Integrative transcriptomic and proteomic analyses reveal a positive role of BES1 in salt tolerance in Arabidopsis

Lei Feng; Yan Li; Yu-Ling Zhou; Guang-Hua Meng; Zhao-Lin Ji; Wen-Hui Lin; Jun-Xian He

doi:10.3389/fpls.2023.1034393

Integrative transcriptomic and proteomic analyses reveal a positive role of BES1 in salt tolerance in Arabidopsis

Front Plant Sci. 2023 Mar 1:14:1034393. doi: 10.3389/fpls.2023.1034393. eCollection 2023.

Authors

Lei Feng¹, Yan Li², Yu-Ling Zhou¹, Guang-Hua Meng¹, Zhao-Lin Ji^{1

3}, Wen-Hui Lin^{4

5}, Jun-Xian He¹

Affiliations

¹ School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China.
² State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Hangzhou, China.
³ College of Plant Protection, Yangzhou University, Yangzhou, China.
⁴ The Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
⁵ Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, Shanghai Jiao Tong University, Shanghai, China.

Abstract

Introduction: Salt stress is a major environmental factor limiting plant growth and development. Previous studies have indicated that the steroidal hormones-brassinosteroids (BRs) are important regulators of plant responses to salt stress. However, the underlying molecular mechanisms have not been fully understood.

Methods: (1) Phenotypic analysis of bes1-D, BES1-RNAi and their wild-type (Col-0) under salt treatments with different concentrations of NaCl. (2) Transcriptomic and proteomic profiling of BES1-regulated genes and proteins under salt treatment; (3) qRT-PCR validation of selected BES1-regulated genes under salt stress; (4) Transient transcriptional assay of BES1 regulation on its putative target genes in Arabidopsis protoplasts; (5) Electrophoresis Mobility Shift Assay (EMSA) of BES1 binding with its potential target genes.

Results and discussion: Phenotypic analysis indicated that bes1-D, a gain-of-function mutant of the BR-regulated transcription factor BES1 in Arabidopsis showed better salt tolerance than the wild-type plant, while a BES1 RNA interference (BES1-RNAi) line was more sensitive to salt stress. Global gene expression profiling and time series clustering analyses identified a total of 1,170 genes whose expression was boosted in bes1-D under salt stress. Further GO enrichment and gene functional network analyses identified several key modules that are regulated by BES1 and most sensitive to salt stress perturbations, including stress response, response to ABA and ROS, flavonoid biosynthesis and transmembrane transport. A comparative proteomic analysis performed under the same stress conditions supported the results from the transcriptome analysis. In addition, transient gene transcription assays in Arabidopsis protoplasts and in vitro DNA binding assays verified that BES1 regulates the expression of some ion transporter genes directly and indirectly. Taken together, our results support a positive role of BES1 in plant salt tolerance.

Keywords: Arabidopsis thaliana; BES1; brassinosteroids; proteomics; salt tolerance; transcriptomics.

Grants and funding

This work was supported by the General Research Fund (CUHK Codes 14148916 and 14104521) and AoE grants (AoE/M-05/12 and AoE/M-403/16) from the Research Grants Council (RGC) of Hong Kong, the National Natural Science Foundation (NSFC)-RGC Joint Scheme (N_CUHK452/17), and the Direct Grants from the Chinese University of Hong Kong to J-XH, and the NSFC-RGC Joint Scheme (Grant No. 31761163003) to W-HL.