ABSTRACT

Cold stress is a major environmental factor that limits plant growth and productivity. Plants have evolved various strategies to adapt to these environmental conditions. To better explain the mechanisms used to survive environmental challenges, we retrieved the cold-responsive genes of Arabidopsis thaliana from the Gene Expression Omnibus (GEO) database. The GEO raw data were normalized by the quantile method, and then the differentially expressed genes (DEGs) under cold stress were screened using the robust rank aggregation (RRA) algorithm, including 261 upregulated and 177 downregulated genes out of more than 20,000 genes. Further, the integrated bioinformatics analyses of PUBMED, PANTHER, DAVID, and STRING indicated that the upregulated DEGs were involved in cellular response to red light, negative regulation of circadian rhythm, photoprotection, monosaccharide transport, cold acclimation, and phosphate ion homeostasis, while the downregulated DEGs were associated with the indole glucosinolate biosynthetic process, regulation of RNA splicing, water transport, cell wall modification, cell wall loosening, cellular water homeostasis, and cell wall homeostasis. Furthermore, the up-regulated DEGs had about four times protein-protein-interactions (PPIs) than the down-regulated DEGs, and the cold-responsive genes were identified using Cytoscape software. Furthermore, qRT-PCR of low-temperature-responsive protein 78 (LTI78), transducin family protein (SWA1), and arginine methyltransferase 11 (PRMT11) were performed to validate the outcome of integrated bioinformatics analysis. Our work will improve our knowledge of cold-responsive mechanisms and these DEGs might be targets for plant cold stress-resistance research.

摘要

冷胁迫是限制植物生长和生产力的主要环境因素。植物已经进化出各种策略来适应这些环境条件。为了更好地解释用于在环境挑战中生存的机制，我们检索了拟南芥的冷响应基因来自基因表达综合 (GEO) 数据库。GEO原始数据通过分位数方法归一化，然后使用稳健秩聚合（RRA）算法筛选冷胁迫下的差异表达基因（DEGs），包括20000多个基因中的261个上调基因和177个下调基因。此外，对 PUBMED、PANTHER、DAVID 和 STRING 的综合生物信息学分析表明，上调的 DEG 参与细胞对红光的反应、昼夜节律的负调节、光保护、单糖转运、冷驯化和磷酸根离子稳态，而下调的 DEG 与吲哚硫代葡萄糖苷生物合成过程、RNA 剪接调节、水转运、细胞壁修饰、细胞壁松散、细胞水稳态有关，和细胞壁稳态。此外，上调的DEGs的蛋白质-蛋白质相互作用（PPI）大约是下调的DEGs的四倍，并且使用Cytoscape软件鉴定了冷响应基因。此外，低温响应蛋白 78 (LTI78 )、转导蛋白家族蛋白 ( SWA1 ) 和精氨酸甲基转移酶 11 (执行PRMT11 ) 以验证综合生物信息学分析的结果。我们的工作将提高我们对冷响应机制的了解，这些 DEG 可能成为植物抗冷胁迫研究的目标。