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Hostetler T, Chen TY, Chang WC. Bioinformatic, structural, and biochemical analysis leads to the discovery of novel isonitrilases and decodes their substrate selectivity. RSC Chem Biol 2025; 6:583-589. [PMID: 39944535 PMCID: PMC11811631 DOI: 10.1039/d4cb00304g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2024] [Accepted: 01/28/2025] [Indexed: 04/04/2025] Open
Abstract
Bacterial species, such as Mycobacterium tuberculosis, utilize isonitrile-containing peptides (INPs) for trace metal trafficking, e.g., copper or zinc. Despite their importance, very few INP structures have been characterized to date. Reported INPs consist of a peptide backbone and β-isonitrile amide moieties. While the peptide backbone can be annotated using an adenylation domain predictor of non-ribosomal peptide synthetase (NRPS), determining the alkyl chain of β-isonitrile amide moieties remains challenging via conventional analytical techniques. In this study, we focus on non-heme iron and 2-oxoglutarate (Fe/2OG) dependent isonitrilases that exhibit inherent selectivity toward the alkyl chain length of the substrate, thus enabling the structural elucidation of INPs. Based on two known isonitrilase structures, we identified eight residue positions that control substrate selectivity. Using a custom Python program that we developed, BioSynthNexus, over 350 Fe/2OG isonitrilase genes were identified. One of these enzymes was engineered through mutations at eight selected positions, effectively modifying its substrate preference to favor either a shorter or a longer alkyl chain. Furthermore, by examining several annotated isonitrilases at eight selected positions, substrate preferences of several isonitrilases were predicted and validated through biochemical assays. Together, these findings allow for effective identification of isonitrilases and INPs, and establish a predictive framework for determining the preferred alkyl chain of β-isonitrile amide moieties.
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Affiliation(s)
- Tyler Hostetler
- Department of Chemistry, North Carolina State University Raleigh NC 27695 USA
| | - Tzu-Yu Chen
- Department of Chemistry, North Carolina State University Raleigh NC 27695 USA
| | - Wei-Chen Chang
- Department of Chemistry, North Carolina State University Raleigh NC 27695 USA
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Flores ADR, Khosla C. Characterization of the Flavin-Dependent Monooxygenase Involved in the Biosynthesis of the Nocardiosis-Associated Polyketide†. Biochemistry 2024; 63:2868-2877. [PMID: 39433512 PMCID: PMC11872153 DOI: 10.1021/acs.biochem.4c00480] [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] [Indexed: 10/23/2024]
Abstract
Some species of the Nocardia genus harbor a highly conserved biosynthetic gene cluster designated as the NOCardiosis-Associated Polyketide (NOCAP) synthase that produces a unique glycolipid natural product. The NOCAP glycolipid is composed of a fully substituted benzaldehyde headgroup linked to a polyfunctional alkyl tail and an O-linked disaccharide composed of 3-α-epimycarose and 2-O-methyl-α-rhamnose. Incorporation of the disaccharide unit is preceded by a critical step involving hydroxylation by NocapM, a flavin monooxygenase. In this study, we employed biochemical, spectroscopic, and kinetic analyses to explore the substrate scope of NocapM. Our findings indicate that NocapM catalyzes hydroxylation of diverse aromatic substrates, although the observed coupling between NADPH oxidation and substrate hydroxylation varies widely from substrate to substrate. Our in-depth biochemical characterization of NocapM provides a solid foundation for future mechanistic studies of this enzyme as well as its utilization as a practical biocatalyst.
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Affiliation(s)
| | - Chaitan Khosla
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- Sarafan ChEM-H, Stanford University, Stanford, California 94305, United States
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Jia K, Sun H, Zhou Y, Zhang W. Biosynthesis of isonitrile lipopeptides. Curr Opin Chem Biol 2024; 81:102470. [PMID: 38788523 PMCID: PMC11323250 DOI: 10.1016/j.cbpa.2024.102470] [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: 02/28/2024] [Revised: 04/25/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024]
Abstract
Isonitrile lipopeptides discovered from Actinobacteria have attracted wide attention due to their fascinating biosynthetic pathways and relevance to the virulence of many human pathogens including Mycobacterium tuberculosis. Specifically, the identification of the new class of isonitrile-forming enzymes that belong to non-heme iron (II) and α-ketoglutarate dependent dioxygenases has intrigued several research groups to investigate their catalytic mechanism. Here we summarize the recent studies on the biosynthesis of isonitrile lipopeptides from Streptomyces and Mycobacterium. The latest research on the core and tailoring enzymes involved in the pathway as well as the isonitrile metabolic enzymes are discussed in this review.
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Affiliation(s)
- Kaimin Jia
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720, United States; California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA 94720, United States
| | - Helen Sun
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720, United States
| | - Yiyan Zhou
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720, United States; California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA 94720, United States.
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Del Rio Flores A, Zhai R, Zhang W. Isonitrile biosynthesis by non-heme iron(II)-dependent oxidases/decarboxylases. Methods Enzymol 2024; 704:143-172. [PMID: 39300646 PMCID: PMC11424024 DOI: 10.1016/bs.mie.2024.06.002] [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] [Indexed: 09/22/2024]
Abstract
The isonitrile group is a compact, electron-rich moiety coveted for its commonplace as a building block and bioorthogonal functionality in synthetic chemistry and chemical biology. Hundreds of natural products containing an isonitrile group with intriguing bioactive properties have been isolated from diverse organisms. Our recent discovery of a conserved biosynthetic gene cluster in some Actinobacteria species highlighted a novel enzymatic pathway to isonitrile formation involving a non-heme iron(II) and α-ketoglutarate-dependent dioxygenase. Here, we focus this chapter on recent advances in understanding and probing the biosynthetic machinery for isonitrile synthesis by non-heme iron(II) and α-ketoglutarate-dependent dioxygenases. We will begin by describing how to harness isonitrile enzymatic machinery through heterologous expression, purification, synthetic strategies, and in vitro biochemical/kinetic characterization. We will then describe a generalizable strategy to probe the mechanism for isonitrile formation by combining various spectroscopic methods. The chapter will also cover strategies to study other enzyme homologs by implementing coupled assays using biosynthetic pathway enzymes. We will conclude this chapter by addressing current challenges and future directions in understanding and engineering isonitrile synthesis.
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Affiliation(s)
- Antonio Del Rio Flores
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, United States
| | - Rui Zhai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, United States.
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Chen TY, Chen J, Ruszczycky MW, Hilovsky D, Hostetler T, Liu X, Zhou J, Chang WC. Variation in biosynthesis and metal-binding properties of isonitrile-containing peptides produced by Mycobacteria versus Streptomyces. ACS Catal 2024; 14:4975-4983. [PMID: 38895101 PMCID: PMC11185824 DOI: 10.1021/acscatal.4c00645] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
A number of bacteria are known to produce isonitrile-containing peptides (INPs) that facilitate metal transport and are important for cell survival; however, considerable structural variation is observed among INPs depending on the producing organism. While non-heme iron 2-oxoglutarate dependent isonitrilases catalyze isonitrile formation, how the natural variation in INP structure is controlled and its implications for INP bioactivity remain open questions. Herein, total chemical synthesis is utilized with X-Ray crystallographic analysis of mycobacterial isonitrilases to provide a structural model of substrate specificity that explains the longer alkyl chains observed in mycobacterial versus Streptomyces INPs. Moreover, proton NMR titration experiments demonstrate that INPs regardless of alkyl chain length are specific for binding copper instead of zinc. These results suggest that isonitrilases may act as gatekeepers in modulating the observed biological distribution of INP structures and this distribution may be primarily related to differing metal transport requirements among the producing strains.
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Affiliation(s)
- Tzu-Yu Chen
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, United States
| | - Jinfeng Chen
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Mark W Ruszczycky
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Dalton Hilovsky
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, United States
| | - Tyler Hostetler
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, United States
| | - Xiaojing Liu
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, United States
| | - Jiahai Zhou
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wei-Chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, United States
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Matsuda K, Maruyama H, Imachi K, Ikeda H, Wakimoto T. Actinobacterial chalkophores: the biosynthesis of hazimycins. J Antibiot (Tokyo) 2024; 77:228-237. [PMID: 38378905 DOI: 10.1038/s41429-024-00706-6] [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: 07/29/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/22/2024]
Abstract
Copper is a transition metal element with significant effects on the morphological development and secondary metabolism of actinobacteria. In some microorganisms, copper-binding natural products are employed to modulate copper homeostasis, although their significance in actinobacteria remains largely unknown. Here, we identified the biosynthetic genes of the diisocyanide natural product hazimycin in Kitasatospora purpeofusca HV058, through gene knock-out and heterologous expression. Biochemical analyses revealed that hazimycin A specifically binds to copper, which diminishes its antimicrobial activity. The presence of a set of putative importer/exporter genes surrounding the biosynthetic genes suggested that hazimycin is a chalkophore that modulates the intracellular copper level. A bioinformatic survey of homologous gene cassettes, as well as the identification of two previously unknown hazimycin-producing Streptomyces strains, indicated that the isocyanide-based mechanism of copper homeostasis is prevalent in actinobacteria.
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Affiliation(s)
- Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan.
| | - Hiroto Maruyama
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Kumiko Imachi
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Haruo Ikeda
- Technology Research Association for Next generation natural products chemistry, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan.
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