The Chloroplast RNA binding protein CP31A shows cold-dependent RNA association and mediates cold-resistance via its acidic domain

Abstract

Chloroplast RNA metabolism is characterized by long-lived mRNAs that undergo a multitude of post-transcriptional processing events. Chloroplast RNA accumulation responds to environmental cues, foremost light and temperature. A large number of nuclear-encoded RNA-binding proteins (RBPs) are required for chloroplast RNA metabolism, but we do not yet know how chloroplast RBPs convert abiotic signals into gene expression changes. Previous studies showed that the chloroplast ribonucleoprotein 31A (CP31A) is required for the stabilization of multiple chloroplast mRNAs in the cold, and that the phosphorylation of CP31A at various residues within its N-terminal acidic domain (AD) can alter its affinity for RNA in vitro. Loss of CP31A leads to cold sensitive plants that exhibit bleached tissue at the center of the vegetative rosette. Here, by applying RIP-Seq, we demonstrated that CP31A shows increased affinity for a large number of chloroplast RNAs in vivo in the cold. Among the main targets of CP31A were RNAs encoding subunits of the NDH complex and loss of CP31A lead to reduced accumulation of ndh transcripts. Deletion analyses revealed that cold-dependent RNA binding and cold resistance of chloroplast development both depend on the AD of CP31A. Together, our analysis established the AD of CP31A as a key mediator of cold acclimation of the chloroplast transcriptome. One sentence summaryCold exposure induces increased RNA association of the RRM protein CP31A, which mediates cold-resistance of Arabidopsis thaliana via its acidic domain