Functions of PPR proteins

Group leader : Philippe GIEGE

Research area

The team research mainly focuses on pentatricopeptide repeat (PPR) proteins, a pivotal class of RNA binding proteins universally found in eukaryotes. Their function is mostly related to the biogenesis of organelles through the fulfilment of essential gene expression processes. Research on PPR proteins has extremely wide implications, going from human health to agriculture. The team contributes to the characterisation of the functional and mechanistic diversity of PPR proteins.

With this research, the team investigates the functional diversity that these essential factors have acquired during the evolution of eukaryotes. In particular, the function of specific PPR proteins called PRORP involved in RNase P activity is explored. Their mode of action is deciphered and interaction networks are determined. Their evolutionary diversity is investigated through the functional characterisation of PRORP in representative model eukaryotes. Because PRORPs have a NYN catalytic domain, we also investigate the diversity of NYN nucleases in plants.

The function of PPR proteins for plant mitochondrial translation is also investigated with a combination of biochemical, structural and reverse genetic approaches. Altogether, this research should help revealing how PPR functions are integrated within the plant cell and how they affect plant physiology.

The team is part of the LabEx consortium MitoCross. It is also funded by different ANR grants.

Projects

Involvement of PPR proteins for plant mitochondria translation

Translation remains the most elusive step of gene expression in plant organelles. The specificities of the translation apparatus in plant mitochondria are investigated by a combination of biochemical and structural approaches, i.e. by single particle cryo-electron microscopy. Results show that Arabidopsis mitoribosomes are characterized by numerous additional protein subunits, in particular PPR proteins, whose exact functions are investigated by reverse genetic methods.

Diversity of NYN nucleases for RNA maturation in organelles

Beyond PRORP proteins that hold RNase P activity, we study other NYN domain nucleases that represent the diversity of these enzymes in plants. One of them, YacP participates in the maturation of mRNAs in chloroplasts. Another enzyme, MNU2 interacts with the PRORP1 protein located in the mitochondria. The study of this NYN domain enzyme complex will help to understand its role in mitochondrial gene expression.

Functions and diversity of PRORP proteins

The integration of PRORP functions within the overall framework of the plant cell is determined through the characterization of PRORP interactomes with proteins and RNA. In order to understand the diversity and evolution of PRORP proteins, these enzymes are characterized in the green alga Chlamydomonas, the malaria parasite Plasmodium and the nematode Romanomermis. The detailed understanding of the diversity of PRORP proteins and comparisons with ribonucleoprotein RNase P are expected to give clues to understand the transition from the prebiotic RNA world to today’s world dominated by proteins.

PRORP proteins mode of action

Specificities of PPR proteins mode of action are exemplarily investigated for PRORP proteins. This project is based on biophysical analyses of these enzymes, in particular, through crystallographic and solution structure analyses of PRORP proteins alone and in complex with pre-tRNA substrates. The dynamics and kinetic parameters of this complex are also analysed with an array of biochemical and biophysical approaches.

PPR proteins for virus resistance

Many plant viruses are characterized by the occurrence of essential tRNA-like structures (TLS) at the 3’ end of their genomic RNA. Because virus replication takes place in the cytosol, the targeting signal of PRORP enzymes is manipulated to induce PRORP accumulation in the cytosol and the cleavage of viral TLS, leading to an arrest of virus replication. After an anlaysis with Arabidopsis and the TYMV, this biotechnological application will be evaluated with plants of economic relevance and an array of plant viruses.

Members

Selected publications

  • WALTZ F., NGUYEN T.T., ARRIVÉ M., BOCHLER A., CHICHER J., HAMMANN P., KUHN L., QUADRADO M., MIREAU H., HASHEM Y. and GIEGÉ P.

    Small is big in Arabidopsis mitochondrial ribosome

    Nature Plants, 5:106-117, 2019. | DOI : 10.1038/s41477-018-0339-yDOI logo

  • BONNARD G., GOBERT A., PINKER F., ARRIVÉ M., SALINAS-GIEGÉ T. and GIEGÉ P.

    Transfer RNA maturation in Chlamydomonas mitochondria, chloroplast and the nucleus by a single RNase P protein

    Plant Journal, 87(3):270-280, 2016. | DOI : 10.1111/tpj.13198DOI logo

  • GOBERT A., PINKER F., FUCHSBAUER O., GUTMANN B., BOUTIN R., ROBLIN P., SAUTER C. and GIEGÉ P.

    Structural insights into protein-only RNase P complexed with tRNA

    Nature Communications, 4:1353, 2013. | DOI : 10.1038/ncomms2358DOI logo

  • GUTMANN B., GOBERT A. and GIEGÉ P.

    PRORP proteins support RNase P activity in both organelles and the nucleus in Arabidopsis

    Genes and Development, 26(10):1022-7, 2012. | DOI : 10.1101/gad.189514.112DOI logo

  • GOBERT A., GUTMANN B., TASCHNER A., GOESSRINGER M., HOLZMANN J., HARTMANN R., ROSSMANITH W. and GIEGÉ P.

    A single Arabidopsis organellar protein has RNase P activity.

    Nature Structural and Molecular Biology, :17, 740-744, 2010.