Pentatricopeptide repeat (PPR) proteins are characterized by tandem repeats of a degenerate 35 amino acid motif [1]. Most of PPR proteins have roles in mitochondria or plastid. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [1,2]. 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 [3,4,5]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins.

Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see <PDOC50005>) [1].

The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organization [6,7]:

• Plant P-subfamily. In the P-subfamily the 35 amino acid repeats are adjacent to each other (i.e. in tandem repeats). This subfamily contains proteins involved in RNA processing (high chlorophyll fluorescence protein 152), translation (chloroplast RNA processing protein 1), splicing (PPR4) and RNA stability (ribosome release factor 1b, PGR3).
• Plant combinatorial and modular proteins (PCMP) subfamily. In the PCMP subfamily classical 35 amino acid repeats are found in association with shorter (31 amino acids) and longer (36 amino acids) repeats. This subfamily contains proteins involved in RNA editing (chlororespiratory reduction proteins 4 and 21) and RNA processing (CRR2, RF1).

Some non-plant PPR proteins are listed below:

• Mammalian leucine-rich PPR motif-containing (LPPRC) protein. It may play a role in translation or stability of mitochondrially encoded cytochrome c oxidase (COX) subunits.
• Drosophila bicoid mRNA stability factor (BSF). BSF binds specifically to bicoid mRNA 3'-untranslated region. BSF plays a role in bicoid RNA stabilization.
• Yeast Pet309 protein. It is involved in translation of the yeast mitochondrial COX1 gene, which encodes subunit I of the cytochrome c oxidase. Pet309 protein is also involved in stabilization of the COX1 mRNA.
• Yeast ATPase expression protein 3 (Aep3). It stabilizes the mitochondrial bicistronic mRNA encoding ATP6 and ATP8, 2 subunits of the proton-translocating ATP synthase.

The profile we developed covers the entire PPR repeat.