Proteins are shared among RNA-protein complexes that form in the 5′ untranslated regions of spinach chloroplast mRNAs

Gene expression in chloroplasts is strongly regulated at the post-transcriptional level. Most post-transcriptional mechanisms require RNA-protein complexes. Here we report an analysis of RNA-protein complexes that form in the 5′ untranslated regions (5′UTRs) of spinach chloroplast mRNAs. Previous studies from our laboratory showed that four ATP synthase 5′UTRs were able to compete with each other for binding by proteins in a chloroplast extract. This implied that at least some of the binding proteins recognized all four of those ATP synthase 5′UTRs. Here, we examine whether the binding proteins are ATP synthase-specific by performing competition-binding assays between an ATP synthase 5′UTR and 5′UTRs from other chloroplast genes. Competition substrates were chosen to represent a wide range of chloroplast mRNAs, including those encoding the photosystems, NADH dehydrogenase, cytochromes and ribosomal subunits, and two previously unexamined ATP synthase subunits. Results from these experiments revealed that, although the ATP synthase-binding proteins do not bind universally to every chloroplast 5′UTR, they do bind to the majority (12/14) of those examined. Thus, these RNA-binding proteins are candidates for factors that link the post-transcriptional expression of many chloroplast genes of disparate function.