Mitochondrial nad3 gene RNA editing in <i>Withania somnifera</i>: Implications for protein structure and stability

Abstract

This study explores RNA editing in the mitochondrial NADH‐dehydrogenase subunit 3 ( nad3) gene of Withania somnifera and examines its effects on gene expression and protein structure under salinity stress conditions. RNA editing, which involves post-transcriptional nucleotide modifications, is crucial in ensuring the functionality of critical proteins. We identified 16 C-to-U RNA editing sites in the nad3 gene using RNA sequencing data, subsequently validated by qRT-PCR. These editing events were consistent across both control and salt stress conditions. The editing of RNA caused big changes to the NAD3 protein’s amino acid sequence, which in turn caused changes to its secondary and tertiary structures. Computational modeling and stability analyses indicated that RNA editing generally stabilized the NAD3 protein, as evidenced by negative Gibbs free energy values. However, it also introduced substantial conformational changes that may influence protein function. Furthermore, molecular docking studies revealed that RNA editing enhanced the binding affinity and interaction profile of the NAD3-NAD1 complex with quinine, with a new interaction involving the LEU21 residue. These findings underscore the importance of RNA editing in modulating protein structure and function to restore an active protein with no effectiveness of salinity on nad3 editing in this plant. Future research should further investigate the broader implications of RNA editing on protein networks.