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Zhang C, Xu Q, Fu J, Wu L, Li Y, Lu Y, Shi Y, Sun H, Li X, Wang L, Hong B. Engineering Streptomyces sp. CPCC 204095 for the targeted high-level production of isatropolone A by elucidating its pathway-specific regulatory mechanism. Microb Cell Fact 2024; 23:113. [PMID: 38622698 PMCID: PMC11020959 DOI: 10.1186/s12934-024-02387-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/05/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Isatropolone A and C, produced by Streptomyces sp. CPCC 204095, belong to an unusual class of non-benzenoid aromatic compounds and contain a rare seven-membered ring structure. Isatropolone A exhibits potent activity against Leishmania donovani, comparable to the only oral drug miltefosine. However, its variably low productivity represents a limitation for this lead compound in the future development of new anti-leishmaniasis drugs to meet unmet clinical needs. RESULTS Here we first elucidated the regulatory cascade of biosynthesis of isatropolones, which consists of two SARP family regulators, IsaF and IsaJ. Through a series of in vivo and in vitro experiments, IsaF was identified as a pathway-specific activator that orchestrates the transcription of the gene cluster essential for isatropolone biosynthesis. Interestingly, IsaJ was found to only upregulate the expression of the cytochrome P450 monooxygenase IsaS, which is crucial for the yield and proportion of isatropolone A and C. Through targeted gene deletions of isaJ or isaS, we effectively impeded the conversion of isatropolone A to C. Concurrently, the facilitation of isaF overexpression governed by selected promoters, prompted the comprehensive activation of the production of isatropolone A. Furthermore, meticulous optimization of the fermentation parameters was conducted. These strategies culminated in the attainment of an unprecedented maximum yield-980.8 mg/L of isatropolone A-achieved in small-scale solid-state fermentation utilizing the genetically modified strains, thereby establishing the highest reported titer to date. CONCLUSION In Streptomyces sp. CPCC 204095, the production of isatropolone A and C is modulated by the SARP regulators IsaF and IsaJ. IsaF serves as a master pathway-specific regulator for the production of isatropolones. IsaJ, on the other hand, only dictates the transcription of IsaS, the enzyme responsible for the conversion of isatropolone A and C. By engineering the expression of these pivotal genes, we have devised a strategy for genetic modification aimed at the selective and high-yield biosynthesis of isatropolone A. This study not only unveils the unique regulatory mechanisms governing isatropolone biosynthesis for the first time, but also establishes an essential engineering framework for the targeted high-level production of isatropolone A.
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Affiliation(s)
- Cong Zhang
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Qianqian Xu
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Jie Fu
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Linzhuan Wu
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Yihong Li
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Yuan Lu
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Yuanyuan Shi
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Hongmin Sun
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Xingxing Li
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
| | - Lifei Wang
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
| | - Bin Hong
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
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Andreo-Vidal A, Yushchuk O, Marinelli F, Binda E. Cross-Talking of Pathway-Specific Regulators in Glycopeptide Antibiotics (Teicoplanin and A40926) Production. Antibiotics (Basel) 2023; 12:antibiotics12040641. [PMID: 37107003 PMCID: PMC10135024 DOI: 10.3390/antibiotics12040641] [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: 03/03/2023] [Revised: 03/19/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Teicoplanin and A40926 (natural precursor of dalbavancin) are clinically relevant glycopeptide antibiotics (GPAs) produced by Actinoplanes teichomyceticus NRRL B-16726 and Nonomuraea gerenzanensis ATCC 39727. Their biosynthetic enzymes are coded within large biosynthetic gene clusters (BGCs), named tei for teicoplanin and dbv for A40926, whose expression is strictly regulated by pathway-specific transcriptional regulators (PSRs), coded by cluster-situated regulatory genes (CSRGs). Herein, we investigated the "cross-talk" between the CSRGs from tei and dbv, through the analysis of GPA production levels in A. teichomyceticus and N. gerenzanensis strains, with knockouts of CSRGs cross-complemented by the expression of heterologous CSRGs. We demonstrated that Tei15* and Dbv4 StrR-like PSRs, although orthologous, were not completely interchangeable: tei15* and dbv4 were only partially able or unable to cross-complement N. gerenzanensis knocked out in dbv4 and A. teichomyceticus knocked out in tei15*, implying that the DNA-binding properties of these PSRs are more different in vivo than it was believed before. At the same time, the unrelated LuxR-like PSRs Tei16* and Dbv3 were able to cross-complement corresponding N. gerenzanensis knocked out in dbv3 and A. teichomyceticus knocked out in tei16*. Moreover, the heterologous expression of dbv3 in A. teichomyceticus led to a significant increase in teicoplanin production. Although the molecular background of these events merits further investigations, our results contribute to a deeper understanding of GPA biosynthesis regulation and offer novel biotechnological tools to improve their production.
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Affiliation(s)
- Andrés Andreo-Vidal
- Department of Biotechnology and Life Sciences, University of Insubria, via J. H. Dunant 3, 21100 Varese, Italy
| | - Oleksandr Yushchuk
- Department of Biotechnology and Life Sciences, University of Insubria, via J. H. Dunant 3, 21100 Varese, Italy
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, via J. H. Dunant 3, 21100 Varese, Italy
| | - Elisa Binda
- Department of Biotechnology and Life Sciences, University of Insubria, via J. H. Dunant 3, 21100 Varese, Italy
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Hansen MH, Stegmann E, Cryle MJ. Beyond vancomycin: recent advances in the modification, reengineering, production and discovery of improved glycopeptide antibiotics to tackle multidrug-resistant bacteria. Curr Opin Biotechnol 2022; 77:102767. [PMID: 35933924 DOI: 10.1016/j.copbio.2022.102767] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/01/2022] [Accepted: 07/12/2022] [Indexed: 11/24/2022]
Abstract
Glycopeptide antibiotics (GPAs), which include vancomycin and teicoplanin, are important last-resort antibiotics used to treat multidrug-resistant Gram-positive bacterial infections. Whilst second-generation GPAs - generated through chemical modification of natural GPAs - have proven successful, the emergence of GPA resistance has underlined the need to develop new members of this compound class. Significant recent advances have been made in GPA research, including gaining an in-depth understanding of their biosynthesis, improving titre in production strains, developing new derivatives via novel chemical modifications and identifying a new mode of action for structurally diverse type-V GPAs. Taken together, these advances demonstrate significant untapped potential for the further development of GPAs to tackle the growing threat of multidrug-resistant bacteria.
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Affiliation(s)
- Mathias H Hansen
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; EMBL Australia, Monash University, Clayton, Victoria 3800, Australia; ARC Centre of Excellence for Innovations in Peptide and Protein Science, Australia
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany; Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; EMBL Australia, Monash University, Clayton, Victoria 3800, Australia; ARC Centre of Excellence for Innovations in Peptide and Protein Science, Australia.
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Xu M, Wang W, Waglechner N, Culp EJ, Guitor AK, Wright GD. Phylogeny-Informed Synthetic Biology Reveals Unprecedented Structural Novelty in Type V Glycopeptide Antibiotics. ACS CENTRAL SCIENCE 2022; 8:615-626. [PMID: 35647273 PMCID: PMC9136965 DOI: 10.1021/acscentsci.1c01389] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Indexed: 06/01/2023]
Abstract
The rise and dissemination of glycopeptide antibiotic (GPA)-resistant pathogens in healthcare settings fuel efforts to discover GPAs that can overcome resistance. Members of the type V subclass of GPAs can evade common GPA resistance mechanisms and offer promise as new drug leads. We characterize five new type V GPAs-rimomycin-A/B/C and misaugamycin-A/B-discovered through a phylogeny-guided genome mining strategy coupled with heterologous production using our GPAHex synthetic biology platform. Rimomycin is a heptapeptide similar to kistamicin but includes an N-methyl-tyrosine at amino acid 6 (AA6) and substitutes 4-hydroxyphenylglycine for tyrosine and 3,5-dihydroxyphenylglycine at positions AA1 and AA3. Misaugamycin is characterized by an unprecedented N-C cross-link between AA2 and AA4 and unique N-terminal acylation by malonyl (misaugamycin-A) or 2-sulfoacetyl (misaugamycin-B) groups. We demonstrate that rimomycin-A/B/C and misaugamycin-A/B are potent antibiotics with activity against GPA-resistant clinical isolates and that the mode of action is consistent with the inhibition of cell division by the evasion of autolysin activity. These discoveries expand the chemical diversity of the type V GPAs, offer new chemical scaffolds for drug development, and demonstrate the application of the GPAHex platform in mining GPA chemical "dark matter".
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Biosynthesis of (±)-Differolide, an Antioxidant Isolate from Streptomyces qaidamensis S10T. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12083741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Streptomyces from unexplored or underexplored environments may be an essential source of discoveries of bioactive molecules. One such example is Streptomyces qaidamensis S10T, which was isolated from a sand sample collected in Qaidam Basin, Qinghai Province, China. Here, we report on (±)-differolide, an antioxidant isolated from S. qaidamensis, and verified with scavenging experiments on 2,2-diphenyl-1-picrylhydrazyl (DPPH). The biosynthetic gene cluster responsible for synthesizing the compound was also identified using comparative genomic methods. These results provide a basis for further study of the biological activities of (±)-differolide, which also make it possible to develop as an antioxidant medicine.
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Qian H, Wei W, Chen XA, Mo XT, Ge M, Zhao QW, Li YQ. Strategy for Producing the High-Quality Glycopeptide Antibiotic A82846B in Amycolatopsis orientalis Based on the CRISPR-Cas12a System. ACS Synth Biol 2021; 10:3009-3016. [PMID: 34628852 DOI: 10.1021/acssynbio.1c00317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oritavancin is a new-generation semisynthetic lipoglycopeptide antibiotic used to prevent the spread of vancomycin-resistant Gram-positive bacteria. The glycopeptide A82846B is the direct precursor of oritavancin. Considering the structural similarity between A82846B and vancomycin, the vancomycin producer Amycolatopsis orientalis was used as a chassis for the construction of a strain producing high-quality A82846B. To construct the A82846B synthetic pathway, we established a highly efficient CRISPR-Cas12a system by optimizing the conditions of conjugation and by screening the regulatory elements in the A. orientalis, which is difficult to be genetically manipulated. The efficiency of gene knockout was almost 100%. The glycosyltransferases module (gtfDE) and glycosyl synthesis module (vcaAEBD) in the vancomycin gene cluster were replaced with the corresponding glycosyltransferases module (gtfABC) and glycosyl synthesis module (evaAEBD) in the A82846B cluster, respectively. A82846B was successfully produced by the artificially constructed synthetic pathway. Moreover, the titer of A82846B was increased 80% by expressing the pathway-specific regulatory strR. This strategy has excellent potential for remodification of natural products to solve antibiotic resistance.
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Affiliation(s)
- Hui Qian
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Wei Wei
- Shanghai Laiyi Center for Biopharmaceutical R&D, Shanghai 200240, China
| | - Xin-Ai Chen
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Xiao-Ting Mo
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Mei Ge
- Shanghai Laiyi Center for Biopharmaceutical R&D, Shanghai 200240, China
| | - Qing-Wei Zhao
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, 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, School of Medicine, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
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