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.
BMC Genomics. 2023 Aug 26;24(1):490. doi: 10.1186/s12864-023-09553-5.
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.
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).
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.
作为生姜中的特征性功能成分，姜辣素具有多种促进健康的特性。长非编码 RNA（lncRNA）作为多种生物过程的关键调控因子。然而，到目前为止，生姜中的 lncRNA 尚未被鉴定，其在姜辣素生物合成中的潜在作用仍不清楚。本研究对中国三种主要生姜品种（乐山黄姜、铜陵白姜和御江 1 号）进行代谢组学和转录组学分析，以了解特定 lncRNA 在姜辣素积累中的潜在作用。
通过代谢组学分析共监测到 744 种代谢物，分为十一类。其中，酚酸类最大组包含 143 种代谢物，包括 21 种姜辣素衍生物。其中，[8]-姜烯酚、[10]-姜辣素和[12]-姜辣素三种姜辣素类似物积累显著。此外，通过转录组学分析，在所有三种比较中，共鉴定出 16346 个 lncRNA，包括 2513、1225 和 2884 个差异表达（DEL）lncRNA 基因。基因本体论富集（GO）分析表明，DEL 主要富集在次生代谢物生物合成过程、植物激素响应和酚类化合物代谢过程中。相关性分析表明，11 个 DE 姜辣素生物合成酶基因（GBEG）和 190 个转录因子基因（TF 基因）的表达水平与三种姜辣素类似物的含量呈强烈的相关系数。此外，鉴定出 7 个和 111 个上游顺式作用 lncRNA 分别对应于 GBEG 和 TF 基因，1200 个和 2225 个上游反式作用 lncRNA。有趣的是，1184 个 DEL 可能作为这些 GBEG 和 TF 基因的共同上游调节剂，如 LNC_008452、LNC_006109、LNC_004340 等。此外，蛋白质-蛋白质相互作用网络（PPI）分析表明，三个 TF 蛋白 MYB4、MYB43 和 WRKY70 可能与四个 GBEG 蛋白（PAL1、PAL2、PAL3 和 4CL-4）相互作用。
基于这些发现，我们首次在全球范围内提出了一个涉及 lncRNA、TF 基因和 GBEG 参与控制姜辣素生物合成的假设调控级联。这些结果不仅为生姜中涉及姜辣素代谢的 lncRNA 提供了新的见解，也为进一步研究相关分子机制奠定了基础。
