Chloroplast mRNAs show a tight coordination across various environmental conditions. This is not a function of transcriptional, but rather of post-transcriptional regulation. Strikingly, their half-lives are massively extended relative to the on in their bacterial ancestors, a prerequisite for extensive post-transcriptional control. In the past, highly specific RNA binding proteins, in particular from the PPR class, have been demonstrated to protect selected, individual mRNAs. How RNA stabilization is coordinated over larger pools of transcripts remains uncharted. This proposal focuses on nuclear-encoded, chloroplast RRM proteins that are characterized by their ability to associate with multiple chloroplast target RNAs. These so-called cpRNPs are related to eukaryotic hnRNPs and are believed to affect their target’s RNA stability and RNA processing – conclusions based mostly on in vitro analyses. The in vivo mechanisms behind these functions remains unclear. By using a combination of ERIC-Seq, iCLIP and reverse genetics, we intend to decode the cpRNPs’ target sites in vivo and connect them with functional insights into the mechanisms of chloroplast RNA stabilization.

Szabo EX, Reichert P, Lehniger MK, Ohmer M, de Francisco Amorim M, Gowik U, Schmitz-Linneweber C, Laubinger S.
Metabolic Labeling of RNAs Uncovers Hidden Features and Dynamics of the Arabidopsis Transcriptome. Plant Cell. 2020;32(4):871-887. doi: 10.1105/tpc.19.00214.

Teubner M, Fuß J, Kühn K, Krause K, Schmitz-Linneweber C.
The RNA recognition motif protein CP33A is a global ligand of chloroplast mRNAs and is essential for plastid biogenesis and plant development. Plant J. 2017; 89(3):472-485. doi: 10.1111/tpj.13396.

Kupsch C, Ruwe R, Gusewski S, Tillich M, Small I, Schmitz-Linneweber C.
Arabidopsis chloroplast RNA binding proteins CP31A and CP29A associate with large transcript pools and confer cold stress tolerance by influencing multiple chloroplast RNA processing steps Plant Cell. 2012;24(10):4266-80. doi: 10.1105/tpc.112.103002