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Li H, Li W, Song K, Liu Y, Zhao G, Du YL. Nitric oxide synthase-guided genome mining identifies a cytochrome P450 enzyme for olefin nitration in bacterial specialized metabolism. Synth Syst Biotechnol 2024; 9:127-133. [PMID: 38304063 PMCID: PMC10831120 DOI: 10.1016/j.synbio.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 02/03/2024] Open
Abstract
The biological signaling molecule nitric oxide (NO) has recently emerged as a metabolic precursor for the creation of microbial natural products with diversified structures and biological activities. Within the biosynthetic gene clusters (BGCs) of these compounds, genes associated with NO production pathways have been pinpointed. In this study, we employ a nitric oxide synthase (NOS)-guided genome mining strategy for the targeted discovery of NO-derived bacterial natural products and NO-utilizing biocatalysts. We show that a conserved NOS-containing BGC, distributed across several actinobacterial genomes, is responsible for the biosynthesis of lajollamycin, a unique nitro-tetraene-containing antibiotic whose biosynthetic mechanism remains elusive. Through a combination of in vivo and in vitro studies, we unveil the first cytochrome P450 enzyme capable of catalyzing olefin nitration in natural product biosynthesis. These results not only expand the current knowledge about biosynthetic nitration processes but also offer an efficient way for targeted identification of NO-utilizing metabolic pathways and novel nitrating biocatalysts.
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Affiliation(s)
- Hu Li
- Polytechnic Institute, Zhejiang University, Hangzhou, 310022, China
| | - Wei Li
- Department of Microbiology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Kaihui Song
- Department of Microbiology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yu Liu
- College of Life Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Guiyun Zhao
- Department of Microbiology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yi-Ling Du
- Polytechnic Institute, Zhejiang University, Hangzhou, 310022, China
- Department of Microbiology, Zhejiang University School of Medicine, Hangzhou, 310058, China
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Kotajima M, Choi JH, Suzuki H, Suzuki T, Wu J, Hirai H, Nelson DC, Ouchi H, Inai M, Dohra H, Kawagishi H. Identification of Biosynthetic and Metabolic Genes of 2-Azahypoxanthine in Lepista sordida Based on Transcriptomic Analysis. JOURNAL OF NATURAL PRODUCTS 2023; 86:710-718. [PMID: 36802627 DOI: 10.1021/acs.jnatprod.2c00789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
2-Azahypoxanthine was isolated from the fairy ring-forming fungus Lepista sordida as a fairy ring-inducing compound. 2-Azahypoxanthine has an unprecedented 1,2,3-triazine moiety, and its biosynthetic pathway is unknown. The biosynthetic genes for 2-azahypoxanthine formation in L. sordida were predicted by a differential gene expression analysis using MiSeq. The results revealed that several genes in the purine and histidine metabolic pathways and the arginine biosynthetic pathway are involved in the biosynthesis of 2-azahypoxanthine. Furthermore, nitric oxide (NO) was produced by recombinant NO synthase 5 (rNOS5), suggesting that NOS5 can be the enzyme involved in the formation of 1,2,3-triazine. The gene encoding hypoxanthine-guanine phosphoribosyltransferase (HGPRT), one of the major phosphoribosyltransferases of purine metabolism, increased when 2-azahypoxanthine content was the highest. Therefore, we hypothesized that HGPRT might catalyze a reversible reaction between 2-azahypoxanthine and 2-azahypoxanthine-ribonucleotide. We proved the endogenous existence of 2-azahypoxanthine-ribonucleotide in L. sordida mycelia by LC-MS/MS for the first time. Furthermore, it was shown that recombinant HGPRT catalyzed reversible interconversion between 2-azahypoxanthine and 2-azahypoxanthine-ribonucleotide. These findings demonstrate that HGPRT can be involved in the biosynthesis of 2-azahypoxanthine via 2-azahypoxanthine-ribonucleotide generated by NOS5.
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Affiliation(s)
| | | | | | - Tomohiro Suzuki
- Center for Bioscience Research and Education, Utsunomiya University, 350 mine-machi, Utsunomiya, Tochigi 321-8505, Japan
| | | | | | - David C Nelson
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521, United States
| | - Hitoshi Ouchi
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Makoto Inai
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
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Takemura H, Choi JH, Fushimi K, Narikawa R, Wu J, Kondo M, Nelson DC, Suzuki T, Ouchi H, Inai M, Hirai H, Kawagishi H. Role of hypoxanthine-guanine phosphoribosyltransferase in the metabolism of fairy chemicals in rice. Org Biomol Chem 2023; 21:2556-2561. [PMID: 36880328 DOI: 10.1039/d3ob00026e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Fairy chemicals (FCs), 2-azahypoxanthine (AHX), imidazole-4-carboxamide (ICA), and 2-aza-8-oxohypoxanthine (AOH), are molecules with many diverse functions in plants. The defined biosynthetic pathway for FCs is a novel purine metabolism in which they are biosynthesized from 5-aminoimidazole-4-carboxamide. Here, we show that one of the purine salvage enzymes, hypoxanthine-guanine phosphoribosyltransferase (HGPRT), recognizes AHX and AOH as substrates. Two novel compounds, AOH ribonucleotide and its ribonucleoside which are the derivatives of AOH, were enzymatically synthesized. The structures were determined by mass spectrometry, 1D and 2D NMR spectroscopy, and X-ray single-crystal diffraction analysis. This report demonstrates the function of HGPRT and the existence of novel purine metabolism associated with the biosynthesis of FCs in rice.
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Affiliation(s)
- Hirohide Takemura
- Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
- Research Fellow of Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Jae-Hoon Choi
- Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan.
- Research Institute for Mushroom Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Keiji Fushimi
- Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Rei Narikawa
- Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Jing Wu
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan.
- Research Institute for Mushroom Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Mitsuru Kondo
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - David C Nelson
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA
| | - Tomohiro Suzuki
- Center for Bioscience Research and Education, Utsunomiya University, 350 Minemachi, Tochigi 321-8505, Japan
| | - Hitoshi Ouchi
- Department of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Makoto Inai
- Department of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Hirofumi Hirai
- Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan.
- Research Institute for Mushroom Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Hirokazu Kawagishi
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan.
- Research Institute for Mushroom Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
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Kotajima M, Choi JH, Suzuki T, Wu J, Hirai H, Nelson DC, Ouchi H, Inai M, Dohra H, Kawagishi H. The role of xanthine dioxygenase in the biosynthetic pathway of 2-aza-8-oxohypoxanthine of Lepista sordida. Biosci Biotechnol Biochem 2023; 87:420-425. [PMID: 36756780 DOI: 10.1093/bbb/zbad005] [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: 11/18/2022] [Accepted: 01/13/2023] [Indexed: 01/20/2023]
Abstract
2-Azahypoxanthine (AHX) and 2-aza-8-oxohypoxanthine (AOH), discovered as causal substances of fairy rings are known to be endogenous in the fairy ring-forming Lepista sordida. In this study, we showed that xanthine dioxygenase, an a-ketoglutarate-dependent dioxygenase, might catalyze the conversion of AHX to AOH in the fungus. Furthermore, this enzyme is the first reported molybdopterin-independent protein of hypoxanthine metabolism.
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Affiliation(s)
- Mihaya Kotajima
- Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Japan
| | - Jae-Hoon Choi
- Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Japan
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Japan
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Japan
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Japan
- Research Institute for Mushroom Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Japan
| | - Tomohiro Suzuki
- Research Institute for Mushroom Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Japan
- Center for Bioscience Research and Education, Utsunomiya University, 350 Mine-machi, Utsunomiya, Tochigi, Japan
| | - Jing Wu
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Japan
- Research Institute for Mushroom Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Japan
| | - Hirofumi Hirai
- Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Japan
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Japan
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Japan
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Japan
- Research Institute for Mushroom Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Japan
| | - David C Nelson
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Hitoshi Ouchi
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Japan
| | - Makoto Inai
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Japan
| | - Hideo Dohra
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Japan
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Japan
- Research Institute for Mushroom Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Japan
| | - Hirokazu Kawagishi
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Japan
- Research Institute for Mushroom Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Japan
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