Academic journal article Genetics

DMR1 (CCM1/YGR150C) of Saccharomyces Cerevisiae Encodes an RNA-Binding Protein from the Pentatricopeptide Repeat Family Required for the Maintenance of the Mitochondrial 15S Ribosomal RNA

Academic journal article Genetics

DMR1 (CCM1/YGR150C) of Saccharomyces Cerevisiae Encodes an RNA-Binding Protein from the Pentatricopeptide Repeat Family Required for the Maintenance of the Mitochondrial 15S Ribosomal RNA

Article excerpt

ABSTRACT

Pentatricopeptide repeat (PPR) proteins form the largest known RNA-binding protein family and are found in all eukaryotes, being particularly abundant in higher plants. PPR proteins localize mostly in mitochondria and chloroplasts, where they modulate organellar genome expression on the post-transcriptional level. The Saccharomyces cerevisiae DMR1 (CCM1, YGR150C) encodes a PPR protein that localizes to mitochondria. Deletion of DMR1 results in a complete and irreversible loss of respiratory capacity and loss of wild-type mtDNA by conversion to ρ^sup -^/ρ^sup 0^ petites, regardless of the presence of introns in mtDNA. The phenotype of the dmr1Δ mitochondria is characterized by fragmentation of the small subunit mitochondrial rRNA (15S rRNA), that can be reversed by wild-type Dmr1p. Other mitochondrial transcripts, including the large subunit mitochondrial rRNA (21S rRNA), are not affected by the lack of Dmr1p. The purified Dmr1 protein specifically binds to different regions of 15S rRNA in vitro, consistent with the deletion phenotype. Dmr1p is therefore the first yeast PPR protein, which has an rRNA target and is probably involved in the biogenesis of mitochondrial ribosomes and translation.

PROGRESS in plant genomics, particularly sequencing of the Arabidopsis thaliana genome, led to the discovery of a large protein family characterized by tandem repeats of a degenerate 35-amino-acid motif and thus named the pentatricopeptide repeat (PPR) family (Small and Peeters 2000; Lurin et al. 2004). This family underwent a striking expansion in terrestrial plants, with typical genomes encoding several hundred PPR proteins; their presence is, however, a common feature of all eukaryotic lineages, including protists, metazoa, and fungi. The number of confirmed PPR proteins encoded by nonplant genomes ranges from ∼30 in protists to 7 in humans and 3 in Saccharomyces cerevisiae (Lightowlers and Chrzanowska-Lightowlers 2008; Schmitz-Linneweber and Sluyter 2008; Davies et al. 2009); it should be noted, however, that due to the degenerate nature of the pentatricopeptidemotif, these numbers may not be exact.

Two common features of the PPR family are the organellar localization and RNA binding. About 50% of the A. thaliana PPR proteins are predicted to be targeted to mitochondria, and 25% to chloroplasts using in silico methods (Lurin et al. 2004). All the seven human PPR proteins are predicted to be mitochondrial, and functional analysis confirms their role in the expression of the mitochondrial genome (Lightowlers and Chrzanowska-Lightowlers 2008; Davies et al. 2009). Three yeast proteins that can be unambiguously assigned to the PPR family: Pet309p (Manthey and McEwen 1995; Perez-Martinez et al. 2003; Tavares-Carreon et al. 2008), Aep3p (Ellis et al. 2004), and Dmr1p also have mitochondrial localization and function. Involvement in mitochondrial genome expression was also confirmed for PPR proteins in Trypanosoma (Pusnik et al. 2007). In contrast, cytoplasmic (Mancebo et al. 2001) or nuclear (Ding et al. 2006) localization of PPR proteins was found only in a few cases. The vast majority of PPR proteins are therefore targeted to mitochondria and/or chloroplasts.

Structural predictions as well as available genetic and biochemical data suggest that the PPR proteins bind RNA and participate in various post-transcriptional steps of organellar gene expression (Andres et al. 2007; Delannoy et al. 2007; Pusnik et al. 2007; Lightowlers and Chrzanowska-Lightowlers 2008; Schmitz- Linneweber and Sluyter 2008). The PPR motif is structurally (and presumably also phylogenetically) related to the tetratricopeptide repeat (TPR) motif, which mediates protein-protein interactions (Blatch and Lassle 1999). A single PPR motif consists of a pair of antiparallel a-helices (A and B) forming in tandem arrays a superhelix that encloses a central groove-a putative ligand-binding site. While in TPR motifs the residues projecting into the groove vary considerably (Das et al. …

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