Biology subjects

Lehniger, M.-K.

Publications and source records attributed to Lehniger, M.-K..

2 recordsLinked to original sources

bioRxiv2019

The Chloroplast RNA binding protein CP31A shows cold-dependent RNA association and mediates cold-resistance via its acidic domain

Chloroplast RNA metabolism is characterized by long-lived mRNAs that undergo a multitude of post-transcriptional processing events. Chloroplast RNA accumulation responds to environmental cues, foremost light and temperature. A large number of nuclear-encoded RNA-binding proteins (RBPs) are required for chloroplast RNA metabolism, but we do not yet know how chloroplast RBPs convert abiotic signals into gene expression changes. Previous studies showed that the chloroplast ribonucleoprotein 31A (CP31A) is required for the stabilization of multiple chloroplast mRNAs in the cold, and that the phosphorylation of CP31A at various residues within its N-terminal acidic domain (AD) can alter its affinity for RNA in vitro. Loss of CP31A leads to cold sensitive plants that exhibit bleached tissue at the center of the vegetative rosette. Here, by applying RIP-Seq, we demonstrated that CP31A shows increased affinity for a large number of chloroplast RNAs in vivo in the cold. Among the main targets of CP31A were RNAs encoding subunits of the NDH complex and loss of CP31A lead to reduced accumulation of ndh transcripts. Deletion analyses revealed that cold-dependent RNA binding and cold resistance of chloroplast development both depend on the AD of CP31A. Together, our analysis established the AD of CP31A as a key mediator of cold acclimation of the chloroplast transcriptome. One sentence summaryCold exposure induces increased RNA association of the RRM protein CP31A, which mediates cold-resistance of Arabidopsis thaliana via its acidic domain

plant biology↗

bioRxiv2019

Metabolic labeling of RNAs uncovers hidden features and dynamics of the Arabidopsis thaliana transcriptome

Transcriptome analysis by RNA sequencing (RNA-seq) has become an indispensable core research tool in modern plant biology. Virtually all RNA-seq studies provide a snapshot of the steady-state transcriptome, which contains valuable information about RNA populations at a given time, but lacks information about the dynamics of RNA synthesis and degradation. Only a few specialized sequencing techniques, such as global run-on sequencing (GRO-seq), have been applied in plants and provide information about RNA synthesis rates. Here, we demonstrate that RNA labeling with a modified, non-toxic uridine analog, 5-ethynyl uridine (5-EU), in Arabidopsis thaliana seedlings provides insight into the dynamic nature of a plant transcriptome. Pulse-labeling with 5-EU allowed the detection and analysis of nascent and unstable RNAs, of RNA processing intermediates generated by splicing, and of chloroplast RNAs. We also conducted pulse-chase experiments with 5-EU, which allowed us to determine RNA stabilities without the need for chemical inhibition of transcription using compounds such as actinomycin and cordycepin. Genome-wide analysis of RNA stabilities by 5-EU pulse-chase experiments revealed that this inhibitor-free RNA stability measurement results in RNA half-lives much shorter than those reported after chemical inhibition of transcription. In summary, our results show that the Arabidopsis nascent transcriptome contains unstable RNAs and RNA processing intermediates, and suggest that half-lives of plant RNAs are largely overestimated. Our results lay the ground for an easy and affordable nascent transcriptome analysis and inhibitor-free analysis of RNA stabilities in plants.

plant biology↗