The E3 ubiquitin ligase mechanism specifying target-directed microRNA degradation (TDMD) is now published! 🎉🍾 We, @bartellab.bsky.social and Schulman lab, describe how 2-RNA factors control protein degradation by recruiting an E3 ligase. @mpibiochem.bsky.social
www.nature.com/articles/s41...
Formation & function of #MembranelessOrganelles! #CryoET structures of #proteasome storage granules inside cells!
Read our paper @cp-cell.bsky.social!
❕Publication: doi.org/10.1016/j.ce...
❕Press Release: www.biochem.mpg.de/en/pressroom
@uoftmedicine.bsky.social
@erc.europa.eu #UPSmeetMet
Many thanks to Brenda, Basti, all co-authors @mpibiochem.bsky.social and collaborators Simon and Benoît @ludwigcancer.bsky.social!
6/6
Occupation of an enzyme exosite to regulate accessability of a phosphodegron to a kinase-E3 ligase cascade is a new mechanism of metabolite-gated protein degradation.
5/6
SAR studies with Trp analogs reveal that only Trp and its synthetic anlog α-methyl Trp, inhibit degron accessibility by structuring a C-terminal region.
This links ligand chemistry to decision-making by the UPS.
4/6
When Trp is limiting, TDO2 is subject to proteasomal degradation to avert tryptophanemia.
By combining CRISPRi screening, biochemistry and cryo-EM, we discovered how Trp is perceived by binding to an exosite on TDO2 to control its phosphorylation-dependent ubiquitylation.
3/6
Since the 1950s, long before the discovery of the ubiquitin-proteasome system, Tryptophan 2,3-dioxygenase (TDO2) emerged as a model for protein stability – a mystery now solved!
2/6
New year, new preprint! 🎊
We are excited to share our recent work on #E3 ligase regulation in #metabolism!
www.biorxiv.org/content/10.6...
#ubiquitin #targetedproteindegradation #chemicalbiology
1/6
Excited to share our latest study on how K29/K48-branched #ubiquitin chains are forged by the #E3 ligase TRIP12, and how this suggests a consensus mechanism for chain formation by HECT E3s!
@natsmb.nature.com
1/7
www.nature.com/articles/s41...
Video
When RNA Degradation 🤝 meets 🤝 Protein Degradation! tinyurl.com/E3TDMD In a collaboration of @bartellab.bsky.social and Schulman lab, we show that, in target-directed microRNA degradation (TDMD), 2-RNA-factors recruit an E3 ligase and induce the degradation of not only a protein but also RNA (1/5).
Small molecules toggling the ubiquitin-proteasome system (UPS) are powerful regulators of protein degradation. Yet, mechanistic knowledge of how endogenous ligands gate UPS decisions remains rudimentary. Here, we define control of UPS access to Tryptophan-2,3-dioxygenase (TDO2), which converts the essential amino acid tryptophan (Trp) to N-formylkynurenine. When Trp concentrations are limiting, TDO2 is degraded to avert tryptophanemia. Using CRISPRi screening and biochemistry, we identify a CK2-FBXW11 kinase-E3 ligase cascade that generates and recognizes tandem TDO2 phosphodegrons when not protected by Trp. Trp binding to an exosite safeguards TDO2 from phosphorylation-dependent ubiquitylation. Effects of Trp analogs on CK2-FBXW11-dependent ubiquitylation indicated that the indole, amino, and carboxylate groups are necessary for substrate shielding. Cryo-EM reveals how these moieties order a region proximal to the phosphodegrons; without Trp, this segment is flexible, enabling phosphorylation-coupled ubiquitylation. Overall, our data uncovered an endogenous small molecule allosterically stabilizing its own metabolizing enzyme through protection from a phosphorylation-ubiquitylation cascade. ### Competing Interest Statement B.A.S. is a member of the scientific advisory boards of Proxygen and Lyterian. The other authors declare no competing interests. Max Planck Society, https://ror.org/01hhn8329 European Union, ERC AdvG, UPSmeetMet, 101098161 to BAS Boehringer Ingelheim Fonds, https://ror.org/00dkye506
