Formation of the Arabidopsis pentatricopeptide repeat family
Formation of the Arabidopsis pentatricopeptide repeat family
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DOI：
10.1104/pp.106.077826
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发表时间：
2006-07-01
期刊：
影响因子：
7.4
通讯作者：
Lecharny, Alain
中科院分区：
文献类型：
--
作者：
Rivals, Eric;Bruyere, Clemence;Lecharny, Alain
在拟南芥 (Arabidopsis thaliana) 中，466 个五肽重复 (PPR) 蛋白是假定的 RNA 结合蛋白，在细胞器中发挥重要作用。大约一半的 PPR 蛋白形成植物组合和模块化蛋白 (PCMP) 亚家族，这是陆地植物特有的。 PCMP 表现出三个 PPR 变体基序的标准模式的大且可变的串联重复。该重复序列与 C 末端的三个非 PPR 基序的关联或不关联定义了 PCMP 的四种不同类别。这些基序的高度结构化排列以及这些排列在四类中的相似重新分配表明基序组织和底物特异性之间的精确关系。本研究试图重建 PCMP 家族的进化场景。我们开发了一种基于两个水平上蛋白质比较的创新方法：即沿蛋白质的基序序列和基序的氨基酸序列。它使我们能够推断蛋白质之间以及蛋白质间和蛋白质内重复之间的进化关系。首先，我们观察到重复从 C 末端向 N 末端区域的极化延伸，表明基序的局部重组。其次，最N端的PPR三基序被证明在与其余重复不同的约束下进化。总而言之，证据表明 PCMP 中 PPR 区域和 C 端区域的进化不同，这表明这些区域具有不同的功能。此外，跨 PCMP 类别观察到的局部序列同质性可能是由于基序的类间改组，或 C 末端非 PPR 基序的删除/插入。
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.