The Chloroplast RNA Binding Protein CP29A supportsrbcLexpression during cold acclimation

Abstract

The chloroplast genome encodes key components of the photosynthetic light reaction machinery and the large subunit of the enzyme central for carbon fixation, RuBisCo. Plants constantly face the challenge of balancing light and dark reactions under varying environmental conditions. Nuclear RNA binding proteins (RBPs) play a crucial role in plant acclimation to these changes through post-transcriptional processes. Mutants of chloroplast gene expression factors often exhibit impaired chloroplast biogenesis, especially in cold conditions. Cold temperatures pose a challenge for plants as they slow down Calvin Cycle enzymes, potentially leading to a shortage of electron acceptors and oxidative damage from excess electrons in the thylakoid membrane. A well-known response of plants to this problem is to increase the production of RuBisCo and other Calvin Cycle enzymes in the cold. The chloroplast RNA binding protein CP29A targetsrbcLmRNA and is essential for cold resistance inArabidopsis thaliana. This effect is confined to the youngest leaf tissue and is linked to its role in enhancing the splicing of various chloroplast RNAs in cold conditions. In this study, we utilized enhanced cross-linking and immunoprecipitation (eCLIP) and RNA- Bind-N-Seq (RBNS) to investigate the RNA targets of CP29A, achieving nucleotide-resolution insights into protein-RNA interaction sites. We discovered that CP29A preferentially binds to mRNAs encoding subunits of photosystem II. Notably, one of the most confidently identified targets of CP29A is the 5’-UTR ofrbcL, where it interacts with a site downstream of the pentatricopeptide repeat protein MRL1, a crucial player inrbcLaccumulation. Arabidopsis mutants lacking CP29A showed no significantrbcLchanges, possibly due to CP29A’s restricted role in a limited number of cells at the base of leaves. In contrast, CRISPR mutants of tobaccoNtCP29Aexhibit photosynthetic deficiencies throughout the entire leaf blade, correlating with a substantial decrease in bothrbcLmRNA and RbcL protein levels. Conclusively, our study establishes CP29A as a pioneer regulator in sustaining optimal RuBisCo expression during cold acclimation, highlighting its integral role in plant cold response mechanisms.