Chloroplast RNA-binding proteins: repair and regulation of chloroplast transcripts

Chloroplast RNA metabolism has greatly diverged from the cyanobacterial ancestral state. The number of processing sites per transcript has increased and novel processing steps not found in bacteria have been acquired. Whereas many of the processing steps are essential for chloroplast development, it is unclear why such steps evolved at all. In this article, two hypotheses seeking to explain the complexity of chloroplast RNA metabolism are explored: the genomic debugging hypothesis and the nuclear regulation hypothesis. The nuclear-encoded RNA processing factors underlying these two alternative, but not mutually exclusive, hypotheses have very different characteristics. We propose that pentatricopeptide repeat (PPR) proteins, with high sequence specificity and essential roles in various RNA-processing steps, act largely as genomic debuggers. By contrast, the chloroplast ribonucleoproteins (cpRNPs), which are strongly modulated by external and internal stimuli, are suggested to be major players in transducing signals to the chloroplast transcript pool.