BackgroundThe complexity of RNA regulation is one of the current frontiers in animal and plant molecular biology research. RNA-binding proteins (RBPs) are characteristically involved in post-transcriptional gene regulation through interaction with RNA. Recently, the mRNA-bound proteome of mammalian cell lines has been successfully cataloged using a new method called interactome capture. This method relies on UV crosslinking of proteins to RNA, purifying the mRNA using complementary oligo-dT beads and identifying the crosslinked proteins using mass spectrometry. We describe here an optimized system of mRNA interactome capture for Arabidopsis thaliana leaf mesophyll protoplasts, a cell type often used in functional cellular assays.ResultsWe established the conditions for optimal protein yield, namely the amount of starting tissue, the duration of UV irradiation and the effect of UV intensity. We demonstrated high efficiency mRNA-protein pull-down by oligo-d(T)25 bead capture. Proteins annotated to have RNA-binding capacity were overrepresented in the obtained medium scale mRNA-bound proteome, indicating the specificity of the method and providing in vivo UV crosslinking experimental evidence for several candidate RBPs from leaf mesophyll protoplasts.ConclusionsThe described method, applied to plant cells, allows identifying proteins as having the capacity to bind mRNA directly. The method can now be scaled and applied to other plant cell types and species to contribute to the comprehensive description of the RBP proteome of plants.Electronic supplementary materialThe online version of this article (doi:10.1186/s13007-016-0142-6) contains supplementary material, which is available to authorized users.

We analyze in detail how the interplay between electronic structure and cluster geometry determines the stability and the fragmentation channels of single Pd-doped cationic Au clusters, PdAu N −1 + (N = 2−20). For this purpose, a combination of photofragmentation experiments and density functional theory calculations was employed. A remarkable agreement between the experiment and the calculations is obtained. Pd doping is found to modify the structure of the Au clusters, in particular altering the two-dimensional to three-dimensional transition size, with direct consequences on the stability of the clusters. Analysis of the electronic density of states of the clusters shows that depending on cluster size, Pd delocalizes one 4d electron, giving an enhanced stability to PdAu 6 + , or remains with all 4d 10 electrons localized, closing an electronic shell in PdAu 9 +. Furthermore, it is observed that for most clusters, Au evaporation is the lowest-energy decay channel, although for some sizes Pd evaporation competes. In particular, PdAu 7 + and PdAu 9 + decay by Pd evaporation due to the high stability of the Au 7 + and Au 9 + fragmentation products.

Far-infrared multiple photon dissociation spectroscopy is used in combination with density functional theory calculations to determine the structures of isolated Aun+ (n ≤ 9) clusters.

The reactivity of small metallic clusters, nanoparticles composed of a countable number of atoms (typically up to ~100 atoms), has attracted much attention due to the fascinating properties these objects possess toward a variety of molecules. Cluster reactivity often is significantly different from the homologous bulk, with gold as prototypical example. Bulk gold is the noblest of all metals, whereas small gold clusters react with carbon monoxide, molecular oxygen, and hydrocarbons, among others. Furthermore, cluster reactivity is strongly size and composition dependent, allowing a wide range of tuning possibilities.The study of cluster reactivity usually follows two routes of investigation. In the first, research aims for fundamental understanding of mechanisms, mainly driven by curiosity. One consequence of the inherent small size of a cluster is that atoms can arrange themselves very differently from the crystallographic structure of the homologous bulk. In addition, quantum confinement effects dominate the electronic structure of a cluster with atom-like electronic shells instead of the Flanders (FWO).