mRNA-miRNA analyses reveal the involvement of CsbHLH1 and miR1446a in the regulation of caffeine biosynthesis in Camellia sinensis

Qifang Jin; Zhong Wang; Devinder Sandhu; Lan Chen; Chenyu Shao; Fanghuizi Shang; Siyi Xie; Feiyi Huang; Zhenyan Chen; Xiangqin Zhang; Jinyu Hu; Guizhi Liu; Qin Su; Mengdi Huang; Zhonghua Liu; Jianan Huang; Na Tian; Shuoqian Liu

doi:10.1093/hr/uhad282

mRNA-miRNA analyses reveal the involvement of CsbHLH1 and miR1446a in the regulation of caffeine biosynthesis in Camellia sinensis

Hortic Res. 2023 Dec 29;11(2):uhad282. doi: 10.1093/hr/uhad282. eCollection 2024 Feb.

Authors

Qifang Jin^{1

2

3}, Zhong Wang^{1

2

3}, Devinder Sandhu⁴, Lan Chen^{1

2

3}, Chenyu Shao^{1

2

3}, Fanghuizi Shang^{1

2

3}, Siyi Xie^{1

2

3}, Feiyi Huang⁵, Zhenyan Chen^{1

2

3}, Xiangqin Zhang^{1

2

3}, Jinyu Hu^{1

2

3}, Guizhi Liu^{1

2

3}, Qin Su^{1

2

3}, Mengdi Huang^{1

2

3}, Zhonghua Liu^{1

2

3}, Jianan Huang^{1

2

3}, Na Tian^{1

2

3}, Shuoqian Liu^{1

2

3}

Affiliations

¹ Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China.
² National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China.
³ CoInnovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China.
⁴ United States Salinity Laboratory, United States Department of Agriculture, Agricultural Research Service, Riverside, CA 92504, USA.
⁵ Tea Research Institute, Hunan Academy of Agricultural Sciences/National Small and Medium Leaf Tea Plant Germplasm Resource Nursery, Changsha 410128, China.

Abstract

Caffeine, a primary flavor component in tea, has been the subject of intense research. With the goal of shedding light on the complex regulatory processes governing caffeine biosynthesis in tea plants, liquid chromatography coupled with mass spectrometry (LC-MS), transcriptomics, and small RNA analyses were employed on diverse tea cultivars such as 'Jianghua Kucha' [including 'Xianghong 3' (XH3H) and 'Kucha 3' (KC3H)], 'Fuding Dabaicha' (FDDB), 'Yaoshan Xiulv' (YSXL), and 'Bixiangzao' (BXZ). The results showed that the caffeine level in 'Jianghua Kucha' was significantly higher than that in other tea plant cultivars. In addition, weighted gene co-expression network analysis indicated that that the CsbHLH1 gene might play a pivotal role as a potential hub gene related to the regulation of caffeine biosynthesis. Subcellular localization analysis showed that the CsbHLH1 protein was localized in the nucleus of the cells. Moreover, CsbHLH1 suppresses the transcription of TCS1 by binding to the TCS1 promoter, as evidenced by a yeast one-hybrid assay, an electrophoretic mobility shift assay, and dual luciferase analysis. In addition, a microRNA, miR1446a, was identified that directly cleaves CsbHLH1, leading to an increase in caffeine levels. Therefore, our findings imply that CsbHLH1 binds to the TCS1 promoter (-971 to -1019 bp) to reduce its expression, thereby negatively regulating caffeine biosynthesis. On the other hand, miR1446a enhances the biosynthesis of caffeine by suppressing the expression of CsbHLH1. This work enhances our understanding of the molecular mechanisms of caffeine biosynthesis in tea plants and offers potential directions for manipulating caffeine levels in future tea cultivation.