Functional characterisation of RNA helicases involved in ribosome biogenesis

The synthesis of cytoplasmic ribosomes in Eukaryotes is best understood in the yeast Saccharomyces cerevisiae. Here, the pathway requires more than 180 non-ribosomal proteins, such as GTPases, nucleases and RNA helicases. In addition, 75 small nucleolar RNAs (snoRNAs) are involved and base-pair with pre-ribosomal RNA, and many are predicted to require helicase activities for their release. Since the knowledge on the 19 RNA helicases involved in ribosome biogenesis is still limited and molecular and regulatory functions of these enzymes seem to be diverse, the elucidation of their roles has remained a challenging task.

We are studying RNA helicase function in S. cerevisiae. Using the UV cross-linking and analysis of cDNAs (CRAC) approach, Solexa deep sequencing and bioinformatics, we have identified RNA binding sites of helicases involved in ribosome biogenesis. We have recently shown that the RNA helicase Prp43 has at least 5 major binding sites on pre-rRNA. Prp43 showed strong binding in helix 44 close to the 3'-end of the 18S rRNA and at several positions in the 25S rRNA where it fulfills diverse functions, such as release of several snoRNAs from pre-ribosomes.

We thus for the first time reported binding sites of eukaryotic RNA helicases on pre-rRNA and could allocate distinct molecular functions to proteins bound at the individual sites. We are currently studying the RNA interactions and molecular functions of RNA helicases in ribosome biogenesis and other pathways.