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Plant and Cell Physiology Advance Access originally published online on October 6, 2009
Plant and Cell Physiology 2009 50(11):1865-1873; doi:10.1093/pcp/pcp132
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© The Author 2009. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use distribution, and reproduction in any medium, provided the original work is properly cited.

Rapid Paper

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

Kei Yura1,2,*, Sintawee Sulaiman3, Yosuke Hatta4, Masafumi Shionyu4 and Mitiko Go4,5,6

1Computational Biology, Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo, 112-8610 Japan
2Center for Informational Biology, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo, 112-8610 Japan
3Bioinformatics Program, King Mongkut’s University of Technology Thonburi, 126 Pracha-utid Road, Bangmod, Toongkru, Thailand
4Department of Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga, 526-0829 Japan
5Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo, 113-8510 Japan
6Research Organization of Information and Systems, 4-3-13, Toranomon, Minato, Tokyo, 105-0001 Japan

*Corresponding author: E-mail, yura.kei{at}ocha.ac.jp; Fax: +81-3-5978-5514.


  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/.

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

Abbreviations: 3D, three-dimensional; PDB, Protein Data Bank.

(Received September 15, 2009; Accepted September 24, 2009)
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