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Sundaraj Y, Abdullah H, Nezhad NG, Rodrigues KF, Sabri S, Baharum SN. Cloning, Expression and Functional Characterization of a Novel α-Humulene Synthase, Responsible for the Formation of Sesquiterpene in Agarwood Originating from Aquilaria malaccensis. Curr Issues Mol Biol 2023; 45:8989-9002. [PMID: 37998741 PMCID: PMC10670791 DOI: 10.3390/cimb45110564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/04/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023] Open
Abstract
This study describes the cloning, expression and functional characterization of α-humulene synthase, responsible for the formation of the key aromatic compound α-humulene in agarwood originating from Aquilaria malaccensis. The partial sesquiterpene synthase gene from the transcriptome data of A. malaccensis was utilized for full-length gene isolation via a 3' RACE PCR. The complete gene, denoted as AmDG2, has an open reading frame (ORF) of 1671 bp and encodes for a polypeptide of 556 amino acids. In silico analysis of the protein highlighted several conserved motifs typically found in terpene synthases such as Asp-rich substrate binding (DDxxD), metal-binding residues (NSE/DTE), and cytoplasmic ER retention (RxR) motifs at their respective sites. The AmDG2 was successfully expressed in the E. coli:pET-28a(+) expression vector whereby an expected band of about 64 kDa in size was detected in the SDS-PAGE gel. In vitro enzyme assay using substrate farnesyl pyrophosphate (FPP) revealed that AmDG2 gave rise to two sesquiterpenes: α-humulene (major) and β-caryophyllene (minor), affirming its identity as α-humulene synthase. On the other hand, protein modeling performed using AlphaFold2 suggested that AmDG2 consists entirely of α-helices with short connecting loops and turns. Meanwhile, molecular docking via AutoDock Vina (Version 1.5.7) predicted that Asp307 and Asp311 act as catalytic residues in the α-humulene synthase. To our knowledge, this is the first comprehensive report on the cloning, expression and functional characterization of α-humulene synthase from agarwood originating from A. malaccensis species. These findings reveal a deeper understanding of the structure and functional properties of the α-humulene synthase and could be utilized for metabolic engineering work in the future.
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Affiliation(s)
- Yasotha Sundaraj
- Metabolomics Research Laboratory, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia;
- Faculty of Engineering and Life Sciences, Universiti Selangor (UNISEL), Bestari Jaya 45600, Selangor, Malaysia;
| | - Hasdianty Abdullah
- Faculty of Engineering and Life Sciences, Universiti Selangor (UNISEL), Bestari Jaya 45600, Selangor, Malaysia;
| | - Nima Ghahremani Nezhad
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia;
| | - Kenneth Francis Rodrigues
- Biotechnology Research Institute, Universiti Malaysia Sabah (UMS), Kota Kinabalu 88400, Sabah, Malaysia;
| | - Suriana Sabri
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia;
| | - Syarul Nataqain Baharum
- Metabolomics Research Laboratory, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia;
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Ali M, Nishawy E, Ramadan WA, Ewas M, Rizk MS, Sief-Eldein AGM, El-Zayat MAS, Hassan AHM, Guo M, Hu GW, Wang S, Ahmed FA, Amar MH, Wang QF. Molecular characterization of a Novel NAD+-dependent farnesol dehydrogenase SoFLDH gene involved in sesquiterpenoid synthases from Salvia officinalis. PLoS One 2022; 17:e0269045. [PMID: 35657794 PMCID: PMC9165828 DOI: 10.1371/journal.pone.0269045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/12/2022] [Indexed: 11/25/2022] Open
Abstract
Salvia officinalis is one of the most important medicinal and aromatic plants in terms of nutritional and medicinal value because it contains a variety of vital active ingredients. Terpenoid compounds, particularly monoterpenes (C10) and sesquiterpenes, are the most important and abundant among these active substances (C15). Terpenes play a variety of roles and have beneficial biological properties in plants. With these considerations, the current study sought to clone theNAD+-dependent farnesol dehydrogenase (SoFLDH, EC: 1.1.1.354) gene from S. officinalis. Functional analysis revealed that, SoFLDH has an open reading frame of 2,580 base pairs that encodes 860 amino acids.SoFLDH has two conserved domains and four types of highly conserved motifs: YxxxK, RXR, RR (X8) W, TGxxGhaG. However, SoFLDH was cloned from Salvia officinalis leaves and functionally overexpressed in Arabidopsis thaliana to investigate its role in sesquiterpenoid synthases. In comparison to the transgenic plants, the wild-type plants showed a slight delay in growth and flowering formation. To this end, a gas chromatography-mass spectrometry analysis revealed that SoFLDH transgenic plants were responsible for numerous forms of terpene synthesis, particularly sesquiterpene. These results provide a base for further investigation on SoFLDH gene role and elucidating the regulatory mechanisms for sesquiterpene synthesis in S. offcinalis. And our study paves the way for the future metabolic engineering of the biosynthesis of useful terpene compounds in S. offcinalis.
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Affiliation(s)
- Mohammed Ali
- Department of Genetic Resources, Desert Research Center, Cairo, Egypt
| | - Elsayed Nishawy
- Department of Genetic Resources, Desert Research Center, Cairo, Egypt
| | - Walaa A. Ramadan
- Genetics and Cytology Department, Biotechnology Research institute, National Research Centre, Giza, Egypt
| | - Mohamed Ewas
- Department of Genetic Resources, Desert Research Center, Cairo, Egypt
| | - Mokhtar Said Rizk
- Department of Genetic Resources, Desert Research Center, Cairo, Egypt
| | | | | | | | - Mingquan Guo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Guang-Wan Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | | | - Fatma A. Ahmed
- Department of Medicinal and Aromatic Plants, Desert Research Center, Cairo, Egypt
| | - Mohamed Hamdy Amar
- Department of Genetic Resources, Desert Research Center, Cairo, Egypt
- * E-mail:
| | - Qing-Feng Wang
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Hubei Minzu University, Enshi, China
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Ali M, Alshehri D, Alkhaibari AM, Elhalem NA, Darwish DBE. Cloning and Characterization of 1,8-Cineole Synthase ( SgCINS) Gene From the Leaves of Salvia guaranitica Plant. FRONTIERS IN PLANT SCIENCE 2022; 13:869432. [PMID: 35498676 PMCID: PMC9051517 DOI: 10.3389/fpls.2022.869432] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 02/28/2022] [Indexed: 05/08/2023]
Abstract
Monoterpenes are one of the most common groups belonging to the terpenoid family, with a C10 structure comprising of two isoprene units. Most of monoterpenes are volatile plant compounds, and they act as signaling molecules between plants and the environment, particularly as defensive compounds against herbivores and pathogens. In this study, 1,8-cineole synthase (SgCINS) gene was identified and cloned from the leaves of Salvia guaranitica plant. To examine the role of SgCINS in insect resistance, we transformed and expressed this gene into tobacco leaves. The metabolic analysis revealed that the production of various types and amount of terpenoid was increased and decreased in SgCINS overexpression and control lines, respectively, suggesting that overexpressing SgCINS in transgenic tobacco plants lead to an increase in the production of various types of terpenoids and other phytochemical compounds. These results indicated why transgenic tobacco was highly resistant against cotton worm than the highly susceptible control plants. Our results demonstrate that the SgCINS gene can play an important role in plants against cotton worm insect attack, and pave the way for using terpenoids genes for improving resistance to insect attack in higher plants.
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Affiliation(s)
- Mohammed Ali
- Egyptian Deserts Gene Bank, North Sinai Research Station, Department of Genetic Resources, Desert Research Center, Cairo, Egypt
- *Correspondence: Mohammed Ali, , , orcid.org/0000-0001-9232-1781
| | - Dikhnah Alshehri
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | | | - Naeema A. Elhalem
- Egyptian Deserts Gene Bank, North Sinai Research Station, Department of Genetic Resources, Desert Research Center, Cairo, Egypt
| | - Doaa Bahaa Eldin Darwish
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
- Department of Botany, Faculty of Science, Mansoura University, Mansoura, Egypt
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Owusu Adjei M, Zhou X, Mao M, Rafique F, Ma J. MicroRNAs Roles in Plants Secondary Metabolism. PLANT SIGNALING & BEHAVIOR 2021; 16:1915590. [PMID: 33938393 PMCID: PMC8205019 DOI: 10.1080/15592324.2021.1915590] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 05/20/2023]
Abstract
Plant growth and development is dependent on the regulation of classes of microRNAs (miRNAs) that have emerged as important gene regulators. These miRNAs can regulate plant gene expression to function. They play an important roles in biological homeostasis and environmental response controls. A wide range of plant biological and metabolic processes, including developmental timing, tissues specific development, and differentiation, depends on miRNAs. They perpetually regulate secondary metabolite functions in different plant family lines. Mapping of molecular phylogenies shows the distribution of secondary metabolism in the plant territory. More importantly, a lot of information related to miRNA regulatory processes in plants is revealed, but the role of miRNAs in secondary metabolism regulation and functions of the metabolites are still unclear. In this review, we pinnacle some potential miRNAs regulating the secondary metabolite biosynthesis activities in plants. This will provide an alternative knowledge for functional studies of secondary metabolism.
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Affiliation(s)
- Mark Owusu Adjei
- College of Landscape Architecture of Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xuzixin Zhou
- College of Landscape Architecture of Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Meiqin Mao
- College of Landscape Architecture of Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Fatima Rafique
- College of Landscape Architecture of Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jun Ma
- College of Landscape Architecture of Sichuan Agricultural University, Chengdu, Sichuan, China
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Satyaveanthan MV, Suhaimi SA, Ng CL, Muhd-Noor ND, Awang A, Lam KW, Hassan M. Purification, biochemical characterisation and bioinformatic analysis of recombinant farnesol dehydrogenase from Theobroma cacao. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 161:143-155. [PMID: 33588320 DOI: 10.1016/j.plaphy.2021.01.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 01/30/2021] [Indexed: 06/12/2023]
Abstract
The juvenile hormones (JH) in plants are suggested to act as a form of plant defensive strategy especially against insect herbivory. The oxidation of farnesol to farnesoic acid is a key step in the juvenile hormone biosynthesis pathway. We herein present the purification and characterisation of the recombinant Theobroma cacao farnesol dehydrogenase enzyme that catalyses oxidation of farnesol to farnesal. The recombinant enzyme was purified to apparent homogeneity by affinity chromatography. The purified enzyme was characterised in terms of its deduced amino acid sequences, phylogeny, substrate specificity, kinetic parameters, structural modeling, and docking simulation. The phylogenetic analysis indicated that the T. cacao farnesol dehydrogenase (TcFolDH) showed a close relationship with A. thaliana farnesol dehydrogenase gene. The TcFolDH monomer had a large N-terminal domain which adopted a typical Rossmann-fold, harboring the GxxGxG motif (NADP(H)-binding domain) and a small C-terminal domain. The enzyme was a homotrimer comprised of subunits with molecular masses of 36 kDa. The TcFolDH was highly specific to NADP+ as coenzyme. The substrate specificity studies showed trans, trans-farnesol was the most preferred substrate for the TcFolDH, suggesting that the purified enzyme was a NADP+-dependent farnesol dehydrogenase. The docking of trans, trans-farnesol and NADP+ into the active site of the enzyme showed the important residues, and their interactions involved in the substrate and coenzyme binding of TcFolDH. Considering the extensive involvement of JH in both insects and plants, an in-depth knowledge on the recombinant production of intermediate enzymes of the JH biosynthesis pathway could help provide a potential method for insect control.
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Affiliation(s)
| | - Saidi-Adha Suhaimi
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, Bangi, Selangor, 43600, Malaysia
| | - Chyan Leong Ng
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, Bangi, Selangor, 43600, Malaysia
| | - Noor-Dina Muhd-Noor
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, Bangi, Selangor, 43600, Malaysia; Enzyme & Microbial Technology Center (EMTech), Faculty of Biotechnology & Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor, 43400, Malaysia
| | - Alias Awang
- Cocoa Research & Development Centre (Bagan Datuk), Malaysian Cocoa Board, P.O. Box 30, Sg. Dulang Road, Sg. Sumun, Perak, 36307, Malaysia
| | - Kok Wai Lam
- Drug and Herbal Research Centre, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, 50300, Malaysia
| | - Maizom Hassan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, Bangi, Selangor, 43600, Malaysia.
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Srinivasan A, S V, Raman K, Srivastava S. Rational metabolic engineering for enhanced alpha-tocopherol production in Helianthus annuus cell culture. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.107256] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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7
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Samad AFA, Rahnamaie-Tajadod R, Sajad M, Jani J, Murad AMA, Noor NM, Ismail I. Regulation of terpenoid biosynthesis by miRNA in Persicaria minor induced by Fusarium oxysporum. BMC Genomics 2019; 20:586. [PMID: 31311515 PMCID: PMC6636069 DOI: 10.1186/s12864-019-5954-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 07/03/2019] [Indexed: 12/24/2022] Open
Abstract
Background Persicaria minor (kesum) is an herbaceous plant with a high level of secondary metabolite compounds, particularly terpenoids. These terpenoid compounds have well-established roles in the pharmaceutical and food industries. Although the terpenoids of P. minor have been studied thoroughly, the involvement of microRNA (miRNA) in terpenoid regulation remains poorly understood and needs to be explored. In this study, P. minor plants were inoculated with the pathogenic fungus Fusarium oxysporum for terpenoid induction. Result SPME GC-MS analysis showed the highest terpenoid accumulation on the 6th day post-inoculation (dpi) compared to the other treatment time points (0 dpi, 3 dpi, and 9 dpi). Among the increased terpenoid compounds, α-cedrene, valencene and β-bisabolene were prominent. P. minor inoculated for 6 days was selected for miRNA library construction using next generation sequencing. Differential gene expression analysis showed that 58 miRNAs belonging to 30 families had significantly altered regulation. Among these 58 differentially expressed genes (DEGs), 33 miRNAs were upregulated, whereas 25 miRNAs were downregulated. Two putative novel pre-miRNAs were identified and validated through reverse transcriptase PCR. Prediction of target transcripts potentially involved in the mevalonate pathway (MVA) was carried out by psRobot software, resulting in four miRNAs: pmi-miR530, pmi-miR6173, pmi-miR6300 and a novel miRNA, pmi-Nov_13. In addition, two miRNAs, miR396a and miR398f/g, were predicted to have their target transcripts in the non-mevalonate pathway (MEP). In addition, a novel miRNA, pmi-Nov_12, was identified to have a target gene involved in green leaf volatile (GLV) biosynthesis. RT-qPCR analysis showed that pmi-miR6173, pmi-miR6300 and pmi-nov_13 were downregulated, while miR396a and miR398f/g were upregulated. Pmi-miR530 showed upregulation at 9 dpi, and dynamic expression was observed for pmi-nov_12. Pmi-6300 and pmi-miR396a cleavage sites were detected through degradome sequence analysis. Furthermore, the relationship between miRNA metabolites and mRNA metabolites was validated using correlation analysis. Conclusion Our findings suggest that six studied miRNAs post-transcriptionally regulate terpenoid biosynthesis in P. minor. This regulatory behaviour of miRNAs has potential as a genetic tool to regulate terpenoid biosynthesis in P. minor. Electronic supplementary material The online version of this article (10.1186/s12864-019-5954-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Abdul Fatah A Samad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, 43600, Bangi, Selangor, Malaysia.,Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | | | - Muhammad Sajad
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM, 43600, Bangi, Selangor, Malaysia.,Department of Plant Breeding and Genetics, University College of Agriculture & Environmental Sciences, The Islamia University of Bahawalpur, Punjab, Pakistan
| | - Jaeyres Jani
- Borneo Medical and Health Research Centre, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| | - Abdul Munir Abdul Murad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, 43600, Bangi, Selangor, Malaysia
| | - Normah Mohd Noor
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM, 43600, Bangi, Selangor, Malaysia
| | - Ismanizan Ismail
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, 43600, Bangi, Selangor, Malaysia. .,Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM, 43600, Bangi, Selangor, Malaysia.
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Muangphrom P, Seki H, Matsumoto S, Nishiwaki M, Fukushima EO, Muranaka T. Identification and characterization of a novel sesquiterpene synthase, 4-amorphen-11-ol synthase, from Artemisia maritima. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2018; 35:113-121. [PMID: 31819713 PMCID: PMC6879386 DOI: 10.5511/plantbiotechnology.18.0324a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 03/24/2018] [Indexed: 06/09/2023]
Abstract
Artemisinin, a sesquiterpene lactone exhibiting effective antimalarial activity, is produced by only Artemisia annua plant. A key step in artemisinin biosynthesis is the cyclization of farnesyl pyrophosphate (FPP) to amorpha-4,11-diene catalyzed by amorpha-4,11-diene synthase (AaADS). Intriguingly, several non-artemisinin-producing Artemisia plants also express genes highly homologous to AaADS. Our previous functional analysis of these homologous enzymes revealed that they catalyzed the synthesis of rare natural sesquiterpenoids. In this study, we analyzed the function of another putative sesquiterpene synthase highly homologous to AaADS from A. maritima. Unlike AaADS, in vivo enzymatic assay showed that this enzyme cyclized FPP to 4-amorphen-11-ol, a precursor of several gastroprotective agents. The discovery of 4-amorphen-11-ol synthase (AmAOS) and the successful de novo production of 4-amorphen-11-ol in engineered yeast demonstrated herein provides insights into the methods used to enhance its production for future application.
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Affiliation(s)
- Paskorn Muangphrom
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Hikaru Seki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Seiya Matsumoto
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Mika Nishiwaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Ery O. Fukushima
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 Japan
- Center for Open Innovation Research and Education, Graduate School of Engineering, Osaka University, 2-1,Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Toshiya Muranaka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 Japan
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Rusdi NA, Goh HH, Sabri S, Ramzi AB, Mohd Noor N, Baharum SN. Functional Characterisation of New Sesquiterpene Synthase from the Malaysian Herbal Plant, Polygonum Minus. Molecules 2018; 23:E1370. [PMID: 29882808 PMCID: PMC6100370 DOI: 10.3390/molecules23061370] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/29/2018] [Accepted: 05/31/2018] [Indexed: 11/16/2022] Open
Abstract
Polygonum minus (syn. Persicaria minor) is a herbal plant that is well known for producing sesquiterpenes, which contribute to its flavour and fragrance. This study describes the cloning and functional characterisation of PmSTPS1 and PmSTPS2, two sesquiterpene synthase genes that were identified from P. minus transcriptome data mining. The full-length sequences of the PmSTPS1 and PmSTPS2 genes were expressed in the E. coli pQE-2 expression vector. The sizes of PmSTPS1 and PmSTPS2 were 1098 bp and 1967 bp, respectively, with open reading frames (ORF) of 1047 and 1695 bp and encoding polypeptides of 348 and 564 amino acids, respectively. The proteins consist of three conserved motifs, namely, Asp-rich substrate binding (DDxxD), metal binding residues (NSE/DTE), and cytoplasmic ER retention (RxR), as well as the terpene synthase family N-terminal domain and C-terminal metal-binding domain. From the in vitro enzyme assays, using the farnesyl pyrophosphate (FPP) substrate, the PmSTPS1 enzyme produced multiple acyclic sesquiterpenes of β-farnesene, α-farnesene, and farnesol, while the PmSTPS2 enzyme produced an additional nerolidol as a final product. The results confirmed the roles of PmSTPS1 and PmSTPS2 in the biosynthesis pathway of P. minus, to produce aromatic sesquiterpenes.
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Affiliation(s)
- Nor Azizun Rusdi
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600 UKM, Selangor, Malaysia.
- Institutes for Tropical Biology and Conservation, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia.
| | - Hoe-Han Goh
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600 UKM, Selangor, Malaysia.
| | - Suriana Sabri
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang 43400, Malaysia.
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang 43400, Malaysia.
| | - Ahmad Bazli Ramzi
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600 UKM, Selangor, Malaysia.
| | - Normah Mohd Noor
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600 UKM, Selangor, Malaysia.
| | - Syarul Nataqain Baharum
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600 UKM, Selangor, Malaysia.
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Annotation of the Corymbia terpene synthase gene family shows broad conservation but dynamic evolution of physical clusters relative to Eucalyptus. Heredity (Edinb) 2018. [PMID: 29523839 DOI: 10.1038/s41437-018-0058-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Terpenes are economically and ecologically important phytochemicals. Their synthesis is controlled by the terpene synthase (TPS) gene family, which is highly diversified throughout the plant kingdom. The plant family Myrtaceae are characterised by especially high terpene concentrations, and considerable variation in terpene profiles. Many Myrtaceae are grown commercially for terpene products including the eucalypts Corymbia and Eucalyptus. Eucalyptus grandis has the largest TPS gene family of plants currently sequenced, which is largely conserved in the closely related E. globulus. However, the TPS gene family has been well studied only in these two eucalypt species. The recent assembly of two Corymbia citriodora subsp. variegata genomes presents an opportunity to examine the conservation of this important gene family across more divergent eucalypt lineages. Manual annotation of the TPS gene family in C. citriodora subsp. variegata revealed a similar overall number, and relative subfamily representation, to that previously reported in E. grandis and E. globulus. Many of the TPS genes were in physical clusters that varied considerably between Eucalyptus and Corymbia, with several instances of translocation, expansion/contraction and loss. Notably, there was greater conservation in the subfamilies involved in primary metabolism than those involved in secondary metabolism, likely reflecting different selective constraints. The variation in cluster size within subfamilies and the broad conservation between the eucalypts in the face of this variation are discussed, highlighting the potential contribution of selection, concerted evolution and stochastic processes. These findings provide the foundation to better understand terpene evolution within the ecologically and economically important Myrtaceae.
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Abstract
Functional genomics encompasses diverse disciplines in molecular biology and bioinformatics to comprehend the blueprint, regulation, and expression of genetic elements that define the physiology of an organism. The deluge of sequencing data in the postgenomics era has demanded the involvement of computer scientists and mathematicians to create algorithms, analytical software, and databases for the storage, curation, and analysis of biological big data. In this chapter, we discuss on the concept of functional genomics in the context of systems biology and provide examples of its application in human genetic disease studies, molecular crop improvement, and metagenomics for antibiotic discovery. An overview of transcriptomics workflow and experimental considerations is also introduced. Lastly, we present an in-house case study of transcriptomics analysis of an aromatic herbal plant to understand the effect of elicitation on the biosynthesis of volatile organic compounds.
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Affiliation(s)
- Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia.
| | - Chyan Leong Ng
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
| | - Kok-Keong Loke
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
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12
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Ker DS, Pang SL, Othman NF, Kumaran S, Tan EF, Krishnan T, Chan KG, Othman R, Hassan M, Ng CL. Purification and biochemical characterization of recombinant Persicaria minor β-sesquiphellandrene synthase. PeerJ 2017; 5:e2961. [PMID: 28265494 PMCID: PMC5333544 DOI: 10.7717/peerj.2961] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 01/05/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Sesquiterpenes are 15-carbon terpenes synthesized by sesquiterpene synthases using farnesyl diphosphate (FPP) as a substrate. Recently, a sesquiterpene synthase gene that encodes a 65 kDa protein was isolated from the aromatic plant Persicaria minor. Here, we report the expression, purification and characterization of recombinant P. minor sesquiterpene synthase protein (PmSTS). Insights into the catalytic active site were further provided by structural analysis guided by multiple sequence alignment. METHODS The enzyme was purified in two steps using affinity and size exclusion chromatography. Enzyme assays were performed using the malachite green assay and enzymatic product was identified using gas chromatography-mass spectrometry (GC-MS) analysis. Sequence analysis of PmSTS was performed using multiple sequence alignment (MSA) against plant sesquiterpene synthase sequences. The homology model of PmSTS was generated using I-TASSER server. RESULTS Our findings suggest that the recombinant PmSTS is mainly expressed as inclusion bodies and soluble aggregate in the E. coli protein expression system. However, the addition of 15% (v/v) glycerol to the protein purification buffer and the removal of N-terminal 24 amino acids of PmSTS helped to produce homogenous recombinant protein. Enzyme assay showed that recombinant PmSTS is active and specific to the C15 substrate FPP. The optimal temperature and pH for the recombinant PmSTS are 30 °C and pH 8.0, respectively. The GC-MS analysis further showed that PmSTS produces β-sesquiphellandrene as a major product and β-farnesene as a minor product. MSA analysis revealed that PmSTS adopts a modified conserved metal binding motif (NSE/DTE motif). Structural analysis suggests that PmSTS may binds to its substrate similarly to other plant sesquiterpene synthases. DISCUSSION The study has revealed that homogenous PmSTS protein can be obtained with the addition of glycerol in the protein buffer. The N-terminal truncation dramatically improved the homogeneity of PmSTS during protein purification, suggesting that the disordered N-terminal region may have caused the formation of soluble aggregate. We further show that the removal of the N-terminus disordered region of PmSTS does not affect the product specificity. The optimal temperature, optimal pH, Km and kcat values of PmSTS suggests that PmSTS shares similar enzyme characteristics with other plant sesquiterpene synthases. The discovery of an altered conserved metal binding motif in PmSTS through MSA analysis shows that the NSE/DTE motif commonly found in terpene synthases is able to accommodate certain level of plasticity to accept variant amino acids. Finally, the homology structure of PmSTS that allows good fitting of substrate analog into the catalytic active site suggests that PmSTS may adopt a sesquiterpene biosynthesis mechanism similar to other plant sesquiterpene synthases.
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Affiliation(s)
- De-Sheng Ker
- Institute of Systems Biology, Universiti Kebangsaan Malaysia , Bangi , Selangor , Malaysia
| | - Sze Lei Pang
- Institute of Systems Biology, Universiti Kebangsaan Malaysia , Bangi , Selangor , Malaysia
| | - Noor Farhan Othman
- Institute of Systems Biology, Universiti Kebangsaan Malaysia , Bangi , Selangor , Malaysia
| | - Sekar Kumaran
- Institute of Systems Biology, Universiti Kebangsaan Malaysia , Bangi , Selangor , Malaysia
| | - Ee Fun Tan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia , Bangi , Selangor , Malaysia
| | - Thiba Krishnan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya , Kuala Lumpur , Malaysia
| | - Kok Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya , Kuala Lumpur , Malaysia
| | - Roohaida Othman
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia; School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Maizom Hassan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia , Bangi , Selangor , Malaysia
| | - Chyan Leong Ng
- Institute of Systems Biology, Universiti Kebangsaan Malaysia , Bangi , Selangor , Malaysia
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Muangphrom P, Seki H, Suzuki M, Komori A, Nishiwaki M, Mikawa R, Fukushima EO, Muranaka T. Functional Analysis of Amorpha-4,11-Diene Synthase (ADS) Homologs from Non-Artemisinin-Producing Artemisia Species: The Discovery of Novel Koidzumiol and (+)-α-Bisabolol Synthases. PLANT & CELL PHYSIOLOGY 2016; 57:1678-1688. [PMID: 27273626 DOI: 10.1093/pcp/pcw094] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/29/2016] [Indexed: 06/06/2023]
Abstract
The production of artemisinin, the most effective antimalarial compound, is limited to Artemisia annua. Enzymes involved in artemisinin biosynthesis include amorpha-4,11-diene synthase (ADS), amorpha-4,11-diene 12-monooxygenase (CYP71AV1) and artemisinic aldehyde Δ(11)13 reductase (DBR2). Although artemisinin and its specific intermediates are not detected in other Artemisia species, we reported previously that CYP71AV1 and DBR2 homologs were expressed in some non-artemisinin-producing Artemisia plants. These homologous enzymes showed similar functions to their counterparts in A. annua and can convert fed intermediates into the following products along the artemisinin biosynthesis in planta These findings suggested a partial artemisinin-producing ability in those species. In this study, we examined genes highly homologous to ADS, the first committed gene in the pathway, in 13 Artemisia species. We detected ADS homologs in A. absinthium, A. kurramensis and A. maritima. We analyzed the enzymatic functions of all of the ADS homologs after obtaining their cDNA. We found that the ADS homolog from A. absinthium exhibited novel activity in the cyclization of farnesyl pyrophosphate (FPP) to koidzumiol, a rare natural sesquiterpenoid. Those from A. kurramensis and A. maritima showed similar, but novel, activities in the cyclization of FPP to (+)-α-bisabolol. The unique functions of the novel sesquiterpene synthases highly homologous to ADS found in this study could provide insight into the molecular basis of the exceptional artemisinin-producing ability in A. annua.
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Affiliation(s)
- Paskorn Muangphrom
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan
| | - Hikaru Seki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan
| | - Munenori Suzuki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan KNC Laboratories Co., Ltd., 3-2-34 Takatsukadai, Nishi-ku, Kobe, Hyogo, 651-2271 Japan
| | - Aya Komori
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan KNC Laboratories Co., Ltd., 3-2-34 Takatsukadai, Nishi-ku, Kobe, Hyogo, 651-2271 Japan
| | - Mika Nishiwaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan
| | - Ryota Mikawa
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan
| | - Ery Odette Fukushima
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan Continuing Professional Development Center, Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan
| | - Toshiya Muranaka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan
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