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Tessier TM, Chowdhury A, Stekel Z, Fux J, Sartori MA, Teyra J, Jarvik N, Chung J, Kurinov I, Sicheri F, Sidhu SS, Singer AU, Zhang W. Structural and functional validation of a highly specific Smurf2 inhibitor. Protein Sci 2024; 33:e4885. [PMID: 38147466 PMCID: PMC10823456 DOI: 10.1002/pro.4885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 12/28/2023]
Abstract
Smurf1 and Smurf2 are two closely related member of the HECT (homologous to E6AP carboxy terminus) E3 ubiquitin ligase family and play important roles in the regulation of various cellular processes. Both were initially identified to regulate transforming growth factor-β and bone morphogenetic protein signaling pathways through regulating Smad protein stability and are now implicated in various pathological processes. Generally, E3 ligases, of which over 800 exist in humans, are ideal targets for inhibition as they determine substrate specificity; however, there are few inhibitors with the ability to precisely target a particular E3 ligase of interest. In this work, we explored a panel of ubiquitin variants (UbVs) that were previously identified to bind Smurf1 or Smurf2. In vitro binding and ubiquitination assays identified a highly specific Smurf2 inhibitor, UbV S2.4, which was able to inhibit ligase activity with high potency in the low nanomolar range. Orthologous cellular assays further demonstrated high specificity of UbV S2.4 toward Smurf2 and no cross-reactivity toward Smurf1. Structural analysis of UbV S2.4 in complex with Smurf2 revealed its mechanism of inhibition was through targeting the E2 binding site. In summary, we investigated several protein-based inhibitors of Smurf1 and Smurf2 and identified a highly specific Smurf2 inhibitor that disrupts the E2-E3 protein interaction interface.
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Affiliation(s)
- Tanner M. Tessier
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphOntarioCanada
| | - Arvid Chowdhury
- Department of Molecular GeneticsUniversity of TorontoTorontoOntarioCanada
| | - Zane Stekel
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphOntarioCanada
| | - Julia Fux
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphOntarioCanada
| | | | | | - Nick Jarvik
- Department of PharmacyUniversity of WaterlooKitchenerOntarioCanada
| | - Jacky Chung
- Department of PharmacyUniversity of WaterlooKitchenerOntarioCanada
| | - Igor Kurinov
- NE‐CAT, Department of Chemistry and Chemical BiologyCornell UniversityArgonneIllinoisUSA
| | - Frank Sicheri
- Lunenfeld‐Tanenbaum Research Institute, Mount Sinai HospitalTorontoOntarioCanada
| | - Sachdev S. Sidhu
- Department of PharmacyUniversity of WaterlooKitchenerOntarioCanada
| | - Alex U. Singer
- Department of PharmacyUniversity of WaterlooKitchenerOntarioCanada
| | - Wei Zhang
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphOntarioCanada
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Hart T, Tong AHY, Chan K, Van Leeuwen J, Seetharaman A, Aregger M, Chandrashekhar M, Hustedt N, Seth S, Noonan A, Habsid A, Sizova O, Nedyalkova L, Climie R, Tworzyanski L, Lawson K, Sartori MA, Alibeh S, Tieu D, Masud S, Mero P, Weiss A, Brown KR, Usaj M, Billmann M, Rahman M, Constanzo M, Myers CL, Andrews BJ, Boone C, Durocher D, Moffat J. Evaluation and Design of Genome-Wide CRISPR/SpCas9 Knockout Screens. G3 (Bethesda) 2017; 7:2719-2727. [PMID: 28655737 PMCID: PMC5555476 DOI: 10.1534/g3.117.041277] [Citation(s) in RCA: 280] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/12/2017] [Indexed: 12/26/2022]
Abstract
The adaptation of CRISPR/SpCas9 technology to mammalian cell lines is transforming the study of human functional genomics. Pooled libraries of CRISPR guide RNAs (gRNAs) targeting human protein-coding genes and encoded in viral vectors have been used to systematically create gene knockouts in a variety of human cancer and immortalized cell lines, in an effort to identify whether these knockouts cause cellular fitness defects. Previous work has shown that CRISPR screens are more sensitive and specific than pooled-library shRNA screens in similar assays, but currently there exists significant variability across CRISPR library designs and experimental protocols. In this study, we reanalyze 17 genome-scale knockout screens in human cell lines from three research groups, using three different genome-scale gRNA libraries. Using the Bayesian Analysis of Gene Essentiality algorithm to identify essential genes, we refine and expand our previously defined set of human core essential genes from 360 to 684 genes. We use this expanded set of reference core essential genes, CEG2, plus empirical data from six CRISPR knockout screens to guide the design of a sequence-optimized gRNA library, the Toronto KnockOut version 3.0 (TKOv3) library. We then demonstrate the high effectiveness of the library relative to reference sets of essential and nonessential genes, as well as other screens using similar approaches. The optimized TKOv3 library, combined with the CEG2 reference set, provide an efficient, highly optimized platform for performing and assessing gene knockout screens in human cell lines.
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Affiliation(s)
- Traver Hart
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | | | - Katie Chan
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | | | | | - Michael Aregger
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | | | - Nicole Hustedt
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada
| | - Sahil Seth
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | - Avery Noonan
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | - Andrea Habsid
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | - Olga Sizova
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | | | - Ryan Climie
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | | | - Keith Lawson
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | | | - Sabriyeh Alibeh
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | - David Tieu
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Ontario M5S3E1, Canada
| | - Sanna Masud
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Ontario M5S3E1, Canada
| | - Patricia Mero
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | - Alexander Weiss
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | - Kevin R Brown
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | - Matej Usaj
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | - Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Mahfuzur Rahman
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | | | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Brenda J Andrews
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Ontario M5S3E1, Canada
- Canadian Institute for Advanced Research, Toronto, Ontario M5G1Z8, Canada
| | - Charles Boone
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Ontario M5S3E1, Canada
- Canadian Institute for Advanced Research, Toronto, Ontario M5G1Z8, Canada
| | - Daniel Durocher
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada
- Department of Molecular Genetics, University of Toronto, Ontario M5S3E1, Canada
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Ontario M5S3E1, Canada
- Canadian Institute for Advanced Research, Toronto, Ontario M5G1Z8, Canada
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