1
|
Renz C, Asimaki E, Meister C, Albanèse V, Petriukov K, Krapoth NC, Wegmann S, Wollscheid HP, Wong RP, Fulzele A, Chen JX, Léon S, Ulrich HD. Ubiquiton-An inducible, linkage-specific polyubiquitylation tool. Mol Cell 2024; 84:386-400.e11. [PMID: 38103558 PMCID: PMC10804999 DOI: 10.1016/j.molcel.2023.11.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 09/28/2023] [Accepted: 11/15/2023] [Indexed: 12/19/2023]
Abstract
The posttranslational modifier ubiquitin regulates most cellular processes. Its ability to form polymeric chains of distinct linkages is key to its diverse functionality. Yet, we still lack the experimental tools to induce linkage-specific polyubiquitylation of a protein of interest in cells. Here, we introduce a set of engineered ubiquitin protein ligases and matching ubiquitin acceptor tags for the rapid, inducible linear (M1-), K48-, or K63-linked polyubiquitylation of proteins in yeast and mammalian cells. By applying the so-called "Ubiquiton" system to proteasomal targeting and the endocytic pathway, we validate this tool for soluble cytoplasmic and nuclear as well as chromatin-associated and integral membrane proteins and demonstrate how it can be used to control the localization and stability of its targets. We expect that the Ubiquiton system will serve as a versatile, broadly applicable research tool to explore the signaling functions of polyubiquitin chains in many biological contexts.
Collapse
Affiliation(s)
- Christian Renz
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Evrydiki Asimaki
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Cindy Meister
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | | | - Kirill Petriukov
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Nils C Krapoth
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Sabrina Wegmann
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | | | - Ronald P Wong
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Amitkumar Fulzele
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Jia-Xuan Chen
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Sébastien Léon
- Université de Paris, CNRS, Institut Jacques Monod, 75013 Paris, France
| | - Helle D Ulrich
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany.
| |
Collapse
|
2
|
Riley AK, Grant M, Snell A, Vichas A, Moorthi S, Urisman A, Castel P, Wan L, Berger AH. The deubiquitinase USP9X regulates RIT1 protein abundance and oncogenic phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569313. [PMID: 38077017 PMCID: PMC10705424 DOI: 10.1101/2023.11.30.569313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
RIT1 is a rare and understudied oncogene in lung cancer. Despite structural similarity to other RAS GTPase proteins such as KRAS, oncogenic RIT1 activity does not appear to be tightly regulated by nucleotide exchange or hydrolysis. Instead, there is a growing understanding that the protein abundance of RIT1 is important for its regulation and function. We previously identified the deubiquitinase USP9X as a RIT1 dependency in RIT1-mutant cells. Here, we demonstrate that both wild-type and mutant forms of RIT1 are substrates of USP9X. Depletion of USP9X leads to decreased RIT1 protein stability and abundance and resensitizes cells to EGFR tyrosine kinase inhibitors. Our work expands upon the current understanding of RIT1 protein regulation and presents USP9X as a key regulator of RIT1-driven oncogenic phenotypes.
Collapse
Affiliation(s)
- Amanda K. Riley
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Michael Grant
- Department of Molecular Oncology, Molecular Medicine Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Aidan Snell
- Department of Molecular Oncology, Molecular Medicine Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Athea Vichas
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sitapriya Moorthi
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Anatoly Urisman
- Department of Pathology, University of California San Francisco, CA, USA
| | - Pau Castel
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Lixin Wan
- Department of Molecular Oncology, Molecular Medicine Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Alice H. Berger
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Herbold Computational Biology Program, Public Health Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Lead contact:
| |
Collapse
|
3
|
Di Mambro T, Vanzolini T, Bianchi M, Crinelli R, Canonico B, Tasini F, Menotta M, Magnani M. Development and in vitro characterization of a humanized scFv against fungal infections. PLoS One 2022; 17:e0276786. [PMID: 36315567 PMCID: PMC9621433 DOI: 10.1371/journal.pone.0276786] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/14/2022] [Indexed: 01/24/2023] Open
Abstract
The resistance and the birth of new intrinsic and multidrug-resistant pathogenic species like C. auris is creating great concern in the antifungal world. Given the limited drug arsenal and the lack of effectiveness of the available compounds, there is an urgent need for innovative approaches. The murine mAb 2G8 was humanized and engineered in silico to develop a single-chain fragment variable (hscFv) antibody against β-1,3-glucans which was then expressed in E. coli. Among the recombinant proteins developed, a soluble candidate with high stability and affinity was obtained. This selected protein is VL-linker-VH oriented, and it is characterized by the presence of two ubiquitin monomers at the N-terminus and a His tag at the C-terminus. This construct, Ub2-hscFv-His, guaranteed stability, solubility, efficient purification and satisfactory recovery of the recombinant product. HscFv can bind β-1,3-glucans both as coated antigens and on C. auris and C. albicans cells similarly to its murine parental and showed long stability and retention of binding ability when stored at 4°, -20° and -80° C. Furthermore, it was efficient in enhancing the antifungal activity of drugs caspofungin and amphotericin B against C. auris. The use of biological drugs as antifungals is limited; here we present a promising hscFv which has the potential to be useful in combination with currently available antifungal drugs.
Collapse
Affiliation(s)
| | - Tania Vanzolini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
- * E-mail:
| | - Marzia Bianchi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Rita Crinelli
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Barbara Canonico
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Filippo Tasini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Michele Menotta
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Mauro Magnani
- Diatheva s.r.l., Cartoceto, Italy
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| |
Collapse
|
4
|
In memoriam: Huib Ovaa, the brain behind the formula (18/12/1973-19/05/2020). Semin Cell Dev Biol 2022; 132:1-4. [PMID: 35753908 DOI: 10.1016/j.semcdb.2022.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|