Ribonomics of Abundant Chloroplast RNA Binding Proteins

Chloroplast gene expression depends on hundreds of nuclear-encoded DNA- and RNA-binding proteins (RBPs). Most of the hitherto analyzed RBPs are highly specific RNA adaptors and show little expression variation under the various conditions tested. These are unlikely to be global regulators of gene expression. By contrast, there is a family of chloroplast proteins named cpRNPs that are sensitive to light, developmental and temperature signals. Also, they are post-translationally modified in response to light, which changes their affinity to RNA.

We identified the genome-wide RNA ligands of cpRNPs using ribonomics approaches and show that they are required for the stability and processing of most chloroplast mRNAs. Two of the ten cpRNPs in Arabidopsis are particularly important under cold stress conditions and one other is essential for seedling development. Since cpRNPs are most closely related to nuclear (and not cyanobacterial) RRM proteins, we conclude that they are a eukaryotic invention to manipulate large sets of chloroplast RNAs under changing environmental conditions.