RNA-protein interaction mediating post-transcriptional regulation in the circadian system

The pepper RNA-binding protein CaRBP1 functions in hypersensitive cell death and defense signaling in the cytoplasm

The regulation of gene expression via post-transcriptional modification by RNA-binding proteins is crucial for plant disease and innate immunity. Here, we report the identification of the pepper (Capsicum annuum) RNA-binding protein1 gene (CaRBP1) as essential for hypersensitive cell death and defense signaling in the cytoplasm. CaRBP1 contains an RNA recognition motif and is rapidly and strongly induced in pepper by avirulent Xanthomonas campestris pv. vesicatoria (Xcv) infection. CaRBP1 displays in vitro RNA- and DNA-binding activity and in planta nucleocytoplasmic localization. Transient expression of CaRBP1 in pepper leaves triggers cell-death and defense responses. Notably, cytoplasmic localization of CaRBP1, mediated by the N-terminal region of CaRBP1, is essential for the hypersensitive cell-death response. Silencing of CaRBP1 in pepper plants significantly enhances susceptibility to avirulent Xcv infection. This is accompanied by compromised hypersensitive cell death, production of reactive oxygen species in oxidative bursts, expression of defense marker genes and accumulation of endogenous salicylic acid and jasmonic acid. Over-expression of CaRBP1 in Arabidopsis confers reduced susceptibility to infection by the biotrophic oomycete Hyaloperonospora arabidopsidis. Together, these results suggest that cytoplasmic localization of CaRBP1 is required for plant signaling of hypersensitive cell-death and defense responses.

Quantitative analysis of single-molecule RNA-protein interaction

RNA-binding proteins impact gene expression at the posttranscriptional level by interacting with cognate cis elements within the transcripts. Here, we apply dynamic single-molecule force spectroscopy to study the interaction of the Arabidopsis glycine-rich RNA-binding protein AtGRP8 with its RNA target. A dwell-time-dependent analysis of the single-molecule data in combination with competition assays and site-directed mutagenesis of both the RNA target and the RNA-binding domain of the protein allowed us to distinguish and quantify two different binding modes. For dwell times <0.21 s an unspecific complex with a lifetime of 0.56 s is observed, whereas dwell times >0.33 s result in a specific interaction with a lifetime of 208 s. The corresponding reaction lengths are 0.28 nm for the unspecific and 0.55 nm for the specific AtGRP8-RNA interactions, indicating formation of a tighter complex with increasing dwell time. These two binding modes cannot be dissected in ensemble experiments. Quantitative titration in RNA bandshift experiments yields an ensemble-averaged equilibrium constant of dissociation of KD = 2 x 10(-7) M. Assuming comparable on-rates for the specific and nonspecific binding modes allows us to estimate their free energies as DeltaG0 = -42 kJ/mol and DeltaG0 = -28 kJ/mol for the specific and nonspecific binding modes, respectively. Thus, we show that single-molecule force spectroscopy with a refined statistical analysis is a potent tool for the analysis of protein-RNA interactions without the drawback of ensemble averaging. This makes it possible to discriminate between different binding modes or sites and to analyze them quantitatively. We propose that this method could be applied to complex interactions of biomolecules in general, and be of particular interest for the investigation of multivalent binding reactions.