1
|
Röth S, Fulcher LJ, Sapkota GP. Advances in targeted degradation of endogenous proteins. Cell Mol Life Sci 2019; 76:2761-2777. [PMID: 31030225 PMCID: PMC6588652 DOI: 10.1007/s00018-019-03112-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/23/2019] [Accepted: 04/16/2019] [Indexed: 01/07/2023]
Abstract
Protein silencing is often employed as a means to aid investigations in protein function and is increasingly desired as a therapeutic approach. Several types of protein silencing methodologies have been developed, including targeting the encoding genes, transcripts, the process of translation or the protein directly. Despite these advances, most silencing systems suffer from limitations. Silencing protein expression through genetic ablation, for example by CRISPR/Cas9 genome editing, is irreversible, time consuming and not always feasible. Similarly, RNA interference approaches warrant prolonged treatments, can lead to incomplete protein depletion and are often associated with off-target effects. Targeted proteolysis has the potential to overcome some of these limitations. The field of targeted proteolysis has witnessed the emergence of many methodologies aimed at targeting specific proteins for degradation in a spatio-temporal manner. In this review, we provide an appraisal of the different targeted proteolytic systems and discuss their applications in understanding protein function, as well as their potential in therapeutics.
Collapse
Affiliation(s)
- Sascha Röth
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Luke J Fulcher
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Gopal P Sapkota
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
| |
Collapse
|
3
|
Hughes DJ, Tiede C, Penswick N, Tang AAS, Trinh CH, Mandal U, Zajac KZ, Gaule T, Howell G, Edwards TA, Duan J, Feyfant E, McPherson MJ, Tomlinson DC, Whitehouse A. Generation of specific inhibitors of SUMO-1- and SUMO-2/3-mediated protein-protein interactions using Affimer (Adhiron) technology. Sci Signal 2017; 10:10/505/eaaj2005. [PMID: 29138295 DOI: 10.1126/scisignal.aaj2005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Because protein-protein interactions underpin most biological processes, developing tools that target them to understand their function or to inform the development of therapeutics is an important task. SUMOylation is the posttranslational covalent attachment of proteins in the SUMO family (SUMO-1, SUMO-2, or SUMO-3), and it regulates numerous cellular pathways. SUMOylated proteins are recognized by proteins with SUMO-interaction motifs (SIMs) that facilitate noncovalent interactions with SUMO. We describe the use of the Affimer system of peptide display for the rapid isolation of synthetic binding proteins that inhibit SUMO-dependent protein-protein interactions mediated by SIMs both in vitro and in cells. Crucially, these synthetic proteins did not prevent SUMO conjugation either in vitro or in cell-based systems, enabling the specific analysis of SUMO-mediated protein-protein interactions. Furthermore, through structural analysis and molecular modeling, we explored the molecular mechanisms that may underlie their specificity in interfering with either SUMO-1-mediated interactions or interactions mediated by either SUMO-2 or SUMO-3. Not only will these reagents enable investigation of the biological roles of SUMOylation, but the Affimer technology used to generate these synthetic binding proteins could also be exploited to design or validate reagents or therapeutics that target other protein-protein interactions.
Collapse
Affiliation(s)
- David J Hughes
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. .,Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews KY16 9ST, UK
| | - Christian Tiede
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Natalie Penswick
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Anna Ah-San Tang
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Chi H Trinh
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Upasana Mandal
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Katarzyna Z Zajac
- BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Thembaninskosi Gaule
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Gareth Howell
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Thomas A Edwards
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | | | | | - Michael J McPherson
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Darren C Tomlinson
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. .,BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Adrian Whitehouse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. .,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| |
Collapse
|
4
|
Josa-Prado F, Henley JM, Wilkinson KA. SUMOylation of Argonaute-2 regulates RNA interference activity. Biochem Biophys Res Commun 2015; 464:1066-1071. [PMID: 26188511 PMCID: PMC4624959 DOI: 10.1016/j.bbrc.2015.07.073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 07/14/2015] [Indexed: 12/21/2022]
Abstract
Post-translational modification of substrate proteins by small ubiquitin-like modifier (SUMO) regulates a vast array of cellular processes. SUMOylation occurs through three sequential enzymatic steps termed E1, E2 and E3. Substrate selection can be determined through interactions between the target protein and the SUMO E2 conjugating enzyme Ubc9 and specificity can be enhanced by substrate interactions with E3 ligase enzymes. We used the putative substrate recognition (PINIT) domain from the SUMO E3 PIAS3 as bait to identify potential SUMO substrates. One protein identified was Argonaute-2 (Ago2), which mediates RNA-induced gene silencing through binding small RNAs and promoting degradation of complimentary target mRNAs. We show that Ago2 can be SUMOylated in mammalian cells by both SUMO1 and SUMO2. SUMOylation occurs primarily at K402, and mutation of the SUMO consensus site surrounding this lysine reduces Ago2-mediated siRNA-induced silencing in a luciferase-based reporter assay. These results identify SUMOylation as a potential regulator of Ago2 activity and open new avenues for research into the mechanisms underlying the regulation of RNA-induced gene silencing. Argonaute-2 (Ago2) is SUMOylated in mammalian cells. SUMOylation of Ago2 takes place primarily at lysine 402. Abolishing Ago2 SUMOylation reduces its functional activity.
Collapse
Affiliation(s)
- Fernando Josa-Prado
- School of Biochemistry, Medical Sciences Building, University Walk, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - Jeremy M Henley
- School of Biochemistry, Medical Sciences Building, University Walk, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - Kevin A Wilkinson
- School of Biochemistry, Medical Sciences Building, University Walk, University of Bristol, Bristol, BS8 1TD, United Kingdom.
| |
Collapse
|