Journal Article

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

Kei Yura, Sintawee Sulaiman, Yosuke Hatta, Masafumi Shionyu and Mitiko Go

in Plant and Cell Physiology

Published on behalf of Japanese Society of Plant Physiologists

Volume 50, issue 11, pages 1865-1873
Published in print November 2009 | ISSN: 0032-0781
Published online October 2009 | e-ISSN: 1471-9053 | DOI: http://dx.doi.org/10.1093/pcp/pcp132

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  • Biochemistry
  • Molecular and Cell Biology
  • Plant Sciences and Forestry

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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/.

Keywords: Chloroplast; Mitochondrion; Molecular evolution; Organelle genome; Protein 3D structure; RNA editing

Journal Article.  4678 words.  Illustrated.

Subjects: Biochemistry ; Molecular and Cell Biology ; Plant Sciences and Forestry

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