Ayaz Aliya, Jalal Abdul, Zhang Xiaoli, Khan Khalid Ali, Hu Chunmei, Li Ying, Hou Xilin
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.
Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
Plants (Basel). 2024 Apr 22;13(8):1160. doi: 10.3390/plants13081160.
Numerous studies have been conducted to investigate the genomic characterization of 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 transcription factors (TFs). However, a comprehensive and systematic investigations regarding the role of 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 genes, gain insight into their expression patterns during ER stress in pak choi, and investigate the protein-to-protein interaction of genes with the ER chaperone BiP. In total, 112 members of the 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 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 genes were discovered to exhibit a wide variety of -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 genes with ER-stress-responsive genes. Moreover, gene expression profiles and protein-protein interaction with ER chaperone further confirmed their roles and capacity to respond to ER stress in pak choi.
已经开展了大量研究来调查基因的基因组特征及其在内质网（ER）应激细胞反应中的作用。这些研究为内质网应激的细胞协同反应提供了有价值的见解，这种反应由转录因子（TFs）介导。然而，现有文献中目前缺乏关于白菜中基因的作用及其在内质网应激反应中的参与情况的全面系统研究。为了填补这一知识空白，启动了本研究，以阐明基因的基因组特征，深入了解它们在白菜内质网应激期间的表达模式，并研究基因与内质网伴侣BiP之间的蛋白质-蛋白质相互作用。通过全面的全基因组分析，总共鉴定出112个基因成员。基于序列相似性、基因结构、保守结构域和响应基序的分析，通过系统发育分析将鉴定出的基因分为10个不同的亚家族。染色体定位和复制事件为它们的基因组背景和进化历史提供了见解。分歧分析估计了它们的进化历史，预测分歧时间范围为73万至8071万年前（百万年前）。发现这些基因的启动子区域表现出各种各样的元件，包括光、激素和应激反应元件。基因本体（GO）富集分析进一步证实了它们在内质网未折叠蛋白反应（UPR）中的作用，而共表达网络分析表明基因与内质网应激反应基因有很强的关系。此外，基因表达谱以及与内质网伴侣的蛋白质-蛋白质相互作用进一步证实了它们在白菜中对内质网应激的反应作用和能力。
