National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab 140306, India.
Department of Biotechnology, Panjab University, Chandigarh 160014, India.
Genes (Basel). 2020 Nov 26;11(12):1412. doi: 10.3390/genes11121412.
Metacaspases (MCs), a class of cysteine-dependent proteases found in plants, fungi, and protozoa, are predominately involved in programmed cell death processes. In this study, we identified metacaspase genes in cultivated and wild rice species. Characterization of metacaspase genes identified both in cultivated subspecies of , , and and in nine wild rice species was performed. Extensive computational analysis was conducted to understand gene structures, phylogenetic relationships, -regulatory elements, expression patterns, and haplotypic variations. Further, the haplotyping study of metacaspase genes was conducted using the whole-genome resequencing data publicly available for 4726 diverse genotype and in-house resequencing data generated for north-east Indian rice lines. Sequence variations observed among wild and cultivated rice species for metacaspase genes were used to understand the duplication and neofunctionalization events. The expression profiles of metacaspase genes were analyzed using RNA-seq transcriptome profiling in rice during different developmental stages and stress conditions. Real-time quantitative PCR analysis of candidate metacaspase genes in rice cultivars Pusa Basmati-1 in response to infection indicated a significant role in the disease resistance mechanism. The information provided here will help to understand the evolution of metacaspases and their role under stress conditions in rice.
植物、真菌和原生动物中发现的天冬氨酸半胱氨酸蛋白酶（MCs）是一类半胱氨酸依赖性蛋白酶，主要参与程序性细胞死亡过程。在这项研究中，我们鉴定了栽培稻和野生稻中的天冬氨酸半胱氨酸蛋白酶基因。对 、 和 栽培亚种以及 9 种野生稻中的天冬氨酸半胱氨酸蛋白酶基因进行了鉴定和特征描述。进行了广泛的计算分析，以了解基因结构、系统发育关系、-调控元件、表达模式和单倍型变异。此外，还利用 4726 个不同基因型的全基因组重测序数据和为印度东北部水稻品系生成的内部重测序数据，对天冬氨酸半胱氨酸蛋白酶基因进行了单倍型研究。观察到野生和栽培稻种中天冬氨酸半胱氨酸蛋白酶基因的序列变异，用于了解重复和新功能化事件。利用水稻不同发育阶段和胁迫条件下的 RNA-seq 转录组分析了天冬氨酸半胱氨酸蛋白酶基因的表达谱。对水稻品种 Pusa Basmati-1 中候选天冬氨酸半胱氨酸蛋白酶基因对 感染的实时定量 PCR 分析表明，它们在抗病机制中起重要作用。本研究提供的信息将有助于了解天冬氨酸半胱氨酸蛋白酶的进化及其在水稻胁迫条件下的作用。
