In-Depth Characterization of bZIP Genes in the Context of Endoplasmic Reticulum (ER) Stress in Brassica campestris ssp. chinensis

Aliya Ayaz; Abdul Jalal; Xiaoli Zhang; Khalid Ali Khan; Chunmei Hu; Ying Li; Xilin Hou

doi:10.3390/plants13081160

In-Depth Characterization of bZIP Genes in the Context of Endoplasmic Reticulum (ER) Stress in Brassica campestris ssp. chinensis

Plants (Basel). 2024 Apr 22;13(8):1160. doi: 10.3390/plants13081160.

Authors

Aliya Ayaz¹, Abdul Jalal², Xiaoli Zhang¹, Khalid Ali Khan³, Chunmei Hu¹, Ying Li¹, Xilin Hou¹

Affiliations

¹ State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Science and Technology/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
² Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
³ Applied College, Center of Bee Research and Its Products (CBRP), Unit of Bee Research and Honey Production, and Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha 61413, Saudi Arabia.

Abstract

Numerous studies have been conducted to investigate the genomic characterization of bZIP genes and their involvement in the cellular response to endoplasmic reticulum (ER) stress. These studies have provided valuable insights into the coordinated cellular response to ER stress, which is mediated by bZIP transcription factors (TFs). However, a comprehensive and systematic investigations regarding the role of bZIP genes and their involvement in ER stress response in pak choi is currently lacking in the existing literature. To address this knowledge gap, the current study was initiated to elucidate the genomic characteristics of bZIP genes, gain insight into their expression patterns during ER stress in pak choi, and investigate the protein-to-protein interaction of bZIP genes with the ER chaperone BiP. In total, 112 members of the BcbZIP genes were identified through a comprehensive genome-wide analysis. Based on an analysis of sequence similarity, gene structure, conserved domains, and responsive motifs, the identified BcbZIP genes were categorized into 10 distinct subfamilies through phylogenetic analysis. Chromosomal location and duplication events provided insight into their genomic context and evolutionary history. Divergence analysis estimated their evolutionary history with a predicted divergence time ranging from 0.73 to 80.71 million years ago (MYA). Promoter regions of the BcbZIP genes were discovered to exhibit a wide variety of cis-elements, including light, hormone, and stress-responsive elements. GO enrichment analysis further confirmed their roles in the ER unfolded protein response (UPR), while co-expression network analysis showed a strong relationship of BcbZIP genes with ER-stress-responsive genes. Moreover, gene expression profiles and protein-protein interaction with ER chaperone BiP further confirmed their roles and capacity to respond to ER stress in pak choi.

Keywords: BcbZIP genes; ER stress; expression profiles; functional analysis; gene interaction network; phylogeny.

Grants and funding

This work was supported by China’s national science and technology basic resources survey project (2023FY101202), and China’s national vegetable industry technology system (CARS-23-A-16).