MBE Advance Access published online on March 14, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn057
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
On the expansion of the pentatricopeptide repeat gene family in plants
1 Centre for Computational Systems Biology, University of Western Australia, Perth, Australia
2 The Centre for Gene Research, Nagoya University, Japan
3 ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, Australia
4 Unité de Recherche en Génomique Végétale (INRA-CNRS-UEVE), 91057 Evry cedex, France
5 Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521 USA
6 Institute of Biology, Humboldt University of Berlin, Chausseestr. 117, 10115 Berlin, Germany
Corresponding Author: Ian Small, Postal address: ARC Centre of Excellence in Plant Energy Biology, Molecular and Chemical Sciences Building (M316), University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia , Email: iansmall{at}uwa.edu.au, Telephone: +61 8 64884499, Fax: +61 8 64884401
Received for publication December 19, 2007. Revision received February 14, 2008. 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 post-transcriptional 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 three 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 three 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 three species also display a bias towards 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 three species.
Key Words: Oryza sativa • Arabidopsis thaliana • Physcomitrella patens • introns • pentatricopeptide repeat • RNA editing