii WSM597, Rhizobium sp. LC145, and Rhizobium sp. Root483D2, respectively. Eight more candidate recombineering systems were generated by combining the new ET-like recombinases with Redγ or Pluγ. The PluγETRHI145 system, RecETh1h2h3h4AGROB6 system, and PluγEThRHI483 system were determined to be the most efficient recombineering system for the type strains A. tumefaciens C58, A. tumefaciens EHA105, and R. rhizogenes NBCR13257, respectively. The utility of these systems was demonstrated by knocking out the istB and istA fusion gene in C58, the celI gene in EHA105, and the 3'-5' exonuclease gene and endoglucanase gene in NBCR13257. Our work provides an effective genetic manipulation strategy for Agrobacterium species. IMPORTANCE Agrobacterium is a powerful transgenic vehicle for the genetic manipulation of numerous plant and fungal species and even animal cells. In addition to improving the utility of Agrobacterium as a transgenic vehicle, genetic engineering tools are important for revealing crucial components that are functionally involved in T-DNA translocation events. This work developed an efficient and versatile recombineering system for Agrobacterium. Successful genome modification of Agrobacterium strains revealed that this new recombineering system could be used for the genetic engineering of Agrobacterium.
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Shen Q, Dai G, Li A, Liu Y, Zhong G, Li X, Ren X, Sui H, Fu J, Jiao N, Zhang Y, Bian X, Zhou H. Genome-Guided Discovery of Highly Oxygenated Aromatic Polyketides, Saccharothrixins D-M, from the Rare Marine Actinomycete Saccharothrix sp. D09. JOURNAL OF NATURAL PRODUCTS 2021; 84:2875-2884. [PMID: 34784196 DOI: 10.1021/acs.jnatprod.1c00617] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Angucyclines and angucyclinones are aromatic polyketides with intriguing structures and therapeutic value. Genome mining of the rare marine actinomycete Saccharothrix sp. D09 led to the identification of a type II polyketide synthase biosynthetic gene cluster, sxn, which encodes several distinct subclasses of oxidoreductases, implying that this strain has the potential to produce novel polycyclic aromatic polyketides with unusual redox modifications. The "one strain-many compounds" (OSMAC) strategy and comparative metabolite analysis facilitated the discovery of 20 angucycline derivatives from the D09 strain, including six new highly oxygenated saccharothrixins D-I (1-6), four new glycosylated saccharothrixins J-M (7-10), and 10 known analogues (11-20). Their structures were elucidated based on detailed HRESIMS, NMR spectroscopic, and X-ray crystallographic analysis. With the help of gene disruption and heterologous expression, we proposed their plausible biosynthetic pathways. In addition, compounds 3, 4, and 8 showed antibacterial activity against Helicobacter pylori with MIC values ranging from 16 to 32 μg/mL. Compound 3 also revealed anti-inflammatory activity by inhibiting the production of NO with an IC50 value of 28 μM.
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Affiliation(s)
- Qiyao Shen
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Guangzhi Dai
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Aiying Li
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yang Liu
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Guannan Zhong
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xiaoju Li
- Core Facilities for Life and Environmental Sciences, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xiangmei Ren
- Core Facilities for Life and Environmental Sciences, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Haiyan Sui
- Core Facilities for Life and Environmental Sciences, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Jun Fu
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Nianzhi Jiao
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, 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, China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
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45
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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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46
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Wang X, Zheng W, Zhou H, Tu Q, Tang YJ, Stewart AF, Zhang Y, Bian X. Improved dsDNA recombineering enables versatile multiplex genome engineering of kilobase-scale sequences in diverse bacteria. Nucleic Acids Res 2021; 50:e15. [PMID: 34792175 PMCID: PMC8860599 DOI: 10.1093/nar/gkab1076] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 09/23/2021] [Accepted: 10/22/2021] [Indexed: 01/21/2023] Open
Abstract
Recombineering assisted multiplex genome editing generally uses single-stranded oligonucleotides for site directed mutational changes. It has proven highly efficient for functional screens and to optimize microbial cell factories. However, this approach is limited to relatively small mutational changes. Here, we addressed the challenges involved in the use of double-stranded DNA substrates for multiplex genome engineering. Recombineering is mediated by phage single-strand annealing proteins annealing ssDNAs into the replication fork. We apply this insight to facilitate the generation of ssDNA from the dsDNA substrate and to alter the speed of replication by elevating the available deoxynucleoside triphosphate (dNTP) levels. Intracellular dNTP concentration was elevated by ribonucleotide reductase overexpression or dNTP addition to establish double-stranded DNA Recombineering-assisted Multiplex Genome Engineering (dReaMGE), which enables rapid and flexible insertional and deletional mutagenesis at multiple sites on kilobase scales in diverse bacteria without the generation of double-strand breaks or disturbance of the mismatch repair system. dReaMGE can achieve combinatorial genome engineering works, for example, alterations to multiple biosynthetic pathways, multiple promoter or gene insertions, variations of transcriptional regulator combinations, within a few days. dReaMGE adds to the repertoire of bacterial genome engineering to facilitate discovery, functional genomics, strain optimization and directed evolution of microbial cell factories.
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Affiliation(s)
- Xue Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Wentao Zheng
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Qiang Tu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Ya-Jie Tang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - A Francis Stewart
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
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47
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Robinson SL, Piel J, Sunagawa S. A roadmap for metagenomic enzyme discovery. Nat Prod Rep 2021; 38:1994-2023. [PMID: 34821235 PMCID: PMC8597712 DOI: 10.1039/d1np00006c] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Indexed: 12/13/2022]
Abstract
Covering: up to 2021Metagenomics has yielded massive amounts of sequencing data offering a glimpse into the biosynthetic potential of the uncultivated microbial majority. While genome-resolved information about microbial communities from nearly every environment on earth is now available, the ability to accurately predict biocatalytic functions directly from sequencing data remains challenging. Compared to primary metabolic pathways, enzymes involved in secondary metabolism often catalyze specialized reactions with diverse substrates, making these pathways rich resources for the discovery of new enzymology. To date, functional insights gained from studies on environmental DNA (eDNA) have largely relied on PCR- or activity-based screening of eDNA fragments cloned in fosmid or cosmid libraries. As an alternative, shotgun metagenomics holds underexplored potential for the discovery of new enzymes directly from eDNA by avoiding common biases introduced through PCR- or activity-guided functional metagenomics workflows. However, inferring new enzyme functions directly from eDNA is similar to searching for a 'needle in a haystack' without direct links between genotype and phenotype. The goal of this review is to provide a roadmap to navigate shotgun metagenomic sequencing data and identify new candidate biosynthetic enzymes. We cover both computational and experimental strategies to mine metagenomes and explore protein sequence space with a spotlight on natural product biosynthesis. Specifically, we compare in silico methods for enzyme discovery including phylogenetics, sequence similarity networks, genomic context, 3D structure-based approaches, and machine learning techniques. We also discuss various experimental strategies to test computational predictions including heterologous expression and screening. Finally, we provide an outlook for future directions in the field with an emphasis on meta-omics, single-cell genomics, cell-free expression systems, and sequence-independent methods.
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Affiliation(s)
| | - Jörn Piel
- Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland.
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48
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Wang X, Isbrandt T, Christensen EØ, Melchiorsen J, Larsen TO, Zhang SD, Gram L. Identification and Verification of the Prodigiosin Biosynthetic Gene Cluster (BGC) in Pseudoalteromonas rubra S4059. Microbiol Spectr 2021; 9:e0117121. [PMID: 34724731 PMCID: PMC8557933 DOI: 10.1128/spectrum.01171-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 11/20/2022] Open
Abstract
Pseudoalteromonas rubra S4059 produces the red pigment prodigiosin, which has pharmaceutical and industrial potential. Here, we targeted a putative prodigiosin-synthesizing transferase PigC, and a pigC in-frame deletion mutant did not produce prodigiosin. However, extractions of the pigC mutant cultures retained antibacterial activity, and bioassay-guided fractionation found antibacterial activity in two fractions of blue color. A precursor of prodigiosin, 4-methoxy-2,2'-bipyrrole-5-carbaldehyde (MBC), was the dominant compound in both the fractions and likely caused the antibacterial activity. Also, a stable blue pigment, di-pyrrolyl-dipyrromethene prodigiosin, was identified from the two fractions. We also discovered antibacterial activity in the sterile filtered (nonextracted) culture supernatant of both wild type and mutant, and both contained a heat-sensitive compound between 30 and 100 kDa. Deletion of prodigiosin production did not affect growth rate or biofilm formation of P. rubra and did not change its fitness, as the mutant and wild type coexisted in equal levels in mixed cultures. In conclusion, a prodigiosin biosynthetic gene cluster (BGC) was identified and verified genetically and chemically in P. rubra S4059 and a stable blue pigment was isolated from the pigC mutant of S4059, suggesting that this strain may produce several prodigiosin-derived compounds of pharmaceutical and/or industrial potential. IMPORTANCE Pigmented Pseudoalteromonas strains are renowned for their production of secondary metabolites, and genome mining has revealed a high number of biosynthetic gene clusters (BGCs) for which the chemistry is unknown. Identification of those BGCs is a prerequisite for linking products to gene clusters and for further exploitation through heterologous expression. In this study, we identified the BGCs for the red, bioactive pigment prodigiosin using genomic, genetic, and metabolomic approaches. We also report here for the first time the production of a stable blue pigment, di-pyrrolyl-dipyrromethene prodigiosin (Dip-PDG), being produced by the pigC mutant of Pseudoalteromonas rubra S4059.
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Affiliation(s)
- Xiyan Wang
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Thomas Isbrandt
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Emil Ørsted Christensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Jette Melchiorsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Thomas Ostenfeld Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Sheng-Da Zhang
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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49
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Wu Q, Luo F, Wang XL, Lin Q, Liu GQ. Angiotensin I-converting enzyme inhibitory peptide: an emerging candidate for vascular dysfunction therapy. Crit Rev Biotechnol 2021; 42:736-755. [PMID: 34634988 DOI: 10.1080/07388551.2021.1948816] [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: 10/20/2022]
Abstract
Abnormal vasoconstriction, inflammation, and vascular remodeling can be promoted by angiotensin II (Ang II) in the renin-angiotensin system (RAS), leading to vascular dysfunction diseases such as hypertension and atherosclerosis. Researchers have recently focused on angiotensin I-converting enzyme inhibitory peptides (ACEIPs), that have desirable efficacy in vascular dysfunction therapy due to Ang II reduction by inhibiting ACE activity. Promising methods for the large-scale preparation of ACEIPs include selective enzymatic hydrolysis and microbial fermentation. Thus far, ACEIPs have been widely reported to be hydrolyzed from protein-rich sources, including animals, plants, and marine organisms, while many emerging microorganism-derived ACEIPs are theoretically biosynthesized through the nonribosomal peptide synthase (NRPS) pathway. Notably, vasodilatation, anti-inflammation, and vascular reconstruction reversal of ACEIPs are strongly correlated. However, the related molecular mechanisms underlying signal transduction regulation in vivo remain unclear. We provide a comprehensive update of the ACE-Ang II-G protein-coupled type 1 angiotensin receptor (AT1R) axis signaling and its functional significance for potential translation into therapeutic strategies, particularly targeting AT1R by ACEIPs, as well as specific related signaling pathways. Future studies are expected to verify the biosynthetic regulatory mechanism of ACEIPs via the NRPS pathway, the effect of gut microbiota metabolism on vascular dysfunction and rigorous studies of ACE-Ang II-AT1R signaling pathways mediated by ACEIPs in large animals and humans.
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Affiliation(s)
- Qiang Wu
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry and Technology, Changsha, China.,College of Food and Chemical Engineering, Shaoyang University, Shaoyang, China
| | - Feijun Luo
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry and Technology, Changsha, China.,College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, China
| | - Xiao-Ling Wang
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry and Technology, Changsha, China
| | - Qinlu Lin
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry and Technology, Changsha, China.,College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, China
| | - Gao-Qiang Liu
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry and Technology, Changsha, China
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50
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Liu T, Ma X, Yu J, Yang W, Wang G, Wang Z, Ge Y, Song J, Han H, Zhang W, Yang D, Liu X, Ma M. Rational generation of lasso peptides based on biosynthetic gene mutations and site-selective chemical modifications. Chem Sci 2021; 12:12353-12364. [PMID: 34603665 PMCID: PMC8480316 DOI: 10.1039/d1sc02695j] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/10/2021] [Indexed: 12/14/2022] Open
Abstract
Lasso peptides are a unique family of natural products whose structures feature a specific threaded fold, which confers these peptides the resistance to thermal and proteolytic degradation. This stability gives lasso peptides excellent pharmacokinetic properties, which together with their diverse reported bioactivities have garnered extensive attention because of their drug development potential. Notably, the threaded fold has proven quite inaccessible by chemical synthesis, which has hindered efficient generation of structurally diverse lasso peptides. We herein report the discovery of a new lasso peptide stlassin (1) by gene activation based on a Streptomyces heterologous expression system. Site-directed mutagenesis on the precursor peptide-encoding gene is carried out systematically, generating 17 stlassin derivatives (2–17 and 21) with residue-replacements at specific positions of 1. The solution NMR structures of 1, 3, 4, 14 and 16 are determined, supporting structural comparisons that ultimately enabled the rational production of disulfide bond-containing derivatives 18 and 19, whose structures do not belong to any of the four classes currently used to classify lasso peptides. Several site-selective chemical modifications are first applied on 16 and 21, efficiently generating new derivatives (20, 22–27) whose structures bear various decorations beyond the peptidyl monotonicity. The high production yields of these stlassin derivatives facilitate biological assays, which show that 1, 4, 16, 20, 21 and 24 possess antagonistic activities against the binding of lipopolysaccharides to toll-like receptor 4 (TLR4). These results demonstrate proof-of-concept for the combined mutational/chemical generation of lasso peptide libraries to support drug lead development. A new class II lasso peptide stlassin (1) was discovered and stlassin derivatives (2–27) were rationally generated by biosynthetic gene mutations and site-selective chemical modifications, expanding the structural diversity of lasso peptides.![]()
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Affiliation(s)
- Tan Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xiaojie Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Jiahui Yu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Wensheng Yang
- School of Medicine, Tongji University 1239 Siping Road Shanghai 200092 China
| | - Guiyang Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Zhengdong Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Yuanjie Ge
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Juan Song
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Hua Han
- School of Medicine, Tongji University 1239 Siping Road Shanghai 200092 China
| | - Wen Zhang
- School of Medicine, Tongji University 1239 Siping Road Shanghai 200092 China
| | - Donghui Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xuehui Liu
- CAS Research Platform for Protein Sciences, Institute of Biophysics, Chinese Academy of Sciences 15 Datun Road, Chao-yang District Beijing 100101 China
| | - Ming Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
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