Pentatricopeptide repeat proteins: I. Involvement in RNA editing in plants

ABSTRACT

Pentatricopeptide repeat (PPR) proteins are encoded in the nucleus and transported to the cell organelles to perform several specific functions, including RNA editing. The modular RNA-specific binding property of the PPR proteins has been extensively used for regulating organellar gene expression in some lower eukaryotes, mammals, and plants. In this review, we focus on the present understanding of the structural–functional relationship in PPR proteins, in three plant species, namely, Arabidopsis thaliana, Zea mays, and Oryza sativa. On the basis of their motif structure, the PPR proteins comprise two major subfamilies, “P” and “PLS”. Based on the domain/motif structure, we have categorized the P subfamily into 4 subgroups, viz., P/DYW like, P/RRM, P/SMR, and P/PRORP; and the PLS subfamily into three subgroups, viz., PLS/E, PLS/E+ and PLS/DYW among the three species to relate their structure with their function(s). On the basis of function(s), they perform, PPR proteins have been classified into two types: first, those proteins that are not involved in RNA editing and, second, those proteins that mediate RNA editing. Structural features of the PPR proteins that are involved in RNA editing are discussed here. Understanding of PPR protein-RNA binding code has led to the development of designer PPR proteins that have proven useful in understanding various post-transcriptional processes, such as RNA editing and development of programmable RNA-editing technology. In the accompanying review article, we discuss prospects of application of designer PPR proteins for crop improvement.

KEYWORDS:

• Designer PPR proteins
• gene expression regulation
• natural PPR proteins
• pentatricopeptide repeat proteins
• PPR protein-RNA binding code