Formation of the Arabidopsis Pentatricopeptide Repeat Family

Eric Rivals 1 Clémence Bruyère 2 Claire Toffano-Nioche 2 Alain Lecharny 2
1 MAB - Méthodes et Algorithmes pour la Bioinformatique
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
Abstract : In Arabidopsis (Arabidopsis thaliana) the 466 pentatricopeptide repeat (PPR) proteins are putative RNA-binding proteins with essential roles in organelles. Roughly half of the PPR proteins form the plant combinatorial and modular protein (PCMP) subfamily, which is land-plant specific. PCMPs exhibit a large and variable tandem repeat of a standard pattern of three PPR variant motifs. The association or not of this repeat with three non-PPR motifs at their C terminus defines four distinct classes of PCMPs. The highly structured arrangement of these motifs and the similar repartition of these arrangements in the four classes suggest precise relationships between motif organization and substrate specificity. This study is an attempt to reconstruct an evolutionary scenario of the PCMP family. We developed an innovative approach based on comparisons of the proteins at two levels: namely the succession of motifs along the protein and the amino acid sequence of the motifs. It enabled us to infer evolutionary relationships between proteins as well as between the inter- and intraprotein repeats. First, we observed a polarized elongation of the repeat from the C terminus toward the N-terminal region, suggesting local recombinations of motifs. Second, the most N-terminal PPR triple motif proved to evolve under different constraints than the remaining repeat. Altogether, the evidence indicates different evolution for the PPR region and the C-terminal one in PCMPs, which points to distinct functions for these regions. Moreover, local sequence homogeneity observed across PCMP classes may be due to interclass shuffling of motifs, or to deletions/insertions of non-PPR motifs at the C terminus.
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https://hal-lirmm.ccsd.cnrs.fr/lirmm-00109042
Contributeur : Eric Rivals <>
Soumis le : lundi 23 octobre 2006 - 15:54:46
Dernière modification le : jeudi 11 janvier 2018 - 06:26:12

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Eric Rivals, Clémence Bruyère, Claire Toffano-Nioche, Alain Lecharny. Formation of the Arabidopsis Pentatricopeptide Repeat Family. Plant Physiology, American Society of Plant Biologists, 2006, 141, pp.825-839. 〈http://www.plantphysiol.org/cgi/content/abstract/141/3/825〉. 〈10.1104/pp.106.077826〉. 〈lirmm-00109042〉

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