title: Identification of RNA editing  sites in cotton (Gossypium hirsutum) chloroplasts and editing events  that affect secondary and three-dimensional protein structures.
abstract: RNA  editing can alter individual nucleotides in primary transcripts, which can  cause the amino acids encoded by edited RNA to deviate from the ones predicted  from the DNA template. We investigated RNA editing sites of protein-coding  genes from the chloroplast genome of cotton. Fifty-four editing sites were  identified in 27 transcripts, which is the highest editing frequency found  until now in angiosperms. All these editing sites were C-to-U conversion,  biased toward ndh genes and U_A context. Examining published editotypes  in various angiosperms, we found that RNA editing mostly converts amino acid  from hydrophilic to hydrophobic and restores evolutionary conserved amino  acids. Using bioinformatics to analyze the effect of editing events on protein  secondary and three-dimensional structures, we found that 21 editing sites can  affect protein secondary structures and seven editing sites can alter  three-dimensional protein structures. These results imply that 24 editing sites  in cotton chloroplast transcripts may play an important role in their protein  structures and functions.
authors.affiliation: College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, PR China.
authors.forename: Y
authors.initials: Y
authors.lastname: Jiang
authors.forename: S L
authors.initials: SL
authors.lastname: Fan
authors.forename: M Z
authors.initials: MZ
authors.lastname: Song
authors.forename: J N
authors.initials: JN
authors.lastname: Yu
authors.forename: S X
authors.initials: SX
authors.lastname: Yu
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000032:analysis; D002736:Chloroplasts / Q000378:metabolism*; D003062:Codon; D018744:DNA, Plant; D003368:Gossypium / Q000235:genetics*; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics*; D016133:Polymerase Chain Reaction; D011487:Protein Conformation; D017393:RNA Editing
chemical_list: D000596:Amino Acids; D003062:Codon; D018744:DNA, Plant; D010940:Plant Proteins