Complex formation of the spinach chloroplast psbA mRNA 5' untranslated region with proteins is dependent on the RNA structure.

RNA-protein interactions are part of many regulatory pathways in gene expression. In chloroplasts of higher plants and of green algae, gene regulation by posttranscriptional processes such as differential regulation of mRNA stability and control of translation plays a major role during chloroplast development and light-dependent protein expression. Regulation here is mediated by interactions of RNA-binding proteins with the respective mRNAs. In this work, structural requirements for protein-RNA complex formation between the 5' untranslated region of the spinach psbA mRNA (encoding the D1 protein of photosystem II) and stromal proteins are analyzed. For this, a combination of temperature gradient gel electrophoresis and gel shift analysis is employed to study several variants of the psbA 5' untranslated region. Supported by theoretical interpretation of the data and analysis of the structures by chemical probing, we show that a certain structure of the RNA is necessary for protein complex formation. Already very subtle structural changes within the RNA interfere with binding and thereby with the biological activity of the mRNA.