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Identification of Sesquiterpene Synthases from the Basidiomycota Coniophora Puteana for the Efficient and Highly Selective Β-Co

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Identification of Sesquiterpene Synthases from the Basidiomycota Coniophora Puteana for the Efficient and Highly Selective Β-Co Mischko et al. Microb Cell Fact (2018) 17:164 https://doi.org/10.1186/s12934-018-1010-z Microbial Cell Factories RESEARCH Open Access Identifcation of sesquiterpene synthases from the Basidiomycota Coniophora puteana for the efcient and highly selective β‑copaene and cubebol production in E. coli Wolfgang Mischko , Max Hirte , Monika Fuchs , Norbert Mehlmer and Thomas B. Brück* Abstract Background: Terpenes are an important and extremely versatile class of secondary metabolites that are commer- cially used in the pharmaceutical, food and cosmetics sectors. Genome mining of diferent fungal collections has revealed the genetic basis for a steadily increasing number of putative terpene synthases without any detailed knowl- edge about their biochemical properties. The analysis and research of this rich genetic source provides a precious basis for the advancing biotechnological production of an almost endless number of valuable natural metabolites. Results: Three annotated terpene synthases from the little investigated Basidiomycota Coniophora puteana were studied in this work. For biochemical characterization, the heterologous expression in E. coli was conducted leading to the identifcation of two sesquiterpene synthases capable of the highly selective generation of β-copaene and cubebol. These compounds are commercially used as food and favor additives. The new enzymes show the high- est reported product selectivity for their main compounds and therefore represent the frst exclusive synthases for β-copaene (62% product selectivity) and cubebol (75% product selectivity) generation. In combination with an opti- mized heterologous microbial production system, we obtained product titers of 215 mg/L β-copaene and 497 mg/L cubebol. Conclusion: The reported product selectivity and our generated terpene titers exceed all published biotechnological data regarding the production of β-copaene and cubebol. This represents a promising and economic alternative to extraction from natural plant sources and the associated complex product purifcation. Keywords: Copaene, Cubebol, Sesquiterpene, Basidiomycota, Coniophora puteana, Heterologous expression, Fermentation, Phylogenetic analysis Background products [2]. All terpenoids are based on the same basic Filamentous fungi are experts at producing highly com- ­C5 isoprene building blocks, dimethylallyl pyrophos- plex natural compounds of commercial interest [1]. phate (DMAPP) and isopentenyl pyrophosphate (IPP), Fungal-derived polyketides have been the main focus which are consecutively fused by head to tail conden- of recent research activities, whereas the identifca- sation. Depending on their carbon chain length, these tion of terpenoids and their biosynthesis in fungi have linear phosphorylated alkenes are universal precursors received little attention although these compounds rep- of mono(C10)-, sesqui(C15)-, di(C20)-, sester(C25)- or resent the most structurally diverse group of natural tri(C30)-terpenes [3]. Te structural diversity within the class of terpenoids results from the complex cyclization of the linear precursors into chemically complex mol- *Correspondence: [email protected] Werner Siemens‑Chair of Synthetic Biotechnology, Department ecules, a reaction catalyzed by the family of terpene syn- of Chemistry, Technical University of Munich, 85748 Garching, Germany thase (TPS) enzymes. More specifcally, sesquiterpene © The Author(s) 2018. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creat​iveco​mmons​.org/licen​ses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creat​iveco​mmons​.org/ publi​cdoma​in/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Mischko et al. Microb Cell Fact (2018) 17:164 Page 2 of 13 synthases (STPSs) transform the linear C15 precursor terpene synthases from C. puteana within an optimized farnesyl pyrophosphate (FPP) into a variety of diferent production construct provided 215 mg/L β-copaene scafolds, which form the structural core of functional- and 497 mg/L cubebol. Te cubebol production titers ized, bioactive sesquiterpenoids (STPs) [2]. Many STPs reported in this study exceeded all other described pro- are lead structures in pharmaceutical applications, duction systems by a factor of 50. encompassing anti-cancer [4, 5], anti-infammatory [6, 7] and antibiotic [8] therapies. STPs also have existing appli- Results cations in the food and cosmetics industries, where they Identifcation and characterization of putative terpene are used as favor and fragrance ingredients [9, 10]. synthase genes in C. puteana As the extraction of these latter compounds from nat- A Basic Local Alignment Search Tool (BLAST) analy- ural sources is often cost-intensive and not suitable to sis of fungal genomes with conserved terpene synthases meet market demands [11], efective biotechnological sequences resulted in the identifcation of a large number production routes are the focus of development eforts of putative terpene synthases (TPSs). However, for the [12]. Due to the rapid progress of modern sequencing majority of TPS candidates, a biochemical and functional techniques, in silico genome mining based on conserved characterization remains to be established. In order to amino acid motifs can be applied to identify putative gain insight into their catalytic function, three putative TPSs [13]. Whole genome projects of diferent mush- TPSs (Copu1: XP_007772164.1; Copu2: XP_007771895.1; room-forming fungi (Basidiomycota) species represent a Copu3: XP_007765978.1) from C. puteana were selected largely unexplored source of investigation and extraction for cloning and functional characterization. Te specifc of rarely characterized STPSs [14, 15]. In this context, selection was made on the basis of characteristic con- numerous putative TPSs have already been annotated served sequence motifs. Moreover, Copu1-3 showed but their catalytic capacities remain to be established closely related amino acid (AA) sequences (55–62% simi- [14]. To exploit the biotechnological potential of fungal larity). A comparison of the AA sequence of Copu1 and biosynthetic pathways, subsequent functional expression Copu2 with the public database showed < 50% similarity and characterization of these enzymes is required. Tis to other listed enzymes, covering all biological realms. By represents the frst step in providing a sustainable supply contrast, Copu3 showed 65% similarity to putative TPS of high-value natural products using microorganisms as sequences, which were not functionally characterized. cell factories [16]. Te AA sequences of all three enzymes contained typi- Based on the available genome data, we were able to cal sequence motifs common to the TPS family, such as select potential TPSs from the Basidiomycota Coni- the highly conserved (N/D)D(L/I/V)x(S/T)xxxE (NSE) ophora puteana, which is classifed as a common wood triad and the aspartate-rich D(D/E)xxD motif, coordi- rotting fungus [17]. At present, only the enzyme systems nating a trinuclear Mg 2+ cluster, which is catalytically involved in C. puteana-dependent wood depolymeriza- essential for the initial hydrolysis of the FPP-derived tion have been characterized in detail [18, 19]. However, pyrophosphate group [22] (see Additional fle 1). A highly there are no reports of any other enzymes involved in conserved arginine residue, indicated as the pyrophos- secondary metabolite production. Terefore, this study phate sensor, is located 46 positions upstream of the NSE focuses on the identifcation and characterization of triad. Additionally, the catalytically important RY-dimer, three putative C. puteana-derived TPSs. We present the which is involved in the formation of hydrogen bonds functional reconstitution of these enzymes in an E. coli to the substrate-derived pyrophosphate, is found 80 AA whole-cell production system. With respect to designing downstream of the NSE triad and close to the C-terminus an efective STP production system, the supply of the FPP [23–25]. precursor needed to be ensured by an adapted co-expres- sion of bottleneck enzymes (DXS, Idi) from the native Heterologous expression of C. puteana TPS genes resulted non-mevalonate pathway (MEP) (Fig. 2a). Tis optimi- in the generation of diverse sesquiterpenes in E. coli zation measure ensured a directed carbon fux towards To study the product profle of Copu1-3, their pre- STP production. Two of the three identifed TPSs from dicted coding sequences were codon-optimized and C. puteana (Copu1-3) could be expressed functionally synthesized for transfer into E. coli expression vectors. in E. coli, resulting in a range of sesquiterpene products. For the heterologous expression, an adapted produc- Te main product of the Copu2 fermentations was the tion system based on a single operon with a constitu- tricyclic β-copaene. By contrast, Copu3 fermentations tive promoter was constructed. Reported bottleneck provided cubebol as the main product, which is approved enzymes from E. coli’s native non-mevalonate path- as a dietary supplement and favoring agent [9, 20] due way (MEP) were selected for co-expression (DXS; to its pronounced cooling efect [21]. Utilizing the new WP_099145004.1 and idi; AAC32208.1) to increase Mischko et al. Microb
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