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PPR proteins are universal in eukaryotes, however, they are particularly numerous in higher plants. Bioinformatic analyses predict that PPR proteins are putative RNA binding proteins targeted to organelles for most of them. So PPR proteins should be involved in many plant specific processes involving RNA, especially in organelles.....

Gene expression processes in plant mitochondria

The expression of mitochondrial genes is completely dependent of nuclear encoded factors. Indeed, for their expression, mitochondrial genes must be transcribed, their RNAs undergo a number of post-transcriptional maturations and they are translated. In plants, post-transcriptional processes include in particular, the maturation of transcript ends, splicing of group II introns and RNA editing. Most of these gene expression processes are specific from higher plant mitochondria and rely entirely on proteins imported from the cytosol. Then, transcripts are translated by a mitochondrial specific translation machinery and can be degraded by a specific degradation process involving polyadenylation. The nature of most proteins involved in these post-transcriptional processes has remained elusive for a very long time. The breakthrough came with the discovery of the pentatricopeptide repeat (PPR) protein family a decade ago. In 2000, as a consequence of the sequencing of Arabidopsis nuclear genome, a novel gene family, unaccounted until this time, representing up to 1 % of the genome was identified. The genes composing this family contained tandem repeats of motifs resembling and evolutively related to tetratricopeptide repeat (TPR) motifs. Hence, it was called PPR (for “pentatricopeptide repeat”) because the tandem repeated PPR motifs are composed of 35 amino acids. PPR proteins were proposed to be putative RNA binding proteins predicted to be localised to organelles for most of them.  Thus, it was proposed that PPR proteins would probably be involved in post-transcriptional processes in plant organelles. A fast growing number of studies now indeed relate the function of all the mitochondrial specific gene expression processes with PPR proteins.

ppr domain structure

Three dimensional domain of PPR proteins, individual PPR repeats and the alpha superhelices formed by the succession of PPR repeats

Communication pathways between mitochondria and the nucleus

Mitochondria are semi-autonomous organelles that have arisen from an endosymbiotic event. They have retained a genome and harbour a complete gene expression machinery. However, the vast majority of mitochondrial proteins are encoded in the nucleus and have to be imported into mitochondria from the cytosol. Thus, mitochondrial biogenesis relies heavily on the coordinated expression of nuclear encoded genes. The mechanisms underlying this coordination and their regulation remain poorly understood. We have recently identified PNM1, a pentatricopeptide repeat (PPR) protein, dual localized to both mitochondria and the nucleus, which could be involved in this regulation. PPR proteins are ubiquitous in eukaryotes but particularly prevalent in higher plants. Most of them are predicted to localize to organelles and to be involved in post-transcriptional processes. In the nucleus PNM1 binds proteins involved in regulating gene expression, especially a TCP transcription factor. This class of proteins was recently shown to control the expression of nuclear genes encoding mitochondrial proteins that contain cis-acting “site II” regulatory elements in their promoter regions. The analysis of mutant plants showed that some genes with site II elements have increased expression levels when PNM1 is not present in the nucleus. This suggests that PNM1 might act as a negative regulator for the expression of an unknown number of genes with site II elements. Altogether, PNM1 might act as a nuclear regulator and / or could be a retrograde messenger molecule from mitochondria to the nucleus for the fine-tuning of nuclear gene expression required for mitochondrial biogenesis.

Confocal imaging and electron microscopy showing the nucleo / mitochondrial localisation of PNMI

tRNA 5’ maturation in eukaryotes

Similar to most transcripts, tRNAs are expressed as precursor molecules. Among the essential tRNA maturation steps, the 5’ leader sequences of tRNAs are removed by an endonuclease called RNase P. This virtually universal enzyme is thus essential to obtain functional tRNAs and is therefore pivotal for translation. RNase P activities from all phyla of life were assumed to be universally performed by ribonucleoprotein enzymes whose catalytic activities are held by ribozymes. This concept was challenged with the recent discovery of protein-only RNase P enzymes called PRORP (for “Proteinaceous RNase P”) in both endosymbiotic organelles and the nucleus of a wide range of eukaryote species. It appears that ribonucleoprotein enzymes have been entirely replaced by proteins for RNase P activity in plants and other eukaryotes. PRORP enzymes are composed of an N-terminal RNA binding domain composed of PPR repeats as well a C-terminal catalytic domain belonging to the NYN family. Beyond tRNAs, PRORP proteins are involved in the maturation of other RNA species such as snoRNA and mRNA. The comparison of PRORP mode of action with ribonucleoprotein RNases P suggests that PRORP proteins have evolved a tRNA recognition process similar to that of ribonucleoprotein RNase P. The comparison of the two systems will give clues to understand the transition from the prebiotic “RNA world” to the present day protein dominated world.


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