RESOPS: A Database for Analyzing the Correspondence of RNA Editing Sites to Protein Three-Dimensional Structures

Abstract

Transcripts from mitochondrial and chloroplast DNA of land plants often undergo cytidine to uridine conversion-type RNA editing events. RESOPS is a newly built database that specializes in displaying RNA editing sites of land plant organelles on protein three-dimensional (3D) structures to help elucidate the mechanisms of RNA editing for gene expression regulation. RESOPS contains the following information: unedited and edited cDNA sequences with notes for the target nucleotides of RNA editing, conceptual translation from the edited cDNA sequence in pseudo-UniProt format, a list of proteins under the influence of RNA editing, multiple amino acid sequence alignments of edited proteins, the location of amino acid residues coded by codons under the influence of RNA editing in protein 3D structures and the statistics of biased distributions of the edited residues with respect to protein structures. Most of the data processing procedures are automated; hence, it is easy to keep abreast of updated genome and protein 3D structural data. In the RESOPS database, we clarified that the locations of residues switched by RNA editing are significantly biased to protein structural cores. The integration of different types of data in the database also help advance the understanding of RNA editing mechanisms. RESOPS is accessible at http://cib.cf.ocha.ac.jp/RNAEDITING/.

The evolution of RNA editing and pentatricopeptide repeat genes

“…Indeed, several studies have conclusively shown that the number of RNA editing sites is strongly positively correlated with genome GC content (Malek et al. , 1996; Smith, 2009; Yura et al. , 2009).…”

Identification of RNA editing sites in cotton (Gossypium hirsutum) chloroplasts and editing events that affect secondary and three-dimensional protein structures

“…Chateigner-Boutin et al (2008) could not clearly determine the impact of the unedited clpP-187. Then, Yura et al (2009) found that the Tyrosine of clpP-187 located on the ClpP surface according to RESOPS, and unedited residue of clpP-187 have almost no effect on the stability and function of ClpP. Similar to clpP-187, the other five sites may not be very important for the stability or function of each corresponding protein.…”

“…Up to date, a number of experiments were performed to test the function of RNA editing. There is growing evidence that most of the unedited proteins have less function than the edited ones (Zito et al, 1997;Sasaki et al, 2001;Yura et al 2009). We used bioinformatics to analyze protein secondary structures of all 27 transcripts in cotton before and after editing.…”

“…The results indicated that seven editing sites in 4 proteins (ndhA-114, ndhD-128, ndhD-225, ndhD-433, ndhC-108, ndhB-204, and ndhB-419) are involved in their corresponding protein 3-D structures. We also analyzed protein 3-D structures of edited transcripts using RESOPS, which is a database for analyzing the correspondence of RNA editing sites to protein 3-D structure (Yura et al, 2009). To date, 41 3-D structures of chloroplast proteins with editing are listed in RESOPS.…”

RNA Editing and Drug Discovery for Cancer Therapy

“…For organellar RNA editing resources, GOBASE [42], REDIdb [43], and PREPACT 2.0 [44] contain the interface for RNA editing data of mitochondrion- and chloroplast-encoded sequences. Some bioinformatics resources of RNA editing in plants [60–63] were not included in Table 1 because they have little relationships to drug discovery. …”