Molecular evolution of pentatricopeptide repeat genes reveals truncation in species lacking an editing target and structural domains under distinct selective pressures.

BMC Evolutionary Biology
Michael L HayesR Michael Mulligan

Abstract

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. 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 t...Continue Reading

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Citations

Mar 26, 2013·FEBS Letters·Hannes RuweDavid B Stern
May 7, 2013·RNA Biology·Mamoru SugitaChieko Sugita
Jun 9, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Heqin LiShanfa Lu
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Oct 17, 2017·The Plant Journal : for Cell and Molecular Biology·Michael F DiazR Michael Mulligan
Apr 27, 2021·Plant Communications·Shengchun LiJiang Zhang

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Methods Mentioned

BETA
PCR

Software Mentioned

HHpred
Clustal W
PAML
MEGA5
PHYML
codeml
ClustalW
Phytozome
aLRT
TBLASTN

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