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

被引:19
作者
Yura, Kei [1 ,2 ]
Sulaiman, Sintawee [3 ]
Hatta, Yosuke [4 ]
Shionyu, Masafumi [4 ]
Go, Mitiko [4 ,5 ,6 ]
机构
[1] Ochanomizu Univ, Grad Sch Humanities & Sci, Bunkyo Ku, Tokyo 1128610, Japan
[2] Ochanomizu Univ, Ctr Informat Biol, Bunkyo Ku, Tokyo 1128610, Japan
[3] King Mongkuts Univ Technol Thonburi, Bioinformat Program, Bangmod, Toongkru, Thailand
[4] Nagahama Inst Biosci & Technol, Fac Biosci, Dept Biosci, Shiga 5260829, Japan
[5] Tokyo Med & Dent Univ, Bunkyo Ku, Tokyo 1138510, Japan
[6] Res Org Informat & Syst, Minato Ku, Tokyo 1050001, Japan
基金
日本学术振兴会;
关键词
Chloroplast; Mitochondrion; Molecular evolution; Organelle genome; Protein 3D structure; RNA editing; PENTATRICOPEPTIDE REPEAT PROTEIN; AMINO-ACID-RESIDUES; DYW PROTEIN; HORNWORT CHLOROPLASTS; PLANT-MITOCHONDRIA; MESSENGER-RNA; TRANSCRIPTS; SEQUENCE; PREDICTION; CREATION;
D O I
10.1093/pcp/pcp132
中图分类号
Q94 [植物学];
学科分类号
071001 ;
摘要
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/.
引用
收藏
页码:1865 / 1873
页数:9
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