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Wu Z, Xia Z, Tang Z, Li J, Liu W. Mutasynthesis generates nine new pyrroindomycins. Org Biomol Chem 2024; 22:2813-2818. [PMID: 38511276 DOI: 10.1039/d4ob00239c] [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: 03/22/2024]
Abstract
Pyrroindomycins (PYRs) represent the only spirotetramate natural products discovered in nature, and possess potent activities against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecium. Their unique structure and impressive biological activities make them attractive targets for synthesis and biosynthesis; however, the discovery and generation of new PYRs remains challenging. To date, only the initial components A and B have been reported. Herein, we report a mutasynthesis approach for the generation of nine new PYRs with varying acyl modifications on their deoxy-trisaccharide moieties. This was achieved by blocking the formation of the acyl group 1,8-dihydropyrrolo[2,3-b]indole (DHPI) via gene pyrK1 inactivation and supplying chemical acyl precursors. The gene pyrK1 encodes a DUF1864 family protein that probably catalyzes the oxidative transformation of L-tryptophan to DHPI, and its deletion results in the abolishment of DHPI-containing PYRs and the accumulation of three new PYRs either without acyl modification or with DHPI replaced by benzoic acid and pyrrole-2-carboxylic acid. Capitalizing on the capacity of the ΔpyrK1 mutant to produce new PYRs, we have successfully developed a mutasynthesis strategy for the generation of six novel PYR analogs with various aromatic acid modifications on their deoxy-trisaccharide moieties, showcasing the potential for generating structurally diverse PYRs. Overall, this research contributes significantly to understanding the biosynthesis of PYRs and offers valuable perspectives on their structural diversity.
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Affiliation(s)
- Zhuhua Wu
- National key Laboratory of Lead druggability Research, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Copernicus Road, Shanghai 201203, China.
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
| | - Zhengxiang Xia
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
- Department of Pharmacy, Stomatological Hospital and Dental School of Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, 399 Middle Yan Chang Road, Shanghai, 200072, China
| | - Zhijun Tang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
| | - Ji'an Li
- National key Laboratory of Lead druggability Research, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Copernicus Road, Shanghai 201203, China.
| | - Wen Liu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
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2
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Fang Z, Zhang Q, Xiong W, Sun L, Tan B, Zhu M, Ma L, Zhang L, Zhu Y, Zhang C. Discovery of Tetronate-Containing Kongjuemycins from a Coral-Associated Actinomycete and Elucidation of Their Biosynthetic Origin. Org Lett 2023; 25:6346-6351. [PMID: 37606755 DOI: 10.1021/acs.orglett.3c02231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Tetronate antibiotics make up a growing family of natural products with a wide variety of biological activities. Herein, we report four new tetronates kongjuemycins (KJMs, 5-8) from a coral-associated actinomycete Pseudonocardia kongjuensis SCSIO 11457, and the identification and characterization of the KJM biosynthetic gene cluster (kjm) by heterologous expression, comparative genomic analysis, isotope labeling, and gene knockout studies. The biosynthesis of KJMs is demonstrated to harness diverse precursors from primary metabolism for building secondary metabolites.
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Affiliation(s)
- Zhuangjie Fang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingbo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Weiliang Xiong
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Lili Sun
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Tan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Mengyi Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Liang Ma
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
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3
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Kokkini M, Oves-Costales D, Sánchez P, Melguizo Á, Mackenzie TA, Pérez-Bonilla M, Martín J, Giusti A, de Witte P, Vicente F, Genilloud O, Reyes F. New Phocoenamicin and Maklamicin Analogues from Cultures of Three Marine-Derived Micromonospora Strains. Mar Drugs 2023; 21:443. [PMID: 37623724 PMCID: PMC10455904 DOI: 10.3390/md21080443] [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: 07/06/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
Antimicrobial resistance can be considered a hidden global pandemic and research must be reinforced for the discovery of new antibiotics. The spirotetronate class of polyketides, with more than 100 bioactive compounds described to date, has recently grown with the discovery of phocoenamicins, compounds displaying different antibiotic activities. Three marine Micromonospora strains (CA-214671, CA-214658 and CA-218877), identified as phocoenamicins producers, were chosen to scale up their production and LC/HRMS analyses proved that EtOAc extracts from their culture broths produce several structurally related compounds not disclosed before. Herein, we report the production, isolation and structural elucidation of two new phocoenamicins, phocoenamicins D and E (1-2), along with the known phocoenamicin, phocoenamicins B and C (3-5), as well as maklamicin (7) and maklamicin B (6), the latter being reported for the first time as a natural product. All the isolated compounds were tested against various human pathogens and revealed diverse strong to negligible activity against methicillin-resistant Staphylococcus aureus, Mycobacterium tuberculosis H37Ra, Enterococcus faecium and Enterococcus faecalis. Their cell viability was also evaluated against the human liver adenocarcinoma cell line (Hep G2), demonstrating weak or no cytotoxicity. Lastly, the safety of the major compounds obtained, phocoenamicin (3), phocoenamicin B (4) and maklamicin (7), was tested against zebrafish eleuthero embryos and all of them displayed no toxicity up to a concentration of 25 μM.
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Affiliation(s)
- Maria Kokkini
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico Ciencias de la Salud, Avda. del Conocimiento 34, Armilla, 18016 Granada, Spain; (D.O.-C.); (P.S.); (Á.M.); (T.A.M.); (M.P.-B.); (J.M.); (F.V.); (O.G.)
| | - Daniel Oves-Costales
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico Ciencias de la Salud, Avda. del Conocimiento 34, Armilla, 18016 Granada, Spain; (D.O.-C.); (P.S.); (Á.M.); (T.A.M.); (M.P.-B.); (J.M.); (F.V.); (O.G.)
| | - Pilar Sánchez
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico Ciencias de la Salud, Avda. del Conocimiento 34, Armilla, 18016 Granada, Spain; (D.O.-C.); (P.S.); (Á.M.); (T.A.M.); (M.P.-B.); (J.M.); (F.V.); (O.G.)
| | - Ángeles Melguizo
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico Ciencias de la Salud, Avda. del Conocimiento 34, Armilla, 18016 Granada, Spain; (D.O.-C.); (P.S.); (Á.M.); (T.A.M.); (M.P.-B.); (J.M.); (F.V.); (O.G.)
| | - Thomas A. Mackenzie
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico Ciencias de la Salud, Avda. del Conocimiento 34, Armilla, 18016 Granada, Spain; (D.O.-C.); (P.S.); (Á.M.); (T.A.M.); (M.P.-B.); (J.M.); (F.V.); (O.G.)
| | - Mercedes Pérez-Bonilla
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico Ciencias de la Salud, Avda. del Conocimiento 34, Armilla, 18016 Granada, Spain; (D.O.-C.); (P.S.); (Á.M.); (T.A.M.); (M.P.-B.); (J.M.); (F.V.); (O.G.)
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico Ciencias de la Salud, Avda. del Conocimiento 34, Armilla, 18016 Granada, Spain; (D.O.-C.); (P.S.); (Á.M.); (T.A.M.); (M.P.-B.); (J.M.); (F.V.); (O.G.)
| | - Arianna Giusti
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, University of Leuven, O & N II Herestraat 49-box 824, 3000 Leuven, Belgium; (A.G.); (P.d.W.)
| | - Peter de Witte
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, University of Leuven, O & N II Herestraat 49-box 824, 3000 Leuven, Belgium; (A.G.); (P.d.W.)
| | - Francisca Vicente
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico Ciencias de la Salud, Avda. del Conocimiento 34, Armilla, 18016 Granada, Spain; (D.O.-C.); (P.S.); (Á.M.); (T.A.M.); (M.P.-B.); (J.M.); (F.V.); (O.G.)
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico Ciencias de la Salud, Avda. del Conocimiento 34, Armilla, 18016 Granada, Spain; (D.O.-C.); (P.S.); (Á.M.); (T.A.M.); (M.P.-B.); (J.M.); (F.V.); (O.G.)
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico Ciencias de la Salud, Avda. del Conocimiento 34, Armilla, 18016 Granada, Spain; (D.O.-C.); (P.S.); (Á.M.); (T.A.M.); (M.P.-B.); (J.M.); (F.V.); (O.G.)
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4
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Zorn K, Back CR, Barringer R, Chadimová V, Manzo‐Ruiz M, Mbatha SZ, Mobarec J, Williams SE, van der Kamp MW, Race PR, Willis CL, Hayes MA. Interrogation of an Enzyme Library Reveals the Catalytic Plasticity of Naturally Evolved [4+2] Cyclases. Chembiochem 2023; 24:e202300382. [PMID: 37305956 PMCID: PMC10946715 DOI: 10.1002/cbic.202300382] [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: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 06/13/2023]
Abstract
Stereoselective carbon-carbon bond forming reactions are quintessential transformations in organic synthesis. One example is the Diels-Alder reaction, a [4+2] cycloaddition between a conjugated diene and a dienophile to form cyclohexenes. The development of biocatalysts for this reaction is paramount for unlocking sustainable routes to a plethora of important molecules. To obtain a comprehensive understanding of naturally evolved [4+2] cyclases, and to identify hitherto uncharacterised biocatalysts for this reaction, we constructed a library comprising forty-five enzymes with reported or predicted [4+2] cycloaddition activity. Thirty-one library members were successfully produced in recombinant form. In vitro assays employing a synthetic substrate incorporating a diene and a dienophile revealed broad-ranging cycloaddition activity amongst these polypeptides. The hypothetical protein Cyc15 was found to catalyse an intramolecular cycloaddition to generate a novel spirotetronate. The crystal structure of this enzyme, along with docking studies, establishes the basis for stereoselectivity in Cyc15, as compared to other spirotetronate cyclases.
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Affiliation(s)
- Katja Zorn
- Compound Synthesis and Management, Discovery SciencesBiopharmaceuticals R&DAstraZenecaPepparedsleden 1431 83MölndalSweden
| | | | - Rob Barringer
- School of BiochemistryUniversity of BristolBristolBS8 1TDUK
| | - Veronika Chadimová
- Compound Synthesis and Management, Discovery SciencesBiopharmaceuticals R&DAstraZenecaPepparedsleden 1431 83MölndalSweden
| | | | | | - Juan‐Carlos Mobarec
- Mechanistic and Structural BiologyBiopharmaceuticals R&DAstraZenecaCambridgeCB21 6GHUK
| | | | | | - Paul R. Race
- School of BiochemistryUniversity of BristolBristolBS8 1TDUK
| | | | - Martin A. Hayes
- Compound Synthesis and Management, Discovery SciencesBiopharmaceuticals R&DAstraZenecaPepparedsleden 1431 83MölndalSweden
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5
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Multifunctional Enzymes in Microbial Secondary Metabolic Processes. Catalysts 2023. [DOI: 10.3390/catal13030581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023] Open
Abstract
Microorganisms possess a strong capacity for secondary metabolite synthesis, which is represented by tightly controlled networks. The absence of any enzymes leads to a change in the original metabolic pathway, with a decrease in or even elimination of a synthetic product, which is not permissible under conditions of normal life activities of microorganisms. In order to improve the efficiency of secondary metabolism, organisms have evolved multifunctional enzymes (MFEs) that can catalyze two or more kinds of reactions via multiple active sites. However, instead of interfering, the multifunctional catalytic properties of MFEs facilitate the biosynthetic process. Among the numerous MFEs considered of vital importance in the life activities of living organisms are the synthases involved in assembling the backbone of compounds using different substrates and modifying enzymes that confer the final activity of compounds. In this paper, we review MFEs in terms of both synthetic and post-modifying enzymes involved in secondary metabolic biosynthesis, focusing on polyketides, non-ribosomal peptides, terpenoids, and a wide range of cytochrome P450s(CYP450s), and provide an overview and describe the recent progress in the research on MFEs.
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6
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Wang H, Zou Y, Li M, Tang Z, Wang J, Tian Z, Strassner N, Yang Q, Zheng Q, Guo Y, Liu W, Pan L, Houk KN. A cyclase that catalyses competing 2 + 2 and 4 + 2 cycloadditions. Nat Chem 2023; 15:177-184. [PMID: 36690833 DOI: 10.1038/s41557-022-01104-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 11/01/2022] [Indexed: 01/24/2023]
Abstract
Cycloaddition reactions are among the most widely used reactions in chemical synthesis. Nature achieves these cyclization reactions with a variety of enzymes, including Diels-Alderases that catalyse concerted 4 + 2 cycloadditions, but biosynthetic enzymes with 2 + 2 cyclase activity have yet to be discovered. Here we report that PloI4, a β-barrel-fold protein homologous to the exo-selective 4 + 2 cyclase that functions in the biosynthesis of pyrroindomycins, catalyses competitive 2 + 2 and 4 + 2 cycloaddition reactions. PloI4 is believed to catalyse an endo-4 + 2 cycloaddition in the biosynthesis of pyrrolosporin A; however, when the substrate precursor of pyrroindomycins was treated with PloI4, an exo-2 + 2 adduct was produced in addition to the exo- and endo-4 + 2 adducts. Biochemical characterizations, computational analyses, (co)crystal structures and mutagenesis outcomes have allowed the catalytic versatility of PloI4 to be rationalized. Mechanistic studies involved the directed engineering of PloI4 to variants that produced the exo-4 + 2, endo-4 + 2 or exo-2 + 2 product preferentially. This work illustrates an enzymatic thermal 2 + 2 cycloaddition and provides evidence of a process through which an enzyme evolves along with its substrate for specialization and activity improvement.
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Affiliation(s)
- Hongbo Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Yike Zou
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Miao Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China.,School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Zhijun Tang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Jiabao Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China.,Department of Chemistry, Shanghai Normal University, Shanghai, China
| | - Zhenhua Tian
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China.,Abiochem Biotechnology Co., Ltd, Shanghai, China
| | - Nina Strassner
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Qian Yang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Qingfei Zheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Yujiao Guo
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China. .,Department of Chemistry, Shanghai Normal University, Shanghai, China.
| | - Lifeng Pan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China. .,School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA.
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7
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Exploring Micromonospora as Phocoenamicins Producers. Mar Drugs 2022; 20:md20120769. [PMID: 36547916 PMCID: PMC9782249 DOI: 10.3390/md20120769] [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: 10/21/2022] [Revised: 12/01/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022] Open
Abstract
Over the past few years, new technological and scientific advances have reinforced the field of natural product discovery. The spirotetronate class of natural products has recently grown with the discovery of phocoenamicins, natural actinomycete derived compounds that possess different antibiotic activities. Exploring the MEDINA's strain collection, 27 actinomycete strains, including three marine-derived and 24 terrestrial strains, were identified as possible phocoenamicins producers and their taxonomic identification by 16S rDNA sequencing showed that they all belong to the Micromonospora genus. Using an OSMAC approach, all the strains were cultivated in 10 different media each, resulting in 270 fermentations, whose extracts were analyzed by LC-HRMS and subjected to High-throughput screening (HTS) against methicillin-resistant Staphylococcus aureus (MRSA), Mycobacterium tuberculosis H37Ra and Mycobacterium bovis. The combination of LC-UV-HRMS analyses, metabolomics analysis and molecular networking (GNPS) revealed that they produce several related spirotetronates not disclosed before. Variations in the culture media were identified as the most determining factor for phocoenamicin production and the best producer strains and media were established. Herein, we reported the chemically diverse production and metabolic profiling of Micromonospora sp. strains, including the known phocoenamicins and maklamicin, reported for the first time as being related to this family of compounds, as well as the bioactivity of their crude extracts. Although our findings do not confirm previous statements about phocoenamicins production only in unique marine environments, they have identified marine-derived Micromonospora species as the best producers of phocoenamicins in terms of both the abundance in their extracts of some major members of the structural class and the variety of molecular structures produced.
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8
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Zhang T, Cai G, Rong X, Xu J, Jiang B, Wang H, Li X, Wang L, Zhang R, He W, Yu L. Mining and characterization of the PKS-NRPS hybrid for epicoccamide A: a mannosylated tetramate derivative from Epicoccum sp. CPCC 400996. Microb Cell Fact 2022; 21:249. [PMID: 36419162 PMCID: PMC9685919 DOI: 10.1186/s12934-022-01975-2] [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: 10/10/2022] [Accepted: 11/16/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Genomic analysis indicated that the genomes of ascomycetes might carry dozens of biosynthetic gene clusters (BGCs), yet many clusters have remained enigmatic. The ascomycete genus Epicoccum, belonging to the family Didymellaceae, is ubiquitous that colonizes different types of substrates and is associated with phyllosphere or decaying vegetation. Species of this genus are prolific producers of bioactive substances. The epicoccamides, as biosynthetically distinct mannosylated tetramate, were first isolated in 2003 from Epicoccum sp. In this study, using a combination of genome mining, chemical identification, genetic deletion, and bioinformatic analysis, we identified the required BGC epi responsible for epicoccamide A biosynthesis in Epicoccum sp. CPCC 400996. RESULTS The unconventional biosynthetic gene cluster epi was obtained from an endophyte Epicoccum sp. CPCC 400996 through AntiSMASH-based genome mining. The cluster epi includes six putative open reading frames (epiA-epiF) altogether, in which the epiA encodes a tetramate-forming polyketide synthase and nonribosomal peptide synthetases (PKS-NRPS hybrid). Sequence alignments and bioinformatic analysis to other metabolic pathways of fungal tetramates, we proposed that the gene cluster epi could be involved in generating epicoccamides. Genetic knockout of epiA completely abolished the biosynthesis of epicoccamide A (1), thereby establishing the correlation between the BGC epi and biosynthesis of epicoccamide A. Bioinformatic adenylation domain signature analysis of EpiA and other fungal PKS-NRPSs (NRPs) indicated that the EpiA is L-alanine incorporating tetramates megasynthase. Furthermore, based on the molecular structures of epicoccamide A and deduced gene functions of the cluster epi, a hypothetic metabolic pathway for biosynthesizing compound 1 was proposed. The corresponding tetramates releasing during epicoccamide A biosynthesis was catalyzed through Dieckmann-type cyclization, in which the reductive (R) domain residing in terminal module of EpiA accomplished the conversion. These results unveiled the underlying mechanism of epicoccamides biosynthesis and these findings might provide opportunities for derivatization of epicoccamides or generation of new chemical entities. CONCLUSION Genome mining and genetic inactivation experiments unveiled a previously uncharacterized PKS - NRPS hybrid-based BGC epi responsible for the generation of epicoccamide A (1) in endophyte Epicoccum sp. CPCC 400996. In addition, based on the gene cluster data, a hypothetical biosynthetic pathway of epicoccamide A was proposed.
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Affiliation(s)
- Tao Zhang
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
| | - Guowei Cai
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China ,grid.452240.50000 0004 8342 6962Medical Research Center, Binzhou Medical University Hospital, Binzhou, 256603 Shandong China
| | - Xiaoting Rong
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China ,grid.510447.30000 0000 9970 6820College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212003 Jiangsu China
| | - Jingwen Xu
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
| | - Bingya Jiang
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
| | - Hao Wang
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
| | - Xinxin Li
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
| | - Lu Wang
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
| | - Ran Zhang
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
| | - Wenni He
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
| | - Liyan Yu
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
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9
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Yang L, Yang D, Wang Q, Li J, Li HL, Pan L. Functional expression and purification of DoxA, a key cytochrome P450 from Streptomyces peucetius ATCC 27952. PeerJ 2022; 10:e14373. [PMID: 36411834 PMCID: PMC9675340 DOI: 10.7717/peerj.14373] [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: 06/28/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022] Open
Abstract
The antitumor drug doxorubicin is widely used in clinical practice. However, the low yield and high cost of this drug highlight the urgent need for cost-effective processes to rapidly manufacture antitumor drugs at scale. In the biosynthesis pathway, the multi-functional cytochrome P450 enzyme DoxA catalyzes the last three steps of hydroxylation. The final conversion of daunorubicin to doxorubicin is the rate-limiting step. In our work, the DoxA has been expressed with the ferredoxin reductase FDR2 and the ferredoxin FDX1 and purified to homogeneous. The reduced carbon monoxide difference spectroscopy, heme concentration, and enzymatic characteristic were characterized. These studies suggest an approach for engineering Streptomyces P450s with functional expression for mechanistic and structural studies.
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Affiliation(s)
- Liyan Yang
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning, China
| | - Dengfeng Yang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, China
| | - Qingyan Wang
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning, China
| | - Juan Li
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning, China
| | - Hong-Liang Li
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, China
| | - Lixia Pan
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning, China
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10
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Saeed AU, Rahman MU, Chen HF, Zheng J. Structural Insight of KSIII (β-Ketoacyl-ACP Synthase)-like Acyltransferase ChlB3 in the Biosynthesis of Chlorothricin. Molecules 2022; 27:molecules27196405. [PMID: 36234941 PMCID: PMC9573744 DOI: 10.3390/molecules27196405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/07/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
Chlorothricin (CHL) belongs to a spirotetronate antibiotic family produced by Streptomyces antibioticus that inhibits pyruvate carboxylase and malate dehydrogenase. For the biosynthesis of CHL, ChlB3 plays a crucial role by introducing the 6-methylsalicylic acid (6MSA) moiety to ChlB2, an acyl carrier protein (ACP). However, the structural insight and catalytic mechanism of ChlB3 was unclear. In the current study, the crystal structure of ChlB3 was solved at 3.1 Å-resolution and a catalytic mechanism was proposed on the basis of conserved residues of structurally related enzymes. ChlB3 is a dimer having the same active sites as CerJ (a structural homologous enzyme) and uses a KSIII-like fold to work as an acyltransferase. The relaxed substrate specificity of ChlB3 was defined by its catalytic efficiencies (kcat/Km) for non-ACP tethered synthetic substrates such as 6MSA-SNAC, acetyl-SNAC, and cyclohexonyl-SNAC. ChlB3 successfully detached the 6MSA moiety from 6MSA-SNAC substrate and this hydrolytic activity demonstrated that ChlB3 has the potential to catalyze non-ACP tethered substrates. Structural comparison indicated that ChlB3 belongs to FabH family and showed 0.6–2.5 Å root mean square deviation (RMSD) with structural homologous enzymes. Molecular docking and dynamics simulations were implemented to understand substrate active site and structural behavior such as the open and closed conformation of the ChlB3 protein. The resultant catalytic and substrate recognition mechanism suggested that ChlB3 has the potential to use non-native substrates and minimize the labor of expressing ACP protein. This versatile acyltransferase activity may pave the way for manufacturing CHL variants and may help to hydrolyze several thioester-based compounds.
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Affiliation(s)
- Asad Ullah Saeed
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mueed Ur Rahman
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Center for Bioinformation Technology, Shanghai 200235, China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- Correspondence:
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11
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Yan X, Zhang J, Tan H, Liu Z, Jiang K, Tian W, Zheng M, Lin Z, Deng Z, Qu X. A Pair of Atypical KAS III Homologues with Initiation and Elongation Functions Program the Polyketide Biosynthesis in Asukamycin. Angew Chem Int Ed Engl 2022; 61:e202200879. [DOI: 10.1002/anie.202200879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Xiaoli Yan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Jun Zhang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Hongqun Tan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
| | - Zhihao Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
| | - Kai Jiang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Wenya Tian
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Mengmeng Zheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
| | - Zhi Lin
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Xudong Qu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
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12
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Yan X, Zhang J, Tan H, Liu Z, Jiang K, Tian W, Zheng M, Lin Z, Deng Z, Qu X. A Pair of Atypical KAS III Homologues with Initiation and Elongation Functions Program the Polyketide Biosynthesis in Asukamycin. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Xiaoli Yan
- Wuhan University School of pharmaceutical Sciences CHINA
| | - Jun Zhang
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Hongqun Tan
- Wuhan University School of Pharmaceutical Sciences CHINA
| | - Zhihao Liu
- Wuhan University School of pharmaceutical Sciences CHINA
| | - Kai Jiang
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Wenya Tian
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Mengmeng Zheng
- Wuhan University School of Pharmaceutical Sciences CHINA
| | - Zhi Lin
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Zixin Deng
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Xudong Qu
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology 800 Dongchuan Rd. 200240 Shanghai CHINA
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13
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Li LY, Hu YL, Sun JL, Yu LB, Shi J, Wang ZR, Guo ZK, Zhang B, Guo WJ, Tan RX, Ge HM. Resistance and phylogeny guided discovery reveals structural novelty of tetracycline antibiotics. Chem Sci 2022; 13:12892-12898. [DOI: 10.1039/d2sc03965f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/20/2022] [Indexed: 11/21/2022] Open
Abstract
Using resistance gene genome mining strategy and refinement with chain length factor, we obtained 25 distinct tetracycline biosynthetic gene clusters and a novel tetracycline. The biosynthesis of the highly modified tetracycline was investigated.
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Affiliation(s)
- Ling Yu Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yi Ling Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Jia Lin Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Long Bo Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Jing Shi
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Zi Ru Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Zhi Kai Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Bio-technology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Bo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Wen Jie Guo
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
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14
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Crowe C, Molyneux S, Sharma SV, Zhang Y, Gkotsi DS, Connaris H, Goss RJM. Halogenases: a palette of emerging opportunities for synthetic biology-synthetic chemistry and C-H functionalisation. Chem Soc Rev 2021; 50:9443-9481. [PMID: 34368824 PMCID: PMC8407142 DOI: 10.1039/d0cs01551b] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Indexed: 12/14/2022]
Abstract
The enzymatic generation of carbon-halogen bonds is a powerful strategy used by both nature and synthetic chemists to tune the bioactivity, bioavailability and reactivity of compounds, opening up the opportunity for selective C-H functionalisation. Genes encoding halogenase enzymes have recently been shown to transcend all kingdoms of life. These enzymes install halogen atoms into aromatic and less activated aliphatic substrates, achieving selectivities that are often challenging to accomplish using synthetic methodologies. Significant advances in both halogenase discovery and engineering have provided a toolbox of enzymes, enabling the ready use of these catalysts in biotransformations, synthetic biology, and in combination with chemical catalysis to enable late stage C-H functionalisation. With a focus on substrate scope, this review outlines the mechanisms employed by the major classes of halogenases, while in parallel, it highlights key advances in the utilisation of the combination of enzymatic halogenation and chemical catalysis for C-H activation and diversification.
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Affiliation(s)
- Charlotte Crowe
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Samuel Molyneux
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Sunil V. Sharma
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Ying Zhang
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Danai S. Gkotsi
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Helen Connaris
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Rebecca J. M. Goss
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
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15
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Tippelt A, Nett M. Saccharomyces cerevisiae as host for the recombinant production of polyketides and nonribosomal peptides. Microb Cell Fact 2021; 20:161. [PMID: 34412657 PMCID: PMC8374128 DOI: 10.1186/s12934-021-01650-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/05/2021] [Indexed: 01/30/2023] Open
Abstract
As a robust, fast growing and genetically tractable organism, the budding yeast Saccharomyces cerevisiae is one of the most widely used hosts in biotechnology. Its applications range from the manufacturing of vaccines and hormones to bulk chemicals and biofuels. In recent years, major efforts have been undertaken to expand this portfolio to include structurally complex natural products, such as polyketides and nonribosomally synthesized peptides. These compounds often have useful pharmacological properties, which make them valuable drugs for the treatment of infectious diseases, cancer, or autoimmune disorders. In nature, polyketides and nonribosomal peptides are generated by consecutive condensation reactions of short chain acyl-CoAs or amino acids, respectively, with the substrates and reaction intermediates being bound to large, multidomain enzymes. For the reconstitution of these multistep catalytic processes, the enzymatic assembly lines need to be functionally expressed and the required substrates must be supplied in reasonable quantities. Furthermore, the production hosts need to be protected from the toxicity of the biosynthetic products. In this review, we will summarize and evaluate the status quo regarding the heterologous production of polyketides and nonribosomal peptides in S. cerevisiae. Based on a comprehensive literature analysis, prerequisites for a successful pathway reconstitution could be deduced, as well as recurring bottlenecks in this microbial host.
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Affiliation(s)
- Anna Tippelt
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Strasse 66, 44227, Dortmund, Germany
| | - Markus Nett
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Strasse 66, 44227, Dortmund, Germany.
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16
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Zhu HJ, Zhang B, Wang L, Wang W, Liu SH, Igarashi Y, Bashiri G, Tan RX, Ge HM. Redox Modifications in the Biosynthesis of Alchivemycin A Enable the Formation of Its Key Pharmacophore. J Am Chem Soc 2021; 143:4751-4757. [PMID: 33736434 DOI: 10.1021/jacs.1c00516] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Redox enzymes play a critical role in transforming nascent scaffolds into structurally complex and biologically active natural products. Alchivemycin A (AVM, 1) is a highly oxidized polycyclic compound with potent antimicrobial activity and features a rare 2H-tetrahydro-4,6-dioxo-1,2-oxazine (TDO) ring system. The scaffold of AVM has previously been shown to be biosynthesized by a hybrid polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS) pathway. In this study, we present a postassembly secondary metabolic network involving six redox enzymes that leads to AVM formation. We characterize this complex redox network using in vivo gene deletions, in vitro biochemical assays, and one-pot enzymatic total synthesis. Importantly, we show that an FAD-dependent monooxygenase catalyzes oxygen insertion into an amide bond to form the key TDO ring in AVM, an unprecedented function of flavoenzymes. We also show that the TDO ring is essential to the antimicrobial activity of AVM, likely through targeting the β-subunit of RNA polymerase. As further evidence, we show that AvmK, a β-subunit of RNA synthase, can confer self-resistance to AVM via target modification. Our findings expand the repertoire of functions of flavoenzymes and provide insight into antimicrobial and biocatalyst development based on AVM.
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Affiliation(s)
- Hong Jie Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Bo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Lan Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Wen Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Shuang He Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Toyama 939-0398, Japan
| | - Ghader Bashiri
- Laboratory of Molecular and Microbial Biochemistry, School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
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17
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Nabi AA, Scott LM, Furkert DP, Sperry J. Synthetic studies toward inducamide C. Org Biomol Chem 2021; 19:416-420. [PMID: 33313627 DOI: 10.1039/d0ob01995j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The alkaloid inducamide C is proposed to contain a very rare benzoxazepine ring. Herein, we report that the benzoxazepine ring in inducamide C is unstable and prone to rearrangement, indicating that structural revision of the natural product may be necessary. In a first-generation synthetic approach, attempts to assemble the benzoxazepine by cyclization of 4-hydroxyinducamide A led to the regioisomeric oxepanoindole, a result of the 4-hydroxyindole (C4-OH) undergoing preferential cyclization instead of the desired chlorosalicylic acid C15-OH. A second-generation approach involved dealkylation of O-isopropylinducamide C, but the same oxepanoindole formed via rearrangement of the proposed inducamide C structure. Computational studies validate preferential formation of the oxepanoindole and the lactone in O-isopropylinducamide C is susceptible to nucleophilic attack. Thus, inducamide C is either highly unstable or in need of structural revision.
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Affiliation(s)
- Ardalan A Nabi
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand.
| | - Lydia M Scott
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand.
| | - Daniel P Furkert
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand.
| | - Jonathan Sperry
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand.
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18
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The biosynthetic pathway to tetromadurin (SF2487/A80577), a polyether tetronate antibiotic. PLoS One 2020; 15:e0239054. [PMID: 32925967 PMCID: PMC7489565 DOI: 10.1371/journal.pone.0239054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/30/2020] [Indexed: 12/03/2022] Open
Abstract
The type I polyketide SF2487/A80577 (herein referred to as tetromadurin) is a polyether tetronate ionophore antibiotic produced by the terrestrial Gram-positive bacterium Actinomadura verrucosospora. Tetromadurin is closely related to the polyether tetronates tetronasin (M139603) and tetronomycin, all of which are characterised by containing a tetronate, cyclohexane, tetrahydropyran, and at least one tetrahydrofuran ring. We have sequenced the genome of Actinomadura verrucosospora to identify the biosynthetic gene cluster responsible for tetromadurin biosynthesis (the mad gene cluster). Based on bioinformatic analysis of the 32 genes present within the cluster a plausible biosynthetic pathway for tetromadurin biosynthesis is proposed. Functional confirmation of the mad gene cluster is obtained by performing in-frame deletions in each of the genes mad10 and mad31, which encode putative cyclase enzymes responsible for cyclohexane and tetrahydropyran formation, respectively. Furthermore, the A. verrucosospora Δmad10 mutant produces a novel tetromadurin metabolite that according to mass spectrometry analysis is analogous to the recently characterised partially cyclised tetronasin intermediate lacking its cyclohexane and tetrahydropyran rings. Our results therefore elucidate the biosynthetic machinery of tetromadurin biosynthesis and lend support for a conserved mechanism of cyclohexane and tetrahydropyran biosynthesis across polyether tetronates.
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19
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Li Y, Zhang J, Zheng J, Guan H, Liu W, Tan H. Co-expression of a SARP Family Activator ChlF2 and a Type II Thioesterase ChlK Led to High Production of Chlorothricin in Streptomyces antibioticus DSM 40725. Front Bioeng Biotechnol 2020; 8:1013. [PMID: 32974326 PMCID: PMC7471628 DOI: 10.3389/fbioe.2020.01013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/03/2020] [Indexed: 11/20/2022] Open
Abstract
Chlorothricin (CHL), produced by Streptomyces antibioticus DSM 40725 (wild-type strain, WT), belongs to a growing family of spirotetronate antibiotics that have biological activities inhibiting pyruvate carboxylase and malate dehydrogenase. ChlF2, a cluster-situated SARP regulator, can activate the transcription of chlJ, chlC3, chlC6, chlE1, chlM, and chlL to control CHL biosynthesis. Co-expression of chlF2 and chlK encoding type II thioesterase in WT strain under the control of Pkan led to high production of chlorothricin by 840% in comparison with that of WT. Since the inhibitory activity of CHL against several Gram-positive bacteria is higher than des-CHL, combinatorial strategies were applied to promote the conversion of des-CHL to CHL. Over-expression of chlB4, encoding a halogenase, combining with the supplementation of sodium chloride led to further 41% increase of CHL production compared to that of F2OE, a chlF2 over-expression strain. These findings provide new insights into the fine-tuned regulation of spirotetronate family of antibiotics and the construction of high-yield engineered strains.
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Affiliation(s)
- Yue Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jihui Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jiazhen Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hanye Guan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Huarong Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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20
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Luo M, Tang L, Dong Y, Huang H, Deng Z, Sun Y. Antibacterial natural products lobophorin L and M from the marine-derived Streptomyces sp. 4506. Nat Prod Res 2020; 35:5581-5587. [DOI: 10.1080/14786419.2020.1797730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Minghe Luo
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and School of Pharmaceutical Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Lingjie Tang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and School of Pharmaceutical Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Yulu Dong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and School of Pharmaceutical Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Hongbo Huang
- School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and School of Pharmaceutical Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and School of Pharmaceutical Sciences, Wuhan University, Wuhan, People’s Republic of China
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21
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Komaki H, Harunari E, Ichikawa N, Hosoyama A, Hamada M, Duangmal K, Thamchaipenet A, Igarashi Y. Draft genome sequence of Actinomadura sp. K4S16 and elucidation of the nonthmicin biosynthetic pathway. J Genomics 2020; 8:53-61. [PMID: 32494308 PMCID: PMC7256010 DOI: 10.7150/jgen.44650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/21/2020] [Indexed: 11/28/2022] Open
Abstract
Actinomadura sp. K4S16 (=NBRC 110471) is a producer of a novel tetronate polyether compound nonthmicin. Here, we report the draft genome sequence of this strain together with features of the organism and assembly, annotation and analysis of the genome sequence. The 9.6 Mb genome of Actinomadura sp. K4S16 encoded 9,004 putative ORFs, of which 7,701 were assigned with COG categories. The genome contained four type-I polyketide synthase (PKS) gene clusters, two type-II PKS gene clusters, and three nonribosomal peptide synthetase (NRPS) gene clusters. Among the type-I PKS gene (t1pks) clusters, a large t1pks cluster was annotated to be responsible for nonthmicin synthesis based on bioinformatic analyses. We also performed feeding experiments using labeled precursors and propose the biosynthetic pathway of nonthmicin.
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Affiliation(s)
- Hisayuki Komaki
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), Kisarazu, Chiba 292-0818, Japan
| | - Enjuro Harunari
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama 939-0398, Japan
| | | | | | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), Kisarazu, Chiba 292-0818, Japan
| | | | | | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama 939-0398, Japan
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22
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Jaremko MJ, Davis TD, Corpuz JC, Burkart MD. Type II non-ribosomal peptide synthetase proteins: structure, mechanism, and protein-protein interactions. Nat Prod Rep 2020; 37:355-379. [PMID: 31593192 PMCID: PMC7101270 DOI: 10.1039/c9np00047j] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Covering: 1990 to 2019 Many medicinally-relevant compounds are derived from non-ribosomal peptide synthetase (NRPS) products. Type I NRPSs are organized into large modular complexes, while type II NRPS systems contain standalone or minimal domains that often encompass specialized tailoring enzymes that produce bioactive metabolites. Protein-protein interactions and communication between the type II biosynthetic machinery and various downstream pathways are critical for efficient metabolite production. Importantly, the architecture of type II NRPS proteins makes them ideal targets for combinatorial biosynthesis and metabolic engineering. Future investigations exploring the molecular basis or protein-protein recognition in type II NRPS pathways will guide these engineering efforts. In this review, we consolidate the broad range of NRPS systems containing type II proteins and focus on structural investigations, enzymatic mechanisms, and protein-protein interactions important to unraveling pathways that produce unique metabolites, including dehydrogenated prolines, substituted benzoic acids, substituted amino acids, and cyclopropanes.
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Affiliation(s)
- Matt J Jaremko
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, USA.
| | - Tony D Davis
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, USA.
| | - Joshua C Corpuz
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, USA.
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, USA.
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23
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Antimicrobial biosynthetic potential and diversity of culturable soil actinobacteria from forest ecosystems of Northeast India. Sci Rep 2020; 10:4104. [PMID: 32139731 PMCID: PMC7057963 DOI: 10.1038/s41598-020-60968-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/06/2020] [Indexed: 02/07/2023] Open
Abstract
Actinobacteria is a goldmine for the discovery of abundant secondary metabolites with diverse biological activities. This study explores antimicrobial biosynthetic potential and diversity of actinobacteria from Pobitora Wildlife Sanctuary and Kaziranga National Park of Assam, India, lying in the Indo-Burma mega-biodiversity hotspot. A total of 107 actinobacteria were isolated, of which 77 exhibited significant antagonistic activity. 24 isolates tested positive for at least one of the polyketide synthase type I, polyketide synthase type II or non-ribosomal peptide synthase genes within their genome. Their secondary metabolite pathway products were predicted to be involved in the production of ansamycin, benzoisochromanequinone, streptogramin using DoBISCUIT database. Molecular identification indicated that these actinobacteria predominantly belonged to genus Streptomyces, followed by Nocardia and Kribbella. 4 strains, viz. Streptomyces sp. PB-79 (GenBank accession no. KU901725; 1313 bp), Streptomyces sp. Kz-28 (GenBank accession no. KY000534; 1378 bp), Streptomyces sp. Kz-32 (GenBank accession no. KY000536; 1377 bp) and Streptomyces sp. Kz-67 (GenBank accession no. KY000540; 1383 bp) showed ~89.5% similarity to the nearest type strain in EzTaxon database and may be considered novel. Streptomyces sp. Kz-24 (GenBank accession no. KY000533; 1367 bp) showed only 96.2% sequence similarity to S. malaysiensis and exhibited minimum inhibitory concentration of 0.024 µg/mL against methicilin resistant Staphylococcus aureus ATCC 43300 and Candida albicans MTCC 227. This study establishes that actinobacteria isolated from the poorly explored Indo-Burma mega-biodiversity hotspot may be an extremely rich reservoir for production of biologically active compounds for human welfare.
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24
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Tan B, Chen S, Zhang Q, Chen Y, Zhu Y, Khan I, Zhang W, Zhang C. Heterologous Expression Leads to Discovery of Diversified Lobophorin Analogues and a Flexible Glycosyltransferase. Org Lett 2020; 22:1062-1066. [PMID: 31971807 DOI: 10.1021/acs.orglett.9b04597] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Bin Tan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Institution of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Siqiang Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Institution of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingbo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Institution of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Yuchan Chen
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Guangzhou 510070, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Institution of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Imran Khan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Institution of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weimin Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Guangzhou 510070, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Institution of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
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25
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Kallscheuer N, Kage H, Milke L, Nett M, Marienhagen J. Microbial synthesis of the type I polyketide 6-methylsalicylate with Corynebacterium glutamicum. Appl Microbiol Biotechnol 2019; 103:9619-9631. [DOI: 10.1007/s00253-019-10121-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/26/2019] [Accepted: 09/04/2019] [Indexed: 12/28/2022]
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26
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Ogawara H. Comparison of Antibiotic Resistance Mechanisms in Antibiotic-Producing and Pathogenic Bacteria. Molecules 2019; 24:E3430. [PMID: 31546630 PMCID: PMC6804068 DOI: 10.3390/molecules24193430] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance poses a tremendous threat to human health. To overcome this problem, it is essential to know the mechanism of antibiotic resistance in antibiotic-producing and pathogenic bacteria. This paper deals with this problem from four points of view. First, the antibiotic resistance genes in producers are discussed related to their biosynthesis. Most resistance genes are present within the biosynthetic gene clusters, but some genes such as paromomycin acetyltransferases are located far outside the gene cluster. Second, when the antibiotic resistance genes in pathogens are compared with those in the producers, resistance mechanisms have dependency on antibiotic classes, and, in addition, new types of resistance mechanisms such as Eis aminoglycoside acetyltransferase and self-sacrifice proteins in enediyne antibiotics emerge in pathogens. Third, the relationships of the resistance genes between producers and pathogens are reevaluated at their amino acid sequence as well as nucleotide sequence levels. Pathogenic bacteria possess other resistance mechanisms than those in antibiotic producers. In addition, resistance mechanisms are little different between early stage of antibiotic use and the present time, e.g., β-lactam resistance in Staphylococcus aureus. Lastly, guanine + cytosine (GC) barrier in gene transfer to pathogenic bacteria is considered. Now, the resistance genes constitute resistome composed of complicated mixture from divergent environments.
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Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, 33-9, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, 522-1, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
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27
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Eida AA, Abugrain ME, Brumsted CJ, Mahmud T. Glycosylation of acyl carrier protein-bound polyketides during pactamycin biosynthesis. Nat Chem Biol 2019; 15:795-802. [PMID: 31308531 PMCID: PMC6642016 DOI: 10.1038/s41589-019-0314-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/29/2019] [Indexed: 11/09/2022]
Abstract
Glycosylation is a common modification reaction in natural products biosynthesis and has been known to be a post assembly line tailoring process in glycosylated polyketide biosynthesis. Here, we show that in pactamycin biosynthesis glycosylation can take place on an acyl carrier protein (ACP)-bound polyketide intermediate. Using in vivo gene inactivation, chemical complementation, and in vitro pathway reconstitution we demonstrate that the 3-aminoacetophenone moiety of pactamycin is derived from 3-aminobenzoic acid by a set of discrete polyketide synthase proteins via a 3-[3-aminophenyl]3-oxopropionyl-ACP intermediate. This ACP-bound intermediate is then glycosylated by an N-glycosyltransferase, PtmJ, providing a sugar precursor for the formation of the aminocyclopentitol core structure of pactamycin. This is the first example of glycosylation of a small molecule while tethered to a carrier protein. Additionally, we demonstrate that PtmO is a hydrolase that is responsible for the release of the ACP-bound product to a free β-ketoacid that subsequently undergoes decarboxylation.
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Affiliation(s)
- Auday A Eida
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, USA
| | - Mostafa E Abugrain
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, USA
| | - Corey J Brumsted
- Department of Chemistry, Oregon State University, Corvallis, OR, USA
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, USA. .,Department of Chemistry, Oregon State University, Corvallis, OR, USA.
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28
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Yi X, Zhao Q, Tian Z, Jia X, Cao W, Liu W, He Q. Insights into the Functionalization of the Methylsalicyclic Moiety during the Biosynthesis of Chlorothricin by Comparative Kinetic Assays of the Activities of Two KAS III‐like Acyltransferases. CHINESE J CHEM 2019. [DOI: 10.1002/cjoc.201900134] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xuan Yi
- Department of Chemistry, Innovative Drug Research CenterShanghai University 99 Shangda Road, Shanghai 200444 China
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence on Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences 345 Lingling Road, Shanghai 200032 China
| | - Qunfei Zhao
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence on Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences 345 Lingling Road, Shanghai 200032 China
| | - Zhenhua Tian
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence on Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences 345 Lingling Road, Shanghai 200032 China
| | - Xinying Jia
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence on Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences 345 Lingling Road, Shanghai 200032 China
| | - Weiguo Cao
- Department of Chemistry, Innovative Drug Research CenterShanghai University 99 Shangda Road, Shanghai 200444 China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence on Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences 345 Lingling Road, Shanghai 200032 China
- Huzhou Center of Bio‐Synthetic Innovation 1366 Hongfeng Road, Huzhou, Zhejiang 313000 China
| | - Qing‐Li He
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine 1200 Cai Lun Road, Shanghai 201203 China
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29
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Nofiani R, Philmus B, Nindita Y, Mahmud T. 3-Ketoacyl-ACP synthase (KAS) III homologues and their roles in natural product biosynthesis. MEDCHEMCOMM 2019; 10:1517-1530. [PMID: 31673313 DOI: 10.1039/c9md00162j] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/29/2019] [Indexed: 11/21/2022]
Abstract
The 3-ketoacyl-ACP synthase (KAS) III proteins are one of the most abundant enzymes in nature, as they are involved in the biosynthesis of fatty acids and natural products. KAS III enzymes catalyse a carbon-carbon bond formation reaction that involves the α-carbon of a thioester and the carbonyl carbon of another thioester. In addition to the typical KAS III enzymes involved in fatty acid and polyketide biosynthesis, there are proteins homologous to KAS III enzymes that catalyse reactions that are different from that of the traditional KAS III enzymes. Those include enzymes that are responsible for a head-to-head condensation reaction, the formation of acetoacetyl-CoA in mevalonate biosynthesis, tailoring processes via C-O bond formation or esterification, as well as amide formation. This review article highlights the diverse reactions catalysed by this class of enzymes and their role in natural product biosynthesis.
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Affiliation(s)
- Risa Nofiani
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA . .,Department of Chemistry , Universitas Tanjungpura , Pontianak , Indonesia
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
| | - Yosi Nindita
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
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30
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Braddock AA, Theodorakis EA. Marine Spirotetronates: Biosynthetic Edifices That Inspire Drug Discovery. Mar Drugs 2019; 17:md17040232. [PMID: 31010150 PMCID: PMC6521127 DOI: 10.3390/md17040232] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 04/13/2019] [Accepted: 04/16/2019] [Indexed: 12/31/2022] Open
Abstract
Spirotetronates are actinomyces-derived polyketides that possess complex structures and exhibit potent and unexplored bioactivities. Due to their anticancer and antimicrobial properties, they have potential as drug hits and deserve further study. In particular, abyssomicin C and tetrocarcin A have shown significant promise against antibiotic-resistant S. aureus and tuberculosis, as well as for the treatment of various lymphomas and solid tumors. Improved synthetic routes to these compounds, particularly the class II spirotetronates, are needed to access sufficient quantities for structure optimization and clinical applications.
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Affiliation(s)
- Alexander A Braddock
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA 92093-0358, USA.
| | - Emmanuel A Theodorakis
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA 92093-0358, USA.
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31
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Tolmie C, Smit MS, Opperman DJ. Native roles of Baeyer–Villiger monooxygenases in the microbial metabolism of natural compounds. Nat Prod Rep 2019; 36:326-353. [DOI: 10.1039/c8np00054a] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Baeyer–Villiger monooxygenases function in the primary metabolism of atypical carbon sources, as well as the synthesis of complex microbial metabolites.
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Affiliation(s)
- Carmien Tolmie
- Department of Biotechnology
- University of the Free State
- Bloemfontein
- South Africa
| | - Martha S. Smit
- Department of Biotechnology
- University of the Free State
- Bloemfontein
- South Africa
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32
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Zheng Q, Gong Y, Guo Y, Zhao Z, Wu Z, Zhou Z, Chen D, Pan L, Liu W. Structural Insights into a Flavin-Dependent [4 + 2] Cyclase that Catalyzes trans-Decalin Formation in Pyrroindomycin Biosynthesis. Cell Chem Biol 2018; 25:718-727.e3. [DOI: 10.1016/j.chembiol.2018.03.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/28/2018] [Accepted: 03/12/2018] [Indexed: 12/13/2022]
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33
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Zheng Q, Wu Z, Sun P, Chen D, Tian Z, Liu W. A linear hydroxymethyl tetramate undergoes an acetylation-elimination process for exocyclic methylene formation in the biosynthetic pathway of pyrroindomycins. Org Biomol Chem 2018; 15:88-91. [PMID: 27942669 DOI: 10.1039/c6ob02567f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We herein report the isolation and characterization of a key linear intermediate in the biosynthetic pathway of pyrroindomycins, the potent spirotetramate natural products produced by Streptomyces rugosporus. This polyene intermediate bears a γ-hydroxymethyl group that is exocyclic to the tetramate moiety, indicating that a serine residue serves as the three-carbon unit for tetramate formation and chain-elongation termination. The further conversion involves an acetylation-elimination of the exocyclic γ-hydroxymethyl group to generate a γ-methylene group, which is indispensable for intramolecular [4 + 2] cross-bridging to construct the characteristic pentacyclic core. The findings presented in this study provide new insights into the biosynthesis of pyrroindomycins, and thus suggest a common paradigm for both spirotetramates and spirotetronates in processing the exocyclic γ-hydroxymethyl group of the five-membered heterocycle.
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Affiliation(s)
- Qingfei Zheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
| | - Zhuhua Wu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
| | - Peng Sun
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China. and Research Center for Marine Drugs, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Dandan Chen
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China. and Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou 313000, China
| | - Zhenhua Tian
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China. and Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou 313000, China
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34
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Identification of a biosynthetic gene cluster for the polyene macrolactam sceliphrolactam in a Streptomyces strain isolated from mangrove sediment. Sci Rep 2018; 8:1594. [PMID: 29371699 PMCID: PMC5785472 DOI: 10.1038/s41598-018-20018-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/11/2018] [Indexed: 11/25/2022] Open
Abstract
Streptomyces are a genus of Actinobacteria capable of producing structurally diverse natural products. Here we report the isolation and characterization of a biosynthetically talented Streptomyces (Streptomyces sp. SD85) from tropical mangrove sediments. Whole-genome sequencing revealed that Streptomyces sp. SD85 harbors at least 52 biosynthetic gene clusters (BGCs), which constitute 21.2% of the 8.6-Mb genome. When cultivated under lab conditions, Streptomyces sp. SD85 produces sceliphrolactam, a 26-membered polyene macrolactam with unknown biosynthetic origin. Genome mining yielded a putative sceliphrolactam BGC (sce) that encodes a type I modular polyketide synthase (PKS) system, several β-amino acid starter biosynthetic enzymes, transporters, and transcriptional regulators. Using the CRISPR/Cas9–based gene knockout method, we demonstrated that the sce BGC is essential for sceliphrolactam biosynthesis. Unexpectedly, the PKS system encoded by sce is short of one module required for assembling the 26-membered macrolactam skeleton according to the collinearity rule. With experimental data disfavoring the involvement of a trans-PKS module, the biosynthesis of sceliphrolactam seems to be best rationalized by invoking a mechanism whereby the PKS system employs an iterative module to catalyze two successive chain extensions with different outcomes. The potential violation of the collinearity rule makes the mechanism distinct from those of other polyene macrolactams.
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35
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Gui C, Zhang S, Zhu X, Ding W, Huang H, Gu YC, Duan Y, Ju J. Antimicrobial Spirotetronate Metabolites from Marine-Derived Micromonospora harpali SCSIO GJ089. JOURNAL OF NATURAL PRODUCTS 2017; 80:1594-1603. [PMID: 28489382 DOI: 10.1021/acs.jnatprod.7b00176] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Two new spirotetronate aglycones, 22-dehydroxymethyl-kijanolide (1) and 8-hydroxy-22-dehydroxymethyl-kijanolide (2), along with seven new spirotetronate glycosides, microsporanates A-F (3-8) and tetrocarcin P (9), together with three known tetrocarcins [tetrocarcins A (10), B (11), and AC6H (12)], were isolated from fermentation broths of the marine-derived Micromonospora harpali SCSIO GJ089. The structures of 1-9 were elucidated on the basis of 1D and 2D NMR and MS spectroscopic data. Compounds 3-8 feature an α,β-unsaturated carbonyl moiety within their spirotetronate skeletons. Moreover, compounds 3-12 displayed strong to moderate antibacterial activities against Gram positive bacteria Bacillus thuringiensis BT01 and B. subtilis BS01 with MIC values ranging from 0.016 to 8.0 μg/mL.
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Affiliation(s)
- Chun Gui
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, People's Republic of China
- University of Chinese Academy of Sciences , 19 Yuquan Road, Beijing 110039, People's Republic of China
| | - Shanwen Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, People's Republic of China
- University of Chinese Academy of Sciences , 19 Yuquan Road, Beijing 110039, People's Republic of China
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine, Central South University, National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery , 172 Tongzipo Road, Changsha 410013, People's Republic of China
| | - Wenjuan Ding
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, People's Republic of China
- University of Chinese Academy of Sciences , 19 Yuquan Road, Beijing 110039, People's Republic of China
| | - Hongbo Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, People's Republic of China
| | - Yu-Cheng Gu
- Syngenta Jealott's Hill International Research Centre , Bracknell, Berkshire RG42 6EY, U.K
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine, Central South University, National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery , 172 Tongzipo Road, Changsha 410013, People's Republic of China
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, People's Republic of China
- University of Chinese Academy of Sciences , 19 Yuquan Road, Beijing 110039, People's Republic of China
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36
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Abstract
The enzymology of 135 assembly lines containing primarily cis-acyltransferase modules is comprehensively analyzed, with greater attention paid to less common phenomena. Diverse online transformations, in which the substrate and/or product of the reaction is an acyl chain bound to an acyl carrier protein, are classified so that unusual reactions can be compared and underlying assembly-line logic can emerge. As a complement to the chemistry surrounding the loading, extension, and offloading of assembly lines that construct primarily polyketide products, structural aspects of the assembly-line machinery itself are considered. This review of assembly-line phenomena, covering the literature up to 2017, should thus be informative to the modular polyketide synthase novice and expert alike.
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Affiliation(s)
- Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States
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37
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Lin CI, McCarty RM, Liu HW. The Enzymology of Organic Transformations: A Survey of Name Reactions in Biological Systems. Angew Chem Int Ed Engl 2017; 56:3446-3489. [PMID: 27505692 PMCID: PMC5477795 DOI: 10.1002/anie.201603291] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Indexed: 01/05/2023]
Abstract
Chemical reactions that are named in honor of their true, or at least perceived, discoverers are known as "name reactions". This Review is a collection of biological representatives of named chemical reactions. Emphasis is placed on reaction types and catalytic mechanisms that showcase both the chemical diversity in natural product biosynthesis as well as the parallels with synthetic organic chemistry. An attempt has been made, whenever possible, to describe the enzymatic mechanisms of catalysis within the context of their synthetic counterparts and to discuss the mechanistic hypotheses for those reactions that are currently active areas of investigation. This Review has been categorized by reaction type, for example condensation, nucleophilic addition, reduction and oxidation, substitution, carboxylation, radical-mediated, and rearrangements, which are subdivided by name reactions.
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Affiliation(s)
- Chia-I Lin
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin, Austin, TX, 78731, USA
| | - Reid M McCarty
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin, Austin, TX, 78731, USA
| | - Hung-Wen Liu
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin, Austin, TX, 78731, USA
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Lin C, McCarty RM, Liu H. Die Enzymologie organischer Umwandlungen: Namensreaktionen in biologischen Systemen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201603291] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Chia‐I. Lin
- Division of Chemical Biology and Medicinal Chemistry College of Pharmacy, and Department of Chemistry University of Texas at Austin Austin TX 78731 USA
| | - Reid M. McCarty
- Division of Chemical Biology and Medicinal Chemistry College of Pharmacy, and Department of Chemistry University of Texas at Austin Austin TX 78731 USA
| | - Hung‐wen Liu
- Division of Chemical Biology and Medicinal Chemistry College of Pharmacy, and Department of Chemistry University of Texas at Austin Austin TX 78731 USA
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Tetrodecamycin: An unusual and interesting tetronate antibiotic. Bioorg Med Chem 2016; 24:6269-6275. [DOI: 10.1016/j.bmc.2016.05.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/08/2016] [Accepted: 05/17/2016] [Indexed: 11/23/2022]
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Abstract
[4 + 2]-Cycloadditions are increasingly being recognized in the biosynthetic pathways of many structurally complex natural products. A relatively small collection of enzymes from these pathways have been demonstrated to increase rates of cyclization and impose stereochemical constraints on the reactions. While mechanistic investigation of these enzymes is just beginning, recent studies have provided new insights with implications for understanding their biosynthetic roles, mechanisms of catalysis, and evolutionary origin.
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Affiliation(s)
- Byung-Sun Jeon
- Department of Chemistry and ‡Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin , Austin, Texas 78712, United States
| | - Shao-An Wang
- Department of Chemistry and ‡Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin , Austin, Texas 78712, United States
| | - Mark W Ruszczycky
- Department of Chemistry and ‡Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin , Austin, Texas 78712, United States
| | - Hung-Wen Liu
- Department of Chemistry and ‡Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin , Austin, Texas 78712, United States
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Hashimoto T, Kuzuyama T. Mechanistic insights into Diels-Alder reactions in natural product biosynthesis. Curr Opin Chem Biol 2016; 35:117-123. [DOI: 10.1016/j.cbpa.2016.09.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/14/2016] [Accepted: 09/17/2016] [Indexed: 10/20/2022]
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Chen M, Liu J, Duan P, Li M, Liu W. Biosynthesis and molecular engineering of templated natural products. Natl Sci Rev 2016. [DOI: 10.1093/nsr/nww045] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Abstract
Bioactive small molecules that are produced by living organisms, often referred to as natural products (NPs), historically play a critical role in the context of both medicinal chemistry and chemical biology. How nature creates these chemical entities with stunning structural complexity and diversity using a limited range of simple substrates has not been fully understood. Focusing on two types of NPs that share a highly evolvable ‘template’-biosynthetic logic, we here provide specific examples to highlight the conceptual and technological leaps in NP biosynthesis and witness the area of progress since the beginning of the twenty-first century. The biosynthesis of polyketides, non-ribosomal peptides and their hybrids that share an assembly-line enzymology of modular multifunctional proteins exemplifies an extended ‘central dogma’ that correlates the genotype of catalysts with the chemotype of products; in parallel, post-translational modifications of ribosomally synthesized peptides involve a number of unusual biochemical mechanisms for molecular maturation. Understanding the biosynthetic processes of these templated NPs would largely facilitate the design, development and utilization of compatible biosynthetic machineries to address the challenge that often arises from structural complexity to the accessibility and efficiency of current chemical synthesis.
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Affiliation(s)
- Ming Chen
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jingyu Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Panpan Duan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Mulin Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
- State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Huzhou Center of Bio-Synthetic Innovation, Huzhou 313000, China
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Minami A, Oikawa H. Recent advances of Diels–Alderases involved in natural product biosynthesis. J Antibiot (Tokyo) 2016; 69:500-6. [DOI: 10.1038/ja.2016.67] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 05/10/2016] [Accepted: 05/13/2016] [Indexed: 01/17/2023]
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Pang B, Wang M, Liu W. Cyclization of polyketides and non-ribosomal peptides on and off their assembly lines. Nat Prod Rep 2016; 33:162-73. [PMID: 26604034 DOI: 10.1039/c5np00095e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Modular polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) are multifunctional megaenzymes that serve as templates to program the assembly of short carboxylic acids and amino acids in a primarily co-linear manner. The variation, combination, permutation and evolution of their functional units (e.g., modules, domains and proteins) along with their association with external enzymes have resulted in the generation of numerous versions of templates, the roles of which have not been fully recognized in the structural diversification of polyketides, non-ribosomal peptides and their hybrids present in nature. In this Highlight, we focus on the assembly-line enzymology and associated chemistry by providing examples of some newly characterized cyclization reactions that occur on and off the assembly lines during and after chain elongation for the purpose of elucidating the template effects of PKSs and NRPSs. A fundamental understanding of the underlying biosynthetic logic would facilitate the elucidation of chemical information contained within the PKS or NRPS templates and benefit the development of strategies for genome mining, biosynthesis-inspired chemical synthesis and combinatorial biosynthesis.
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Affiliation(s)
- Bo Pang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
| | - Min Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China. and Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou 313000, China
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Tang XL, Dai P, Gao H, Wang CX, Chen GD, Hong K, Hu D, Yao XS. A Single Gene Cluster for Chalcomycins and Aldgamycins: Genetic Basis for Bifurcation of Their Biosynthesis. Chembiochem 2016; 17:1241-9. [PMID: 27191535 DOI: 10.1002/cbic.201600118] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Indexed: 01/27/2023]
Abstract
Aldgamycins are 16-membered macrolide antibiotics with a rare branched-chain sugar d-aldgarose or decarboxylated d-aldgarose at C-5. In our efforts to clone the gene cluster for aldgamycins from a marine-derived Streptomyces sp. HK-2006-1 capable of producing both aldgamycins and chalcomycins, we found that both are biosynthesized from a single gene cluster. Whole-genome sequencing combined with gene disruption established the entire gene cluster of aldgamycins: nine new genes are incorporated with the previously identified chalcomycin gene cluster. Functional analysis of these genes revealed that almDI/almDII, (encoding α/β subunits of pyruvate dehydrogenase) triggers the biosynthesis of aldgamycins, whereas almCI (encoding an oxidoreductase) initiates chalcomycins biosynthesis. This is the first report that aldgamycins and chalcomycins are derived from a single gene cluster and of the genetic basis for bifurcation in their biosynthesis.
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Affiliation(s)
- Xiao-Long Tang
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, No. 103 Wenhua Road, Shenyang, 110016, China
| | - Ping Dai
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, China
| | - Hao Gao
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, China
| | - Chuan-Xi Wang
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, China
| | - Guo-Dong Chen
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, China
| | - Kui Hong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, No. 185 Donghu Road, Wuhan, 430071, China
| | - Dan Hu
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, China.
| | - Xin-Sheng Yao
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, No. 103 Wenhua Road, Shenyang, 110016, China. .,Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, China.
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Abstract
The inducamides are a family of chlorinated alkaloids featuring an amide arising from union of an l-tryptophan to a rare chlorosalicylic acid unit, the production of which is linked to a chemically induced mutation in the RNA polymerase of Streptomyces sp. (SNC-109-M3). The synthesis of inducamides A and B has been accomplished by the coupling of 6-hydroxy-3-chloro-2-methylbenzoic acid with l-6-chlorotryptophan and l-tryptophan, respectively, followed by ester hydrolysis. The spectroscopic data and optical rotation for each synthetic sample confirm the structures of these silent secondary metabolites and their biosynthesis from l-tryptophan.
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Affiliation(s)
- Lydia M Scott
- School of Chemical Sciences, University of Auckland , 23 Symonds Street, Auckland, New Zealand
| | - Jonathan Sperry
- School of Chemical Sciences, University of Auckland , 23 Symonds Street, Auckland, New Zealand
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Pang B, Zhong G, Tang Z, Liu W. Enzymatic [4+2] Cycloadditions in the Biosynthesis of Spirotetramates and Spirotetronates. Methods Enzymol 2016; 575:39-63. [PMID: 27417924 DOI: 10.1016/bs.mie.2016.02.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The Diels-Alder reaction is a quintessential type of [4+2] cycloaddition that remains one of the most intriguing transformations in synthetic chemistry. This reaction has long been envisaged to participate in the biosynthesis of a number of cyclohexene-containing natural products, although the question of whether a bona fide Diels-Alderase exists remains unsolved. In nature, there are remarkably few enzymes known to have the activity of [4+2] cycloaddition. These enzymes are phylogenetically distinct and are often classified according to the specific chemical structures. The variation of protein ancestors and in many cases the instability/complexity of the substrates and products pose a significant challenge in identification of the [4+2] cycloaddition catalysts using general homology-based mining approaches. We here provide the detailed description of the multiple comparison-based strategy and methods for the characterization of two distinct types of dedicated [4+2] cyclases (eg, PyrE3 and PyrI4) in the biosynthesis of spirotetramates and spirotetronates, where they act in tandem for coordinated cross-bridging of a linear polyene intermediate into a enantiomerically pure pentacyclic core. The search of new protein scaffolds with the [4+2] cycloaddition activity could enrich the pool of the candidates for mechanistic examination of a true enzymatic Diels-Alder reaction. The protocols presented in this study would also be applicable to the study of other functionally similar but phylogenetically different proteins, eg, the spiroketal cyclases.
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Affiliation(s)
- B Pang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, PR China
| | - G Zhong
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, PR China
| | - Z Tang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, PR China
| | - W Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, PR China; Huzhou Center of Bio-Synthetic Innovation, Huzhou, PR China.
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48
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Liao L, Chen R, Jiang M, Tian X, Liu H, Yu Y, Fan C, Chen B. Bioprospecting potential of halogenases from Arctic marine actinomycetes. BMC Microbiol 2016; 16:34. [PMID: 26964536 PMCID: PMC4785625 DOI: 10.1186/s12866-016-0662-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 03/05/2016] [Indexed: 11/14/2022] Open
Abstract
Background Halometabolites, an important group of natural products, generally require halogenases for their biosynthesis. Actinomycetes from the Arctic Ocean have rarely been investigated for halogenases and their gene clusters associated, albeit great potential of halometabolite production has been predicted. Therefore, we initiated this research on the screening of halogenases from Arctic marine actinomycetes isolates to explore their genetic potential of halometabolite biosynthesis. Results Nine halogenase genes were discovered from sixty Arctic marine actinomycetes using in-house designed or previously reported PCR primers. Four representative genotypes were further cloned to obtain full coding regions through genome walking. The resulting halogenases were predicted to be involved in halogenation of indole groups, antitumor agent ansamitocin-like substrates, or unknown peptide-like compounds. Genome sequencing revealed a potential gene cluster containing the halogenase predicted to catalyze peptide-like compounds. However, the gene cluster was probably silent under the current conditions. Conclusions PCR-based screening of halogenase genes is a powerful and efficient tool to conduct bioprospecting of halometabolite-producing actinomycetes from the Arctic. Genome sequencing can also identify cryptic gene clusters potentially producing new halometabolites, which might be easily missed by traditional isolation and chemical characterization. In addition, our study indicates that great genetic potential of new halometabolites can be expected from mostly untapped actinomycetes from the polar regions. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0662-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Li Liao
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, 451 Jinqiao Road, Shanghai, 200136, China
| | - Ruiqin Chen
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, 451 Jinqiao Road, Shanghai, 200136, China.,College of Bioengineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Ming Jiang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20030, China
| | - Xiaoqing Tian
- Key Laboratory of East China Sea & Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, China
| | - Huan Liu
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, 451 Jinqiao Road, Shanghai, 200136, China.,College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Yong Yu
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, 451 Jinqiao Road, Shanghai, 200136, China
| | - Chenqi Fan
- Key Laboratory of East China Sea & Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, China
| | - Bo Chen
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, 451 Jinqiao Road, Shanghai, 200136, China.
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Enzyme-Dependent [4 + 2] Cycloaddition Depends on Lid-like Interaction of the N-Terminal Sequence with the Catalytic Core in PyrI4. Cell Chem Biol 2016; 23:352-60. [DOI: 10.1016/j.chembiol.2016.01.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/13/2016] [Accepted: 01/17/2016] [Indexed: 11/23/2022]
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50
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Li Y, Li J, Tian Z, Xu Y, Zhang J, Liu W, Tan H. Coordinative Modulation of Chlorothricin Biosynthesis by Binding of the Glycosylated Intermediates and End Product to a Responsive Regulator ChlF1. J Biol Chem 2016; 291:5406-17. [PMID: 26750095 DOI: 10.1074/jbc.m115.695874] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Indexed: 11/06/2022] Open
Abstract
Chlorothricin, isolated from Streptomyces antibioticus, is a parent member of spirotetronate family of antibiotics that have long been appreciated for their remarkable biological activities. ChlF1 plays bifunctional roles in chlorothricin biosynthesis by binding to its target genes (chlJ, chlF1, chlG, and chlK). The dissociation constants of ChlF1 to these genes are ∼ 102-140 nm. A consensus sequence, 5'-GTAANNATTTAC-3', was found in these binding sites. ChlF1 represses the transcription of chlF1, chlG, and chlK but activates chlJ, which encodes a key enzyme acyl-CoA carboxyl transferase involved in the chlorothricin biosynthesis. We demonstrate that the end product chlorothricin and likewise its biosynthetic intermediates (demethylsalicycloyl chlorothricin and deschloro-chlorothricin) can act as signaling molecules to modulate the binding of ChlF1 to its target genes. Intriguingly, a correlation between the antibacterial activity and binding ability of signaling molecules to the regulator ChlF1 is clearly observed. These features of the signaling molecules are associated with the glycosylation of spirotetronate macrolide aglycone. The findings provide new insights into the TetR family regulators responding to special structure of signaling molecules, and we reveal the regulatory mini-network mediated by ChlF1 in chlorothricin biosynthesis for the first time.
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Affiliation(s)
- Yue Li
- From the State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China, the University of Chinese Academy of Sciences, Beijing 100101, China, and
| | - Jingjing Li
- From the State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China, the University of Chinese Academy of Sciences, Beijing 100101, China, and
| | - Zhenhua Tian
- the State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yu Xu
- the State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jihui Zhang
- From the State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen Liu
- the State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Huarong Tan
- From the State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China,
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