Formation of the Arabidopsis Pentatricopeptide Repeat Family

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.

The Pentatricopeptide Repeat GeneOTP43Is Required fortrans-Splicing of the Mitochondrialnad1Intron 1 inArabidopsis thaliana

“…In addition to these splicing factors, one highly specific factor has been identified that is required for the trans-splicing of rps12 intron 1 in chloroplasts (SchmitzLinneweber et al, 2006). This rps12 RNA splicing factor is a pentatricopeptide repeat (PPR) protein, one of a very large family in Arabidopsis of at least 450 proteins (Aubourg et al, 2000;Lurin et al, 2004;Rivals et al, 2006). They are characterized by tandemly repeated, degenerate, 35-amino acid motifs and have been proposed to be sequence-specific RNA binding proteins (Small and Peeters, 2000).…”

Insights into PPR Gene Family in Cajanus Cajan and Other Legume Species

“…PRORP (proteinaceous RNaseP) sub-class possess metallonuclease domain which are involved in processing of mitochondrial tRNA, for example arabidopsis PRORP3 protein [20]. The classical P motif when interspersed by L motifs (36 amino acids) and S motifs (31 amino acids) in triplets constitute PLS sub-class, wherein this ordered association could have variable number of S motif repeats [21]. PLS-PPRs also possess additional C terminal domains designated as E (extended), E + (slightly longer than E domain) and DYW (characterised by Asp-Tyr-Trp triplet at terminating end).…”

Multi-relational Data Mining for Tetratricopeptide Repeats (TPR)-Like Superfamily Members in Leishmania spp.: Acting-by-Connecting Proteins

“…PPR-containing proteins (PPRPs) occur predominantly in eukaryotes [10] (particularly abundant in plants), while it has been suggested that each of the highly variable PPRPs is a genespecific regulator of plant organellar RNA metabolism. HAT repeats are less abundant and HAT-containing proteins (HATPs) appear to be components of macromolecular complexes that are required for RNA processing [10][11][12][15][16].…”

“…TPRs exhibit a large degree of sequence diversity and structural conservation (two antiparallel alpha-helices separated by a turn) that might act as scaffolds for the assembly of different multiprotein complexes [13] including the peroxisomal import receptor and the NADPH oxidase [14]. Similar to TPR, PPR and HAT motifs also have repetitive patterns characterized by tandem array of repeats, where the number of motifs seems to influence the affinity and specificity of the repeat-containing protein for RNA [12,[15][16]. PPR-containing proteins (PPRPs) occur predominantly in eukaryotes [10] (particularly abundant in plants), while it has been suggested that each of the highly variable PPRPs is a genespecific regulator of plant organellar RNA metabolism.…”

“…The curvature created by the superhelical nature predetermines the target proteins that can bind to them [20]. TPRs, PPRs and HAT (all together referred as TPR-like motifs), form a large superfamily or the clan TPR-like [7][8][9][10][11][12][13][14][15][16]. Homologous structural repeat units are often highly divergent at the sequence level, a feature that makes their prediction challenging.…”