Focused Genome Mining of Structurally Related Sesterterpenes: Enzymatic Formation of Enantiomeric and Diastereomeric Products

Narita, Koji; Sato, Hajime; Minami, Atsushi; Kudo, Kosei; Gao, Lei; Liu, Chengwei; Ozaki, Taro; Kodama, Motoichiro; Lei, Xiaoguang; Taniguchi, Tohru; Monde, Kenji; Yamazaki, Mami; Uchiyama, Masanobu; Oikawa, Hideaki

doi:10.1021/acs.orglett.7b03418

Cited by 50 publications

(54 citation statements)

References 18 publications

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“…We recently reported sesterfisherol synthase NfSS 3 that is a representative enzyme of fungal sesterterpene synthase and closely related enzymes 4 . Isotopic labeling experiments with [1- 13 C, 2 H 3 ]acetate and (8,8- 2 H 2 ) geranylgeranyl diphosphate indicated that the 13 C-labeling pattern of sesterfisherol ( 1 ) is identical to that of GFPP, and multiple hydrogen shifts take place during the cyclization process.…”

Section: Introductionmentioning

confidence: 99%

Theoretical Study of Sesterfisherol Biosynthesis: Computational Prediction of Key Amino Acid Residue in Terpene Synthase

Sato

Narita

Minami

et al. 2018

Sci Rep

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The cyclization mechanisms involved in the biosynthesis of sesterterpenes are not fully understood. For example, there are two plausible reaction pathways for sesterfisherol biosynthesis, which differ in the order of ring cyclization: A-D-B/C (Path a) and A-B-C/D (Path b). It is difficult to capture intermediates of terpene cyclization, which is a complex, domino-type reaction, and so here we employed a combination of experimental and computational methods. Density functional theory calculations revealed unexpected intermediates and transition states, and implied that C–H···π interaction between a carbocation intermediate and an aromatic residue of sesterfisherol synthase (NfSS) plays a critical role, serving to accelerate the 1,2-H shift (thereby preventing triquinane carbocation formation) and to protect reactive carbocation intermediates from bases such as pyrophosphate or water in the active site. Site-directed mutagenesis of NfSS guided by docking simulations confirmed that phenylalanine F191 is a critical amino acid residue for sesterfisherol synthase, as the F191A mutant of NfSS produces novel sesterterpenes, but not sesterfisherol. Although both pathways are energetically viable, on the basis of our computational and experimental results, NfSS-mediated sesterfisherol biosynthesis appears to proceed via Path a. These findings may also provide new insight into the cyclization mechanisms in related sesterterpene synthases.

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Section: Introductionmentioning

confidence: 99%

Theoretical Study of Sesterfisherol Biosynthesis: Computational Prediction of Key Amino Acid Residue in Terpene Synthase

Sato

Narita

Minami

et al. 2018

Sci Rep

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“…6B). 45) The structure of Bm2, including its absolute configuration, is the same as that of the tetracyclic carbocation, whereas the other three products are diastereomers of the bicyclic and tricyclic carbocations. This observation suggested that clade I CPF-TSs can generate various enantiomeric and diastereomeric cation intermediates that give rise to a diverse array of structural derivatives.…”

Section: Genome Mining Of Novel Nps From Silent Bgcsmentioning

confidence: 99%

Heterologous production of fungal natural products: Reconstitution of biosynthetic gene clusters in model host <i>Aspergillus oryzae</i>

Oikawa

2020

Proc. Jpn. Acad., Ser. B

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While exploring phytotoxic metabolites from phytopathogenic fungi in the 1970s, we became interested in biosynthetic enzymes that catalyze Diels–Alder reactions involving biosynthesis of several phytotoxins that we isolated. Target enzymes were successfully characterized, and this triggered the identification of various Diels–Alderases in a recent decade. Through our Diels–Alderase project in 1990s, we recognized a highly efficient expression system of various biosynthetic genes with Aspergillus oryzae as a host. With the development of tools such as genomic data and bioinformatics analysis to identify biosynthetic gene clusters for natural products, we developed a highly reliable methodology such as hot spot knock-in to elucidate the biosynthetic pathways of representative fungal metabolites including phytotoxic substances. This methodology allows total biosynthesis of natural products and genome mining using silent biosynthetic gene clusters to obtain novel bioactive metabolites. Further applications of this technology are discussed.

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“…A detailed theoretical study of sesterfisherol biosynthesis was published by Sato et al (Narita et al, 2017; Sato et al, 2018b). While they were exploring the cyclization mechanisms of sesterfisherol, a deep minima was found that required extraordinarily high energy, which was different from the activation energy in terpene biosynthesis.…”

Section: Terpenoidsmentioning

confidence: 99%

Acceleration of Mechanistic Investigation of Plant Secondary Metabolism Based on Computational Chemistry

2019

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This review describes the application of computational chemistry to plant secondary metabolism, focusing on the biosynthetic mechanisms of terpene/terpenoid, alkaloid, flavonoid, and lignin as representative examples. Through these biosynthetic studies, we exhibit several computational methods, including density functional theory (DFT) calculations, theozyme calculation, docking simulation, molecular dynamics (MD) simulation, and quantum mechanics/molecular mechanics (QM/MM) calculation. This review demonstrates how modern computational chemistry can be employed as an effective tool for revealing biosynthetic mechanisms and the potential of computational chemistry—for example, elucidating how enzymes regulate regio- and stereoselectivity, finding the key catalytic residue of an enzyme, and assessing the viability of hypothetical pathways. Furthermore, insights for the next research objective involving application of computational chemistry to plant secondary metabolism are provided herein. This review will be helpful for plant scientists who are not well versed with computational chemistry.

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Focused Genome Mining of Structurally Related Sesterterpenes: Enzymatic Formation of Enantiomeric and Diastereomeric Products

Cited by 50 publications

References 18 publications

Theoretical Study of Sesterfisherol Biosynthesis: Computational Prediction of Key Amino Acid Residue in Terpene Synthase

Theoretical Study of Sesterfisherol Biosynthesis: Computational Prediction of Key Amino Acid Residue in Terpene Synthase

Heterologous production of fungal natural products: Reconstitution of biosynthetic gene clusters in model host <i>Aspergillus oryzae</i>

Acceleration of Mechanistic Investigation of Plant Secondary Metabolism Based on Computational Chemistry

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