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Zhang W, Yang Y, Zhu X, Yang S, Liao X, Li H, Li Z, Liao Q, Tang J, Zhao G, Wu L. Integrated analyses of metabolomics and transcriptomics reveal the potential regulatory roles of long non-coding RNAs in gingerol biosynthesis. BMC Genomics 2023; 24:490. [PMID: 37633894 PMCID: PMC10464350 DOI: 10.1186/s12864-023-09553-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 08/03/2023] [Indexed: 08/28/2023] Open
Abstract
BACKGROUND As the characteristic functional component in ginger, gingerols possess several health-promoting properties. Long non-coding RNAs (lncRNAs) act as crucial regulators of diverse biological processes. However, lncRNAs in ginger are not yet identified so far, and their potential roles in gingerol biosynthesis are still unknown. In this study, metabolomic and transcriptomic analyses were performed in three main ginger cultivars (leshanhuangjiang, tonglingbaijiang, and yujiang 1 hao) in China to understand the potential roles of the specific lncRNAs in gingerol accumulation. RESULTS A total of 744 metabolites were monitored by metabolomics analysis, which were divided into eleven categories. Among them, the largest group phenolic acid category contained 143 metabolites, including 21 gingerol derivatives. Of which, three gingerol analogs, [8]-shogaol, [10]-gingerol, and [12]-shogaol, accumulated significantly. Moreover, 16,346 lncRNAs, including 2,513, 1,225, and 2,884 differentially expressed (DE) lncRNA genes (DELs), were identified in all three comparisons by transcriptomic analysis. Gene ontology enrichment (GO) analysis showed that the DELs mainly enriched in the secondary metabolite biosynthetic process, response to plant hormones, and phenol-containing compound metabolic process. Correlation analysis revealed that the expression levels of 11 DE gingerol biosynthesis enzyme genes (GBEGs) and 190 transcription factor genes (TF genes), such as MYB1, ERF100, WRKY40, etc. were strongly correlation coefficient with the contents of the three gingerol analogs. Furthermore, 7 and 111 upstream cis-acting lncRNAs, 1,200 and 2,225 upstream trans-acting lncRNAs corresponding to the GBEGs and TF genes were identified, respectively. Interestingly, 1,184 DELs might function as common upstream regulators to these GBEGs and TFs genes, such as LNC_008452, LNC_006109, LNC_004340, etc. Furthermore, protein-protein interaction networks (PPI) analysis indicated that three TF proteins, MYB4, MYB43, and WRKY70 might interact with four GBEG proteins (PAL1, PAL2, PAL3, and 4CL-4). CONCLUSION Based on these findings, we for the first time worldwide proposed a putative regulatory cascade of lncRNAs, TFs genes, and GBEGs involved in controlling of gingerol biosynthesis. These results not only provide novel insights into the lncRNAs involved in gingerol metabolism, but also lay a foundation for future in-depth studies of the related molecular mechanism.
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Affiliation(s)
- Wenlin Zhang
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, 402160, China
- College of Food Science, Southwest University, Beibei, 400715, China
| | - Yang Yang
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, China
| | - Xuedong Zhu
- Southeast Chongqing Academy of Agricultural Sciences, Fuling, 408000, China
| | - Suyu Yang
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, China
| | - Ximei Liao
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, China
| | - Honglei Li
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, 402160, China
| | - Zhexin Li
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, 402160, China
| | - Qinhong Liao
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, 402160, China
| | - Jianmin Tang
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, 402160, China.
| | - Guohua Zhao
- College of Food Science, Southwest University, Beibei, 400715, China.
| | - Lin Wu
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, China.
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Zeng H, Li X, Zhou D, Wang N, Yu X, Long L, Cheng H, Zhou S, Shen Z, Zhou W. Qihu Preparation Ameliorates Diabetes by Activating the AMPK Signaling Pathway in db/db Mice. Diabetes Metab Syndr Obes 2021; 14:3229-3241. [PMID: 34285530 PMCID: PMC8286761 DOI: 10.2147/dmso.s312137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 07/02/2021] [Indexed: 02/05/2023] Open
Abstract
PURPOSE To examine the pharmacological effects of Qihu on type 2 diabetes mellitus using db/db mice. MATERIALS AND METHODS Thirty-seven db/db mice were randomly divided into the following 5 groups: diabetes model control group (DM group; n = 7), administered with the adjuvant 0.3% carboxymethyl cellulose-Na; positive control group (Met group; n = 8), administered with metformin (0.13 g/kg bodyweight); Qihu-L group (n = 7), administered with a low dose of Qihu (0.75 g/kg bodyweight), Qihu-M group (n = 7), administered with a medium dose of Qihu (1.5 g/kg bodyweight); Qihu-H group (n = 8), administered with a high dose of Qihu (3.0 g/kg bodyweight). BKS mice (n = 8) were used as the negative control group. The db/db mice were administered with drugs through oral gavage for 28 days. The random blood glucose levels, glucose tolerance test, bodyweight, food intake, and blood lipid levels of the mice were measured during the experimental period. The liver and pancreas tissues were collected for pathological, quantitative real-time polymerase chain reaction, and Western blotting analyses. RESULTS Compared with the DM group, the Qihu groups exhibited decreased bodyweight gain. The blood glucose levels in the Qihu-L, Qihu-M, and Qihu-H were 31.46%, 43.73%, and 51.83%, respectively, lower than those in the DM group. The triglyceride levels were significantly downregulated and the swelling and steatosis of the hepatocytes were significantly lower in the Qihu-M and Qihu-H groups than in the DM group. Qihu downregulated the expression of IL-1β, IL-6, and TXNIP and upregulated the AMP-activated protein kinase (AMPK) signaling pathway in the pancreas and liver tissues of db/db mice. CONCLUSION The anti-diabetic effects of Qihu are mediated through the activation of the AMPK/Txnip signaling and the downregulation of the secretion of inflammatory factors in db/db mice.
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Affiliation(s)
- Hongfang Zeng
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, People’s Republic of China
- Chongqing Key Laboratory of Drug Metabolism, Chongqing, People’s Republic of China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, People’s Republic of China
| | - Xiaoli Li
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, People’s Republic of China
- Chongqing Key Laboratory of Drug Metabolism, Chongqing, People’s Republic of China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, People’s Republic of China
| | - Duanfang Zhou
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, People’s Republic of China
- Chongqing Key Laboratory of Drug Metabolism, Chongqing, People’s Republic of China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, People’s Republic of China
| | - Ning Wang
- West China Biopharm Research Institute, West China Hospital, Chengdu, Sichuan Province, 610041, People’s Republic of China
| | - Xiaoping Yu
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, People’s Republic of China
- Chongqing Key Laboratory of Drug Metabolism, Chongqing, People’s Republic of China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, People’s Republic of China
| | - Liangyuan Long
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, People’s Republic of China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, People’s Republic of China
| | - Hao Cheng
- China Company 18th, College of Pharmacy, Army Medical University, Chongqing, 400038, People’s Republic of China
- Department of Pharmacy, Medical Security Center, the 925 Hospital, Joint Logistic Support Force, Guiyang, Guizhou Province, 550005, People’s Republic of China
| | - Shuyu Zhou
- China Company 18th, College of Pharmacy, Army Medical University, Chongqing, 400038, People’s Republic of China
| | - Zhengze Shen
- Department of Pharmacy, Yongchuan Hospital Affiliated to Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Weiying Zhou
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, People’s Republic of China
- Chongqing Key Laboratory of Drug Metabolism, Chongqing, People’s Republic of China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, People’s Republic of China
- Correspondence: Weiying Zhou Department of Pharmacology, College of Pharmacy, Chongqing Medical University, 1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, People’s Republic of ChinaTel/Fax +86 23 684 85161 Email
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