Toward a Mechanistic Understanding Of The Roles Of Pentatricopeptide Repeat Proteins In Organellar Gene Expression: Beyond The Code For RNA Recognition

The pentatricopeptide repeat (PPR) protein family is a remarkable family of RNA binding proteins that holds special promise for the rational design of specified RNA binding properties and for the engineering of switches to control organelle gene expression. PPR proteins harbor tandem arrays of a degenerate helical repeat that form a surface for binding single-stranded RNA. Virtually all PPR proteins localize to mitochondria or chloroplasts, where they influence the editing, splicing, stability, translation, or processing of one or several RNAs. PPR tracts bind RNA via a modular 1-repeat/1-nt mechanism, and they have the potential to form RNA binding surfaces of unprecedented length. These features underlie the unusual evolutionary history and functional repertoire of the PPR family. For example, the ability of a PPR tract to sequester a long RNA segment can account for many reported effects of PPR proteins on RNA processing, stability and translation.  In collaboration with Ian Small’s group, we demonstrated a “code” for nucleotide recognition involving two amino acids in each PPR motif. The simplicity of these mechanisms suggests that PPR proteins can be exploited to modulate RNA function both within and outside of their natural organellar context. However, the prediction of binding site repertoires for PPR tracts remains problematic due to gaps in our understanding of PPR-RNA interactions. I will discuss the challenges ahead, as we seek to develop this understanding to the point that we can reliably predict the repertoire of binding sites for natural PPR proteins, and design PPR tracts with desired RNA sequence specificities and affinities.