Research update: evolutionary conserved RNA-binding proteins

During the last years, hundreds of novel RNA-binding proteins (RBPs) have been detected in mammalian cell lines. Now, we mapped the mRNA-bound proteome of a complete organism: the yeast S. cerevisiae. Additionally, we determined the mRNA interactome of human hepatocytic cells (HuH-7).

Having comprehensive information on RBPs from a eukaryotic single cell organism and from mammalian cell lines, we defined a conserved core mRNA interactome of eukaryotic mRNA-binders. The core consists of many well-established RNA-binding proteins but also of many enzymes from diverse biochemical pathways and glycolysis emerges as hot-spot of conserved RBPs.

We also identified another interesting difference among some conserved eukaryotic RBPs in their overall RNA-binding architecture: throughout evolution, a steady increase in the repetition of short amino acid tripeptide motifs in unstructured regions of proteins could be observed.

Literature:

Beckmann BM, Horos R, Fischer B, Castello A, Eichelbaum K, Alleaume A-M, Schwarzl T, Curk T, Foehr S, Huber W, Krijgsveld J & Hentze MW.  The RNA-binding proteomes from yeast to man harbour conserved enigmRBPs. Nature Communications (2015); 6:10127

 

Research update: Mapping RNA-binding sites in proteins

Understanding RNA-protein interactions requires researchers to investigate both binding partners: RNA and RNA-binding proteins (RBPs). Unfortunately, methods to study both molecules are differentially well developed. Whereas new high-throughput techniques for RNA research such as PAR-CLIP or iCLIP allow to pinpoint protein binding sites in RNA at nucleotide resolution for millions of sequences, we so far could not do the complementary experiment: mapping interaction sites of RNA within proteins in an unbiased and high throughput fashion.

Participating in a study from Henning Urlaubs lab (MPI Göttingen, Germany), we could now develop a mass-spectrometry-based technique that maps more than 250 RNA interactions in 124 proteins: RNPxl. The method was tested in human and yeast cells and allows to identify those amino acids in RBPs which were interacting with RNA.

 

Literature:

Kramer K, Sachsenberg T, Beckmann BM, Qamar S, Boon K-L, Hentze MW, Kohlbacher O & Urlaub H. Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteinsNature Methods (2014); 11(10):1064-1070