1
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Tsukamoto T, Takahashi K, Someya K, Kusakabe T, Kato K. Synthesis of the Proposed Structure of Urupocidin A. Org Lett 2025; 27:4519-4523. [PMID: 40254888 DOI: 10.1021/acs.orglett.5c01046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2025]
Abstract
The proposed structure of urupocidin A was synthesized. The bicyclic guanidino core was constructed by Pd(II) catalyzed cyclization-carbonylation-cyclization cascade reactions of the acyclic propargyl guanidine. The N-hydroxy guanidino functionality was protected as a THP ether.
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Affiliation(s)
- Takuya Tsukamoto
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Keisuke Takahashi
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Kyoka Someya
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Taichi Kusakabe
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Keisuke Kato
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
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2
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Bjarnesen D, Lanza L, Presini F, Giovannini PP, Müller M. Diversity of ThDP-Dependent Enzymes Forming Chiral Tertiary Alcohols. Chembiochem 2025:e2500200. [PMID: 40228089 DOI: 10.1002/cbic.202500200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2025] [Revised: 04/07/2025] [Accepted: 04/08/2025] [Indexed: 04/16/2025]
Abstract
Thiamine diphosphate (ThDP)-dependent enzymes are well known biocatalysts for CC bond-forming reactions. While this enzyme class is mainly investigated for the formation of acyloins of secondary alcohols, recent studies have expanded its scope to utilize ketones as electrophiles in asymmetric carboligation reactions for the formation of tertiary alcohols. Chiral tertiary alcohols are ubiquitous motifs in natural products and important building blocks for the synthesis of bioactive compounds. ThDP-dependent enzymes are emerging as one of the most promising classes of biocatalysts for synthesizing a wide range of products due to the variety of possible substrate combinations, accessible starting materials, high enantioselectivity, and advantageous self-regeneration of the catalytic ThDP cofactor. This review provides an overview of the ThDP-dependent enzymes (e.g., decarboxylase, DC; transketolase, TK; α-keto acid dehydrogenase 2, αKADH2) that form tertiary alcohols, focusing on the substrate scope and diversity of physiological functions. The available toolbox and the characterized reactions shall serve as a starting point for future studies. Inspired by nature, an even broader diversity of classes and substrate specificities is expected in this field.
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Affiliation(s)
- Daniela Bjarnesen
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Lucrezia Lanza
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Francesco Presini
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via L. Borsari 46, 44121, Ferrara, Italy
| | - Pier Paolo Giovannini
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via L. Borsari 46, 44121, Ferrara, Italy
| | - Michael Müller
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
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3
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Seshadri K, Abad AND, Nagasawa KK, Yost KM, Johnson CW, Dror MJ, Tang Y. Synthetic Biology in Natural Product Biosynthesis. Chem Rev 2025; 125:3814-3931. [PMID: 40116601 DOI: 10.1021/acs.chemrev.4c00567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2025]
Abstract
Synthetic biology has played an important role in the renaissance of natural products research during the post-genomics era. The development and integration of new tools have transformed the workflow of natural product discovery and engineering, generating multidisciplinary interest in the field. In this review, we summarize recent developments in natural product biosynthesis from three different aspects. First, advances in bioinformatics, experimental, and analytical tools to identify natural products associated with predicted biosynthetic gene clusters (BGCs) will be covered. This will be followed by an extensive review on the heterologous expression of natural products in bacterial, fungal and plant organisms. The native host-independent paradigm to natural product identification, pathway characterization, and enzyme discovery is where synthetic biology has played the most prominent role. Lastly, strategies to engineer biosynthetic pathways for structural diversification and complexity generation will be discussed, including recent advances in assembly-line megasynthase engineering, precursor-directed structural modification, and combinatorial biosynthesis.
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Affiliation(s)
- Kaushik Seshadri
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Abner N D Abad
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Kyle K Nagasawa
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Karl M Yost
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Colin W Johnson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Moriel J Dror
- Department of Bioengineering, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, United States
- Department of Bioengineering, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, United States
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4
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Angeli C, Atienza-Sanz S, Schröder S, Hein A, Li Y, Argyrou A, Osipyan A, Terholsen H, Schmidt S. Recent Developments and Challenges in the Enzymatic Formation of Nitrogen-Nitrogen Bonds. ACS Catal 2025; 15:310-342. [PMID: 39781334 PMCID: PMC11705231 DOI: 10.1021/acscatal.4c05268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2024] [Revised: 12/04/2024] [Accepted: 12/06/2024] [Indexed: 01/12/2025]
Abstract
The biological formation of nitrogen-nitrogen (N-N) bonds represents intriguing reactions that have attracted much attention in the past decade. This interest has led to an increasing number of N-N bond-containing natural products (NPs) and related enzymes that catalyze their formation (referred to in this review as NNzymes) being elucidated and studied in greater detail. While more detailed information on the biosynthesis of N-N bond-containing NPs, which has only become available in recent years, provides an unprecedented source of biosynthetic enzymes, their potential for biocatalytic applications has been minimally explored. With this review, we aim not only to provide a comprehensive overview of both characterized NNzymes and hypothetical biocatalysts with putative N-N bond forming activity, but also to highlight the potential of NNzymes from a biocatalytic perspective. We also present and compare conventional synthetic approaches to linear and cyclic hydrazines, hydrazides, diazo- and nitroso-groups, triazenes, and triazoles to allow comparison with enzymatic routes via NNzymes to these N-N bond-containing functional groups. Moreover, the biosynthetic pathways as well as the diversity and reaction mechanisms of NNzymes are presented according to the direct functional groups currently accessible to these enzymes.
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Affiliation(s)
- Charitomeni Angeli
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, The Netherlands
| | - Sara Atienza-Sanz
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, The Netherlands
| | - Simon Schröder
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, The Netherlands
| | - Annika Hein
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, The Netherlands
| | - Yongxin Li
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, The Netherlands
| | - Alexander Argyrou
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, The Netherlands
| | - Angelina Osipyan
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, The Netherlands
| | - Henrik Terholsen
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, The Netherlands
| | - Sandy Schmidt
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, The Netherlands
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5
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Krug L, Bjarnesen D, Lanza L, Lindemann L, Fessner ND, Müller M. Identification of Kibdelomycin and Related Biosynthetic Gene Clusters and Characterization of the C-Branching of Amycolose. Angew Chem Int Ed Engl 2024; 63:e202403535. [PMID: 38951114 DOI: 10.1002/anie.202403535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 07/03/2024]
Abstract
Many bacterial natural products contain C-branched sugars, including components from the outer cell wall or antibiotically active metabolites. The enzymatic C-branching of keto sugars leading to longer side chains (≥C2) is catalyzed by thiamine diphosphate (ThDP)-dependent enzymes. Chiral tertiary α-hydroxy ketones are formed in this process. The ThDP-dependent enzymes that catalyze C-branching reactions belong to one of three enzymatic superfamilies: decarboxylases, transketolases, and α-ketoacid dehydrogenases 2, but branching of keto sugars has only been demonstrated for decarboxylases. In this study, we showed that an α-ketoacid dehydrogenase is responsible for C-branching of the deoxyketo sugar amycolose in the biosynthesis of kibdelomycin in Kibdelosporangium sp. MA7385. In addition, we characterized an amino transferase in the same biosynthetic gene cluster (BGC) that accepts a sterically demanding tertiary α-hydroxy ketone in a downstream reaction. Subsequently, we identified approximately 400 similar BGCs in silico, suggesting that there is a large diversity of possible ThDP-dependent enzymes catalyzing the C-branching of keto sugars and subsequent modifications.
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Affiliation(s)
- Leonhard Krug
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Daniela Bjarnesen
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Lucrezia Lanza
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Lucia Lindemann
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Nico D Fessner
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Michael Müller
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
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6
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Motter J, Benckendorff CMM, Westarp S, Sunde-Brown P, Neubauer P, Kurreck A, Miller GJ. Purine nucleoside antibiotics: recent synthetic advances harnessing chemistry and biology. Nat Prod Rep 2024; 41:873-884. [PMID: 38197414 PMCID: PMC11188666 DOI: 10.1039/d3np00051f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Indexed: 01/11/2024]
Abstract
Covering: 2019 to 2023Nucleoside analogues represent one of the most important classes of small molecule pharmaceuticals and their therapeutic development is successfully established within oncology and for the treatment of viral infections. However, there are currently no nucleoside analogues in clinical use for the management of bacterial infections. Despite this, a significant number of clinically recognised nucleoside analogues are known to possess some antibiotic activity, thereby establishing a potential source for new therapeutic discovery in this area. Furthermore, given the rise in antibiotic resistance, the discovery of new clinical candidates remains an urgent global priority and natural product-derived nucleoside analogues may also present a rich source of discovery space for new modalities. This Highlight, covering work published from 2019 to 2023, presents a current perspective surrounding the synthesis of natural purine nucleoside antibiotics. By amalgamating recent efforts from synthetic chemistry with advances in biosynthetic understanding and the use of recombinant enzymes, prospects towards different structural classes of purines are detailed.
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Affiliation(s)
- Jonas Motter
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, D-13355, Berlin, Germany
| | - Caecilie M M Benckendorff
- School of Chemical and Physical Sciences and Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, UK.
| | - Sarah Westarp
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, D-13355, Berlin, Germany
- BioNukleo GmbH, Ackerstraße 76, 13355 Berlin, Germany.
| | - Peter Sunde-Brown
- School of Chemical and Physical Sciences and Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, UK.
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, D-13355, Berlin, Germany
| | - Anke Kurreck
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, D-13355, Berlin, Germany
- BioNukleo GmbH, Ackerstraße 76, 13355 Berlin, Germany.
| | - Gavin J Miller
- School of Chemical and Physical Sciences and Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, UK.
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7
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Liao Y, Wang XJ, Ma GL, Candra H, Qiu En SL, Khandelwal S, Liang ZX. Biosynthesis of Octacosamicin A: Uncommon Starter/extender Units and Product Releasing via Intermolecular Amidation. Chembiochem 2024; 25:e202300590. [PMID: 37908177 DOI: 10.1002/cbic.202300590] [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: 08/22/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/02/2023]
Abstract
Octacosamicin A is an antifungal metabolite featuring a linear polyene-polyol chain flanked by N-hydroxyguanidine and glycine moieties. We report here that sub-inhibitory concentrations of streptomycin elicited the production of octacosamicin A in Amycolatopsis azurea DSM 43854T . We identified the biosynthetic gene cluster (oca BGC) that encodes a modular polyketide synthase (PKS) system for assembling the polyene-polyol chain of octacosamicin A. Our analysis suggested that the N-hydroxyguanidine unit originates from a 4-guanidinobutyryl-CoA starter unit, while the PKS incorporates an α-hydroxyketone moiety using a (2R)-hydroxymalonyl-CoA extender unit. The modular PKS system contains a non-canonical terminal module that lacks thioesterase (TE) and acyl carrier protein (ACP) domains, indicating the biosynthesis is likely to employ an unconventional and cryptic off-loading mechanism that attaches glycine to the polyene-polyol chain via an intermolecular amidation reaction.
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Affiliation(s)
- Yanghui Liao
- School of Biological Sciences, Nanyang Technological University, Singapore, 67551, Singapore
| | - Xue-Jiao Wang
- School of Biological Sciences, Nanyang Technological University, Singapore, 67551, Singapore
| | - Guang-Lei Ma
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314102, China
| | - Hartono Candra
- School of Biological Sciences, Nanyang Technological University, Singapore, 67551, Singapore
| | - Sean Lee Qiu En
- School of Biological Sciences, Nanyang Technological University, Singapore, 67551, Singapore
| | - Srashti Khandelwal
- School of Biological Sciences, Nanyang Technological University, Singapore, 67551, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore, 67551, Singapore
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8
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Hibi G, Shiraishi T, Umemura T, Nemoto K, Ogura Y, Nishiyama M, Kuzuyama T. Discovery of type II polyketide synthase-like enzymes for the biosynthesis of cispentacin. Nat Commun 2023; 14:8065. [PMID: 38052796 PMCID: PMC10698177 DOI: 10.1038/s41467-023-43731-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 11/18/2023] [Indexed: 12/07/2023] Open
Abstract
Type II polyketide synthases (PKSs) normally synthesize polycyclic aromatic compounds in nature, and the potential to elaborate further diverse skeletons was recently revealed by the discovery of a polyene subgroup. Here, we show a type II PKS machinery for the biosynthesis of a five-membered nonaromatic skeleton contained in the nonproteinogenic amino acid cispentacin and the plant toxin coronatine. We successfully produce cispentacin in a heterologous host and reconstruct its biosynthesis using seven recombinant proteins in vitro. Biochemical analyses of each protein reveal the unique enzymatic reactions, indicating that a heterodimer of type II PKS-like enzymes (AmcF-AmcG) catalyzes a single C2 elongation as well as a subsequent cyclization on the acyl carrier protein (AmcB) to form a key intermediate with a five-membered ring. The subsequent reactions, which are catalyzed by a collection of type II PKS-like enzymes, are also peculiar. This work further expands the definition of type II PKS and illuminates an unexplored genetic resource for natural products.
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Affiliation(s)
- Genki Hibi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Taro Shiraishi
- 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, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Tatsuki Umemura
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kenji Nemoto
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yusuke Ogura
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Makoto Nishiyama
- 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, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Tomohisa Kuzuyama
- 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, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
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9
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Makris C, Leckrone JK, Butler A. Tistrellabactins A and B Are Photoreactive C-Diazeniumdiolate Siderophores from the Marine-Derived Strain Tistrella mobilis KA081020-065. JOURNAL OF NATURAL PRODUCTS 2023; 86:1770-1778. [PMID: 37341506 PMCID: PMC10391617 DOI: 10.1021/acs.jnatprod.3c00230] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Indexed: 06/22/2023]
Abstract
The C-diazeniumdiolate group in the amino acid graminine is emerging as a new microbially produced Fe(III) coordinating ligand in siderophores, which is photoreactive. While the few siderophores reported from this class have only been isolated from soil-associated microbes, here we report the first C-diazeniumdiolate siderophores tistrellabactins A and B, isolated from the bioactive marine-derived strain Tistrella mobilis KA081020-065. The structural characterization of the tistrellabactins reveals unique biosynthetic features including an NRPS module iteratively loading glutamine residues and a promiscuous adenylation domain yielding either tistrellabactin A with an asparagine residue or tistrellabactin B with an aspartic acid residue at analogous positions. Beyond the function of scavenging Fe(III) for growth, these siderophores are photoreactive upon irradiation with UV light, releasing the equivalent of nitric oxide (NO) and an H atom from the C-diazeniumdiolate group. Fe(III)-tistrellabactin is also photoreactive, with both the C-diazeniumdiolate and the β-hydroxyaspartate residues undergoing photoreactions, resulting in a photoproduct without the ability to chelate Fe(III).
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Affiliation(s)
- Christina Makris
- Department of Chemistry &
Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - Jamie K. Leckrone
- Department of Chemistry &
Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - Alison Butler
- Department of Chemistry &
Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
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10
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Tao XB, LaFrance S, Xing Y, Nava AA, Martin H, Keasling J, Backman TH. ClusterCAD 2.0: an updated computational platform for chimeric type I polyketide synthase and nonribosomal peptide synthetase design. Nucleic Acids Res 2022; 51:D532-D538. [PMID: 36416273 PMCID: PMC9825560 DOI: 10.1093/nar/gkac1075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/14/2022] [Accepted: 10/25/2022] [Indexed: 11/24/2022] Open
Abstract
Megasynthase enzymes such as type I modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) play a central role in microbial chemical warfare because they can evolve rapidly by shuffling parts (catalytic domains) to produce novel chemicals. If we can understand the design rules to reshuffle these parts, PKSs and NRPSs will provide a systematic and modular way to synthesize millions of molecules including pharmaceuticals, biomaterials, and biofuels. However, PKS and NRPS engineering remains difficult due to a limited understanding of the determinants of PKS and NRPS fold and function. We developed ClusterCAD to streamline and simplify the process of designing and testing engineered PKS variants. Here, we present the highly improved ClusterCAD 2.0 release, available at https://clustercad.jbei.org. ClusterCAD 2.0 boasts support for PKS-NRPS hybrid and NRPS clusters in addition to PKS clusters; a vastly enlarged database of curated PKS, PKS-NRPS hybrid, and NRPS clusters; a diverse set of chemical 'starters' and loading modules; the new Domain Architecture Cluster Search Tool; and an offline Jupyter Notebook workspace, among other improvements. Together these features massively expand the chemical space that can be accessed by enzymes engineered with ClusterCAD.
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Affiliation(s)
- Xavier B Tao
- Department of Chemistry, University of California, Berkeley, CA 94720, USA,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sarah LaFrance
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA,Biofuels and Bioproducts Division, Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA,QB3 Institute, University of California, Berkeley, CA 94720, USA
| | - Yifei Xing
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA
| | - Alberto A Nava
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Hector Garcia Martin
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA,Biofuels and Bioproducts Division, Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA,Department of Energy Agile BioFoundry, Emeryville, CA 94608, USA
| | - Jay D Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA,Biofuels and Bioproducts Division, Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA,Department of Bioengineering, University of California, Berkeley, CA 94720, USA,QB3 Institute, University of California, Berkeley, CA 94720, USA,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark 2800Copenhagen, Denmark,Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
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11
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Makris C, Carmichael JR, Zhou H, Butler A. C-Diazeniumdiolate Graminine in the Siderophore Gramibactin Is Photoreactive and Originates from Arginine. ACS Chem Biol 2022; 17:3140-3147. [PMID: 36354305 PMCID: PMC9679993 DOI: 10.1021/acschembio.2c00593] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/24/2022] [Indexed: 11/12/2022]
Abstract
Siderophores are synthesized by microbes to facilitate iron acquisition required for growth. Catecholate, hydroxamate, and α-hydroxycarboxylate groups comprise well-established ligands coordinating Fe(III) in siderophores. Recently, a C-type diazeniumdiolate ligand in the newly identified amino acid graminine (Gra) was found in the siderophore gramibactin (Gbt) produced by Paraburkholderia graminis DSM 17151. The N-N bond in the diazeniumdiolate is a distinguishing feature of Gra, yet the origin and reactivity of this C-type diazeniumdiolate group has remained elusive until now. Here, we identify l-arginine as the direct precursor to l-Gra through the isotopic labeling of l-Arg, l-ornithine, and l-citrulline. Furthermore, these isotopic labeling studies establish that the N-N bond in Gra must be formed between the Nδ and Nω of the guanidinium group in l-Arg. We also show the diazeniumdiolate groups in apo-Gbt are photoreactive, with loss of nitric oxide (NO) and H+ from each d-Gra yielding E/Z oxime isomers in the photoproduct. With the loss of Gbt's ability to chelate Fe(III) upon exposure to UV light, our results hint at this siderophore playing a larger ecological role. Not only are NO and oximes important in plant biology for communication and defense, but so too are NO-releasing compounds and oximes attractive in medicinal applications.
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Affiliation(s)
| | | | - Hongjun Zhou
- Department of Chemistry &
Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - Alison Butler
- Department of Chemistry &
Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
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12
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Huang W, Fan S, Gao J, Luo S, Tang S, Liu J, Wang X. Total Synthesis of Complex Peptidyl Nucleoside Antibiotics: Asymmetric De Novo Syntheses of Miharamycin B and Its Biosynthetic Precursor. Angew Chem Int Ed Engl 2022; 61:e202204907. [DOI: 10.1002/anie.202204907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Wenjun Huang
- State Key Laboratory of Applied Organic Chemistry Department of Chemistry and School of Pharmacy Lanzhou University Lanzhou 730000 P. R. China
| | - Shuai Fan
- State Key Laboratory of Applied Organic Chemistry Department of Chemistry and School of Pharmacy Lanzhou University Lanzhou 730000 P. R. China
| | - Jiahui Gao
- State Key Laboratory of Applied Organic Chemistry Department of Chemistry and School of Pharmacy Lanzhou University Lanzhou 730000 P. R. China
| | - Shangwen Luo
- State Key Laboratory of Applied Organic Chemistry Department of Chemistry and School of Pharmacy Lanzhou University Lanzhou 730000 P. R. China
| | - Shouchu Tang
- State Key Laboratory of Applied Organic Chemistry Department of Chemistry and School of Pharmacy Lanzhou University Lanzhou 730000 P. R. China
| | - Jian Liu
- State Key Laboratory of Applied Organic Chemistry Department of Chemistry and School of Pharmacy Lanzhou University Lanzhou 730000 P. R. China
| | - Xiaolei Wang
- State Key Laboratory of Applied Organic Chemistry Department of Chemistry and School of Pharmacy Lanzhou University Lanzhou 730000 P. R. China
- State Key Laboratory of Veterinary Etiological Biology College of Veterinary Medicine Lanzhou University Lanzhou 730000 P. R. China
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13
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Huang W, Fan S, Gao J, Luo S, Tang S, Liu J, Wang X. Total Synthesis of Complex Peptidyl Nucleoside Antibiotics: Asymmetric De Novo Syntheses of Miharamycin B and Its Biosynthetic Precursor. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Wenjun Huang
- State Key Laboratory of Applied Organic Chemistry Department of Chemistry and School of Pharmacy Lanzhou University Lanzhou 730000 P. R. China
| | - Shuai Fan
- State Key Laboratory of Applied Organic Chemistry Department of Chemistry and School of Pharmacy Lanzhou University Lanzhou 730000 P. R. China
| | - Jiahui Gao
- State Key Laboratory of Applied Organic Chemistry Department of Chemistry and School of Pharmacy Lanzhou University Lanzhou 730000 P. R. China
| | - Shangwen Luo
- State Key Laboratory of Applied Organic Chemistry Department of Chemistry and School of Pharmacy Lanzhou University Lanzhou 730000 P. R. China
| | - Shouchu Tang
- State Key Laboratory of Applied Organic Chemistry Department of Chemistry and School of Pharmacy Lanzhou University Lanzhou 730000 P. R. China
| | - Jian Liu
- State Key Laboratory of Applied Organic Chemistry Department of Chemistry and School of Pharmacy Lanzhou University Lanzhou 730000 P. R. China
| | - Xiaolei Wang
- State Key Laboratory of Applied Organic Chemistry Department of Chemistry and School of Pharmacy Lanzhou University Lanzhou 730000 P. R. China
- State Key Laboratory of Veterinary Etiological Biology College of Veterinary Medicine Lanzhou University Lanzhou 730000 P. R. China
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14
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D’Ambrosio HK, Ganley JG, Keeler AM, Derbyshire ER. A single amino acid residue controls acyltransferase activity in a polyketide synthase from Toxoplasma gondii. iScience 2022; 25:104443. [PMID: 35874921 PMCID: PMC9301873 DOI: 10.1016/j.isci.2022.104443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 04/12/2022] [Accepted: 05/16/2022] [Indexed: 11/17/2022] Open
Abstract
Type I polyketide synthases (PKSs) are multidomain, multimodule enzymes capable of producing complex polyketide metabolites. These modules contain an acyltransferase (AT) domain, which selects acyl-CoA substrates to be incorporated into the metabolite scaffold. Herein, we reveal the sequences of three AT domains from a polyketide synthase (TgPKS2) from the apicomplexan parasite Toxoplasma gondii. Phylogenic analysis indicates these ATs (AT1, AT2, and AT3) are distinct from domains in well-characterized microbial biosynthetic gene clusters. Biochemical investigations revealed that AT1 and AT2 hydrolyze malonyl-CoA but the terminal AT3 domain is non-functional. We further identify an "on-off switch" residue that controls activity such that a single amino acid change in AT3 confers hydrolysis activity while the analogous mutation in AT2 eliminates activity. This biochemical analysis of AT domains from an apicomplexan PKS lays the foundation for further molecular and structural studies on PKSs from T. gondii and other protists.
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Affiliation(s)
- Hannah K. D’Ambrosio
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
| | - Jack G. Ganley
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
| | - Aaron M. Keeler
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
| | - Emily R. Derbyshire
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, NC 27710, USA
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15
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Zhang Y, Pham TM, Kayrouz C, Ju KS. Biosynthesis of Argolaphos Illuminates the Unusual Biochemical Origins of Aminomethylphosphonate and N ε-Hydroxyarginine Containing Natural Products. J Am Chem Soc 2022; 144:9634-9644. [PMID: 35616638 DOI: 10.1021/jacs.2c00627] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Phosphonate natural products have a history of successful application in medicine and biotechnology due to their ability to inhibit essential cellular pathways. This has inspired efforts to discover phosphonate natural products by prioritizing microbial strains whose genomes encode uncharacterized biosynthetic gene clusters (BGCs). Thus, success in genome mining is dependent on establishing the fundamental principles underlying the biosynthesis of inhibitory chemical moieties to facilitate accurate prediction of BGCs and the bioactivities of their products. Here, we report the complete biosynthetic pathway for the argolaphos phosphonopeptides. We uncovered the biochemical origins of aminomethylphosphonate (AMPn) and Nε-hydroxyarginine, two noncanonical amino acids integral to the antimicrobial function of argolaphos. Critical to this pathway were dehydrogenase and transaminase enzymes dedicated to the conversion of hydroxymethylphosphonate to AMPn. The interconnected activities of both enzymes provided a solution to overcome unfavorable energetics, empower cofactor regeneration, and mediate intermediate toxicity during these transformations. Sequential ligation of l-arginine and l-valine was afforded by two GCN5-related N-acetyltransferases in a tRNA-dependent manner. AglA was revealed to be an unusual heme-dependent monooxygenase that hydroxylated the Nε position of AMPn-Arg. As the first biochemically characterized member of the YqcI/YcgG protein family, AglA enlightens the potential functions of this elusive group, which remains biochemically distinct from the well-established P450 monooxygenases. The widespread distribution of AMPn and YqcI/YcgG genes among actinobacterial genomes suggests their involvement in diverse metabolic pathways and cellular functions. Our findings illuminate new paradigms in natural product biosynthesis and realize a significant trove of AmPn and Nε-hydroxyarginine natural products that await discovery.
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Affiliation(s)
- Yeying Zhang
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Tiffany M Pham
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Chase Kayrouz
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Kou-San Ju
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States.,Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, Columbus, Ohio 43210, United States.,Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210, United States.,Infectious Diseases Institute, The Ohio State University, Columbus, Ohio 43210, United States
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16
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Chu L, Luo X, Zhu T, Cao Y, Zhang L, Deng Z, Gao J. Harnessing phosphonate antibiotics argolaphos biosynthesis enables a synthetic biology-based green synthesis of glyphosate. Nat Commun 2022; 13:1736. [PMID: 35365617 PMCID: PMC8976061 DOI: 10.1038/s41467-022-29188-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/03/2022] [Indexed: 01/16/2023] Open
Abstract
Glyphosate is a widely used herbicide with an annual production of more than one million tons globally. Current commercialized production processes of glyphosate are generally associated with manufacturing hazards and toxic wastes. Recently, many countries have strengthened environmental supervision and law enforcement on glyphosate manufacturing. Therefore, a green source of glyphosate is required. Here, we characterize the genes required for producing aminomethylphosphonate (AMP), one of the intermediates in the biosynthesis of the potent antibiotics argolaphos. We apply a synthetic biology strategy to improve AMP production in Streptomyces lividans, with fermentation titers of 52 mg L-1, a 500-fold improvement over the original strain. Furthermore, we develop an efficient and practical chemical process for converting AMP to glyphosate. Our findings highlight one greenness-driven alternative in the production of glyphosate.
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Affiliation(s)
- Leixia Chu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
- Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Xiaoxia Luo
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, College of Life Science & Technology, Tarim University, Alar, Xinjiang, 843300, China
| | - Taoting Zhu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
- Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Yingying Cao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
- Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Lili Zhang
- Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Jiangtao Gao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China.
- Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China.
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17
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Zhang WH, Wang F, Wang YL, You S, Pan HX, Tang GL. Identification and Characterization of Enzymes Catalyzing Early Steps in Miharamycin and Amipurimycin Biosynthesis. Org Lett 2021; 23:8761-8765. [PMID: 34747180 DOI: 10.1021/acs.orglett.1c03254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The biochemical elucidation of the early biosynthetic pathways of miharamycins and amipurimycin revealed the roles of several enzymes, which include GMP hydrolase, represented by MihD/ApmD, and hypothetical proteins, MihI/ApmI, unexpectedly exhibiting the dual function of the guanylglucuronic acid assembly and GMP cleavage. In addition, MihE, a carbonyl reductase that functions on the C2 branch of high-carbon sugars, and MihF, a rare guanine O-methyltransferase, were also functionally verified.
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Affiliation(s)
- Wen-He Zhang
- School of Life Sciences and Biopharmaceuticals, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Fei Wang
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences (CAS), Hangzhou 310024, China
| | - Yi-Lin Wang
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences (CAS), Hangzhou 310024, China
| | - Song You
- School of Life Sciences and Biopharmaceuticals, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Hai-Xue Pan
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences (CAS), Hangzhou 310024, China
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of CAS, CAS, Shanghai 200032, China
| | - Gong-Li Tang
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences (CAS), Hangzhou 310024, China
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of CAS, CAS, Shanghai 200032, China
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18
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Perali RS, Boddu UR, Sankar DC. [1,2]- vs [2,3]-Wittig Rearrangement in Carbohydrate Derived Alkenyl Systems. Org Lett 2021; 23:3850-3853. [PMID: 33929209 DOI: 10.1021/acs.orglett.1c00988] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A simple and efficient strategy for the regio- and stereoselective synthesis of carbon-branched sugar derivatives is described. The successful implementation of Wittig rearrangement on substrates derived by Ferrier rearrangement of various glycals and 3-O-alkenyl glycals is studied extensively. A highly selective [1,2]- or [2,3]-Wittig rearrangement is revealed that provides a novel class of stereodefined 3-C-branched glycals and C-glycosides, which are otherwise difficult to obtain.
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Affiliation(s)
- Ramu Sridhar Perali
- School of Chemistry, University of Hyderabad, Gachibowli, Hyderabad 500 046, India
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19
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Yu B, Wang S. Solving the Structural Puzzles of Amipurimycin and Miharamycins Enabled by Stereodivergent Total Synthesis. CHEM REC 2021; 21:3015-3028. [PMID: 33835677 DOI: 10.1002/tcr.202100057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 11/09/2022]
Abstract
The efforts toward the synthesis of amipurimycin and miharamycin A/B, two peptidyl nucleoside antibiotics bearing a unique nine carbon C3-branched pyranosyl amino acid core, are accounted. Highlighted is our stereodivergent total synthesis of all the possible diastereoisomers of amipurimycin, which has enabled us to solve the structural puzzles of amipurimycin and miharamycin A/B after ∼50 years of their discovery.
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Affiliation(s)
- Biao Yu
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou, 310024, China.,State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Shengyang Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China.,Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, 201203, China
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20
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Schneider NO, Tassoulas LJ, Zeng D, Laseke AJ, Reiter NJ, Wackett LP, Maurice MS. Solving the Conundrum: Widespread Proteins Annotated for Urea Metabolism in Bacteria Are Carboxyguanidine Deiminases Mediating Nitrogen Assimilation from Guanidine. Biochemistry 2020; 59:3258-3270. [PMID: 32786413 DOI: 10.1021/acs.biochem.0c00537] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Free guanidine is increasingly recognized as a relevant molecule in biological systems. Recently, it was reported that urea carboxylase acts preferentially on guanidine, and consequently, it was considered to participate directly in guanidine biodegradation. Urea carboxylase combines with allophanate hydrolase to comprise the activity of urea amidolyase, an enzyme predominantly found in bacteria and fungi that catalyzes the carboxylation and subsequent hydrolysis of urea to ammonia and carbon dioxide. Here, we demonstrate that urea carboxylase and allophanate hydrolase from Pseudomonas syringae are insufficient to catalyze the decomposition of guanidine. Rather, guanidine is decomposed to ammonia through the combined activities of urea carboxylase, allophanate hydrolase, and two additional proteins of the DUF1989 protein family, expansively annotated as urea carboxylase-associated family proteins. These proteins comprise the subunits of a heterodimeric carboxyguanidine deiminase (CgdAB), which hydrolyzes carboxyguanidine to N-carboxyurea (allophanate). The genes encoding CgdAB colocalize with genes encoding urea carboxylase and allophanate hydrolase. However, 25% of urea carboxylase genes, including all fungal urea amidolyases, do not colocalize with cgdAB. This subset of urea carboxylases correlates with a notable Asp to Asn mutation in the carboxyltransferase active site. Consistent with this observation, we demonstrate that fungal urea amidolyase retains a strong substrate preference for urea. The combined activities of urea carboxylase, carboxyguanidine deiminase and allophanate hydrolase represent a newly recognized pathway for the biodegradation of guanidine. These findings reinforce the relevance of guanidine as a biological metabolite and reveal a broadly distributed group of enzymes that act on guanidine in bacteria.
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Affiliation(s)
- Nicholas O Schneider
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53201-1881, United States
| | - Lambros J Tassoulas
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota 55108-6106, United States.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108-6106, United States
| | - Danyun Zeng
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201-1881, United States
| | - Amanda J Laseke
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53201-1881, United States
| | - Nicholas J Reiter
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201-1881, United States
| | - Lawrence P Wackett
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota 55108-6106, United States.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108-6106, United States
| | - Martin St Maurice
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53201-1881, United States
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21
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Nonn M, Binder A, Volk B, Kiss L. Stereo- and regiocontrolled synthesis of highly functionalized cyclopentanes with multiple chiral centers. SYNTHETIC COMMUN 2020. [DOI: 10.1080/00397911.2020.1733612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Melinda Nonn
- Institute of Pharmaceutical Chemistry, University of Szeged, Szeged, Hungary
- Interdisciplinary Excellence Centre, Institute of Pharmaceutical Chemistry, University of Szeged, Szeged, Hungary
- MTA-SZTE Stereochemistry Research Group, Hungarian Academy of Sciences, Szeged, Hungary
| | - Adrienn Binder
- Institute of Pharmaceutical Chemistry, University of Szeged, Szeged, Hungary
| | - Balázs Volk
- Directorate of Drug Substance Development, Egis Pharmaceuticals Plc., Budapest, Hungary
| | - Loránd Kiss
- Institute of Pharmaceutical Chemistry, University of Szeged, Szeged, Hungary
- Interdisciplinary Excellence Centre, Institute of Pharmaceutical Chemistry, University of Szeged, Szeged, Hungary
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22
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Wang F, Zhang WH, Zhao J, Kang WJ, Wang S, Yu B, Pan HX, Tang GL. Characterization of Miharamycin Biosynthesis Reveals a Hybrid NRPS-PKS to Synthesize High-Carbon Sugar from a Complex Nucleoside. J Am Chem Soc 2020; 142:5996-6000. [PMID: 32167762 DOI: 10.1021/jacs.0c01778] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Miharamycins are peptidyl nucleoside antibiotics with a unique branched C9 pyranosyl amino acid core and a rare 2-aminopurine moiety. Inactivation of 19 genes in the biosynthetic gene cluster and identification of several unexpected intermediates suggest an alternative biosynthetic pathway, which is further supported by feeding experiments and in vitro characterization of an unusual adenylation domain recognizing a complex nucleoside derivative as the substrate. These results thereby provide an unprecedented biosynthetic route of high-carbon sugar catalyzed by atypical hybrid nonribosomal peptide synthetase-polyketide synthase.
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Affiliation(s)
- Fei Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Wen-He Zhang
- School of Life Sciences and Biopharmaceutical Sciences, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Juan Zhao
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wen-Jia Kang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Shengyang Wang
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Biao Yu
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hai-Xue Pan
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Gong-Li Tang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China.,State Key Laboratory of Bio-Organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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23
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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: 26] [Impact Index Per Article: 4.3] [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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24
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Hill RA, Sutherland A. Hot off the Press. Nat Prod Rep 2019. [DOI: 10.1039/c9np90045d] [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
A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as burlemarxione A from Clusia burle-marxii.
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