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Wang Y, Shu H, Qu Y, Jin X, Liu J, Peng W, Wang L, Hao M, Xia M, Zhao Z, Dong K, Di Y, Tian M, Hao F, Xia C, Zhang W, Ba X, Feng Y, Wei M. PKM2 functions as a histidine kinase to phosphorylate PGAM1 and increase glycolysis shunts in cancer. EMBO J 2024; 43:2368-2396. [PMID: 38750259 PMCID: PMC11183095 DOI: 10.1038/s44318-024-00110-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 03/24/2024] [Accepted: 03/27/2024] [Indexed: 06/19/2024] Open
Abstract
Phosphoglycerate mutase 1 (PGAM1) is a key node enzyme that diverts the metabolic reactions from glycolysis into its shunts to support macromolecule biosynthesis for rapid and sustainable cell proliferation. It is prevalent that PGAM1 activity is upregulated in various tumors; however, the underlying mechanism remains unclear. Here, we unveil that pyruvate kinase M2 (PKM2) moonlights as a histidine kinase in a phosphoenolpyruvate (PEP)-dependent manner to catalyze PGAM1 H11 phosphorylation, that is essential for PGAM1 activity. Moreover, monomeric and dimeric but not tetrameric PKM2 are efficient to phosphorylate and activate PGAM1. In response to epidermal growth factor signaling, Src-catalyzed PGAM1 Y119 phosphorylation is a prerequisite for PKM2 binding and the subsequent PGAM1 H11 phosphorylation, which constitutes a discrepancy between tumor and normal cells. A PGAM1-derived pY119-containing cell-permeable peptide or Y119 mutation disrupts the interaction of PGAM1 with PKM2 and PGAM1 H11 phosphorylation, dampening the glycolysis shunts and tumor growth. Together, these results identify a function of PKM2 as a histidine kinase, and illustrate the importance of enzyme crosstalk as a regulatory mode during metabolic reprogramming and tumorigenesis.
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Affiliation(s)
- Yang Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, 130024, Changchun, Jilin, China
| | - Hengyao Shu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, 130024, Changchun, Jilin, China
| | - Yanzhao Qu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, 130024, Changchun, Jilin, China
| | - Xin Jin
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, 130024, Changchun, Jilin, China
| | - Jia Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, 130024, Changchun, Jilin, China
| | - Wanting Peng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, 130024, Changchun, Jilin, China
| | - Lihua Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, 130024, Changchun, Jilin, China
| | - Miao Hao
- Science Research Center, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, 130033, Changchun, Jilin, China
| | - Mingjie Xia
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, 130024, Changchun, Jilin, China
| | - Zhexuan Zhao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, 130024, Changchun, Jilin, China
| | - Kejian Dong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, 130024, Changchun, Jilin, China
| | - Yao Di
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, 130024, Changchun, Jilin, China
| | - Miaomiao Tian
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, 130024, Changchun, Jilin, China
| | - Fengqi Hao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, 130024, Changchun, Jilin, China
| | - Chaoyi Xia
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, 130024, Changchun, Jilin, China
| | - Wenxia Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, 130024, Changchun, Jilin, China
| | - Xueqing Ba
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, 130024, Changchun, Jilin, China.
| | - Yunpeng Feng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, 130024, Changchun, Jilin, China.
| | - Min Wei
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, 130024, Changchun, Jilin, China.
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2
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Allen MC, Karplus PA, Mehl RA, Cooley RB. Genetic Encoding of Phosphorylated Amino Acids into Proteins. Chem Rev 2024; 124:6592-6642. [PMID: 38691379 DOI: 10.1021/acs.chemrev.4c00110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Reversible phosphorylation is a fundamental mechanism for controlling protein function. Despite the critical roles phosphorylated proteins play in physiology and disease, our ability to study individual phospho-proteoforms has been hindered by a lack of versatile methods to efficiently generate homogeneous proteins with site-specific phosphoamino acids or with functional mimics that are resistant to phosphatases. Genetic code expansion (GCE) is emerging as a transformative approach to tackle this challenge, allowing direct incorporation of phosphoamino acids into proteins during translation in response to amber stop codons. This genetic programming of phospho-protein synthesis eliminates the reliance on kinase-based or chemical semisynthesis approaches, making it broadly applicable to diverse phospho-proteoforms. In this comprehensive review, we provide a brief introduction to GCE and trace the development of existing GCE technologies for installing phosphoserine, phosphothreonine, phosphotyrosine, and their mimics, discussing both their advantages as well as their limitations. While some of the technologies are still early in their development, others are already robust enough to greatly expand the range of biologically relevant questions that can be addressed. We highlight new discoveries enabled by these GCE approaches, provide practical considerations for the application of technologies by non-GCE experts, and also identify avenues ripe for further development.
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Affiliation(s)
- Michael C Allen
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
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3
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Gupta S, Saha M, Singh R, Ahmed SB, Asati V. Multistage in silico approach to identify novel quinoline derivatives as potential c-kit kinase inhibitors. J Biomol Struct Dyn 2024:1-18. [PMID: 38287494 DOI: 10.1080/07391102.2024.2308759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 01/15/2024] [Indexed: 01/31/2024]
Abstract
The type II-C-KIT signaling network has been extensively studied for its potential as a target for cancer treatment, leading to the investigation of quinoline derivatives as compounds with inhibitory effects on c-Kit kinase. In this study, a multistage approach was employed, including the creation of pharmacophore models, 3D QSAR analysis, virtual screening, docking investigations, and molecular dynamics stimulation. The pharmacophore evaluation included a data set of 29 ligands, which resulted in the generation of the ADDHR_1pharmacophore model as the most promising, with a survival score of 5.6812. The main objective was to utilize the atom-based 3D-QSAR approach for generating robust 3D-QSAR models aimed at identifying new TypeII-C-kit kinase inhibitors. The evaluations of these models have convincingly demonstrated their high predictive power (Q2 = 0.6547, R2 = 0.9947). Using atom-based 3D-QSAR data, a total of 7564 novel compounds were generated from R-group enumeration. Molecular docking and MM-GBSA study revealed that compound A1 exhibited the highest binding score of -9.30 kcal/mol and a Δ GBind value of -90.56 kcal/mol. The ZINC compounds were then screened using the pharmacophore model, followed by virtual screening, which identified ZINC65798256, ZINC09317958, ZINC73187176, and ZINC76176670 as potential candidates with promising docking scores. Among these, ZINC65798256 demonstrated the best binding interactions with amino acid residues, ASP810, LYS623, CYS673, and THR670 (PDB ID: 1T46). To further analyze the structural features and molecular interactions, molecular dynamics simulation was conducted for a time scale of 100 ns.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shankar Gupta
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, Punjab, India
| | - Moumita Saha
- Department of Pharmaceutical Analysis, ISF College of Pharmacy, Moga, Punjab, India
| | - Rajveer Singh
- Department of Pharmacognosy, ISF College of Pharmacy, Moga, Punjab, India
| | - Samia Ben Ahmed
- Department of Chemistry, College of Sciences, King Khalid University, Abha, Saudi Arabia
| | - Vivek Asati
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, Punjab, India
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Sim PF, Chek MF, Nguyen NTH, Nishimura T, Inaba T, Hakoshima T, Suetsugu S. The SH3 binding site in front of the WH1 domain contributes to the membrane binding of the BAR domain protein endophilin A2. J Biochem 2023; 175:57-67. [PMID: 37812440 DOI: 10.1093/jb/mvad065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/22/2023] [Accepted: 08/31/2023] [Indexed: 10/10/2023] Open
Abstract
The Bin-Amphiphysin-Rvs (BAR) domain of endophilin binds to the cell membrane and shapes it into a tubular shape for endocytosis. Endophilin has a Src-homology 3 (SH3) domain at their C-terminal. The SH3 domain interacts with the proline-rich motif (PRM) that is found in proteins such as neural Wiskott-Aldrich syndrome protein (N-WASP). Here, we re-examined the binding sites of the SH3 domain of endophilin in N-WASP by machine learning-based prediction and identified the previously unrecognized binding site. In addition to the well-recognized PRM at the central proline-rich region, we found a PRM in front of the N-terminal WASP homology 1 (WH1) domain of N-WASP (NtPRM) as a binding site of the endophilin SH3 domain. Furthermore, the diameter of the membrane tubules in the presence of NtPRM mutant was narrower and wider than that in the presence of N-WASP and in its absence, respectively. Importantly, the NtPRM of N-WASP was involved in the membrane localization of endophilin A2 in cells. Therefore, the NtPRM contributes to the binding of endophilin to N-WASP in membrane remodeling.
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Affiliation(s)
- Pei Fang Sim
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Min Fey Chek
- Institute for Research Initiatives, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Nhung Thi Hong Nguyen
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Tamako Nishimura
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Takehiko Inaba
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Toshio Hakoshima
- Institute for Research Initiatives, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Shiro Suetsugu
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
- Data Science Center, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
- Center for Digital Green-innovation, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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5
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Wang Y, Shu H, Liu J, Jin X, Wang L, Qu Y, Xia M, Peng P, Feng Y, Wei M. EGF promotes PKM2 O-GlcNAcylation by stimulating O-GlcNAc transferase phosphorylation at Y976 and their subsequent association. J Biol Chem 2022; 298:102340. [PMID: 35931120 PMCID: PMC9436816 DOI: 10.1016/j.jbc.2022.102340] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 11/30/2022] Open
Abstract
Epidermal growth factor (EGF) is one of the most well-characterized growth factors and plays a crucial role in cell proliferation and differentiation. Its receptor EGFR has been extensively explored as a therapeutic target against multiple types of cancers, such as lung cancer and glioblastoma. Recent studies have established a connection between deregulated EGF signaling and metabolic reprogramming, especially rewiring in aerobic glycolysis, which is also known as the Warburg effect and recognized as a hallmark in cancer. Pyruvate kinase M2 (PKM2) is a rate-limiting enzyme controlling the final step of glycolysis and serves as a major regulator of the Warburg effect. We previously showed that PKM2 T405/S406 O-GlcNAcylation, a critical mark important for PKM2 detetramerization and activity, was markedly upregulated by EGF. However, the mechanism by which EGF regulates PKM2 O-GlcNAcylation still remains uncharacterized. Here, we demonstrated that EGF promoted O-GlcNAc transferase (OGT) binding to PKM2 by stimulating OGT Y976 phosphorylation. As a consequence, we found PKM2 O-GlcNAcylation and detetramerization were upregulated, leading to a significant decrease in PKM2 activity. Moreover, distinct from PKM2, we observed that the association of additional phosphotyrosine-binding proteins with OGT was also enhanced when Y976 was phosphorylated. These proteins included STAT1, STAT3, STAT5, PKCδ, and p85, which are reported to be O-GlcNAcylated. Together, we show EGF-dependent Y976 phosphorylation is critical for OGT-PKM2 interaction and propose that this posttranslational modification might be important for substrate selection by OGT.
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Affiliation(s)
- Yang Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, Changchun, Jilin, 130024, China
| | - Hengyao Shu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, Changchun, Jilin, 130024, China
| | - Jia Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, Changchun, Jilin, 130024, China
| | - Xin Jin
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, Changchun, Jilin, 130024, China
| | - Lihua Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, Changchun, Jilin, 130024, China
| | - Yanzhao Qu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, Changchun, Jilin, 130024, China
| | - Mingjie Xia
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, Changchun, Jilin, 130024, China
| | - Pinghui Peng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, Changchun, Jilin, 130024, China
| | - Yunpeng Feng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, Changchun, Jilin, 130024, China.
| | - Min Wei
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 5268 Renmin Street, Changchun, Jilin, 130024, China.
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6
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Banerjee SL, Lessard F, Chartier FJM, Jacquet K, Osornio-Hernandez AI, Teyssier V, Ghani K, Lavoie N, Lavoie JN, Caruso M, Laprise P, Elowe S, Lambert JP, Bisson N. EPH receptor tyrosine kinases phosphorylate the PAR-3 scaffold protein to modulate downstream signaling networks. Cell Rep 2022; 40:111031. [PMID: 35793621 DOI: 10.1016/j.celrep.2022.111031] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 04/26/2022] [Accepted: 06/13/2022] [Indexed: 11/03/2022] Open
Abstract
EPH receptors (EPHRs) constitute the largest family among receptor tyrosine kinases in humans. They are mainly involved in short-range cell-cell communication events that regulate cell adhesion, migration, and boundary formation. However, the molecular mechanisms by which EPHRs control these processes are less understood. To address this, we unravel EPHR-associated complexes under native conditions using mass-spectrometry-based BioID proximity labeling. We obtain a composite proximity network from EPHA4, -B2, -B3, and -B4 that comprises 395 proteins, most of which were not previously linked to EPHRs. We examine the contribution of several BioID-identified candidates via loss-of-function in an EPHR-dependent cell-segregation assay. We find that the signaling scaffold PAR-3 is required for cell sorting and that EPHRs directly phosphorylate PAR-3. We also delineate a signaling complex involving the C-terminal SRC kinase (CSK), whose recruitment to PAR-3 is dependent on EPHR signals. Our work describes signaling networks by which EPHRs regulate cellular phenotypes.
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Affiliation(s)
- Sara L Banerjee
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, QC, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, Canada
| | - Frédéric Lessard
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, QC, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, Canada
| | - François J M Chartier
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, QC, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, Canada
| | - Kévin Jacquet
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, QC, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada
| | - Ana I Osornio-Hernandez
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, QC, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, Canada
| | - Valentine Teyssier
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, QC, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, Canada
| | - Karim Ghani
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, QC, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada
| | - Noémie Lavoie
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, QC, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, Canada
| | - Josée N Lavoie
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, QC, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, QC, Canada
| | - Manuel Caruso
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, QC, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, QC, Canada
| | - Patrick Laprise
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, QC, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, QC, Canada
| | - Sabine Elowe
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, QC, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, Canada; Department of Pediatrics, Université Laval, Québec, QC, Canada
| | - Jean-Philippe Lambert
- Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada; Department of Molecular Medicine, Université Laval, Québec, QC, Canada; Centre de recherche en données massives de l'Université Laval, Québec, QC, Canada; Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Endocrinologie-néphrologie, Québec, QC, Canada
| | - Nicolas Bisson
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, QC, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, QC, Canada.
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7
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Dionne U, Percival LJ, Chartier FJM, Landry CR, Bisson N. SRC homology 3 domains: multifaceted binding modules. Trends Biochem Sci 2022; 47:772-784. [PMID: 35562294 DOI: 10.1016/j.tibs.2022.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/30/2022] [Accepted: 04/11/2022] [Indexed: 12/15/2022]
Abstract
The assembly of complexes following the detection of extracellular signals is often controlled by signaling proteins comprising multiple peptide binding modules. The SRC homology (SH)3 family represents the archetypical modular protein interaction module, with ~300 annotated SH3 domains in humans that regulate an impressive array of signaling processes. We review recent findings regarding the allosteric contributions of SH3 domains host protein context, their phosphoregulation, and their roles in phase separation that challenge the simple model in which SH3s are considered to be portable domains binding to specific proline-rich peptide motifs.
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Affiliation(s)
- Ugo Dionne
- Centre de recherche sur le cancer et Centre de recherche du CHU de Québec - Université Laval, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada
| | - Lily J Percival
- Centre de recherche sur le cancer et Centre de recherche du CHU de Québec - Université Laval, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada; School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, The Michael Smith Building, Manchester, UK
| | - François J M Chartier
- Centre de recherche sur le cancer et Centre de recherche du CHU de Québec - Université Laval, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada
| | - Christian R Landry
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada; Institute of Integrative and Systems Biology, Université Laval, Quebec, QC, Canada; Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Quebec, QC, Canada; Department of Biology, Université Laval, Quebec, QC, Canada.
| | - Nicolas Bisson
- Centre de recherche sur le cancer et Centre de recherche du CHU de Québec - Université Laval, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Quebec, QC, Canada.
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8
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Abstract
The EPH receptor tyrosine kinases and their signaling partners, the EPHRINS, comprise a large class of cell signaling molecules that plays diverse roles in development. As cell membrane-anchored signaling molecules, they regulate cellular organization by modulating the strength of cellular contacts, usually by impacting the actin cytoskeleton or cell adhesion programs. Through these cellular functions, EPH/EPHRIN signaling often regulates tissue shape. Indeed, recent evidence indicates that this signaling family is ancient and associated with the origin of multicellularity. Though extensively studied, our understanding of the signaling mechanisms employed by this large family of signaling proteins remains patchwork, and a truly "canonical" EPH/EPHRIN signal transduction pathway is not known and may not exist. Instead, several foundational evolutionarily conserved mechanisms are overlaid by a myriad of tissue -specific functions, though common themes emerge from these as well. Here, I review recent advances and the related contexts that have provided new understanding of the conserved and varied molecular and cellular mechanisms employed by EPH/EPHRIN signaling during development.
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Affiliation(s)
- Jeffrey O Bush
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, United States; Program in Craniofacial Biology, University of California San Francisco, San Francisco, CA, United States; Institute for Human Genetics, University of California San Francisco, San Francisco, CA, United States; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, United States.
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9
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ASAI D, KANG JH, KATAYAMA Y. Old but Still Useful [γ-<sup>32</sup>P]ATP —Development of Peptide Substrates for Protein Kinases by <sup>32</sup>P-Based Enzyme Activity Assay—. BUNSEKI KAGAKU 2022. [DOI: 10.2116/bunsekikagaku.71.179] [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]
Affiliation(s)
- Daisuke ASAI
- Laboratory of Microbiology, Showa Pharmaceutical University
| | - Jeong-Hun KANG
- Division of Biopharmaceutics and Pharmacokinetics, National Cerebral and Cardiovascular Center Research Institute
| | - Yoshiki KATAYAMA
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University
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10
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Aboualizadeh F, Yao Z, Guan J, Drecun L, Pathmanathan S, Snider J, Umapathy G, Kotlyar M, Jurisica I, Palmer R, Stagljar I. Mapping the Phospho-dependent ALK Interactome to Identify Novel Components in ALK Signaling. J Mol Biol 2021; 433:167283. [PMID: 34606829 DOI: 10.1016/j.jmb.2021.167283] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/27/2021] [Accepted: 09/27/2021] [Indexed: 10/25/2022]
Abstract
Protein-protein interactions (PPIs) play essential roles in Anaplastic Lymphoma Kinase (ALK) signaling. Systematic characterization of ALK interactors helps elucidate novel ALK signaling mechanisms and may aid in the identification of novel therapeutics targeting related diseases. In this study, we used the Mammalian Membrane Two-Hybrid (MaMTH) system to map the phospho-dependent ALK interactome. By screening a library of 86 SH2 domain-containing full length proteins, 30 novel ALK interactors were identified. Many of their interactions are correlated to ALK phosphorylation activity: oncogenic ALK mutations potentiate the interactions and ALK inhibitors attenuate the interactions. Among the novel interactors, NCK2 was further verified in neuroblastoma cells using co-immunoprecipitation. Modulation of ALK activity by addition of inhibitors lead to concomitant changes in the tyrosine phosphorylation status of NCK2 in neuroblastoma cells, strongly supporting the functionality of the ALK/NCK2 interaction. Our study provides a resource list of potential novel ALK signaling components for further study.
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Affiliation(s)
| | - Zhong Yao
- Donnelly Centre, University of Toronto, Ontario, Canada
| | - Jikui Guan
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-40530, Sweden
| | - Luka Drecun
- Donnelly Centre, University of Toronto, Ontario, Canada
| | | | - Jamie Snider
- Donnelly Centre, University of Toronto, Ontario, Canada
| | - Ganesh Umapathy
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-40530, Sweden
| | - Max Kotlyar
- Krembil Research Institute, University Health Network, Ontario, Canada
| | - Igor Jurisica
- Krembil Research Institute, University Health Network, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Ontario, Canada; Department of Computer Science, University of Toronto, Ontario, Canada; Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Ruth Palmer
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-40530, Sweden
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Ontario, Canada; Mediterranean Institute for Life Sciences, Meštrovićevo Šetalište 45, Split, Croatia; School of Medicine, University of Split, Split, Croatia. https://twitter.com/stagljar
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11
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Abstract
The non-catalytic region of tyrosine kinase (Nck) family of adaptors, consisting of Nck1 and Nck2, contributes to selectivity and specificity in the flow of cellular information by recruiting components of signaling networks. Known to play key roles in cytoskeletal remodeling, Nck adaptors modulate host cell-pathogen interactions, immune cell receptor activation, cell adhesion and motility, and intercellular junctions in kidney podocytes. Genetic inactivation of both members of the Nck family results in embryonic lethality; however, viability of mice lacking either one of these adaptors suggests partial functional redundancy. In this Cell Science at a Glance and the accompanying poster, we highlight the molecular organization and functions of the Nck family, focusing on key interactions and pathways, regulation of cellular processes, development, homeostasis and pathogenesis, as well as emerging and non-redundant functions of Nck1 compared to those of Nck2. This article thus aims to provide a timely perspective on the biology of Nck adaptors and their potential as therapeutic targets.
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Affiliation(s)
- Briana C. Bywaters
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 7783, USA
| | - Gonzalo M. Rivera
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 7783, USA
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12
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Light TP, Gomez-Soler M, Wang Z, Karl K, Zapata-Mercado E, Gehring MP, Lechtenberg BC, Pogorelov TV, Hristova K, Pasquale EB. A cancer mutation promotes EphA4 oligomerization and signaling by altering the conformation of the SAM domain. J Biol Chem 2021; 297:100876. [PMID: 34139238 PMCID: PMC8260879 DOI: 10.1016/j.jbc.2021.100876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 05/20/2021] [Accepted: 06/13/2021] [Indexed: 12/24/2022] Open
Abstract
The Eph receptor tyrosine kinases and their ephrin ligands regulate many physiological and pathological processes. EphA4 plays important roles in nervous system development and adult homeostasis, while aberrant EphA4 signaling has been implicated in neurodegeneration. EphA4 may also affect cancer malignancy, but the regulation and effects of EphA4 signaling in cancer are poorly understood. A correlation between decreased patient survival and high EphA4 mRNA expression in melanoma tumors that also highly express ephrinA ligands suggests that enhanced EphA4 signaling may contribute to melanoma progression. A search for EphA4 gain-of-function mutations in melanoma uncovered a mutation of the highly conserved leucine 920 in the EphA4 sterile alpha motif (SAM) domain. We found that mutation of L920 to phenylalanine (L920F) potentiates EphA4 autophosphorylation and signaling, making it the first documented EphA4 cancer mutation that increases kinase activity. Quantitative Föster resonance energy transfer and fluorescence intensity fluctuation (FIF) analyses revealed that the L920F mutation induces a switch in EphA4 oligomer size, from a dimer to a trimer. We propose this switch in oligomer size as a novel mechanism underlying EphA4-linked tumorigenesis. Molecular dynamics simulations suggest that the L920F mutation alters EphA4 SAM domain conformation, leading to the formation of EphA4 trimers that assemble through two aberrant SAM domain interfaces. Accordingly, EphA4 wild-type and the L920F mutant are affected differently by the SAM domain and are differentially regulated by ephrin ligand stimulation. The increased EphA4 activation induced by the L920F mutation, through the novel mechanism we uncovered, supports a functional role for EphA4 in promoting pathogenesis.
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Affiliation(s)
- Taylor P Light
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Maricel Gomez-Soler
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Zichen Wang
- Department of Chemistry, Center for Biophysics and Quantitative Biology, Beckman Institute for Advanced Science and Technology, and National Center for Supercomputing Applications, School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kelly Karl
- Program in Molecular Biophysics, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Elmer Zapata-Mercado
- Program in Molecular Biophysics, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Marina P Gehring
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Bernhard C Lechtenberg
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Taras V Pogorelov
- Department of Chemistry, Center for Biophysics and Quantitative Biology, Beckman Institute for Advanced Science and Technology, and National Center for Supercomputing Applications, School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kalina Hristova
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, USA; Program in Molecular Biophysics, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, USA.
| | - Elena B Pasquale
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA.
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13
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Alfaidi M, Scott ML, Orr AW. Sinner or Saint?: Nck Adaptor Proteins in Vascular Biology. Front Cell Dev Biol 2021; 9:688388. [PMID: 34124074 PMCID: PMC8187788 DOI: 10.3389/fcell.2021.688388] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/28/2021] [Indexed: 12/28/2022] Open
Abstract
The Nck family of modular adaptor proteins, including Nck1 and Nck2, link phosphotyrosine signaling to changes in cytoskeletal dynamics and gene expression that critically modulate cellular phenotype. The Nck SH2 domain interacts with phosphotyrosine at dynamic signaling hubs, such as activated growth factor receptors and sites of cell adhesion. The Nck SH3 domains interact with signaling effectors containing proline-rich regions that mediate their activation by upstream kinases. In vascular biology, Nck1 and Nck2 play redundant roles in vascular development and postnatal angiogenesis. However, recent studies suggest that Nck1 and Nck2 differentially regulate cell phenotype in the adult vasculature. Domain-specific interactions likely mediate these isoform-selective effects, and these isolated domains may serve as therapeutic targets to limit specific protein-protein interactions. In this review, we highlight the function of the Nck adaptor proteins, the known differences in domain-selective interactions, and discuss the role of individual Nck isoforms in vascular remodeling and function.
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Affiliation(s)
- Mabruka Alfaidi
- Department of Pathology and Translational Pathobiology, Louisiana State University Health - Shreveport, Shreveport, LA, United States
| | - Matthew L Scott
- Department of Pathology and Translational Pathobiology, Louisiana State University Health - Shreveport, Shreveport, LA, United States
| | - Anthony Wayne Orr
- Department of Pathology and Translational Pathobiology, Louisiana State University Health - Shreveport, Shreveport, LA, United States.,Department of Cell Biology and Anatomy, LSU Health - Shreveport, Shreveport, LA, United States.,Department of Molecular & Cellular Physiology, LSU Health - Shreveport, Shreveport, LA, United States
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14
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Protein context shapes the specificity of SH3 domain-mediated interactions in vivo. Nat Commun 2021; 12:1597. [PMID: 33712617 PMCID: PMC7954794 DOI: 10.1038/s41467-021-21873-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 02/17/2021] [Indexed: 02/07/2023] Open
Abstract
Protein–protein interactions (PPIs) between modular binding domains and their target peptide motifs are thought to largely depend on the intrinsic binding specificities of the domains. The large family of SRC Homology 3 (SH3) domains contribute to cellular processes via their ability to support such PPIs. While the intrinsic binding specificities of SH3 domains have been studied in vitro, whether each domain is necessary and sufficient to define PPI specificity in vivo is largely unknown. Here, by combining deletion, mutation, swapping and shuffling of SH3 domains and measurements of their impact on protein interactions in yeast, we find that most SH3s do not dictate PPI specificity independently from their host protein in vivo. We show that the identity of the host protein and the position of the SH3 domains within their host are critical for PPI specificity, for cellular functions and for key biophysical processes such as phase separation. Our work demonstrates the importance of the interplay between a modular PPI domain such as SH3 and its host protein in establishing specificity to wire PPI networks. These findings will aid understanding how protein networks are rewired during evolution and in the context of mutation-driven diseases such as cancer. The SRC Homology 3 (SH3) domains mediate protein–protein interactions (PPIs). Here, the authors assess the SH3-mediated PPIs in yeast, and show that the identity of the protein itself and the position of the SH3 both affect the interaction specificity and thus the PPI-dependent cellular functions.
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15
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Vélot L, Lessard F, Bérubé-Simard FA, Tav C, Neveu B, Teyssier V, Boudaoud I, Dionne U, Lavoie N, Bilodeau S, Pouliot F, Bisson N. Proximity-dependent Mapping of the Androgen Receptor Identifies Kruppel-like Factor 4 as a Functional Partner. Mol Cell Proteomics 2021; 20:100064. [PMID: 33640491 PMCID: PMC8050775 DOI: 10.1016/j.mcpro.2021.100064] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/15/2022] Open
Abstract
Prostate cancer (PCa) is the most frequently diagnosed cancer in men and the third cause of cancer mortality. PCa initiation and growth are driven by the androgen receptor (AR). The AR is activated by androgens such as testosterone and controls prostatic cell proliferation and survival. Here, we report an AR signaling network generated using BioID proximity labeling proteomics in androgen-dependent LAPC4 cells. We identified 31 AR-associated proteins in nonstimulated cells. Strikingly, the AR signaling network increased to 182 and 200 proteins, upon 24 h or 72 h of androgenic stimulation, respectively, for a total of 267 nonredundant AR-associated candidates. Among the latter group, we identified 213 proteins that were not previously reported in databases. Many of these new AR-associated proteins are involved in DNA metabolism, RNA processing, and RNA polymerase II transcription. Moreover, we identified 44 transcription factors, including the Kru¨ppel-like factor 4 (KLF4), which were found interacting in androgen-stimulated cells. Interestingly, KLF4 repressed the well-characterized AR-dependent transcription of the KLK3 (PSA) gene; AR and KLF4 also colocalized genome-wide. Taken together, our data report an expanded high-confidence proximity network for AR, which will be instrumental to further dissect the molecular mechanisms underlying androgen signaling in PCa cells. BioID proteomics identifies 267 androgen receptor (AR)-associated candidates Krüppel-like factor 4 (KLF4) is a new AR interaction partner AR and KLF4 colocalize genome-wide on >4000 genes, including KLK3 (PSA) KLF4 acts as a repressor for the AR target gene KLK3 (PSA)
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Affiliation(s)
- Lauriane Vélot
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, Quebec, Canada
| | - Frédéric Lessard
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, Quebec, Canada
| | - Félix-Antoine Bérubé-Simard
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada
| | - Christophe Tav
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; Centre de recherche en données massives de l'Université Laval, Québec, Québec, Canada
| | - Bertrand Neveu
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada
| | - Valentine Teyssier
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, Quebec, Canada
| | - Imène Boudaoud
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada
| | - Ugo Dionne
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, Quebec, Canada
| | - Noémie Lavoie
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, Quebec, Canada
| | - Steve Bilodeau
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; Centre de recherche en données massives de l'Université Laval, Québec, Québec, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculté de Médecine, Université Laval, Québec, Quebec, Canada
| | - Frédéric Pouliot
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; Department of Surgery, Faculté de Médecine, Université Laval, Québec, Quebec, Canada.
| | - Nicolas Bisson
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, Quebec, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculté de Médecine, Université Laval, Québec, Quebec, Canada.
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16
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LY75 Ablation Mediates Mesenchymal-Epithelial Transition (MET) in Epithelial Ovarian Cancer (EOC) Cells Associated with DNA Methylation Alterations and Suppression of the Wnt/β-Catenin Pathway. Int J Mol Sci 2020; 21:ijms21051848. [PMID: 32156068 PMCID: PMC7084525 DOI: 10.3390/ijms21051848] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/26/2020] [Accepted: 03/05/2020] [Indexed: 02/07/2023] Open
Abstract
Growing evidence demonstrates that epithelial-mesenchymal transition (EMT) plays an important role in epithelial ovarian cancer (EOC) progression and spreading; however, its molecular mechanisms remain poorly defined. We have previously shown that the antigen receptor LY75 can modulate EOC cell phenotype and metastatic potential, as LY75 depletion directed mesenchymal-epithelial transition (MET) in EOC cell lines with mesenchymal phenotype. We used the LY75-mediated modulation of EMT as a model to investigate for DNA methylation changes during EMT in EOC cells, by applying the reduced representation bisulfite sequencing (RRBS) methodology. Numerous genes have displayed EMT-related DNA methylation patterns alterations in their promoter/exon regions. Ten selected genes, whose DNA methylation alterations were further confirmed by alternative methods, were further identified, some of which could represent new EOC biomarkers/therapeutic targets. Moreover, our methylation data were strongly indicative for the predominant implication of the Wnt/β-catenin pathway in the EMT-induced DNA methylation variations in EOC cells. Consecutive experiments, including alterations in the Wnt/β-catenin pathway activity in EOC cells with a specific inhibitor and the identification of LY75-interacting partners by a proteomic approach, were strongly indicative for the direct implication of the LY75 receptor in modulating the Wnt/β-catenin signaling in EOC cells.
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17
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Liang LY, Patel O, Janes PW, Murphy JM, Lucet IS. Eph receptor signalling: from catalytic to non-catalytic functions. Oncogene 2019; 38:6567-6584. [PMID: 31406248 DOI: 10.1038/s41388-019-0931-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/23/2019] [Accepted: 07/24/2019] [Indexed: 12/26/2022]
Abstract
Eph receptors, the largest subfamily of receptor tyrosine kinases, are linked with proliferative disease, such as cancer, as a result of their deregulated expression or mutation. Unlike other tyrosine kinases that have been clinically targeted, the development of therapeutics against Eph receptors remains at a relatively early stage. The major reason is the limited understanding on the Eph receptor regulatory mechanisms at a molecular level. The complexity in understanding Eph signalling in cells arises due to following reasons: (1) Eph receptors comprise 14 members, two of which are pseudokinases, EphA10 and EphB6, with relatively uncharacterised function; (2) activation of Eph receptors results in dimerisation, oligomerisation and formation of clustered signalling centres at the plasma membrane, which can comprise different combinations of Eph receptors, leading to diverse downstream signalling outputs; (3) the non-catalytic functions of Eph receptors have been overlooked. This review provides a structural perspective of the intricate molecular mechanisms that drive Eph receptor signalling, and investigates the contribution of intra- and inter-molecular interactions between Eph receptors intracellular domains and their major binding partners. We focus on the non-catalytic functions of Eph receptors with relevance to cancer, which are further substantiated by exploring the role of the two pseudokinase Eph receptors, EphA10 and EphB6. Throughout this review, we carefully analyse and reconcile the existing/conflicting data in the field, to allow researchers to further the current understanding of Eph receptor signalling.
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Affiliation(s)
- Lung-Yu Liang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Onisha Patel
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Peter W Janes
- Olivia Newton-John Cancer Research Institute, 145 Studley Road, Heidelberg, VIC, 3084, Australia
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.
| | - Isabelle S Lucet
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.
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18
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Malagrinò F, Troilo F, Bonetti D, Toto A, Gianni S. Mapping the allosteric network within a SH3 domain. Sci Rep 2019; 9:8279. [PMID: 31164678 PMCID: PMC6547694 DOI: 10.1038/s41598-019-44656-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 05/21/2019] [Indexed: 11/09/2022] Open
Abstract
SH3 domains are very abundant protein-protein interactions modules, involved in the regulation of several cellular processes. Whilst they have been associated to allosteric communication pathways between contiguous domains in multi-domain proteins, there is lack of information regarding the intra-domain allosteric cross-talk within the SH3 moiety. Here we scrutinize the presence of an allosteric network in the C-terminal SH3 domain of Grb2 protein, upon binding the Grb2-associated binding 2 protein. To explore allostery, we performed double mutant cycle analysis, a powerful quantitative approach based on mutagenesis in conjunction with kinetic experiments. Data reveal the presence of an unexpected allosteric sparse network that modulates the affinity between the SH3 domain and its physiological partner.
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Affiliation(s)
- Francesca Malagrinò
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy
| | - Francesca Troilo
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy
| | - Daniela Bonetti
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy
| | - Angelo Toto
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy
| | - Stefano Gianni
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy.
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19
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Merő B, Radnai L, Gógl G, Tőke O, Leveles I, Koprivanacz K, Szeder B, Dülk M, Kudlik G, Vas V, Cserkaszky A, Sipeki S, Nyitray L, Vértessy BG, Buday L. Structural insights into the tyrosine phosphorylation-mediated inhibition of SH3 domain-ligand interactions. J Biol Chem 2019; 294:4608-4620. [PMID: 30659095 DOI: 10.1074/jbc.ra118.004732] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 01/17/2019] [Indexed: 01/01/2023] Open
Abstract
Src homology 3 (SH3) domains bind proline-rich linear motifs in eukaryotes. By mediating inter- and intramolecular interactions, they regulate the functions of many proteins involved in a wide variety of signal transduction pathways. Phosphorylation at different tyrosine residues in SH3 domains has been reported previously. In several cases, the functional consequences have also been investigated. However, a full understanding of the effects of tyrosine phosphorylation on the ligand interactions and cellular functions of SH3 domains requires detailed structural, atomic-resolution studies along with biochemical and biophysical analyses. Here, we present the first crystal structures of tyrosine-phosphorylated human SH3 domains derived from the Abelson-family kinases ABL1 and ABL2 at 1.6 and 1.4 Å resolutions, respectively. The structures revealed that simultaneous phosphorylation of Tyr89 and Tyr134 in ABL1 or the homologous residues Tyr116 and Tyr161 in ABL2 induces only minor structural perturbations. Instead, the phosphate groups sterically blocked the ligand-binding grooves, thereby strongly inhibiting the interaction with proline-rich peptide ligands. Although some crystal contact surfaces involving phosphotyrosines suggested the possibility of tyrosine phosphorylation-induced dimerization, we excluded this possibility by using small-angle X-ray scattering (SAXS), dynamic light scattering (DLS), and NMR relaxation analyses. Extensive analysis of relevant databases and literature revealed not only that the residues phosphorylated in our model systems are well-conserved in other human SH3 domains, but that the corresponding tyrosines are known phosphorylation sites in vivo in many cases. We conclude that tyrosine phosphorylation might be a mechanism involved in the regulation of the human SH3 interactome.
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Affiliation(s)
| | | | - Gergő Gógl
- the Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest H-1117, Hungary
| | - Orsolya Tőke
- Laboratory for NMR Spectroscopy, Research Center for Natural Sciences (RCNS), Hungarian Academy of Sciences, Magyar tudósok körútja 2, Budapest H-1117, Hungary
| | - Ibolya Leveles
- From the Institute of Enzymology and.,the Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Szt. Gellért tér 4, Budapest H-1111, Hungary, and
| | | | | | | | | | - Virág Vas
- From the Institute of Enzymology and
| | | | - Szabolcs Sipeki
- the Department of Medical Chemistry, Semmelweis University Medical School, Tűzoltó u. 37-47, Budapest H-1094, Hungary
| | - László Nyitray
- the Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest H-1117, Hungary
| | - Beáta G Vértessy
- From the Institute of Enzymology and.,the Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Szt. Gellért tér 4, Budapest H-1111, Hungary, and
| | - László Buday
- From the Institute of Enzymology and .,the Department of Medical Chemistry, Semmelweis University Medical School, Tűzoltó u. 37-47, Budapest H-1094, Hungary
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