Splice Variants of Superoxide Dismutases in Rice and Their Expression Profiles under Abiotic Stresses.

Ajay Saini,Yong-Fang Li,Ramanjulu Sunkar,Jai S Rohila,Ganesan Govindan

doi:10.3390/ijms22083997

Abstract

The superoxide dismutases (SODs) play vital roles in controlling cellular reactive oxygen species (ROS) that are generated both under optimal as well as stress conditions in plants. The rice genome harbors seven SOD genes (CSD1, CSD2, CSD3, CSD4, FSD1, FSD2, and MSD) that encode seven constitutive transcripts. Of these, five (CSD2, CSD3, CSD4, FSD1, and MSD) utilizes an alternative splicing (AS) strategy and generate seven additional splice variants (SVs) or mRNA variants, i.e., three for CSD3, and one each for CSD2, CSD4, FSD1, and MSD. The exon-intron organization of these SVs revealed variations in the number and length of exons and/or untranslated regions (UTRs). We determined the expression patterns of SVs along with their constitutive forms of SODs in rice seedlings exposed to salt, osmotic, cold, heavy metal (Cu+2) stresses, as well as copper-deprivation. The results revealed that all seven SVs were transcriptionally active in both roots and shoots. When compared to their corresponding constitutive transcripts, the profiles of five SVs were almost similar, while two specific SVs (CSD3-SV4 and MSD-SV2) differed significantly, and the differences were also apparent between shoots and roots suggesting that the specific SVs are likely to play important roles in a tissue-specific and stress-specific manner. Overall, the present study has provided a comprehensive analysis of the SVs of SODs and their responses to stress conditions in shoots and roots of rice seedlings.

Highlights

In eukaryotes, splicing of intron-containing precursor messenger RNAs generates mature mRNA [1,2,3]
A survey of the Nipponbare rice genome identified a total of seven superoxide dismutases (SODs) genes, which were further categorized into CSDs (CuZn-SODs), FSDs (Fe-SODs), and MSD (Mn-SOD)
‘a’ Genomic locus is as per the information at Rice Genome Annotation Project website. ‘b’ Isoelectric point and molecular weight (MW) of protein sequences were estimated using the ‘Compute pI/Mw software tool’ at ExPASy. ‘# ’ Splice variant sequence that showed variation in the untranslated regions (UTRs). ‘c’ The splice variant sequences were searched against GenBank (EST) database

Summary

Introduction

In eukaryotes, splicing of intron-containing precursor messenger RNAs (pre-mRNAs) generates mature mRNA [1,2,3]. Splicing provides an opportunity for generating diverse mature transcripts with alternative combinations of exons/untranslated regions (UTRs) via specific events, such as the intron retention, exon skipping, alternative splice sites, and mutually exclusive exons, by a process known as ‘alternative splicing’. AS enhances the transcriptome and proteome diversity with altered stability, properties, and subcellular localization in an organism that can affect a variety of cellular processes [3,5,6]. Previous studies have estimated that more than 60% of the intron containing pre-mRNAs in Arabidopsis undergo AS [7,8].

Methods

Results

Conclusion