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Tomescu MS, Sooklal SA, Ntsowe T, Naicker P, Darnhofer B, Archer R, Stoychev S, Swanevelder D, Birner-Grünberger R, Rumbold K. Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato). PLoS One 2021; 16:e0253741. [PMID: 34283859 PMCID: PMC8291589 DOI: 10.1371/journal.pone.0253741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 06/11/2021] [Indexed: 11/19/2022] Open
Abstract
The corm of Hypoxis hemerocallidea, commonly known as the African potato, is used in traditional medicine to treat several medical conditions such as urinary infections, benign prostate hyperplasia, inflammatory conditions and testicular tumours. The metabolites contributing to the medicinal properties of H. hemerocallidea have been identified in several studies and, more recently, the active terpenoids of the plant were profiled. However, the biosynthetic pathways and the enzymes involved in the production of the terpene metabolites in H. hemerocallidea have not been characterised at a transcriptomic or proteomic level. In this study, total RNA extracted from the corm, leaf and flower tissues of H. hemerocallidea was sequenced on the Illumina HiSeq 2500 platform. A total of 143,549 transcripts were assembled de novo using Trinity and 107,131 transcripts were functionally annotated using the nr, GO, COG, KEGG and SWISS-PROT databases. Additionally, the proteome of the three tissues were sequenced using LC-MS/MS, revealing aspects of secondary metabolism and serving as data validation for the transcriptome. Functional annotation led to the identification of numerous terpene synthases such as nerolidol synthase, germacrene D synthase, and cycloartenol synthase amongst others. Annotations also revealed a transcript encoding the terpene synthase phytoalexin momilactone A synthase. Differential expression analysis using edgeR identified 946 transcripts differentially expressed between the three tissues and revealed that the leaf upregulates linalool synthase compared to the corm and the flower tissues. The transcriptome as well as the proteome of Hypoxis hemerocallidea presented here provide a foundation for future research.
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Affiliation(s)
- Mihai-Silviu Tomescu
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Selisha Ann Sooklal
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, UNISA, Johannesburg, South Africa
| | - Thuto Ntsowe
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
| | - Previn Naicker
- Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Barbara Darnhofer
- ACIB GmbH, Graz, Austria
- Institute for Pathology, Medical University of Graz, Graz, Austria
- Omics Center Graz, BioTechMed, Graz, Austria
| | - Robert Archer
- National Herbarium, South African National Biodiversity Institute, Pretoria, South Africa
| | - Stoyan Stoychev
- Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Dirk Swanevelder
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
| | - Ruth Birner-Grünberger
- ACIB GmbH, Graz, Austria
- Institute for Pathology, Medical University of Graz, Graz, Austria
- Omics Center Graz, BioTechMed, Graz, Austria
| | - Karl Rumbold
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
- * E-mail:
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Sooklal SA, Mpangase PT, Tomescu MS, Aron S, Hazelhurst S, Archer RH, Rumbold K. Functional characterisation of the transcriptome from leaf tissue of the fluoroacetate-producing plant, Dichapetalum cymosum, in response to mechanical wounding. Sci Rep 2020; 10:20539. [PMID: 33239700 PMCID: PMC7688953 DOI: 10.1038/s41598-020-77598-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/13/2020] [Indexed: 12/21/2022] Open
Abstract
Dichapetalum cymosum produces the toxic fluorinated metabolite, fluoroacetate, presumably as a defence mechanism. Given the rarity of fluorinated metabolites in nature, the biosynthetic origin and function of fluoroacetate have been of particular interest. However, the mechanism for fluorination in D. cymosum was never elucidated. More importantly, there is a severe lack in knowledge on a genetic level for fluorometabolite-producing plants, impeding research on the subject. Here, we report on the first transcriptome for D. cymosum and investigate the wound response for insights into fluorometabolite production. Mechanical wounding studies were performed and libraries of the unwounded (control) and wounded (30 and 60 min post wounding) plant were sequenced using the Illumina HiSeq platform. A combined reference assembly generated 77,845 transcripts. Using the SwissProt, TrEMBL, GO, eggNOG, KEGG, Pfam, EC and PlantTFDB databases, a 69% annotation rate was achieved. Differential expression analysis revealed the regulation of 364 genes in response to wounding. The wound responses in D. cymosum included key mechanisms relating to signalling cascades, phytohormone regulation, transcription factors and defence-related secondary metabolites. However, the role of fluoroacetate in inducible wound responses remains unclear. Bacterial fluorinases were searched against the D. cymosum transcriptome but transcripts with homology were not detected suggesting the presence of a potentially different fluorinating enzyme in plants. Nevertheless, the transcriptome produced in this study significantly increases genetic resources available for D. cymosum and will assist with future research into fluorometabolite-producing plants.
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Affiliation(s)
- Selisha A Sooklal
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Phelelani T Mpangase
- Sydney Brenner Institute for Molecular Biosciences, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Mihai-Silviu Tomescu
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Shaun Aron
- Sydney Brenner Institute for Molecular Biosciences, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Biosciences, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Robert H Archer
- National Herbarium, South African National Biodiversity Institute, Pretoria, 0186, South Africa
| | - Karl Rumbold
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, 2000, South Africa.
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Tshabalala TN, Tomescu MS, Prior A, Balakrishnan V, Sayed Y, Dirr HW, Achilonu I. Energetics of Glutathione Binding to Human Eukaryotic Elongation Factor 1 Gamma: Isothermal Titration Calorimetry and Molecular Dynamics Studies. Protein J 2016; 35:448-458. [PMID: 27844275 DOI: 10.1007/s10930-016-9688-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The energetics of ligand binding to human eukaryotic elongation factor 1 gamma (heEF1γ) was investigated using reduced glutathione (GSH), oxidised glutathione (GSSG), glutathione sulfonate and S-hexylglutathione as ligands. The experiments were conducted using isothermal titration calorimetry, and the findings were supported using computational studies. The data show that the binding of these ligands to heEF1γ is enthalpically favourable and entropically driven (except for the binding of GSSG). The full length heEF1γ binds GSSG with lower affinity (K d = 115 μM), with more hydrogen-bond contacts (ΔH = -73.8 kJ/mol) and unfavourable entropy (-TΔS = 51.7 kJ/mol) compared to the glutathione transferase-like N-terminus domain of heEF1γ, which did not show preference to any specific ligand. Computational free binding energy calculations from the 10 ligand poses show that GSSG and GSH consistently bind heEF1γ, and that both ligands bind at the same site with a folded bioactive conformation. This study reveals the possibility that heEF1γ is a glutathione-binding protein.
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Affiliation(s)
- Thabiso N Tshabalala
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, 2050, South Africa
| | - Mihai-Silviu Tomescu
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, 2050, South Africa
| | - Allan Prior
- School of Chemistry, University of the Witwatersrand, Johannesburg, 2050, South Africa
| | - Vijayakumar Balakrishnan
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, 2050, South Africa
| | - Yasien Sayed
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, 2050, South Africa
| | - Heini W Dirr
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, 2050, South Africa
| | - Ikechukwu Achilonu
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, 2050, South Africa.
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