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An L, Wang Z, Cui Y, Bai Y, Yao Y, Yao X, Wu K. Comparative Analysis of Hulless Barley Transcriptomes to Regulatory Effects of Phosphorous Deficiency. Life (Basel) 2024; 14:904. [PMID: 39063656 PMCID: PMC11278117 DOI: 10.3390/life14070904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 07/11/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Hulless barley is a cold-resistant crop widely planted in the northwest plateau of China. It is also the main food crop in this region. Phosphorus (P), as one of the important essential nutrient elements, regulates plant growth and defense. This study aimed to analyze the development and related molecular mechanisms of hulless barley under P deficiency and explore the regulatory genes so as to provide a basis for subsequent molecular breeding research. Transcriptome analysis was performed on the root and leaf samples of hulless barley cultured with different concentrations of KH2PO4 (1 mM and 10 μM) Hoagland solution. A total of 46,439 genes were finally obtained by the combined analysis of leaf and root samples. Among them, 325 and 453 genes had more than twofold differences in expression. These differentially expressed genes (DEGs) mainly participated in the abiotic stress biosynthetic process through Gene Ontology prediction. Moreover, the Kyoto Encyclopedia of Genes and Genomes showed that DEGs were mainly involved in photosynthesis, plant hormone signal transduction, glycolysis, phenylpropanoid biosynthesis, and synthesis of metabolites. These pathways also appeared in other abiotic stresses. Plants initiated multiple hormone synergistic regulatory mechanisms to maintain growth under P-deficient conditions. Transcription factors (TFs) also proved these predictions. The enrichment of ARR-B TFs, which positively regulated the phosphorelay-mediated cytokinin signal transduction, and some other TFs (AP2, GRAS, and ARF) was related to plant hormone regulation. Some DEGs showed different values in their FPKM (fragment per kilobase of transcript per million mapped reads), but the expression trends of genes responding to stress and phosphorylation remained highly consistent. Therefore, in the case of P deficiency, the first response of plants was the expression of stress-related genes. The effects of this stress on plant metabolites need to be further studied to improve the relevant regulatory mechanisms so as to further understand the importance of P in the development and stress resistance of hulless barley.
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Affiliation(s)
- Likun An
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (L.A.); (Z.W.); (Y.C.); (Y.B.); (Y.Y.); (X.Y.)
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining 810016, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining 810016, China
| | - Ziao Wang
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (L.A.); (Z.W.); (Y.C.); (Y.B.); (Y.Y.); (X.Y.)
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining 810016, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining 810016, China
| | - Yongmei Cui
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (L.A.); (Z.W.); (Y.C.); (Y.B.); (Y.Y.); (X.Y.)
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining 810016, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining 810016, China
| | - Yixiong Bai
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (L.A.); (Z.W.); (Y.C.); (Y.B.); (Y.Y.); (X.Y.)
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining 810016, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining 810016, China
| | - Youhua Yao
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (L.A.); (Z.W.); (Y.C.); (Y.B.); (Y.Y.); (X.Y.)
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining 810016, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining 810016, China
| | - Xiaohua Yao
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (L.A.); (Z.W.); (Y.C.); (Y.B.); (Y.Y.); (X.Y.)
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining 810016, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining 810016, China
| | - Kunlun Wu
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (L.A.); (Z.W.); (Y.C.); (Y.B.); (Y.Y.); (X.Y.)
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining 810016, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining 810016, China
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Li Y, Zhao ZA, Hu J, Lei T, Chen Q, Li J, Yang L, Hu D, Gao S. MeJA-induced hairy roots in Plumbago auriculata L. by RNA-seq profiling and key synthase provided new insights into the sustainable production of plumbagin and saponins. FRONTIERS IN PLANT SCIENCE 2024; 15:1411963. [PMID: 39070915 PMCID: PMC11272555 DOI: 10.3389/fpls.2024.1411963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/04/2024] [Indexed: 07/30/2024]
Abstract
Naturally synthesized secondary metabolites in plants are considered an important source of drugs, food additives, etc. Among them, research on natural plant medicinal components and their synthesis mechanisms has always been of high concern. We identified a novel medicinal floral crop, Plumbago auriculata L., that can be treated with methyl jasmonate (MeJA) for the rapid or sustainable production of natural bioactives from hairy roots. In the study, we globally analyzed the changes in the accumulation of plumbagin and others in the hairy roots of Plumbago auriculata L. hairy roots (PAHR) 15834 in P. auriculata L. based on 100 μmol/L of MeJA treatment by RNA-seq profiling, and we found that there was a significant increase in the accumulation of plumbagin and saponin before 24 h. To explain the principle of co-accumulation, it showed that MeJA induced JA signaling and the shikimic acid pathway, and the methylvaleric acid (MVA) pathway was activated downstream subsequently by the Mfuzz and weighted gene co-expression analysis. Under the shared metabolic pathway, the high expression of PAL3 and HMGR promoted the activity of the "gateway enzymes" phenylalanine ammonia lyase (PAL) and 3-hydroxy-3-methylglutaryl CoA reductase (HMGR), which respectively induced the high expression of key reaction enzyme genes, including chalcone synthase (CHS), isopentenyl diphosphate (IPP), and farnesyl pyrophosphate synthase (FPS), that led to the synthesis of plumbagin and saponin. We speculated that large amounts of ketones and/or aldehydes were formed under the action of these characteristic enzymes, ultimately achieving their co-accumulation through polyketone and high-level sugar and amino acid metabolism. The study results provided a theoretical basis for carrying out the factory refinement and biosynthesis of plumbagin and saponins and also provided new ideas for fully exploiting multifunctional agricultural crops and plants and developing new agricultural by-products.
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Affiliation(s)
- Yirui Li
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Zi-an Zhao
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Ju Hu
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
- College of Biology and Pharmacy, Yulin Normal University, Yulin, China
| | - Ting Lei
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Qibing Chen
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Jiani Li
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Lijuan Yang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Di Hu
- School of Fine Arts and Calligraphy, Sichuan Normal University, Chengdu, China
| | - Suping Gao
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
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Jalota K, Sharma V, Agarwal C, Jindal S. Eco-friendly approaches to phytochemical production: elicitation and beyond. NATURAL PRODUCTS AND BIOPROSPECTING 2024; 14:5. [PMID: 38195902 PMCID: PMC10776560 DOI: 10.1007/s13659-023-00419-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 11/19/2023] [Indexed: 01/11/2024]
Abstract
Highly ameliorated phytochemicals from plants are recognized to have numerous beneficial effects on human health. However, obtaining secondary metabolites directly from wild plants is posing a great threat to endangered plant species due to their over exploitation. Moreover, due to complicated structure and stereospecificity chemical synthesis of these compounds is a troublesome procedure. As a result, sustainable and ecofriendly in vitro strategy has been adopted for phytochemicals production. But, lack of fully differentiated cells lowers down cultured cells productivity. Consequently, for enhancing yield of metabolites produced by cultured plant cells a variety of methodologies has been followed one such approach includes elicitation of culture medium that provoke stress responses in plants enhancing synthesis and storage of bioactive compounds. Nevertheless, for conclusive breakthrough in synthesizing bioactive compounds at commercial level in-depth knowledge regarding metabolic responses to elicitation in plant cell cultures is needed. However, technological advancement has led to development of molecular based approaches like metabolic engineering and synthetic biology which can serve as promising path for phytochemicals synthesis. This review article deals with classification, stimulating effect of elicitors on cultured cells, parameters of elicitors and action mechanism in plants, modern approaches like metabolic engineering for future advances.
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Affiliation(s)
- Kritika Jalota
- Division of Molecular Biology and Genetic Engineering, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, 144411, India
| | - Vikas Sharma
- Division of Molecular Biology and Genetic Engineering, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, 144411, India
| | | | - Suruchi Jindal
- Division of Molecular Biology and Genetic Engineering, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, 144411, India.
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System network analysis of Rosmarinus officinalis transcriptome and metabolome-Key genes in biosynthesis of secondary metabolites. PLoS One 2023; 18:e0282316. [PMID: 36862714 PMCID: PMC9980811 DOI: 10.1371/journal.pone.0282316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 02/13/2023] [Indexed: 03/03/2023] Open
Abstract
Medicinal plants contain valuable compounds that have attracted worldwide interest for their use in the production of natural drugs. The presence of compounds such as rosmarinic acid, carnosic acid, and carnosol in Rosmarinus officinalis has made it a plant with unique therapeutic effects. The identification and regulation of the biosynthetic pathways and genes will enable the large-scale production of these compounds. Hence, we studied the correlation between the genes involved in biosynthesis of the secondary metabolites in R. officinalis using proteomics and metabolomics data by WGCNA. We identified three modules as having the highest potential for the metabolite engineering. Moreover, the hub genes highly connected to particular modules, TFs, PKs, and transporters were identified. The TFs of MYB, C3H, HB, and C2H2 were the most likely candidates associated with the target metabolic pathways. The results indicated that the hub genes including Copalyl diphosphate synthase (CDS), Phenylalanine ammonia lyase (PAL), Cineole synthase (CIN), Rosmarinic acid synthase (RAS), Tyrosine aminotransferase (TAT), Cinnamate 4-hydroxylase (C4H), and MYB58 are responsible for biosynthesis of important secondary metabolites. Thus, we confirmed these results using qRT-PCR after treating R. officinalis seedlings with methyl jasmonate. These candidate genes may be employed for genetic and metabolic engineering research to increase R. officinalis metabolite production.
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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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