Pentatricopeptide Repeat Domain-Containing Proteins in Mammals and Budding Yeast

Abstract

Copyright: © 2012 Piva MA, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The pentatricopeptide repeat (PPR) family is composed of three degenerated domains that span between 31 and 36 amino acids [1]. PPR motifs occur in tandem arrays of two to 26 units per protein [2]. Each motif is predicted to comprise two anti-parallel α-helices that contain several projecting amino acidic side groups; therefore the arrays would form a superhelix with a binding surface that is suitable to interact with selected bases [3] and, through basic amino acids, with phosphate groups of RNA molecules [4]. The minimal requirement to bind RNA sequences with high affinity [2] and specificity [5,6] is thought to be a pair of tandem repeats [4]. PPR-containing proteins mainly participate in post-transcriptional events, such as RNA editing [7], translation [8], stability [5], processing [9], and splicing [10]. Nuclear genomes of land plants encode between 400 and 600 members of the PPR family [11], whose products are predicted to be mostly localized in chloroplasts and mitochondria [1]. To date, the TPRpred algorithm [12] has detected seven mammalian PPR proteins [13], albeit with different probabilities (indicated as percentage between parenthesis immediately after the abbreviated name): leucine-rich pentatricopeptide repeat cassette protein (LRPPRC; 100%), mitochondrial DNA-directed (MtRPOL; 2%), RNA polymerase (mitochondrial protein of the small subunit 27 (MRPS27; 93%), mitochondrial RNase P protein 3 (MRPP3; 10%), pentatricopeptide repeat-containing protein 1 (PTCD1; 100%), pentatricopeptide repeat-containing protein 2 (PTCD2; 97%), and pentatricopeptide repeat-containing protein 3 (PTCD3; 100%). These proteins are predicted to contain between two and 20 PPR domains. However, only a few of these motifs have been experimentally proven to be involved in the activity of the corresponding protein. The nuclearencoded LRPPRC has 20 PPR motifs, arrayed in four clusters of six, two, four, and seven, respectively. The last motif stands alone. Even though 19 N-terminal PPR domains are required for full RNA binding activity in vitro, the replacement by β-galactosidase of the last 120 C-terminal amino acids (1272–1392), which deletes 15 amino acids of the 19th motif and the entire 20th motif, causes embryonic lethality in mice [6]. LRPPRC localizes in the mitochondria matrix and forms an RNA-dependent complex with the stem-loop interacting RNA binding protein (SLIRP) that stabilizes mRNAs encoded by the mitochondrial DNA H strand [14]. A single alanine to valine mutation (A354V) [15] located outside the PPR motifs, restricts the import of LRPPRC protein into mitochondria [16]. This replacement causes a severe form of Leigh syndrome, characterized by cytochrome c oxidase deficiency that leads to metabolic and/ or neurological fatal episodes [15,17]. The structure of a single-subunit RNA polymerase transcribes the human mitochondrial genome [18] has been solved [19]. It possesses two PPR motifs in tandem, between amino acids 263-296 and 297-330, spatially separated from the active site. The PPR domains are indirectly important for enzymatic activity: when deleted, the polymerase cannot initiate transcription [19]. MRPS27 has been annotated as a member of the mitoribosome small subunit [20] and is predicted to possess six PPR motifs. MRPS27 associates to the Era G-protein-like1 (ERAL1), a RNA chaperone that contributes to the assembly of the mitoribosome small subunit by protecting the ribosomal RNA (rRNA) from degradation [21]. PTCD1 is a mitochondrial matrix protein [22] with nine predicted PPR domains. PTCD1 binds to leucyl-tRNAs and reduces their levels, thus negatively affecting mitochondrial translation in osteosarcoma cell lines [22]. PTCD2 has five predicted PPR domains and is required to process the NADH dehydrogenase subunit 5 (ND5)cytochrome b (COB) pre-mRNA into the corresponding mature transcripts. Lack of PTCD2 causes a dramatic decrease of complex III activity, especially in the heart [23]. PTCD3 has 15 predicted PPR motifs and specifically binds the rRNA of the mitoribosome small subunit, but it is not required for rRNA stability [24]. PTCD3 is now considered a constitutive member of the mitochondrial ribosome [25], even though it has also been found in the mitochondrial transcriptional complex along with transcripts, RNA polymerase, and a putative RNA helicase [26].