Evolutionary Understanding of Metacaspase Genes in Cultivated and Wild Oryza Species and Its Role in Disease Resistance Mechanism in Rice.

Ruchi Bansal,Rushil Mandlik,Akshay Singh,Tilak Raj Sharma,Humira Sonah,Pallavi Dhiman,Nitika Rana,Rupesh Deshmukh

doi:10.3390/genes11121412

Ruchi Bansal, Rushil Mandlik + Show 6 more

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https://doi.org/10.3390/genes11121412

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Abstract

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 Oryza sativa, japonica, and indica and in nine wild rice species was performed. Extensive computational analysis was conducted to understand gene structures, phylogenetic relationships, cis-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 Magnaporthe oryzae 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.

Highlights

Plants are able to engage in programmed cell death, which can be defined as a schematic mode of action that mediates cell death both under stress and at developmental phases of life [1,2].The phenomenon of programmed cell death is thoroughly characterized in higher animals where caspases are found to have the key role [3,4]
Eight metacaspase genes were found in O. brachyantha, O. sativa subsp. indica, O. glumaepatula, O. barthii, O. meridionalis, O. nivara, and O. punctata genomes and nine in O. longistaminata, O. sativa subsp
The role of metacaspase genes under stress and developmental processes in plants has been demonstrated in several studies

Summary

Introduction

Plants are able to engage in programmed cell death, which can be defined as a schematic mode of action that mediates cell death both under stress and at developmental phases of life [1,2]. The phenomenon of programmed cell death is thoroughly characterized in higher animals where caspases are found to have the key role [3,4]. Very little is known about the programmed cell death in plants and fungi, which lack caspases [5]. Metacaspases and paracaspases, which are structurally related to caspases, are present in plants and fungi [6]. The metacaspases and paracaspases belong to the C14 family of proteases. Metacaspases can be found in all eukaryotic lineages except for a strict absence in animals [7].

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