The Chloroplast Ribonucleoprotein CP33B Quantitatively Binds the psbA mRNA

Abstract

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 <i>psbA</i> mRNA, which shows light-dependent translation. Recently, the chloroplast ribonucleoprotein CP33B was identified as a ligand of the <i>psbA</i> 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 <i>psbA</i> over all other chloroplast RNAs and associates with the vast majority of the <i>psbA</i> transcript pool. The RNA sequence target motif, determined in vitro, does not fully explain CP33B’s preference for <i>psbA</i>, suggesting that there are other determinants of specificity in vivo.