Identification of soybean trans-factors associated with plastid RNA editing sites.

Nureyev F Rodrigues,Rogerio Margis,Fábio C S Nogueira,Gilberto B Domont

doi:10.1590/1678-4685-gmb-2019-0067

Abstract

RNA editing is a posttranscriptional process that changes nucleotide sequences, among which cytosine-to-uracil by a deamination reaction can revert non-neutral codon mutations. Pentatricopeptide repeat (PPR) proteins comprise a family of RNA-binding proteins, with members acting as editing trans-factors that recognize specific RNA cis-elements and perform the deamination reaction. PPR proteins are classified into P and PLS subfamilies. In this work, we have designed RNA biotinylated probes based in soybean plastid RNA editing sites to perform trans-factor specific protein isolation. Soybean cis-elements from these three different RNA probes show differences in respect to other species. Pulldown samples were submitted to mass spectrometry for protein identification. Among detected proteins, five corresponded to PPR proteins. More than one PPR protein, with distinct functional domains, was pulled down with each one of the RNA probes. Comparison of the soybean PPR proteins to Arabidopsis allowed identification of the closest homologous. Differential gene expression analysis demonstrated that the PPR locus Glyma.02G174500 doubled its expression under salt stress, which correlates with the increase of its potential rps14 editing. The present study represents the first identification of RNA editing trans-factors in soybean. Data also indicated that potential multiple trans-factors should interact with RNA cis-elements to perform the RNA editing.

Highlights

The evolutionary history of chloroplasts underwent several selective and adaptive processes, along terrestrial colonization
Recognition sequences from atpF-92, ndhB-1481, and rps14-80 editing sites were analyzed at 30 upstream and 20 downstream nucleotides in eight species (Figure 1)
In vitro RNA editing demonstrated that deletions, insertions, and mutations in cis-elements could lead to changes in a protein that recognize an editing site between plant species without loss of RNA editing (Neuwirt et al, 2005)

Summary

Introduction

The evolutionary history of chloroplasts underwent several selective and adaptive processes, along terrestrial colonization. Massive transfers of genetic information to the host genome and its functional assimilation led to retraction in the endosymbiotic genome (Timmis et al, 2004). A strong selective pressure acted to maintain the remaining endosymbiotic genetic information. Posttranscriptional processes were selected by promoting the maintenance of essential sequences for gene expression and functional proteins. Nation reactions, respectively (Chateigner-Boutin and Small, 2010; Takenaka et al, 2013). These changes are necessary for RNA maturation, to generate start or stop codons, or even to result in changes in amino acid identity (Schallenberg-Rüdinger and Knoop, 2016)

Methods

Results

Conclusion