Unveiling Chloroplast RNA Editing Events Using Next Generation Small RNA Sequencing Data

Nureyev F Rodrigues,Ana P Christoff,Guilherme C Da Fonseca,Rogerio Margis,Franceli R Kulcheski

doi:10.3389/fpls.2017.01686

Nureyev F Rodrigues, Ana P Christoff + Show 3 more

Open Access

https://doi.org/10.3389/fpls.2017.01686

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Abstract

Organellar RNA editing involves the modification of nucleotide sequences to maintain conserved protein functions, mainly by reverting non-neutral codon mutations. The loss of plastid editing events, resulting from mutations in RNA editing factors or through stress interference, leads to developmental, physiological and photosynthetic alterations. Recently, next generation sequencing technology has generated the massive discovery of sRNA sequences and expanded the number of sRNA data. Here, we present a method to screen chloroplast RNA editing using public sRNA libraries from Arabidopsis, soybean and rice. We mapped the sRNAs against the nuclear, mitochondrial and plastid genomes to confirm predicted cytosine to uracil (C-to-U) editing events and identify new editing sites in plastids. Among the predicted editing sites, 40.57, 34.78, and 25.31% were confirmed using sRNAs from Arabidopsis, soybean and rice, respectively. SNP analysis revealed 58.2, 43.9, and 37.5% new C-to-U changes in the respective species and identified known and new putative adenosine to inosine (A-to-I) RNA editing in tRNAs. The present method and data reveal the potential of sRNA as a reliable source to identify new and confirm known editing sites.

Highlights

Chloroplasts are notable examples of successful endosymbiosis in the early origin of modern life forms
We propose that small RNAs (sRNA) sequencing data could represent an additional resource to identify chloroplast RNA editing events, in addition to other approaches, such as strand-specific RNA sequencing and Single Nucleotide Polymorphism (SNP)
The sRNA libraries sequenced without plastid RNA isolation were mapped to Arabidopsis, soybean and rice chloroplast genomes using an in-house pipeline (Figure 1)

Summary

Introduction

Chloroplasts are notable examples of successful endosymbiosis in the early origin of modern life forms These organelles possess their own gene expression machinery, with complex posttranscriptional processes and fine nucleus-cytosol crosstalk. These organelles undergo a posttranscriptional process called RNA editing, corresponding to nucleotide changes from cytosine to uracil (C-to-U) and less frequently from uracil to cytosine (U-to-C), in some sites of coding sequences (Tillich et al, 2006; Chateigner-Boutin and Small, 2010) These nucleotide changes correct the codons to encode appropriate amino acids, maintaining the functional amino acid sequence of the evolutionarily conserved protein (Takenaka et al, 2013). The A-to-I editing in position 34 of the tRNAArg (ACG) produces the wobble nucleotide described as essential for efficient chloroplast

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