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Polito JT, Lange I, Barton KE, Srividya N, Lange BM. Characterization of a Unique Pair of Ferredoxin and Ferredoxin NADP + Reductase Isoforms That Operates in Non-Photosynthetic Glandular Trichomes. PLANTS (BASEL, SWITZERLAND) 2024; 13:409. [PMID: 38337942 PMCID: PMC10857128 DOI: 10.3390/plants13030409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/18/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024]
Abstract
Our recent investigations indicated that isoforms of ferredoxin (Fd) and ferredoxin NADP+ reductase (FNR) play essential roles for the reductive steps of the 2C-methyl-D-erythritol 4-phosphate (MEP) pathway of terpenoid biosynthesis in peppermint glandular trichomes (GTs). Based on an analysis of several transcriptome data sets, we demonstrated the presence of transcripts for a leaf-type FNR (L-FNR), a leaf-type Fd (Fd I), a root-type FNR (R-FNR), and two root-type Fds (Fd II and Fd III) in several members of the mint family (Lamiaceae). The present study reports on the biochemical characterization of all Fd and FNR isoforms of peppermint (Mentha × piperita L.). The redox potentials of Fd and FNR isoforms were determined using photoreduction methods. Based on a diaphorase assay, peppermint R-FNR had a substantially higher specificity constant (kcat/Km) for NADPH than L-FNR. Similar results were obtained with ferricyanide as an electron acceptor. When assayed for NADPH-cytochrome c reductase activity, the specificity constant with the Fd II and Fd III isoforms (when compared to Fd I) was slightly higher for L-FNR and substantially higher for R-FNR. Based on real-time quantitative PCR assays with samples representing various peppermint organs and cell types, the Fd II gene was expressed very highly in metabolically active GTs (but also present at lower levels in roots), whereas Fd III was expressed at low levels in both roots and GTs. Our data provide evidence that high transcript levels of Fd II, and not differences in the biochemical properties of the encoded enzyme when compared to those of Fd III, are likely to support the formation of copious amounts of monoterpene via the MEP pathway in peppermint GTs. This work has laid the foundation for follow-up studies to further investigate the roles of a unique R-FNR-Fd II pair in non-photosynthetic GTs of the Lamiaceae.
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Affiliation(s)
| | | | | | | | - B. Markus Lange
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-7411, USA; (J.T.P.); (I.L.); (K.E.B.); (N.S.)
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Chauhan AS, Tiwari M, Indoliya Y, Mishra SK, Lavania UC, Chauhan PS, Chakrabarty D, Tripathi RD. Identification and validation of reference genes in vetiver ( Chrysopogon zizanioides) root transcriptome. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:613-627. [PMID: 37363421 PMCID: PMC10284770 DOI: 10.1007/s12298-023-01315-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 06/27/2023]
Abstract
Vetiver [Vetiveria zizanioides (L.) Roberty] is a perennial C-4 grass traditionally valued for its aromatic roots/root essential oil. Owing to its deep penetrating web-forming roots, the grass is now widely used across the globe for phytoremediation and the conservation of soil and water. This study has used the transcriptome data of vetiver roots in its two distinct geographic morphotypes (North Indian type A and South Indian type B) for reference gene(s) identification. Further, validation of reference genes using various abiotic stresses such as heat, cold, salt, and drought was carried out. The de novo assembly based on differential genes analysis gave 1,36,824 genes (PRJNA292937). Statistical tests like RefFinder, NormFinder, BestKeeper, geNorm, and Delta-Ct software were applied on 346 selected contigs. Eleven selected genes viz., GAPs, UBE2W, RP, OSCam2, MUB, RPS, Core histone 1, Core histone 2, SAMS, GRCWSP, PLDCP along with Actin were used for qRT-PCR analysis. Finally, the study identified the five best reference genes GAPs, OsCam2, MUB, Core histone 1, and SAMS along with Actin. The two optimal reference genes SAMS and Core histone 1 were identified with the help of qbase + software. The findings of the present analyses have value in the identification of suitable reference gene(s) in transcriptomic and molecular data analysis concerning various phenotypes related to abiotic stress and developmental aspects, as well as a quality control measure in gene expression experiments. Identifying reference genes in vetiver appears important as it allows for accurate normalization of gene expression data in qRT-PCR experiments. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01315-7.
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Affiliation(s)
- Abhishek Singh Chauhan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
- Molecular Biology and Biotechnology Division, CSIR – National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Madhu Tiwari
- Molecular Biology and Biotechnology Division, CSIR – National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Yuvraj Indoliya
- Molecular Biology and Biotechnology Division, CSIR – National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Shashank Kumar Mishra
- Microbial Technologies Division, CSIR – National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Umesh Chandra Lavania
- CSIR – National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Puneet Singh Chauhan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
- Microbial Technologies Division, CSIR – National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Debasis Chakrabarty
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
- Molecular Biology and Biotechnology Division, CSIR – National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Rudra Deo Tripathi
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
- Plant Ecology and Environmental Science Division, CSIR – National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
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Bharati R, Sen MK, Kumar R, Gupta A, Žiarovská J, Fernández-Cusimamani E, Leuner O. Systematic Identification of Suitable Reference Genes for Quantitative Real-Time PCR Analysis in Melissa officinalis L. PLANTS (BASEL, SWITZERLAND) 2023; 12:470. [PMID: 36771553 PMCID: PMC9919226 DOI: 10.3390/plants12030470] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Melissa officinalis L. is well known for its lemon-scented aroma and various pharmacological properties. Despite these valuable properties, the genes involved in the biosynthetic pathways in M. officinalis are not yet well-explored when compared to other members of the mint family. For that, gene expression studies using quantitative real-time PCR (qRT-PCR) are an excellent tool. Although qRT-PCR can provide accurate results, its accuracy is highly reliant on the expression and stability of the reference gene used for normalization. Hence, selecting a suitable experiment-specific reference gene is very crucial to obtain accurate results. However, to date, there are no reports for experiment-specific reference genes in M. officinalis. Therefore, in the current study, ten commonly used reference genes were assessed for their suitability as optimal reference genes in M. officinalis under various abiotic stress conditions and different plant organs. The candidate genes were ranked based on BestKeeper, comparative ΔCt, geNorm, NormFinder, and RefFinder. Based on the results, we recommend the combination of EF-1α and GAPDH as the best reference genes to normalize gene expression studies in M. officinalis. On the contrary, HLH71 was identified as the least-performing gene. Thereafter, the reliability of the optimal gene combination was assessed by evaluating the relative gene expression of the phenylalanine ammonia lyase (PAL) gene under two elicitor treatments (gibberellic acid and jasmonic acid). PAL is a crucial gene involved directly or indirectly in the production of various economically important secondary metabolites in plants. Suitable reference genes for each experimental condition are also discussed. The findings of the current study form a basis for current and future gene expression studies in M. officinalis and other related species.
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Affiliation(s)
- Rohit Bharati
- Department of Crop Sciences and Agroforestry, The Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic
| | - Madhab Kumar Sen
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic
| | - Ram Kumar
- Department of Plant Protection, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic
| | - Aayushi Gupta
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic
| | - Jana Žiarovská
- Research Centre AgroBioTech, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
| | - Eloy Fernández-Cusimamani
- Department of Crop Sciences and Agroforestry, The Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic
| | - Olga Leuner
- Department of Crop Sciences and Agroforestry, The Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic
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Bharati R, Sen MK, Kumar R, Gupta A, Sur VP, Melnikovová I, Fernández-Cusimamani E. Selection and Validation of the Most Suitable Reference Genes for Quantitative Real-Time PCR Normalization in Salvia rosmarinus under In Vitro Conditions. PLANTS (BASEL, SWITZERLAND) 2022; 11:2878. [PMID: 36365331 PMCID: PMC9655146 DOI: 10.3390/plants11212878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/12/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Salvia rosmarinus L. (rosemary) is known to have a wide range of pharmacological effects including antidiabetic, anticarcinogenic, and antitumorigenic properties owing to its secondary metabolites. Studies aiming to elevate these metabolites have utilized various elicitors and stresses under in vitro conditions, although underlying molecular mechanisms remain unexplored. Gene expression studies using RT-qPCR might provide valuable information regarding how plant and plant cells interact and perceive various treatments and elicitors. However, despite being able to calculate accurate fold changes, the accuracy of the RT-qPCR data highly depends on the expression of reference genes. To the best of our knowledge, there is no information available on the stable reference genes in rosemary under in vitro conditions. Thus, in this paper, we assessed the stability of seven commonly used reference genes under different elicitor and stress conditions using RT-qPCR. Thereafter, the five most commonly used software and algorithms (comparative ΔCt, BestKeeper, NormFinder, geNorm, and RefFinder) were used to rank the candidates based on their expression stabilities. In conclusion, we recommend using a combination of F1-ATPase, ATP synthase and ACCase to normalize the gene expression experiments in rosemary under in vitro conditions. The selected reference genes were verified using 4-coumarate-CoA ligase, a pharmacologically important gene, whose expression might alter under nanoparticle treatment. Additionally, reference genes for several plant tissues, elicitors, and stresses are also proposed. The conclusions obtained from this current study will accelerate the future molecular work in S. rosmarinus and other related species.
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Affiliation(s)
- Rohit Bharati
- Department of Crop Sciences and Agroforestry, The Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague 6, Czech Republic
| | - Madhab Kumar Sen
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague 6, Czech Republic
| | - Ram Kumar
- Department of Plant Protection, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague 6, Czech Republic
| | - Aayushi Gupta
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague 6, Czech Republic
| | - Vishma Pratap Sur
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Ingrid Melnikovová
- Department of Crop Sciences and Agroforestry, The Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague 6, Czech Republic
| | - Eloy Fernández-Cusimamani
- Department of Crop Sciences and Agroforestry, The Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague 6, Czech Republic
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Stable reference gene selection for quantitative real-time PCR normalization in passion fruit (Passiflora edulis Sims.). Mol Biol Rep 2022; 49:5985-5995. [PMID: 35357624 DOI: 10.1007/s11033-022-07382-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 03/16/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Passiflora edulis is a tropical fruit with high nutrient and medicinal values that is widely planted in southern China. However, the molecular biology of P. edulis has not been well studied. There are few reports regarding the choice of reference genes for gene expression studies of passion fruit. METHODS AND RESULTS By using three algorithms, implemented in geNorm, NormFinder and BestKeeper, we have selected ten candidate reference genes to explore their transcriptional expression stability in various tissues and under cold stress conditions. EF1 and HIS were stably expressed in five tissues. Ts and OTU were stably in vegetative organs. 50 S and Liom were stably in reproductive organs. The transcriptional abundance of EF1 and UBQ was stable in cold-treated and recovery treated leaf samples of P. edulis. In all samples, EF1 and Ts exhibited the highest expression stability. Evaluation of selected genes using simple statistical methods (ANOVA and post hoc analysis). Overall, EF1 emerged as the optimum reference gene for qRT-PCR normalize in P. edulis. In addition, the qRT-PCR analysis revealed that expression of ICE1 increases with the duration of cold treatment. CONCLUSIONS In this study, we successfully screened stable reference genes from 10 candidates in P. edulis and verified the results by analyzing the expression level of ICE1. The results provide reliable and effective reference genes for future research on gene expression analysis in P. edulis, and lay a foundation for follow-up research on functional genes in P. edulis.
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Rodríguez-Parra A, Picazo-Aragonés J, Balao F. Evaluation of Reference Genes in the Polyploid Complex Dianthus broteri (Caryophyllaceae) Using qPCR. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040518. [PMID: 35214851 PMCID: PMC8878694 DOI: 10.3390/plants11040518] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/07/2022] [Accepted: 02/09/2022] [Indexed: 05/14/2023]
Abstract
Dianthus broteri is an endemic complex which is considered the largest polyploid series within the Dianthus genus. This polyploid species involves four cytotypes (2×, 4×, 6× and 12×) with spatial and ecological segregation. The study of gene expression in polyploid species must be very rigorous because of the effects of duplications on gene regulation. In these cases, real-time polymerase chain reaction (qPCR) is the most appropriate technique for determining the gene expression profile because of its high sensitivity. The relative quantification strategy using qPCR requires genes with stable expression, known as reference genes, for normalization. In this work, we evaluated the stability of 13 candidate genes to be considered reference genes in leaf and petal tissues in Dianthus broteri. Several statistical analyses were used to determine the most stable candidate genes: Bayesian analysis, network analysis based on equivalence tests, geNorm and BestKeeper algorithms. In the leaf tissue, the most stable candidate genes were TIP41, TIF5A, PP2A and SAMDC. Similarly, the most adequate reference genes were H3.1, TIP41, TIF5A and ACT7 in the petal tissue. Therefore, we suggest that the best reference genes to compare different ploidy levels for both tissues in D. broteri are TIP41 and TIF5A.
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Gopalam R, Datey A, Bijoor S, Chakravortty D, Tumaney AW. Biochemical Characterization of Acyl-CoA: Lysophosphatidylcholine Acyltransferase (LPCAT) Enzyme from the Seeds of Salvia hispanica. Mol Biotechnol 2021; 63:963-972. [PMID: 34129179 DOI: 10.1007/s12033-021-00354-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/08/2021] [Indexed: 11/26/2022]
Abstract
Salvia hispanica (chia) is the highest reported terrestrial plant source of alpha-linolenic acid (ALA, ~ 65%), an ω-3 polyunsaturated fatty acid with numerous health benefits. The molecular basis of high ALA accumulation in chia is yet to be understood. We have identified lysophosphatidylcholine acyltransferase (LPCAT) gene from the developing seed transcriptome data of chia and carried out its biochemical characterization through heterologous expression in Saccharomyces cerevisiae. Expression profiling showed that the enzyme was active throughout the seed development, indicating a pivotal role in oil biosynthesis. The enzyme could utilize both saturated and unsaturated lysophosphatidylcholine substrates at the same rate, to synthesize phosphatidylcholine (PC). The enzyme also exhibited lysophosphatidic acid acyltransferase (LPAAT) activity, by preferring lysophosphatidic acid substrate. Substrate specificity studies showed that the enzyme preferred both monounsaturated and polyunsaturated fatty acyl CoAs over saturated CoAs. This activity may play a key role in enriching the PC fraction with polyunsaturated fatty acids (PUFAs). PUFAs present on PC can be transferred to oil through the action of other acyltransferases. Our results describe a new LPCAT enzyme that can be used to biotechnologically alter oilseed crops to incorporate more PUFA in its seed oil.
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Affiliation(s)
- Rahul Gopalam
- Department of Lipid Science, CSIR-Central Food Technological Research Institute (CSIR-CFTRI), Mysore, 570020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Akshay Datey
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, 560012, India
| | - Sharath Bijoor
- Department of Lipid Science, CSIR-Central Food Technological Research Institute (CSIR-CFTRI), Mysore, 570020, India
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, 560012, India
| | - Ajay W Tumaney
- Department of Lipid Science, CSIR-Central Food Technological Research Institute (CSIR-CFTRI), Mysore, 570020, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Gopalam R, Tumaney AW. Functional characterization of acyltransferases from Salvia hispanica that can selectively catalyze the formation of trilinolenin. PHYTOCHEMISTRY 2021; 186:112712. [PMID: 33706110 DOI: 10.1016/j.phytochem.2021.112712] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 06/12/2023]
Abstract
Salvia hispanica (chia) is an important oilseed crop cultivated commercially in South America, Australia, and India. It is the richest terrestrial natural source of α-linolenic acid (ALA), an ω-3 polyunsaturated fatty acid with varied health benefits. In this study, we have measured the total lipid content, fatty acid composition in four phases of seed development and analyzed the major triacylglycerol (TAG) molecular species present in Indian chia seed oil. We found that the mature seeds produced 28% oil, 65% of ALA, and trilinolenin as the major TAG species. To make TAG rich in ALA, there should be specialized enzymes that can efficiently transfer ALA to TAG. To study this hypothesis, we performed a characterization of TAG synthesizing enzymes present in chia. We have identified two acyl CoA:diacylglycerol acyltransferases (ShDGAT1 and ShDGAT2) and one phospholipid:diacylglycerol acyltransferase (ShPDAT1) from the chia transcriptome data. Functional characterization of these enzymes was conducted by heterologous expression in a TAG deficient mutant of Saccharomyces cerevisiae. Substrate specificity studies showed that ShDGAT2-1 and ShPDAT1 exhibited a strong preference towards substrates containing ALA and could incorporate 45% and 80% ALA into TAG, respectively. Both enzymes incorporated ALA in a concentration-dependent manner into TAG and were able to form trilinolenin in yeast. Our results provide a first insight into the high ALA accumulation in chia and the first demonstration of trilinolenin formation by DGAT2. The two identified enzymes (ShDGAT2-1 and ShPDAT1) can be used to metabolically engineer other oilseed crops to produce high levels of ALA.
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Affiliation(s)
- Rahul Gopalam
- Department of Lipid Science, CSIR-Central Food Technological Research Institute (CSIR-CFTRI), Mysore, 570 020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ajay W Tumaney
- Department of Lipid Science, CSIR-Central Food Technological Research Institute (CSIR-CFTRI), Mysore, 570 020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Fulvio F, Martinelli T, Paris R. Selection and validation of reference genes for RT-qPCR normalization in different tissues of milk thistle (Silybum marianum, Gaert.). Gene 2021; 768:145272. [PMID: 33122080 DOI: 10.1016/j.gene.2020.145272] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/06/2020] [Accepted: 10/21/2020] [Indexed: 12/31/2022]
Abstract
Quantitative reverse transcription PCR is a sensitive technique for evaluating transcriptional profiles in different experimental datasets. To obtain a reliable quantification of the transcripts level, data normalization with stable reference genes is required. Stable reference genes are identified after analysis of their transcripts profile in every new experiment and species of interest. In Silybum marianum, a widely cultivated officinal plant, only few gene expression studies exist, and reference genes for RT-qPCR studies in the diverse plant tissues have never been investigated before. In this work, the expression stability of 10 candidate reference genes was evaluated in leaves, roots, stems and fruits of S. marianum grown under physiological environmental condition. The stability values for each candidate reference gene were calculated by four canonical statistical algorithms GeNorm, NormFinder, Bestkeeper and ΔCt method in different subsets of samples, then they were ranked with RefFinder from the most to the least suitable for normalization. Best combinations of reference genes are finally proposed for different experimental data sets, including all tissues, vegetative, and reproductive tissues separately. Three target genes putatively involved in important biosynthetic pathway leading to key metabolites in the fruits of milk thistle, such as silymarin and fatty acids, were analyzed with the chosen panels of reference genes, in comparison to the ones used in previous papers. To the best of our knowledge, this is the first report on a reliable and systematic identification and validation of the reference genes for RT-qPCR normalization to study gene expression in S. marianum.
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Affiliation(s)
- Flavia Fulvio
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di ricerca Cerealicoltura e Colture Industriali, Via di Corticella 133, 40128 Bologna, Italy
| | - Tommaso Martinelli
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di ricerca Cerealicoltura e Colture Industriali, Via di Corticella 133, 40128 Bologna, Italy; Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di ricerca Difesa e Certificazione, Via di Lanciola 12/A, Loc. Cascine del Riccio, 50125 Firenze, Italy
| | - Roberta Paris
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di ricerca Cerealicoltura e Colture Industriali, Via di Corticella 133, 40128 Bologna, Italy.
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Wimberley J, Cahill J, Atamian HS. De novo Sequencing and Analysis of Salvia hispanica Tissue-Specific Transcriptome and Identification of Genes Involved in Terpenoid Biosynthesis. PLANTS 2020; 9:plants9030405. [PMID: 32213996 PMCID: PMC7154873 DOI: 10.3390/plants9030405] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/16/2020] [Accepted: 03/19/2020] [Indexed: 12/11/2022]
Abstract
Salvia hispanica (commonly known as chia) is gaining popularity worldwide as a healthy food supplement due to its low saturated fatty acid and high polyunsaturated fatty acid content, in addition to being rich in protein, fiber, and antioxidants. Chia leaves contain plethora of secondary metabolites with medicinal properties. In this study, we sequenced chia leaf and root transcriptomes using the Illumina platform. The short reads were assembled into contigs using the Trinity software and annotated against the Uniprot database. The reads were de novo assembled into 103,367 contigs, which represented 92.8% transcriptome completeness and a diverse set of Gene Ontology terms. Differential expression analysis identified 6151 and 8116 contigs significantly upregulated in the leaf and root tissues, respectively. In addition, we identified 30 contigs belonging to the Terpene synthase (TPS) family and demonstrated their evolutionary relationships to tomato TPS family members. Finally, we characterized the expression of S. hispanica TPS members in leaves subjected to abiotic stresses and hormone treatments. Abscisic acid had the most pronounced effect on the expression of the TPS genes tested in this study. Our work provides valuable community resources for future studies aimed at improving and utilizing the beneficial constituents of this emerging healthy food source.
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Affiliation(s)
- James Wimberley
- Computational and Data Sciences Program, Chapman University, Orange, CA 92866, USA;
- Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
| | | | - Hagop S. Atamian
- Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
- Biological Sciences Program, Chapman University, Orange, CA 92866, USA
- Correspondence: ; Tel.: +1-(714)-289-2023
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Jamshidi Goharrizi K, Moosavi SS, Amirmahani F, Salehi F, Nazari M. Assessment of changes in growth traits, oxidative stress parameters, and enzymatic and non-enzymatic antioxidant defense mechanisms in Lepidium draba plant under osmotic stress induced by polyethylene glycol. PROTOPLASMA 2020; 257:459-473. [PMID: 31776775 DOI: 10.1007/s00709-019-01457-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 11/08/2019] [Indexed: 06/10/2023]
Abstract
Lepidium draba is a weed with the medicinal properties which few researches have been done on it. In this study, some traits, related to the osmotic stress, in 14-day-old L. draba sprouts that were grown 9 days in the presence of various doses of polyethylene glycol 6000 (PEG 6000) including 0, 3, 6, 9, and 12%, with different osmotic potentials (- 0.04, - 0.12, - 0.23, - 0.34, and - 0.48 MPa, respectively) were investigated. Based on our results, germination percentage besides stem and root lengths decreased with increasing the concentrations of PEG. The contents of electrolyte leakage, malondialdehyde, other aldehydes, total protein, free amino acids, total soluble carbohydrate as well as free proline increased with increasing the concentrations of PEG. Also, for the first time, our results have proven that under osmotic stress, there is an adverse relationship between hydrogen peroxide content and the activity of catalase, peroxidase, ascorbate peroxidase, and guaiacol peroxidase enzymes, such that hydrogen peroxide content decreased with induction of PEG up to 6% and after that increased, while the activity of catalase, peroxidase, ascorbate peroxidase, and guaiacol peroxidase enzymes increased up to 6% PEG and after that decreased. The expression levels of catalase, peroxidase, ascorbate peroxidase, and guaiacol peroxidase genes showed the same pattern as was seen for these enzyme activities. According to the results of this study, it can be deduced that decreasing H2O2 content cannot be the main reason for other oxidative stress parameters to decrease. In this study, P5CS and P5CR gene expression levels increased with increasing levels of PEG up to 12% which was completely similar to free proline content. Based on our results, L. draba can be considered as a semi-tolerant plant to osmotic stress.
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Affiliation(s)
| | - Sayyed Saeed Moosavi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran.
| | - Farzane Amirmahani
- Genetic Division, Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran
| | - Fatemeh Salehi
- Department of Ecology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Maryam Nazari
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
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Identification and functional characterization of Buglossoides arvensis microsomal fatty acid desaturation pathway genes involved in polyunsaturated fatty acid synthesis in seeds. J Biotechnol 2019; 308:130-140. [PMID: 31843519 DOI: 10.1016/j.jbiotec.2019.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/09/2019] [Accepted: 12/12/2019] [Indexed: 01/05/2023]
Abstract
Buglossoides arvensis seed oil is the richest natural source of stearidonic acid (SDA), an ω-3 fatty acid with nutraceutical potential superior to α-linolenic acid (ALA). The molecular basis of polyunsaturated fatty acid synthesis in B. arvensis is unknown. Here, we describe the identification of B. arvensis fatty acid desaturase2 (BaFAD2), fatty acid desaturase3 (BaFAD3), and Delta-6-desaturase (BaD6D-1 and BaD6D-2) genes by mining the transcriptome of developing seeds and their functional characterization by heterologous expression in Saccharomyces cerevisiae. In silico analysis of their encoded protein sequences showed conserved histidine-boxes and signature motifs essential for desaturase activity. Expression profiling of these genes showed higher transcript abundance in reproductive tissues than in vegetative tissues, and their expression varied with temperature stress treatments. Yeast expressing BaFAD2 was found to desaturate both oleic acid and palmitoleic acid into linoleic acid (LA) and hexadecadienoic acid, respectively. Fatty acid supplementation studies in yeast expressing BaFAD3 and BaD6D-1 genes revealed that the encoded enzyme activities of BaFAD3 efficiently converted LA to ALA, and BaD6D-1 converted LA to γ-linolenic acid and ALA to SDA, but with an apparent preference to LA. BaD6D-2 did not show the encoded enzyme activity and is not a functional D6D. Our results provide an insight into SDA biosynthesis in B. arvensis and expand the repository of fatty acid desaturase targets available for biotechnological production of SDA in traditional oilseed crops.
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Olsen S, Krause K. A rapid preparation procedure for laser microdissection-mediated harvest of plant tissues for gene expression analysis. PLANT METHODS 2019; 15:88. [PMID: 31388345 PMCID: PMC6676614 DOI: 10.1186/s13007-019-0471-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/26/2019] [Indexed: 05/31/2023]
Abstract
BACKGROUND Gene expression changes that govern essential biological processes can occur at the cell-specific level. To gain insight into such events, laser microdissection is applied to cut out specific cells or tissues from which RNA for gene expression analysis is isolated. However, the preparation of plant tissue sections for laser microdissection and subsequent RNA isolation usually involves fixation and embedding, processes that are often time-consuming and can lower the yield and quality of isolated RNA. RESULTS Infection sites of the parasitic plant Cuscuta reflexa growing on its compatible host plant Pelargonium zonale were sectioned using a vibratome and dried on glass slides at 4 °C before laser microdissection. High quality RNA (RQI > 7) was isolated from 1 mm2, 3 mm2 and 6 mm2 total surface areas of laser microdissection-harvested C. reflexa tissue, with the yield of RNA correlating to the amount of collected material (on average 7 ng total RNA/mm2). The expression levels of two parasite genes previously found to be highly expressed during host plant infection were shown to differ individually between specific regions of the infection site. By drying plant sections under low pressure to reduce the dehydration time, the induced expression of two wound-related genes during preparation was avoided. CONCLUSIONS Plants can be prepared quickly and easily for laser microdissection by direct sectioning of fresh tissue followed by dehydration on glass slides. We show that RNA isolated from material treated in this manner maintains high quality and enables the investigation of differential gene expression at a high morphological resolution.
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Affiliation(s)
- Stian Olsen
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
| | - Kirsten Krause
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
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Selection and validation of reference genes for quantitative real-time PCR in Rosmarinus officinalis L. in various tissues and under elicitation. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101246] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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