Final Report Summary - DEAD2THEEND (RNA poly(A) tail: the beginning of the end)
Our group studies the molecular mechanisms of eukaryotic mRNA turnover. The turnover of mRNAs has emerged as a key step in the regulation of eukaryotic gene expression, not only under different physiological conditions but also during development and differentiation. Eukaryotic mRNAs are generally protected from degradation by the specialized ends they are endowed with: the poly(A) tail at the 3' end and the cap structure at the 5' end. The turnover of mRNAs starts with the removal of these specialized structures. The first and rate-limiting step is the gradual erosion of the poly(A) tail, which is carried out by the Pan2-Pan3 and Ccr4-Not complexes. The product of the deadenylases is then accessible to the downstream enzymatic activities that either degrade the mRNA in the 3'-5' direction (via the exosome and Ski complexes) or remove the cap structure and degrade in the 5'-3' direction (via the decapping-Lsm complexes and Xrn1).
We study the macromolecular complexes that consecutively deadenylate and degrade mRNAs. In particular, we are interested in how these nano-machines are constructed, how they recognize RNA substrates, how they carry out their chemical reactions and how they interact with each other. All the enzymatic activities of these complexes and most of the regulatory subunits are evolutionarily conserved.
In the past five years, we have made tremendous progress in elucidating the mechanisms of the Pan2-Pan3, Ccr4-Not, exosome, Ski and Lsm complexes. We have determined atomic snapshots of all the core complexes: the 200 kDa Pan2-Pan3 core, the 400 kDa exosome core, the 370 kDa Ski core, as well as the 8-subunit Lsm-Pat1 core and almost all the modules of Ccr4-Not. Instrumental for the structure determination of these large molecular machines was the biochemical characterization of their properties that we have dissected. The results we obtained have elucidated the principles with which the catalytically active subunits coordinate with the regulatory subunits. These studies have revealed how these complexes assemble with unusual and unexpected stoichiometry and how protein-protein interaction modules coordinate with the catalytic modules to regulate substrate specificities and enzymatic activities.
We study the macromolecular complexes that consecutively deadenylate and degrade mRNAs. In particular, we are interested in how these nano-machines are constructed, how they recognize RNA substrates, how they carry out their chemical reactions and how they interact with each other. All the enzymatic activities of these complexes and most of the regulatory subunits are evolutionarily conserved.
In the past five years, we have made tremendous progress in elucidating the mechanisms of the Pan2-Pan3, Ccr4-Not, exosome, Ski and Lsm complexes. We have determined atomic snapshots of all the core complexes: the 200 kDa Pan2-Pan3 core, the 400 kDa exosome core, the 370 kDa Ski core, as well as the 8-subunit Lsm-Pat1 core and almost all the modules of Ccr4-Not. Instrumental for the structure determination of these large molecular machines was the biochemical characterization of their properties that we have dissected. The results we obtained have elucidated the principles with which the catalytically active subunits coordinate with the regulatory subunits. These studies have revealed how these complexes assemble with unusual and unexpected stoichiometry and how protein-protein interaction modules coordinate with the catalytic modules to regulate substrate specificities and enzymatic activities.