1
|
Gu B, Goldfuss B, Dickschat JS. Two Sesterterpene Synthases from Lentzea atacamensis Demonstrate the Role of Conformational Variability in Terpene Biosynthesis. Angew Chem Int Ed Engl 2024; 63:e202401539. [PMID: 38372063 DOI: 10.1002/anie.202401539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/20/2024]
Abstract
Mining of two multiproduct sesterterpene synthases from Lentzea atacamensis resulted in the identification of the synthases for lentzeadiene (LaLDS) and atacamatriene (LaATS). The main product of LaLDS (lentzeadiene) is a new compound, while one of the side products (lentzeatetraene) is the enantiomer of brassitetraene B and the other side product (sestermobaraene F) is known from a surprisingly distantly related sesterterpene synthase. LaATS produces six new compounds, one of which is the enantiomer of the known sesterterpene Bm1. Notably, for both enzymes the products cannot all be explained from one and the same starting conformation of geranylfarnesyl diphosphate, demonstrating the requirement of conformational flexibility of the substrate in the enzymes' active sites. For lentzeadiene an intriguing thermal [1,5]-sigmatropic rearrangement was discovered, reminiscent of the biosynthesis of vitamin D3. All enzyme reactions and the [1,5]-sigmatropic rearrangement were investigated through isotopic labeling experiments and DFT calculations. The results also emphasize the importance of conformational changes during terpene cyclizations.
Collapse
Affiliation(s)
- Binbin Gu
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Bernd Goldfuss
- Department for Chemistry, University of Cologne, Greinstraße 4, 50939, Cologne, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| |
Collapse
|
2
|
Tessmer I. The roles of non-productive complexes of DNA repair proteins with DNA lesions. DNA Repair (Amst) 2023; 129:103542. [PMID: 37453245 DOI: 10.1016/j.dnarep.2023.103542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/30/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
A multitude of different types of lesions is continuously introduced into the DNA inside our cells, and their rapid and efficient repair is fundamentally important for the maintenance of genomic stability and cellular viability. This is achieved by a number of DNA repair systems that each involve different protein factors and employ versatile strategies to target different types of DNA lesions. Intriguingly, specialized DNA repair proteins have also evolved to form non-functional complexes with their target lesions. These proteins allow the marking of innocuous lesions to render them visible for DNA repair systems and can serve to directly recruit DNA repair cascades. Moreover, they also provide links between different DNA repair mechanisms or even between DNA lesions and transcription regulation. I will focus here in particular on recent findings from single molecule analyses on the alkyltransferase-like protein ATL, which is believed to initiate nucleotide excision repair (NER) of non-native NER target lesions, and the base excision repair (BER) enzyme hOGG1, which recruits the oncogene transcription factor Myc to gene promoters under oxidative stress.
Collapse
Affiliation(s)
- Ingrid Tessmer
- Rudolf Virchow Center, University of Würzburg, Josef Schneider Str. 2, 97080 Würzburg, Germany
| |
Collapse
|
3
|
Faylo JL, Christianson DW. Visualizing transiently associated catalytic domains in assembly-line biosynthesis using cryo-electron microscopy. J Struct Biol 2021; 213:107802. [PMID: 34606906 PMCID: PMC8665010 DOI: 10.1016/j.jsb.2021.107802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/28/2021] [Indexed: 11/25/2022]
Abstract
While cryo-electron microscopy (cryo-EM) has revolutionized the structure determination of supramolecular protein complexes that are refractory to structure determination by X-ray crystallography, structure determination by cryo-EM can nonetheless be complicated by excessive conformational flexibility or structural heterogeneity resulting from weak or transient protein-protein association. Since such transient complexes are often critical for function, specialized approaches must be employed for the determination of meaningful structure-function relationships. Here, we outline examples in which transient protein-protein interactions have been visualized successfully by cryo-EM in the biosynthesis of fatty acids, polyketides, and terpenes. These studies demonstrate the utility of chemical crosslinking to stabilize transient protein-protein complexes for cryo-EM structural analysis, as well as the use of partial signal subtraction and localized reconstruction to extract useful structural information out of cryo-EM data collected from inherently dynamic systems. While these approaches do not always yield atomic resolution insights on protein-protein interactions, they nonetheless enable direct experimental observation of complexes in assembly-line biosynthesis that would otherwise be too fleeting for structural analysis.
Collapse
Affiliation(s)
- Jacque L Faylo
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.
| |
Collapse
|
4
|
Yang R, Du Z, Qiu T, Sun J, Shen Y, Huang L. Discovery and Functional Characterization of a Diverse Diterpene Synthase Family in the Medicinal Herb Isodon lophanthoides Var. gerardiana. Plant Cell Physiol 2021; 62:1423-1435. [PMID: 34133748 DOI: 10.1093/pcp/pcab089] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 06/09/2021] [Accepted: 06/16/2021] [Indexed: 06/12/2023]
Abstract
Isodon lophanthoides var. gerardiana (Lamiaceae), also named xihuangcao, is a traditional Chinese medicinal herb that exhibits a broad range of pharmacological activities. Abietane-type diterpenoids are the characteristic constituents of I. lophanthoides, yet their biosynthesis has not been elucidated. Although the aerial parts are the most commonly used organs of I. lophanthoides, metabolite profiling by gas chromatography-mass spectrometry showed the underground parts also contain large amounts of labdane diterpenoids including abietatriene, miltiradiene and ferruginol, which are distinct from the 13-hydroxy-8(14)-abietene detected in the aerial parts. Comparative transcriptome analysis of root and leaf samples identified a diverse diterpene synthase family including 6 copalyl diphosphate synthase (IlCPS1-6) and 5 kaurene synthase-like (IlKSL1-5). Here we report the functional characterization of six of these enzymes using yeast heterologous expression system. Both IlCPS1 and IlCPS3 synthesized (+)-copalyl diphosphate (CPP), in combination with IlKSL1 resulted in miltiradiene, precursor of abietane-type diterpenoids, while coupling with IlKSL5 led to the formation of hydroxylated diterpene scaffold nezukol. Expression profiling and phylogenetic analysis further support the distinct evolutionary relationship and spatial distribution of IlCPS1 and IlCPS3. IlCPS2 converted GGPP into labda-7,13E-dien-15-ol diphosphate. IlCPS6 was identified as ent-CPS, indicating a role in gibberellin metabolism. We further identified a single residue that determined the water addition of nezukol synthase IlKSL5. Substitution of alanine 513 with isoleucine completely altered the product outcome from hydroxylated nezukol to isopimara-7,15-diene. Together, these findings elucidated the early steps of bioactive abietane-type diterpenoid biosynthesis in I. lophanthoides and the catalytic mechanism of nezukol synthase.
Collapse
Affiliation(s)
- Ruikang Yang
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, 12 Jichang Rd, Guangzhou 510405, China
| | - Zuying Du
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, 12 Jichang Rd, Guangzhou 510405, China
- The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Ting Qiu
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, 12 Jichang Rd, Guangzhou 510405, China
- The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Jie Sun
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of biotechnology and bioengineering, Zhejiang University of Technology, 18 Chaowang Rd Hangzhou 310014, Zhejiang, China
| | - Yanting Shen
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, 232 Waihuan Rd, Guangzhou 510006, China
| | - Lili Huang
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, 12 Jichang Rd, Guangzhou 510405, China
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, 232 Waihuan Rd, Guangzhou 510006, China
| |
Collapse
|
5
|
Xu B, Tantillo DJ, Rudolf JD. Mechanistic Insights into the Formation of the 6,10-Bicyclic Eunicellane Skeleton by the Bacterial Diterpene Synthase Bnd4. Angew Chem Int Ed Engl 2021; 60:23159-23163. [PMID: 34378291 PMCID: PMC8511055 DOI: 10.1002/anie.202109641] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Indexed: 11/05/2022]
Abstract
The eunicellane diterpenoids are a unique family of natural products seen in marine organisms, plants, and bacteria. We used a series of biochemical, bioinformatics, and theoretical experiments to investigate the mechanism of the first diterpene synthase known to form the eunicellane skeleton. Deuterium labeling studies and quantum chemical calculations support that Bnd4, from Streptomyces sp. (CL12-4), forms the 6,10-bicyclic skeleton through a 1,10-cyclization, 1,3-hydride shift, and 1,14-cyclization cascade. Bnd4 also demonstrated sesquiterpene cyclase activity and the ability to prenylate small molecules. Bnd4 possesses a unique D94 NxxxD motif and mutation experiments confirmed an absolute requirement for D94 as well as E169.
Collapse
Affiliation(s)
- Baofu Xu
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Dean J Tantillo
- Department of Chemistry, University of California-Davis, Davis, CA, 95616, USA
| | - Jeffrey D Rudolf
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| |
Collapse
|
6
|
Ghodke PP, Guengerich FP. DNA polymerases η and κ bypass N 2-guanine-O 6-alkylguanine DNA alkyltransferase cross-linked DNA-peptides. J Biol Chem 2021; 297:101124. [PMID: 34461101 PMCID: PMC8463853 DOI: 10.1016/j.jbc.2021.101124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 11/27/2022] Open
Abstract
DNA-protein cross-links are formed when proteins become covalently trapped with DNA in the presence of exogenous or endogenous alkylating agents. If left unrepaired, they inhibit transcription as well as DNA unwinding during replication and may result in genome instability or even cell death. The DNA repair protein O6-alkylguanine DNA-alkyltransferase (AGT) is known to form DNA cross-links in the presence of the carcinogen 1,2-dibromoethane, resulting in G:C to T:A transversions and other mutations in both bacterial and mammalian cells. We hypothesized that AGT-DNA cross-links would be processed by nuclear proteases to yield peptides small enough to be bypassed by translesion (TLS) polymerases. Here, a 15-mer and a 36-mer peptide from the active site of AGT were cross-linked to the N2 position of guanine via conjugate addition of a thiol containing a peptide dehydroalanine moiety. Bypass studies with DNA polymerases (pols) η and κ indicated that both can accurately bypass the cross-linked DNA peptides. The specificity constant (kcat/Km) for steady-state incorporation of the correct nucleotide dCTP increased by 6-fold with human (h) pol κ and 3-fold with hpol η, with hpol η preferentially inserting nucleotides in the order dC > dG > dA > dT. LC-MS/MS analysis of the extension product also revealed error-free bypass of the cross-linked 15-mer peptide by hpol η. We conclude that a bulky 15-mer AGT peptide cross-linked to the N2 position of guanine can retard polymerization, but that overall fidelity is not compromised because only correct bases are inserted and extended.
Collapse
Affiliation(s)
- Pratibha P Ghodke
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
| |
Collapse
|
7
|
Helfrich F, Scheidig AJ. Structural and catalytic characterization of Blastochloris viridis and Pseudomonas aeruginosa homospermidine synthases supports the essential role of cation-π interaction. Acta Crystallogr D Struct Biol 2021; 77:1317-1335. [PMID: 34605434 PMCID: PMC8489232 DOI: 10.1107/s2059798321008937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 08/27/2021] [Indexed: 11/16/2022] Open
Abstract
Polyamines influence medically relevant processes in the opportunistic pathogen Pseudomonas aeruginosa, including virulence, biofilm formation and susceptibility to antibiotics. Although homospermidine synthase (HSS) is part of the polyamine metabolism in various strains of P. aeruginosa, neither its role nor its structure has been examined so far. The reaction mechanism of the nicotinamide adenine dinucleotide (NAD+)-dependent bacterial HSS has previously been characterized based on crystal structures of Blastochloris viridis HSS (BvHSS). This study presents the crystal structure of P. aeruginosa HSS (PaHSS) in complex with its substrate putrescine. A high structural similarity between PaHSS and BvHSS with conservation of the catalytically relevant residues is demonstrated, qualifying BvHSS as a model for mechanistic studies of PaHSS. Following this strategy, crystal structures of single-residue variants of BvHSS are presented together with activity assays of PaHSS, BvHSS and BvHSS variants. For efficient homospermidine production, acidic residues are required at the entrance to the binding pocket (`ionic slide') and near the active site (`inner amino site') to attract and bind the substrate putrescine via salt bridges. The tryptophan residue at the active site stabilizes cationic reaction components by cation-π interaction, as inferred from the interaction geometry between putrescine and the indole ring plane. Exchange of this tryptophan for other amino acids suggests a distinct catalytic requirement for an aromatic interaction partner with a highly negative electrostatic potential. These findings substantiate the structural and mechanistic knowledge on bacterial HSS, a potential target for antibiotic design.
Collapse
Affiliation(s)
- F. Helfrich
- Zoological Institute, University of Kiel, Am Botanischen Garten 1–9, 24118 Kiel, Germany
| | - Axel J. Scheidig
- Zoological Institute, University of Kiel, Am Botanischen Garten 1–9, 24118 Kiel, Germany
| |
Collapse
|
8
|
Schotte C, Lukat P, Deuschmann A, Blankenfeldt W, Cox RJ. Understanding and Engineering the Stereoselectivity of Humulene Synthase. Angew Chem Int Ed Engl 2021; 60:20308-20312. [PMID: 34180566 PMCID: PMC8457177 DOI: 10.1002/anie.202106718] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/21/2021] [Indexed: 11/09/2022]
Abstract
The non-canonical terpene cyclase AsR6 is responsible for the formation of 2E,6E,9E-humulene during the biosynthesis of the tropolone sesquiterpenoid (TS) xenovulene A. The structures of unliganded AsR6 and of AsR6 in complex with an in crystallo cyclized reaction product and thiolodiphosphate reveal a new farnesyl diphosphate binding motif that comprises a unique binuclear Mg2+ -cluster and an essential K289 residue that is conserved in all humulene synthases involved in TS formation. Structure-based site-directed mutagenesis of AsR6 and its homologue EupR3 identify a single residue, L285/M261, that controls the production of either 2E,6E,9E- or 2Z,6E,9E-humulene. A possible mechanism for the observed stereoselectivity was investigated using different isoprenoid precursors and results demonstrate that M261 has gatekeeping control over product formation.
Collapse
Affiliation(s)
- Carsten Schotte
- Institute for Organic Chemistry and BMWZLeibniz Universität HannoverSchneiderberg 3830167HannoverGermany
| | - Peer Lukat
- Structure and Function of ProteinsHelmholtz Centre for Infection ResearchInhoffenstr. 738124BraunschweigGermany
| | - Adrian Deuschmann
- Institute for Organic Chemistry and BMWZLeibniz Universität HannoverSchneiderberg 3830167HannoverGermany
| | - Wulf Blankenfeldt
- Structure and Function of ProteinsHelmholtz Centre for Infection ResearchInhoffenstr. 738124BraunschweigGermany
- Institute for Biochemistry, Biotechnology and BioinformaticsTechnische Universität BraunschweigSpielmannstr. 738106BraunschweigGermany
| | - Russell J. Cox
- Institute for Organic Chemistry and BMWZLeibniz Universität HannoverSchneiderberg 3830167HannoverGermany
| |
Collapse
|
9
|
Ashaari NS, Ab Rahim MH, Sabri S, Lai KS, Song AAL, Abdul Rahim R, Ong Abdullah J. Kinetic studies and homology modeling of a dual-substrate linalool/nerolidol synthase from Plectranthus amboinicus. Sci Rep 2021; 11:17094. [PMID: 34429465 PMCID: PMC8385045 DOI: 10.1038/s41598-021-96524-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 08/11/2021] [Indexed: 02/07/2023] Open
Abstract
Linalool and nerolidol are terpene alcohols that occur naturally in many aromatic plants and are commonly used in food and cosmetic industries as flavors and fragrances. In plants, linalool and nerolidol are biosynthesized as a result of respective linalool synthase and nerolidol synthase, or a single linalool/nerolidol synthase. In our previous work, we have isolated a linalool/nerolidol synthase (designated as PamTps1) from a local herbal plant, Plectranthus amboinicus, and successfully demonstrated the production of linalool and nerolidol in an Escherichia coli system. In this work, the biochemical properties of PamTps1 were analyzed, and its 3D homology model with the docking positions of its substrates, geranyl pyrophosphate (C10) and farnesyl pyrophosphate (C15) in the active site were constructed. PamTps1 exhibited the highest enzymatic activity at an optimal pH and temperature of 6.5 and 30 °C, respectively, and in the presence of 20 mM magnesium as a cofactor. The Michaelis-Menten constant (Km) and catalytic efficiency (kcat/Km) values of 16.72 ± 1.32 µM and 9.57 × 10-3 µM-1 s-1, respectively, showed that PamTps1 had a higher binding affinity and specificity for GPP instead of FPP as expected for a monoterpene synthase. The PamTps1 exhibits feature of a class I terpene synthase fold that made up of α-helices architecture with N-terminal domain and catalytic C-terminal domain. Nine aromatic residues (W268, Y272, Y299, F371, Y378, Y379, F447, Y517 and Y523) outlined the hydrophobic walls of the active site cavity, whilst residues from the RRx8W motif, RxR motif, H-α1 and J-K loops formed the active site lid that shielded the highly reactive carbocationic intermediates from the solvents. The dual substrates use by PamTps1 was hypothesized to be possible due to the architecture and residues lining the catalytic site that can accommodate larger substrate (FPP) as demonstrated by the protein modelling and docking analysis. This model serves as a first glimpse into the structural insights of the PamTps1 catalytic active site as a multi-substrate linalool/nerolidol synthase.
Collapse
Affiliation(s)
- Nur Suhanawati Ashaari
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Mohd Hairul Ab Rahim
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
- Department of Industrial Biotechnology, Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, 26300, Gambang, Kuantan, Pahang, Malaysia
| | - Suriana Sabri
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Kok Song Lai
- Health Sciences Division, Abu Dhabi Women's College, Higher Colleges of Technology, 41012, Abu Dhabi, United Arab Emirates
| | - Adelene Ai-Lian Song
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Raha Abdul Rahim
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Janna Ong Abdullah
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia.
| |
Collapse
|
10
|
Huang JQ, Li DM, Li JX, Lin JL, Tian X, Wang LJ, Chen XY, Fang X. 1,10/1,11-Cyclization catalyzed by diverged plant sesquiterpene synthases is dependent on a single residue. Org Biomol Chem 2021; 19:6650-6656. [PMID: 34264250 DOI: 10.1039/d1ob00827g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The exquisite chemodiversity of terpenoids is the product of the large diverse terpene synthase (TPS) superfamily. Here, by using structural and phylogenetic analyses and site-directed mutagenesis, we identified a residue (Cys440 in Nicotiana tabacum 5-epi-aristolochene synthase) proximal to an ion-binding motif common to all TPSs and named the preNSE/DTE residue, which determines the product specificity of sesquiterpene synthases from different plant species. In sesquiterpene synthases catalyzing 1,10-cyclization (1,10-cyclases) of farnesyl diphosphate, mutation of the residue in both specific and promiscuous 1,10-cyclases from different lineages leads to the accumulation of monocyclic germacrene A-11-ol, which is "short-circuited" from complex cyclization cascades, suggesting a key role of this residue in generating the first common intermediate of 1,10-cyclization. Altering this residue in a specific 1,11-cyclase results in alternative 1,10-cyclization products. Moreover, the preNSE/DTE residue can be harnessed to engineer highly specific sesquiterpene synthases for an improved proportion of high-value terpenoids, such as patchoulol, a main constituent of several traditional Chinese medicines that could treat SARS-CoV-2.
Collapse
Affiliation(s)
- Jin-Quan Huang
- Yunnan University, Kunming, PR China and National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, PR China
| | - Dong-Mei Li
- Yunnan University, Kunming, PR China and State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, PR China.
| | - Jian-Xu Li
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, PR China
| | - Jia-Ling Lin
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, PR China and School of Life Science and Technology, ShanghaiTech University, Shanghai, PR China
| | - Xiu Tian
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, PR China
| | - Ling-Jian Wang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, PR China
| | - Xiao-Ya Chen
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, PR China
| | - Xin Fang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, PR China.
| |
Collapse
|
11
|
Liang D, Li W, Yan X, Caiyin Q, Zhao G, Qiao J. Molecular and Functional Evolution of the Spermatophyte Sesquiterpene Synthases. Int J Mol Sci 2021; 22:ijms22126348. [PMID: 34198531 PMCID: PMC8232007 DOI: 10.3390/ijms22126348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/07/2021] [Accepted: 06/10/2021] [Indexed: 12/23/2022] Open
Abstract
Sesquiterpenes are important defense and signal molecules for plants to adapt to the environment, cope with stress, and communicate with the outside world, and their evolutionary history is closely related to physiological functions. In this study, the information of plant sesquiterpene synthases (STSs) with identified functions were collected and sorted to form a dataset containing about 500 members. The phylogeny of spermatophyte functional STSs was constructed based on the structural comparative analysis to reveal the sequence–structure–function relationships. We propose the evolutionary history of plant sesquiterpene skeletons, from chain structure to small rings, followed by large rings for the first time and put forward a more detailed function-driven hypothesis. Then, the evolutionary origins and history of spermatophyte STSs are also discussed. In addition, three newly identified STSs CaSTS2, CaSTS3, and CaSTS4 were analyzed in this functional evolutionary system, and their germacrene D products were consistent with the functional prediction. This demonstrates an application of the structure-based phylogeny in predicting STS function. This work will help us to understand evolutionary patterns and dynamics of plant sesquiterpenes and STSs and screen or design STSs with specific product profiles as functional elements for synthetic biology application.
Collapse
Affiliation(s)
- Dongmei Liang
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (D.L.); (W.L.); (X.Y.); (Q.C.); (G.Z.)
- Key Laboratory of Systems Bioengineering, Tianjin University, Ministry of Education, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Weiguo Li
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (D.L.); (W.L.); (X.Y.); (Q.C.); (G.Z.)
- Key Laboratory of Systems Bioengineering, Tianjin University, Ministry of Education, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Xiaoguang Yan
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (D.L.); (W.L.); (X.Y.); (Q.C.); (G.Z.)
- Key Laboratory of Systems Bioengineering, Tianjin University, Ministry of Education, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Qinggele Caiyin
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (D.L.); (W.L.); (X.Y.); (Q.C.); (G.Z.)
- Key Laboratory of Systems Bioengineering, Tianjin University, Ministry of Education, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Guangrong Zhao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (D.L.); (W.L.); (X.Y.); (Q.C.); (G.Z.)
- Key Laboratory of Systems Bioengineering, Tianjin University, Ministry of Education, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Jianjun Qiao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (D.L.); (W.L.); (X.Y.); (Q.C.); (G.Z.)
- Key Laboratory of Systems Bioengineering, Tianjin University, Ministry of Education, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology, Tianjin University, Ministry of Education, Tianjin 300072, China
- Correspondence: ; Tel.: +86-22-8740-2107
| |
Collapse
|
12
|
Faylo JL, van Eeuwen T, Kim HJ, Gorbea Colón JJ, Garcia BA, Murakami K, Christianson DW. Structural insight on assembly-line catalysis in terpene biosynthesis. Nat Commun 2021; 12:3487. [PMID: 34108468 PMCID: PMC8190136 DOI: 10.1038/s41467-021-23589-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 05/05/2021] [Indexed: 12/20/2022] Open
Abstract
Fusicoccadiene synthase from Phomopsis amygdali (PaFS) is a unique bifunctional terpenoid synthase that catalyzes the first two steps in the biosynthesis of the diterpene glycoside Fusicoccin A, a mediator of 14-3-3 protein interactions. The prenyltransferase domain of PaFS generates geranylgeranyl diphosphate, which the cyclase domain then utilizes to generate fusicoccadiene, the tricyclic hydrocarbon skeleton of Fusicoccin A. Here, we use cryo-electron microscopy to show that the structure of full-length PaFS consists of a central octameric core of prenyltransferase domains, with the eight cyclase domains radiating outward via flexible linker segments in variable splayed-out positions. Cryo-electron microscopy and chemical crosslinking experiments additionally show that compact conformations can be achieved in which cyclase domains are more closely associated with the prenyltransferase core. This structural analysis provides a framework for understanding substrate channeling, since most of the geranylgeranyl diphosphate generated by the prenyltransferase domains remains on the enzyme for cyclization to form fusicoccadiene.
Collapse
Affiliation(s)
- Jacque L Faylo
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States
| | - Trevor van Eeuwen
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Hee Jong Kim
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Jose J Gorbea Colón
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Kenji Murakami
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States.
| |
Collapse
|
13
|
Schriever K, Saenz-Mendez P, Rudraraju RS, Hendrikse NM, Hudson EP, Biundo A, Schnell R, Syrén PO. Engineering of Ancestors as a Tool to Elucidate Structure, Mechanism, and Specificity of Extant Terpene Cyclase. J Am Chem Soc 2021; 143:3794-3807. [PMID: 33496585 PMCID: PMC8023661 DOI: 10.1021/jacs.0c10214] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Indexed: 12/21/2022]
Abstract
Structural information is crucial for understanding catalytic mechanisms and to guide enzyme engineering efforts of biocatalysts, such as terpene cyclases. However, low sequence similarity can impede homology modeling, and inherent protein instability presents challenges for structural studies. We hypothesized that X-ray crystallography of engineered thermostable ancestral enzymes can enable access to reliable homology models of extant biocatalysts. We have applied this concept in concert with molecular modeling and enzymatic assays to understand the structure activity relationship of spiroviolene synthase, a class I terpene cyclase, aiming to engineer its specificity. Engineering a surface patch in the reconstructed ancestor afforded a template structure for generation of a high-confidence homology model of the extant enzyme. On the basis of structural considerations, we designed and crystallized ancestral variants with single residue exchanges that exhibited tailored substrate specificity and preserved thermostability. We show how the two single amino acid alterations identified in the ancestral scaffold can be transferred to the extant enzyme, conferring a specificity switch that impacts the extant enzyme's specificity for formation of the diterpene spiroviolene over formation of sesquiterpenes hedycaryol and farnesol by up to 25-fold. This study emphasizes the value of ancestral sequence reconstruction combined with enzyme engineering as a versatile tool in chemical biology.
Collapse
Affiliation(s)
- Karen Schriever
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Science
for Life Laboratory, KTH Royal Institute
of Technology, 114 28 Stockholm, Sweden
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Department
of Fibre and Polymer Technology, KTH Royal
Institute of Technology, 114 28 Stockholm, Sweden
| | - Patricia Saenz-Mendez
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Science
for Life Laboratory, KTH Royal Institute
of Technology, 114 28 Stockholm, Sweden
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Department
of Fibre and Polymer Technology, KTH Royal
Institute of Technology, 114 28 Stockholm, Sweden
| | | | - Natalie M. Hendrikse
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Science
for Life Laboratory, KTH Royal Institute
of Technology, 114 28 Stockholm, Sweden
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Department
of Fibre and Polymer Technology, KTH Royal
Institute of Technology, 114 28 Stockholm, Sweden
- Swedish
Orphan Biovitrum AB, 112
76 Stockholm, Sweden
| | - Elton P. Hudson
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Science
for Life Laboratory, KTH Royal Institute
of Technology, 114 28 Stockholm, Sweden
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Department
of Protein Science, KTH Royal Institute
of Technology, 114 28 Stockholm, Sweden
| | - Antonino Biundo
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Science
for Life Laboratory, KTH Royal Institute
of Technology, 114 28 Stockholm, Sweden
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Department
of Fibre and Polymer Technology, KTH Royal
Institute of Technology, 114 28 Stockholm, Sweden
| | - Robert Schnell
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, 17 165 Stockholm, Sweden
| | - Per-Olof Syrén
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Science
for Life Laboratory, KTH Royal Institute
of Technology, 114 28 Stockholm, Sweden
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Department
of Fibre and Polymer Technology, KTH Royal
Institute of Technology, 114 28 Stockholm, Sweden
- Wallenberg
Wood Science Center, Teknikringen 56−58, 100 44 Stockholm, Sweden
| |
Collapse
|
14
|
Durairaj J, Melillo E, Bouwmeester HJ, Beekwilder J, de Ridder D, van Dijk ADJ. Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases. PLoS Comput Biol 2021; 17:e1008197. [PMID: 33750949 PMCID: PMC8016262 DOI: 10.1371/journal.pcbi.1008197] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 04/01/2021] [Accepted: 02/15/2021] [Indexed: 12/19/2022] Open
Abstract
Sesquiterpene synthases (STSs) catalyze the formation of a large class of plant volatiles called sesquiterpenes. While thousands of putative STS sequences from diverse plant species are available, only a small number of them have been functionally characterized. Sequence identity-based screening for desired enzymes, often used in biotechnological applications, is difficult to apply here as STS sequence similarity is strongly affected by species. This calls for more sophisticated computational methods for functionality prediction. We investigate the specificity of precursor cation formation in these elusive enzymes. By inspecting multi-product STSs, we demonstrate that STSs have a strong selectivity towards one precursor cation. We use a machine learning approach combining sequence and structure information to accurately predict precursor cation specificity for STSs across all plant species. We combine this with a co-evolutionary analysis on the wealth of uncharacterized putative STS sequences, to pinpoint residues and distant functional contacts influencing cation formation and reaction pathway selection. These structural factors can be used to predict and engineer enzymes with specific functions, as we demonstrate by predicting and characterizing two novel STSs from Citrus bergamia.
Collapse
Affiliation(s)
- Janani Durairaj
- Bioinformatics Group, Department of Plant Sciences, Wageningen University and Research, Wageningen, The Netherlands
| | | | - Harro J. Bouwmeester
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Jules Beekwilder
- Bioscience, Wageningen Plant Research, Wageningen University and Research, Wageningen, The Netherlands
- Laboratory of Plant Physiology, Department of Plant Sciences, Wageningen University and Research, Wageningen, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Department of Plant Sciences, Wageningen University and Research, Wageningen, The Netherlands
| | - Aalt D. J. van Dijk
- Bioinformatics Group, Department of Plant Sciences, Wageningen University and Research, Wageningen, The Netherlands
- Biometris, Department of Plant Sciences, Wageningen University and Research, Wageningen, The Netherlands
| |
Collapse
|
15
|
Lackus ND, Morawetz J, Xu H, Gershenzon J, Dickschat JS, Köllner TG. The Sesquiterpene Synthase PtTPS5 Produces (1 S,5 S,7 R,10 R)-Guaia-4(15)-en-11-ol and (1 S,7 R,10 R)-Guaia-4-en-11-ol in Oomycete-Infected Poplar Roots. Molecules 2021; 26:555. [PMID: 33494506 PMCID: PMC7866031 DOI: 10.3390/molecules26030555] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/17/2021] [Accepted: 01/19/2021] [Indexed: 01/15/2023] Open
Abstract
Pathogen infection often leads to the enhanced formation of specialized plant metabolites that act as defensive barriers against microbial attackers. In this study, we investigated the formation of potential defense compounds in roots of the Western balsam poplar (Populus trichocarpa) upon infection with the generalist root pathogen Phytophthora cactorum (Oomycetes). P. cactorum infection led to an induced accumulation of terpenes, aromatic compounds, and fatty acids in poplar roots. Transcriptome analysis of uninfected and P. cactorum-infected roots revealed a terpene synthase gene PtTPS5 that was significantly induced upon pathogen infection. PtTPS5 had been previously reported as a sesquiterpene synthase producing two unidentified sesquiterpene alcohols as major products and hedycaryol as a minor product. Using heterologous expression in Escherichia coli, enzyme assays with deuterium-labeled substrates, and NMR analysis of reaction products, we could identify the major PtTPS5 products as (1S,5S,7R,10R)-guaia-4(15)-en-11-ol and (1S,7R,10R)-guaia-4-en-11-ol, with the former being a novel compound. The transcript accumulation of PtTPS5 in uninfected and P. cactorum-infected poplar roots matched the accumulation of (1S,5S,7R,10R)-guaia-4(15)-en-11-ol, (1S,7R,10R)-guaia-4-en-11-ol, and hedycaryol in this tissue, suggesting that PtTPS5 likely contributes to the pathogen-induced formation of these compounds in planta.
Collapse
Affiliation(s)
- Nathalie D. Lackus
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745 Jena, Germany; (N.D.L.); (J.M.); (J.G.)
| | - Jennifer Morawetz
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745 Jena, Germany; (N.D.L.); (J.M.); (J.G.)
| | - Houchao Xu
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany; (H.X.); (J.S.D.)
| | - Jonathan Gershenzon
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745 Jena, Germany; (N.D.L.); (J.M.); (J.G.)
| | - Jeroen S. Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany; (H.X.); (J.S.D.)
| | - Tobias G. Köllner
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745 Jena, Germany; (N.D.L.); (J.M.); (J.G.)
| |
Collapse
|
16
|
Yang M, Liu G, Yamamura Y, Chen F, Fu J. Divergent Evolution of the Diterpene Biosynthesis Pathway in Tea Plants ( Camellia sinensis) Caused by Single Amino Acid Variation of ent-Kaurene Synthase. J Agric Food Chem 2020; 68:9930-9939. [PMID: 32841021 DOI: 10.1021/acs.jafc.0c03488] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Most plant terpenoids are classified as secondary metabolites. A small portion of them are products of primary metabolism biosynthesized by relatively conserved pathways. Gibberellins (GAs), which are essential for plant growth and development, are diterpenoid phytohormones. (E,E,E)-Geranylgeranyl diphosphate (GGPP) is the precursor for both GAs and other diterpenoids of secondary metabolism. ent-Kaurene biosynthesis from GGPP is a key step of GA formation, which is catalyzed by two sequential and dedicated diterpene synthases (diTPSs): ent-copalyl diphosphate synthase (CPS) and ent-kaurene synthase (KS) of the terpene synthase gene family. Sharing a common evolutionary origin, CPS and KS belong to different TPS subfamilies. Tea plant (Camellia sinensis), the subject of this study, is a leaf-based economic crop. Budbreak mainly manipulated by GAs is a primary factor for targeted tea breeding. The key genes for gibberellin biosynthesis are known; however, they have not yet been characterized in tea plants. Here, we identified and functionally characterized three diterpene biosynthesis-related genes, including one CPS and two highly similar KSs in tea plants. These genes were initially identified through transcriptome sequencing. The functional characterization determined by enzymatic activity assay indicated that CsCPS could catalyze GGPP to form ent-copalyl diphosphate (ent-CPP), which was further used as the substrate by CsKS1 to produce ent-kaurene or by CsKS2 to produce 16α-hydroxy-ent-kaurane with ent-kaurene as a minor product, respectively. We demonstrated that the divergent evolution of diterpene biosynthesis in tea plants resulted from gene duplication of KSs, followed by functional divergence caused by single amino acid variation. This study would provide an insight into the diterpenoid metabolism and GA biosynthesis in tea plants to further understand leaf bud development or insect resistance and to provide a genetic basis for tea plant breeding.
Collapse
Affiliation(s)
- Mei Yang
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Hangzhou 310008, China
| | - Guanhua Liu
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Hangzhou 310008, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yoshimi Yamamura
- Faculty of Medicine and Pharmaceutical Sciences for Research, University of Toyama, Toyama 9300194, Japan
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jianyu Fu
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Hangzhou 310008, China
| |
Collapse
|
17
|
Edani BH, Grabińska KA, Zhang R, Park EJ, Siciliano B, Surmacz L, Ha Y, Sessa WC. Structural elucidation of the cis-prenyltransferase NgBR/DHDDS complex reveals insights in regulation of protein glycosylation. Proc Natl Acad Sci U S A 2020; 117:20794-20802. [PMID: 32817466 PMCID: PMC7456142 DOI: 10.1073/pnas.2008381117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Cis-prenyltransferase (cis-PTase) catalyzes the rate-limiting step in the synthesis of glycosyl carrier lipids required for protein glycosylation in the lumen of endoplasmic reticulum. Here, we report the crystal structure of the human NgBR/DHDDS complex, which represents an atomic resolution structure for any heterodimeric cis-PTase. The crystal structure sheds light on how NgBR stabilizes DHDDS through dimerization, participates in the enzyme's active site through its C-terminal -RXG- motif, and how phospholipids markedly stimulate cis-PTase activity. Comparison of NgBR/DHDDS with homodimeric cis-PTase structures leads to a model where the elongating isoprene chain extends beyond the enzyme's active site tunnel, and an insert within the α3 helix helps to stabilize this energetically unfavorable state to enable long-chain synthesis to occur. These data provide unique insights into how heterodimeric cis-PTases have evolved from their ancestral, homodimeric forms to fulfill their function in long-chain polyprenol synthesis.
Collapse
Affiliation(s)
- Ban H Edani
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Kariona A Grabińska
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Rong Zhang
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Eon Joo Park
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Benjamin Siciliano
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Liliana Surmacz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Ya Ha
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520;
| | - William C Sessa
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520;
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| |
Collapse
|
18
|
Liu R, Zhang H, Wu W, Li H, An Z, Zhou F. C7-Prenylation of Tryptophan-Containing Cyclic Dipeptides by 7-Dimethylallyl Tryptophan Synthase Significantly Increases the Anticancer and Antimicrobial Activities. Molecules 2020; 25:E3676. [PMID: 32806659 PMCID: PMC7463755 DOI: 10.3390/molecules25163676] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/05/2020] [Accepted: 08/10/2020] [Indexed: 02/07/2023] Open
Abstract
Prenylated natural products have interesting pharmacological properties and prenylation reactions play crucial roles in controlling the activities of biomolecules. They are difficult to synthesize chemically, but enzymatic synthesis production is a desirable pathway. Cyclic dipeptide prenyltransferase catalyzes the regioselective Friedel-Crafts alkylation of tryptophan-containing cyclic dipeptides. This class of enzymes, which belongs to the dimethylallyl tryptophan synthase superfamily, is known to be flexible to aromatic prenyl receptors, while mostly retaining its typical regioselectivity. In this study, seven tryptophan-containing cyclic dipeptides 1a-7a were converted to their C7-regularly prenylated derivatives 1b-7b in the presence of dimethylallyl diphosphate (DMAPP) by using the purified 7-dimethylallyl tryptophan synthase (7-DMATS) as catalyst. The HPLC analysis of the incubation mixture and the NMR analysis of the separated products showed that the stereochemical structure of the substrate had a great influence on their acceptance by 7-DMATS. Determination of the kinetic parameters proved that cyclo-l-Trp-Gly (1a) consisting of a tryptophanyl and glycine was accepted as the best substrate with a KM value of 169.7 μM and a turnover number of 0.1307 s-1. Furthermore, docking studies simulated the prenyl transfer reaction of 7-DMATS and it could be concluded that the highest affinity between 7-DMATS and 1a. Preliminary results have been clearly shown that prenylation at C7 led to a significant increase of the anticancer and antimicrobial activities of the prenylated derivatives 1b-7b in all the activity test experiment, especially the prenylated product 4b.
Collapse
Affiliation(s)
- Rui Liu
- College of Life Science, Shanxi Datong University, Datong 037009, China; (R.L.); (H.L.)
- Applied Biotechnology Institute, Shanxi Datong University, Datong 037009, China; (W.W.); (Z.A.); (F.Z.)
| | - Hongchi Zhang
- College of Life Science, Shanxi Datong University, Datong 037009, China; (R.L.); (H.L.)
- Applied Biotechnology Institute, Shanxi Datong University, Datong 037009, China; (W.W.); (Z.A.); (F.Z.)
| | - Weiqiang Wu
- Applied Biotechnology Institute, Shanxi Datong University, Datong 037009, China; (W.W.); (Z.A.); (F.Z.)
| | - Hui Li
- College of Life Science, Shanxi Datong University, Datong 037009, China; (R.L.); (H.L.)
- Applied Biotechnology Institute, Shanxi Datong University, Datong 037009, China; (W.W.); (Z.A.); (F.Z.)
| | - Zhipeng An
- Applied Biotechnology Institute, Shanxi Datong University, Datong 037009, China; (W.W.); (Z.A.); (F.Z.)
| | - Feng Zhou
- Applied Biotechnology Institute, Shanxi Datong University, Datong 037009, China; (W.W.); (Z.A.); (F.Z.)
| |
Collapse
|
19
|
Lemke C, Whitham O, Peters RJ. Magnesium-specific ring expansion/contraction catalysed by the class II diterpene cyclase from pleuromutilin biosynthesis. Org Biomol Chem 2020; 18:5586-5588. [PMID: 32672326 PMCID: PMC7430159 DOI: 10.1039/d0ob01422b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The class II diterpene cyclase (DTC) from pleuromutilin biosynthesis uniquely mediates 'A' ring contraction of the initially formed decalin bicycle, yielding mutildienyl diphosphate (MPP). Catalysis requires a divalent metal cation co-factor. Intriguingly, selectively with magnesium, this DTC catalyzes ring expansion/contraction between MPP and halimadienyl diphosphate, providing some catalytic insight.
Collapse
Affiliation(s)
- Cody Lemke
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA.
| | - Owen Whitham
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA.
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA.
| |
Collapse
|
20
|
Ashaari NS, Ab. Rahim MH, Sabri S, Lai KS, Song AAL, Abdul Rahim R, Wan Abdullah WMAN, Ong Abdullah J. Functional characterization of a new terpene synthase from Plectranthus amboinicus. PLoS One 2020; 15:e0235416. [PMID: 32614884 PMCID: PMC7332032 DOI: 10.1371/journal.pone.0235416] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/15/2020] [Indexed: 12/21/2022] Open
Abstract
Plectranthus amboinicus (Lour.) Spreng is an aromatic medicinal herb known for its therapeutic and nutritional properties attributed by the presence of monoterpene and sesquiterpene compounds. Up until now, research on terpenoid biosynthesis has focused on a few mint species with economic importance such as thyme and oregano, yet the terpene synthases responsible for monoterpene production in P. amboinicus have not been described. Here we report the isolation, heterologous expression and functional characterization of a terpene synthase involved in P. amboinicus terpenoid biosynthesis. A putative monoterpene synthase gene (PamTps1) from P. amboinicus was isolated with an open reading frame of 1797 bp encoding a predicted protein of 598 amino acids with molecular weight of 69.6 kDa. PamTps1 shares 60–70% amino acid sequence similarity with other known terpene synthases of Lamiaceae. The in vitro enzymatic activity of PamTps1 demonstrated the conversion of geranyl pyrophosphate and farnesyl pyrophosphate exclusively into linalool and nerolidol, respectively, and thus PamTps1 was classified as a linalool/nerolidol synthase. In vivo activity of PamTps1 in a recombinant Escherichia coli strain revealed production of linalool and nerolidol which correlated with its in vitro activity. This outcome validated the multi-substrate usage of this enzyme in producing linalool and nerolidol both in in vivo and in vitro systems. The transcript level of PamTps1 was prominent in the leaf during daytime as compared to the stem. Gas chromatography-mass spectrometry (GC-MS) and quantitative real-time PCR analyses showed that maximal linalool level was released during the daytime and lower at night following a diurnal circadian pattern which correlated with the PamTps1 expression pattern. The PamTps1 cloned herein provides a molecular basis for the terpenoid biosynthesis in this local herb that could be exploited for valuable production using metabolic engineering in both microbial and plant systems.
Collapse
Affiliation(s)
- Nur Suhanawati Ashaari
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Mohd Hairul Ab. Rahim
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Suriana Sabri
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Kok Song Lai
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi, United Arab of Emirates
| | - Adelene Ai-Lian Song
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Raha Abdul Rahim
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | | | - Janna Ong Abdullah
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, Malaysia
- * E-mail:
| |
Collapse
|
21
|
Cerda A, Moreno JC, Acosta D, Godoy F, Cáceres JC, Cabrera R, Stange C. Functional characterisation and in silico modelling of MdPSY2 variants and MdPSY5 phytoene synthases from Malus domestica. J Plant Physiol 2020; 249:153166. [PMID: 32422487 DOI: 10.1016/j.jplph.2020.153166] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 03/23/2020] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
Carotenoids are plastid isoprenoid pigments that play critical roles in light harvesting, photoprotection, and phytohormone biosynthesis. They are also vitamin-A precursors and antioxidant molecules important for human nutrition. Apples (e.g. Malus x domestica Borkh), one of the most widely consumed fruits with high nutrient levels, have a very low carotenoid concentration in flesh, compared with other fruits and vegetables. This could be explained by a deficiency in carotenoid synthesis/accumulation and/or accelerated degradation. We analysed the contribution of M. domestica cv. 'Fuji' phytoene synthase (PSY) in the biosynthesis of carotenoids and determined that among four MdPSY genes present in the organism, MdPSY2 and MdPSY5 are highly expressed in leaves and during fruit ripening in line with an increment in carotenoid content in fruits. Furthermore, two representative polymorphic MdPSY2 variants were found, one with a Tyr358Phe substitution (MdPSY2_F) and the other that additionally has a six-amino-acid deletion in the signal peptide (MdPSY2_CG). MdPSY2, MdPSY5, MdPSY2_F and MdPSY2_CG are all localised in plastids. Interestingly, the polymorphic MdPSY2_F and MdPSY2_CG variants show lower enzymatic activity than the wild-type form in a heterologous complementation assay, which could be attributed to the Tyr358Phe substitution close to the active-site pocket, as was suggested by 3-D modelling analysis. The presence of polymorphic MdPSY2 variants with lower enzymatic activity could be partially responsible for the low carotenoid content in Fuji apple fruits.
Collapse
Affiliation(s)
- Ariel Cerda
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653 Ñuñoa, Santiago, Chile
| | - Juan C Moreno
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg1 D-14476, Potsdam-Golm, Germany
| | - Daniel Acosta
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653 Ñuñoa, Santiago, Chile
| | - Francisca Godoy
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653 Ñuñoa, Santiago, Chile
| | - Juan Carlos Cáceres
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653 Ñuñoa, Santiago, Chile
| | - Ricardo Cabrera
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653 Ñuñoa, Santiago, Chile
| | - Claudia Stange
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653 Ñuñoa, Santiago, Chile.
| |
Collapse
|
22
|
Blank PN, Barnett AA, Ronnebaum TA, Alderfer KE, Gillott BN, Christianson DW, Himmelberger JA. Structural studies of geranylgeranylglyceryl phosphate synthase, a prenyltransferase found in thermophilic Euryarchaeota. Acta Crystallogr D Struct Biol 2020; 76:542-557. [PMID: 32496216 PMCID: PMC7271946 DOI: 10.1107/s2059798320004878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 04/05/2020] [Indexed: 12/26/2022] Open
Abstract
Archaea are uniquely adapted to thrive in harsh environments, and one of these adaptations involves the archaeal membrane lipids, which are characterized by their isoprenoid alkyl chains connected via ether linkages to glycerol 1-phosphate. The membrane lipids of the thermophilic and acidophilic euryarchaeota Thermoplasma volcanium are exclusively glycerol dibiphytanyl glycerol tetraethers. The first committed step in the biosynthetic pathway of these archaeal lipids is the formation of the ether linkage between glycerol 1-phosphate and geranylgeranyl diphosphate, and is catalyzed by the enzyme geranylgeranylglyceryl phosphate synthase (GGGPS). The 1.72 Å resolution crystal structure of GGGPS from T. volcanium (TvGGGPS) in complex with glycerol and sulfate is reported here. The crystal structure reveals TvGGGPS to be a dimer, which is consistent with the absence of the aromatic anchor residue in helix α5a that is required for hexamerization in other GGGPS homologs; the hexameric quaternary structure in GGGPS is thought to provide thermostability. A phylogenetic analysis of the Euryarchaeota and a parallel ancestral state reconstruction investigated the relationship between optimal growth temperature and the ancestral sequences. The presence of an aromatic anchor residue is not explained by temperature as an ecological parameter. An examination of the active site of the TvGGGPS dimer revealed that it may be able to accommodate longer isoprenoid substrates, supporting an alternative pathway of isoprenoid membrane-lipid synthesis.
Collapse
Affiliation(s)
- P. N. Blank
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - A. A. Barnett
- Department of Biology, DeSales University, 2755 Station Avenue, Center Valley, PA 18034, USA
| | - T. A. Ronnebaum
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - K. E. Alderfer
- Department of Chemistry and Physics, DeSales University, 2755 Station Avenue, Center Valley, PA 18034, USA
| | - B. N. Gillott
- Department of Chemistry and Physics, DeSales University, 2755 Station Avenue, Center Valley, PA 18034, USA
| | - D. W. Christianson
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - J. A. Himmelberger
- Department of Chemistry and Physics, DeSales University, 2755 Station Avenue, Center Valley, PA 18034, USA
| |
Collapse
|
23
|
Khalique A, Mattijssen S, Haddad AF, Chaudhry S, Maraia RJ. Targeting mitochondrial and cytosolic substrates of TRIT1 isopentenyltransferase: Specificity determinants and tRNA-i6A37 profiles. PLoS Genet 2020; 16:e1008330. [PMID: 32324744 PMCID: PMC7200024 DOI: 10.1371/journal.pgen.1008330] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 05/05/2020] [Accepted: 03/18/2020] [Indexed: 11/29/2022] Open
Abstract
The tRNA isopentenyltransferases (IPTases), which add an isopentenyl group to N6 of A37 (i6A37) of certain tRNAs, are among a minority of enzymes that modify cytosolic and mitochondrial tRNAs. Pathogenic mutations to the human IPTase, TRIT1, that decrease i6A37 levels, cause mitochondrial insufficiency that leads to neurodevelopmental disease. We show that TRIT1 encodes an amino-terminal mitochondrial targeting sequence (MTS) that directs mitochondrial import and modification of mitochondrial-tRNAs. Full understanding of IPTase function must consider the tRNAs selected for modification, which vary among species, and in their cytosol and mitochondria. Selection is principally via recognition of the tRNA A36-A37-A38 sequence. An exception is unmodified tRNATrpCCA-A37-A38 in Saccharomyces cerevisiae, whereas tRNATrpCCA is readily modified in Schizosaccharomyces pombe, indicating variable IPTase recognition systems and suggesting that additional exceptions may account for some of the tRNA-i6A37 paucity in higher eukaryotes. Yet TRIT1 had not been characterized for restrictive type substrate-specific recognition. We used i6A37-dependent tRNA-mediated suppression and i6A37-sensitive northern blotting to examine IPTase activities in S. pombe and S. cerevisiae lacking endogenous IPTases on a diversity of tRNA-A36-A37-A38 substrates. Point mutations to the TRIT1 MTS that decrease human mitochondrial import, decrease modification of mitochondrial but not cytosolic tRNAs in both yeasts. TRIT1 exhibits clear substrate-specific restriction against a cytosolic-tRNATrpCCA-A37-A38. Additional data suggest that position 32 of tRNATrpCCA is a conditional determinant for substrate-specific i6A37 modification by the restrictive IPTases, Mod5 and TRIT1. The cumulative biochemical and phylogenetic sequence analyses provide new insights into IPTase activities and determinants of tRNA-i6A37 profiles in cytosol and mitochondria.
Collapse
Affiliation(s)
- Abdul Khalique
- Intramural Research Program of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, of the National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sandy Mattijssen
- Intramural Research Program of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, of the National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alexander F. Haddad
- Intramural Research Program of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, of the National Institutes of Health, Bethesda, Maryland, United States of America
| | - Shereen Chaudhry
- Intramural Research Program of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, of the National Institutes of Health, Bethesda, Maryland, United States of America
| | - Richard J. Maraia
- Intramural Research Program of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, of the National Institutes of Health, Bethesda, Maryland, United States of America
- Commissioned Corps, United States Public Health Service, Rockville, Maryland, United States of America
| |
Collapse
|
24
|
Workman SD, Strynadka NCJ. A Slippery Scaffold: Synthesis and Recycling of the Bacterial Cell Wall Carrier Lipid. J Mol Biol 2020; 432:4964-4982. [PMID: 32234311 DOI: 10.1016/j.jmb.2020.03.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 03/18/2020] [Accepted: 03/25/2020] [Indexed: 01/20/2023]
Abstract
The biosynthesis of bacterial cell envelope polysaccharides such as peptidoglycan relies on the use of a dedicated carrier lipid both for the assembly of precursors at the cytoplasmic face of the plasma membrane and for the translocation of lipid linked oligosaccharides across the plasma membrane into the periplasmic space. This dedicated carrier lipid, undecaprenyl phosphate, results from the dephosphorylation of undecaprenyl pyrophosphate, which is generated de novo in the cytoplasm by undecaprenyl pyrophosphate synthase and released as a by-product when newly synthesized glycans are incorporated into the existing cell envelope. The de novo synthesis of undecaprenyl pyrophosphate has been thoroughly characterized from a structural and mechanistic standpoint; however, its dephosphorylation to the active carrier lipid form, both in the course of de novo synthesis and recycling, has only been begun to be studied in depth in recent years. This review provides an overview of bacterial carrier lipid synthesis and presents the current state of knowledge regarding bacterial carrier lipid recycling.
Collapse
Affiliation(s)
- Sean D Workman
- Department of Biochemistry and Molecular Biology and the Center for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada V6T 1Z3
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and the Center for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada V6T 1Z3.
| |
Collapse
|
25
|
Abstract
Covering: up to July 2019 Terpene synthases (TSs) are responsible for generating much of the structural diversity found in the superfamily of terpenoid natural products. These elegant enzymes mediate complex carbocation-based cyclization and rearrangement cascades with a variety of electron-rich linear and cyclic substrates. For decades, two main classes of TSs, divided by how they generate the reaction-triggering initial carbocation, have dominated the field of terpene enzymology. Recently, several novel and unconventional TSs that perform TS-like reactions but do not resemble canonical TSs in sequence or structure have been discovered. In this review, we identify 12 families of non-canonical TSs and examine their sequences, structures, functions, and proposed mechanisms. Nature provides a wide diversity of enzymes, including prenyltransferases, methyltransferases, P450s, and NAD+-dependent dehydrogenases, as well as completely new enzymes, that utilize distinctive reaction mechanisms for TS chemistry. These unique non-canonical TSs provide immense opportunities to understand how nature evolved different tools for terpene biosynthesis by structural and mechanistic characterization while affording new probes for the discovery of novel terpenoid natural products and gene clusters via genome mining. With every new discovery, the dualistic paradigm of TSs is contradicted and the field of terpene chemistry and enzymology continues to expand.
Collapse
Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Chin-Yuan Chang
- Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan, Republic of China
| |
Collapse
|
26
|
Abstract
Isotopic labeling experiments performed with a newly identified bacterial trichoacorenol synthase established a 1,5-hydride shift occurring in the cyclization mechanism. During EI-MS analysis, major fragments of the sesquiterpenoid were shown to arise via cryptic hydrogen movements. Therefore, the interpretation of earlier results regarding the cyclization mechanism obtained by feeding experiments in Trichoderma is revised.
Collapse
Affiliation(s)
- Jan Rinkel
- Kekulé Institute of Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Strasse 153121BonnGermany
| | - Jeroen S. Dickschat
- Kekulé Institute of Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Strasse 153121BonnGermany
| |
Collapse
|
27
|
Rinkel J, Steiner ST, Bian G, Chen R, Liu T, Dickschat JS. A Family of Related Fungal and Bacterial Di- and Sesterterpenes: Studies on Fusaterpenol and Variediene. Chembiochem 2020; 21:486-491. [PMID: 31476106 PMCID: PMC7065159 DOI: 10.1002/cbic.201900462] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Indexed: 01/28/2023]
Abstract
The absolute configuration of fusaterpenol (GJ1012E) has been revised by an enantioselective deuteration strategy. A bifunctional enzyme with a terpene synthase and a prenyltransferase domain from Aspergillus brasiliensis was characterised as variediene synthase, and the absolute configuration of its product was elucidated. The uniform absolute configurations of these and structurally related di- and sesterterpenes together with a common stereochemical course for the geminal methyl groups of GGPP unravel a similar conformational fold of the substrate in the active sites of the terpene synthases. For variediene, a thermal reaction observed during GC/MS analysis was studied in detail for which a surprising mechanism was uncovered.
Collapse
Affiliation(s)
- Jan Rinkel
- Kekulé Institute of Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Strasse 153121BonnGermany
| | - Simon T. Steiner
- Kekulé Institute of Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Strasse 153121BonnGermany
| | - Guangkai Bian
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education andWuhan University School of Pharmaceutical Sciences185 Dunghu RoadWuhan430071P. R. China
| | - Rong Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education andWuhan University School of Pharmaceutical Sciences185 Dunghu RoadWuhan430071P. R. China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education andWuhan University School of Pharmaceutical Sciences185 Dunghu RoadWuhan430071P. R. China
| | - Jeroen S. Dickschat
- Kekulé Institute of Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Strasse 153121BonnGermany
| |
Collapse
|
28
|
Subramanian M, Marudhamuthu M. Hitherto Unknown Terpene Synthase Organization in Taxol-Producing Endophytic Bacteria Isolated from Marine Macroalgae. Curr Microbiol 2020; 77:918-923. [PMID: 31970484 DOI: 10.1007/s00284-020-01878-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/07/2020] [Indexed: 11/27/2022]
Abstract
Taxol is a successful anti-cancer drug, which extensively studied in Taxus spp. However, microbial endophytes also reported as taxol producers, and especially fungal endophytes extensively studied for the taxol biosynthesis pathway. Although it was well considered, the taxol biosynthesis pathway remains undisclosed since its discovery in bacteria. To decipher this gap, we isolated and identified the endophytic bacteria such as Bacillus flexus strain DMTMMB08, Bacillus licheniformis strain DMTMMB10, and Oceanobacillus picturae strain DMTMMB24, which are unprecedented for taxol production. Subsequently, the genome annotation of these bacteria exhibited the isoprene biosynthesis pathway and terpene synthase profile. Feasibly, this is the very first report on taxol-producing endophytic bacteria from the non-Taxus host and solitary investigation on its genome analysis. The genomic insight into the bacterial system for taxol biosynthesis leads to understanding the terpene synthesis and evolution. This piece of work could expand our perception of the diversity of terpenes and their related natural products.
Collapse
Affiliation(s)
- Mugesh Subramanian
- Department of Microbial Technology, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamilnadu, India
| | - Murugan Marudhamuthu
- Department of Microbial Technology, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamilnadu, India.
| |
Collapse
|
29
|
Thorpe JH, Wall ID, Sinnamon RH, Taylor AN, Stavenger RA. Cocktailed fragment screening by X-ray crystallography of the antibacterial target undecaprenyl pyrophosphate synthase from Acinetobacter baumannii. Acta Crystallogr F Struct Biol Commun 2020; 76:40-46. [PMID: 31929185 PMCID: PMC6957112 DOI: 10.1107/s2053230x19017199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/24/2019] [Indexed: 11/10/2022] Open
Abstract
Direct soaking of protein crystals with small-molecule fragments grouped into complementary clusters is a useful technique when assessing the potential of a new crystal system to support structure-guided drug discovery. It provides a robustness check prior to any extensive crystal screening, a double check for assay binding cutoffs and structural data for binding pockets that may or may not be picked out in assay measurements. The structural output from this technique for three novel fragment molecules identified to bind to the antibacterial target Acinetobacter baumannii undecaprenyl pyrophosphate synthase are reported, and the different physicochemical requirements of a successful antibiotic are compared with traditional medicines.
Collapse
Affiliation(s)
- James H. Thorpe
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, England
| | - Ian D. Wall
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, England
| | - Robert H. Sinnamon
- GlaxoSmithKline, Upper Providence, 1250 South Collegeville Road, PO Box 5089, Collegeville, PA 19426-0989, USA
| | - Amy N. Taylor
- GlaxoSmithKline, Upper Providence, 1250 South Collegeville Road, PO Box 5089, Collegeville, PA 19426-0989, USA
| | - Robert A. Stavenger
- GlaxoSmithKline, Upper Providence, 1250 South Collegeville Road, PO Box 5089, Collegeville, PA 19426-0989, USA
| |
Collapse
|
30
|
Malkowski SN, Spencer TCJ, Breaker RR. Evidence that the nadA motif is a bacterial riboswitch for the ubiquitous enzyme cofactor NAD . RNA 2019; 25:1616-1627. [PMID: 31467147 PMCID: PMC6859854 DOI: 10.1261/rna.072538.119] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 07/29/2019] [Indexed: 05/04/2023]
Abstract
The nadA motif is a riboswitch candidate present in various Acidobacteria species that was previously identified by bioinformatic analysis of bacterial DNA data sets. More than 100 unique representatives have been identified exclusively upstream of nadA genes, which code for an enzyme in the biosynthetic pathway of the ubiquitous coenzyme NAD+ The architecture of nadA motif RNAs suggests they use structurally similar tandem ligand-binding aptamer domains to control translation initiation. Biochemical analyses reveal that the first domain selectively binds ligands carrying an adenosine 5'-diphosphate (5' ADP) moiety, including NAD+ and its reduced form, NADH. Genetic analyses indicate that a tandem nadA motif RNA suppresses gene expression when NAD+ is abundant, and that both aptamer domains are required for maximal gene regulation. However, we have not observed selective binding of the nicotinamide moiety of NAD+ or binding by the second putative aptamer in vitro, despite sequence and structural similarities between the tandem domains.
Collapse
Affiliation(s)
- Sarah N Malkowski
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Tara C J Spencer
- Department of Biology, Howard University, Washington, D.C. 20059, USA
| | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA
| |
Collapse
|
31
|
Hu L, Chen Q, Wang Y, Zhang N, Meng P, Liu T, Bu Y. Sp1 Mediates the Constitutive Expression and Repression of the PDSS2 Gene in Lung Cancer Cells. Genes (Basel) 2019; 10:E977. [PMID: 31783675 PMCID: PMC6947312 DOI: 10.3390/genes10120977] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/14/2019] [Accepted: 11/19/2019] [Indexed: 01/29/2023] Open
Abstract
Prenyl diphosphate synthase subunit 2 (PDSS2) is the first key enzyme in the CoQ10 biosynthesis pathway, and contributes to various metabolic and nephritic diseases. It has been reported that PDSS2 is downregulated in several types of tumors and acts as a potential tumor suppressor gene to inhibit the proliferation and migration of cancer cells. However, the regulatory mechanism of PDSS2 expression remains elusive. In the present study, we first identified and characterized the PDSS2 promoter region. We established four different luciferase reporter constructs which mainly cover the 2 kb region upstream of the PDSS2 gene transcription initiation site. Series luciferase reporter assay demonstrated that all four constructs have prominent promoter activity, and the core promoter of PDSS2 is mainly located within the 202 bp region near its transcription initiation site. Transcription factor binding site analysis revealed that the PDSS2 promoter contains binding sites for canonical transcription factors such as Sp1 and GATA-1. Overexpression of Sp1 significantly inhibited PDSS2 promoter activity, as well as its endogenous expression, at both mRNA and protein levels in lung cancer cells. Site-directed mutagenesis assay further confirmed that the Sp1 binding sites are essential for proximal prompter activity of PDSS2. Consistently, a selective Sp1 inhibitor, mithramycin A, treatment repressed the PDSS2 promoter activity, as well as its endogenous expression. Chromatin immunoprecipitation (ChIP) assay revealed that Sp1 binds to the PDSS2 promoter in vivo. Of note, the expression of Sp1 and PDSS2 are negatively correlated, and higher Sp1 expression with low PDSS2 expression is significantly associated with poor prognosis in lung cancer. Taken together, our results strongly suggest the essential role of Sp1 in maintaining the basic constitutive expression of PDSS2, and the pathogenic implication of Sp1-mediated PDSS2 transcriptional repression in lung cancer cells.
Collapse
Affiliation(s)
- Lanyue Hu
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; (L.H.); (Q.C.); (Y.W.); (N.Z.); (P.M.); (T.L.)
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Quanmei Chen
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; (L.H.); (Q.C.); (Y.W.); (N.Z.); (P.M.); (T.L.)
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Yitao Wang
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; (L.H.); (Q.C.); (Y.W.); (N.Z.); (P.M.); (T.L.)
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Na Zhang
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; (L.H.); (Q.C.); (Y.W.); (N.Z.); (P.M.); (T.L.)
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Peixin Meng
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; (L.H.); (Q.C.); (Y.W.); (N.Z.); (P.M.); (T.L.)
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Tong Liu
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; (L.H.); (Q.C.); (Y.W.); (N.Z.); (P.M.); (T.L.)
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Youquan Bu
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; (L.H.); (Q.C.); (Y.W.); (N.Z.); (P.M.); (T.L.)
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| |
Collapse
|
32
|
Nemoto N, Miyazono KI, Tanokura M, Yamagishi A. Crystal structure of (S)-3-O-geranylgeranylglyceryl phosphate synthase from Thermoplasma acidophilum in complex with the substrate sn-glycerol 1-phosphate. Acta Crystallogr F Struct Biol Commun 2019; 75:470-479. [PMID: 31282866 PMCID: PMC6613444 DOI: 10.1107/s2053230x19007453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/22/2019] [Indexed: 01/17/2023] Open
Abstract
(S)-3-O-Geranylgeranylglyceryl phosphate synthase (GGGPS) catalyzes the initial ether-bond formation between sn-glycerol 1-phosphate (G1P) and geranylgeranyl pyrophosphate to synthesize (S)-3-O-geranylgeranylglyceryl phosphate in the production of an archaeal cell-membrane lipid molecule. Archaeal GGGPS proteins are divided into two groups (group I and group II). In this study, the crystal structure of the archaeal group II GGGPS from Thermoplasma acidophilum (TaGGGPS) was determined at 2.35 Å resolution. The structure of TaGGGPS showed that it has a TIM-barrel fold, the third helix of which is disordered (α3*), and that it forms a homodimer, although a pre-existing structure of an archaeal group II GGGPS (from Methanothermobacter thermautotrophicus) showed a hexameric form. The structure of TaGGGPS showed the precise G1P-recognition mechanism of an archaeal group II GGGPS. The structure of TaGGGPS and molecular-dynamics simulation analysis showed fluctuation of the β2-α2, α3* and α5a regions, which is predicted to be important for substrate uptake and/or product release by TaGGGPS.
Collapse
Affiliation(s)
- Naoki Nemoto
- Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
- Department of Life Science, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Ken-ichi Miyazono
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masaru Tanokura
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akihiko Yamagishi
- Department of Life Science, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| |
Collapse
|
33
|
Kuchay S, Wang H, Marzio A, Jain K, Homer H, Fehrenbacher N, Philips MR, Zheng N, Pagano M. GGTase3 is a newly identified geranylgeranyltransferase targeting a ubiquitin ligase. Nat Struct Mol Biol 2019; 26:628-636. [PMID: 31209342 PMCID: PMC6609460 DOI: 10.1038/s41594-019-0249-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 05/10/2019] [Indexed: 11/25/2022]
Abstract
Protein prenylation is believed to be catalyzed by three heterodimeric enzymes: FTase, GGTase1 and GGTase2. Here we report the identification of a previously unknown human prenyltransferase complex consisting of an orphan prenyltransferase α-subunit, PTAR1, and the catalytic β-subunit of GGTase2, RabGGTB. This enzyme, which we named GGTase3, geranylgeranylates FBXL2 to allow its localization at cell membranes, where this ubiquitin ligase mediates the polyubiquitylation of membrane-anchored proteins. In cells, FBXL2 is specifically recognized by GGTase3 despite having a typical carboxy-terminal CaaX prenylation motif that is predicted to be recognized by GGTase1. Our crystal structure analysis of the full-length GGTase3-FBXL2-SKP1 complex reveals an extensive multivalent interface specifically formed between the leucine-rich repeat domain of FBXL2 and PTAR1, which unmasks the structural basis of the substrate-enzyme specificity. By uncovering a missing prenyltransferase and its unique mode of substrate recognition, our findings call for a revision of the 'prenylation code'.
Collapse
Affiliation(s)
- Shafi Kuchay
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA
- Perlmutter NYU Cancer Center, New York University School of Medicine, New York, NY, USA
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Hui Wang
- Department of Pharmacology, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Antonio Marzio
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Perlmutter NYU Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Kunj Jain
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Perlmutter NYU Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Harrison Homer
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Perlmutter NYU Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Nicole Fehrenbacher
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Perlmutter NYU Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Mark R Philips
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Perlmutter NYU Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Ning Zheng
- Department of Pharmacology, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA.
- Perlmutter NYU Cancer Center, New York University School of Medicine, New York, NY, USA.
| |
Collapse
|
34
|
Chen Y, Bai B, Yan H, Wen F, Qin D, Jander G, Xia Q, Wang G. Systemic disruption of the homeostasis of transfer RNA isopentenyltransferase causes growth and development abnormalities in Bombyx mori. Insect Mol Biol 2019; 28:380-391. [PMID: 30548717 DOI: 10.1111/imb.12561] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Isopentenylation at A37 (i6 A37) of some transfer RNAs (tRNAs) plays a vital role in regulating the efficiency and fidelity of protein synthesis. However, whether insects, which are well known for their highly efficient protein synthesis machinery, employ this regulatory mechanism remains uninvestigated. In the current study, a candidate tRNA isopentenyltransferase (IPT) gene with three alternative splicing isoforms (BmIPT1-BmIPT3) was identified in Bombyx mori (silkworm). Only BmIPT1 could complement a yeast mutant lacking tRNA IPT. Phylogenetic analysis showed that silkworm tRNA IPT is conserved in the Lepidoptera. BmIPT was expressed in all B. mori tissues and organs that were investigated, but was expressed at a significantly higher level in silk glands of the fourth instar compared to the first day of the fifth instar. Interestingly, BmIPT was expressed at a significantly higher level in the domesticated silkworm, B. mori, than in wild Bombyx mandarina in multiple tissues and organs. Knock-down of BmIPT by RNA interference caused severe abnormalities in silk spinning and metamorphosis. Constitutive overexpression of BmIPT1 using a cytoplasmic actin 4 promoter in B. mori raised its messenger RNA level more than sixfold compared with nontransgenic insects and led to significant decreases in the body weight and cocoon shell ratio. Together, these results confirm the first functional tRNA IPT in insects and show that a suitable expression level of tRNA IPT is vital for silk spinning, normal growth, and metamorphosis. Thus, i6 A modification at position A37 in tRNA probably plays an important role in B. mori protein synthesis.
Collapse
Affiliation(s)
- Y Chen
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - B Bai
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - H Yan
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - F Wen
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - D Qin
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - G Jander
- Boyce Thompson Institute, Ithaca, NY, USA
| | - Q Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, China
| | - G Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, China
| |
Collapse
|
35
|
Dhiman RK, Pujari V, Kincaid JM, Ikeh MA, Parish T, Crick DC. Characterization of MenA (isoprenyl diphosphate:1,4-dihydroxy-2-naphthoate isoprenyltransferase) from Mycobacterium tuberculosis. PLoS One 2019; 14:e0214958. [PMID: 30978223 PMCID: PMC6461227 DOI: 10.1371/journal.pone.0214958] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 03/22/2019] [Indexed: 12/18/2022] Open
Abstract
The menaquinone biosynthetic pathway presents a promising drug target against Mycobacterium tuberculosis and potentially other Gram-positive pathogens. In the present study, the essentiality, steady state kinetics of MenA from M. tuberculosis and the mechanism of MenA inhibition by Ro 48-8071 were characterized. MenA [isoprenyl diphosphate:1,4-dihydroxy-2-naphthoate (DHNA) isoprenyltransferase] catalyzes a critical reaction in menaquinone biosynthesis that involves the conversion of cytosolic DHNA, to membrane bound demethylmenaquinone by transferring a hydrophobic 45-carbon isoprenoid chain (in the case of mycobacteria) to the ring nucleus of DHNA. Rv0534c previously identified as the gene encoding MenA in M. tuberculosis complemented a menA deletion in E. coli and an E. coli host expressing Rv0534c exhibited an eight-fold increase in MenA specific activity over the control strain harboring empty vector under similar assay conditions. Expression of Rv0534c is essential for mycobacterial survival and the native enzyme from M. tuberculosis H37Rv was characterized using membrane preparations as it was not possible to solubilize and purify the recombinant enzyme. The enzyme is absolutely dependent on the presence of a divalent cation for optimal activity with Mg+2 being the most effective and is active over a wide pH range, with pH 8.5 being optimal. The apparent Km values for DHNA and farnesyl diphosphate were found to be 8.2 and 4.3 μM, respectively. Ro 48-8071, a compound previously reported to inhibit mycobacterial MenA activity, is non-competitive with regard to DHNA and competitive with regard to the isoprenyldiphosphate substrate.
Collapse
Affiliation(s)
- Rakesh K. Dhiman
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States of America
| | - Venugopal Pujari
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States of America
| | - James M. Kincaid
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States of America
| | - Melanie A. Ikeh
- Queen Mary University of London, Barts & The London School of Medicine and Dentistry, London, United Kingdom
| | - Tanya Parish
- Queen Mary University of London, Barts & The London School of Medicine and Dentistry, London, United Kingdom
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States of America
| | - Dean C. Crick
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States of America
| |
Collapse
|
36
|
Ko TP, Xiao X, Guo RT, Huang JW, Liu W, Chen CC. Substrate-analogue complex structure of Mycobacterium tuberculosis decaprenyl diphosphate synthase. Acta Crystallogr F Struct Biol Commun 2019; 75:212-216. [PMID: 30950820 PMCID: PMC6450523 DOI: 10.1107/s2053230x19001213] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 01/22/2019] [Indexed: 12/03/2022] Open
Abstract
Decaprenyl diphosphate synthase from Mycobacterium tuberculosis (MtDPPS, also known as Rv2361c) catalyzes the consecutive elongation of ω,E,Z-farnesyl diphosphate (EZ-FPP) by seven isoprene units by forming new cis double bonds. The protein folds into a butterfly-like homodimer like most other cis-type prenyltransferases. The starting allylic substrate EZ-FPP is bound to the S1 site and the homoallylic substrate to be incorporated, isopentenyl diphosphate, is bound to the S2 site. Here, a 1.55 Å resolution structure of MtDPPS in complex with the substrate analogues geranyl S-thiodiphosphate (GSPP) and isopentenyl S-thiodiphosphate bound to their respective sites in one subunit clearly shows the active-site configuration and the magnesium-coordinated geometry for catalysis. The ligand-binding mode of GSPP in the other subunit indicates a possible pathway of product translocation from the S2 site to the S1 site, as required for the next step of the reaction. The preferred binding of negatively charged effectors to the S1 site also suggests a promising direction for inhibitor design.
Collapse
Affiliation(s)
- Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Xiansha Xiao
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, People’s Republic of China
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 43420, People’s Republic of China
| | - Jian-Wen Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 43420, People’s Republic of China
| | - Weidong Liu
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, People’s Republic of China
| | - Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 43420, People’s Republic of China
| |
Collapse
|
37
|
Su P, Gao L, Liu S, Guan H, Wang J, Zhang Y, Zhao Y, Hu T, Tu L, Zhou J, Ma B, Liu X, Huang L, Gao W. Probing the function of protein farnesyltransferase in Tripterygium wilfordii. Plant Cell Rep 2019; 38:211-220. [PMID: 30506368 DOI: 10.1007/s00299-018-2363-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/25/2018] [Indexed: 06/09/2023]
Abstract
We found two subunits FTase/GGTaseI-α and FTase-β formed a heterodimer to transfer a farnesyl group from FPP to protein N-dansyl-GCVLS, confirming they are responsible for protein farnesylation in planta. Tripterygium wilfordii is a medicinal plant with a broad spectrum of anti-inflammatory, immunosuppressive and anti-cancer activities. Recently, a number of studies have focused on investigating the biosynthetic pathways of its bioactive compounds, whereas little attention has been paid to the enzymes which play important roles in regulating diverse developmental processes of T. wilfordii. In this study, we report for the first time the identification and characterization of two subunits of farnesyltransferase (FTase), farnesyltransferase/geranylgeranyltransferase I-α (TwFTase/GGTase I-α) and farnesyltransferase-β (TwFTase-β), in this important medicinal plant. Cell-free in vivo assays, yeast two-hybrid (Y2H) and pull-down assays showed that the two subunits interact with each other to form a heterodimer to perform the role of specifically transferring a farnesyl group from FPP to the CAAX-box protein N-dansyl-GCVLS. Furthermore, we discovered that the two subunits had the same cytoplasmic localization pattern and displayed the same tissue expression pattern. These results indicated that we identified a functional TwFTase enzyme which contains two functionally complementary subunits TwFTase/GGTase I-α and TwFTase-β, which provides us promising genetic targets to construct transgenic plants or screen for more adaptable T. wilfordii mutants, which are able to survive in changing environments.
Collapse
Affiliation(s)
- Ping Su
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 10069, China
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Linhui Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 10069, China
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Shuang Liu
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Hongyu Guan
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 10069, China
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China
- Beijing University of Chinese Medicine Third Affiliated Hospital, Beijing, 100029, China
| | - Jian Wang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yifeng Zhang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 10069, China
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yujun Zhao
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Tianyuan Hu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 10069, China
| | - Lichan Tu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 10069, China
| | - Jiawei Zhou
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 10069, China
| | - Baowei Ma
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 10069, China
| | - Xihong Liu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 10069, China
| | - Luqi Huang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Wei Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 10069, China.
| |
Collapse
|
38
|
Durairaj J, Di Girolamo A, Bouwmeester HJ, de Ridder D, Beekwilder J, van Dijk AD. An analysis of characterized plant sesquiterpene synthases. Phytochemistry 2019; 158:157-165. [PMID: 30446165 DOI: 10.1016/j.phytochem.2018.10.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 10/23/2018] [Accepted: 10/24/2018] [Indexed: 05/04/2023]
Abstract
Plants exhibit a vast array of sesquiterpenes, C15 hydrocarbons which often function as herbivore-repellents or pollinator-attractants. These in turn are produced by a diverse range of sesquiterpene synthases. A comprehensive analysis of these enzymes in terms of product specificity has been hampered by the lack of a centralized resource of sufficient functionally annotated sequence data. To address this, we have gathered 262 plant sesquiterpene synthase sequences with experimentally characterized products. The annotated enzyme sequences allowed for an analysis of terpene synthase motifs, leading to the extension of one motif and recognition of a variant of another. In addition, putative terpene synthase sequences were obtained from various resources and compared with the annotated sesquiterpene synthases. This analysis indicated regions of terpene synthase sequence space which so far are unexplored experimentally. Finally, we present a case describing mutational studies on residues altering product specificity, for which we analyzed conservation in our database. This demonstrates an application of our database in choosing likely-functional residues for mutagenesis studies aimed at understanding or changing sesquiterpene synthase product specificity.
Collapse
Affiliation(s)
- Janani Durairaj
- Bioinformatics Group, Department of Plant Sciences, Wageningen University, Netherlands.
| | - Alice Di Girolamo
- Laboratory of Plant Physiology, Department of Plant Sciences, Wageningen University, Netherlands.
| | - Harro J Bouwmeester
- Swammerdam Institute for Life Sciences, University of Amsterdam, Netherlands.
| | - Dick de Ridder
- Bioinformatics Group, Department of Plant Sciences, Wageningen University, Netherlands.
| | - Jules Beekwilder
- Laboratory of Plant Physiology, Department of Plant Sciences, Wageningen University, Netherlands; Bioscience, Wageningen Plant Research, Wageningen University, Netherlands.
| | - Aalt Dj van Dijk
- Bioinformatics Group, Department of Plant Sciences, Wageningen University, Netherlands; Biometris, Department of Plant Sciences, Wageningen University, Netherlands.
| |
Collapse
|
39
|
Ko TP, Huang CH, Lai SJ, Chen Y. Structure of undecaprenyl pyrophosphate synthase from Acinetobacter baumannii. Acta Crystallogr F Struct Biol Commun 2018; 74:765-769. [PMID: 30511669 PMCID: PMC6277960 DOI: 10.1107/s2053230x18012931] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 09/13/2018] [Indexed: 04/06/2024] Open
Abstract
Undecaprenyl pyrophosphate (UPP) is an important carrier of the oligosaccharide component in peptidoglycan synthesis. Inhibition of UPP synthase (UPPS) may be an effective strategy in combating the pathogen Acinetobacter baumannii, which has evolved to be multidrug-resistant. Here, A. baumannii UPPS (AbUPPS) was cloned, expressed, purified and crystallized, and its structure was determined by X-ray diffraction. Each chain of the dimeric protein folds into a central β-sheet with several surrounding α-helices, including one at the C-terminus. In the active site, two molecules of citrate interact with the side chains of the catalytic aspartate and serine. These observations may provide a structural basis for inhibitor design against AbUPPS.
Collapse
Affiliation(s)
- Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chi-Hung Huang
- Department of Biotechnology, HungKuang University, Taichung, Taiwan
| | - Shu-Jung Lai
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yeh Chen
- Department of Biotechnology, HungKuang University, Taichung, Taiwan
| |
Collapse
|
40
|
Wang P, Wang Y. Cytotoxic and mutagenic properties of O6-alkyl-2'-deoxyguanosine lesions in Escherichia coli cells. J Biol Chem 2018; 293:15033-15042. [PMID: 30068548 PMCID: PMC6166734 DOI: 10.1074/jbc.ra118.004676] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/19/2018] [Indexed: 11/06/2022] Open
Abstract
Environmental exposure and cellular metabolism can give rise to DNA alkylation, which can occur on the nitrogen and oxygen atoms of nucleobases, as well as on the phosphate backbone. Although O6-alkyl-2'-deoxyguanosine (O6-alkyl-dG) lesions are known to be associated with cancer, not much is known about how the alkyl group structures in these lesions affect their repair and replicative bypass in vivo or how translesion synthesis DNA polymerases influence the latter process. To answer these questions, here we synthesized oligodeoxyribonucleotides harboring seven O6-alkyl-dG lesions, with the alkyl group being Me, Et, nPr, iPr, nBu, iBu, or sBu, and examined the impact of these lesions on DNA replication in Escherichia coli cells. We found that replication past all the O6-alkyl-dG lesions was highly efficient and that SOS-induced DNA polymerases play redundant roles in bypassing these lesions. Moreover, these lesions directed exclusively the G → A mutation, the frequency of which increased with the size of the alkyl group on the DNA. This could be attributed to the varied repair efficiencies of these lesions by O6-alkylguanine DNA alkyltransferase (MGMT) in cells, which involve the MGMT Ogt and, to a lesser extent, Ada. In conclusion, our study provides important new knowledge about the repair of the O6-alkyl-dG lesions and their recognition by the E. coli DNA replication machinery. Our results suggest that the lesions' carcinogenic potentials may be attributed, at least in part, to their strong mutagenic potential and their efficient bypass by the DNA replication machinery.
Collapse
Affiliation(s)
- Pengcheng Wang
- From the Department of Chemistry, University of California, Riverside, California 92521-0403
| | - Yinsheng Wang
- From the Department of Chemistry, University of California, Riverside, California 92521-0403
| |
Collapse
|
41
|
Huynh F, Grundy DJ, Jenkins RL, Miller DJ, Allemann RK. Sesquiterpene Synthase-Catalysed Formation of a New Medium-Sized Cyclic Terpenoid Ether from Farnesyl Diphosphate Analogues. Chembiochem 2018; 19:1834-1838. [PMID: 29802753 PMCID: PMC6334173 DOI: 10.1002/cbic.201800218] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Indexed: 11/08/2022]
Abstract
Terpene synthases catalyse the first step in the conversion of prenyl diphosphates to terpenoids. They act as templates for their substrates to generate a reactive conformation, from which a Mg2+ -dependent reaction creates a carbocation-PPi ion pair that undergoes a series of rearrangements and (de)protonations to give the final terpene product. This tight conformational control was exploited for the (R)-germacrene A synthase- and germacradien-4-ol synthase-catalysed formation of a medium-sized cyclic terpenoid ether from substrates containing nucleophilic functional groups. Farnesyl diphosphate analogues with a 10,11-epoxide or an allylic alcohol were efficiently converted to a 11-membered cyclic terpenoid ether that was characterised by HRMS and NMR spectroscopic analyses. Further experiments showed that other sesquiterpene synthases, including aristolochene synthase, δ-cadinene synthase and amorphadiene synthase, yielded this novel terpenoid from the same substrate analogues. This work illustrates the potential of terpene synthases for the efficient generation of structurally and functionally novel medium-sized terpene ethers.
Collapse
Affiliation(s)
- Florence Huynh
- School of ChemistryCardiff UniversityMain BuildingPark PlaceCardiffCF10 3ATUK
| | - Daniel J. Grundy
- School of ChemistryCardiff UniversityMain BuildingPark PlaceCardiffCF10 3ATUK
| | - Robert L. Jenkins
- School of ChemistryCardiff UniversityMain BuildingPark PlaceCardiffCF10 3ATUK
| | - David J. Miller
- School of ChemistryCardiff UniversityMain BuildingPark PlaceCardiffCF10 3ATUK
| | - Rudolf K. Allemann
- School of ChemistryCardiff UniversityMain BuildingPark PlaceCardiffCF10 3ATUK
| |
Collapse
|
42
|
Zhang Y, Liu K, Zhu X, Wu Y, Zhang S, Chen H, Ling J, Wang Y, Fang X. Rice tocopherol deficiency 1 encodes a homogentisate phytyltransferase essential for tocopherol biosynthesis and plant development in rice. Plant Cell Rep 2018; 37:775-787. [PMID: 29427065 DOI: 10.1007/s00299-018-2266-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/29/2018] [Indexed: 06/08/2023]
Abstract
RTD1 encodes a homogentisate phytyltransferase catalyzing a key step in rice tocopherol biosynthesis, confers cold tolerance and regulates rice development by affecting the accumulation of DELLA protein SLENDER RICE1. Tocopherols are one of the most important lipid-soluble antioxidants having indispensable roles in living organisms. The physiological functions of tocopherols have been comprehensively characterized in animals and artificial membranes. However, genetic and molecular functions of tocopherols in plants are less understood. This study aimed to isolate a tocopherol-deficient mutant rtd1 in rice. The rtd1 mutant showed overall growth retardation throughout the growth period. Most of the agronomic traits were impaired in rtd1. Map-based cloning revealed that the RTD1 gene encoded a homogentisate phytyltransferase, a key enzyme catalyzing the committed step in tocopherol biosynthesis. RTD1 was preferentially expressed in green leafy tissues, and the protein was located in chloroplasts. Cold tolerance was found to be reduced in rtd1. The cold-related C-repeat-binding factor (CBF)/dehydration-responsive element-binding protein 1 (DREB1) genes were significantly upregulated in rtd1 under natural growth conditions. Moreover, rtd1 exhibited a reduced response to gibberellin (GA).The transcript and protein levels of DELLA protein-coding gene SLENDER RICE 1 (SLR1) in rice was increased in rtd1. However, the GA content was not changed, suggesting a transcriptional, not posttranslational, regulation of SLR1. These findings implied that tocopherols play important roles in regulating rice growth and development.
Collapse
Affiliation(s)
- Yunhui Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences/The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210014, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Kai Liu
- Institute of Agricultural Sciences in Jiangsu Coastal Areas, Yancheng, 224002, China
| | - Xiaomei Zhu
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences/The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210014, China
| | - Yan Wu
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences/The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210014, China
| | - Suobing Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences/The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210014, China
| | - Haiyuan Chen
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences/The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210014, China
| | - Jing Ling
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences/The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210014, China
| | - Yingjie Wang
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences/The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210014, China
| | - Xianwen Fang
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences/The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210014, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
| |
Collapse
|
43
|
Sato H, Narita K, Minami A, Yamazaki M, Wang C, Suemune H, Nagano S, Tomita T, Oikawa H, Uchiyama M. Theoretical Study of Sesterfisherol Biosynthesis: Computational Prediction of Key Amino Acid Residue in Terpene Synthase. Sci Rep 2018; 8:2473. [PMID: 29410538 PMCID: PMC5802712 DOI: 10.1038/s41598-018-20916-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/17/2018] [Indexed: 01/07/2023] Open
Abstract
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.
Collapse
Affiliation(s)
- Hajime Sato
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Elements Chemistry Laboratory, RIKEN, and RIKEN Center for Sustainable Resource Science (Wako campus), 2-1 Hirosawa, Wako-shi, Saitama-ken, 351-0198, Japan.
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan.
| | - Koji Narita
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Atsushi Minami
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
| | - Chao Wang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Elements Chemistry Laboratory, RIKEN, and RIKEN Center for Sustainable Resource Science (Wako campus), 2-1 Hirosawa, Wako-shi, Saitama-ken, 351-0198, Japan
| | - Hironori Suemune
- Department of Engineering, Graduate School of Sustainability Science, Tottori University, Tottori, 680-8552, Japan
| | - Shingo Nagano
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, 680-8552, Japan
| | - Takeo Tomita
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hideaki Oikawa
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Elements Chemistry Laboratory, RIKEN, and RIKEN Center for Sustainable Resource Science (Wako campus), 2-1 Hirosawa, Wako-shi, Saitama-ken, 351-0198, Japan.
| |
Collapse
|
44
|
Loizzi M, González V, Miller DJ, Allemann RK. Nucleophilic Water Capture or Proton Loss: Single Amino Acid Switch Converts δ-Cadinene Synthase into Germacradien-4-ol Synthase. Chembiochem 2018; 19:100-105. [PMID: 29115742 PMCID: PMC5814876 DOI: 10.1002/cbic.201700531] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Indexed: 11/07/2022]
Abstract
δ-Cadinene synthase is a sesquiterpene cyclase that utilises the universal achiral precursor farnesyl diphosphate (FDP) to generate predominantly the bicyclic sesquiterpene δ-cadinene and about 2 % germacradien-4-ol, which is also generated from FDP by the cyclase germacradien-4-ol synthase. Herein, the mechanism by which sesquiterpene synthases discriminate between deprotonation and reaction with a nucleophilic water molecule was investigated by site-directed mutagenesis of δ-cadinene synthase. If W279 in δ-cadinene synthase was replaced with various smaller amino acids, the ratio of alcohol versus hydrocarbon product was directly proportional to the van der Waals volume of the amino acid side chain. DCS-W279A is a catalytically highly efficient germacradien-4-ol synthase (kcat /KM =1.4×10-3 μm s-1 ) that produces predominantly germacradien-4-ol in addition to 11 % δ-cadinene. Water capture is not achieved through strategic positioning of a water molecule in the active site, but through a coordinated series of loop movements that allow bulk water access to the final carbocation in the active site prior to product release.
Collapse
Affiliation(s)
- Marianna Loizzi
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
| | - Veronica González
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
| | - David J. Miller
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
| | - Rudolf K. Allemann
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
| |
Collapse
|
45
|
Jin B, Cui G, Guo J, Tang J, Duan L, Lin H, Shen Y, Chen T, Zhang H, Huang L. Functional Diversification of Kaurene Synthase-Like Genes in Isodon rubescens. Plant Physiol 2017; 174:943-955. [PMID: 28381502 PMCID: PMC5462038 DOI: 10.1104/pp.17.00202] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/03/2017] [Indexed: 05/11/2023]
Abstract
Ent-kaurene diterpenoids are the largest group of known Isodon diterpenoids. Among them, oridonin is accumulated in the leaves, and is the most frequently studied compound because of its antitumor and antibacterial activities. We have identified five copalyl diphosphate synthase (CPS) and six kaurene synthase-like (KSL) genes by transcriptome profiling of Isodon rubescens leaves. An in vitro assay assigns ten of them to five different diterpene biosynthesis pathways, except IrCPS3 that has a mutation in the catalytic motif. The Lamiaceae-specific clade genes (IrCPS1 and IrCPS2) synthesize the intermediate copalyl diphosphate (normal-CPP), while IrCPS4 and IrCPS5 synthesize the intermediate ent-copalyl diphosphate (ent-CPP). IrKSL2, IrKSL4, and IrKSL5 react with ent-CPP to produce an ent-isopimaradiene-like compound, ent-atiserene and ent-kaurene, respectively. Correspondingly, the Lamiaceae-specific clade genes IrKSL1 or IrKSL3 combined with normal-CPP led to the formation of miltiradiene. The compound then underwent aromatization and oxidization with a cytochrome P450 forming two related compounds, abietatriene and ferruginol, which were detected in the root bark. IrKSL6 reacts with normal-CPP to produce isopimaradiene. IrKSL3 and IrKSL6 have the γβα tridomain structure, as these proteins tend to possess the bidomain structure of IrKSL1, highlighting the evolutionary history of KSL gene domain loss and further elucidating chemical diversity evolution from a macroevolutionary stance in Lamiaceae.
Collapse
Affiliation(s)
- Baolong Jin
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China (B.J., G.C., J.G., J.T., H.L., Y.S., T.C., H.Z., L.H.); and
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (L.D.)
| | - Guanghong Cui
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China (B.J., G.C., J.G., J.T., H.L., Y.S., T.C., H.Z., L.H.); and
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (L.D.)
| | - Juan Guo
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China (B.J., G.C., J.G., J.T., H.L., Y.S., T.C., H.Z., L.H.); and
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (L.D.)
| | - Jinfu Tang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China (B.J., G.C., J.G., J.T., H.L., Y.S., T.C., H.Z., L.H.); and
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (L.D.)
| | - Lixin Duan
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China (B.J., G.C., J.G., J.T., H.L., Y.S., T.C., H.Z., L.H.); and
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (L.D.)
| | - Huixin Lin
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China (B.J., G.C., J.G., J.T., H.L., Y.S., T.C., H.Z., L.H.); and
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (L.D.)
| | - Ye Shen
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China (B.J., G.C., J.G., J.T., H.L., Y.S., T.C., H.Z., L.H.); and
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (L.D.)
| | - Tong Chen
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China (B.J., G.C., J.G., J.T., H.L., Y.S., T.C., H.Z., L.H.); and
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (L.D.)
| | - Huabei Zhang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China (B.J., G.C., J.G., J.T., H.L., Y.S., T.C., H.Z., L.H.); and
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (L.D.)
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China (B.J., G.C., J.G., J.T., H.L., Y.S., T.C., H.Z., L.H.); and
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (L.D.)
| |
Collapse
|
46
|
Hansen NL, Nissen JN, Hamberger B. Two residues determine the product profile of the class II diterpene synthases TPS14 and TPS21 of Tripterygium wilfordii. Phytochemistry 2017; 138:52-56. [PMID: 28279524 DOI: 10.1016/j.phytochem.2017.02.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/16/2017] [Accepted: 02/22/2017] [Indexed: 05/22/2023]
Abstract
The medicinal plant Tripterygium wilfordii (Celastraceae) contains a pair of class II diterpene synthases (diTPS) of specialized labdane-type metabolism that, despite remarkably close homology, form strikingly different products. TwTPS21 catalyzes bicyclization of the linear C20 precursor geranylgeranyl diphosphate to ent-copal-8-ol diphosphate, while TwTPS14 forms kolavenyl diphosphate. To determine the amino acid signature controlling the functional divergence of the homologues, we modeled their structures based on an existing crystal structure of the Arabidopsis ent-copalyl diphosphate synthase, archetypal of diTPSs in general metabolism of gibberellin phytohormones. Of the residues differing between TwTPS21 and TwTPS14 two located to the predicted active site, and we hypothesized that these are responsible for the functional differentiation of the enzymes. Using site-directed mutagenesis, we generated a panel of six variants, where one, or both positions were exchanged between the enzymes. In coupled heterologous assays with a corresponding class I diTPS, TwTPS2, complete product interchange was observed in variants with both reciprocal mutations, while substitutions of either residue gave mixed product profiles. Two mutants, TwTPS14:Y265H and TwTPS21:A325V, also produced ent-copalyl diphosphate, highlighting the evolutionary potential of enzymes of this family to drive rapid diversification of plant diterpene biosynthesis through neo-functionalization. Our study contributes to the understanding of structure-function relation in plant class II diTPSs and complements previous mutational studies of Arabidopsis ent-copalyl diphosphate synthase with additional examples from the specialized metabolism of T. wilfordii.
Collapse
Affiliation(s)
- Nikolaj L Hansen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Denmark; Center for Synthetic Biology "bioSYNergy" and Copenhagen Plant Sciences Centre, Denmark
| | - Jakob N Nissen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Denmark; Center for Synthetic Biology "bioSYNergy" and Copenhagen Plant Sciences Centre, Denmark
| | - Björn Hamberger
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Denmark; Center for Synthetic Biology "bioSYNergy" and Copenhagen Plant Sciences Centre, Denmark.
| |
Collapse
|
47
|
Pelot KA, Hagelthorn LM, Addison JB, Zerbe P. Biosynthesis of the oxygenated diterpene nezukol in the medicinal plant Isodon rubescens is catalyzed by a pair of diterpene synthases. PLoS One 2017; 12:e0176507. [PMID: 28445526 PMCID: PMC5405970 DOI: 10.1371/journal.pone.0176507] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/11/2017] [Indexed: 01/09/2023] Open
Abstract
Plants produce an immense diversity of natural products (i.e. secondary or specialized metabolites) that offer a rich source of known and potentially new pharmaceuticals and other desirable bioproducts. The Traditional Chinese Medicinal plant Isodon rubescens (Lamiaceae) contains an array of bioactive labdane-related diterpenoid natural products. Of these, the ent-kauranoid oridonin is the most prominent specialized metabolite that has been extensively studied for its potent antimicrobial and anticancer efficacy. Mining of a previously established transcriptome of I. rubescens leaf tissue identified seven diterpene synthase (diTPSs) candidates. Here we report the functional characterization of four I. rubescens diTPSs. IrTPS5 and IrTPS3 were identified as an ent-copalyl diphosphate (CPP) synthase and a (+)-CPP synthase, respectively. Distinct transcript abundance of IrTPS5 and the predicted ent-CPP synthase IrTPS1 suggested a role of IrTPS5 in specialized ent-kaurene metabolism possibly en route to oridonin. Nicotiana benthamiana co-expression assays demonstrated that IrTPS4 functions sequentially with IrTPS3 to form miltiradiene. In addition, IrTPS2 converted the IrTPS3 product (+)-CPP into the hydroxylated tricyclic diterpene nezukol not previously identified in I. rubescens. Metabolite profiling verified the presence of nezukol in I. rubescens leaf tissue. The proposed IrTPS2-catalyzed reaction mechanism proceeds via the common ionization of the diphosphate group of (+)-CPP, followed by formation of an intermediary pimar-15-en-8-yl+ carbocation and neutralization of the carbocation by water capture at C-8 to yield nezukol, as confirmed by nuclear magnetic resonance (NMR) analysis. Oxygenation activity is rare for the family of class I diTPSs and offers new catalysts for developing metabolic engineering platforms to produce a broader spectrum of bioactive diterpenoid natural products.
Collapse
Affiliation(s)
- Kyle A. Pelot
- Department of Plant Biology, University of California-Davis, Davis, California, United States of America
| | - Lynne M. Hagelthorn
- Department of Plant Biology, University of California-Davis, Davis, California, United States of America
| | - J. Bennett Addison
- Department of Chemistry, University of California-Davis, Davis, California, United States of America
| | - Philipp Zerbe
- Department of Plant Biology, University of California-Davis, Davis, California, United States of America
| |
Collapse
|
48
|
Adal AM, Sarker LS, Lemke AD, Mahmoud SS. Isolation and functional characterization of a methyl jasmonate-responsive 3-carene synthase from Lavandula x intermedia. Plant Mol Biol 2017; 93:641-657. [PMID: 28258552 DOI: 10.1007/s11103-017-0588-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/23/2017] [Indexed: 06/06/2023]
Abstract
A methyl jasmonate responsive 3-carene synthase (Li3CARS) gene was isolated from Lavandula x intermedia and functionally characterized in vitro. Lavenders produce essential oils consisting mainly of monoterpenes, including the potent antimicrobial and insecticidal monoterpene 3-carene. In this study we isolated and functionally characterized a leaf-specific, methyl jasmonate (MeJA)-responsive monoterpene synthase (Li3CARS) from Lavandula x intermedia. The ORF excluding transit peptides encoded a 64.9 kDa protein that was expressed in E. coli, and purified with Ni-NTA agarose affinity chromatography. The recombinant Li3CARS converted GPP into 3-carene as the major product, with K m and k cat of 3.69 ± 1.17 µM and 2.01 s-1 respectively. Li3CARS also accepted NPP as a substrate to produce multiple products including a small amount of 3-carene. The catalytic efficiency of Li3CARS to produce 3-carene was over ten fold higher for GPP (k cat /K m = 0.56 µM-1s-1) than NPP (k cat /K m = 0.044 µM-1s-1). Production of distinct end product profiles from different substrates (GPP versus NPP) by Li3CARS indicates that monoterpene metabolism may be controlled in part through substrate availability. Li3CARS transcripts were found to be highly abundant in leaves (16-fold) as compared to flower tissues. The transcriptional activity of Li3CARS correlated with 3-carene production, and was up-regulated (1.18- to 3.8-fold) with MeJA 8-72 h post-treatment. The results suggest that Li3CARS may have a defensive role in Lavandula.
Collapse
Affiliation(s)
- Ayelign M Adal
- Department of Biology, University of British Columbia, 1177 Research Rd, Kelowna, BC. V1V 1V7, Canada
| | - Lukman S Sarker
- Department of Biology, University of British Columbia, 1177 Research Rd, Kelowna, BC. V1V 1V7, Canada
| | - Ashley D Lemke
- Department of Biology, University of British Columbia, 1177 Research Rd, Kelowna, BC. V1V 1V7, Canada
| | - Soheil S Mahmoud
- Department of Biology, University of British Columbia, 1177 Research Rd, Kelowna, BC. V1V 1V7, Canada.
| |
Collapse
|
49
|
Piechulla B, Bartelt R, Brosemann A, Effmert U, Bouwmeester H, Hippauf F, Brandt W. The α-Terpineol to 1,8-Cineole Cyclization Reaction of Tobacco Terpene Synthases. Plant Physiol 2016; 172:2120-2131. [PMID: 27729471 PMCID: PMC5129724 DOI: 10.1104/pp.16.01378] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 10/05/2016] [Indexed: 05/06/2023]
Abstract
Flowers of Nicotiana species emit a characteristic blend including the cineole cassette monoterpenes. This set of terpenes is synthesized by multiproduct enzymes, with either 1,8-cineole or α-terpineol contributing most to the volatile spectrum, thus referring to cineole or terpineol synthase, respectively. To understand the molecular and structural requirements of the enzymes that favor the biochemical formation of α-terpineol and 1,8-cineole, site-directed mutagenesis, in silico modeling, and semiempiric calculations were performed. Our results indicate the formation of α-terpineol by a nucleophilic attack of water. During this attack, the α-terpinyl cation is stabilized by π-stacking with a tryptophan side chain (tryptophan-253). The hypothesized catalytic mechanism of α-terpineol-to-1,8-cineole conversion is initiated by a catalytic dyad (histidine-502 and glutamate-249), acting as a base, and a threonine (threonine-278) providing the subsequent rearrangement from terpineol to cineol by catalyzing the autoprotonation of (S)-(-)-α-terpineol, which is the favored enantiomer product of the recombinant enzymes. Furthermore, by site-directed mutagenesis, we were able to identify amino acids at positions 147, 148, and 266 that determine the different terpineol-cineole ratios in Nicotiana suaveolens cineole synthase and Nicotiana langsdorffii terpineol synthase. Since amino acid 266 is more than 10 Å away from the active site, an indirect effect of this amino acid exchange on the catalysis is discussed.
Collapse
Affiliation(s)
- Birgit Piechulla
- Institute of Biological Sciences, Biochemistry, University of Rostock, 18059 Rostock, Germany (B.P., A.B., U.E., F.H.);
- Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (R.B., W.B.); and
- Plant Sciences, University of Wageningen, 6708PB Wageningen, The Netherlands (H.B.)
| | - Richard Bartelt
- Institute of Biological Sciences, Biochemistry, University of Rostock, 18059 Rostock, Germany (B.P., A.B., U.E., F.H.)
- Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (R.B., W.B.); and
- Plant Sciences, University of Wageningen, 6708PB Wageningen, The Netherlands (H.B.)
| | - Anne Brosemann
- Institute of Biological Sciences, Biochemistry, University of Rostock, 18059 Rostock, Germany (B.P., A.B., U.E., F.H.)
- Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (R.B., W.B.); and
- Plant Sciences, University of Wageningen, 6708PB Wageningen, The Netherlands (H.B.)
| | - Uta Effmert
- Institute of Biological Sciences, Biochemistry, University of Rostock, 18059 Rostock, Germany (B.P., A.B., U.E., F.H.)
- Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (R.B., W.B.); and
- Plant Sciences, University of Wageningen, 6708PB Wageningen, The Netherlands (H.B.)
| | - Harro Bouwmeester
- Institute of Biological Sciences, Biochemistry, University of Rostock, 18059 Rostock, Germany (B.P., A.B., U.E., F.H.)
- Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (R.B., W.B.); and
- Plant Sciences, University of Wageningen, 6708PB Wageningen, The Netherlands (H.B.)
| | - Frank Hippauf
- Institute of Biological Sciences, Biochemistry, University of Rostock, 18059 Rostock, Germany (B.P., A.B., U.E., F.H.)
- Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (R.B., W.B.); and
- Plant Sciences, University of Wageningen, 6708PB Wageningen, The Netherlands (H.B.)
| | - Wolfgang Brandt
- Institute of Biological Sciences, Biochemistry, University of Rostock, 18059 Rostock, Germany (B.P., A.B., U.E., F.H.)
- Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (R.B., W.B.); and
- Plant Sciences, University of Wageningen, 6708PB Wageningen, The Netherlands (H.B.)
| |
Collapse
|
50
|
Nguyen TD, Faraldos JA, Vardakou M, Salmon M, O'Maille PE, Ro DK. Discovery of germacrene A synthases in Barnadesia spinosa: The first committed step in sesquiterpene lactone biosynthesis in the basal member of the Asteraceae. Biochem Biophys Res Commun 2016; 479:622-627. [PMID: 27697527 DOI: 10.1016/j.bbrc.2016.09.165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 09/30/2016] [Indexed: 12/21/2022]
Abstract
The Andes-endemic Barnadesioideae lineage is the oldest surviving and phylogenetically basal subfamily of the Asteraceae (Compositae), a prolific group of flowering plants with world-wide distribution (∼24,000 species) marked by a rich diversity of sesquiterpene lactones (STLs). Intriguingly, there is no evidence that members of the Barnadesioideae produce STLs, specialized metabolites thought to have contributed to the adaptive success of the Asteraceae family outside South America. The biosynthesis of STLs requires the intimate expression and functional integration of germacrene A synthase (GAS) and germacrene A oxidase (GAO) to sequentially cyclize and oxidize farnesyl diphosphate into the advanced intermediate germacrene A acid leading to diverse STLs. Our previous discovery of GAO activity conserved across all major subfamilies of Asteraceae, including the phylogenetically basal lineage of Barnadesioideae, prompted further investigation of the presence of the gateway GAS in Barnadesioideae. Herein we isolated two terpene synthases (BsGAS1/BsGAS2) from the basal Barnadesia spinosa (Barnadesioideae) that displayed robust GAS activity when reconstituted in yeast and characterized in vitro. Despite the apparent lack of STLs in the Barnadesioideae, this work unambiguously confirms the presence of GAS in the basal genera of the Asteraceae. Phylogenetic analysis reveals that the two BsGASs fall into two distinct clades of the Asteraceae's GASs, and BsGAS1 clade is only retained in the evolutionary closer Cichorioideae subfamily, implicating BsGAS2 is likely the ancestral base of most GASs found in the lineages outside the Barnadesioideae. Taken together, these results show the enzymatic capacities of GAS and GAO emerged prior to the subsequent radiation of STL-producing Asteraceae subfamilies.
Collapse
Affiliation(s)
- Trinh-Don Nguyen
- University of Calgary, Department of Biological Sciences, Calgary, T2N 1N4, Canada
| | - Juan A Faraldos
- John Innes Centre, Department of Metabolic Biology, Norwich, NR4 7UH, United Kingdom
| | - Maria Vardakou
- John Innes Centre, Department of Metabolic Biology, Norwich, NR4 7UH, United Kingdom
| | - Melissa Salmon
- John Innes Centre, Department of Metabolic Biology, Norwich, NR4 7UH, United Kingdom
| | - Paul E O'Maille
- John Innes Centre, Department of Metabolic Biology, Norwich, NR4 7UH, United Kingdom; Institute of Food Research, Food and Health Programme, Norwich, NR4 7UA, United Kingdom.
| | - Dae-Kyun Ro
- University of Calgary, Department of Biological Sciences, Calgary, T2N 1N4, Canada.
| |
Collapse
|