RNA editing is defined as the insertion, deletion, and replacement of nucleotide bases that occurs after transcription, which usually results in difference between RNA genetic information and the genome template (Liscovitch-Brauer et al., 2017; Walkley and Li, 2017; Zahn, 2017; Peng et al., 2018). For instance, the transcript of maize chloroplast gene 50S ribosomal protein L2 (rpl2) can only create the initiation codons after uridine replacement of cytidine (Hoch et al., 1991). In 1986, Dutch etbiologist Benne et al. discovered an RNA editing event in the mitochondrial gene cytochrome c oxidase subunit II (cox2) of trypanosomes firstly (Benne et al., 1986), they found that the insertion of four uridines caused the cox2 gene to form a continuous open reading frame, resulting in changes in genetic information. In 1989, Hiesel et al. revealed that RNA editing also exists in primrose mitochondria (Hiesel et al., 1989). Subsequently, more and more RNA editing events were confirmed. To date, RNA editing has been found in primitive eukaryotes, vertebrates, plants, fungi and viruses (Palladino et al., 2000; Bahn et al., 2012; Alon et al., 2015; Guo et al., 2015; Riemondy et al., 2018; Zaidan et al., 2018).
In the case of higher plants, RNA editing mainly appears in the coding regions of mitochondrial and chloroplast genes, of which the most common editing style is cytidines (C) substituting uridines (U) (Covello and Gray, 1989; Tillich et al., 2006; Takenaka et al., 2013). So far, in higher plants, the total number of RNA editing sites in chloroplast genome (20–60) is much less than that of mitochondrial genome (300–600). During the process of RNA editing in higher plants, the editing factor recognizes a 20 ~ 25 nucleotide sequence upstream of the editing site, and the editing factors required for different RNA editing sites may differ (Yagi et al., 2014; Yan et al., 2018). A large number of studies have shown that RNA editing alters the genetic information from the genome and enriches the expression products of genes; on the other hand, it provides new genetic structures and functions for the evolution of organisms (Small et al., 2020; Lukeš et al., 2021). For the mammals, the regulation of RNA editing event has been widely studied. For example, the RNA editing in mammals has been proved to be dynamic landscape between tissues and more potential factors of editing have been discovered to be involved in the editing events (Tan et al., 2017; Blanc et al., 2019).
RNA editing in plant is mainly mediated by editing complex involving editing factors such as Pentapeptide repeat protein (PPR) protein and MORF protein (Tian et al., 2019). The PPR proteins are the largest class of RNA editing factors in plants, which is encoded by nuclear genes and located in mitochondria or chloroplast, playing a role of site-specific recognition in editing (Yagi et al., 2013; Yagi et al., 2014; Ichinose and Sugita, 2017). PPR proteins have two subfamilies, P-type and PLS-type, the P-type consists of the 35-amino acid classic PPR (P) motif, while the PLS-type consists of the classic P-motif and its variants L (35 or 36 amino acids) and S (31 amino acids) (Manna, 2015). In fact, a plant-specific conserved E domain often exists at the C-terminus of the PLS type. Generally in plant organelles, it is the PLS-type PPR protein that recognizes the specific editing sites (Shikanai, 2015; Yan et al., 2018). However, the target relationship of PPR protein catalyzing RNA editing site is still unclear.
Previous studies have revealed that RNA editing is specific in terms of tissues and developmental stages, suggesting that RNA editing may function as a regulatory device in plastid gene expression (Bock et al., 1993; Zeltz et al., 1993; Miyata and Sugita, 2004). Taking spinach as an example, reduced editing was observed in the photosystem II reaction center subunit VI (psbF) and PSII reaction center subunit XII (psbL) transcript from seeds and roots. Tissue-specific and development-specific RNA editing were also detected in the bryophyte ribosomal protein S14 (rps14) gene in previous studies (Miyata and Sugita, 2004). Tseng also observed that the RNA editing efficiency of Arabidopsis plastid mRNA was variable among different tissues (Tseng et al., 2013). Actually, earlier researches on RNA editing mainly focused on selected genes based on experimental methods with disadvantage of low throughput. With the rapid improvement of genomic and transcriptome sequencing technology, more and more genomes of plants have been sequenced and a great quantity of RNA-seq data have also been generated, which offers an opportunity to test the function and regulatory mechanism of RNA editing in plant growth and development. In the future, the regulation and function of RNA editing in plants and their effects on traits, especially some essential agronomic traits, will attract more people's attention (Small et al., 2020).
As a model plant, tobacco (Nicotiana tabacum) plays a key role in plant molecular research, and is also an important worldwide economical plant. In this study, in order to illustrate the tissue distribution characteristics of RNA editing in plant, we identified and analyzed RNA editing sites in four tobacco tissues (roots, stems, leaves, and flowers) based on transcriptome data. And then, the dynamic landscape of C-to-U RNA editing sites was analyzed and we discovered that editing sites were distributed differently in the four tissues, among which the editing sites in the root were the least, which might be related to the physiological function requirements for the roots. Simultaneously, we also analyzed the expression levels of RNA editing factors PPR genes in the four tissues, and its heterogeneity of expression levels might partly explain the varied RNA editing events happening in different tissues. Our findings show that RNA editing are differentially regulated in various types of tissues (non-green vs green), and may contribute to functional differentiation of tobacco tissues.