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Plant Physiology 141:825-839 (2006)
© 2006 American Society of Plant Biologists

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GENOME ANALYSIS

Formation of the Arabidopsis Pentatricopeptide Repeat Family1,[W]

Eric Rivals, Clémence Bruyère, Claire Toffano-Nioche and Alain Lecharny*

Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5506, Université de Montpellier II, 34392 Montpellier cedex 5, France (E.R.); and Institut de Biotechnologie des Plantes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8618, Université Paris-Sud, 91405 Orsay cedex, France (C.B., C.T.-N., A.L.)

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.

1 This work was supported by the Action Concertée Incitative Informatique, Mathématiques, Physique pour la Biologie "Repevol" (grant to E.R.).

The author responsible for the distribution of materials integral to the finding presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Alain Lecharny (lecharny{at}ibp.u-psud.fr).

[W] The online version of this article contains Web-only data.

www.plantphysiol.org/cgi/doi/10.1104/pp.106.077826.

* Corresponding author; lecharny{at}ibp.u-psud.fr; fax 33–1–69–15–34–25.

Received January 25, 2006; returned for revision May 5, 2006; accepted May 8, 2006.




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