RRC ID 21151
著者 Hayes ML, Giang K, Mulligan RM.
タイトル Molecular evolution of pentatricopeptide repeat genes reveals truncation in species lacking an editing target and structural domains under distinct selective pressures.
ジャーナル BMC Evol Biol
Abstract BACKGROUND:Pentatricopeptide repeat (PPR) proteins are required for numerous RNA processing events in plant organelles including C-to-U editing, splicing, stabilization, and cleavage. Fifteen PPR proteins are known to be required for RNA editing at 21 sites in Arabidopsis chloroplasts, and belong to the PLS class of PPR proteins. In this study, we investigate the co-evolution of four PPR genes (CRR4, CRR21, CLB19, and OTP82) and their six editing targets in Brassicaceae species. PPR genes are composed of approximately 10 to 20 tandem repeats and each repeat has two α-helical regions, helix A and helix B, that are separated by short coil regions. Each repeat and structural feature was examined to determine the selective pressures on these regions.
RESULTS:All of the PPR genes examined are under strong negative selection. Multiple independent losses of editing site targets are observed for both CRR21 and OTP82. In several species lacking the known editing target for CRR21, PPR genes are truncated near the 17th PPR repeat. The coding sequences of the truncated CRR21 genes are maintained under strong negative selection; however, the 3' UTR sequences beyond the truncation site have substantially diverged. Phylogenetic analyses of four PPR genes show that sequences corresponding to helix A are high compared to helix B sequences. Differential evolutionary selection of helix A versus helix B is observed in both plant and mammalian PPR genes.
CONCLUSION:PPR genes and their cognate editing sites are mutually constrained in evolution. Editing sites are frequently lost by replacement of an edited C with a genomic T. After the loss of an editing site, the PPR genes are observed with three outcomes: first, few changes are detected in some cases; second, the PPR gene is present as a pseudogene; and third, the PPR gene is present but truncated in the C-terminal region. The retention of truncated forms of CRR21 that are maintained under strong negative selection even in the absence of an editing site target suggests that unrecognized function(s) might exist for this PPR protein. PPR gene sequences that encode helix A are under strong selection, and could be involved in RNA substrate recognition.
巻・号 12
ページ 66
公開日 2012-5-14
DOI 10.1186/1471-2148-12-66
PII 1471-2148-12-66
PMID 22583633
PMC PMC3441922
MeSH Amino Acid Sequence Arabidopsis / genetics* Arabidopsis Proteins / genetics* Chloroplasts / genetics DNA, Plant / genetics Evolution, Molecular* Models, Molecular Molecular Sequence Data Phylogeny RNA Editing* Selection, Genetic* Tandem Repeat Sequences
IF 3.058
引用数 17
WOS 分野 GENETICS & HEREDITY EVOLUTIONARY BIOLOGY
リソース情報
シロイヌナズナ / 植物培養細胞・遺伝子 sjo02300 sjo02100 sjo02600 sjs00500 sjs00200