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Del Rio Flores A, Narayanamoorthy M, Cai W, Zhai R, Yang S, Shen Y, Seshadri K, De Matias K, Xue Z, Zhang W. Biosynthesis of Isonitrile Lipopeptide Metallophores from Pathogenic Mycobacteria. Biochemistry 2023; 62:824-834. [PMID: 36638317 PMCID: PMC9905339 DOI: 10.1021/acs.biochem.2c00611] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Isonitrile lipopeptides (INLPs) are known to be related to the virulence of pathogenic mycobacteria by mediating metal transport, but their biosynthesis remains obscure. In this work, we use in vitro biochemical assays, site-directed mutagenesis, chemical synthesis, and spectroscopy techniques to scrutinize the activity of core enzymes required for INLP biosynthesis in mycobacteria. Compared to environmental Streptomyces, pathogenic Mycobacterium employ a similar chemical logic and enzymatic machinery in INLP biosynthesis, differing mainly in the fatty-acyl chain length, which is controlled by multiple enzymes in the pathway. Our in-depth study on the non-heme iron(II) and α-ketoglutarate-dependent dioxygenase for isonitrile generation, including Rv0097 from Mycobacterium tuberculosis (Mtb), demonstrates that it recognizes a free-standing small molecule substrate, different from the recent hypothesis that a carrier protein is required for Rv0097 in Mtb. A key residue in Rv0097 is further identified to dictate the varied fatty-acyl chain length specificity between Streptomyces and Mycobacterium.
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Affiliation(s)
- Antonio Del Rio Flores
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Maanasa Narayanamoorthy
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Wenlong Cai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Rui Zhai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Siyue Yang
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Yuanbo Shen
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Kaushik Seshadri
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Kyle De Matias
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Zhaoqiang Xue
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
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Del Rio Flores A, Barber CC, Narayanamoorthy M, Gu D, Shen Y, Zhang W. Biosynthesis of Isonitrile- and Alkyne-Containing Natural Products. Annu Rev Chem Biomol Eng 2022; 13:1-24. [PMID: 35236086 PMCID: PMC9811556 DOI: 10.1146/annurev-chembioeng-092120-025140] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Natural products are a diverse class of biologically produced compounds that participate in fundamental biological processes such as cell signaling, nutrient acquisition, and interference competition. Unique triple-bond functionalities like isonitriles and alkynes often drive bioactivity and may serve as indicators of novel chemical logic and enzymatic machinery. Yet, the biosynthetic underpinnings of these groups remain only partially understood, constraining the opportunity to rationally engineer biomolecules with these functionalities for applications in pharmaceuticals, bioorthogonal chemistry, and other value-added chemical processes. Here, we focus our review on characterized biosynthetic pathways for isonitrile and alkyne functionalities, their bioorthogonal transformations, and prospects for engineering their biosynthetic machinery for biotechnological applications.
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Affiliation(s)
- Antonio Del Rio Flores
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA; ,
| | - Colin C Barber
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA;
| | | | - Di Gu
- Department of Chemistry, University of California, Berkeley, California, USA; , ,
| | - Yuanbo Shen
- Department of Chemistry, University of California, Berkeley, California, USA; , ,
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA; ,
- Chan Zuckerberg Biohub, San Francisco, California, USA
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Del Rio Flores A, Kastner DW, Du Y, Narayanamoorthy M, Shen Y, Cai W, Vennelakanti V, Zill NA, Dell LB, Zhai R, Kulik HJ, Zhang W. Probing the Mechanism of Isonitrile Formation by a Non-Heme Iron(II)-Dependent Oxidase/Decarboxylase. J Am Chem Soc 2022; 144:5893-5901. [PMID: 35254829 PMCID: PMC8986608 DOI: 10.1021/jacs.1c12891] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The isonitrile moiety is an electron-rich functionality that decorates various bioactive natural products isolated from diverse kingdoms of life. Isonitrile biosynthesis was restricted for over a decade to isonitrile synthases, a family of enzymes catalyzing a condensation reaction between l-Trp/l-Tyr and ribulose-5-phosphate. The discovery of ScoE, a non-heme iron(II) and α-ketoglutarate-dependent dioxygenase, demonstrated an alternative pathway employed by nature for isonitrile installation. Biochemical, crystallographic, and computational investigations of ScoE have previously been reported, yet the isonitrile formation mechanism remains obscure. In the present work, we employed in vitro biochemistry, chemical synthesis, spectroscopy techniques, and computational simulations that enabled us to propose a plausible molecular mechanism for isonitrile formation. Our findings demonstrate that the ScoE reaction initiates with C5 hydroxylation of (R)-3-((carboxymethyl)amino)butanoic acid to generate 1, which undergoes dehydration, presumably mediated by Tyr96 to synthesize 2 in a trans configuration. (R)-3-isocyanobutanoic acid is finally generated through radical-based decarboxylation of 2, instead of the common hydroxylation pathway employed by this enzyme superfamily.
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Affiliation(s)
- Antonio Del Rio Flores
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States 94720
| | - David W. Kastner
- Department of Bioengineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States 02139
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States 02139
| | - Yongle Du
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States 94720
| | - Maanasa Narayanamoorthy
- Department of Chemistry, University of California, Berkeley, California, United States 94720
| | - Yuanbo Shen
- Department of Chemistry, University of California, Berkeley, California, United States 94720
| | - Wenlong Cai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States 94720
| | - Vyshnavi Vennelakanti
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States 02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States 02139
| | - Nicholas A. Zill
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States 94720
| | - Luisa B. Dell
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States 94720
| | - Rui Zhai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States 94720
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States 02139
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States 94720
- Chan Zuckerberg Biohub, San Francisco, California, United States 94158
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Tao H, Mori T, Chen H, Lyu S, Nonoyama A, Lee S, Abe I. Molecular insights into the unusually promiscuous and catalytically versatile Fe(II)/α-ketoglutarate-dependent oxygenase SptF. Nat Commun 2022; 13:95. [PMID: 35013177 PMCID: PMC8748661 DOI: 10.1038/s41467-021-27636-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/01/2021] [Indexed: 11/23/2022] Open
Abstract
Non-heme iron and α-ketoglutarate-dependent (Fe/αKG) oxygenases catalyze various oxidative biotransformations. Due to their catalytic flexibility and high efficiency, Fe/αKG oxygenases have attracted keen attention for their application as biocatalysts. Here, we report the biochemical and structural characterizations of the unusually promiscuous and catalytically versatile Fe/αKG oxygenase SptF, involved in the biosynthesis of fungal meroterpenoid emervaridones. The in vitro analysis revealed that SptF catalyzes several continuous oxidation reactions, including hydroxylation, desaturation, epoxidation, and skeletal rearrangement. SptF exhibits extremely broad substrate specificity toward various meroterpenoids, and efficiently produced unique cyclopropane-ring-fused 5/3/5/5/6/6 and 5/3/6/6/6 scaffolds from terretonins. Moreover, SptF also hydroxylates steroids, including androsterone, testosterone, and progesterone, with different regiospecificities. Crystallographic and structure-based mutagenesis studies of SptF revealed the molecular basis of the enzyme reactions, and suggested that the malleability of the loop region contributes to the remarkable substrate promiscuity. SptF exhibits great potential as a promising biocatalyst for oxidation reactions.
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Affiliation(s)
- Hui Tao
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.
- PRESTO, Japan Science and Technology Agency, Saitama, Japan.
| | - Heping Chen
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Shuang Lyu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Shoukou Lee
- Sumitomo Dainippon Pharma Co., Ltd, Osaka, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.
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