MBE Advance Access originally published online on March 14, 2008
Molecular Biology and Evolution 2008 25(6):1120-1128; doi:10.1093/molbev/msn057
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Research Articles |
On the Expansion of the Pentatricopeptide Repeat Gene Family in Plants
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* Centre for Computational Systems Biology, University of Western Australia, Perth, Australia
The Centre for Gene Research, Nagoya University, Japan
ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, Australia
Unité de Recherche en Génomique Végétale (INRA-CNRS-UEVE) Evry, France
|| Department of Botany and Plant Sciences, University of California, Riverside
¶ Institute of Biology, Humboldt University of Berlin, Berlin, Germany
E-mail: iansmall{at}uwa.edu.au
Accepted for publication February 26, 2008.
Pentatricopeptide repeat (PPR) proteins form a huge family in plants (450 members in Arabidopsis and 477 in rice) defined by tandem repetitions of characteristic sequence motifs. Some of these proteins have been shown to play a role in posttranscriptional processes within organelles, and they are thought to be sequence-specific RNA-binding proteins. The origins of this family are obscure as they are lacking from almost all prokaryotes, and the spectacular expansion of the family in land plants is equally enigmatic. In this study, we investigate the growth of the family in plants by undertaking a genome-wide identification and comparison of the PPR genes of 3 organisms: the flowering plants Arabidopsis thaliana and Oryza sativa and the moss Physcomitrella patens. A large majority of the PPR genes in each of the flowering plants are intron less. In contrast, most of the 103 PPR genes in Physcomitrella are intron rich. A phylogenetic comparison of the PPR genes in all 3 species shows similarities between the intron-rich PPR genes in Physcomitrella and the few intron-rich PPR genes in higher plants. Intron-poor PPR genes in all 3 species also display a bias toward a position of their introns at their 5' ends. These results provide compelling evidence that one or more waves of retrotransposition were responsible for the expansion of the PPR gene family in flowering plants. The differing numbers of PPR proteins are highly correlated with differences in organellar RNA editing between the 3 species.
Key Words: Oryza sativa • Arabidopsis thaliana • Physcomitrella patens • introns • pentatricopeptide repeat • RNA editing
Geoffrey McFadden, Associate Editor