Elucidating specificity and mechanism of the ubiquitination machinery
Final Report Abstract
Ubiquitination is a central posttranslational modification in eukaryotic cells that regulates the lifetimes, abundance, localization, functions, and interactions of the modified proteins. This requires that ubiquitination, in turn, is specific and tightly controlled. As a consequence, de-regulation of the ubiquitin system is linked to various human diseases, rendering this system a surging arena for therapeutic efforts. Ubiquitination reactions are driven by a cascade of ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2), and ubiquitin ligase (E3) activities, counteracted by deubiquitinases. E3s typically drive substrate recognition and can determine the specificity of modification, together with their cooperating E2. This project focused on dissecting the structural mechanisms of E2s and HECT-type E3s – two diseaserelevant, yet therapeutically unexploited classes of ubiquitination enzymes. Using structural, biochemical, biophysical, and cell biological approaches, we unveiled two structurally and functionally distinct autoinhibition mechanisms in the human E2 UBE2S, a key regulator of the cell cycle. The conformational transitions of UBE2S between its active and inhibited states that we discovered, provide a paradigm for how mutually exclusive intra- and intermolecular interactions modulate the concentrations and activities of E2s, thereby contributing to the precision of ubiquitin signaling. Moreover, we delineated how the HECT-type ligases HUWE1 and E6AP interact with ubiquitin substrates, uncovering critical determinants of specificity, catalysis, regulation, and conformational dynamics of their catalytic domain. We also contributed to the development of a chemical biology-based crosslinking strategy to reconstitute ternary complexes of E2s and HECT-type ligases, respectively, with two ubiquitin substrates. Structural analysis of these complexes will provide keys to understanding specificity in ubiquitin modifications and associated functions. Besides these research accomplishments, the Emmy Noether Programme has allowed me to establish an internationally visible research team, gain expertise as a supervisor and mentor, and secure attractive external offers, leading me to proceed to a position as an Independent Group Leader at the Max Planck Institute for Multidisciplinary Sciences in Göttingen.
Publications
- (2017) A conformational switch regulates the ubiquitin ligase HUWE1. eLife 6: e21036
Sander B, Xu W, Eilers M, Popov N, Lorenz S
(See online at https://doi.org/10.7554/elife.21036) - (2018) Developing small-molecule inhibitors of HECT-type ubiquitin ligases for therapeutic applications: challenges and opportunities. ChemBioChem 19: 2123-2135
Chen D, Gehringer M, Lorenz S
(See online at https://doi.org/10.1002/cbic.201800321) - (2018) Structural mechanisms of HECT-type ubiquitin ligases. Biol Chem 399: 127-145
Lorenz S
(See online at https://doi.org/10.1515/hsz-2017-0184) - (2019) Autoinhibition mechanism of the ubiquitin-conjugating enzyme UBE2S by autoubiquitination. Structure 27: 1195-1210
Liess A, Kucerova A, Schweimer K, Yu L, Roumeliotis T, Diebold M, Dybkov O, Sotriffer C, Urlaub H, Choudhary J, Mansfeld J, Lorenz S
(See online at https://doi.org/10.1016/j.str.2019.05.008) - (2019) Enzymatic logic of ubiquitin chain assembly. Front Physiol 10: 835
Deol KK, Lorenz S, Strieter ER
(See online at https://doi.org/10.3389/fphys.2019.00835) - (2019) Non-proteolytic ubiquitination of Hexokinase 2 by HectH9 controls tumorigenesis, energy metabolism and ROS inhibited cancer stem cell expansion. Nat Commun 10: 2625
Lee H-J, Li C-F, Ruan D, He J, Montal ED, Lorenz S, Girnun GD, Chang C-H
(See online at https://doi.org/10.1038/s41467-019-10374-y) - (2019) Studies of ubiquitin recognition by the HECT ligase E6AP provide insight into its linkage specificity. J Biol Chem 94: 6113-6129
Ries L, Deol KK, Sander B, Letzelter M-A, Strieter E, Lorenz S
(See online at https://doi.org/10.1074/jbc.ra118.007014) - (2020) Dimerization regulates the human APC/C-associated ubiquitin-conjugating enzyme UBE2S. Sci Signal 13: eaba8208
Liess A, Kucerova A, Schweimer K, Urlaub H, Mansfeld J, Lorenz S
(See online at https://doi.org/10.1126/scisignal.aba8208) - (2021) Identification of an atypical interaction site in the BTB domain of the MYC-interacting zinc-finger protein 1. Structure 29: 1230-1240
Orth B, Sander B, Möglich A, Diederichs K, Eilers M, Lorenz S
(See online at https://doi.org/10.1016/j.str.2021.06.005) - (2021) Reconstitution and structural analysis of a HECT ligase-ubiquitin complex via an activity-based probe. ACS Chem Biol 16: 1615-1621
Nair R, Seenivasan A, Liu B, Chen D, Lowe E, Lorenz S
(See online at https://doi.org/10.1021/acschembio.1c00433)
