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Guedes JG, Ribeiro R, Carqueijeiro I, Guimarães AL, Bispo C, Archer J, Azevedo H, Fonseca NA, Sottomayor M. The leaf idioblastome of the medicinal plant Catharanthus roseus is associated with stress resistance and alkaloid metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:274-299. [PMID: 37804484 PMCID: PMC10735432 DOI: 10.1093/jxb/erad374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 10/06/2023] [Indexed: 10/09/2023]
Abstract
Catharanthus roseus leaves produce a range of monoterpenoid indole alkaloids (MIAs) that include low levels of the anticancer drugs vinblastine and vincristine. The MIA pathway displays a complex architecture spanning different subcellular and cell type localizations, and is under complex regulation. As a result, the development of strategies to increase the levels of the anticancer MIAs has remained elusive. The pathway involves mesophyll specialized idioblasts where the late unsolved biosynthetic steps are thought to occur. Here, protoplasts of C. roseus leaf idioblasts were isolated by fluorescence-activated cell sorting, and their differential alkaloid and transcriptomic profiles were characterized. This involved the assembly of an improved C. roseus transcriptome from short- and long-read data, IDIO+. It was observed that C. roseus mesophyll idioblasts possess a distinctive transcriptomic profile associated with protection against biotic and abiotic stresses, and indicative that this cell type is a carbon sink, in contrast to surrounding mesophyll cells. Moreover, it is shown that idioblasts are a hotspot of alkaloid accumulation, suggesting that their transcriptome may hold the key to the in-depth understanding of the MIA pathway and the success of strategies leading to higher levels of the anticancer drugs.
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Affiliation(s)
- Joana G Guedes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- Programa Doutoral em Biologia Molecular e Celular (MCbiology), Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313 Porto, Portugal
| | - Rogério Ribeiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
| | - Inês Carqueijeiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Ana Luísa Guimarães
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
| | - Cláudia Bispo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - John Archer
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Herlander Azevedo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
| | - Nuno A Fonseca
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Mariana Sottomayor
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
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Ahmed J, Sajjad Y, Gatasheh MK, Ibrahim KE, Huzafa M, Khan SA, Situ C, Abbasi AM, Hassan A. Genome-wide identification of NAC transcription factors and regulation of monoterpenoid indole alkaloid biosynthesis in Catharanthus roseus. FRONTIERS IN PLANT SCIENCE 2023; 14:1286584. [PMID: 38223288 PMCID: PMC10785006 DOI: 10.3389/fpls.2023.1286584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/01/2023] [Indexed: 01/16/2024]
Abstract
NAC transcription factors (TFs) are crucial to growth and defense responses in plants. Though NACs have been characterized for their role in several plants, comprehensive information regarding their role in Catharanthus roseus, a perennial ornamental plant, is lacking. Homology modelling was employed to identify and characterize NACs in C. roseus. In-vitro propagation of C. roseus plants was carried out using cell suspension and nodal culture and were elicited with two auxin-antagonists, 5-fluoro Indole Acetic Acid (5-F-IAA) and α-(phenyl ethyl-2-oxo)-Indole-Acetic-Acid (PEO-IAA) for the enhanced production of monoterpenoid indole alkaloids (MIAs) namely catharanthine, vindoline, and vinblastine. Analyses revealed the presence of 47 putative CrNAC genes in the C. roseus genome, primarily localized in the nucleus. Phylogenetic analysis categorized these CrNACs into eight clusters, demonstrating the highest synteny with corresponding genes in Camptotheca acuminata. Additionally, at least one defense or hormone-responsive cis-acting element was identified in the promoter region of all the putative CrNACs. Of the two elicitors, 5-F-IAA was effective at 200 µM to elicit a 3.07-fold increase in catharanthine, 2.76-fold in vindoline, and 2.4-fold in vinblastine production in nodal culture. While a relatively lower increase in MIAs was recorded in suspension culture. Validation of RNA-Seq by qRT-PCR showed upregulated expression of stress-related genes (CrNAC-07 and CrNAC-24), and downregulated expression of growth-related gene (CrNAC-25) in elicited nodal culture of C. roseus. Additionally, the expression of genes involved in the biosynthesis of MIAs was significantly upregulated upon elicitation. The current study provides the first report on the role of CrNACs in regulating the biosynthesis of MIAs.
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Affiliation(s)
- Jawad Ahmed
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad, Pakistan
- Institute for Global Food Security, School of Biological Sciences, Queens University Belfast, Belfast, United Kingdom
| | - Yasar Sajjad
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad, Pakistan
| | - Mansour K. Gatasheh
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Khalid Elfaki Ibrahim
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Huzafa
- Department of Plant Sciences, Quaid-e-Azam University, Islamabad, Pakistan, Pakistan
| | - Sabaz Ali Khan
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad, Pakistan
| | - Chen Situ
- Institute for Global Food Security, School of Biological Sciences, Queens University Belfast, Belfast, United Kingdom
| | - Arshad Mehmood Abbasi
- Department of Environmental Sciences, COMSATS University, Islamabad, Abbottabad, Pakistan
| | - Amjad Hassan
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad, Pakistan
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Lawas LMF, Kamileen MO, Buell CR, O'Connor SE, Leisner CP. Transcriptome-based identification and functional characterization of iridoid synthase involved in monotropein biosynthesis in blueberry. PLANT DIRECT 2023; 7:e512. [PMID: 37440931 PMCID: PMC10333835 DOI: 10.1002/pld3.512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 05/08/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023]
Abstract
Blueberries (Vaccinium spp.) are well known for their nutritional quality, and recent work has shown that Vaccinium spp. also produce iridoids, which are specialized metabolites with potent health-promoting benefits. The iridoid glycoside monotropein, which has anti-inflammatory and antinociceptive activities, has been detected in several wild blueberry species but in only a few cultivated highbush blueberry cultivars. How monotropein is produced in blueberry and the genes involved in its biosynthesis remain to be elucidated. Using a monotropein-positive (M+) and monotropein-negative (M-) cultivar of blueberry, we employed transcriptomics and comparative genomics to identify candidate genes in the blueberry iridoid biosynthetic pathway. Orthology analysis was completed using de novo transcript assemblies for both the M+ and M- blueberry cultivars along with the known iridoid-producing plant species Catharanthus roseus to identify putative genes involved in key steps in the early iridoid biosynthetic pathway. From the identified orthologs, we functionally characterized iridoid synthase (ISY), a key enzyme involved in formation of the iridoid scaffold, from both the M+ and M- cultivars. Detection of nepetalactol suggests that ISY from both the M+ and M- cultivars produce functional enzymes that catalyze the formation of iridoids. Transcript accumulation of the putative ISY gene did not correlate with monotropein production, suggesting other genes in the monotropein biosynthetic pathway may be more directly responsible for differential accumulation of the metabolite in blueberry. Mutual rank analysis revealed that ISY is co-expressed with UDP-glucuronosyltransferase, which encodes an enzyme downstream of the ISY step. Results from this study contribute new knowledge in our understanding of iridoid biosynthesis in blueberry and could lead to development of new cultivars with increased human health benefits.
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Affiliation(s)
| | - Mohamed O. Kamileen
- Department of Natural Product BiosynthesisMax Planck Institute for Chemical EcologyJenaGermany
| | - C. Robin Buell
- Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
- Department of Crop and Soil SciencesInstitute of Plant Breeding, Genetics, & Genomics, University of GeorgiaAthensGeorgiaUSA
| | - Sarah E. O'Connor
- Department of Natural Product BiosynthesisMax Planck Institute for Chemical EcologyJenaGermany
| | - Courtney P. Leisner
- Department of Biological SciencesAuburn UniversityAuburnAlabamaUSA
- School of Plant and Environmental SciencesVirginia TechBlacksburgVirginiaUSA
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Wu P, Wang X, Guo J, Zhang S, Li Q, Zhang M, Fang Q, Luo B, Wang H, He W. Analysis of the difference between early-bolting and non-bolting roots of Angelica dahurica based on transcriptome sequencing. Sci Rep 2023; 13:7847. [PMID: 37188680 DOI: 10.1038/s41598-023-34554-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 05/03/2023] [Indexed: 05/17/2023] Open
Abstract
Angelica dahurica (Fisch. ex Hoffm.) Benth.et Hook.f.var.formosana (Boiss.) Shan et Yuan (A. dahurica) is a well-known medicinal plant that has a wide range of applications in the pharmaceutical, food, cosmetic, and other industries. However, the issue of early bolting has emerged as a major hindrance to its production. This problem not only reduces the yield of A. dahurica, but also has an impact on its active ingredients. To date, the molecular factors that contribute to early bolting and its impact on the growth of A. dahurica have not been thoroughly investigated. Therefore, we conducted a transcriptome study using the Illumina NovaSeq 6000 on two developmental types: early-bolting and non-bolting (normal) roots of A. dahurica. We obtained 2,185 up-regulated and 1,414 down-regulated genes in total. Many of the identified transcripts were related to genes involved in early bolting. The gene ontology analysis revealed several differentially expressed genes that are crucial in various pathways, primarily associated with cellular, molecular, and biological processes. Additionally, the morphological characteristics and coumarin content in the early bolting roots of A. dahurica were significantly altered. This study provides insight into the transcriptomic regulation of early bolting in A. dahurica, which can potentially be utilized to enhance its medicinal properties.
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Affiliation(s)
- Ping Wu
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
| | - Xiaoyu Wang
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
| | - Junxia Guo
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
| | - Songli Zhang
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
| | - Qingmiao Li
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China.
| | - Mei Zhang
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
| | - Qingmao Fang
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
| | - Bin Luo
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
| | - Hongsu Wang
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
| | - Weijin He
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
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5
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March of molecular breeding techniques in the genetic enhancement of herbal medicinal plants: present and future prospects. THE NUCLEUS 2022. [DOI: 10.1007/s13237-022-00406-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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6
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Soltani N, Firouzabadi FN, Shafeinia A, Shirali M, Sadr AS. De Novo transcriptome assembly and differential expression analysis of catharanthus roseus in response to salicylic acid. Sci Rep 2022; 12:17803. [PMID: 36280677 PMCID: PMC9592577 DOI: 10.1038/s41598-022-20314-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/12/2022] [Indexed: 01/19/2023] Open
Abstract
The anti-cancer vinblastine and vincristine alkaloids can only be naturally found in periwinkle (Catharanthus roseus). Both of these alkaloids' accumulations are known to be influenced by salicylic acid (SA). The transcriptome data to reveal the induction effect (s) of SA, however, seem restricted at this time. In this study, the de novo approach of transcriptome assembly was performed on the RNA-Sequencing (RNA-Seq) data in C. roseus. The outcome demonstrated that SA treatment boosted the expression of all the genes in the Terpenoid Indole Alkaloids (TIAs) pathway that produces the vinblastine and vincristine alkaloids. These outcomes supported the time-course measurements of vincristine alkaloid, the end product of the TIAs pathway, and demonstrated that SA spray had a positive impact on transcription and alkaloid synthesis. Additionally, the abundance of transcription factor families including bHLH, C3H, C2H2, MYB, MYB-related, AP2/ ERF, NAC, bZIP, and WRKY suggests a role for a variety of transcription families in response to the SA stimuli. Di-nucleotide and tri-nucleotide SSRs were the most prevalent SSR markers in microsatellite analyses, making up 39% and 34% of all SSR markers, respectively, out of the 77,192 total SSRs discovered.
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Affiliation(s)
- Narges Soltani
- Production Engineering and Plant Genetics Department, Faculty of Agriculture and Natural Resources, Lorestan University, P.O. Box 465, Khorramabad, Iran
| | - Farhad Nazarian Firouzabadi
- Production Engineering and Plant Genetics Department, Faculty of Agriculture and Natural Resources, Lorestan University, P.O. Box 465, Khorramabad, Iran.
| | - Alireza Shafeinia
- Department of Plant Production & Genetics, Faculty of Agriculture, Agricultural Sciences & Natural Resources, University of Khuzestan, Mollasani, Iran
| | - Masoud Shirali
- Agri-Food and Biosciences Institute, Hillsborough, BT26 6DR, UK
- School of Biological Sciences, Queen's University Belfast, Belfast, BT9 5AJ, UK
| | - Ayeh Sadat Sadr
- South of Iran Aquaculture Research Institute (SIARI), Iranian Fisheries Science Research Institute, Agricultural Research Education and Extension Organization (AREEO), Ahvaz, Iran.
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7
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Schnabel A, Athmer B, Manke K, Schumacher F, Cotinguiba F, Vogt T. Identification and characterization of piperine synthase from black pepper, Piper nigrum L. Commun Biol 2021; 4:445. [PMID: 33833371 PMCID: PMC8032705 DOI: 10.1038/s42003-021-01967-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 03/03/2021] [Indexed: 01/19/2023] Open
Abstract
Black pepper (Piper nigrum L.) is the world's most popular spice and is also used as an ingredient in traditional medicine. Its pungent perception is due to the interaction of its major compound, piperine (1-piperoyl-piperidine) with the human TRPV-1 or vanilloid receptor. We now identify the hitherto concealed enzymatic formation of piperine from piperoyl coenzyme A and piperidine based on a differential RNA-Seq approach from developing black pepper fruits. This enzyme is described as piperine synthase (piperoyl-CoA:piperidine piperoyl transferase) and is a member of the BAHD-type of acyltransferases encoded by a gene that is preferentially expressed in immature fruits. A second BAHD-type enzyme, also highly expressed in immature black pepper fruits, has a rather promiscuous substrate specificity, combining diverse CoA-esters with aliphatic and aromatic amines with similar efficiencies, and was termed piperamide synthase. Recombinant piperine and piperamide synthases are members of a small gene family in black pepper. They can be used to facilitate the microbial production of a broad range of medicinally relevant aliphatic and aromatic piperamides based on a wide array of CoA-donors and amine-derived acceptors, offering widespread applications.
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Affiliation(s)
- Arianne Schnabel
- Leibniz Institute of Plant Biochemistry, Dept. Cell and Metabolic Biology, Halle (Saale), Germany
| | - Benedikt Athmer
- Leibniz Institute of Plant Biochemistry, Dept. Cell and Metabolic Biology, Halle (Saale), Germany
| | - Kerstin Manke
- Leibniz Institute of Plant Biochemistry, Dept. Cell and Metabolic Biology, Halle (Saale), Germany
| | | | - Fernando Cotinguiba
- Instituto de Pesquisas de Produtos Naturais (IPPN), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro/RJ, Brasil
| | - Thomas Vogt
- Leibniz Institute of Plant Biochemistry, Dept. Cell and Metabolic Biology, Halle (Saale), Germany.
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Carqueijeiro I, Koudounas K, Dugé de Bernonville T, Sepúlveda LJ, Mosquera A, Bomzan DP, Oudin A, Lanoue A, Besseau S, Lemos Cruz P, Kulagina N, Stander EA, Eymieux S, Burlaud-Gaillard J, Blanchard E, Clastre M, Atehortùa L, St-Pierre B, Giglioli-Guivarc’h N, Papon N, Nagegowda DA, O’Connor SE, Courdavault V. Alternative splicing creates a pseudo-strictosidine β-d-glucosidase modulating alkaloid synthesis in Catharanthus roseus. PLANT PHYSIOLOGY 2021; 185:836-856. [PMID: 33793899 PMCID: PMC8133614 DOI: 10.1093/plphys/kiaa075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 11/24/2020] [Indexed: 05/08/2023]
Abstract
Deglycosylation is a key step in the activation of specialized metabolites involved in plant defense mechanisms. This reaction is notably catalyzed by β-glucosidases of the glycosyl hydrolase 1 (GH1) family such as strictosidine β-d-glucosidase (SGD) from Catharanthus roseus. SGD catalyzes the deglycosylation of strictosidine, forming a highly reactive aglycone involved in the synthesis of cytotoxic monoterpene indole alkaloids (MIAs) and in the crosslinking of aggressor proteins. By exploring C. roseus transcriptomic resources, we identified an alternative splicing event of the SGD gene leading to the formation of a shorter isoform of this enzyme (shSGD) that lacks the last 71-residues and whose transcript ratio with SGD ranges from 1.7% up to 42.8%, depending on organs and conditions. Whereas it completely lacks β-glucosidase activity, shSGD interacts with SGD and causes the disruption of SGD multimers. Such disorganization drastically inhibits SGD activity and impacts downstream MIA synthesis. In addition, shSGD disrupts the metabolic channeling of downstream biosynthetic steps by hampering the recruitment of tetrahydroalstonine synthase in cell nuclei. shSGD thus corresponds to a pseudo-enzyme acting as a regulator of MIA biosynthesis. These data shed light on a peculiar control mechanism of β-glucosidase multimerization, an organization common to many defensive GH1 members.
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Affiliation(s)
- Inês Carqueijeiro
- EA2106 “Biomolécules et Biotechnologies Végétales,” Université de Tours, 37200 Tours, France
| | - Konstantinos Koudounas
- EA2106 “Biomolécules et Biotechnologies Végétales,” Université de Tours, 37200 Tours, France
| | | | - Liuda Johana Sepúlveda
- EA2106 “Biomolécules et Biotechnologies Végétales,” Université de Tours, 37200 Tours, France
- Laboratorio de Biotecnología, Universidad de Antioquia, Sede de Investigación Universitaria, 50010 Medellin, Colombia
| | - Angela Mosquera
- EA2106 “Biomolécules et Biotechnologies Végétales,” Université de Tours, 37200 Tours, France
- Laboratorio de Biotecnología, Universidad de Antioquia, Sede de Investigación Universitaria, 50010 Medellin, Colombia
| | - Dikki Pedenla Bomzan
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru 560065, India
| | - Audrey Oudin
- EA2106 “Biomolécules et Biotechnologies Végétales,” Université de Tours, 37200 Tours, France
| | - Arnaud Lanoue
- EA2106 “Biomolécules et Biotechnologies Végétales,” Université de Tours, 37200 Tours, France
| | - Sébastien Besseau
- EA2106 “Biomolécules et Biotechnologies Végétales,” Université de Tours, 37200 Tours, France
| | - Pamela Lemos Cruz
- EA2106 “Biomolécules et Biotechnologies Végétales,” Université de Tours, 37200 Tours, France
| | - Natalja Kulagina
- EA2106 “Biomolécules et Biotechnologies Végétales,” Université de Tours, 37200 Tours, France
| | - Emily A Stander
- EA2106 “Biomolécules et Biotechnologies Végétales,” Université de Tours, 37200 Tours, France
| | - Sébastien Eymieux
- INSERM U1259, Plateforme IBiSA de Microscopie Electronique, Université de Tours, 37200 Tours, France
| | - Julien Burlaud-Gaillard
- INSERM U1259, Plateforme IBiSA de Microscopie Electronique, Université de Tours, 37200 Tours, France
| | - Emmanuelle Blanchard
- INSERM U1259, Plateforme IBiSA de Microscopie Electronique, Université de Tours, 37200 Tours, France
- Centre Hospitalier Régional de Tours, 37170 Tours, France
| | - Marc Clastre
- EA2106 “Biomolécules et Biotechnologies Végétales,” Université de Tours, 37200 Tours, France
| | - Lucia Atehortùa
- Laboratorio de Biotecnología, Universidad de Antioquia, Sede de Investigación Universitaria, 50010 Medellin, Colombia
| | - Benoit St-Pierre
- EA2106 “Biomolécules et Biotechnologies Végétales,” Université de Tours, 37200 Tours, France
| | | | - Nicolas Papon
- EA3142 “Groupe d'Etude des Interactions Hôte-Pathogène,” Université d’Angers, 49035 Angers, France
| | - Dinesh A Nagegowda
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru 560065, India
| | - Sarah E O’Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Vincent Courdavault
- EA2106 “Biomolécules et Biotechnologies Végétales,” Université de Tours, 37200 Tours, France
- Author for communication:
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George J, Kahlke T, Abbriano RM, Kuzhiumparambil U, Ralph PJ, Fabris M. Metabolic Engineering Strategies in Diatoms Reveal Unique Phenotypes and Genetic Configurations With Implications for Algal Genetics and Synthetic Biology. Front Bioeng Biotechnol 2020; 8:513. [PMID: 32582656 PMCID: PMC7290003 DOI: 10.3389/fbioe.2020.00513] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/30/2020] [Indexed: 12/23/2022] Open
Abstract
Diatoms are photosynthetic microeukaryotes that dominate phytoplankton populations and have increasing applicability in biotechnology. Uncovering their complex biology and elevating strains to commercial standards depends heavily on robust genetic engineering tools. However, engineering microalgal genomes predominantly relies on random integration of transgenes into nuclear DNA, often resulting in detrimental “position-effects” such as transgene silencing, integration into transcriptionally-inactive regions, and endogenous sequence disruption. With the recent development of extrachromosomal transgene expression via independent episomes, it is timely to investigate both strategies at the phenotypic and genomic level. Here, we engineered the model diatom Phaeodactylum tricornutum to produce the high-value heterologous monoterpenoid geraniol, which, besides applications as fragrance and insect repellent, is a key intermediate of high-value pharmaceuticals. Using high-throughput phenotyping we confirmed the suitability of episomes for synthetic biology applications and identified superior geraniol-yielding strains following random integration. We used third generation long-read sequencing technology to generate a complete analysis of all transgene integration events including their genomic locations and arrangements associated with high-performing strains at a genome-wide scale with subchromosomal detail, never before reported in any microalga. This revealed very large, highly concatenated insertion islands, offering profound implications on diatom functional genetics and next generation genome editing technologies, and is key for developing more precise genome engineering approaches in diatoms, including possible genomic safe harbour locations to support high transgene expression for targeted integration approaches. Furthermore, we have demonstrated that exogenous DNA is not integrated inadvertently into the nuclear genome of extrachromosomal-expression clones, an important characterisation of this novel engineering approach that paves the road to synthetic biology applications.
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Affiliation(s)
- Jestin George
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia
| | - Tim Kahlke
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia
| | - Raffaela M Abbriano
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia
| | | | - Peter J Ralph
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia
| | - Michele Fabris
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia.,CSIRO Synthetic Biology Future Science Platform, Brisbane, QLD, Australia
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10
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Fabris M, George J, Kuzhiumparambil U, Lawson CA, Jaramillo-Madrid AC, Abbriano RM, Vickers CE, Ralph P. Extrachromosomal Genetic Engineering of the Marine Diatom Phaeodactylum tricornutum Enables the Heterologous Production of Monoterpenoids. ACS Synth Biol 2020; 9:598-612. [PMID: 32032487 DOI: 10.1021/acssynbio.9b00455] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Geraniol is a commercially relevant plant-derived monoterpenoid that is a main component of rose essential oil and used as insect repellent. Geraniol is also a key intermediate compound in the biosynthesis of the monoterpenoid indole alkaloids (MIAs), a group of over 2000 compounds that include high-value pharmaceuticals. As plants naturally produce extremely small amounts of these molecules and their chemical synthesis is complex, industrially sourcing these compounds is costly and inefficient. Hence, microbial hosts suitable to produce MIA precursors through synthetic biology and metabolic engineering are currently being sought. Here, we evaluated the suitability of a eukaryotic microalga, the marine diatom Phaeodactylum tricornutum, for the heterologous production of monoterpenoids. Profiling of endogenous metabolism revealed that P. tricornutum, unlike other microbes employed for industrial production of terpenoids, accumulates free pools of the precursor geranyl diphosphate. To evaluate the potential for larger synthetic biology applications, we engineered P. tricornutum through extrachromosomal, episome-based expression, for the heterologous biosynthesis of the MIA intermediate geraniol. By profiling the production of geraniol resulting from various genetic and cultivation arrangements, P. tricornutum reached the maximum geraniol titer of 0.309 mg/L in phototrophic conditions. This work provides (i) a detailed analysis of P. tricornutum endogenous terpenoid metabolism, (ii) a successful demonstration of extrachromosomal expression for metabolic pathway engineering with potential gene-stacking applications, and (iii) a convincing proof-of-concept of the suitability of P. tricornutum as a novel production platform for heterologous monoterpenoids, with potential for complex pathway engineering aimed at the heterologous production of MIAs.
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Affiliation(s)
- Michele Fabris
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW 2007, Australia
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia
| | - Jestin George
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW 2007, Australia
| | | | - Caitlin A. Lawson
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW 2007, Australia
| | | | - Raffaela M. Abbriano
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW 2007, Australia
| | - Claudia E. Vickers
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Peter Ralph
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW 2007, Australia
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11
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Sanchez-Muï Oz R, Almagro L, Cusido RM, Bonfill M, Palazon J, Moyano E. Transfecting Taxus � media Protoplasts to Study Transcription Factors BIS2 and TSAR2 as Activators of Taxane-Related Genes. PLANT & CELL PHYSIOLOGY 2020; 61:576-583. [PMID: 31841159 DOI: 10.1093/pcp/pcz225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/29/2019] [Indexed: 06/10/2023]
Abstract
Taxane diterpenes are secondary metabolites with an important pharmacological role in the treatment of cancer. Taxus spp. biofactories have been used for taxane production, but the lack of knowledge about the taxane biosynthetic pathway and its molecular regulation hinders their optimal function. The difficulties in introducing foreign genes in Taxus spp. genomes hinder the study of the molecular mechanisms involved in taxane production, and a new approach is required to overcome them. In this study, a reliable, simple and fast method to obtain Taxus � media protoplasts was developed, allowing their manipulation in downstream assays for the study of physiological changes in Taxus spp. cells. Using this method, Taxus protoplasts were transiently transfected for the first time, corroborating their suitability for transfection assays and the study of specific physiological responses. The two assayed transcription factors (BIS2 and TSAR2) had a positive effect on the expression of several taxane-related genes, suggesting their potential use for the improvement of taxane yields. Furthermore, the results indicate that the developed method is suitable for obtaining T. � media protoplasts for transfection with the aim of unraveling regulatory mechanisms in taxane production.
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Affiliation(s)
- Raul Sanchez-Muï Oz
- Departament de Ci�ncies Experimentals i de la Salut, Universitat Pompeu Fabra, Avda. Dr. Aiguader 80, E-08003 Barcelona, Spain
| | - Lorena Almagro
- Departamento de Biolog�a vegetal, Facultad de Biolog�a, Universidad de Murcia, E-30100 Murcia, Spain
| | - Rosa M Cusido
- Departament de Biologia, Sanitat i Medi Ambient, Secci� de Fisiologia Vegetal, Facultat de Farmacia, Universitat de Barcelona, E-08028 Barcelona, Spain
| | - Mercedes Bonfill
- Departament de Biologia, Sanitat i Medi Ambient, Secci� de Fisiologia Vegetal, Facultat de Farmacia, Universitat de Barcelona, E-08028 Barcelona, Spain
| | - Javier Palazon
- Departament de Biologia, Sanitat i Medi Ambient, Secci� de Fisiologia Vegetal, Facultat de Farmacia, Universitat de Barcelona, E-08028 Barcelona, Spain
| | - Elisabeth Moyano
- Departament de Ci�ncies Experimentals i de la Salut, Universitat Pompeu Fabra, Avda. Dr. Aiguader 80, E-08003 Barcelona, Spain
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12
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Agtuca BJ, Stopka SA, Tuleski TR, do Amaral FP, Evans S, Liu Y, Xu D, Monteiro RA, Koppenaal DW, Paša-Tolić L, Anderton CR, Vertes A, Stacey G. In-Situ Metabolomic Analysis of Setaria viridis Roots Colonized by Beneficial Endophytic Bacteria. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:272-283. [PMID: 31544655 DOI: 10.1094/mpmi-06-19-0174-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Over the past decades, crop yields have risen in parallel with increasing use of fossil fuel-derived nitrogen (N) fertilizers but with concomitant negative impacts on climate and water resources. There is a need for more sustainable agricultural practices, and biological nitrogen fixation (BNF) could be part of the solution. A variety of nitrogen-fixing, epiphytic, and endophytic plant growth-promoting bacteria (PGPB) are known to stimulate plant growth. However, compared with the rhizobium-legume symbiosis, little mechanistic information is available as to how PGPB affect plant metabolism. Therefore, we investigated the metabolic changes in roots of the model grass species Setaria viridis upon endophytic colonization by Herbaspirillum seropedicae SmR1 (fix+) or a fix- mutant strain (SmR54) compared with uninoculated roots. Endophytic colonization of the root is highly localized and, hence, analysis of whole-root segments dilutes the metabolic signature of those few cells impacted by the bacteria. Therefore, we utilized in-situ laser ablation electrospray ionization mass spectrometry to sample only those root segments at or adjacent to the sites of bacterial colonization. Metabolites involved in purine, zeatin, and riboflavin pathways were significantly more abundant in inoculated plants, while metabolites indicative of nitrogen, starch, and sucrose metabolism were reduced in roots inoculated with the fix- strain or uninoculated, presumably due to N limitation. Interestingly, compounds, involved in indole-alkaloid biosynthesis were more abundant in the roots colonized by the fix- strain, perhaps reflecting a plant defense response.
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Affiliation(s)
- Beverly J Agtuca
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
| | - Sylwia A Stopka
- Department of Chemistry, The George Washington University, Washington, DC 20052, U.S.A
| | - Thalita R Tuleski
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, CP 19046, 81.531-990 Curitiba, PR, Brazil
| | - Fernanda P do Amaral
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
| | - Sterling Evans
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
| | - Yang Liu
- Department of Electrical Engineering and Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri Columbia
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri Columbia
| | - Rose Adele Monteiro
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, CP 19046, 81.531-990 Curitiba, PR, Brazil
| | - David W Koppenaal
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, U.S.A
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, U.S.A
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, U.S.A
| | - Akos Vertes
- Department of Chemistry, The George Washington University, Washington, DC 20052, U.S.A
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
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13
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Chen X, Wang DD, Fang X, Chen XY, Mao YB. Plant Specialized Metabolism Regulated by Jasmonate Signaling. PLANT & CELL PHYSIOLOGY 2019; 60:2638-2647. [PMID: 31418777 DOI: 10.1093/pcp/pcz161] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 08/06/2019] [Indexed: 05/22/2023]
Abstract
As sessile and autotrophic organisms, plants have evolved sophisticated pathways to produce a rich array of specialized metabolites, many of which are biologically active and function as defense substances in protecting plants from herbivores and pathogens. Upon stimuli, these structurally diverse small molecules may be synthesized or constitutively accumulated. Jasmonate acids (JAs) are the major defense phytohormone involved in transducing external signals (such as wounding) to activate defense reactions, including, in particular, the reprogramming of metabolic pathways that initiate and enhance the production of defense compounds against insect herbivores and pathogens. In this review, we summarize the progress of recent research on the control of specialized metabolic pathways in plants by JA signaling, with an emphasis on the molecular regulation of terpene and alkaloid biosynthesis. We also discuss the interplay between JA signaling and various signaling pathways during plant defense responses. These studies provide valuable data for breeding insect-proof crops and pave the way to engineering the production of valuable metabolites in future.
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Affiliation(s)
- Xueying Chen
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Shanghai 200032, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Shanghai 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
| | - Dan-Dan Wang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Shanghai 200032, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Shanghai 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
| | - Xin Fang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Xiao-Ya Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Shanghai 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
| | - Ying-Bo Mao
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Shanghai 200032, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Shanghai 200032, China
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14
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Ma X, Meng Y, Wang P, Tang Z, Wang H, Xie T. Bioinformatics-assisted, integrated omics studies on medicinal plants. Brief Bioinform 2019; 21:1857-1874. [PMID: 32706024 DOI: 10.1093/bib/bbz132] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/03/2019] [Accepted: 09/19/2019] [Indexed: 12/14/2022] Open
Abstract
The immense therapeutic and economic values of medicinal plants have attracted increasing attention from the worldwide researchers. It has been recognized that production of the authentic and high-quality herbal drugs became the prerequisite for maintaining the healthy development of the traditional medicine industry. To this end, intensive research efforts have been devoted to the basic studies, in order to pave a way for standardized authentication of the plant materials, and bioengineering of the metabolic pathways in the medicinal plants. In this paper, the recent advances of omics studies on the medicinal plants were summarized from several aspects, including phenomics and taxonomics, genomics, transcriptomics, proteomics and metabolomics. We proposed a multi-omics data-based workflow for medicinal plant research. It was emphasized that integration of the omics data was important for plant authentication and mechanistic studies on plant metabolism. Additionally, the computational tools for proper storage, efficient processing and high-throughput analyses of the omics data have been introduced into the workflow. According to the workflow, authentication of the medicinal plant materials should not only be performed at the phenomics level but also be implemented by genomic and metabolomic marker-based examination. On the other hand, functional genomics studies, transcriptional regulatory networks and protein-protein interactions will contribute greatly for deciphering the secondary metabolic pathways. Finally, we hope that our work could inspire further efforts on the bioinformatics-assisted, integrated omics studies on the medicinal plants.
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Affiliation(s)
- Xiaoxia Ma
- Hangzhou Normal University, Hangzhou 311121, P.R. China.,Holistic Integrative Pharmacy Institutes, Hangzhou Normal University, Hangzhou 311121, P.R. China.,Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province and Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, P.R. China.,College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, P.R. China
| | - Yijun Meng
- Hangzhou Normal University, Hangzhou 311121, P.R. China.,College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, P.R. China
| | - Pu Wang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, P.R. China
| | - Zhonghai Tang
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, P.R. China
| | - Huizhong Wang
- Hangzhou Normal University, Hangzhou 311121, P.R. China.,College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, P.R. China
| | - Tian Xie
- Hangzhou Normal University, Hangzhou 311121, P.R. China.,Holistic Integrative Pharmacy Institutes, Hangzhou Normal University, Hangzhou 311121, P.R. China.,Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province and Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, P.R. China
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15
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Yamamoto K, Takahashi K, Caputi L, Mizuno H, Rodriguez-Lopez CE, Iwasaki T, Ishizaki K, Fukaki H, Ohnishi M, Yamazaki M, Masujima T, O'Connor SE, Mimura T. The complexity of intercellular localisation of alkaloids revealed by single-cell metabolomics. THE NEW PHYTOLOGIST 2019; 224:848-859. [PMID: 31436868 DOI: 10.1111/nph.16138] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 06/19/2019] [Indexed: 05/27/2023]
Abstract
Catharanthus roseus is a medicinal plant well known for producing bioactive compounds such as vinblastine and vincristine, which are classified as terpenoid indole alkaloids (TIAs). Although the leaves of this plant are the main source of these antitumour drugs, much remains unknown on how TIAs are biosynthesised from a central precursor, strictosidine, to various TIAs in planta. Here, we have succeeded in showing, for the first time in leaf tissue of C. roseus, cell-specific TIAs localisation and accumulation with 10 μm spatial resolution Imaging mass spectrometry (Imaging MS) and live single-cell mass spectrometry (single-cell MS). These metabolomic studies revealed that most TIA precursors (iridoids) are localised in the epidermal cells, but major TIAs including serpentine and vindoline are localised instead in idioblast cells. Interestingly, the central TIA intermediate strictosidine also accumulates in both epidermal and idioblast cells of C. roseus. Moreover, we also found that vindoline accumulation increases in laticifer cells as the leaf expands. These discoveries highlight the complexity of intercellular localisation in plant specialised metabolism.
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Affiliation(s)
- Kotaro Yamamoto
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Hyogo, 657-8501, Japan
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Katsutoshi Takahashi
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Koutou-ku, Tokyo, 135-0064, Japan
| | - Lorenzo Caputi
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Hajime Mizuno
- Laboratory of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Shizuoka, 422-8526, Japan
| | - Carlos E Rodriguez-Lopez
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Tetsushi Iwasaki
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Hyogo, 657-8501, Japan
| | - Kimitsune Ishizaki
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Hyogo, 657-8501, Japan
| | - Hidehiro Fukaki
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Hyogo, 657-8501, Japan
| | - Miwa Ohnishi
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Hyogo, 657-8501, Japan
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Chiba, 263-8522, Japan
| | - Tsutomu Masujima
- Quantitative Biology Centre (QBiC), RIKEN, Suita, Osaka, 565-0874, Japan
| | - Sarah E O'Connor
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Tetsuro Mimura
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Hyogo, 657-8501, Japan
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16
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She J, Yan H, Yang J, Xu W, Su Z. croFGD: Catharanthus roseus Functional Genomics Database. Front Genet 2019; 10:238. [PMID: 30967897 PMCID: PMC6438902 DOI: 10.3389/fgene.2019.00238] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 03/04/2019] [Indexed: 01/14/2023] Open
Abstract
Catharanthus roseus is a medicinal plant, which can produce monoterpene indole alkaloid (MIA) metabolites with biological activity and is rich in vinblastine and vincristine. With release of the scaffolded genome sequence of C. roseus, it is necessary to annotate gene functions on the whole-genome level. Recently, 53 RNA-seq datasets are available in public with different tissues (flower, root, leaf, seedling, and shoot) and different treatments (MeJA, PnWB infection and yeast elicitor). We used in-house data process pipeline with the combination of PCC and MR algorithms to construct a co-expression network exploring multi-dimensional gene expression (global, tissue preferential, and treat response) through multi-layered approaches. In the meanwhile, we added miRNA-target pairs, predicted PPI pairs into the network and provided several tools such as gene set enrichment analysis, functional module enrichment analysis, and motif analysis for functional prediction of the co-expression genes. Finally, we have constructed an online croFGD database (http://bioinformatics.cau.edu.cn/croFGD/). We hope croFGD can help the communities to study the C. roseus functional genomics and make novel discoveries about key genes involved in some important biological processes.
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Affiliation(s)
- Jiajie She
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Hengyu Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jiaotong Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
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17
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Costa LM, Sakakibara H. Sixty Years of Plant and Cell Physiology. PLANT & CELL PHYSIOLOGY 2019; 60:1-3. [PMID: 30605543 DOI: 10.1093/pcp/pcy244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
| | - Hitoshi Sakakibara
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- RIKEN Center for Sustainable Resource Sciences, Yokohama, Japan
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18
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Nishanth MJ, Sheshadri SA, Rathore SS, Srinidhi S, Simon B. Expression analysis of Cell wall invertase under abiotic stress conditions influencing specialized metabolism in Catharanthus roseus. Sci Rep 2018; 8:15059. [PMID: 30305670 PMCID: PMC6180051 DOI: 10.1038/s41598-018-33415-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 09/28/2018] [Indexed: 12/04/2022] Open
Abstract
Catharanthus roseus is a commercial source for anti-cancer terpenoid indole alkaloids (TIAs: vincristine and vinblastine). Inherent levels of these TIAs are very low, hence research studies need to focus on enhancing their levels in planta. Since primary metabolism provides precursors for specialized-metabolism, elevating the former can achieve higher amounts of the latter. Cell Wall Invertase (CWIN), a key enzyme in sucrose-metabolism catalyses the breakdown of sucrose into glucose and fructose, which serve as carbon-skeleton for specialized-metabolites. Understanding CWIN regulation could unravel metabolic-engineering approaches towards enhancing the levels of TIAs in planta. Our study is the first to characterize CWIN at gene-expression level in the medicinal plant, C. roseus. The CWINs and their inter-relationship with sucrose and TIA metabolism was studied at gene and metabolite levels. It was found that sucrose-supplementation to C. roseus leaves significantly elevated the monomeric TIAs (vindoline, catharanthine) and their corresponding genes. This was further confirmed in cross-species, wherein Nicotiana benthamiana leaves transiently-overexpressing CrCWIN2 showed significant upregulation of specialized-metabolism genes: NbPAL2, Nb4CL, NbCHS, NbF3H, NbANS, NbHCT and NbG10H. The specialized metabolites- cinnamic acid, coumarin, and fisetin were significantly upregulated. Thus, the present study provides a valuable insight into metabolic-engineering approaches towards augmenting the levels of therapeutic TIAs.
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Affiliation(s)
- M J Nishanth
- Phytoengineering Lab, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, Tamil Nadu, India
| | - S A Sheshadri
- Phytoengineering Lab, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, Tamil Nadu, India
| | - Sudarshan Singh Rathore
- Actinomycetes Bioprospecting Lab, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, Tamil Nadu, India
| | - S Srinidhi
- Phytoengineering Lab, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, Tamil Nadu, India
| | - Bindu Simon
- Phytoengineering Lab, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, Tamil Nadu, India.
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19
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Molecular authentication of Anthemis deserti Boiss. (Asteraceae) based on ITS2 region of nrDNA gene sequence. Saudi J Biol Sci 2018; 26:155-159. [PMID: 30622420 PMCID: PMC6319191 DOI: 10.1016/j.sjbs.2018.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/11/2018] [Accepted: 09/13/2018] [Indexed: 11/05/2022] Open
Abstract
The dried plant material of medicinally important Anthemis deserti Boiss. (family: Asteraceae) especially when it remains in the powdered form often look similar to Anthemis melampodina Del.; and therefore, difficult to distinguish, finally lead to chances of adulteration. The adulteration in medicinal plants effects on the efficacy of the drugs. The molecular authentication of herbal plant materials such as based on the internal transcribed spacer 2 (ITS2) sequences of nuclear ribosomal DNA (nrDNA) is considered as more reliable method compared to other the biochemical or histological methods. The present study aims to molecular authentication ofA. deserti based on molecular phylogenetic analyses of ITS2 gene sequence of nrDNA region. The ITS2 region of nrDNA of A. deserti were sequenced, and the molecular phylogenetic analyses were performed together with the GenBank sequences. The Maximum Parsimony tree revealed the close relationships of A. deserti with A. melampodina; however, the Neighbor-Joining and Maximum Likelihood tree clearly revealed that A. deserti is distinct from A. melampodina, which is also supported by the differences in nucleotides at five diffident positions (i.e. 22, 28, 87, 175 and 198) in the DNA sequence alignment.
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20
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An engineered combinatorial module of transcription factors boosts production of monoterpenoid indole alkaloids in Catharanthus roseus. Metab Eng 2018; 48:150-162. [PMID: 29852273 DOI: 10.1016/j.ymben.2018.05.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/24/2018] [Accepted: 05/25/2018] [Indexed: 11/21/2022]
Abstract
To fend off microbial pathogens and herbivores, plants have evolved a wide range of defense strategies such as physical barriers, or the production of anti-digestive proteins or bioactive specialized metabolites. Accumulation of the latter compounds is often regulated by transcriptional activation of the biosynthesis pathway genes by the phytohormone jasmonate-isoleucine. Here, we used our recently developed flower petal transformation method in the medicinal plant Catharanthus roseus to shed light on the complex regulatory mechanisms steering the jasmonate-modulated biosynthesis of monoterpenoid indole alkaloids (MIAs), to which the anti-cancer compounds vinblastine and vincristine belong. By combinatorial overexpression of the transcriptional activators BIS1, ORCA3 and MYC2a, we provide an unprecedented insight into the modular transcriptional control of MIA biosynthesis. Furthermore, we show that the expression of an engineered de-repressed MYC2a triggers a tremendous reprogramming of the MIA pathway, finally leading to massively increased accumulation of at least 23 MIAs. The current study unveils an innovative approach for future metabolic engineering efforts for the production of valuable bioactive plant compounds in non-model plants.
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21
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Larsen B, Fuller VL, Pollier J, Van Moerkercke A, Schweizer F, Payne R, Colinas M, O’Connor SE, Goossens A, Halkier BA. Identification of Iridoid Glucoside Transporters in Catharanthus roseus. PLANT & CELL PHYSIOLOGY 2017; 58:1507-1518. [PMID: 28922750 PMCID: PMC5921532 DOI: 10.1093/pcp/pcx097] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 07/06/2017] [Indexed: 05/02/2023]
Abstract
Monoterpenoid indole alkaloids (MIAs) are plant defense compounds and high-value pharmaceuticals. Biosynthesis of the universal MIA precursor, secologanin, is organized between internal phloem-associated parenchyma (IPAP) and epidermis cells. Transporters for intercellular transport of proposed mobile pathway intermediates have remained elusive. Screening of an Arabidopsis thaliana transporter library expressed in Xenopus oocytes identified AtNPF2.9 as a putative iridoid glucoside importer. Eight orthologs were identified in Catharanthus roseus, of which three, CrNPF2.4, CrNPF2.5 and CrNPF2.6, were capable of transporting the iridoid glucosides 7-deoxyloganic acid, loganic acid, loganin and secologanin into oocytes. Based on enzyme expression data and transporter specificity, we propose that several enzymes of the biosynthetic pathway are present in both IPAP and epidermis cells, and that the three transporters are responsible for transporting not only loganic acid, as previously proposed, but multiple intermediates. Identification of the iridoid glucoside-transporting CrNPFs is an important step toward understanding the complex orchestration of the seco-iridioid pathway.
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Affiliation(s)
- Bo Larsen
- DynaMo Center, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Victoria L. Fuller
- DynaMo Center, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Jacob Pollier
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Alex Van Moerkercke
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Fabian Schweizer
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Richard Payne
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, UK
| | - Maite Colinas
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Sarah E. O’Connor
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, UK
| | - Alain Goossens
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Barbara A. Halkier
- DynaMo Center, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
- Corresponding author: E-mail, ; Fax, +45 35333333
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22
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Rai A, Saito K, Yamazaki M. Integrated omics analysis of specialized metabolism in medicinal plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:764-787. [PMID: 28109168 DOI: 10.1111/tpj.13485] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 05/19/2023]
Abstract
Medicinal plants are a rich source of highly diverse specialized metabolites with important pharmacological properties. Until recently, plant biologists were limited in their ability to explore the biosynthetic pathways of these metabolites, mainly due to the scarcity of plant genomics resources. However, recent advances in high-throughput large-scale analytical methods have enabled plant biologists to discover biosynthetic pathways for important plant-based medicinal metabolites. The reduced cost of generating omics datasets and the development of computational tools for their analysis and integration have led to the elucidation of biosynthetic pathways of several bioactive metabolites of plant origin. These discoveries have inspired synthetic biology approaches to develop microbial systems to produce bioactive metabolites originating from plants, an alternative sustainable source of medicinally important chemicals. Since the demand for medicinal compounds are increasing with the world's population, understanding the complete biosynthesis of specialized metabolites becomes important to identify or develop reliable sources in the future. Here, we review the contributions of major omics approaches and their integration to our understanding of the biosynthetic pathways of bioactive metabolites. We briefly discuss different approaches for integrating omics datasets to extract biologically relevant knowledge and the application of omics datasets in the construction and reconstruction of metabolic models.
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Affiliation(s)
- Amit Rai
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
| | - Kazuki Saito
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
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23
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Allard PM, Genta-Jouve G, Wolfender JL. Deep metabolome annotation in natural products research: towards a virtuous cycle in metabolite identification. Curr Opin Chem Biol 2017; 36:40-49. [DOI: 10.1016/j.cbpa.2016.12.022] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/20/2016] [Accepted: 12/22/2016] [Indexed: 12/20/2022]
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24
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Dugé de Bernonville T, Carqueijeiro I, Lanoue A, Lafontaine F, Sánchez Bel P, Liesecke F, Musset K, Oudin A, Glévarec G, Pichon O, Besseau S, Clastre M, St-Pierre B, Flors V, Maury S, Huguet E, O'Connor SE, Courdavault V. Folivory elicits a strong defense reaction in Catharanthus roseus: metabolomic and transcriptomic analyses reveal distinct local and systemic responses. Sci Rep 2017; 7:40453. [PMID: 28094274 PMCID: PMC5240345 DOI: 10.1038/srep40453] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 12/06/2016] [Indexed: 11/22/2022] Open
Abstract
Plants deploy distinct secondary metabolisms to cope with environment pressure and to face bio-aggressors notably through the production of biologically active alkaloids. This metabolism-type is particularly elaborated in Catharanthus roseus that synthesizes more than a hundred different monoterpene indole alkaloids (MIAs). While the characterization of their biosynthetic pathway now reaches completion, still little is known about the role of MIAs during biotic attacks. As a consequence, we developed a new plant/herbivore interaction system by challenging C. roseus leaves with Manduca sexta larvae. Transcriptomic and metabolic analyses demonstrated that C. roseus respond to folivory by both local and systemic processes relying on the activation of specific gene sets and biosynthesis of distinct MIAs following jasmonate production. While a huge local accumulation of strictosidine was monitored in attacked leaves that could repel caterpillars through its protein reticulation properties, newly developed leaves displayed an increased biosynthesis of the toxic strictosidine-derived MIAs, vindoline and catharanthine, produced by up-regulation of MIA biosynthetic genes. In this context, leaf consumption resulted in a rapid death of caterpillars that could be linked to the MIA dimerization observed in intestinal tracts. Furthermore, this study also highlights the overall transcriptomic control of the plant defense processes occurring during herbivory.
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Affiliation(s)
- Thomas Dugé de Bernonville
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Inês Carqueijeiro
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Arnaud Lanoue
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Florent Lafontaine
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Paloma Sánchez Bel
- Metabolic Integration and Cell Signaling Group, Plant Physiology Section, Department of CAMN, Universitat Jaume I, Spain
| | - Franziska Liesecke
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Karine Musset
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS/Université François-Rabelais de Tours, Tours, France
| | - Audrey Oudin
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Gaëlle Glévarec
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Olivier Pichon
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Sébastien Besseau
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Marc Clastre
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Benoit St-Pierre
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Victor Flors
- Metabolic Integration and Cell Signaling Group, Plant Physiology Section, Department of CAMN, Universitat Jaume I, Spain
| | - Stéphane Maury
- Université d'Orléans, CoST, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), EA 1207, USC1328 INRA, Orléans, France
| | - Elisabeth Huguet
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS/Université François-Rabelais de Tours, Tours, France
| | - Sarah E O'Connor
- The John Innes Centre, Department of Biological Chemistry, Norwich NR4 7UH, United Kingdom
| | - Vincent Courdavault
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
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25
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A single-step method for RNA isolation from tropical crops in the field. Sci Rep 2016; 6:38368. [PMID: 27922073 PMCID: PMC5138593 DOI: 10.1038/srep38368] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 11/09/2016] [Indexed: 11/08/2022] Open
Abstract
The RNAzol RT reagent was used to provide pure RNA from human cells. We develop a protocol using RNAzol RT reagent to extract pure RNA from plants tissues and demonstrate that this RNA extraction method works not only at room temperature but also at elevated temperatures and provides the simplest and most effective single-step method to extract pure and undegraded RNA directly from tropical plants in the field. RNA extraction directly in a complex field environment opens up the way for studying gene-environment interactions at transcriptome level to decipher the complex regulatory network involved in multiple-stress responses.
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26
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Mertens J, Van Moerkercke A, Vanden Bossche R, Pollier J, Goossens A. Clade IVa Basic Helix-Loop-Helix Transcription Factors Form Part of a Conserved Jasmonate Signaling Circuit for the Regulation of Bioactive Plant Terpenoid Biosynthesis. PLANT & CELL PHYSIOLOGY 2016; 57:2564-2575. [PMID: 27694525 DOI: 10.1093/pcp/pcw168] [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: 06/24/2016] [Accepted: 09/23/2016] [Indexed: 05/18/2023]
Abstract
Plants produce many bioactive, specialized metabolites to defend themselves when facing various stress situations. Their biosynthesis is directed by a tightly controlled regulatory circuit that is elicited by phytohormones such as jasmonate (JA). The basic helix-loop-helix (bHLH) transcription factors (TFs) bHLH iridoid synthesis 1 (BIS1) and Triterpene Saponin Activating Regulator (TSAR) 1 and 2, from Catharanthus roseus and Medicago truncatula, respectively, all belong to clade IVa of the bHLH protein family and activate distinct terpenoid pathways, thereby mediating monoterpenoid indole alkaloid (MIA) and triterpene saponin (TS) accumulation, respectively, in these two species. In this study, we report that promoters of the genes encoding the enzymes involved in the specific terpenoid pathway of one of these species can be transactivated by the orthologous bHLH factor from the other species through recognition of the same cis-regulatory elements. Accordingly, ectopic expression of CrBIS1 in M. truncatula hairy roots up-regulated the expression of all genes required for soyasaponin production, resulting in strongly increased levels of soyasaponins in the transformed roots. Likewise, transient expression of MtTSAR1 and MtTSAR2 in C. roseus petals led to up-regulation of the genes involved in the iridoid branch of the MIA pathway. Together, our data illustrate the functional similarity of these JA-inducible TFs and indicate that recruitment of defined cis-regulatory elements constitutes an important aspect of the evolution of conserved regulatory modules for the activation of species-specific terpenoid biosynthesis pathways by common signals such as the JA phytohormones.
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Affiliation(s)
- Jan Mertens
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
- These authors contributed equally to this work
| | - Alex Van Moerkercke
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
- These authors contributed equally to this work
| | - Robin Vanden Bossche
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Jacob Pollier
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Alain Goossens
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
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27
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Zhao L, Shao Z, Shanks JV. Anticancer Drugs. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807833.ch8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Le Zhao
- Iowa State University; Department of Chemical and Biological Engineering; 4140 Biorenewables Research Laboratory, 617 Bissell Road Ames 50011 IA USA
| | - Zengyi Shao
- Iowa State University; Department of Chemical and Biological Engineering; 4140 Biorenewables Research Laboratory, 617 Bissell Road Ames 50011 IA USA
| | - Jacqueline V Shanks
- Iowa State University; Department of Chemical and Biological Engineering; 4140 Biorenewables Research Laboratory, 617 Bissell Road Ames 50011 IA USA
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28
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Bahieldin A, Atef A, Shokry AM, Al-Karim S, Al Attas SG, Gadallah NO, Edris S, Al-Kordy MA, Hassan SM, Abo-Aba S, El-Domyati FM. Transcription factors regulating uspA genes in Catharanthus roseus. C R Biol 2016; 340:1-6. [PMID: 27890577 DOI: 10.1016/j.crvi.2016.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 10/14/2016] [Accepted: 10/20/2016] [Indexed: 11/15/2022]
Abstract
RNA-Seq of the Catharanthus roseus SRA database was done in order to detect putative universal stress proteins (USPs) and their possible controlling factors. Previous analysis indicated the existence and characterization of uspA-like genes. In silico analysis of RNA-Seq database in several plant tissues revealed the possible functions and regulations of some uspA-like transcripts whose transcription factors (TFs) that might drive their expression were detected. BLAST indicated the existence of TF superfamilies erf (ethylene-responsive TF), bHLH (basic helix-loop-helix) and WRKY that might regulate several uspA-like genes. This data was proven via semi-quantitative RT-PCR in four plant tissues. Several of these transcription factor superfamilies are known for their action in the plant defense against biotic and abiotic stresses.
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Affiliation(s)
- Ahmed Bahieldin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, 21589 Jeddah, Saudi Arabia; Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt.
| | - Ahmed Atef
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, 21589 Jeddah, Saudi Arabia.
| | - Ahmed M Shokry
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, 21589 Jeddah, Saudi Arabia; Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt.
| | - Saleh Al-Karim
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, 21589 Jeddah, Saudi Arabia.
| | - Sanaa G Al Attas
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, 21589 Jeddah, Saudi Arabia.
| | - Nour O Gadallah
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, 21589 Jeddah, Saudi Arabia; Genetics and Cytology Department, Genetic Engineering and Biotechnology Division, National Research Center, Dokki, Egypt.
| | - Sherif Edris
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, 21589 Jeddah, Saudi Arabia; Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt; Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, King Abdulaziz University (KAU), Jeddah, Saudi Arabia.
| | - Magdy A Al-Kordy
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, 21589 Jeddah, Saudi Arabia; Genetics and Cytology Department, Genetic Engineering and Biotechnology Division, National Research Center, Dokki, Egypt
| | - Sabah M Hassan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, 21589 Jeddah, Saudi Arabia; Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt.
| | - Salah Abo-Aba
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, 21589 Jeddah, Saudi Arabia; Microbial Genetics Department, Genetic Engineering and Biotechnology Division, National Research Centre, Giza, Egypt.
| | - Fotouh M El-Domyati
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, 21589 Jeddah, Saudi Arabia; Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt.
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29
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Van Moerkercke A, Steensma P, Gariboldi I, Espoz J, Purnama PC, Schweizer F, Miettinen K, Vanden Bossche R, De Clercq R, Memelink J, Goossens A. The basic helix-loop-helix transcription factor BIS2 is essential for monoterpenoid indole alkaloid production in the medicinal plant Catharanthus roseus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:3-12. [PMID: 27342401 DOI: 10.1111/tpj.13230] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 06/01/2016] [Accepted: 06/03/2016] [Indexed: 05/07/2023]
Abstract
Monoterpenoid indole alkaloids (MIAs) are produced as plant defence compounds. In the medicinal plant Catharanthus roseus, they comprise the anticancer compounds vinblastine and vincristine. The iridoid (monoterpenoid) pathway forms one of the two branches that feed MIA biosynthesis and its activation is regulated by the transcription factor (TF) basic helix-loop-helix (bHLH) iridoid synthesis 1 (BIS1). Here, we describe the identification and characterisation of BIS2, a jasmonate (JA)-responsive bHLH TF expressed preferentially in internal phloem-associated parenchyma cells, which transactivates promoters of iridoid biosynthesis genes and can homodimerise or form heterodimers with BIS1. Stable overexpression of BIS2 in C. roseus suspension cells and transient ectopic expression of BIS2 in C. roseus petal limbs resulted in increased transcript accumulation of methylerythritol-4-phosphate and iridoid pathway genes, but not of other MIA genes or triterpenoid genes. Transcript profiling also indicated that BIS2 expression is part of an amplification loop, as it is induced by overexpression of either BIS1 or BIS2. Accordingly, silencing of BIS2 in C. roseus suspension cells completely abolished the JA-induced upregulation of the iridoid pathway genes and subsequent MIA accumulation, despite the presence of induced BIS1, indicating that BIS2 is essential for MIA production in C. roseus.
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Affiliation(s)
- Alex Van Moerkercke
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Priscille Steensma
- Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
| | - Ivo Gariboldi
- Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
| | - Javiera Espoz
- Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
| | - Purin C Purnama
- Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
| | - Fabian Schweizer
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Karel Miettinen
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Robin Vanden Bossche
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Rebecca De Clercq
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Johan Memelink
- Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
| | - Alain Goossens
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium.
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30
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Goossens J, Fernández-Calvo P, Schweizer F, Goossens A. Jasmonates: signal transduction components and their roles in environmental stress responses. PLANT MOLECULAR BIOLOGY 2016; 68:1333-1347. [PMID: 27927998 DOI: 10.1093/jxb/erw440] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Jasmonates, oxylipin-type plant hormones, are implicated in diverse aspects of plant growth development and interaction with the environment. Following diverse developmental and environmental cues, jasmonate is produced, conjugated to the amino acid isoleucine and perceived by a co-receptor complex composed of the Jasmonate ZIM-domain (JAZ) repressor proteins and an E3 ubiquitin ligase complex containing the F-box CORONATINE INSENSITIVE 1 (COI1). This event triggers the degradation of the JAZ proteins and the release of numerous transcription factors, including MYC2 and its homologues, which are otherwise bound and inhibited by the JAZ repressors. Here, we will review the role of the COI1, JAZ and MYC2 proteins in the interaction of the plant with its environment, illustrating the significance of jasmonate signalling, and of the proteins involved, for responses to both biotic stresses caused by insects and numerous microbial pathogens and abiotic stresses caused by adverse climatic conditions. It has also become evident that crosstalk with other hormone signals, as well as light and clock signals, plays an important role in the control and fine-tuning of these stress responses. Finally, we will discuss how several pathogens exploit the jasmonate perception and early signalling machinery to decoy the plants defence systems.
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Affiliation(s)
- Jonas Goossens
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Patricia Fernández-Calvo
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Fabian Schweizer
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, Technologiepark 927, 9052, Ghent, Belgium.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
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31
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Sun J, Manmathan H, Sun C, Peebles CAM. Examining the transcriptional response of overexpressing anthranilate synthase in the hairy roots of an important medicinal plant Catharanthus roseus by RNA-seq. BMC PLANT BIOLOGY 2016; 16:108. [PMID: 27154243 PMCID: PMC4859987 DOI: 10.1186/s12870-016-0794-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 04/29/2016] [Indexed: 05/04/2023]
Abstract
BACKGROUND Clinically important anti-cancer drugs vinblastine and vincristine are solely synthesized by the terpenoid indole alkaloid (TIA) pathway in Catharanthus roseus. Anthranilate synthase (AS) is a rate-limiting enzyme in the TIA pathway. The transgenic C. roseus hairy root line overexpressing a feedback insensitive ASα subunit under the control of an inducible promoter and the ASβ subunit constitutively was previously created for the overproduction of TIAs. However, both increases and decreases in TIAs were detected after overexpressing ASα. Although genetic modification is targeted to one gene in the TIA pathway, it could trigger global transcriptional changes that can directly or indirectly affect TIA biosynthesis. In this study, Illumina sequencing and RT-qPCR were used to detect the transcriptional responses to overexpressing AS, which can increase understanding of the complex regulation of the TIA pathway and further inspire rational metabolic engineering for enhanced TIA production in C. roseus hairy roots. RESULTS Overexpressing AS in C. roseus hairy roots altered the transcription of most known TIA pathway genes and regulators after 12, 24, and 48 h induction detected by RT-qPCR. Changes in the transcriptome of C. roseus hairy roots was further investigated 18 hours after ASα induction and compared to the control hairy roots using RNA-seq. A unigene set of 30,281 was obtained by de novo assembly of the sequencing reads. Comparison of the differentially expressed transcriptional profiles resulted in 2853 differentially expressed transcripts. Functional annotation of these transcripts revealed a complex and systematically transcriptome change in ASαβ hairy roots. Pathway analysis shows alterations in many pathways such as aromatic amino acid biosynthesis, jasmonic acid (JA) biosynthesis and other secondary metabolic pathways after perturbing AS. Moreover, many genes in overall stress response were differentially expressed after overexpressing ASα. CONCLUSION The transcriptomic analysis illustrates overexpressing AS stimulates the overall stress response and affects the metabolic networks in C. roseus hairy roots. The up-regulation of endogenous JA biosynthesis pathway indicates the involvement of JA signal transduction to regulate TIA biosynthesis in ASαβ engineered roots and explained why many of the transcripts for TIA genes and regulators are seen to increase with AS overexpression.
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Affiliation(s)
- Jiayi Sun
- Chemical and Biological Engineering Department, Colorado State University, Campus delivery 1370, Fort Collins, 80523, USA
| | - Harish Manmathan
- Soil and Crop Sciences Department, Colorado State University, Campus deliver 1170, Fort Collins, Colorado, 80523, USA
| | - Cheng Sun
- Department of biology, Colorado State University, 1878 Campus Delivery, Fort Collins, Colorado, 80521, USA
- Key Laboratory of Pollinating Insect Biology of the Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agriculture Science, Beijing, 10093, China
| | - Christie A M Peebles
- Chemical and Biological Engineering Department, Colorado State University, Campus delivery 1370, Fort Collins, 80523, USA.
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Alagna F, Geu-Flores F, Kries H, Panara F, Baldoni L, O'Connor SE, Osbourn A. Identification and Characterization of the Iridoid Synthase Involved in Oleuropein Biosynthesis in Olive (Olea europaea) Fruits. J Biol Chem 2016; 291:5542-5554. [PMID: 26709230 PMCID: PMC4786697 DOI: 10.1074/jbc.m115.701276] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/21/2015] [Indexed: 01/19/2023] Open
Abstract
The secoiridoids are the main class of specialized metabolites present in olive (Olea europaea L.) fruit. In particular, the secoiridoid oleuropein strongly influences olive oil quality because of its bitterness, which is a desirable trait. In addition, oleuropein possesses a wide range of pharmacological properties, including antioxidant, anti-inflammatory, and anti-cancer activities. In accordance, obtaining high oleuropein varieties is a main goal of molecular breeding programs. Here we use a transcriptomic approach to identify candidate genes belonging to the secoiridoid pathway in olive. From these candidates, we have functionally characterized the olive homologue of iridoid synthase (OeISY), an unusual terpene cyclase that couples an NAD (P)H-dependent 1,4-reduction step with a subsequent cyclization, and we provide evidence that OeISY likely generates the monoterpene scaffold of oleuropein in olive fruits. OeISY, the first pathway gene characterized for this type of secoiridoid, is a potential target for breeding programs in a high value secoiridoid-accumulating species.
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Affiliation(s)
- Fiammetta Alagna
- From the Departments of Metabolic Biology and; the Institute of Biosciences and Bio-resources, National Research Council (CNR), 06128 Perugia, Italy,.
| | - Fernando Geu-Flores
- the Copenhagen Plant Science Centre & Section for Plant Biochemistry, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark, and
| | - Hajo Kries
- Biological Chemistry, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Francesco Panara
- the ENEA Trisaia Research Center, 75026 Rotondella, Matera, Italy
| | - Luciana Baldoni
- the Institute of Biosciences and Bio-resources, National Research Council (CNR), 06128 Perugia, Italy
| | - Sarah E O'Connor
- Biological Chemistry, John Innes Centre, Norwich NR4 7UH, United Kingdom
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Han R, Rai A, Nakamura M, Suzuki H, Takahashi H, Yamazaki M, Saito K. De Novo Deep Transcriptome Analysis of Medicinal Plants for Gene Discovery in Biosynthesis of Plant Natural Products. Methods Enzymol 2016; 576:19-45. [DOI: 10.1016/bs.mie.2016.03.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Udomsom N, Rai A, Suzuki H, Okuyama J, Imai R, Mori T, Nakabayashi R, Saito K, Yamazaki M. Function of AP2/ERF Transcription Factors Involved in the Regulation of Specialized Metabolism in Ophiorrhiza pumila Revealed by Transcriptomics and Metabolomics. FRONTIERS IN PLANT SCIENCE 2016; 7:1861. [PMID: 28018397 PMCID: PMC5145908 DOI: 10.3389/fpls.2016.01861] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 11/25/2016] [Indexed: 05/20/2023]
Abstract
The hairy roots (HR) of Ophiorrhiza pumila produce camptothecin (CPT), a monoterpenoid indole alkaloid used as a precursor in the synthesis of chemotherapeutic drugs. O. pumila HR culture is considered as a promising alternative source of CPT, however, the knowledge about the biosynthetic pathway and regulatory mechanism is still limited. In this study, five genes that encode AP2/ERF transcription factors, namely OpERF1-OpERF5, were isolated from HR of O. pumila. Phylogenetic analysis of AP2/ERF protein sequences suggested the close evolutionary relationship of OpERF1 with stress-responsive ERF factors in Arabidopsis and of OpERF2 with ERF factors reported to regulate alkaloid production, such as ORCA3 in Catharanthus roseus, NIC2 locus ERF in tobacco, and JRE4 in tomato. We generated the transgenic HR lines of O. pumila, ERF1i and ERF2i, in which the expression of OpERF1 and OpERF2, respectively, was suppressed using RNA interference technique. The transcriptome and metabolome of these suppressed HR were analyzed for functional characterization of OpERF1 and OpERF2. Although significant changes were not observed in the metabolome, including CPT and related compounds, the suppression of OpERF2 resulted in reduced expression of genes in the 2-C-methyl-d-erythritol 4-phosphate and secologanin-strictosidine pathways, which supply a precursor, strictosidine, for CPT biosynthesis. Furthermore, while it was not conclusive for OpERF1, enrichment analysis of differentially expressed genes in the suppressed HR showed that the gene ontology terms for oxidation-reduction, presumably involved in secondary metabolite pathways, were enriched in the ERF2i downregulated gene set. These results suggest a positive role of OpERF2 in regulating specialized metabolism in O. pumila.
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Affiliation(s)
- Nirin Udomsom
- Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba UniversityChiba, Japan
| | - Amit Rai
- Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba UniversityChiba, Japan
| | - Hideyuki Suzuki
- Department of Research and Development, Kazusa DNA Research InstituteChiba, Japan
| | - Jun Okuyama
- Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba UniversityChiba, Japan
| | - Ryosuke Imai
- Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba UniversityChiba, Japan
| | - Tetsuya Mori
- RIKEN Center for Sustainable Resource ScienceKanagawa, Japan
| | - Ryo Nakabayashi
- RIKEN Center for Sustainable Resource ScienceKanagawa, Japan
| | - Kazuki Saito
- Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba UniversityChiba, Japan
- RIKEN Center for Sustainable Resource ScienceKanagawa, Japan
| | - Mami Yamazaki
- Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba UniversityChiba, Japan
- *Correspondence: Mami Yamazaki
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Ganie SH, Upadhyay P, Das S, Prasad Sharma M. Authentication of medicinal plants by DNA markers. PLANT GENE 2015; 4:83-99. [PMID: 32289060 PMCID: PMC7103949 DOI: 10.1016/j.plgene.2015.10.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 10/01/2015] [Accepted: 10/07/2015] [Indexed: 11/21/2022]
Abstract
Medicinal plants have been used worldwide for centuries to maintain health and to treat diseases, more so chronic diseases. However, adulteration and use of spurious materials as substitutes have become a major concern for users and industry for reasons of safety and efficacy. Therefore, authentication of medicinal plants is of utmost importance. Morphological, anatomical, chemical and DNA markers solve the problem by differentiating the genuine material from the adulterants, substitutes and spurious drugs. DNA markers use nucleotide sequences to identify species; it takes preference over the other two markers being not age dependent, tissue specific and having a higher discriminating power. Therefore, characterization of plants with such markers is an ideal approach for identification of medicinal plant species and populations/varieties of the same species. Availability of certified taxonomic specimens in herbaria is certainly required for unambiguous confirmation through final visual comparison and analysis.
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Affiliation(s)
| | - Priti Upadhyay
- Dept. of Botany, University of Delhi, Delhi 110007, India
| | - Sandip Das
- Dept. of Botany, University of Delhi, Delhi 110007, India
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Truong AD, Hong YH, Lillehoj HS. RNA-seq Profiles of Immune Related Genes in the Spleen of Necrotic Enteritis-afflicted Chicken Lines. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:1496-511. [PMID: 26323406 PMCID: PMC4554858 DOI: 10.5713/ajas.15.0143] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/10/2015] [Accepted: 04/20/2015] [Indexed: 11/27/2022]
Abstract
The study aimed to compare the necrotic enteritis (NE)-induced transcriptome differences between the spleens of Marek’s disease resistant chicken line 6.3 and susceptible line 7.2 co-infected with Eimeria maxima/Clostridium perfringens using RNA-Seq. Total RNA from the spleens of two chicken lines were used to make libraries, generating 42,736,296 and 42,617,720 usable reads, which were assembled into groups of 29,897 and 29,833 mRNA genes, respectively. The transcriptome changes were investigated using the differentially expressed genes (DEGs) package, which indicated 3,255, 2,468 and 2,234 DEGs of line 6.3, line 7.2, and comparison between two lines, respectively (fold change ≥2, p<0.01). The transcription levels of 14 genes identified were further examined using qRT-PCR. The results of qRT-PCR were consistent with the RNA-seq data. All of the DEGs were analysed using gene ontology terms, the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and the DEGs in each term were found to be more highly expressed in line 6.3 than in line 7.2. RNA-seq analysis indicated 139 immune related genes, 44 CD molecular genes and 150 cytokines genes which were differentially expressed among chicken lines 6.3 and 7.2 (fold change ≥2, p<0.01). Novel mRNA analysis indicated 15,518 novel genes, for which the expression was shown to be higher in line 6.3 than in line 7.2 including some immune-related targets. These findings will help to understand host-pathogen interaction in the spleen and elucidate the mechanism of host genetic control of NE, and provide basis for future studies that can lead to the development of marker-based selection of highly disease-resistant chickens.
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Affiliation(s)
- Anh Duc Truong
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Services, U. S. Department of Agriculture, Beltsville, MD 20705, USA
| | - Yeong Ho Hong
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Services, U. S. Department of Agriculture, Beltsville, MD 20705, USA
| | - Hyun S Lillehoj
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Services, U. S. Department of Agriculture, Beltsville, MD 20705, USA
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Bahieldin A, Atef A, Shokry AM, Al-Karim S, Al Attas SG, Gadallah NO, Edris S, Al-Kordy MA, Omer AMS, Sabir JSM, Ramadan AM, Al-Hajar ASM, Makki RM, Hassan SM, El-Domyati FM. Structural identification of putative USPs in Catharanthus roseus. C R Biol 2015; 338:643-9. [PMID: 26318047 DOI: 10.1016/j.crvi.2015.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 07/18/2015] [Indexed: 10/23/2022]
Abstract
Nucleotide sequences of the C. roseus SRA database were assembled and translated in order to detect putative universal stress proteins (USPs). Based on the known conserved USPA domain, 24 Pfam putative USPA proteins in C. roseus were detected and arranged in six architectures. The USPA-like domain was detected in all architectures, while the protein kinase-like (or PK-like), (tyr)PK-like and/or U-box domains are shown downstream it. Three other domains were also shown to coexist with the USPA domain in C. roseus putative USPA sequences. These domains are tetratricopeptide repeat (or TPR), apolipophorin III (or apoLp-III) and Hsp90 co-chaperone Cdc37. Subsequent analysis divided USPA-like domains based on the ability to bind ATP. The multiple sequence alignment indicated the occurrence of eight C. roseus residues of known features of the bacterial 1MJH secondary structure. The data of the phylogenetic tree indicated several distinct groups of USPA-like domains confirming the presence of high level of sequence conservation between the plant and bacterial USPA-like sequences.
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Affiliation(s)
- Ahmed Bahieldin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia; Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt.
| | - Ahmed Atef
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia.
| | - Ahmed M Shokry
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia; Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt.
| | - Saleh Al-Karim
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia.
| | - Sanaa G Al Attas
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia.
| | - Nour O Gadallah
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia; Genetics and Cytology Department, Genetic Engineering and Biotechnology Division, National Research Center, Dokki, Egypt.
| | - Sherif Edris
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia; Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt; Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, King Abdulaziz University (KAU), Jeddah, Saudi Arabia.
| | - Magdy A Al-Kordy
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia; Genetics and Cytology Department, Genetic Engineering and Biotechnology Division, National Research Center, Dokki, Egypt.
| | - Abdulkader M Shaikh Omer
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia.
| | - Jamal S M Sabir
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia.
| | - Ahmed M Ramadan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia; Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt.
| | - Abdulrahman S M Al-Hajar
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia.
| | - Rania M Makki
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia.
| | - Sabah M Hassan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia; Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt.
| | - Fotouh M El-Domyati
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia; Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt.
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Dugé de Bernonville T, Foureau E, Parage C, Lanoue A, Clastre M, Londono MA, Oudin A, Houillé B, Papon N, Besseau S, Glévarec G, Atehortùa L, Giglioli-Guivarc'h N, St-Pierre B, De Luca V, O'Connor SE, Courdavault V. Characterization of a second secologanin synthase isoform producing both secologanin and secoxyloganin allows enhanced de novo assembly of a Catharanthus roseus transcriptome. BMC Genomics 2015; 16:619. [PMID: 26285573 PMCID: PMC4541752 DOI: 10.1186/s12864-015-1678-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 06/01/2015] [Indexed: 01/14/2023] Open
Abstract
Background Transcriptome sequencing offers a great resource for the study of non-model plants such as Catharanthus roseus, which produces valuable monoterpenoid indole alkaloids (MIAs) via a complex biosynthetic pathway whose characterization is still undergoing. Transcriptome databases dedicated to this plant were recently developed by several consortia to uncover new biosynthetic genes. However, the identification of missing steps in MIA biosynthesis based on these large datasets may be limited by the erroneous assembly of close transcripts and isoforms, even with the multiple available transcriptomes. Results Secologanin synthases (SLS) are P450 enzymes that catalyze an unusual ring-opening reaction of loganin in the biosynthesis of the MIA precursor secologanin. We report here the identification and characterization in C. roseus of a new isoform of SLS, SLS2, sharing 97 % nucleotide sequence identity with the previously characterized SLS1. We also discovered that both isoforms further oxidize secologanin into secoxyloganin. SLS2 had however a different expression profile, being the major isoform in aerial organs that constitute the main site of MIA accumulation. Unfortunately, we were unable to find a current C. roseus transcriptome database containing simultaneously well reconstructed sequences of SLS isoforms and accurate expression levels. After a pair of close mRNA encoding tabersonine 16-hydroxylase (T16H1 and T16H2), this is the second example of improperly assembled transcripts from the MIA pathway in the public transcriptome databases. To construct a more complete transcriptome resource for C. roseus, we re-processed previously published transcriptome data by combining new single assemblies. Care was particularly taken during clustering and filtering steps to remove redundant contigs but not transcripts encoding potential isoforms by monitoring quality reconstruction of MIA genes and specific SLS and T16H isoforms. The new consensus transcriptome allowed a precise estimation of abundance of SLS and T16H isoforms, similar to qPCR measurements. Conclusions The C. roseus consensus transcriptome can now be used for characterization of new genes of the MIA pathway. Furthermore, additional isoforms of genes encoding distinct MIA biosynthetic enzymes isoforms could be predicted suggesting the existence of a higher level of complexity in the synthesis of MIA, raising the question of the evolutionary events behind what seems like redundancy. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1678-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas Dugé de Bernonville
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, 37200, Tours, France.
| | - Emilien Foureau
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, 37200, Tours, France.
| | - Claire Parage
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, 37200, Tours, France.
| | - Arnaud Lanoue
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, 37200, Tours, France.
| | - Marc Clastre
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, 37200, Tours, France.
| | - Monica Arias Londono
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, 37200, Tours, France. .,Universidad de Antioquia, Laboratorio de Biotecnología, Sede de Investigación Universitaria, Medellín, Colombia.
| | - Audrey Oudin
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, 37200, Tours, France.
| | - Benjamin Houillé
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, 37200, Tours, France.
| | - Nicolas Papon
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, 37200, Tours, France.
| | - Sébastien Besseau
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, 37200, Tours, France.
| | - Gaëlle Glévarec
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, 37200, Tours, France.
| | - Lucia Atehortùa
- Universidad de Antioquia, Laboratorio de Biotecnología, Sede de Investigación Universitaria, Medellín, Colombia.
| | - Nathalie Giglioli-Guivarc'h
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, 37200, Tours, France.
| | - Benoit St-Pierre
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, 37200, Tours, France.
| | - Vincenzo De Luca
- Department of Biological Sciences, Brock University, 500 Glenridge Avenue, St Catharines, Ontario, L2S 3A1, Canada.
| | - Sarah E O'Connor
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK.
| | - Vincent Courdavault
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, 37200, Tours, France.
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The bHLH transcription factor BIS1 controls the iridoid branch of the monoterpenoid indole alkaloid pathway in Catharanthus roseus. Proc Natl Acad Sci U S A 2015; 112:8130-5. [PMID: 26080427 DOI: 10.1073/pnas.1504951112] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Plants make specialized bioactive metabolites to defend themselves against attackers. The conserved control mechanisms are based on transcriptional activation of the respective plant species-specific biosynthetic pathways by the phytohormone jasmonate. Knowledge of the transcription factors involved, particularly in terpenoid biosynthesis, remains fragmentary. By transcriptome analysis and functional screens in the medicinal plant Catharanthus roseus (Madagascar periwinkle), the unique source of the monoterpenoid indole alkaloid (MIA)-type anticancer drugs vincristine and vinblastine, we identified a jasmonate-regulated basic helix-loop-helix (bHLH) transcription factor from clade IVa inducing the monoterpenoid branch of the MIA pathway. The bHLH iridoid synthesis 1 (BIS1) transcription factor transactivated the expression of all of the genes encoding the enzymes that catalyze the sequential conversion of the ubiquitous terpenoid precursor geranyl diphosphate to the iridoid loganic acid. BIS1 acted in a complementary manner to the previously characterized ethylene response factor Octadecanoid derivative-Responsive Catharanthus APETALA2-domain 3 (ORCA3) that transactivates the expression of several genes encoding the enzymes catalyzing the conversion of loganic acid to the downstream MIAs. In contrast to ORCA3, overexpression of BIS1 was sufficient to boost production of high-value iridoids and MIAs in C. roseus suspension cell cultures. Hence, BIS1 might be a metabolic engineering tool to produce sustainably high-value MIAs in C. roseus plants or cultures.
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Lin PC, Hu WC, Lee SC, Chen YL, Lee CY, Chen YR, Liu LYD, Chen PY, Lin SS, Chang YC. Application of an Integrated Omics Approach for Identifying Host Proteins That Interact With Odontoglossum ringspot virus Capsid Protein. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:711-26. [PMID: 25625820 DOI: 10.1094/mpmi-08-14-0246-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The glutamic acid at position 100 (E(100)) in the capsid protein (CP) of Odontoglossum ringspot virus (ORSV) plays an important role in long-distance viral movement in Nicotiana benthamiana. The ORSV(E100A) mutant, which has a glutamic acid to alanine substitution, shows a loss of systemic infectivity in N. benthamiana. Transmission electron microscopy and size-exclusion chromatography assays showed that E(100) is essential for CP-CP interaction and viral particle assembly. To identify the ORSV triggering or response genes and CP-interacting proteins (CP-IP), an integrated omics approach based on next-generation sequencing and proteomics profiling was used in this study. The whole-transcriptomes of healthy and ORSV-infected leaves of N. benthamiana were analyzed, and the gene information was used to create a N. benthamiana protein database that was used for protein identification following mass spectrometry analysis. The integrated omics approach identified several putative host proteins that interact with ORSV CP(WT) and were categorized as photosystem subunits, defense-associated proteins, and cell division components. The expression pattern and CP interaction of these CP-IP were examined by semiquantitative reverse transcription polymerase chain reaction and an in vitro binding assay, respectively, to verify the in silico data. Among these proteins, a proteinase inhibitor of N. benthamiana (NbPI2) was highly associated with CP(E100A) as compared with CP(WT), and NbPI1 and NbPI2 were highly induced in ORSV-infected plants. NbPI1- and NbPI2-silenced plants (via a Tobacco rattle virus-induced gene-silencing system) did not exhibit a difference in ORSV infection. Thus, whether NbPI1 and NbPI2 play a role in plant immunity requires further investigation. In summary, the integrated omics approach provides massive and valuable information to identify the ORSV CP-IP and these CP-IP will help us to understand the movement of this virus and plant-virus interaction.
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Affiliation(s)
- Pin-Chun Lin
- 1 Department of Plant Pathology and Microbiology, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
- 2 Institute of Biotechnology, National Taiwan University, 81, Chang-Xing St., Taipei, Taiwan
| | - Wen-Chi Hu
- 1 Department of Plant Pathology and Microbiology, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
| | - Shu-Chuan Lee
- 1 Department of Plant Pathology and Microbiology, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
| | - Ying-Lan Chen
- 4 Agricultural Biotechnology Research Center, Academia Sinica, 128, Academia Rd, Sec. 2, Taipei, Taiwan
- 5 Institute of Plant Biology and Department of Life Science, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
| | - Chi-Ying Lee
- 4 Agricultural Biotechnology Research Center, Academia Sinica, 128, Academia Rd, Sec. 2, Taipei, Taiwan
| | - Yet-Ran Chen
- 4 Agricultural Biotechnology Research Center, Academia Sinica, 128, Academia Rd, Sec. 2, Taipei, Taiwan
| | - Li-Yu Daisy Liu
- 6 Department of Agronomy, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
| | - Po-Yen Chen
- 1 Department of Plant Pathology and Microbiology, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
| | - Shih-Shun Lin
- 2 Institute of Biotechnology, National Taiwan University, 81, Chang-Xing St., Taipei, Taiwan
- 3 Genome and Systems Biology Degree Program, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
- 4 Agricultural Biotechnology Research Center, Academia Sinica, 128, Academia Rd, Sec. 2, Taipei, Taiwan
| | - Ya-Chun Chang
- 1 Department of Plant Pathology and Microbiology, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
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Kumar S, Bhatia S. Isolation of Catharanthus roseus (L.) G. Don Nuclei and Measurement of Rate of Tryptophan decarboxylase Gene Transcription Using Nuclear Run-On Transcription Assay. PLoS One 2015; 10:e0127892. [PMID: 26024519 PMCID: PMC4449189 DOI: 10.1371/journal.pone.0127892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 04/21/2015] [Indexed: 11/27/2022] Open
Abstract
Background An accurate assessment of transcription ‘rate’ is often desired to describe the promoter activity. In plants, isolation of transcriptionally active nuclei and their subsequent use in nuclear run-on assays has been challenging and therefore limit an accurate measurement of gene transcription ‘rate’. Catharanthus roseus has emerged as a model medicinal plant as it exhibits an unsurpassed spectrum of chemodiversity, producing over 130 alkaloids through the terpenoid indole alkaloid (TIA) pathway and therefore serves as a ‘molecular hub’ to understand gene expression profiles. Results The protocols presented here streamline, adapt and optimize the existing methods of nuclear run-on assay for use in C. roseus. Here, we fully describe all the steps to isolate transcriptionally active nuclei from C. roseus leaves and utilize them to perform nuclear run-on transcription assay. Nuclei isolated by this method transcribed at a level consistent with their response to external stimuli, as transcription rate of TDC gene was found to be higher in response to external stimuli i.e. when seedlings were subjected to UV-B light or to methyl jasmonate (MeJA). However, the relative transcript abundance measured parallel through qRT-PCR was found to be inconsistent with the synthesis rate indicating that some post transcriptional events might have a role in transcript stability in response to stimuli. Conclusions Our study provides an optimized, efficient and inexpensive method of isolation of intact nuclei and nuclear ‘run-on’ transcription assay to carry out in-situ measurement of gene transcription rate in Catharanthus roseus. This would be valuable in investigating the transcriptional and post transcriptional response of other TIA pathway genes in C. roseus. Isolated nuclei may also provide a resource that could be used for performing the chip assay as well as serve as the source of nuclear proteins for in-vitro EMSA studies. Moreover, nascent nuclear run-on transcript could be further subjected to RNA-Seq for global nuclear run-on assay (GNRO-Seq) for genome wide in-situ measurement of transcription rate of plant genes.
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Affiliation(s)
- Santosh Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box 10531, New Delhi, 110067, India
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box 10531, New Delhi, 110067, India
- * E-mail:
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Dugé de Bernonville T, Clastre M, Besseau S, Oudin A, Burlat V, Glévarec G, Lanoue A, Papon N, Giglioli-Guivarc'h N, St-Pierre B, Courdavault V. Phytochemical genomics of the Madagascar periwinkle: Unravelling the last twists of the alkaloid engine. PHYTOCHEMISTRY 2015; 113:9-23. [PMID: 25146650 DOI: 10.1016/j.phytochem.2014.07.023] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 07/11/2014] [Accepted: 07/15/2014] [Indexed: 05/12/2023]
Abstract
The Madagascar periwinkle produces a large palette of Monoterpenoid Indole Alkaloids (MIAs), a class of complex alkaloids including some of the most valuable plant natural products with precious therapeutical values. Evolutionary pressure on one of the hotspots of biodiversity has obviously turned this endemic Malagasy plant into an innovative alkaloid engine. Catharanthus is a unique taxon producing vinblastine and vincristine, heterodimeric MIAs with complex stereochemistry, and also manufactures more than 100 different MIAs, some shared with the Apocynaceae, Loganiaceae and Rubiaceae members. For over 60 years, the quest for these powerful anticancer drugs has inspired biologists, chemists, and pharmacists to unravel the chemistry, biochemistry, therapeutic activity, cell and molecular biology of Catharanthus roseus. Recently, the "omics" technologies have fuelled rapid progress in deciphering the last secret of strictosidine biosynthesis, the central precursor opening biosynthetic routes to several thousand MIA compounds. Dedicated C. roseus transcriptome, proteome and metabolome databases, comprising organ-, tissue- and cell-specific libraries, and other phytogenomic resources, were developed for instance by PhytoMetaSyn, Medicinal Plant Genomic Resources and SmartCell consortium. Tissue specific library screening, orthology comparison in species with or without MIA-biochemical engines, clustering of gene expression profiles together with various functional validation strategies, largely contributed to enrich the toolbox for plant synthetic biology and metabolic engineering of MIA biosynthesis.
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Affiliation(s)
- Thomas Dugé de Bernonville
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Marc Clastre
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Sébastien Besseau
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Audrey Oudin
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Vincent Burlat
- Université de Toulouse, UPS, UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617 Auzeville, F-31326 Castanet-Tolosan, France; CNRS, UMR 5546, BP 42617 Auzeville, F-31326 Castanet-Tolosan, France
| | - Gaëlle Glévarec
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Arnaud Lanoue
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Nicolas Papon
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | | | - Benoit St-Pierre
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Vincent Courdavault
- Université François-Rabelais de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France.
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Kellner F, Kim J, Clavijo BJ, Hamilton JP, Childs KL, Vaillancourt B, Cepela J, Habermann M, Steuernagel B, Clissold L, McLay K, Buell CR, O'Connor SE. Genome-guided investigation of plant natural product biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:680-92. [PMID: 25759247 DOI: 10.1111/tpj.12827] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 02/27/2015] [Accepted: 03/04/2015] [Indexed: 05/02/2023]
Abstract
The medicinal plant Madagascar periwinkle, Catharanthus roseus (L.) G. Don, produces hundreds of biologically active monoterpene-derived indole alkaloid (MIA) metabolites and is the sole source of the potent, expensive anti-cancer compounds vinblastine and vincristine. Access to a genome sequence would enable insights into the biochemistry, control, and evolution of genes responsible for MIA biosynthesis. However, generation of a near-complete, scaffolded genome is prohibitive to small research communities due to the expense, time, and expertise required. In this study, we generated a genome assembly for C. roseus that provides a near-comprehensive representation of the genic space that revealed the genomic context of key points within the MIA biosynthetic pathway including physically clustered genes, tandem gene duplication, expression sub-functionalization, and putative neo-functionalization. The genome sequence also facilitated high resolution co-expression analyses that revealed three distinct clusters of co-expression within the components of the MIA pathway. Coordinated biosynthesis of precursors and intermediates throughout the pathway appear to be a feature of vinblastine/vincristine biosynthesis. The C. roseus genome also revealed localization of enzyme-rich genic regions and transporters near known biosynthetic enzymes, highlighting how even a draft genome sequence can empower the study of high-value specialized metabolites.
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Affiliation(s)
- Franziska Kellner
- Department of Biological Chemistry, The John Innes Centre, Norwich, NR4 7UH, UK
| | - Jeongwoon Kim
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | | | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Brieanne Vaillancourt
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Jason Cepela
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Marc Habermann
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | | | | | | | - Carol Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Sarah E O'Connor
- Department of Biological Chemistry, The John Innes Centre, Norwich, NR4 7UH, UK
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Kim T, Dreher K, Nilo-Poyanco R, Lee I, Fiehn O, Lange BM, Nikolau BJ, Sumner L, Welti R, Wurtele ES, Rhee SY. Patterns of metabolite changes identified from large-scale gene perturbations in Arabidopsis using a genome-scale metabolic network. PLANT PHYSIOLOGY 2015; 167:1685-1698. [PMID: 25670818 PMCID: PMC4378150 DOI: 10.1104/pp.114.252361] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 02/06/2015] [Indexed: 05/29/2023]
Abstract
Metabolomics enables quantitative evaluation of metabolic changes caused by genetic or environmental perturbations. However, little is known about how perturbing a single gene changes the metabolic system as a whole and which network and functional properties are involved in this response. To answer this question, we investigated the metabolite profiles from 136 mutants with single gene perturbations of functionally diverse Arabidopsis (Arabidopsis thaliana) genes. Fewer than 10 metabolites were changed significantly relative to the wild type in most of the mutants, indicating that the metabolic network was robust to perturbations of single metabolic genes. These changed metabolites were closer to each other in a genome-scale metabolic network than expected by chance, supporting the notion that the genetic perturbations changed the network more locally than globally. Surprisingly, the changed metabolites were close to the perturbed reactions in only 30% of the mutants of the well-characterized genes. To determine the factors that contributed to the distance between the observed metabolic changes and the perturbation site in the network, we examined nine network and functional properties of the perturbed genes. Only the isozyme number affected the distance between the perturbed reactions and changed metabolites. This study revealed patterns of metabolic changes from large-scale gene perturbations and relationships between characteristics of the perturbed genes and metabolic changes.
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Affiliation(s)
- Taehyong Kim
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.)
| | - Kate Dreher
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.)
| | - Ricardo Nilo-Poyanco
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.)
| | - Insuk Lee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.)
| | - Oliver Fiehn
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.)
| | - Bernd Markus Lange
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.)
| | - Basil J Nikolau
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.)
| | - Lloyd Sumner
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.)
| | - Ruth Welti
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.)
| | - Eve S Wurtele
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.)
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.)
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Costa LM. Editorial: Plant and Cell Physiology--past, present and future. PLANT & CELL PHYSIOLOGY 2015; 56:1-3. [PMID: 25756139 DOI: 10.1093/pcp/pcu207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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Goossens A. It is easy to get huge candidate gene lists for plant metabolism now, but how to get beyond? MOLECULAR PLANT 2015; 8:2-5. [PMID: 25578267 DOI: 10.1016/j.molp.2014.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 07/08/2014] [Accepted: 08/05/2014] [Indexed: 06/04/2023]
Affiliation(s)
- Alain Goossens
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium.
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Ohyanagi H, Takano T, Terashima S, Kobayashi M, Kanno M, Morimoto K, Kanegae H, Sasaki Y, Saito M, Asano S, Ozaki S, Kudo T, Yokoyama K, Aya K, Suwabe K, Suzuki G, Aoki K, Kubo Y, Watanabe M, Matsuoka M, Yano K. Plant Omics Data Center: an integrated web repository for interspecies gene expression networks with NLP-based curation. PLANT & CELL PHYSIOLOGY 2015; 56:e9. [PMID: 25505034 PMCID: PMC4301748 DOI: 10.1093/pcp/pcu188] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 11/24/2014] [Indexed: 05/20/2023]
Abstract
Comprehensive integration of large-scale omics resources such as genomes, transcriptomes and metabolomes will provide deeper insights into broader aspects of molecular biology. For better understanding of plant biology, we aim to construct a next-generation sequencing (NGS)-derived gene expression network (GEN) repository for a broad range of plant species. So far we have incorporated information about 745 high-quality mRNA sequencing (mRNA-Seq) samples from eight plant species (Arabidopsis thaliana, Oryza sativa, Solanum lycopersicum, Sorghum bicolor, Vitis vinifera, Solanum tuberosum, Medicago truncatula and Glycine max) from the public short read archive, digitally profiled the entire set of gene expression profiles, and drawn GENs by using correspondence analysis (CA) to take advantage of gene expression similarities. In order to understand the evolutionary significance of the GENs from multiple species, they were linked according to the orthology of each node (gene) among species. In addition to other gene expression information, functional annotation of the genes will facilitate biological comprehension. Currently we are improving the given gene annotations with natural language processing (NLP) techniques and manual curation. Here we introduce the current status of our analyses and the web database, PODC (Plant Omics Data Center; http://bioinf.mind.meiji.ac.jp/podc/), now open to the public, providing GENs, functional annotations and additional comprehensive omics resources.
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Affiliation(s)
- Hajime Ohyanagi
- School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan CREST, JST, Saitama, 332-0012 Japan Tsukuba Division, Mitsubishi Space Software Co., Ltd., Tsukuba, 305-0032 Japan Plant Genetics Laboratory, National Institute of Genetics, Mishima, 411-8540 Japan These authors contributed equally to this work
| | - Tomoyuki Takano
- School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan CREST, JST, Saitama, 332-0012 Japan These authors contributed equally to this work
| | - Shin Terashima
- School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan CREST, JST, Saitama, 332-0012 Japan These authors contributed equally to this work
| | - Masaaki Kobayashi
- School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan CREST, JST, Saitama, 332-0012 Japan
| | - Maasa Kanno
- School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan
| | - Kyoko Morimoto
- School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan
| | - Hiromi Kanegae
- School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan
| | - Yohei Sasaki
- School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan CREST, JST, Saitama, 332-0012 Japan
| | - Misa Saito
- School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan
| | - Satomi Asano
- School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan CREST, JST, Saitama, 332-0012 Japan
| | - Soichi Ozaki
- School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan CREST, JST, Saitama, 332-0012 Japan
| | - Toru Kudo
- School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan CREST, JST, Saitama, 332-0012 Japan
| | - Koji Yokoyama
- School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan
| | - Koichiro Aya
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601 Japan
| | - Keita Suwabe
- Graduate School of Bioresources, Mie University, Tsu, 514-8507 Japan
| | - Go Suzuki
- Division of Natural Science, Osaka Kyoiku University, Kashiwara, 582-8582 Japan
| | - Koh Aoki
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, 599-8531 Japan
| | - Yasutaka Kubo
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530 Japan
| | - Masao Watanabe
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan
| | - Makoto Matsuoka
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601 Japan
| | - Kentaro Yano
- School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan CREST, JST, Saitama, 332-0012 Japan
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Mata-Pérez C, Sánchez-Calvo B, Begara-Morales JC, Luque F, Jiménez-Ruiz J, Padilla MN, Fierro-Risco J, Valderrama R, Fernández-Ocaña A, Corpas FJ, Barroso JB. Transcriptomic profiling of linolenic acid-responsive genes in ROS signaling from RNA-seq data in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2015; 6:122. [PMID: 25852698 PMCID: PMC4362301 DOI: 10.3389/fpls.2015.00122] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 02/14/2015] [Indexed: 05/20/2023]
Abstract
Linolenic acid (Ln) released from chloroplast membrane galactolipids is a precursor of the phytohormone jasmonic acid (JA). The involvement of this hormone in different plant biological processes, such as responses to biotic stress conditions, has been extensively studied. However, the role of Ln in the regulation of gene expression during abiotic stress situations mediated by cellular redox changes and/or by oxidative stress processes remains poorly understood. An RNA-seq approach has increased our knowledge of the interplay among Ln, oxidative stress and ROS signaling that mediates abiotic stress conditions. Transcriptome analysis with the aid of RNA-seq in the absence of oxidative stress revealed that the incubation of Arabidopsis thaliana cell suspension cultures (ACSC) with Ln resulted in the modulation of 7525 genes, of which 3034 genes had a 2-fold-change, being 533 up- and 2501 down-regulated genes, respectively. Thus, RNA-seq data analysis showed that an important set of these genes were associated with the jasmonic acid biosynthetic pathway including lypoxygenases (LOXs) and Allene oxide cyclases (AOCs). In addition, several transcription factor families involved in the response to biotic stress conditions (pathogen attacks or herbivore feeding), such as WRKY, JAZ, MYC, and LRR were also modified in response to Ln. However, this study also shows that Ln has the capacity to modulate the expression of genes involved in the response to abiotic stress conditions, particularly those mediated by ROS signaling. In this regard, we were able to identify new targets such as galactinol synthase 1 (GOLS1), methionine sulfoxide reductase (MSR) and alkenal reductase in ACSC. It is therefore possible to suggest that, in the absence of any oxidative stress, Ln is capable of modulating new sets of genes involved in the signaling mechanism mediated by additional abiotic stresses (salinity, UV and high light intensity) and especially in stresses mediated by ROS.
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Affiliation(s)
- Capilla Mata-Pérez
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
| | - Beatriz Sánchez-Calvo
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
| | - Juan C. Begara-Morales
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
| | - Francisco Luque
- Department of Experimental Biology, Center for Advanced Studies in Olive Grove and Olive Oils, University of JaénJaén, Spain
| | - Jaime Jiménez-Ruiz
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
| | - María N. Padilla
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
| | - Jesús Fierro-Risco
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
| | - Raquel Valderrama
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
| | - Ana Fernández-Ocaña
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
| | - Francisco J. Corpas
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry, Cellular and Molecular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranada, Spain
| | - Juan B. Barroso
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
- Department of Experimental Biology, Center for Advanced Studies in Olive Grove and Olive Oils, University of JaénJaén, Spain
- *Correspondence: Juan B. Barroso, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of Jaén, Campus Las Lagunillas s/n, Jaén 23071, Spain e-mail:
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Munkert J, Pollier J, Miettinen K, Van Moerkercke A, Payne R, Müller-Uri F, Burlat V, O'Connor SE, Memelink J, Kreis W, Goossens A. Iridoid synthase activity is common among the plant progesterone 5β-reductase family. MOLECULAR PLANT 2015; 8:136-52. [PMID: 25578278 DOI: 10.1016/j.molp.2014.11.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 09/15/2014] [Indexed: 05/21/2023]
Abstract
Catharanthus roseus, the Madagascar periwinkle, synthesizes bioactive monoterpenoid indole alkaloids, including the anti-cancer drugs vinblastine and vincristine. The monoterpenoid branch of the alkaloid pathway leads to the secoiridoid secologanin and involves the enzyme iridoid synthase (IS), a member of the progesterone 5β-reductase (P5βR) family. IS reduces 8-oxogeranial to iridodial. Through transcriptome mining, we show that IS belongs to a family of six C. roseus P5βR genes. Characterization of recombinant CrP5βR proteins demonstrates that all but CrP5βR3 can reduce progesterone and thus can be classified as P5βRs. Three of them, namely CrP5βR1, CrP5βR2, and CrP5βR4, can also reduce 8-oxogeranial, pointing to a possible redundancy with IS (corresponding to CrP5βR5) in secoiridoid synthesis. In-depth functional analysis by subcellular protein localization, gene expression analysis, in situ hybridization, and virus-induced gene silencing indicate that besides IS, CrP5βR4 may also participate in secoiridoid biosynthesis. We cloned a set of P5βR genes from angiosperm plant species not known to produce iridoids and demonstrate that the corresponding recombinant proteins are also capable of using 8-oxogeranial as a substrate. This suggests that IS activity is intrinsic to angiosperm P5βR proteins and has evolved early during evolution.
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Affiliation(s)
- Jennifer Munkert
- Department of Biology, University of Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Jacob Pollier
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Karel Miettinen
- Sylvius Laboratory, Institute of Biology Leiden, Leiden University, Leiden 2333 BE, The Netherlands
| | - Alex Van Moerkercke
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Richard Payne
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, UK
| | - Frieder Müller-Uri
- Department of Biology, University of Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Vincent Burlat
- Université de Toulouse, UPS, UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617 Auzeville, F-31326 Castanet-Tolosan, France; CNRS, UMR 5546, BP 42617, F-31326 Castanet-Tolosan, France
| | - Sarah E O'Connor
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, UK
| | - Johan Memelink
- Sylvius Laboratory, Institute of Biology Leiden, Leiden University, Leiden 2333 BE, The Netherlands
| | - Wolfgang Kreis
- Department of Biology, University of Erlangen-Nuremberg, 91058 Erlangen, Germany.
| | - Alain Goossens
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.
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Aya K, Kobayashi M, Tanaka J, Ohyanagi H, Suzuki T, Yano K, Takano T, Yano K, Matsuoka M. De Novo Transcriptome Assembly of a Fern, Lygodium japonicum, and a Web Resource Database, Ljtrans DB. ACTA ACUST UNITED AC 2014; 56:e5. [DOI: 10.1093/pcp/pcu184] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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