The Chloroplast Ribonucleoprotein CP33B Quantitatively Binds the mRNA.

Chloroplast RNAs are stabilized and processed by a multitude of nuclear-encoded RNA-binding proteins, often in response to external stimuli like light and temperature. A particularly interesting RNA-based regulation occurs with the mRNA, which shows light-dependent translation. Recently, the chloroplast ribonucleoprotein CP33B was identified as a ligand of the mRNA. We here characterized the interaction of CP33B with chloroplast RNAs in greater detail using a combination of RIP-chip, quantitative dot-blot, and RNA-Bind-n-Seq experiments. We demonstrate that CP33B prefers over all other chloroplast RNAs and associates with the vast majority of the transcript pool. The RNA sequence target motif, determined in vitro, does not fully explain CP33B's preference for , suggesting that there are other determinants of specificity in vivo.