Skip to main content
European Commission logo print header

Structural and functional studies on how the Ski complex activates the exosome to degrade RNA

Final Report Summary - EXOSOME-SKI-COMPLEX (Structural and functional studies on how the Ski complex activates the exosome to degrade RNA)

Objectives of the completed project
The aim of the completed project was to understand how the 10 subunit exosome (Exo10) and Ski complex function together to degrade RNA substrates. The main objectives are to find out:
• How are the catalytic activities (a nuclease and a helicase) organized and how do they communicate?
• How is an RNA substrate recruited, unwound and degraded?
• How does the Ski complex provoke RNA degradation?
• What is the role of Ski7?
A combination of structural and functional studies of the Ski2387Exo10 complex has been employed to answer these questions. We expected to acquire a crystal- or electron microscopy structures of the entire ca. 800 kDa complex or sub-complexes of the Ski2387 and Ski7Exo10 as a basis for functional in vitro and in vivo studies that should elucidate the functioning of this important cellular RNA degradation machinery.

Outcome of the project
In the course of the project, we were able to solve several crystal structures and gain structural information on the whole molecule of Ski7, from N to C-terminus. The structures lead especially to a better understanding of the role of Ski7 in the cell but moreover help to model more precisely the spacial arrangement of the Ski-complex and exosome.
• With its very N-terminal domain, Ski7 binds the Ski-complex, exclusively interacting with the C-terminal portion of Ski3.
• With the second part of the N-terminus, the cytosolic Ski7 wraps around the exosome in a manner very similar to its nuclear counterpart Rrp6 although their sequences are very different.
• The C-terminal GTP-binding domain of Ski7 is not involved in the interaction of Ski-complex and exosome. It carries the fold of a typical translational GTPase, like its closest homologue Hbs1. However in the active site of Ski7, residues crucial in GTP hydrolysis are not conserved and Ski7 might have evolved for stable GTP binding (in collaboration with the laboratory of Rachel Green, Baltimore, USA) and binding to the ribosome.

In conclusion the Ski7 N-terminus seems to act solely as adaptor between both complexes not interfering with their catalytically active moieties. Combining the two the substructures lead to an improved working model for the holo-complex.

Furthermore, we found that the Ski-complex can directly bind to the ribosome, having a co-translational function, probably when ribosomes get stalled on faulty messenger RNA (mRNA) and a cryo electron microscopic structure of the Ski-complex on the ribosome was solved (in collaboration with the laboratory of Roland Beckmann, LMU Munich, Germany).