Pentatricopeptide Repeat Proteins: In vivo functions and biochemical mechanisms.

The pentatricopeptide repeat (PPR) is a recently recognized repeat motif (Small and Peeters, TIBS, 2000) represented in a very large protein family in plants, and in small protein families in other eucaryotes. Genetic analysis of a handful of PPR proteins suggest that this family plays a particularly central and broad role in modulating the expression of mitochondrial and chloroplast genes. PPR proteins comprise one of the largest protein families in plants (~450 members in Arabidopsis). Prior studies suggest that most PPR proteins mediate specific post-transcriptional steps in organellar gene expression, and that they do so via direct interaction with RNA. Despite their key role as integrators of nuclear and organellar functions, very little is known about the biochemical mechanisms through which PPR proteins act. Extrapolation from data for the related TPR motif suggests that PPR proteins belong to the broader class of helical repeat proteins, and that they might bind RNA along a surface created by stacked helices from consecutive repeating units. We are aiming to establish a biochemical framework for understanding PPR proteins and their mode of RNA recognition through in vitro experiments with PPR proteins whose biological functions and in vivo RNA ligands are well-characterized. The in vivo functions and RNA ligands of selected PPR proteins are established by genetic and RIP-chip assays, respectively. We are currently studying the biophysical properties of several such proteins and their interactions with their native RNA ligands using in vitro assays with purified recombinant proteins.

Publications

Schmitz-Linneweber C, Williams-Carrier R, Williams-Voelker PM, Kroeger TS, Vichas A, and Barkan A. (2006) A pentatricopeptide repeat protein facilitates the trans-splicing of the maize chloroplast rps12 pre-mRNA. Plant Cell, 18: 2650-63.

Schmitz-Linneweber C, Williams-Carrier R, Barkan A. (2005) RNA Immunoprecipitation and Microarray Analysis Show a Chloroplast Pentatricopeptide Repeat Protein to Be Associated with the 5' Region of mRNAs Whose Translation It Activates The Plant Cell 17:2791-2804

Williams P.M. and A. Barkan (2003) A chloroplast-localized PPR protein required for plastid ribosome accumulation. Plant J 365:675-86.

Fisk, D.G., M.B. Walker, and A. Barkan (1999) Molecular cloning of the maize gene crp1 reveals similarity between regulators of mitochondrial and chloroplast gene expression. EMBO J 18:2621-30.

Barkan A, Walker M, Nolasco M, and Johnson D (1994) A nuclear mutation in maize blocks the processing and translation of several chloroplast mRNAs and provides evidence for the differential translation of alternative mRNA forms. EMBO J., 13: 3170-3181.