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Li W, Cheng Z, Zhao Z, Li H, Liu Y, Lu X, Zhao G, Du YL. Discovery of a Bacterial Hydrazine Transferase That Constructs the N-Aminolactam Pharmacophore in Albofungin Biosynthesis. J Am Chem Soc 2024; 146:13399-13405. [PMID: 38698691 DOI: 10.1021/jacs.4c02311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Structural motifs containing nitrogen-nitrogen (N-N) bonds are prevalent in a large number of clinical drugs and bioactive natural products. Hydrazine (N2H4) serves as a widely utilized building block for the preparation of these N-N-containing molecules in organic synthesis. Despite its common use in chemical processes, no enzyme has been identified to catalyze the incorporation of free hydrazine in natural product biosynthesis. Here, we report that a hydrazine transferase catalyzes the condensation of N2H4 and an aromatic polyketide pathway intermediate, leading to the formation of a rare N-aminolactam pharmacophore in the biosynthesis of broad-spectrum antibiotic albofungin. These results expand the current knowledge on the biosynthetic mechanism for natural products with N-N units and should facilitate future development of biocatalysts for the production of N-N-containing chemicals.
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Affiliation(s)
- Wei Li
- Department of Microbiology and Department of Pharmacy of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Ziyang Cheng
- Department of Microbiology and Department of Pharmacy of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Zhijie Zhao
- Department of Microbiology and Department of Pharmacy of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Hu Li
- Department of Microbiology and Department of Pharmacy of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yu Liu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xingyu Lu
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Instrumentation and Service Center for Molecular Sciences, Westlake University, Hangzhou 310024, China
| | - Guiyun Zhao
- Department of Microbiology and Department of Pharmacy of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yi-Ling Du
- Department of Microbiology and Department of Pharmacy of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
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2
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Matsuda K, Wakimoto T. Bacterial Hydrazine Biosynthetic Pathways Featuring Cupin/Methionyl tRNA Synthetase-like Enzymes. Chembiochem 2024; 25:e202300874. [PMID: 38458972 DOI: 10.1002/cbic.202300874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/26/2024] [Accepted: 03/08/2024] [Indexed: 03/10/2024]
Abstract
Nitrogen-Nitrogen (N-N) bond-containing functional groups in natural products and synthetic drugs play significant roles in exerting biological activities. The mechanisms of N-N bond formation in natural organic molecules have garnered increasing attention over the decades. Recent advances have illuminated various enzymatic and nonenzymatic strategies, and our understanding of natural N-N bond construction is rapidly expanding. A group of didomain proteins with zinc-binding cupin/methionyl-tRNA synthetase (MetRS)-like domains, also known as hydrazine synthetases, generates amino acid-based hydrazines, which serve as key biosynthetic precursors of diverse N-N bond-containing functionalities such as hydrazone, diazo, triazene, pyrazole, and pyridazinone groups. In this review, we summarize the current knowledge on hydrazine synthetase mechanisms and the various pathways employing this unique bond-forming machinery.
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Affiliation(s)
- Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
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3
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Matsuda K, Nakahara Y, Choirunnisa AR, Arima K, Wakimoto T. Phylogeny-guided Characterization of Bacterial Hydrazine Biosynthesis Mediated by Cupin/methionyl tRNA Synthetase-like Enzymes. Chembiochem 2024; 25:e202300838. [PMID: 38403952 DOI: 10.1002/cbic.202300838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/27/2024] [Accepted: 02/25/2024] [Indexed: 02/27/2024]
Abstract
Cupin/methionyl-tRNA synthetase (MetRS)-like didomain enzymes catalyze nitrogen-nitrogen (N-N) bond formation between Nω-hydroxylamines and amino acids to generate hydrazines, key biosynthetic intermediates of various natural products containing N-N bonds. While the combination of these two building blocks leads to the creation of diverse hydrazine products, the full extent of their structural diversity remains largely unknown. To explore this, we herein conducted phylogeny-guided genome-mining of related hydrazine biosynthetic pathways consisting of two enzymes: flavin-dependent Nω-hydroxylating monooxygenases (NMOs) that produce Nω-hydroxylamine precursors and cupin/MetRS-like enzymes that couple the Nω-hydroxylamines with amino acids via N-N bonds. A phylogenetic analysis identified the largely unexplored sequence spaces of these enzyme families. The biochemical characterization of NMOs demonstrated their capabilities to produce various Nω-hydroxylamines, including those previously not known as precursors of N-N bonds. Furthermore, the characterization of cupin/MetRS-like enzymes identified five new hydrazine products with novel combinations of building blocks, including one containing non-amino acid building blocks: 1,3-diaminopropane and putrescine. This study substantially expanded the variety of N-N bond forming pathways mediated by cupin/MetRS-like enzymes.
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Affiliation(s)
- Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Yuto Nakahara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Atina Rizkiya Choirunnisa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Kuga Arima
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
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4
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Zheng Z, Xiong J, Bu J, Ren D, Lee YH, Yeh YC, Lin CI, Parry R, Guo Y, Liu HW. Reconstitution of the Final Steps in the Biosynthesis of Valanimycin Reveals the Origin of Its Characteristic Azoxy Moiety. Angew Chem Int Ed Engl 2024; 63:e202315844. [PMID: 37963815 PMCID: PMC10843709 DOI: 10.1002/anie.202315844] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/11/2023] [Accepted: 11/14/2023] [Indexed: 11/16/2023]
Abstract
Valanimycin is an azoxy-containing natural product isolated from the fermentation broth of Streptomyces viridifaciens MG456-hF10. While the biosynthesis of valanimycin has been partially characterized, how the azoxy group is constructed remains obscure. Herein, the membrane protein VlmO and the putative hydrazine synthetase ForJ from the formycin biosynthetic pathway are demonstrated to catalyze N-N bond formation converting O-(l-seryl)-isobutyl hydroxylamine into N-(isobutylamino)-l-serine. Subsequent installation of the azoxy group is shown to be catalyzed by the non-heme diiron enzyme VlmB in a reaction in which the N-N single bond in the VlmO/ForJ product is oxidized by four electrons to yield the azoxy group. The catalytic cycle of VlmB appears to begin with a resting μ-oxo diferric complex in VlmB, as supported by Mössbauer spectroscopy. This study also identifies N-(isobutylamino)-d-serine as an alternative substrate for VlmB leading to two azoxy regioisomers. The reactions catalyzed by the kinase VlmJ and the lyase VlmK during the final steps of valanimycin biosynthesis are established as well. The biosynthesis of valanimycin was thus fully reconstituted in vitro using the enzymes VlmO/ForJ, VlmB, VlmJ and VlmK. Importantly, the VlmB-catalyzed reaction represents the first example of enzyme-catalyzed azoxy formation and is expected to proceed by an atypical mechanism.
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Affiliation(s)
- Ziyang Zheng
- Department of Chemistry, University of Texas at Austin, Austin, TX-78712, USA
| | - Jin Xiong
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA-15213, USA
| | - Junling Bu
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX-78712, USA
| | - Daan Ren
- Department of Chemistry, University of Texas at Austin, Austin, TX-78712, USA
| | - Yu-Hsuan Lee
- Department of Chemistry, University of Texas at Austin, Austin, TX-78712, USA
| | - Yu-Cheng Yeh
- Department of Chemistry, University of Texas at Austin, Austin, TX-78712, USA
| | - Chia-I Lin
- Department of Chemistry, University of Texas at Austin, Austin, TX-78712, USA
| | - Ronald Parry
- Department of Chemistry, Rice University, Houston, TX-77005, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA-15213, USA
| | - Hung-Wen Liu
- Department of Chemistry, University of Texas at Austin, Austin, TX-78712, USA
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX-78712, USA
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5
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Shi J, Zang X, Zhao Z, Shen Z, Li W, Zhao G, Zhou J, Du YL. Conserved Enzymatic Cascade for Bacterial Azoxy Biosynthesis. J Am Chem Soc 2023; 145:27131-27139. [PMID: 38018127 DOI: 10.1021/jacs.3c12018] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
Azoxy compounds exhibit a wide array of biological activities and possess distinctive chemical properties. Although there has been considerable interest in the biosynthetic mechanisms of azoxy metabolites, the enzymatic basis responsible for azoxy bond formation has remained largely enigmatic. In this study, we unveil the enzyme cascade that constructs the azoxy bond in valanimycin biosynthesis. Our research demonstrates that a pair of metalloenzymes, comprising a membrane-bound hydrazine synthase and a nonheme diiron azoxy synthase, collaborate to convert an unstable pathway intermediate to an azoxy product through a hydrazine-azo-azoxy pathway. Additionally, by characterizing homologues of this enzyme pair from other azoxy metabolite pathways, we propose that this two-enzyme cascade could represent a conserved enzymatic strategy for azoxy bond formation in bacteria. These findings provide significant mechanistic insights into biological N-N bond formation and should facilitate the targeted isolation of bioactive azoxy compounds through genome mining.
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Affiliation(s)
- Jingkun Shi
- Department of Microbiology, and Department of Pharmacy of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xin Zang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zhijie Zhao
- Department of Microbiology, and Department of Pharmacy of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Zhuanglin Shen
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wei Li
- Department of Microbiology, and Department of Pharmacy of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Guiyun Zhao
- Department of Microbiology, and Department of Pharmacy of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jiahai Zhou
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yi-Ling Du
- Department of Microbiology, and Department of Pharmacy of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
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6
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Tanaka Y, Nagano H, Okano M, Kishimoto T, Tatsukawa A, Kunitake H, Fukumoto A, Anzai Y, Arakawa K. Isolation of Hydrazide-alkenes with Different Amino Acid Origins from an Azoxy-alkene-Producing Mutant of Streptomyces rochei 7434AN4. JOURNAL OF NATURAL PRODUCTS 2023; 86:2185-2192. [PMID: 37624992 DOI: 10.1021/acs.jnatprod.3c00476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2023]
Abstract
A triple mutant (strain KA57) of Streptomyces rochei 7434AN4 produces an azoxy-alkene compound, KA57A, which was not detected in a parent strain or other single and double mutants. This strain accumulated several additional minor components, whose structures were elucidated. HPLC analysis of strain KA57 indicated the presence of two UV active components (KA57D1 and KA57D2) as minor components. They exhibited a maximum UV absorbance at 218 nm, whereas a UV absorbance of azoxy-alkene KA57A was detected at 236 nm, suggesting that both KA57D1 and KA57D2 contain a different chromophore from KA57A. KA57D1 has a molecular formula of C12H22N2O2, and NMR analysis revealed KA57D1 is a novel hydrazide-alkene compound, (Z)-N-acetyl-N'-(hex-1-en-1-yl)isobutylhydrazide. Labeling studies indicated that nitrogen Nβ of KA57D1 is derived from l-glutamic acid, and the isobutylamide unit (C-1 to C-3, 2-Me, and Nα) originates from valine. KA57D2 has a molecular formula of C13H24N2O2, and its structure was determined to be (Z)-N-acetyl-N'-(hex-1-en-1-yl)-2-methylbutanehydrazide, in which a 2-methylbutanamide unit was shown to originate from isoleucine. Different biogenesis of the Nα atom (l-serine for KA57A, l-valine for KA57D1, and l-isoleucine for KA57D2) indicates the relaxed substrate recognition for nitrogen-nitrogen bond formation in the biosyntheses of KA57A, KA57D1, and KA57D2.
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Affiliation(s)
- Yu Tanaka
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
- Hiroshima Research Center for Healthy Aging (HiHA), Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Haruka Nagano
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
- Hiroshima Research Center for Healthy Aging (HiHA), Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Mei Okano
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
- Hiroshima Research Center for Healthy Aging (HiHA), Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Takuya Kishimoto
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Ayaka Tatsukawa
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Hirofumi Kunitake
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Atsushi Fukumoto
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Toho University, Chiba 274-8510, Japan
| | - Yojiro Anzai
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Toho University, Chiba 274-8510, Japan
| | - Kenji Arakawa
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
- Hiroshima Research Center for Healthy Aging (HiHA), Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
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7
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Shikai Y, Kawai S, Katsuyama Y, Ohnishi Y. In vitro characterization of nonribosomal peptide synthetase-dependent O-(2-hydrazineylideneacetyl)serine synthesis indicates a stepwise oxidation strategy to generate the α-diazo ester moiety of azaserine. Chem Sci 2023; 14:8766-8776. [PMID: 37621439 PMCID: PMC10445470 DOI: 10.1039/d3sc01906c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/02/2023] [Indexed: 08/26/2023] Open
Abstract
Azaserine, a natural product containing a diazo group, exhibits anticancer activity. In this study, we investigated the biosynthetic pathway to azaserine. The putative azaserine biosynthetic gene (azs) cluster, which contains 21 genes, including those responsible for hydrazinoacetic acid (HAA) synthesis, was discovered using bioinformatics analysis of the Streptomyces fragilis genome. Azaserine was produced by the heterologous expression of the azs cluster in Streptomyces albus. In vitro enzyme assays using recombinant Azs proteins revealed the azaserine biosynthetic pathway as follows. AzsSPTF and carrier protein (CP) AzsQ are used to synthesize the 2-hydrazineylideneacetyl (HDA) moiety attached to AzsQ from HAA. AzsD transfers the HDA moiety to the C-terminal CP domain of AzsN. The heterocyclization (Cy) domain of the nonribosomal peptide synthetase AzsO synthesizes O-(2-hydrazineylideneacetyl)serine (HDA-Ser) attached to its CP domain from l-serine and HDA moiety-attached AzsN. The thioesterase AzsB hydrolyzes it to yield HDA-Ser, which appears to be converted to azaserine by oxidation. Bioinformatics analysis of the Cy domain of AzsO showed that it has a conserved DxxxxD motif; however, two conserved amino acid residues (Thr and Asp) important for heterocyclization are substituted for Asn. Site-directed mutagenesis of two Asp residues in the DxxxxD motif (D193 and D198) and two substituted Asn residues (N414 and N447) indicated that these four residues are important for ester bond synthesis. These results showed that the diazo ester of azasrine is synthesized by the stepwise oxidation of the HAA moiety and provided another strategy to biosynthesize the diazo group.
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Affiliation(s)
- Yusuke Shikai
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Seiji Kawai
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo Bunkyo-ku Tokyo 113-8657 Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo Bunkyo-ku Tokyo 113-8657 Japan
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8
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Kawai S, Yamada A, Du D, Sugai Y, Katsuyama Y, Ohnishi Y. Identification and Analysis of the Biosynthetic Gene Cluster for the Hydrazide-Containing Aryl Polyene Spinamycin. ACS Chem Biol 2023; 18:1821-1828. [PMID: 37498311 DOI: 10.1021/acschembio.3c00248] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Natural products containing nitrogen-nitrogen (N-N) bonds have attracted much attention because of their bioactivities and chemical features. Several recent studies have revealed the nitrous acid-dependent N-N bond-forming machinery. However, the catalytic mechanisms of hydrazide synthesis using nitrous acid remain unknown. Herein, we focused on spinamycin, a hydrazide-containing aryl polyene produced by Streptomyces albospinus JCM3399. In the S. albospinus genome, we discovered a putative spinamycin biosynthetic gene (spi) cluster containing genes that encode a type II polyketide synthase and genes for the secondary metabolism-specific nitrous acid biosynthesis pathway. A gene inactivation experiment showed that this cluster was responsible for spinamycin biosynthesis. A feeding experiment using stable isotope-labeled sodium nitrite and analysis of nitrous acid-synthesizing enzymes in vitro strongly indicated that one of the nitrogen atoms of the hydrazide group was derived from nitrous acid. In vitro substrate specificity analysis of SpiA3, which is responsible for loading a starter substrate onto polyketide synthase, indicated that N-N bond formation occurs after starter substrate loading. In vitro analysis showed that the AMP-dependent ligase SpiA7 catalyzes the diazotization of an amino group on a benzene ring without a hydroxy group, resulting in a highly reactive diazo intermediate, which may be the key step in hydrazide group formation. Therefore, we propose the overall biosynthetic pathway of spinamycin. This study expands our knowledge of N-N bond formation in microbial secondary metabolism.
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Affiliation(s)
- Seiji Kawai
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akito Yamada
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Danyao Du
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yoshinori Sugai
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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9
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Van Cura D, Ng TL, Huang J, Hager H, Hartwig JF, Keasling JD, Balskus EP. Discovery of the Azaserine Biosynthetic Pathway Uncovers a Biological Route for α-Diazoester Production. Angew Chem Int Ed Engl 2023; 62:e202304646. [PMID: 37151182 PMCID: PMC10330308 DOI: 10.1002/anie.202304646] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/09/2023]
Abstract
Azaserine is a bacterial metabolite containing a biologically unusual and synthetically enabling α-diazoester functional group. Herein, we report the discovery of the azaserine (aza) biosynthetic gene cluster from Glycomyces harbinensis. Discovery of related gene clusters reveals previously unappreciated azaserine producers, and heterologous expression of the aza gene cluster confirms its role in azaserine assembly. Notably, this gene cluster encodes homologues of hydrazonoacetic acid (HYAA)-producing enzymes, implicating HYAA in α-diazoester biosynthesis. Isotope feeding and biochemical experiments support this hypothesis. These discoveries indicate that a 2-electron oxidation of a hydrazonoacetyl intermediate is required for α-diazoester formation, constituting a distinct logic for diazo biosynthesis. Uncovering this biological route for α-diazoester synthesis now enables the production of a highly versatile carbene precursor in cells, facilitating approaches for engineering complete carbene-mediated biosynthetic transformations in vivo.
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Affiliation(s)
- Devon Van Cura
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Tai L Ng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Jing Huang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Harry Hager
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - John F Hartwig
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Jay D Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
- Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institute for Advanced Technologies, Shenzhen, China
- Center for Biosustainability, Danish Technical University, Lyngby, Denmark
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
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10
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Wei ZW, Niikura H, Wang M, Ryan KS. Identification of the Azaserine Biosynthetic Gene Cluster Implicates Hydrazine as an Intermediate to the Diazo Moiety. Org Lett 2023; 25:4061-4065. [PMID: 37235858 DOI: 10.1021/acs.orglett.3c01229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Azaserine (1) is a natural product and nonproteinogenic amino acid containing a diazo group. Here we report the biosynthetic gene cluster for 1 from Glycomyces harbinensis. We then use isotopic feeding, gene deletion, and biochemical experiments to support a pathway whereby hydrazinoacetic acid (2) and a peptidyl carrier protein-loaded serine (3) are intermediates on route to the final natural product 1.
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Affiliation(s)
- Zi-Wang Wei
- Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Haruka Niikura
- Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Menghua Wang
- Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Katherine S Ryan
- Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
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11
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Zhang Y, Li J, Liu X, Gao W, Song S, Rong Y, Tan L, Glukhareva TV, Bakulev VA, Fan Z. Exploration of Fungicidal Activity and Mode of Action of Ferimzone Analogs. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:3705-3718. [PMID: 36763904 DOI: 10.1021/acs.jafc.2c08504] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Lead discovery and molecular target identification are important for developing novel pesticides. Scaffold hopping, an effective approach of modern medicinal and agrochemical chemistry for a rational design of target molecules, is aiming to design novel molecules with similar structures and similar/better biological performance. Herein, 24 new ferimzone derivatives were designed and synthesized by a scaffold-hopping strategy. In vitro bioassays indicated that compound 5o showed similar potency to ferimzone against Cercospora arachidicola and 2-fold higher potency than ferimzone against Alternaria solani. Compounds 5q, 6a, and 6d displayed fungicidal activity with EC50 values ranging from 1.17 to 3.84 μg/mL against Rhizoctonia solani, and compounds 5q and 6a displayed 1.6-1.8-fold higher activity than ferimzone against Fusarium graminearum. The in vivo bioassays at 200 μg/mL indicated that compound 5q was more potent than ferimzone against Pyricularia oryzae (90% vs 70% efficacy, respectively). Density functional theory (DFT) calculations elucidated the structure-energy relationship. Although the mode of action of ferimzone is still unclear, studies suggested that compound 5q significantly inhibited the growth and reproduction of R. solani, and its energy metabolism pathways (e.g., starch, sucrose, lipids, and glutathione) were seriously downregulated after a 5q treatment.
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Affiliation(s)
- Yue Zhang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Jing Li
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Xiaoyu Liu
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Wei Gao
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Shuoshuo Song
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Yaping Rong
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Linyu Tan
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Tatiana V Glukhareva
- TOS Department, Ural Federal University named after the first President of Russia B. N. Yeltsin, 19 Mira strasse, 620002 Yekaterinburg, Russia
| | - Vasiliy A Bakulev
- TOS Department, Ural Federal University named after the first President of Russia B. N. Yeltsin, 19 Mira strasse, 620002 Yekaterinburg, Russia
| | - Zhijin Fan
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
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12
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Hou A, Dickschat JS. Labelling studies in the biosynthesis of polyketides and non-ribosomal peptides. Nat Prod Rep 2023; 40:470-499. [PMID: 36484402 DOI: 10.1039/d2np00071g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: 2015 to 2022In this review, we discuss the recent advances in the use of isotopically labelled compounds to investigate the biosynthesis of polyketides, non-ribosomally synthesised peptides, and their hybrids. Also, we highlight the use of isotopes in the elucidation of their structures and investigation of enzyme mechanisms. The biosynthetic pathways of selected examples are presented in detail to reveal the principles of the discussed labelling experiments. The presented examples demonstrate that the application of isotopically labelled compounds is still the state of the art and can provide valuable information for the biosynthesis of natural products.
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Affiliation(s)
- Anwei Hou
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, West 7th Avenue No. 32, 300308 Tianjin, China.,Institute of Microbiology, Jiangxi Academy of Sciences, Changdong Road No. 7777, 330096 Nanchang, China
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.
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13
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Liu W, Lu Z, Yuan S, Jiang X, Xian M. Identification and mechanistic analysis of a bifunctional enzyme involved in the C-N and N-N bond formation. Biochem Biophys Res Commun 2022; 635:154-160. [DOI: 10.1016/j.bbrc.2022.10.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/01/2022] [Accepted: 10/10/2022] [Indexed: 11/02/2022]
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14
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Genetic and Biochemical Characterization of Halogenation and Drug Transportation Genes Encoded in the Albofungin Biosynthetic Gene Cluster. Appl Environ Microbiol 2022; 88:e0080622. [PMID: 36000868 PMCID: PMC9469721 DOI: 10.1128/aem.00806-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Albofungin, a hexacyclic aromatic natural product, exhibits broad-spectrum antimicrobial activity. Its biosynthesis, regulation, and resistance remain elusive. Here, we report the albofungin (abf) biosynthetic gene cluster (BGC) from its producing strain Streptomyces tumemacerans JCM5050. The nascent abf BGC encodes 70 putative genes, including regulators, transporters, type II polyketide synthases (PKSs), oxidoreductase, and tailoring enzymes. To validate the intactness and functionality of the BGC, we developed an Escherichia coli-Streptomyces shuttle bacterial artificial chromosome system, whereby the abf BGC was integrated into the genome of a nonproducing host via heterologous conjugation, wherefrom albofungin can be produced, confirming that the BGC is in effect. We then delimited the boundaries of the BGC by means of in vitro CRISPR-Cas9 DNA editing, concluding a minimal but essential 60-kb abf BGC ranging from orfL to abf58. The orfA gene encoding a reduced flavin adenine dinucleotide (FADH2)-dependent halogenase was examined and is capable of transforming albofungin to halogen-substituted congeners in vivo and in vitro. The orfL gene encoding a transporter was examined in vivo. The presence/absence of orfA or orfL demonstrated that the MIC of albofungin is subject to alteration when an extracellular polysaccharide intercellular adhesin was formed. Despite that halogenation of albofungin somewhat increases binding affinity to transglycosylase (TGase), albofungin with/without a halogen substituent manifests similar in vitro antimicrobial activity. Halogenation, however, limits overall dissemination and effectiveness given a high secretion rate, weak membrane permeability, and high hydrophobicity of the resulting products, whereby the functions of orfA and orfL are correlated with drug detoxification/resistance for the first time. IMPORTANCE Albofungin, a natural product produced from Streptomycetes, exhibits bioactivities against bacteria, fungi, and tumor cells. The biosynthetic logic, regulations, and resistance of albofungin remain yet to be addressed. Herein, the minimal albofungin (abf) biosynthetic gene cluster (BGC) from the producing strain Streptomyces tumemacerans JCM5050 was precisely delimited using the Escherichia coli-Streptomyces shuttle bacterial artificial chromosome system, of which the gene essentiality was established in vivo and in vitro. Next, we characterized two genes orfA and orfL encoded in the abf BGC, which act as a reduced flavin adenine dinucleotide (FADH2)-dependent halogenase and an albofungin-congeners transporter, respectively. While each testing microorganism exhibited different sensitivities to albofungins, the MIC values of albofungins against testing strains with/without orfA and/or orfL were subject to considerable changes. Halogen-substituted albofungins mediated by OrfA manifested overall compromised dissemination and effectiveness, revealing for the first time that two functionally distinct proteins OrfA and OrfL are associated together, exerting a novel “belt and braces” mechanism in antimicrobial detoxification/resistance.
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15
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Matsuda K, Arima K, Akiyama S, Yamada Y, Abe Y, Suenaga H, Hashimoto J, Shin-Ya K, Nishiyama M, Wakimoto T. A Natural Dihydropyridazinone Scaffold Generated from a Unique Substrate for a Hydrazine-Forming Enzyme. J Am Chem Soc 2022; 144:12954-12960. [PMID: 35771530 DOI: 10.1021/jacs.2c05269] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Nitrogen-nitrogen bond-containing functional groups are rare, but they are found in a considerably wide class of natural products. Recent clarifications of the biosynthetic routes for such functional groups shed light onto overlooked biosynthetic genes distributed across the bacterial kingdom, highlighting the presence of yet-to-be identified natural products with peculiar functional groups. Here, the genome-mining approach targeting a unique hydrazine-forming gene led to the discovery of actinopyridazinones A (1) and B (2), the first natural products with dihydropyridazinone rings. The structure of actinopyridazinone A was unambiguously established by total synthesis. Biosynthetic studies unveiled the structural diversity of natural hydrazines derived from this family of N-N bond-forming enzymes.
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Affiliation(s)
- Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan.,Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education, Hokkaido University, Kita 12, Nishi 6, Sapporo 060-0812, Japan
| | - Kuga Arima
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan
| | - Satoko Akiyama
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan
| | - Yuito Yamada
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan
| | - Yo Abe
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan
| | - Hikaru Suenaga
- National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium (JBIC), Tokyo 135-0064, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Makoto Nishiyama
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.,Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan.,Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education, Hokkaido University, Kita 12, Nishi 6, Sapporo 060-0812, Japan
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16
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Nunez Avila AG, Deschênes-Simard B, Arnold JE, Morency M, Chartrand D, Maris T, Berger G, Day GM, Hanessian S, Wuest JD. Surprising Chemistry of 6-Azidotetrazolo[5,1- a]phthalazine: What a Purported Natural Product Reveals about the Polymorphism of Explosives. J Org Chem 2022; 87:6680-6694. [PMID: 35504046 DOI: 10.1021/acs.joc.2c00369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
6-Azidotetrazolo[5,1-a]phthalazine (ATPH) is a nitrogen-rich compound of surprisingly broad interest. It is purported to be a natural product, yet it is closely related to substances developed as explosives and is highly polymorphic despite having a nearly planar structure with little flexibility. Seven solid forms of ATPH have been characterized by single-crystal X-ray diffraction. The structures show diverse patterns of molecular organization, including both stacked sheets and herringbone packing. In all cases, N···N and C-H···N interactions play key roles in ensuring molecular cohesion. The high polymorphism of ATPH appears to arise in part from the ability of virtually every atom of nitrogen and hydrogen in the molecule to take part in close N···N and C-H···N contacts. As a result, adjacent molecules can adopt many different relative orientations that are energetically similar, thereby generating a polymorphic landscape with an unusually high density of potential structures. This landscape has been explored in detail by the computational prediction of crystal structures. Studying ATPH has provided insights into the field of energetic materials, where access to multiple polymorphs can be used to improve performance and clarify how it depends on molecular packing. In addition, our work with ATPH shows how valuable insights into molecular crystallization, often gleaned from statistical analyses of structural databases, can also come from in-depth empirical and theoretical studies of single compounds that show distinctive behavior.
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Affiliation(s)
| | | | - Joseph E Arnold
- School of Chemistry, University of Southampton, University Road, Southampton SO17 1BJ, U.K
| | - Mathieu Morency
- Département de Chimie, Université de Montréal, Montréal, Québec H2V 0B3, Canada
| | - Daniel Chartrand
- Département de Chimie, Université de Montréal, Montréal, Québec H2V 0B3, Canada
| | - Thierry Maris
- Département de Chimie, Université de Montréal, Montréal, Québec H2V 0B3, Canada
| | - Gilles Berger
- Microbiologie, Chimie bioorganique et macromoléculaire, Faculté de Pharmacie, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Bruxelles 1050, Belgium
| | - Graeme M Day
- School of Chemistry, University of Southampton, University Road, Southampton SO17 1BJ, U.K
| | - Stephen Hanessian
- Département de Chimie, Université de Montréal, Montréal, Québec H2V 0B3, Canada
| | - James D Wuest
- Département de Chimie, Université de Montréal, Montréal, Québec H2V 0B3, Canada
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17
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He HY, Niikura H, Du YL, Ryan KS. Synthetic and biosynthetic routes to nitrogen-nitrogen bonds. Chem Soc Rev 2022; 51:2991-3046. [PMID: 35311838 DOI: 10.1039/c7cs00458c] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The nitrogen-nitrogen bond is a core feature of diverse functional groups like hydrazines, nitrosamines, diazos, and pyrazoles. Such functional groups are found in >300 known natural products. Such N-N bond-containing functional groups are also found in significant percentage of clinical drugs. Therefore, there is wide interest in synthetic and enzymatic methods to form nitrogen-nitrogen bonds. In this review, we summarize synthetic and biosynthetic approaches to diverse nitrogen-nitrogen-bond-containing functional groups, with a focus on biosynthetic pathways and enzymes.
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Affiliation(s)
- Hai-Yan He
- Department of Chemistry, University of British Columbia, Vancouver, Canada. .,Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Haruka Niikura
- Department of Chemistry, University of British Columbia, Vancouver, Canada.
| | - Yi-Ling Du
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
| | - Katherine S Ryan
- Department of Chemistry, University of British Columbia, Vancouver, Canada.
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18
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Ma GL, Candra H, Pang LM, Xiong J, Ding Y, Tran HT, Low ZJ, Ye H, Liu M, Zheng J, Fang M, Cao B, Liang ZX. Biosynthesis of Tasikamides via Pathway Coupling and Diazonium-Mediated Hydrazone Formation. J Am Chem Soc 2022; 144:1622-1633. [DOI: 10.1021/jacs.1c10369] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Guang-Lei Ma
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Hartono Candra
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Li Mei Pang
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Juan Xiong
- School of Pharmacy, Fudan University, Shanghai 201203, P. R. China
| | - Yichen Ding
- Temasek Life Sciences Laboratory Limited, Research Link, National University of Singapore, 117604 Singapore
| | - Hoa Thi Tran
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Zhen Jie Low
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Hong Ye
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Min Liu
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798 Singapore
| | - Jie Zheng
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798 Singapore
| | - Mingliang Fang
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798 Singapore
| | - Bin Cao
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798 Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551 Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
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19
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Zhang M, Kong L, Gong R, Iorio M, Donadio S, Deng Z, Sosio M, Chen W. Biosynthesis of C-nucleoside antibiotics in actinobacteria: recent advances and future developments. Microb Cell Fact 2022; 21:2. [PMID: 34983520 PMCID: PMC8724604 DOI: 10.1186/s12934-021-01722-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/14/2021] [Indexed: 12/13/2022] Open
Abstract
Epidemic diseases and antibiotic resistance are urgent threats to global health, and human is confronted with an unprecedented dilemma to conquer them by expediting development of new natural product related drugs. C-nucleoside antibiotics, a remarkable group of microbial natural products with diverse biological activities, feature a heterocycle base linked with a ribosyl moiety via an unusual C-glycosidic bond, and have played significant roles in healthcare and for plant protection. Elucidating how nature biosynthesizes such a group of antibiotics has provided the basis for engineered biosynthesis as well as targeted genome mining of more C-nucleoside antibiotics towards improved properties. In this review, we mainly summarize the recent advances on the biosynthesis of C-nucleoside antibiotics, and we also tentatively discuss the future developments on rationally accessing C-nucleoside diversities in a more efficient and economical way via synthetic biology strategies.
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Affiliation(s)
- Meng Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Liyuan Kong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Rong Gong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | | | | | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.,State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | | | - Wenqing Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.
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20
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Zhao G, Peng W, Song K, Shi J, Lu X, Wang B, Du YL. Molecular basis of enzymatic nitrogen-nitrogen formation by a family of zinc-binding cupin enzymes. Nat Commun 2021; 12:7205. [PMID: 34893622 PMCID: PMC8664883 DOI: 10.1038/s41467-021-27523-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 11/19/2021] [Indexed: 11/26/2022] Open
Abstract
Molecules with a nitrogen-nitrogen (N-N) bond in their structures exhibit various biological activities and other unique properties. A few microbial proteins are recently emerging as dedicated N-N bond forming enzymes in natural product biosynthesis. However, the details of these biochemical processes remain largely unknown. Here, through in vitro biochemical characterization and computational studies, we report the molecular basis of hydrazine bond formation by a family of di-domain enzymes. These enzymes are widespread in bacteria and sometimes naturally exist as two standalone enzymes. We reveal that the methionyl-tRNA synthase-like domain/protein catalyzes ATP-dependent condensation of two amino acids substrates to form a highly unstable ester intermediate, which is subsequently captured by the zinc-binding cupin domain/protein and undergoes redox-neutral intramolecular rearrangement to give the N-N bond containing product. These results provide important mechanistic insights into enzymatic N-N bond formation and should facilitate future development of novel N-N forming biocatalyst.
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Affiliation(s)
- Guiyun Zhao
- grid.13402.340000 0004 1759 700XState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, 310003 Hangzhou, China ,grid.13402.340000 0004 1759 700XInstitute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, 310058 Hangzhou, China
| | - Wei Peng
- grid.12955.3a0000 0001 2264 7233State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, China
| | - Kaihui Song
- grid.13402.340000 0004 1759 700XInstitute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, 310058 Hangzhou, China
| | - Jingkun Shi
- grid.13402.340000 0004 1759 700XInstitute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, 310058 Hangzhou, China
| | - Xingyu Lu
- grid.494629.40000 0004 8008 9315Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Instrumentation and Service Center for Molecular Sciences, Westlake University, 310024 Hangzhou, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, China.
| | - Yi-Ling Du
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, 310003, Hangzhou, China. .,Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, 310058, Hangzhou, China.
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21
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Del Rio Flores A, Twigg FF, Du Y, Cai W, Aguirre DQ, Sato M, Dror MJ, Narayanamoorthy M, Geng J, Zill NA, Zhai R, Zhang W. Biosynthesis of triacsin featuring an N-hydroxytriazene pharmacophore. Nat Chem Biol 2021; 17:1305-1313. [PMID: 34725510 PMCID: PMC8605994 DOI: 10.1038/s41589-021-00895-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 09/09/2021] [Indexed: 01/08/2023]
Abstract
Triacsins are an intriguing class of specialized metabolites possessing a conserved N-hydroxytriazene moiety not found in any other known natural products. Triacsins are notable as potent acyl-CoA synthetase inhibitors in lipid metabolism, yet their biosynthesis has remained elusive. Through extensive mutagenesis and biochemical studies, we here report all enzymes required to construct and install the N-hydroxytriazene pharmacophore of triacsins. Two distinct ATP-dependent enzymes were revealed to catalyze the two consecutive N-N bond formation reactions, including a glycine-utilizing, hydrazine-forming enzyme (Tri28) and a nitrite-utilizing, N-nitrosating enzyme (Tri17). This study paves the way for future mechanistic interrogation and biocatalytic application of enzymes for N-N bond formation.
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Affiliation(s)
- Antonio Del Rio Flores
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States
| | - Frederick F Twigg
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States
| | - Yongle Du
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States
| | - Wenlong Cai
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States
| | - Daniel Q Aguirre
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States
| | - Michio Sato
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Moriel J Dror
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States
| | | | - Jiaxin Geng
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, United States
| | - Nicholas A Zill
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States
| | - Rui Zhai
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States.
- Chan Zuckerberg Biohub, San Francisco, CA, United States.
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22
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Albuquerque P, Ribeiro I, Correia S, Mucha AP, Tamagnini P, Braga-Henriques A, Carvalho MDF, Mendes MV. Complete Genome Sequence of Two Deep-Sea Streptomyces Isolates from Madeira Archipelago and Evaluation of Their Biosynthetic Potential. Mar Drugs 2021; 19:md19110621. [PMID: 34822492 PMCID: PMC8622039 DOI: 10.3390/md19110621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/28/2021] [Accepted: 10/28/2021] [Indexed: 11/22/2022] Open
Abstract
The deep-sea constitutes a true unexplored frontier and a potential source of innovative drug scaffolds. Here, we present the genome sequence of two novel marine actinobacterial strains, MA3_2.13 and S07_1.15, isolated from deep-sea samples (sediments and sponge) and collected at Madeira archipelago (NE Atlantic Ocean; Portugal). The de novo assembly of both genomes was achieved using a hybrid strategy that combines short-reads (Illumina) and long-reads (PacBio) sequencing data. Phylogenetic analyses showed that strain MA3_2.13 is a new species of the Streptomyces genus, whereas strain S07_1.15 is closely related to the type strain of Streptomyces xinghaiensis. In silico analysis revealed that the total length of predicted biosynthetic gene clusters (BGCs) accounted for a high percentage of the MA3_2.13 genome, with several potential new metabolites identified. Strain S07_1.15 had, with a few exceptions, a predicted metabolic profile similar to S. xinghaiensis. In this work, we implemented a straightforward approach for generating high-quality genomes of new bacterial isolates and analyse in silico their potential to produce novel NPs. The inclusion of these in silico dereplication steps allows to minimize the rediscovery rates of traditional natural products screening methodologies and expedite the drug discovery process.
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Affiliation(s)
- Pedro Albuquerque
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (P.A.); (P.T.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Inês Ribeiro
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; (I.R.); (S.C.); (A.P.M.); (M.d.F.C.)
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Sofia Correia
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; (I.R.); (S.C.); (A.P.M.); (M.d.F.C.)
| | - Ana Paula Mucha
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; (I.R.); (S.C.); (A.P.M.); (M.d.F.C.)
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Edifício FC4, 4169-007 Porto, Portugal
| | - Paula Tamagnini
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (P.A.); (P.T.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Edifício FC4, 4169-007 Porto, Portugal
| | - Andreia Braga-Henriques
- OOM—Oceanic Observatory of Madeira & MARE—Marine and Environmental Sciences Centre, ARDITI—Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação, Caminho da Penteada, 9020-105 Funchal, Portugal;
- Regional Directorate for Fisheries, Regional Secretariat for the Sea and Fisheries, Government of the Azores, Rua Cônsul Dabney—Colónia Alemã, 9900-014 Horta, Portugal
| | - Maria de Fátima Carvalho
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; (I.R.); (S.C.); (A.P.M.); (M.d.F.C.)
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Marta V. Mendes
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (P.A.); (P.T.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Correspondence:
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23
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Abstract
Natural products are an important source of medicinal seeds. The discovery of novel biosynthetic enzymes from nature is important for their use as biocatalysts for the enzymatic synthesis of useful natural products. In addition, genetics and structural biology developments have enabled the engineering of enzymes for the production of unnatural analogs of bioactive natural products. In this review, I describe the recent research on these two topics, the exploitation of a novel secondary metabolite enzyme involved in the biosynthesis of the sulfonamide natural product antibiotic SB-203208, and the production of unnatural bioactive depsipeptides by reconstruction of the modular enzyme assembly lines in the microbial host.
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Affiliation(s)
- Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
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24
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Kawai S, Sugaya Y, Hagihara R, Tomita H, Katsuyama Y, Ohnishi Y. Complete Biosynthetic Pathway of Alazopeptin, a Tripeptide Consisting of Two Molecules of 6-Diazo-5-oxo-l-norleucine and One Molecule of Alanine. Angew Chem Int Ed Engl 2021; 60:10319-10325. [PMID: 33624374 DOI: 10.1002/anie.202100462] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Indexed: 11/06/2022]
Abstract
DON (6-diazo-5-oxo-l-norleucine), a diazo-containing amino acid, has been studied for more than 60 years as a potent antitumor agent, but its biosynthesis has not been elucidated. Here we reveal the complete biosynthetic pathway of alazopeptin, the tripeptide Ala-DON-DON, which has antitumor activity, by gene inactivation and in vitro analysis of recombinant enzymes. We also established heterologous production of N-acetyl-DON in Streptomyces albus. DON is synthesized from lysine by three enzymes and converted to alazopeptin by five enzymes and one carrier protein. Most interestingly, transmembrane protein AzpL was indicated to catalyze diazotization using 5-oxolysine and nitrous acid as substrates. Site-directed mutagenesis of AzpL indicated that the hydroxy group of Tyr-93 is important for the diazotization. These findings expand our knowledge of the enzymology of N-N bond formation.
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Affiliation(s)
- Seiji Kawai
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yuko Sugaya
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Ryota Hagihara
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hiroya Tomita
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
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25
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Kawai S, Sugaya Y, Hagihara R, Tomita H, Katsuyama Y, Ohnishi Y. Complete Biosynthetic Pathway of Alazopeptin, a Tripeptide Consisting of Two Molecules of 6‐Diazo‐5‐oxo‐
l
‐norleucine and One Molecule of Alanine. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Seiji Kawai
- Department of Biotechnology Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Yuko Sugaya
- Department of Biotechnology Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Ryota Hagihara
- Department of Biotechnology Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Hiroya Tomita
- Department of Biotechnology Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Yohei Katsuyama
- Department of Biotechnology Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Bunkyo-ku Tokyo 113-8657 Japan
| | - Yasuo Ohnishi
- Department of Biotechnology Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Bunkyo-ku Tokyo 113-8657 Japan
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26
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Chen L, Deng Z, Zhao C. Nitrogen-Nitrogen Bond Formation Reactions Involved in Natural Product Biosynthesis. ACS Chem Biol 2021; 16:559-570. [PMID: 33721494 DOI: 10.1021/acschembio.1c00052] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Construction of nitrogen-nitrogen bonds involves sophisticated biosynthetic mechanisms to overcome the difficulties inherent to the nucleophilic nitrogen atom of amine. Over the past decade, a multitude of reactions responsible for nitrogen-nitrogen bond formation in natural product biosynthesis have been uncovered. On the basis of the intrinsic properties of these reactions, this Review classifies these reactions into three categories: comproportionation, rearrangement, and radical recombination reactions. To expound the metallobiochemistry underlying nitrogen-nitrogen bond formation reactions, we discuss the enzymatic mechanisms in comparison to well characterized canonical heme-dependent enzymes, mononuclear nonheme iron-dependent enzymes, and nonheme di-iron enzymes. We also illuminate the intermediary properties of nitrogen oxide species NO2-, NO+, and N2O3 in nitrogen-nitrogen bond formation reactions with clues derived from inorganic nitrogen metabolism driven by anammox bacteria and nitrifying bacteria. These multidimentional discussions will provide further insights into the mechanistic proposals of nitrogen-nitrogen bond formation in natural product biosynthesis.
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Affiliation(s)
- Linyue Chen
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
| | - Zixin Deng
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
| | - Changming Zhao
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
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27
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Paul CE, Eggerichs D, Westphal AH, Tischler D, van Berkel WJH. Flavoprotein monooxygenases: Versatile biocatalysts. Biotechnol Adv 2021; 51:107712. [PMID: 33588053 DOI: 10.1016/j.biotechadv.2021.107712] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/27/2021] [Accepted: 02/06/2021] [Indexed: 12/13/2022]
Abstract
Flavoprotein monooxygenases (FPMOs) are single- or two-component enzymes that catalyze a diverse set of chemo-, regio- and enantioselective oxyfunctionalization reactions. In this review, we describe how FPMOs have evolved from model enzymes in mechanistic flavoprotein research to biotechnologically relevant catalysts that can be applied for the sustainable production of valuable chemicals. After a historical account of the development of the FPMO field, we explain the FPMO classification system, which is primarily based on protein structural properties and electron donor specificities. We then summarize the most appealing reactions catalyzed by each group with a focus on the different types of oxygenation chemistries. Wherever relevant, we report engineering strategies that have been used to improve the robustness and applicability of FPMOs.
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Affiliation(s)
- Caroline E Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Daniel Eggerichs
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dirk Tischler
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands.
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28
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Hou F, Wan Y, Gan Q, Xian M, Huang W. Identification of 8-Azaguanine Biosynthesis-Related Genes Provides Insight Into the Enzymatic and Non-enzymatic Biosynthetic Pathway for 1,2,3-Triazole. Front Bioeng Biotechnol 2020; 8:603514. [PMID: 33251204 PMCID: PMC7674941 DOI: 10.3389/fbioe.2020.603514] [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: 09/07/2020] [Accepted: 10/14/2020] [Indexed: 12/02/2022] Open
Abstract
8-Azaguanine (1) is a special 1,2,3-triazole containing natural product that possesses potent antibacterial and antitumor activities. In the present study, the entire 8-azaguanine biosynthetic gene cluster was located from Streptomyces CGMCC4.1633. Targeted gene disruption, heterologous expression analysis, and feeding experiments identified crucial genes for 8-azaguanine production. Moreover, we characterized the structure of two novel metabolites, analyzed NO (or reactive nitrogen species) related genes 8-azgA/B and radical SAM enzyme homologous 8-AzgG, and verified the non-enzymatic ring formation reaction of 8-azaguanine 1,2,3-triazole. All of the data and presumptions provide insight into the timing and mechanism of the enzymatic and non-enzymatic pathway that produce 8-azaguanine-type 1,2,3-triazole.
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Affiliation(s)
- Feifei Hou
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Department of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Yupeng Wan
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Department of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Qi Gan
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Mo Xian
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Wei Huang
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
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29
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Katsuyama Y, Matsuda K. Recent advance in the biosynthesis of nitrogen–nitrogen bond–containing natural products. Curr Opin Chem Biol 2020; 59:62-68. [DOI: 10.1016/j.cbpa.2020.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/22/2020] [Accepted: 05/06/2020] [Indexed: 12/21/2022]
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30
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Wibowo M, Ding L. Chemistry and Biology of Natural Azoxy Compounds. JOURNAL OF NATURAL PRODUCTS 2020; 83:3482-3491. [PMID: 33197183 DOI: 10.1021/acs.jnatprod.0c00725] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Azoxy compounds belong to a small yet intriguing group of natural products sharing a common functional group with the general structure RN═N+(O-)R. Their intriguing chemical structures, diverse biological activities, and important industrial applications have received attention from researchers in natural product chemistry, total synthesis, and biosynthesis. This review presents current updates about the structural diversity of natural azoxy compounds isolated from different organisms and highlights the enzymes and biological logic involved in their construction. We assume that the identification of key enzymes will provide efficient tools in biocatalysis to generate new azoxy compounds, while genome mining may result in novel natural azoxy compounds of medical and industrial interest.
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Affiliation(s)
- Mario Wibowo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs. Lyngby, Denmark
| | - Ling Ding
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs. Lyngby, Denmark
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31
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Mügge C, Heine T, Baraibar AG, van Berkel WJH, Paul CE, Tischler D. Flavin-dependent N-hydroxylating enzymes: distribution and application. Appl Microbiol Biotechnol 2020; 104:6481-6499. [PMID: 32504128 PMCID: PMC7347517 DOI: 10.1007/s00253-020-10705-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/18/2020] [Accepted: 05/24/2020] [Indexed: 02/06/2023]
Abstract
Amino groups derived from naturally abundant amino acids or (di)amines can be used as "shuttles" in nature for oxygen transfer to provide intermediates or products comprising N-O functional groups such as N-hydroxy, oxazine, isoxazolidine, nitro, nitrone, oxime, C-, S-, or N-nitroso, and azoxy units. To this end, molecular oxygen is activated by flavin, heme, or metal cofactor-containing enzymes and transferred to initially obtain N-hydroxy compounds, which can be further functionalized. In this review, we focus on flavin-dependent N-hydroxylating enzymes, which play a major role in the production of secondary metabolites, such as siderophores or antimicrobial agents. Flavoprotein monooxygenases of higher organisms (among others, in humans) can interact with nitrogen-bearing secondary metabolites or are relevant with respect to detoxification metabolism and are thus of importance to understand potential medical applications. Many enzymes that catalyze N-hydroxylation reactions have specific substrate scopes and others are rather relaxed. The subsequent conversion towards various N-O or N-N comprising molecules is also described. Overall, flavin-dependent N-hydroxylating enzymes can accept amines, diamines, amino acids, amino sugars, and amino aromatic compounds and thus provide access to versatile families of compounds containing the N-O motif. Natural roles as well as synthetic applications are highlighted. Key points • N-O and N-N comprising natural and (semi)synthetic products are highlighted. • Flavin-based NMOs with respect to mechanism, structure, and phylogeny are reviewed. • Applications in natural product formation and synthetic approaches are provided. Graphical abstract .
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Affiliation(s)
- Carolin Mügge
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - Thomas Heine
- Environmental Microbiology, Faculty of Chemistry and Physics, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Alvaro Gomez Baraibar
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany
- Rottendorf Pharma GmbH, Ostenfelder Str. 51-61, 59320, Ennigerloh, Germany
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
| | - Caroline E Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, HZ 2629, Delft, The Netherlands
| | - Dirk Tischler
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany.
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32
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Kurosawa S, Matsuda K, Hasebe F, Shiraishi T, Shin-Ya K, Kuzuyama T, Nishiyama M. Guanidyl modification of the 1-azabicyclo[3.1.0]hexane ring in ficellomycin essential for its biological activity. Org Biomol Chem 2020; 18:5137-5144. [PMID: 32582897 DOI: 10.1039/d0ob00339e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The 1-azabicyclo[3.1.0]hexane ring is a key moiety in natural products for biological activities against bacteria, fungi, and tumor through DNA alkylation. Ficellomycin is a dipeptide that consists of l-valine and a non-proteinogenic amino acid with the 1-azabicyclo[3.1.0]hexane ring structure. Although the biosynthetic gene cluster of ficellomycin has been identified, the biosynthetic pathway currently remains unclear. We herein report the final stage of ficellomycin biosynthesis involving ring modifications and successive dipeptide formation. After the ring is formed, the hydroxy group of the ring is converted into the guanidyl unit by three enzymes, which include an aminotransferase with a novel inter ω-ω amino-transferring activity. In the last step, the resulting 1-azabicyclo[3.1.0]hexane ring-containing amino acid is connected with l-valine by an amino acid ligase to yield ficellomycin. The present study revealed a new machinery that expands the structural and biological diversities of natural products.
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Affiliation(s)
- Sumire Kurosawa
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8567, Japan.
| | - Kenichi Matsuda
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8567, Japan.
| | - Fumihito Hasebe
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8567, Japan.
| | - Taro Shiraishi
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8567, Japan. and Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8567, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Tomohisa Kuzuyama
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8567, Japan. and Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8567, Japan
| | - Makoto Nishiyama
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8567, Japan. and Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8567, Japan
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33
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Zhao G, Guo YY, Yao S, Shi X, Lv L, Du YL. Nitric oxide as a source for bacterial triazole biosynthesis. Nat Commun 2020; 11:1614. [PMID: 32235841 PMCID: PMC7109123 DOI: 10.1038/s41467-020-15420-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/02/2020] [Indexed: 11/09/2022] Open
Abstract
The heterocycle 1,2,3-triazole is among the most versatile chemical scaffolds and has been widely used in diverse fields. However, how nature creates this nitrogen-rich ring system remains unknown. Here, we report the biosynthetic route to the triazole-bearing antimetabolite 8-azaguanine. We reveal that its triazole moiety can be assembled through an enzymatic and non-enzymatic cascade, in which nitric oxide is used as a building block. These results expand our knowledge of the physiological role of nitric oxide synthase in building natural products with a nitrogen-nitrogen bond, and should also inspire the development of synthetic biology approaches for triazole production.
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Affiliation(s)
- Guiyun Zhao
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Yuan-Yang Guo
- School of Chemistry and Chemical Engineering, Henan Normal University, 453007, Xinxiang, China
| | - Shunyu Yao
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Xinjie Shi
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Longxian Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, 310003, Hangzhou, China
| | - Yi-Ling Du
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China. .,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, 310003, Hangzhou, China.
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34
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Wang M, Niikura H, He H, Daniel‐Ivad P, Ryan KS. Biosynthesis of the N–N‐Bond‐Containing Compound
l
‐Alanosine. Angew Chem Int Ed Engl 2020; 59:3881-3885. [DOI: 10.1002/anie.201913458] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/30/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Menghua Wang
- Department of Chemistry The University of British Columbia Vancouver British Columbia Canada
| | - Haruka Niikura
- Department of Chemistry The University of British Columbia Vancouver British Columbia Canada
| | - Hai‐Yan He
- Department of Chemistry The University of British Columbia Vancouver British Columbia Canada
| | - Phillip Daniel‐Ivad
- Department of Chemistry The University of British Columbia Vancouver British Columbia Canada
| | - Katherine S. Ryan
- Department of Chemistry The University of British Columbia Vancouver British Columbia Canada
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35
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Wang M, Niikura H, He H, Daniel‐Ivad P, Ryan KS. Biosynthesis of the N–N‐Bond‐Containing Compound
l
‐Alanosine. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201913458] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Menghua Wang
- Department of Chemistry The University of British Columbia Vancouver British Columbia Canada
| | - Haruka Niikura
- Department of Chemistry The University of British Columbia Vancouver British Columbia Canada
| | - Hai‐Yan He
- Department of Chemistry The University of British Columbia Vancouver British Columbia Canada
| | - Phillip Daniel‐Ivad
- Department of Chemistry The University of British Columbia Vancouver British Columbia Canada
| | - Katherine S. Ryan
- Department of Chemistry The University of British Columbia Vancouver British Columbia Canada
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36
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Sulzbach M, Kunjapur AM. The Pathway Less Traveled: Engineering Biosynthesis of Nonstandard Functional Groups. Trends Biotechnol 2020; 38:532-545. [PMID: 31954529 DOI: 10.1016/j.tibtech.2019.12.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 12/02/2019] [Accepted: 12/06/2019] [Indexed: 12/12/2022]
Abstract
The field of metabolic engineering has achieved biochemical routes for conversion of renewable inputs to structurally diverse chemicals, but these products contain a limited number of chemical functional groups. In this review, we provide an overview of the progression of uncommon or 'nonstandard' functional groups from the elucidation of their biosynthetic machinery to the pathway optimization framework of metabolic engineering. We highlight exemplary efforts from primarily the last 5 years for biosynthesis of aldehyde, ester, terminal alkyne, terminal alkene, fluoro, epoxide, nitro, nitroso, nitrile, and hydrazine functional groups. These representative nonstandard functional groups vary in development stage and showcase the pipeline of chemical diversity that could soon appear within customized, biologically produced molecules.
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Affiliation(s)
- Morgan Sulzbach
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711, USA
| | - Aditya M Kunjapur
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711, USA.
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37
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Comparative Investigation into Formycin A and Pyrazofurin A Biosynthesis Reveals Branch Pathways for the Construction of C-Nucleoside Scaffolds. Appl Environ Microbiol 2020; 86:AEM.01971-19. [PMID: 31676476 DOI: 10.1128/aem.01971-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/25/2019] [Indexed: 12/23/2022] Open
Abstract
Formycin A (FOR-A) and pyrazofurin A (PRF-A) are purine-related C-nucleoside antibiotics in which ribose and a pyrazole-derived base are linked by a C-glycosidic bond. However, the logic underlying the biosynthesis of these molecules has remained largely unexplored. Here, we report the discovery of the pathways for FOR-A and PRF-A biosynthesis from diverse actinobacteria and propose that their biosynthesis is likely initiated by a lysine N 6-monooxygenase. Moreover, we show that forT and prfT (involved in FOR-A and PRF-A biosynthesis, respectively) mutants are correspondingly capable of accumulating the unexpected pyrazole-related intermediates 4-amino-3,5-dicarboxypyrazole and 3,5-dicarboxy-4-oxo-4,5-dihydropyrazole. We also decipher the enzymatic mechanism of ForT/PrfT for C-glycosidic bond formation in FOR-A/PRF-A biosynthesis. To our knowledge, ForT/PrfT represents an example of β-RFA-P (β-ribofuranosyl-aminobenzene 5'-phosphate) synthase-like enzymes governing C-nucleoside scaffold construction in natural product biosynthesis. These data establish a foundation for combinatorial biosynthesis of related purine nucleoside antibiotics and also open the way for target-directed genome mining of PRF-A/FOR-A-related antibiotics.IMPORTANCE FOR-A and PRF-A are C-nucleoside antibiotics known for their unusual chemical structures and remarkable biological activities. Deciphering the enzymatic mechanism for the construction of a C-nucleoside scaffold during FOR-A/PRF-A biosynthesis will not only expand the biochemical repertoire for novel enzymatic reactions but also permit target-oriented genome mining of FOR-A/PRF-A-related C-nucleoside antibiotics. Moreover, the availability of FOR-A/PRF-A biosynthetic gene clusters will pave the way for the rational generation of designer FOR-A/PRF-A derivatives with enhanced/selective bioactivity via synthetic biology strategies.
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38
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Antwi I, Chiorean S, van Belkum MJ, Vederas JC. Unveiling the active isomer of cycloalanopine, a cyclic opine from Lactobacillus rhamnosus LS8, through synthesis and analog production. RSC Med Chem 2020; 11:528-531. [DOI: 10.1039/d0md00033g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/23/2020] [Indexed: 11/21/2022] Open
Abstract
Stereochemistry of the antimicrobial isomer of a cyclic opine was determined by synthesis using oxidative cyclisation of a bis-hydrazide.
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Affiliation(s)
- Isaac Antwi
- Department of Chemistry
- University of Alberta
- Edmonton
- Canada
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39
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Abstract
Natural nonproteinogenic amino acids vastly outnumber the well-known 22 proteinogenic amino acids. Such amino acids are generated in specialized metabolic pathways. In these pathways, diverse biosynthetic transformations, ranging from isomerizations to the stereospecific functionalization of C-H bonds, are employed to generate structural diversity. The resulting nonproteinogenic amino acids can be integrated into more complex natural products. Here we review recently discovered biosynthetic routes to freestanding nonproteinogenic α-amino acids, with an emphasis on work reported between 2013 and mid-2019.
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Affiliation(s)
- Jason B Hedges
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Katherine S Ryan
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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40
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Ng TL, McCallum ME, Zheng CR, Wang JX, Wu KJY, Balskus EP. The l-Alanosine Gene Cluster Encodes a Pathway for Diazeniumdiolate Biosynthesis. Chembiochem 2019; 21:1155-1160. [PMID: 31643127 DOI: 10.1002/cbic.201900565] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Indexed: 12/29/2022]
Abstract
N-Nitroso-containing natural products are bioactive metabolites with antibacterial and anticancer properties. In particular, compounds containing the diazeniumdiolate (N-nitrosohydroxylamine) group display a wide range of bioactivities ranging from cytotoxicity to metal chelation. Despite the importance of this structural motif, knowledge of its biosynthesis is limited. Herein we describe the discovery of a biosynthetic gene cluster in Streptomyces alanosinicus ATCC 15710 responsible for producing the diazeniumdiolate natural product l-alanosine. Gene disruption and stable isotope feeding experiments identified essential biosynthetic genes and revealed the source of the N-nitroso group. Additional biochemical characterization of the biosynthetic enzymes revealed that the non-proteinogenic amino acid l-2,3-diaminopropionic acid (l-Dap) is synthesized and loaded onto a free-standing peptidyl carrier protein (PCP) domain in l-alanosine biosynthesis, which we propose may be a mechanism of handling unstable intermediates generated en route to the diazeniumdiolate. These discoveries will facilitate efforts to determine the biochemistry of diazeniumdiolate formation.
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Affiliation(s)
- Tai L Ng
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Monica E McCallum
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Christine R Zheng
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Jennifer X Wang
- Small Molecule Mass Spectrometry Facility, Faculty of Arts and Sciences Division of Science, Harvard University, 52 Oxford Street, Cambridge, MA, 02138, USA
| | - Kelvin J Y Wu
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
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41
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Zhao G, Yao S, Rothchild KW, Liu T, Liu Y, Lian J, He H, Ryan KS, Du Y. The Biosynthetic Gene Cluster of Pyrazomycin—A C‐Nucleoside Antibiotic with a Rare Pyrazole Moiety. Chembiochem 2019; 21:644-649. [DOI: 10.1002/cbic.201900449] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Guiyun Zhao
- Institute of Pharmaceutical Biotechnology and The First Affiliated HospitalZhejiang University School of Medicine 866 Yuhangtang Road Hangzhou 310058 P. R. China
| | - Shunyu Yao
- Institute of Pharmaceutical Biotechnology and The First Affiliated HospitalZhejiang University School of Medicine 866 Yuhangtang Road Hangzhou 310058 P. R. China
| | - Kristina W. Rothchild
- Department of ChemistryThe University of British Columbia 2036 Main Mall Vancouver BC V6T 1Z1 Canada
| | - Tengfei Liu
- Institute of Biological Engineering, College of Chemical and Biological EngineeringZhejiang University 38 Zheda Road Hangzhou 310027 P. R. China
| | - Yu Liu
- College of Life SciencesZhejiang University 866 Yuhangtang Road Hangzhou 310058 P. R. China
| | - Jiazhang Lian
- Institute of Biological Engineering, College of Chemical and Biological EngineeringZhejiang University 38 Zheda Road Hangzhou 310027 P. R. China
| | - Hai‐Yan He
- Department of ChemistryThe University of British Columbia 2036 Main Mall Vancouver BC V6T 1Z1 Canada
| | - Katherine S. Ryan
- Department of ChemistryThe University of British Columbia 2036 Main Mall Vancouver BC V6T 1Z1 Canada
| | - Yi‐Ling Du
- Institute of Pharmaceutical Biotechnology and The First Affiliated HospitalZhejiang University School of Medicine 866 Yuhangtang Road Hangzhou 310058 P. R. China
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42
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Ren D, Wang S, Ko Y, Geng Y, Ogasawara Y, Liu H. Identification of the
C
‐Glycoside Synthases during Biosynthesis of the Pyrazole‐
C
‐Nucleosides Formycin and Pyrazofurin. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Daan Ren
- Department of Chemistry and Division of Chemical Biology and Medicinal Chemistry College of Pharmacy University of Texas at Austin Austin TX 78712 USA
| | - Shao‐An Wang
- Department of Chemistry and Division of Chemical Biology and Medicinal Chemistry College of Pharmacy University of Texas at Austin Austin TX 78712 USA
| | - Yeonjin Ko
- Department of Chemistry and Division of Chemical Biology and Medicinal Chemistry College of Pharmacy University of Texas at Austin Austin TX 78712 USA
| | - Yujie Geng
- Department of Chemistry and Division of Chemical Biology and Medicinal Chemistry College of Pharmacy University of Texas at Austin Austin TX 78712 USA
| | - Yasushi Ogasawara
- Department of Chemistry and Division of Chemical Biology and Medicinal Chemistry College of Pharmacy University of Texas at Austin Austin TX 78712 USA
- Current address: Graduate School of Engineering Sapporo Hokkaido 060-8628 Japan
| | - Hung‐wen Liu
- Department of Chemistry and Division of Chemical Biology and Medicinal Chemistry College of Pharmacy University of Texas at Austin Austin TX 78712 USA
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43
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Ren D, Wang SA, Ko Y, Geng Y, Ogasawara Y, Liu HW. Identification of the C-Glycoside Synthases during Biosynthesis of the Pyrazole-C-Nucleosides Formycin and Pyrazofurin. Angew Chem Int Ed Engl 2019; 58:16512-16516. [PMID: 31518483 PMCID: PMC6911263 DOI: 10.1002/anie.201910356] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Indexed: 12/18/2022]
Abstract
C-Nucleosides are characterized by a C-C rather than a C-N linkage between the heterocyclic base and the ribofuranose ring. While the biosynthesis of pseudouridine-C-nucleosides has been studied, less is known about the pyrazole-C-nucleosides such as the formycins and pyrazofurin. Herein, genome screening of Streptomyces candidus NRRL 3601 led to the discovery of the pyrazofurin biosynthetic gene cluster pyf. In vitro characterization of gene product PyfQ demonstrated that it is able to catalyze formation of the C-glycoside carboxyhydroxypyrazole ribonucleotide (CHPR) from 4-hydroxy-1H-pyrazole-3,5-dicarboxylic acid and phosphoribosyl pyrophosphate (PRPP). Similarly, ForT, the PyfQ homologue in the formycin pathway, can catalyze the coupling of 4-amino-1H-pyrazole-3,5-dicarboxylic acid and PRPP to form carboxyaminopyrazole ribonucleotide. Finally, PyfP and PyfT are shown to catalyze amidation of CHPR to pyrazofurin 5'-phosphate thereby establishing the latter stages of both pyrazofurin and formycin biosynthesis.
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Affiliation(s)
| | | | - Yeonjin Ko
- Department of Chemistry and Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712 (USA)
| | - Yujie Geng
- Department of Chemistry and Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712 (USA)
| | | | - 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 (USA)
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44
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Guo YY, Li ZH, Xia TY, Du YL, Mao XM, Li YQ. Molecular mechanism of azoxy bond formation for azoxymycins biosynthesis. Nat Commun 2019; 10:4420. [PMID: 31594923 PMCID: PMC6783550 DOI: 10.1038/s41467-019-12250-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 08/27/2019] [Indexed: 01/07/2023] Open
Abstract
Azoxy bond is an important chemical bond and plays a crucial role in high energy density materials. However, the biosynthetic mechanism of azoxy bond remains enigmatic. Here we report that the azoxy bond biosynthesis of azoxymycins is an enzymatic and non-enzymatic coupling cascade reaction. In the first step, nonheme diiron N-oxygenase AzoC catalyzes the oxidization of amine to its nitroso analogue. Redox coenzyme pairs then facilitate the mutual conversion between nitroso group and hydroxylamine via the radical transient intermediates, which efficiently dimerize to azoxy bond. The deficiency of nucleophilic reactivity in AzoC is proposed to account for the enzyme's non-canonical oxidization of amine to nitroso product. Free nitrogen radicals induced by coenzyme pairs are proposed to be responsible for the efficient non-enzymatic azoxy bond formation. This mechanism study will provide molecular basis for the biosynthesis of azoxy high energy density materials and other valuable azoxy chemicals.
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Affiliation(s)
- Yuan-Yang Guo
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China.,School of Chemistry and Chemical Engineering, Henan Normal University, 453007, Xinxiang, China
| | - Zhen-Hua Li
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Tian-Yu Xia
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Yi-Ling Du
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Xu-Ming Mao
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China.
| | - Yong-Quan Li
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China.
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45
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Recent advances in the biosynthesis of nucleoside antibiotics. J Antibiot (Tokyo) 2019; 72:913-923. [PMID: 31554958 DOI: 10.1038/s41429-019-0236-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 08/24/2019] [Accepted: 09/07/2019] [Indexed: 01/27/2023]
Abstract
Nucleoside antibiotics are a diverse class of natural products with promising biomedical activities. These compounds contain a saccharide core and a nucleobase. Despite the large number of nucleoside antibiotics that have been reported, biosynthetic studies on these compounds have been limited compared with those on other types of natural products such as polyketides, peptides, and terpenoids. Due to recent advances in genome sequencing technology, the biosynthesis of nucleoside antibiotics has rapidly been clarified. This review covering 2009-2019 focuses on recent advances in the biosynthesis of nucleoside antibiotics.
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46
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Abstract
Bacterial natural products display astounding structural diversity, which, in turn, endows them with a remarkable range of biological activities that are of significant value to modern society. Such structural features are generated by biosynthetic enzymes that construct core scaffolds or perform peripheral modifications, and can thus define natural product families, introduce pharmacophores and permit metabolic diversification. Modern genomics approaches have greatly enhanced our ability to access and characterize natural product pathways via sequence-similarity-based bioinformatics discovery strategies. However, many biosynthetic enzymes catalyse exceptional, unprecedented transformations that continue to defy functional prediction and remain hidden from us in bacterial (meta)genomic sequence data. In this Review, we highlight exciting examples of unusual enzymology that have been uncovered recently in the context of natural product biosynthesis. These suggest that much of the natural product diversity, including entire substance classes, awaits discovery. New approaches to lift the veil on the cryptic chemistries of the natural product universe are also discussed.
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47
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Twigg FF, Cai W, Huang W, Liu J, Sato M, Perez TJ, Geng J, Dror MJ, Montanez I, Tong TL, Lee H, Zhang W. Identifying the Biosynthetic Gene Cluster for Triacsins with an N-Hydroxytriazene Moiety. Chembiochem 2019; 20:1145-1149. [PMID: 30589194 PMCID: PMC6590916 DOI: 10.1002/cbic.201800762] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Indexed: 11/05/2022]
Abstract
Triacsins are a family of natural products having in common an N-hydroxytriazene moiety not found in any other known secondary metabolites. Though many studies have examined the biological activity of triacsins in lipid metabolism, their biosynthesis has remained unknown. Here we report the identification of the triacsin biosynthetic gene cluster in Streptomyces aureofaciens ATCC 31442. Bioinformatic analysis of the gene cluster led to the discovery of the tacrolimus producer Streptomyces tsukubaensis NRRL 18488 as a new triacsin producer. In addition to targeted gene disruption to identify necessary genes for triacsin production, stable isotope feeding was performed in vivo to advance the understanding of N-hydroxytriazene biosynthesis.
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Affiliation(s)
- Frederick F Twigg
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, 2151 Berkeley Way, Berkeley, CA, 94704, USA
| | - Wenlong Cai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, 2151 Berkeley Way, Berkeley, CA, 94704, USA
| | - Wei Huang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, 2151 Berkeley Way, Berkeley, CA, 94704, USA
| | - Joyce Liu
- Department of Bioengineering, University of California, Berkeley, 2151 Berkeley Way, Berkeley, CA, 94704, USA
| | - Michio Sato
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, 2151 Berkeley Way, Berkeley, CA, 94704, USA
| | - Tynan J Perez
- Department of Chemistry, University of California, Berkeley, 2151 Berkeley Way, Berkeley, CA, 94704, USA
| | - Jiaxin Geng
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, 94704, USA
| | - Moriel J Dror
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, 2151 Berkeley Way, Berkeley, CA, 94704, USA
| | - Ismael Montanez
- Department of Chemistry, University of California, Berkeley, 2151 Berkeley Way, Berkeley, CA, 94704, USA
| | - Tate L Tong
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, 2151 Berkeley Way, Berkeley, CA, 94704, USA
| | - Hyunsu Lee
- Department of Chemistry, University of California, Berkeley, 2151 Berkeley Way, Berkeley, CA, 94704, USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, 2151 Berkeley Way, Berkeley, CA, 94704, USA
- Chan Zuckerberg Biohub, 499 Illinois St., San Francisco, CA, 94158, USA
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48
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Wang SA, Ko Y, Zeng J, Geng Y, Ren D, Ogasawara Y, Irani S, Zhang Y, Liu HW. Identification of the Formycin A Biosynthetic Gene Cluster from Streptomyces kaniharaensis Illustrates the Interplay between Biological Pyrazolopyrimidine Formation and de Novo Purine Biosynthesis. J Am Chem Soc 2019; 141:6127-6131. [PMID: 30942582 DOI: 10.1021/jacs.9b00241] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Formycin A is a potent purine nucleoside antibiotic with a C-glycosidic linkage between the ribosyl moiety and the pyrazolopyrimidine base. Herein, a cosmid is identified from the Streptomyces kaniharaensis genome library that contains the for gene cluster responsible for the biosynthesis of formycin. Subsequent gene deletion experiments and in vitro characterization of the forBCH gene products established their catalytic functions in formycin biosynthesis. Results also demonstrated that PurH from de novo purine biosynthesis plays a key role in pyrazolopyrimidine formation during biosynthesis of formycin A. The participation of PurH in both pathways represents a good example of how primary and secondary metabolism are interlinked.
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49
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Caranto JD. The emergence of nitric oxide in the biosynthesis of bacterial natural products. Curr Opin Chem Biol 2019; 49:130-138. [DOI: 10.1016/j.cbpa.2018.11.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/28/2018] [Accepted: 11/09/2018] [Indexed: 12/16/2022]
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50
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He HY, Henderson AC, Du YL, Ryan KS. Two-Enzyme Pathway Links l-Arginine to Nitric Oxide in N-Nitroso Biosynthesis. J Am Chem Soc 2019; 141:4026-4033. [DOI: 10.1021/jacs.8b13049] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hai-Yan He
- Department of Chemistry, University of British Columbia, Vancouver, Canada
| | | | - Yi-Ling Du
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
| | - Katherine S. Ryan
- Department of Chemistry, University of British Columbia, Vancouver, Canada
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