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Abstract
Covering: from 2000 up to the very early part of 2023S-Adenosyl-L-methionine (SAM) is a naturally occurring trialkyl sulfonium molecule that is typically associated with biological methyltransfer reactions. However, SAM is also known to donate methylene, aminocarboxypropyl, adenosyl and amino moieties during natural product biosynthetic reactions. The reaction scope is further expanded as SAM itself can be modified prior to the group transfer such that a SAM-derived carboxymethyl or aminopropyl moiety can also be transferred. Moreover, the sulfonium cation in SAM has itself been found to be critical for several other enzymatic transformations. Thus, while many SAM-dependent enzymes are characterized by a methyltransferase fold, not all of them are necessarily methyltransferases. Furthermore, other SAM-dependent enzymes do not possess such a structural feature suggesting diversification along different evolutionary lineages. Despite the biological versatility of SAM, it nevertheless parallels the chemistry of sulfonium compounds used in organic synthesis. The question thus becomes how enzymes catalyze distinct transformations via subtle differences in their active sites. This review summarizes recent advances in the discovery of novel SAM utilizing enzymes that rely on Lewis acid/base chemistry as opposed to radical mechanisms of catalysis. The examples are categorized based on the presence of a methyltransferase fold and the role played by SAM within the context of known sulfonium chemistry.
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Affiliation(s)
- Yu-Hsuan Lee
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| | - Daan Ren
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| | - Byungsun Jeon
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| | - Hung-Wen Liu
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA
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2
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Zheng X, Li Y, Guan M, Wang L, Wei S, Li YC, Chang CY, Xu Z. Biomimetic Total Synthesis of the Spiroindimicin Family of Natural Products. Angew Chem Int Ed Engl 2022; 61:e202208802. [PMID: 35904849 DOI: 10.1002/anie.202208802] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Indexed: 12/24/2022]
Abstract
A unified strategy for the biomimetic total synthesis of the spiroindimicin family of natural products was reported. Key transformations include a one-pot two-enzyme-catalyzed oxidative dimerization of L-tryptophan/5-chloro-L-tryptophan to afford the bis-indole precursors chromopyrrolic acid/5',5''-dichloro-chromopyrrolic acid, and regioselective C3'-C2'' and C3'-C4'' bond formation converting a common bis-indole skeleton to two skeletally different natural products, including (±)-spiroindimicins D and G with a [5,5] spiro-ring skeleton, and (±)-spiroindimicins A and H with a [5,6] spiro-ring skeleton, respectively.
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Affiliation(s)
- Xikang Zheng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
| | - Yan Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
| | - Mengtie Guan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
| | - Lingyue Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
| | - Shilong Wei
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
| | - Yi-Cheng Li
- Department of Biological Sciences and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, P. R. China
| | - Chin-Yuan Chang
- Department of Biological Sciences and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, P. R. China
| | - Zhengren Xu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
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3
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Zheng X, Li Y, Guan M, Wang L, Wei S, Li YC, Chang CY, Xu Z. Biomimetic Total Synthesis of the Spiroindimicin Family of Natural Products. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xikang Zheng
- Peking University State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences CHINA
| | - Yan Li
- Peking University State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences CHINA
| | - Mengtie Guan
- Peking University State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences CHINA
| | - Lingyue Wang
- Peking University State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences CHINA
| | - Shilong Wei
- Peking University State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences CHINA
| | - Yi-Cheng Li
- National Yang Ming Chiao Tung University Department of Biological Sciences and Technology TAIWAN
| | - Chin-Yuan Chang
- National Yang Ming Chiao Tung University Department of Biological Sciences and Technology TAIWAN
| | - Zhengren Xu
- Peking University State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences 38 Xueyuan Road, Haidian District 100191 Beijing CHINA
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4
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Shi S, Cui L, Zhang K, Zeng Q, Li Q, Ma L, Long L, Tian X. Streptomyces marincola sp. nov., a Novel Marine Actinomycete, and Its Biosynthetic Potential of Bioactive Natural Products. Front Microbiol 2022; 13:860308. [PMID: 35572650 PMCID: PMC9096227 DOI: 10.3389/fmicb.2022.860308] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 02/24/2022] [Indexed: 12/28/2022] Open
Abstract
Marine actinomycetes are an important source of antibiotics, but many of them are yet to be explored in terms of taxonomy, ecology, and functional activity. In this study, two marine actinobacterial strains, designated SCSIO 64649T and SCSIO 03032, were isolated, and the potential for bioactive natural product discovery was evaluated based on genome mining, compound detection, and antimicrobial activity. Phylogenetic analysis of the 16S rRNA gene sequences showed that strain SCSIO 64649T formed a single clade with SCSIO 03032 (similarity 99.5%) and sister clades with the species Streptomyces specialis DSM 41924T (97.1%) and Streptomyces manganisoli MK44T (96.8%). The whole genome size of strain SCSIO 64649T was 6.63 Mbp with a 73.6% G + C content. The average nucleotide identity and digital DNA–DNA hybridization between strain SCSIO 64649T and its closest related species were well below the thresholds recommended for species delineation. Therefore, according to the results of polyphasic taxonomy analysis, the strains SCSIO 64649T and SCSIO 03032 are proposed to represent a novel species named Streptomyces marincola sp. nov. Furthermore, strains SCSIO 64649T and 03032 encode 37 putative biosynthetic gene clusters, and in silico analysis revealed that this new species has a high potential to produce unique natural products, such as a novel polyene polyketide compounds, two mayamycin analogs, and a series of post-translationally modified peptides. In addition, other important bioactive natural products, such as heronamide F, piericidin A1, and spiroindimicin A, were also detected in strain SCSIO 64649T. Finally, this new species’ metabolic crude extract showed a strong antimicrobial activity. Thanks to the integration of all these analyses, this study demonstrates that the novel species Streptomyces marincola has a unique and novel secondary metabolite biosynthetic potential that not only is beneficial to possible marine hosts but that could also be exploited for industrial applications.
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Affiliation(s)
- Songbiao Shi
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Chinese Academy of Sciences, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Linqing Cui
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Chinese Academy of Sciences, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Kun Zhang
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Chinese Academy of Sciences, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qi Zeng
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Chinese Academy of Sciences, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qinglian Li
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Chinese Academy of Sciences, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Liang Ma
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Chinese Academy of Sciences, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Lijuan Long
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Chinese Academy of Sciences, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Xinpeng Tian
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Chinese Academy of Sciences, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
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5
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Seipp K, Geske L, Opatz T. Marine Pyrrole Alkaloids. Mar Drugs 2021; 19:514. [PMID: 34564176 PMCID: PMC8471394 DOI: 10.3390/md19090514] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/05/2021] [Accepted: 09/07/2021] [Indexed: 12/13/2022] Open
Abstract
Nitrogen heterocycles are essential parts of the chemical machinery of life and often reveal intriguing structures. They are not only widespread in terrestrial habitats but can also frequently be found as natural products in the marine environment. This review highlights the important class of marine pyrrole alkaloids, well-known for their diverse biological activities. A broad overview of the marine pyrrole alkaloids with a focus on their isolation, biological activities, chemical synthesis, and derivatization covering the decade from 2010 to 2020 is provided. With relevant structural subclasses categorized, this review shall provide a clear and timely synopsis of this area.
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Affiliation(s)
| | | | - Till Opatz
- Department of Chemistry, Organic Chemistry Section, Johannes Gutenberg University, Duesbergweg 10–14, 55128 Mainz, Germany; (K.S.); (L.G.)
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6
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Zhang Z, Ray S, Imlay L, Callaghan LT, Niederstrasser H, Mallipeddi PL, Posner BA, Wetzel DM, Phillips MA, Smith MW. Total synthesis of (+)-spiroindimicin A and congeners unveils their antiparasitic activity. Chem Sci 2021; 12:10388-10394. [PMID: 34377425 PMCID: PMC8336461 DOI: 10.1039/d1sc02838c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/25/2021] [Indexed: 12/02/2022] Open
Abstract
The spiroindimicins are a unique class of chlorinated indole alkaloids characterized by three heteroaromatic rings structured around a congested spirocyclic stereocenter. Here, we report the first total synthesis of (+)-spiroindimicin A, which bears a challenging C-3′/C-5′′-linked spiroindolenine. We detail our initial efforts to effect a biomimetic oxidative spirocyclization from its proposed natural precursor, lynamicin D, and describe how these studies shaped our final abiotic 9-step solution to this complex alkaloid built around a key Pd-catalyzed asymmetric spirocyclization. Scalable access to spiroindimicins A, H, and their congeners has enabled discovery of their activity against several parasites relevant to human health, providing potential starting points for new therapeutics for the neglected tropical diseases leishmaniasis and African sleeping sickness. Spiroindimicins A and H have been synthesized for the first time via a key palladium-catalyzed spirocyclization. Access to these alkaloids and several congeners has allowed the discovery of their antiparasitic properties.![]()
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Affiliation(s)
- Zhen Zhang
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Sneha Ray
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Leah Imlay
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Lauren T Callaghan
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA .,Department of Pediatrics, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Hanspeter Niederstrasser
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Prema Latha Mallipeddi
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Bruce A Posner
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Dawn M Wetzel
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA .,Department of Pediatrics, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Margaret A Phillips
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Myles W Smith
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
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7
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Abstract
Lankacidins are a class of polyketide natural products isolated from Streptomyces spp. that show promising antimicrobial activity. Owing to their complex molecular architectures and chemical instability, structural assignment and derivatization of lankacidins are challenging tasks. Herein we describe three fully synthetic approaches to lankacidins that enable access to new structural variability within the class. We use these routes to systematically generate stereochemical derivatives of both cyclic and acyclic lankacidins. Additionally, we access a new series of lankacidins bearing a methyl group at the C4 position, a modification intended to increase chemical stability. In the course of this work, we discovered that the reported structures for two natural products of the lankacidin class were incorrect, and we determine the correct structures of 2,18-seco-lankacidinol B and iso-lankacidinol. We also evaluate the ability of several iso- and seco-lankacidins to inhibit the growth of bacteria and to inhibit translation in vitro. This work grants insight into the rich chemical complexity of this class of antibiotics and provides an avenue for further structural derivatization.
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Affiliation(s)
- Lingchao Cai
- Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jinagsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing, 210037 Jiangsu, China
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California 94158, United States
| | - Yanmin Yao
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California 94158, United States
| | - Seul Ki Yeon
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California 94158, United States
| | - Ian B Seiple
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California 94158, United States
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8
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Ma L, Zhang W, Liu Z, Huang Y, Zhang Q, Tian X, Zhang C, Zhu Y. Complete genome sequence of Streptomyces sp. SCSIO 03032 isolated from Indian Ocean sediment, producing diverse bioactive natural products. Mar Genomics 2020; 55:100803. [PMID: 33517980 DOI: 10.1016/j.margen.2020.100803] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/19/2020] [Accepted: 06/25/2020] [Indexed: 12/13/2022]
Abstract
Streptomyces sp. SCSIO 03032, isolated from a deep-sea sediment sample (-3412 m) from the Indian Ocean, produces several classes of bioactive compounds including α-pyridone antibiotics (piericidins), polycyclic macrolactams (heronamides) and bisindole alkaloids (spiroindimicins, indimicins and lynamicins). Here we report the complete genome sequence of Streptomyces sp. SCSIO 03032, which consists of a 6,287,975 bp linear chromosome. The genome analysis reveals the presence of 29 putative biosynthetic gene clusters for secondary metabolites, including those for piericidins, heronamides and spiroindimicins/indimicins/lynamicins. The genome sequence suggests that Streptomyces sp. SCSIO 03032 could be a producer for novel bioactive natural products with potential applications in drug discovery.
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Affiliation(s)
- Liang Ma
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy 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; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Wenjun Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy 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; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Zhiwen Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy 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; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Yanbing Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy 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; Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning 530007, China
| | - Qingbo Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy 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; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Xinpeng Tian
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy 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; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Changsheng Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy 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; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Yiguang Zhu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy 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; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.
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9
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Widmann C, Ismail M, Sewald N, Niemann HH. Structure of apo flavin-dependent halogenase Xcc4156 hints at a reason for cofactor-soaking difficulties. Acta Crystallogr D Struct Biol 2020; 76:687-697. [PMID: 32627741 PMCID: PMC7336383 DOI: 10.1107/s2059798320007731] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 06/05/2020] [Indexed: 01/18/2023] Open
Abstract
Flavin-dependent halogenases regioselectively introduce halide substituents into electron-rich substrates under mild reaction conditions. For the enzyme Xcc4156 from Xanthomonas campestris, the structure of a complex with the cofactor flavin adenine dinucleotide (FAD) and a bromide ion would be of particular interest as this enzyme exclusively brominates model substrates in vitro. Apo Xcc4156 crystals diffracted to 1.6 Å resolution. The structure revealed an open substrate-binding site lacking the loop regions that close off the active site and contribute to substrate binding in tryptophan halogenases. Therefore, Xcc4156 might accept larger substrates, possibly even peptides. Soaking of apo Xcc4156 crystals with FAD led to crumbling of the intergrown crystals. Around half of the crystals soaked with FAD did not diffract, while in the others there was no electron density for FAD. The FAD-binding loop, which changes its conformation between the apo and the FAD-bound form in related enzymes, is involved in a crystal contact in the apo Xcc4156 crystals. The conformational change that is predicted to occur upon FAD binding would disrupt this crystal contact, providing a likely explanation for the destruction of the apo crystals in the presence of FAD. Soaking with only bromide did not result in bromide bound to the catalytic halide-binding site. Simultaneous soaking with FAD and bromide damaged the crystals more severely than soaking with only FAD. Together, these latter two observations suggest that FAD and bromide bind to Xcc4156 with positive cooperativity. Thus, apo Xcc4156 crystals provide functional insight into FAD and bromide binding, even though neither the cofactor nor the halide is visible in the structure.
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Affiliation(s)
- Christiane Widmann
- Structural Biochemistry (BCIV), Department of Chemistry, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Mohamed Ismail
- Organic and Bioorganic Chemistry (OC III), Department of Chemistry, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Norbert Sewald
- Organic and Bioorganic Chemistry (OC III), Department of Chemistry, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Hartmut H. Niemann
- Structural Biochemistry (BCIV), Department of Chemistry, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
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10
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Chu L, Huang J, Muhammad M, Deng Z, Gao J. Genome mining as a biotechnological tool for the discovery of novel marine natural products. Crit Rev Biotechnol 2020; 40:571-589. [PMID: 32308042 DOI: 10.1080/07388551.2020.1751056] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Compared to terrestrial environments, the oceans harbor a variety of environments, creating higher biodiversity, which gives marine natural products a high occurrence of significant biology and novel chemistry. However, traditional bioassay-guided isolation and purification strategies are severely limiting the discovery of additional novel natural products from the ocean. With an increasing number of marine microorganisms being sequenced, genome mining is gradually becoming a powerful tool to retrieve novel marine natural products. In this review, we have summarized genome mining approaches used to analyze key enzymes of biosynthetic pathways and predict the chemical structure of new gene clusters by introducing successful stories that used genome mining strategy to identify new marine-derived compounds. Furthermore, we also put forward challenges for genome mining techniques and their proposed solutions. The detailed analysis of the genome mining strategy will help researchers to understand this novel technique and its application. With the development of a genome sequence, genome mining strategies will be applied more widely, which will drive rapid development in the field of marine natural product development.
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Affiliation(s)
- Leixia Chu
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jinping Huang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mustafa Muhammad
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiangtao Gao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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11
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A Co-Culturing Approach Enables Discovery and Biosynthesis of a Bioactive Indole Alkaloid Metabolite. Molecules 2020; 25:molecules25020256. [PMID: 31936318 PMCID: PMC7024260 DOI: 10.3390/molecules25020256] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/26/2019] [Accepted: 01/03/2020] [Indexed: 12/19/2022] Open
Abstract
Whole-genome sequence data of the genus Streptomyces have shown a far greater chemical diversity of metabolites than what have been discovered under typical laboratory fermentation conditions. In our previous natural product discovery efforts on Streptomyces sp. MA37, a bacterium isolated from the rhizosphere soil sample in Legon, Ghana, we discovered a handful of specialised metabolites from this talented strain. However, analysis of the draft genome of MA37 suggested that most of the encoded biosynthetic gene clusters (BGCs) remained cryptic or silent, and only a small fraction of BGCs for the production of specialised metabolites were expressed when cultured in our laboratory conditions. In order to induce the expression of the seemingly silent BGCs, we have carried out a co-culture experiment by growing the MA37 strain with the Gram-negative bacterium Pseudomonas sp. in a co-culture chamber that allows co-fermentation of two microorganisms with no direct contact but allows exchange of nutrients, metabolites, and other chemical cues. This co-culture approach led to the upregulation of several metabolites that were not previously observed in the monocultures of each strain. Moreover, the co-culture induced the expression of the cryptic indole alkaloid BGC in MA37 and led to the characterization of the known indolocarbazole alkaloid, BE-13793C 1. Neither bacterium produced compound 1 when cultured alone. The structure of 1 was elucidated by Nuclear Magnetic Resonance (NMR), mass spectrometry analyses and comparison of experimental with literature data. A putative biosynthetic pathway of 1 was proposed. Furthermore, BE-13793C 1 showed strong anti-proliferative activity against HT-29 (ATCC HTB-38) cells but no toxic effect to normal lung (ATCC CCL-171) cells. To the best of our knowledge, this is the first report for the activity of 1 against HT-29. No significant antimicrobial and anti-trypanosomal activities for 1 were observed. This research provides a solid foundation for the fact that a co-culture approach paves the way for increasing the chemical diversity of strain MA37. Further characterization of other upregulated metabolites in this strain is currently ongoing in our laboratory.
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12
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Extreme Environment Streptomyces: Potential Sources for New Antibacterial and Anticancer Drug Leads? Int J Microbiol 2019; 2019:5283948. [PMID: 31354829 PMCID: PMC6636559 DOI: 10.1155/2019/5283948] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/22/2019] [Indexed: 01/20/2023] Open
Abstract
Antimicrobial resistance (AR) is recognized as one of the greatest threats to public health and in global concern. Consequently, the increased morbidity and mortality, which are associated with multidrug resistance bacteria, urgently require the discovery of novel and more efficient drugs. Conversely, cancer is a growing complex human disease that demands new drugs with no or fewer side effects. Most of the drugs currently used in the health care systems were of Streptomyces origin or their synthetic forms. Natural product researches from Streptomyces have been genuinely spectacular over the recent years from extreme environments. It is because of technical advances in isolation, fermentation, spectroscopy, and genomic studies which led to the efficient recovering of Streptomyces and their new chemical compounds with distinct activities. Expanding the use of the last line of antibiotics and demand for new drugs will continue to play an essential role for the potent Streptomyces from previously unexplored environmental sources. In this context, deep-sea, desert, cryo, and volcanic environments have proven to be a unique habitat of more extreme, and of their adaptation to extreme living, environments attribute to novel antibiotics. Extreme Streptomyces have been an excellent source of a new class of compounds which include alkaloids, angucycline, macrolide, and peptides. This review covers novel drug leads with antibacterial and cytotoxic activities isolated from deep-sea, desert, cryo, and volcanic environment Streptomyces from 2009 to 2019. The structure and chemical classes of the compounds, their relevant bioactivities, and the sources of organisms are presented.
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Chen LY, Cui HT, Su C, Bai FW, Zhao XQ. Analysis of the complete genome sequence of a marine-derived strain Streptomyces sp. S063 CGMCC 14582 reveals its biosynthetic potential to produce novel anti-complement agents and peptides. PeerJ 2019; 7:e6122. [PMID: 30627488 PMCID: PMC6321760 DOI: 10.7717/peerj.6122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/12/2018] [Indexed: 12/12/2022] Open
Abstract
Genome sequences of marine streptomycetes are valuable for the discovery of useful enzymes and bioactive compounds by genome mining. However, publicly available complete genome sequences of marine streptomycetes are still limited. Here, we present the complete genome sequence of a marine streptomycete Streptomyces sp. S063 CGMCC 14582. Species delineation based on the pairwise digital DNA-DNA hybridization and genome comparison ANI (average nucleotide identity) value showed that Streptomyces sp. S063 CGMCC 14582 possesses a unique genome that is clearly different from all of the other available genomes. Bioactivity tests showed that Streptomyces sp. S063 CGMCC 14582 produces metabolites with anti-complement activities, which are useful for treatment of numerous diseases that arise from inappropriate activation of the human complement system. Analysis of the genome reveals no biosynthetic gene cluster (BGC) which shows even low similarity to that of the known anti-complement agents was detected in the genome, indicating that Streptomyces sp. S063 CGMCC 14582 may produce novel anti-complement agents of microbial origin. Four BGCs which are potentially involved in biosynthesis of non-ribosomal peptides were disrupted, but no decrease of anti-complement activities was observed, suggesting that these four BGCs are not involved in biosynthesis of the anti-complement agents. In addition, LC-MS/MS analysis and subsequent alignment through the Global Natural Products Social Molecular Networking (GNPS) platform led to the detection of novel peptides produced by the strain. Streptomyces sp. S063 CGMCC 14582 grows rapidly and is salt tolerant, which benefits efficient secondary metabolite production via seawater-based fermentation. Our results indicate that Streptomyces sp. S063 has great potential to produce novel bioactive compounds, and also is a good host for heterologous production of useful secondary metabolites for drug discovery.
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Affiliation(s)
- Liang-Yu Chen
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,School Life Science and Biotechnology, Dalian University of Technology, Dalian, Liaoning, China
| | - Hao-Tian Cui
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chun Su
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Feng-Wu Bai
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Liu Z, Ma L, Zhang L, Zhang W, Zhu Y, Chen Y, Zhang W, Zhang C. Functional characterization of the halogenase SpmH and discovery of new deschloro-tryptophan dimers. Org Biomol Chem 2019; 17:1053-1057. [DOI: 10.1039/c8ob02775g] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Inactivation of the halogenase gene spmH led to discovery of four new deschloro-tryptophan dimers. SpmH was further biochemically characterized in vitro as an l-tryptophan 5-halogenase.
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Affiliation(s)
- Zhiwen Liu
- 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
| | - 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
| | - 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
| | - Wenjun 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
| | - 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
| | - Yuchan Chen
- State Key Laboratory of Applied Microbiology Southern China
- Guangdong Institute of Microbiology
- Guangzhou 510070
- China
| | - Weimin Zhang
- State Key Laboratory of Applied Microbiology Southern China
- Guangdong Institute of Microbiology
- Guangzhou 510070
- 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
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Nepal KK, Wang G. Streptomycetes: Surrogate hosts for the genetic manipulation of biosynthetic gene clusters and production of natural products. Biotechnol Adv 2019; 37:1-20. [PMID: 30312648 PMCID: PMC6343487 DOI: 10.1016/j.biotechadv.2018.10.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/04/2018] [Accepted: 10/05/2018] [Indexed: 12/23/2022]
Abstract
Due to the worldwide prevalence of multidrug-resistant pathogens and high incidence of diseases such as cancer, there is an urgent need for the discovery and development of new drugs. Nearly half of the FDA-approved drugs are derived from natural products that are produced by living organisms, mainly bacteria, fungi, and plants. Commercial development is often limited by the low yield of the desired compounds expressed by the native producers. In addition, recent advances in whole genome sequencing and bioinformatics have revealed an abundance of cryptic biosynthetic gene clusters within microbial genomes. Genetic manipulation of clusters in the native host is commonly used to awaken poorly expressed or silent gene clusters, however, the lack of feasible genetic manipulation systems in many strains often hinders our ability to engineer the native producers. The transfer of gene clusters into heterologous hosts for expression of partial or entire biosynthetic pathways is an approach that can be used to overcome this limitation. Heterologous expression also facilitates the chimeric fusion of different biosynthetic pathways, leading to the generation of "unnatural" natural products. The genus Streptomyces is especially known to be a prolific source of drugs/antibiotics, its members are often used as heterologous expression hosts. In this review, we summarize recent applications of Streptomyces species, S. coelicolor, S. lividans, S. albus, S. venezuelae and S. avermitilis, as heterologous expression systems.
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Affiliation(s)
- Keshav K Nepal
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 U.S. 1 North, Fort Pierce, FL 34946, USA
| | - Guojun Wang
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 U.S. 1 North, Fort Pierce, FL 34946, USA.
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