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Patil RS, Sharma S, Bhaskarwar AV, Nambiar S, Bhat NA, Koppolu MK, Bhukya H. TetR and OmpR family regulators in natural product biosynthesis and resistance. Proteins 2023. [PMID: 37874037 DOI: 10.1002/prot.26621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 08/30/2023] [Accepted: 10/06/2023] [Indexed: 10/25/2023]
Abstract
This article provides a comprehensive review and sequence-structure analysis of transcription regulator (TR) families, TetR and OmpR/PhoB, involved in specialized secondary metabolite (SSM) biosynthesis and resistance. Transcription regulation is a fundamental process, playing a crucial role in orchestrating gene expression to confer a survival advantage in response to frequent environmental stress conditions. This process, coupled with signal sensing, enables bacteria to respond to a diverse range of intra and extracellular signals. Thus, major bacterial signaling systems use a receptor domain to sense chemical stimuli along with an output domain responsible for transcription regulation through DNA-binding. Sensory and output domains on a single polypeptide chain (one component system, OCS) allow response to stimuli by allostery, that is, DNA-binding affinity modulation upon signal presence/absence. On the other hand, two component systems (TCSs) allow cross-talk between the sensory and output domains as they are disjoint and transmit information by phosphorelay to mount a response. In both cases, however, TRs play a central role. Biosynthesis of SSMs, which includes antibiotics, is heavily regulated by TRs as it diverts the cell's resources towards the production of these expendable compounds, which also have clinical applications. These TRs have evolved to relay information across specific signals and target genes, thus providing a rich source of unique mechanisms to explore towards addressing the rapid escalation in antimicrobial resistance (AMR). Here, we focus on the TetR and OmpR family TRs, which belong to OCS and TCS, respectively. These TR families are well-known examples of regulators in secondary metabolism and are ubiquitous across different bacteria, as they also participate in a myriad of cellular processes apart from SSM biosynthesis and resistance. As a result, these families exhibit higher sequence divergence, which is also evident from our bioinformatic analysis of 158 389 and 77 437 sequences from TetR and OmpR family TRs, respectively. The analysis of both sequence and structure allowed us to identify novel motifs in addition to the known motifs responsible for TR function and its structural integrity. Understanding the diverse mechanisms employed by these TRs is essential for unraveling the biosynthesis of SSMs. This can also help exploit their regulatory role in biosynthesis for significant pharmaceutical, agricultural, and industrial applications.
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Affiliation(s)
- Rachit S Patil
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Siddhant Sharma
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Aditya V Bhaskarwar
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Souparnika Nambiar
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Niharika A Bhat
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Mani Kanta Koppolu
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Hussain Bhukya
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
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2
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Canko A, Athanassopoulou GD, Psycharis V, Raptopoulou CP, Herniman JM, Mouchtouris V, Foscolos AS, Couladouros EA, Vidali VP. First total synthesis of type II abyssomicins: (±)-abyssomicin 2 and (±)-neoabyssomicin B. Org Biomol Chem 2023; 21:3761-3765. [PMID: 37083981 DOI: 10.1039/d3ob00476g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
The intramolecular Diels-Alder reaction (IMDA) of a butenolide derivative, as an entry to the type II abyssomicin scaffold, and the total synthesis of (±)-abyssomicin 2 and (±)-neoabyssomicin B are reported for the first time. A facile route to the IMDA precursor, the formation of a type I intermediate and two paths to (±)-neoabyssomicin B are also discussed.
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Affiliation(s)
- Aleksander Canko
- Institute of Nanoscience & Nanotechnology, NCSR "Demokritos", Ag. Paraskevi, Athens, Greece.
- Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | | | - Vassilis Psycharis
- Institute of Nanoscience & Nanotechnology, NCSR "Demokritos", Ag. Paraskevi, Athens, Greece.
| | - Catherine P Raptopoulou
- Institute of Nanoscience & Nanotechnology, NCSR "Demokritos", Ag. Paraskevi, Athens, Greece.
| | - Julie M Herniman
- Faculty of Engineering and Physical Sciences, School of Chemistry, University of Southampton, Highfield, Southampton, UK
| | - Vasileios Mouchtouris
- Nano-Science Center and Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Angeliki Sofia Foscolos
- Institute of Nanoscience & Nanotechnology, NCSR "Demokritos", Ag. Paraskevi, Athens, Greece.
| | - Elias A Couladouros
- Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Veroniki P Vidali
- Institute of Nanoscience & Nanotechnology, NCSR "Demokritos", Ag. Paraskevi, Athens, Greece.
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3
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Tian W, Chen X, Zhang J, Zheng M, Wei G, Deng Z, Qu X. Biosynthesis of Tetronates by a Nonribosomal Peptide Synthetase-Polyketide Synthase System. Org Lett 2023; 25:1628-1632. [PMID: 36876998 DOI: 10.1021/acs.orglett.3c00103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
A cryptic tetronate biosynthetic pathway was identified in Kitasatospora niigatensis DSM 44781 via heterologous expression. Distinct from the currently known biosynthetic pathways, this system utilizes a partially functional nonribosomal peptide synthetase and a broadly selective polyketide synthase to direct the assembly and lactonization of the tetronate scaffold. By employing a permissive crotonyl-CoA reductase/carboxylase to provide different extender units, seven new tetronates (kitaniitetronins A-G) were obtained via precursor-directed biosynthesis.
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Affiliation(s)
- Wenya Tian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xinru Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Jun Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mengmeng Zheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Guangzheng Wei
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Xudong Qu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
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4
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Devine AJ, Parnell AE, Back CR, Lees NR, Johns ST, Zulkepli AZ, Barringer R, Zorn K, Stach JEM, Crump MP, Hayes MA, van der Kamp MW, Race PR, Willis CL. The Role of Cytochrome P450 AbyV in the Final Stages of Abyssomicin C Biosynthesis. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202213053. [PMID: 38516347 PMCID: PMC10952897 DOI: 10.1002/ange.202213053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Indexed: 03/23/2024]
Abstract
Abyssomicin C and its atropisomer are potent inhibitors of bacterial folate metabolism. They possess complex polycyclic structures, and their biosynthesis has been shown to involve several unusual enzymatic transformations. Using a combination of synthesis and in vitro assays we reveal that AbyV, a cytochrome P450 enzyme from the aby gene cluster, catalyses a key late-stage epoxidation required for the installation of the characteristic ether-bridged core of abyssomicin C. The X-ray crystal structure of AbyV has been determined, which in combination with molecular dynamics simulations provides a structural framework for our functional data. This work demonstrates the power of combining selective carbon-13 labelling with NMR spectroscopy as a sensitive tool to interrogate enzyme-catalysed reactions in vitro with no need for purification.
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Affiliation(s)
| | | | | | | | | | | | - Rob Barringer
- School of BiochemistryUniversity of BristolBS81TDBristolUK
| | - Katja Zorn
- BioPharmaceuticals R&DAstraZenecaPepparedsleden 143183MölndalSweden
| | - James E. M. Stach
- School of Natural and Environmental SciencesNewcastle UniversityNE17RUNewcastle-upon-TyneUK
| | | | - Martin A. Hayes
- BioPharmaceuticals R&DAstraZenecaPepparedsleden 143183MölndalSweden
| | | | - Paul R. Race
- School of BiochemistryUniversity of BristolBS81TDBristolUK
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5
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Devine AJ, Parnell AE, Back CR, Lees NR, Johns ST, Zulkepli AZ, Barringer R, Zorn K, Stach JEM, Crump MP, Hayes MA, van der Kamp MW, Race PR, Willis CL. The Role of Cytochrome P450 AbyV in the Final Stages of Abyssomicin C Biosynthesis. Angew Chem Int Ed Engl 2023; 62:e202213053. [PMID: 36314667 PMCID: PMC10107801 DOI: 10.1002/anie.202213053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/16/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022]
Abstract
Abyssomicin C and its atropisomer are potent inhibitors of bacterial folate metabolism. They possess complex polycyclic structures, and their biosynthesis has been shown to involve several unusual enzymatic transformations. Using a combination of synthesis and in vitro assays we reveal that AbyV, a cytochrome P450 enzyme from the aby gene cluster, catalyses a key late-stage epoxidation required for the installation of the characteristic ether-bridged core of abyssomicin C. The X-ray crystal structure of AbyV has been determined, which in combination with molecular dynamics simulations provides a structural framework for our functional data. This work demonstrates the power of combining selective carbon-13 labelling with NMR spectroscopy as a sensitive tool to interrogate enzyme-catalysed reactions in vitro with no need for purification.
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Affiliation(s)
- Andrew J Devine
- School of Chemistry, University of Bristol, BS81TS, Bristol, UK
| | - Alice E Parnell
- School of Biochemistry, University of Bristol, BS81TD, Bristol, UK
| | - Catherine R Back
- School of Biochemistry, University of Bristol, BS81TD, Bristol, UK
| | - Nicholas R Lees
- School of Chemistry, University of Bristol, BS81TS, Bristol, UK
| | - Samuel T Johns
- School of Biochemistry, University of Bristol, BS81TD, Bristol, UK
| | - Ainul Z Zulkepli
- School of Biochemistry, University of Bristol, BS81TD, Bristol, UK
| | - Rob Barringer
- School of Biochemistry, University of Bristol, BS81TD, Bristol, UK
| | - Katja Zorn
- BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - James E M Stach
- School of Natural and Environmental Sciences, Newcastle University, NE17RU, Newcastle-upon-Tyne, UK
| | - Matthew P Crump
- School of Chemistry, University of Bristol, BS81TS, Bristol, UK
| | - Martin A Hayes
- BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden
| | | | - Paul R Race
- School of Biochemistry, University of Bristol, BS81TD, Bristol, UK
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6
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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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7
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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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8
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Little RF, Hertweck C. Chain release mechanisms in polyketide and non-ribosomal peptide biosynthesis. Nat Prod Rep 2021; 39:163-205. [PMID: 34622896 DOI: 10.1039/d1np00035g] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Review covering up to mid-2021The structure of polyketide and non-ribosomal peptide natural products is strongly influenced by how they are released from their biosynthetic enzymes. As such, Nature has evolved a diverse range of release mechanisms, leading to the formation of bioactive chemical scaffolds such as lactones, lactams, diketopiperazines, and tetronates. Here, we review the enzymes and mechanisms used for chain release in polyketide and non-ribosomal peptide biosynthesis, how these mechanisms affect natural product structure, and how they could be utilised to introduce structural diversity into the products of engineered biosynthetic pathways.
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Affiliation(s)
- Rory F Little
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
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9
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Abyssomicins-A 20-Year Retrospective View. Mar Drugs 2021; 19:md19060299. [PMID: 34073764 PMCID: PMC8225091 DOI: 10.3390/md19060299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 12/15/2022] Open
Abstract
Abyssomicins represent a new family of polycyclic macrolactones. The first described compounds of the abyssomicin family were abyssomicin B, C, atrop-C, and D, produced by the marine actinomycete strain Verrucosispora maris AB-18-032, which was isolated from a sediment collected in the Sea of Japan. Among the described abyssomicins, only abyssomicin C and atrop-abyssomicin C show a high antibiotic activity against Gram-positive bacteria, including multi-resistant and vancomycin-resistant strains. The inhibitory activity is caused by a selective inhibition of the enzyme 4-amino-4-deoxychorismate synthase, which catalyzes the transformation of chorismate to para-aminobenzoic acid, an intermediate in the folic acid pathway.
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10
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Bunbamrung N, Kittisrisopit S, Intaraudom C, Dramae A, Thawai C, Niemhom N, Harding DJ, Auncharoen P, Pittayakhajonwut P. Abyssomicin derivatives from the rhizosphere soil actinomycete Microbispora rhizosphaerae sp. nov. TBRC6028. PHYTOCHEMISTRY 2021; 185:112700. [PMID: 33647781 DOI: 10.1016/j.phytochem.2021.112700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
Three undescribed abyssomicin derivatives, including microbimisin, abyssomicins Z1, and Z2, were isolated from the soil actinomycete Microbispora rhizosphaerae sp. nov. TBRC6028. Chemical structures were determined by NMR spectroscopic data (1H, 13C, COSY, HSQC, HMBC, and NOESY spectra) and the absolute configurations were verified by single-crystal X-ray diffraction analyses together with the ECD spectral data. Microbimisin and abyssomicin Z1 exhibited weak antibacterial activity against Bacillus cereus with MIC values of 25.0 and 50.0 μg/mL without cytotoxicity against MCF-7 and Vero cells at the concentration of 50 μg/mL.
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Affiliation(s)
- Nantiya Bunbamrung
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phaholyothin Road, Klong Luang, Pathumthani, 12120, Thailand
| | - Suchada Kittisrisopit
- Department of biology, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand
| | - Chakapong Intaraudom
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phaholyothin Road, Klong Luang, Pathumthani, 12120, Thailand
| | - Aibrohim Dramae
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phaholyothin Road, Klong Luang, Pathumthani, 12120, Thailand
| | - Chitti Thawai
- Department of biology, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand; Antinobacterial Research Unit, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand; Center of Excellence in Applied Biosciences, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand
| | - Nantawan Niemhom
- Scientific Instruments Centre, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand
| | - David J Harding
- Functional Materials and Nanotechnology Center of Excellence, Walailak University, Thasala, Nakhon Si Thammarat, 80160, Thailand
| | - Patchanee Auncharoen
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phaholyothin Road, Klong Luang, Pathumthani, 12120, Thailand
| | - Pattama Pittayakhajonwut
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phaholyothin Road, Klong Luang, Pathumthani, 12120, Thailand.
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11
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Songsumanus A, Kuncharoen N, Kudo T, Yuki M, Ohkuma M, Igarashi Y, Tanasupawat S. Actinomadura decatromicini sp. nov., isolated from mountain soil in Thailand. J Antibiot (Tokyo) 2021; 74:51-58. [PMID: 32724099 DOI: 10.1038/s41429-020-0353-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/27/2020] [Accepted: 07/02/2020] [Indexed: 11/08/2022]
Abstract
A novel actinomycete strain CYP1-5T was isolated from the mountain soil sample collected from Chaiyaphum province, Thailand and its taxonomic position was clarified by using a polyphasic taxonomic approach. The chemotaxonomic properties of strain CYP1-5T were consistent within the genus Actinomadura. Cell-wall peptidoglycan of this strain contained meso-diaminopimelic acid. Galactose, madurose, and ribose were presented as the diagnostic sugars in whole-cell hydrolysates. The major menaquinone was MK-9(H6). Major cellular fatty acids were iso-C16:0 and C16:0. Phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, and phosphatidylinositol mannoside were observed as predominant phospholipids. Based on the results of phylogenetic analyses of 16S rRNA gene sequence, strain CYP1-5T was constituent with the genus Actinomadura and was closely related to Actinomadura syzygii GKU157T (99.5%) and Actinomadura chibensis IFM 10266T (= JCM 14158T) (98.2%). The draft genome size of strain CYP1-5T was 9.30 Mb with 72.2 mol% of G + C content. Strain CYP1-5T showed ANIb values of 94.9% with A. syzygii GKU157T and 93.2% with A. chibensis JCM 14158T. Phenotypic characteristics, phylogenetic analysis and genome data support that strain CYP1-5T could be discriminated from its closest relatives, representing a novel species of the genus Actinomadura, for which the name Actinomadura decatromicini sp. nov. is proposed. The type strain is CYP1-5T (= JCM 16996T = KCTC 19916T = TISTR 2901T).
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Affiliation(s)
| | - Nattakorn Kuncharoen
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Masahiro Yuki
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Yasuhiro Igarashi
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand.
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12
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Mo X, Yang S. Complete Genome of Nocamycin-Producing Strain Saccharothrix syringae NRRL B-16468 Reveals the Biosynthetic Potential for Secondary Metabolites. Curr Microbiol 2020; 78:107-113. [PMID: 33136202 DOI: 10.1007/s00284-020-02272-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/22/2020] [Indexed: 11/29/2022]
Abstract
The bacterium Saccharothrix syringae NRRL B-16468 is the producer of nocamycin I and nocamycin II which feature tetramic acid and bicyclic ketal groups. In this study, we presented the complete genome of S. syringae NRRL B-16468 obtained from ARS Culture Collection. It contains a circular chromosome of 10,929,570 bp with an average GC content of 73.49%, 9316 genes, 12 rRNAs and 54 tRNAs. Bioinformatics analyses of the genome has demonstrated that it harbors 55 putative biosynthetic gene clusters (BGCs) involved in synthesizing diverse secondary metabolites. The backbones of the natural products synthesized by these BGCs encoding for type I polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS) and hybrid type I PKS-NRPS were analyzed, furthermore, the natural products synthesized by these BGCs with > 40% similarity to known BGCs were described in detail. The complete genome of S. syringae reveals its capacity in producing diverse bioactive natural products, and it will also shed lights on mining novel secondary metabolites from S. syringae through rational strategies.
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Affiliation(s)
- Xuhua Mo
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Song Yang
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
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13
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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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14
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Iglesias A, Latorre-Pérez A, Stach JEM, Porcar M, Pascual J. Out of the Abyss: Genome and Metagenome Mining Reveals Unexpected Environmental Distribution of Abyssomicins. Front Microbiol 2020; 11:645. [PMID: 32351480 PMCID: PMC7176366 DOI: 10.3389/fmicb.2020.00645] [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: 10/24/2019] [Accepted: 03/20/2020] [Indexed: 12/27/2022] Open
Abstract
Natural products have traditionally been discovered through the screening of culturable microbial isolates from diverse environments. The sequencing revolution allowed the identification of dozens of biosynthetic gene clusters (BGCs) within single bacterial genomes, either from cultured or uncultured strains. However, we are still far from fully exploiting the microbial reservoir, as most of the species are non-model organisms with complex regulatory systems that can be recalcitrant to engineering approaches. Genomic and metagenomic data produced by laboratories worldwide covering the range of natural and artificial environments on Earth, are an invaluable source of raw information from which natural product biosynthesis can be accessed. In the present work, we describe the environmental distribution and evolution of the abyssomicin BGC through the analysis of publicly available genomic and metagenomic data. Our results demonstrate that the selection of a pathway-specific enzyme to direct genome mining is an excellent strategy; we identified 74 new Diels–Alderase homologs and unveiled a surprising prevalence of the abyssomicin BGC within terrestrial habitats, mainly soil and plant-associated. We also identified five complete and 12 partial new abyssomicin BGCs and 23 new potential abyssomicin BGCs. Our results strongly support the potential of genome and metagenome mining as a key preliminary tool to inform bioprospecting strategies aimed at the identification of new bioactive compounds such as -but not restricted to- abyssomicins.
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Affiliation(s)
- Alba Iglesias
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - James E M Stach
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.,Centre for Synthetic Biology and the Bioeconomy, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Manuel Porcar
- Darwin Bioprospecting Excellence S.L., Paterna, Spain.,Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, Paterna, Spain
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15
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Rego A, Sousa AGG, Santos JP, Pascoal F, Canário J, Leão PN, Magalhães C. Diversity of Bacterial Biosynthetic Genes in Maritime Antarctica. Microorganisms 2020; 8:microorganisms8020279. [PMID: 32085500 PMCID: PMC7074882 DOI: 10.3390/microorganisms8020279] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 02/06/2023] Open
Abstract
Bacterial natural products (NPs) are still a major source of new drug leads. Polyketides (PKs) and non-ribosomal peptides (NRP) are two pharmaceutically important families of NPs and recent studies have revealed Antarctica to harbor endemic polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes, likely to be involved in the production of novel metabolites. Despite this, the diversity of secondary metabolites genes in Antarctica is still poorly explored. In this study, a computational bioprospection approach was employed to study the diversity and identity of PKS and NRPS genes to one of the most biodiverse areas in maritime Antarctica—Maxwell Bay. Amplicon sequencing of soil samples targeting ketosynthase (KS) and adenylation (AD) domains of PKS and NRPS genes, respectively, revealed abundant and unexplored chemical diversity in this peninsula. About 20% of AD domain sequences were only distantly related to characterized biosynthetic genes. Several PKS and NRPS genes were found to be closely associated to recently described metabolites including those from uncultured and candidate phyla. The combination of new approaches in computational biology and new culture-dependent and -independent strategies is thus critical for the recovery of the potential novel chemistry encoded in Antarctica microorganisms.
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Affiliation(s)
- Adriana Rego
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal; (A.R.); (A.G.G.S.); (J.P.S.); (F.P.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
| | - António G. G. Sousa
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal; (A.R.); (A.G.G.S.); (J.P.S.); (F.P.)
| | - João P. Santos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal; (A.R.); (A.G.G.S.); (J.P.S.); (F.P.)
- Institute F.-A. Forel, Earth and Environmental Sciences, Faculty of Sciences, University of Geneva, 66, Boulevard Carl-Vogt, 1211 Genève 4, Switzerland
| | - Francisco Pascoal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal; (A.R.); (A.G.G.S.); (J.P.S.); (F.P.)
| | - João Canário
- Centro de Química Estrutural at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal;
| | - Pedro N. Leão
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal; (A.R.); (A.G.G.S.); (J.P.S.); (F.P.)
- Correspondence: (P.N.L); (C.M.)
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal; (A.R.); (A.G.G.S.); (J.P.S.); (F.P.)
- Faculty of Sciences, University of Porto, 4150-179 Porto, Portugal
- School of Science, University of Waikato, Hamilton 3216, New Zealand
- Correspondence: (P.N.L); (C.M.)
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16
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Zhang J, Li B, Qin Y, Karthik L, Zhu G, Hou C, Jiang L, Liu M, Ye X, Liu M, Hsiang T, Dai H, Zhang L, Liu X. A new abyssomicin polyketide with anti-influenza A virus activity from a marine-derived Verrucosispora sp. MS100137. Appl Microbiol Biotechnol 2020; 104:1533-1543. [PMID: 31894364 DOI: 10.1007/s00253-019-10217-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/16/2019] [Accepted: 10/22/2019] [Indexed: 12/29/2022]
Abstract
Marine microorganisms live in dramatically different environments and have attracted much attention for their structurally unique natural products with potential strong biological activity. Based on the one strain-many compounds (OSMAC) strategy and liquid chromatography mass spectrometry (LC-MS) methods, our continuing efforts on the investigation of novel active compounds from marine Verrucosispora sp. MS100137 has led to the identification of a new polycyclic metabolite, abyssomicin Y (1), together with six known abyssomicin and proximicin analogs (2-7). Abyssomicin Y is a type I abyssomicin with an epoxide group at C-8 and C-9. Compounds 1-3 showed potent inhibitory effects against the influenza A virus; their observed inhibition rates were 97.9%, 98.3%, and 95.9%, respectively, at a concentration of 10 μM, and they displayed lower cytotoxicity than 4. The structures were determined by different NMR techniques and HRMS experiments. This investigation revealed that OSMAC could serve as a useful method for enabling the activation of the silent genes in the microorganism and for the formation of previously unreported active secondary metabolites.
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Affiliation(s)
- Jingyu Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Bixiao Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.,Institute of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui Province, China.,Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yujie Qin
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Loganathan Karthik
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.,Sri Shakthi Institute of Engineering and Technology (Autonomous), Coimbatore, Tamil Nadu, India
| | - Guoliang Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Chengjian Hou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Lan Jiang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Miaomiao Liu
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD, 4111, Australia
| | - Xin Ye
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mei Liu
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Huanqin Dai
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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17
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Diversity of PKS and NRPS gene clusters between Streptomyces abyssomicinicus sp. nov. and its taxonomic neighbor. J Antibiot (Tokyo) 2019; 73:141-151. [PMID: 31853029 DOI: 10.1038/s41429-019-0261-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/23/2019] [Accepted: 11/12/2019] [Indexed: 11/08/2022]
Abstract
Streptomyces sp. CHI39, isolated from a rock soil sample, is a producer of abyssomicin I. The taxonomic status was clarified by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain was closely related to Streptomyces fragilis, with similarity of 99.9%. Strain CHI39 comprised LL-diaminopimelic acid, glutamic acid, glycine, and alanine in its peptidoglycan. The predominant menaquinones were MK-9(H6), and major fatty acids were anteiso-C15:0, anteiso-C17:0, and iso-C16:0. The chemotaxonomic features matched those described for the genus Streptomyces. Genome sequencing was conducted for strain CHI39 and S. fragilis NBRC 12862T. The results of digital DNA-DNA hybridization along with differences in phenotypic characteristics between the strains suggested strain CHI39 to be a novel species, for which Streptomyces abyssomicinicus sp. nov. is proposed; the type strain is CHI39T (=NBRC 110469T). Next, we surveyed polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) gene clusters in genomes of S. abyssomicinicus CHI39T and S. fragilis NBRC 12862T. These strains encoded 9 and 12 clusters, respectively, among which only four clusters were shared between them while the others are specific in each strain. This suggests that strains classified to distinct species each harbor many specific secondary metabolite-biosynthetic pathways even if the strains are taxonomically close.
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18
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Marsh CO, Lees NR, Han L, Byrne MJ, Mbatha SZ, Maschio L, Pagden‐Ratcliffe S, Duke PW, Stach JEM, Curnow P, Willis CL, Race PR. A Natural Diels‐Alder Biocatalyst Enables Efficient [4+2] Cycloaddition Under Harsh Reaction Conditions. ChemCatChem 2019. [DOI: 10.1002/cctc.201901285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Carl O. Marsh
- School of BiochemistryUniversity of Bristol Bristol BS8 1TD UK
- BrisSynBio Synthetic Biology Research CentreUniversity of Bristol Bristol BS8 1TQ UK
| | | | - Li‐Chen Han
- BrisSynBio Synthetic Biology Research CentreUniversity of Bristol Bristol BS8 1TQ UK
- School of ChemistryUniversity of Bristol Bristol BS8 1TS UK
| | - Matthew J. Byrne
- School of BiochemistryUniversity of Bristol Bristol BS8 1TD UK
- BrisSynBio Synthetic Biology Research CentreUniversity of Bristol Bristol BS8 1TQ UK
| | | | - Laurence Maschio
- School of BiochemistryUniversity of Bristol Bristol BS8 1TD UK
- BrisSynBio Synthetic Biology Research CentreUniversity of Bristol Bristol BS8 1TQ UK
| | | | - Phillip W. Duke
- Defense Science and Technology Laboratory Porton Down SP4 0JQ UK
| | - James E. M. Stach
- School of Natural and Environmental SciencesNewcastle University Newcastle-upon-Tyne NE1 7RU UK
- Centre for Synthetic Biology and the BioeconomyNewcastle University Newcastle-upon-Tyne NE2 4AX UK
| | - Paul Curnow
- School of BiochemistryUniversity of Bristol Bristol BS8 1TD UK
- BrisSynBio Synthetic Biology Research CentreUniversity of Bristol Bristol BS8 1TQ UK
| | - Christine L. Willis
- BrisSynBio Synthetic Biology Research CentreUniversity of Bristol Bristol BS8 1TQ UK
- School of ChemistryUniversity of Bristol Bristol BS8 1TS UK
| | - Paul R. Race
- School of BiochemistryUniversity of Bristol Bristol BS8 1TD UK
- BrisSynBio Synthetic Biology Research CentreUniversity of Bristol Bristol BS8 1TQ UK
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19
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Zhao YL, Cheng Y. Construction of Complex Bisether-Bridged Medium-Sized Cyclic Compounds from o-(1-(Acyloxy)propargyl)benzaldehydes under Base and Acid Catalysis. J Org Chem 2019; 84:11114-11124. [PMID: 31419137 DOI: 10.1021/acs.joc.9b01677] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report herein our serendipitous discovery of the rapid and straightforward accesses to unprecedented diverse complex molecular structures from readily available starting materials. Catalyzed by 1,8-diazabicyclo[5.4.0]undec-7-ene under mild conditions, o-(1-(acyloxy)propargyl)benzaldehydes 1 underwent efficient and selective dimerization reactions to produce novel complex bisether-bridged tricyclic products 3 and 4. The reactions proceeded most probably through dimerizations between 3-methylene-3H-isochromene intermediate and its zwitterionic resonance structures which were generated from a concerted 6-π electrocyclic ring closure reaction from the initially formed (2-formylphenyl)allene intermediates derived directly from o-(1-(acyloxy)propargyl)benzaldehydes. Treatment of the resulting product simply with NaOEt in ethanol and aqueous HCl, respectively, enabled further development of complex molecular diversities.
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Affiliation(s)
- Yun-Long Zhao
- College of Chemistry , Beijing Normal University , Beijing 100875 , China
| | - Ying Cheng
- College of Chemistry , Beijing Normal University , Beijing 100875 , China
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20
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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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21
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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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22
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Lees NR, Han LC, Byrne MJ, Davies JA, Parnell AE, Moreland PEJ, Stach JEM, van der Kamp MW, Willis CL, Race PR. An Esterase-like Lyase Catalyzes Acetate Elimination in Spirotetronate/Spirotetramate Biosynthesis. Angew Chem Int Ed Engl 2019; 58:2305-2309. [PMID: 30664319 DOI: 10.1002/anie.201812105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Indexed: 11/09/2022]
Abstract
Spirotetronate and spirotetramate natural products include a multitude of compounds with potent antimicrobial and antitumor activities. Their biosynthesis incorporates many unusual biocatalytic steps, including regio- and stereo-specific modifications, cyclizations promoted by Diels-Alderases, and acetylation-elimination reactions. Here we focus on the acetate elimination catalyzed by AbyA5, implicated in the formation of the key Diels-Alder substrate to give the spirocyclic system of the antibiotic abyssomicin C. Using synthetic substrate analogues, it is shown that AbyA5 catalyzes stereospecific acetate elimination, establishing the (R)-tetronate acetate as a biosynthetic intermediate. The X-ray crystal structure of AbyA5, the first of an acetate-eliminating enzyme, reveals a deviant acetyl esterase fold. Molecular dynamics simulations and enzyme assays show the use of a His-Ser dyad to catalyze either elimination or hydrolysis, via disparate mechanisms, under substrate control.
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Affiliation(s)
- Nicholas R Lees
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.,BrisSynBio Synthetic Biology Research Centre, University of Bristol, Bristol, BS8 1TQ, UK
| | - Li-Chen Han
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.,BrisSynBio Synthetic Biology Research Centre, University of Bristol, Bristol, BS8 1TQ, UK
| | - Matthew J Byrne
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK.,BrisSynBio Synthetic Biology Research Centre, University of Bristol, Bristol, BS8 1TQ, UK
| | - Jonathan A Davies
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.,BrisSynBio Synthetic Biology Research Centre, University of Bristol, Bristol, BS8 1TQ, UK
| | - Alice E Parnell
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK.,BrisSynBio Synthetic Biology Research Centre, University of Bristol, Bristol, BS8 1TQ, UK
| | - Pollyanna E J Moreland
- School of Biology, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK.,Centre for Synthetic Biology and the Bioeconomy, Newcastle-upon-Tyne, NE2 4AX, UK
| | - James E M Stach
- School of Biology, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK.,Centre for Synthetic Biology and the Bioeconomy, Newcastle-upon-Tyne, NE2 4AX, UK
| | - Marc W van der Kamp
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK.,BrisSynBio Synthetic Biology Research Centre, University of Bristol, Bristol, BS8 1TQ, UK
| | - Christine L Willis
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.,BrisSynBio Synthetic Biology Research Centre, University of Bristol, Bristol, BS8 1TQ, UK
| | - Paul R Race
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK.,BrisSynBio Synthetic Biology Research Centre, University of Bristol, Bristol, BS8 1TQ, UK
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23
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Lees NR, Han LC, Byrne MJ, Davies JA, Parnell AE, Moreland PEJ, Stach JEM, van der Kamp MW, Willis CL, Race PR. An Esterase-like Lyase Catalyzes Acetate Elimination in Spirotetronate/Spirotetramate Biosynthesis. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Nicholas R. Lees
- School of Chemistry; University of Bristol; Bristol BS8 1TS UK
- BrisSynBio Synthetic Biology Research Centre; University of Bristol; Bristol BS8 1TQ UK
| | - Li-Chen Han
- School of Chemistry; University of Bristol; Bristol BS8 1TS UK
- BrisSynBio Synthetic Biology Research Centre; University of Bristol; Bristol BS8 1TQ UK
| | - Matthew J. Byrne
- School of Biochemistry; University of Bristol; Bristol BS8 1TD UK
- BrisSynBio Synthetic Biology Research Centre; University of Bristol; Bristol BS8 1TQ UK
| | - Jonathan A. Davies
- School of Chemistry; University of Bristol; Bristol BS8 1TS UK
- BrisSynBio Synthetic Biology Research Centre; University of Bristol; Bristol BS8 1TQ UK
| | - Alice E. Parnell
- School of Biochemistry; University of Bristol; Bristol BS8 1TD UK
- BrisSynBio Synthetic Biology Research Centre; University of Bristol; Bristol BS8 1TQ UK
| | - Pollyanna E. J. Moreland
- School of Biology; Newcastle University; Newcastle-upon-Tyne NE1 7RU UK
- Centre for Synthetic Biology and the Bioeconomy; Newcastle-upon-Tyne NE2 4AX UK
| | - James E. M. Stach
- School of Biology; Newcastle University; Newcastle-upon-Tyne NE1 7RU UK
- Centre for Synthetic Biology and the Bioeconomy; Newcastle-upon-Tyne NE2 4AX UK
| | - Marc W. van der Kamp
- School of Biochemistry; University of Bristol; Bristol BS8 1TD UK
- BrisSynBio Synthetic Biology Research Centre; University of Bristol; Bristol BS8 1TQ UK
| | - Christine L. Willis
- School of Chemistry; University of Bristol; Bristol BS8 1TS UK
- BrisSynBio Synthetic Biology Research Centre; University of Bristol; Bristol BS8 1TQ UK
| | - Paul R. Race
- School of Biochemistry; University of Bristol; Bristol BS8 1TD UK
- BrisSynBio Synthetic Biology Research Centre; University of Bristol; Bristol BS8 1TQ UK
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24
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25
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Li Q, Ding W, Yao Z, Tu J, Wang L, Huang H, Li S, Ju J. AbmV Catalyzes Tandem Ether Installation and Hydroxylation during Neoabyssomicin/Abyssomicin Biosynthesis. Org Lett 2018; 20:4854-4857. [PMID: 30070849 DOI: 10.1021/acs.orglett.8b01997] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Qinglian Li
- 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, 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, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Ziwei Yao
- 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, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Jiajia Tu
- 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, China
| | - Liyan Wang
- College of Bio and Marine Sciences, Shenzhen University, 3688 Nanhai Ave, Shenzhen 518060, 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, China
| | - Shengying Li
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266000 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, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
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Review on Abyssomicins: Inhibitors of the Chorismate Pathway and Folate Biosynthesis. Molecules 2018; 23:molecules23061371. [PMID: 29882815 PMCID: PMC6100094 DOI: 10.3390/molecules23061371] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 05/30/2018] [Accepted: 06/04/2018] [Indexed: 11/16/2022] Open
Abstract
Antifolates targeting folate biosynthesis within the shikimate-chorismate-folate metabolic pathway are ideal and selective antimicrobials, since higher eukaryotes lack this pathway and rely on an exogenous source of folate. Resistance to the available antifolates, inhibiting the folate pathway, underlines the need for novel antibiotic scaffolds and molecular targets. While para-aminobenzoic acid synthesis within the chorismate pathway constitutes a novel molecular target for antifolates, abyssomicins are its first known natural inhibitors. This review describes the abyssomicin family, a novel spirotetronate polyketide Class I antimicrobial. It summarizes synthetic and biological studies, structural, biosynthetic, and biological properties of the abyssomicin family members. This paper aims to explain their molecular target, mechanism of action, structure⁻activity relationship, and to explore their biological and pharmacological potential. Thirty-two natural abyssomicins and numerous synthetic analogues have been reported. The biological activity of abyssomicins includes their antimicrobial activity against Gram-positive bacteria and mycobacteria, antitumor properties, latent human immunodeficiency virus (HIV) reactivator, anti-HIV and HIV replication inducer properties. Their antimalarial properties have not been explored yet. Future analoging programs using the structure⁻activity relationship data and synthetic approaches may provide a novel abyssomicin structure that is active and devoid of cytotoxicity. Abyssomicin J and atrop-o-benzyl-desmethylabyssomicin C constitute promising candidates for such programs.
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Tu J, Li S, Chen J, Song Y, Fu S, Ju J, Li Q. Characterization and heterologous expression of the neoabyssomicin/abyssomicin biosynthetic gene cluster from Streptomyces koyangensis SCSIO 5802. Microb Cell Fact 2018; 17:28. [PMID: 29463238 PMCID: PMC5819245 DOI: 10.1186/s12934-018-0875-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/09/2018] [Indexed: 11/10/2022] Open
Abstract
Background The deep-sea-derived microbe Streptomyces koyangensis SCSIO 5802 produces neoabyssomicins A–B (1–2) and abyssomicins 2 (3) and 4 (4). Neoabyssomicin A (1) augments human immunodeficiency virus-1 (HIV-1) replication whereas abyssomicin 2 (3) selectively reactivates latent HIV and is also active against Gram-positive pathogens including methicillin-resistant Staphylococcus aureus (MRSA). Structurally, neoabyssomicins A–B constitute a new subtype within the abyssomicin family and feature unique structural traits characteristic of extremely interesting biosynthetic transformations. Results In this work, the biosynthetic gene cluster (BGC) for the neoabyssomicins and abyssomicins, composed of 28 opening reading frames, was identified in S. koyangensis SCSIO 5802, and its role in neoabyssomicin/abyssomicin biosynthesis was confirmed via gene inactivation and heterologous expression experiments. Bioinformatics and genomics analyses enabled us to propose a biosynthetic pathway for neoabyssomicin/abyssomicin biosynthesis. Similarly, a protective export system by which both types of compounds are secreted from the S. koyangensis producer was identified, as was a four-component ABC transporter-based import system central to neoabyssomicin/abyssomicin biosynthesis. Furthermore, two regulatory genes, abmI and abmH, were unambiguously shown to be positive regulators of neoabyssomicin/abyssomicin biosynthesis. Consistent with their roles as positive regulatory genes, the overexpression of abmI and abmH (independent of each other) was shown to improve neoabyssomicin/abyssomicin titers. Conclusions These studies provide new insight into the biosynthesis of the abyssomicin class of natural products, and highlight important exploitable features of its BGC for future efforts. Elucidation of the neoabyssomicin/abyssomicin BGC now enables combinatorial biosynthetic initiatives aimed at improving both the titers and pharmaceutical properties of these important natural products-based drug leads. Electronic supplementary material The online version of this article (10.1186/s12934-018-0875-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiajia Tu
- 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, China.,School of Pharmacy, Zunyi Medical University, 201 Dalian Road, Zunyi, 563000, China
| | - Siting Li
- 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, China.,College of Bio and Marine Sciences, Shenzhen University, 3688 Nanhai Ave, Shenzhen, 518060, China
| | - Jiang Chen
- 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, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 110039, China
| | - Yongxiang Song
- 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, China
| | - Shaobin Fu
- School of Pharmacy, Zunyi Medical University, 201 Dalian Road, Zunyi, 563000, 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, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 110039, China
| | - Qinglian Li
- 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, China.
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Song Y, Li Q, Qin F, Sun C, Liang H, Wei X, Wong NK, Ye L, Zhang Y, Shao M, Ju J. Neoabyssomicins A–C, polycyclic macrolactones from the deep-sea derived Streptomyces koyangensis SCSIO 5802. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.07.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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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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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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32
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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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34
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New antibiotics from Nature’s chemical inventory. Bioorg Med Chem 2016; 24:6227-6252. [DOI: 10.1016/j.bmc.2016.09.014] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/07/2016] [Indexed: 01/07/2023]
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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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Ghosh S, Kuisiene N, Cheeptham N. The cave microbiome as a source for drug discovery: Reality or pipe dream? Biochem Pharmacol 2016; 134:18-34. [PMID: 27867014 DOI: 10.1016/j.bcp.2016.11.018] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/15/2016] [Indexed: 01/04/2023]
Abstract
This review highlights cave habitats, cave microbiomes and their potential for drug discovery. Such studies face many challenges, including access to remote and pristine caves, and sample collection and transport. Inappropriate physical and chemical growth conditions in the laboratory for the isolation and cultivation of cave microorganisms pose many complications including length of cultivation; some cave microorganisms can take weeks and even months to grow. Additionally, DNA extraction from cave environmental samples may be difficult due to the high concentration of various minerals that are natural DNA blocking agents. Once cave microorganisms are grown in the lab, other problems often arise, such as maintenance of pure culture, consistency of antimicrobial activity and fermentation conditions for antimicrobial production. In this review, we suggest that, although based on what has been done in the field, there is potential in using cave microorganisms to produce antimicrobial agents, one needs to be highly committed and prepared.
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Affiliation(s)
- Soumya Ghosh
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, Canada
| | - Nomeda Kuisiene
- Department of Microbiology and Biotechnology, Vilnius University, Lithuania
| | - Naowarat Cheeptham
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, Canada.
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Liu L, Salam N, Jiao JY, Jiang HC, Zhou EM, Yin YR, Ming H, Li WJ. Diversity of Culturable Thermophilic Actinobacteria in Hot Springs in Tengchong, China and Studies of their Biosynthetic Gene Profiles. MICROBIAL ECOLOGY 2016; 72:150-162. [PMID: 27048448 DOI: 10.1007/s00248-016-0756-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 03/21/2016] [Indexed: 06/05/2023]
Abstract
The class Actinobacteria has been a goldmine for the discovery of antibiotics and has attracted interest from both academics and industries. However, an absence of novel approaches during the last few decades has limited the discovery of new microbial natural products useful for industries. Scientists are now focusing on the ecological aspects of diverse environments including unexplored or underexplored habitats and extreme environments in the search for new metabolites. This paper reports on the diversity of culturable actinobacteria associated with hot springs located in Tengchong County, Yunnan Province, southwestern China. A total of 58 thermophilic actinobacterial strains were isolated from the samples collected from ten hot springs distributed over three geothermal fields (e.g., Hehua, Rehai, and Ruidian). Phylogenetic positions and their biosynthetic profiles were analyzed by sequencing 16S rRNA gene and three biosynthetic gene clusters (KS domain of PKS-I, KSα domain of PKS-II and A domain of NRPS). On the basis of 16S rRNA gene phylogenetic analysis, the 58 strains were affiliated with 12 actinobacterial genera: Actinomadura Micromonospora, Microbispora, Micrococcus, Nocardiopsis, Nonomuraea, Promicromonospora, Pseudonocardia, Streptomyces, Thermoactinospora, Thermocatellispora, and Verrucosispora, of which the two novel genera Thermoactinospora and Thermocatellisopora were recently described from among these strains. Considering the biosynthetic potential of these actinobacterial strains, 22 were positive for PCR amplification of at least one of the three biosynthetic gene clusters (PKS-I, PKS-II, and NRPS). These actinobacteria were further subjected to antimicrobial assay against five opportunistic human pathogens (Acinetobacter baumannii, Escherichia coli, Micrococcus luteus, Staphylococcus aureus and Streptococcus faecalis). All of the 22 strains that were positive for PCR amplification of at least one of the biosynthetic gene domains exhibited antimicrobial activities against at least one of the five test organisms. Among the remaining 36 actinobacteria that are negative for PCR amplification of the domains for the biosynthetic genes, 33 strains showed antimicrobial activities against at least one of the five test pathogens. In summary, the findings presented in this study emphasized the importance of underexplored habitats such as Tengchong hot springs as potential sources for search of bioactive molecules.
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Affiliation(s)
- Lan Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Jian-Yu Jiao
- Yunnan Institute of Microbiology, Yunnan University, Kunming, China
- Medical Faculty of Kunming University of Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Hong-Chen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.
| | - En-Min Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Yi-Rui Yin
- Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Hong Ming
- Yunnan Institute of Microbiology, Yunnan University, Kunming, China
- College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
- Yunnan Institute of Microbiology, Yunnan University, Kunming, China.
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Liu J, Bedell TA, West JG, Sorensen EJ. Design and Synthesis of Molecular Scaffolds with Anti-infective Activity. Tetrahedron 2016; 72:3579-3592. [PMID: 27284210 PMCID: PMC4894353 DOI: 10.1016/j.tet.2016.01.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | - T. Aaron Bedell
- Department of Chemistry, Princeton University, Frick Chemical Laboratory, Princeton, New Jersey 08544, USA
| | - Julian G. West
- Department of Chemistry, Princeton University, Frick Chemical Laboratory, Princeton, New Jersey 08544, USA
| | - Erik J. Sorensen
- Department of Chemistry, Princeton University, Frick Chemical Laboratory, Princeton, New Jersey 08544, USA
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Byrne MJ, Lees NR, Han LC, van der Kamp MW, Mulholland AJ, Stach JEM, Willis CL, Race PR. The Catalytic Mechanism of a Natural Diels–Alderase Revealed in Molecular Detail. J Am Chem Soc 2016; 138:6095-8. [DOI: 10.1021/jacs.6b00232] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Matthew J. Byrne
- School
of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
- BrisSynBio
Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
| | - Nicholas R. Lees
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Li-Chen Han
- BrisSynBio
Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Marc W. van der Kamp
- School
of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
- BrisSynBio
Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Adrian J. Mulholland
- BrisSynBio
Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - James E. M. Stach
- School
of Biology, Newcastle University, Ridley Building, Newcastle NE1 7RU, United Kingdom
- Centre
for Synthetic Biology and the Bioeconomy, Newcastle University, Baddiley-Clark Building, Newcastle NE2 4AX, United Kingdom
| | - Christine L. Willis
- BrisSynBio
Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Paul R. Race
- School
of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
- BrisSynBio
Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
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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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Anti-MRSA and anti-TB metabolites from marine-derived Verrucosispora sp. MS100047. Appl Microbiol Biotechnol 2016; 100:7437-47. [PMID: 26975378 DOI: 10.1007/s00253-016-7406-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 01/31/2016] [Accepted: 02/18/2016] [Indexed: 02/05/2023]
Abstract
Microbes belonging to the genus Verrucosispora possess significant chemical diversity and biological properties. They have attracted the interests of many researchers and are becoming promising resources in the marine natural product research field. A bioassay-guided isolation from the crude extract of Verrucosispora sp. strain MS100047, isolated from sediments collected from the South China Sea, has led to the identification of a new salicylic derivative, glycerol 1-hydroxy-2,5-dimethyl benzoate (1), along with three known compounds, brevianamide F (2), abyssomicin B (3), and proximicin B (4). Compound 1 showed selective activity against methicillin-resistant Staphylococcus aureus (MRSA) with a minimum inhibitory concentration (MIC) value of 12.5 μg/mL. Brevianamide F (2), which was isolated from actinomycete for the first time, showed a good anti-BCG activity with a MIC value of 12.5 μg/mL that has not been reported previously in literatures. Proximicin B (4) showed significant anti-MRSA (MIC = 3.125 μg/mL), anti-BCG (MIC = 6.25 μg/mL), and anti-tuberculosis (TB) (MIC = 25 μg/mL) activities. This is the first report on the anti-tubercular activities of proximicins. In addition, Verrucosispora sp. strain MS100047 was found to harbor 18 putative secondary metabolite gene clusters based on genomic sequence analysis. These include the biosynthetic loci encoding polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) consistent with abyssomicins and proximicins, respectively. The biosynthetic pathways of these isolated compounds have been proposed. These results indicate that MS100047 possesses a great potential as a source of active secondary metabolites.
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References. Antibiotics (Basel) 2015. [DOI: 10.1128/9781555819316.refs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Daduang R, Kitani S, Hashimoto J, Thamchaipenet A, Igarashi Y, Shin-ya K, Ikeda H, Nihira T. Characterization of the biosynthetic gene cluster for maklamicin, a spirotetronate-class antibiotic of the endophytic Micromonospora sp. NBRC 110955. Microbiol Res 2015; 180:30-9. [DOI: 10.1016/j.micres.2015.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/08/2015] [Accepted: 07/11/2015] [Indexed: 10/23/2022]
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Lacoske M, Theodorakis EA. Spirotetronate polyketides as leads in drug discovery. JOURNAL OF NATURAL PRODUCTS 2015; 78:562-75. [PMID: 25434976 PMCID: PMC4380204 DOI: 10.1021/np500757w] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Indexed: 05/05/2023]
Abstract
The discovery of chlorothricin (1) defined a new family of microbial metabolites with potent antitumor antibiotic properties collectively referred to as spirotetronate polyketides. These microbial metabolites are structurally distinguished by the presence of a spirotetronate motif embedded within a macrocyclic core. Glycosylation at the periphery of this core contributes to the structural complexity and bioactivity of this motif. The spirotetronate family displays impressive chemical structures, potent bioactivities, and significant pharmacological potential. This review groups the family members based on structural and biosynthetic considerations and summarizes synthetic and biological studies that aim to elucidate their mode of action and explore their pharmacological potential.
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Affiliation(s)
- Michelle
H. Lacoske
- Department of Chemistry and
Biochemistry, University of California,
San Diego, 9500 Gilman
Drive, La Jolla, California 92093-0358, United States
| | - Emmanuel A. Theodorakis
- Department of Chemistry and
Biochemistry, University of California,
San Diego, 9500 Gilman
Drive, La Jolla, California 92093-0358, United States
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45
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An enzymatic [4+2] cyclization cascade creates the pentacyclic core of pyrroindomycins. Nat Chem Biol 2015; 11:259-65. [DOI: 10.1038/nchembio.1769] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 02/04/2015] [Indexed: 01/16/2023]
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Hashimoto T, Hashimoto J, Teruya K, Hirano T, Shin-ya K, Ikeda H, Liu HW, Nishiyama M, Kuzuyama T. Biosynthesis of versipelostatin: identification of an enzyme-catalyzed [4+2]-cycloaddition required for macrocyclization of spirotetronate-containing polyketides. J Am Chem Soc 2015; 137:572-5. [PMID: 25551461 PMCID: PMC4308742 DOI: 10.1021/ja510711x] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Versipelostatin
(VST) is an unusual 17-membered macrocyclic polyketide
product that contains a spirotetronate skeleton. In this study, the
entire VST biosynthetic gene cluster (vst) spanning
108 kb from Streptomyces versipellis 4083-SVS6 was
identified by heterologous expression using a bacterial artificial
chromosome vector. Here, we demonstrate that an enzyme, VstJ, catalyzes
the stereoselective [4+2]-cycloaddition between the conjugated diene
and the exocyclic olefin of a newly identified tetronate-containing
intermediate to form the spirotetronate skeleton during VST biosynthesis.
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Affiliation(s)
- Takuya Hashimoto
- Biotechnology Research Center, The University of Tokyo , 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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León B, Navarro G, Dickey BJ, Stepan G, Tsai A, Jones GS, Morales ME, Barnes T, Ahmadyar S, Tsiang M, Geleziunas R, Cihlar T, Pagratis N, Tian Y, Yu H, Linington RG. Abyssomicin 2 reactivates latent HIV-1 by a PKC- and HDAC-independent mechanism. Org Lett 2015; 17:262-5. [PMID: 25560385 DOI: 10.1021/ol503349y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Screening of a marine natural products library afforded three new analogues of the tetronic acid containing polyketide abyssomicin family and identified abyssomicin 2 as a selective reactivator of latent HIV virus. Examination of the mode of action of this new latent HIV reactivating agent demonstrated that it functions via a distinct mechanism compared to that of existing reactivating agents and is effective at reactivating latent virus in a subset of primary patient cell lines.
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Affiliation(s)
- Brian León
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States
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Smyth JE, Butler NM, Keller PA. A twist of nature – the significance of atropisomers in biological systems. Nat Prod Rep 2015; 32:1562-83. [DOI: 10.1039/c4np00121d] [Citation(s) in RCA: 293] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This review encompasses the synthesis and identification of recently detected natural atropisomers with potential therapeutic activity.
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Affiliation(s)
- Jamie E. Smyth
- School of Chemistry
- University of Wollongong
- Wollongong
- Australia 2522
| | | | - Paul A. Keller
- School of Chemistry
- University of Wollongong
- Wollongong
- Australia 2522
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49
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Abstract
Microbes produce a huge array of secondary metabolites endowed with important ecological functions. These molecules, which can be catalogued as natural products, have long been exploited in medical fields as antibiotics, anticancer and anti-infective agents. Recent years have seen considerable advances in elucidating natural-product biosynthesis and many drugs used today are natural products or natural-product derivatives. The major contribution to recent knowledge came from application of genomics to secondary metabolism and was facilitated by all relevant genes being organised in a contiguous DNA segment known as gene cluster. Clustering of genes regulating biosynthesis in bacteria is virtually universal. Modular gene clusters can be mixed and matched during evolution to generate structural diversity in natural products. Biosynthesis of many natural products requires the participation of complex molecular machines known as polyketide synthases and non-ribosomal peptide synthetases. Discovery of new evolutionary links between the polyketide synthase and fatty acid synthase pathways may help to understand the selective advantages that led to evolution of secondary-metabolite biosynthesis within bacteria. Secondary metabolites confer selective advantages, either as antibiotics or by providing a chemical language that allows communication among species, with other organisms and their environment. Herewith, we discuss these aspects focusing on the most clinically relevant bioactive molecules, the thiotemplated modular systems that include polyketide synthases, non-ribosomal peptide synthetases and fatty acid synthases. We begin by describing the evolutionary and physiological role of marine natural products, their structural/functional features, mechanisms of action and biosynthesis, then turn to genomic and metagenomic approaches, highlighting how the growing body of information on microbial natural products can be used to address fundamental problems in environmental evolution and biotechnology.
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Vieweg L, Reichau S, Schobert R, Leadlay PF, Süssmuth RD. Recent advances in the field of bioactive tetronates. Nat Prod Rep 2014; 31:1554-84. [DOI: 10.1039/c4np00015c] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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