1
|
Hammond FR, Lewis A, Pollara G, Tomlinson GS, Noursadeghi M, Kiss-Toth E, Elks PM. Tribbles1 is host protective during in vivo mycobacterial infection. eLife 2024; 13:e95980. [PMID: 38896446 PMCID: PMC11186633 DOI: 10.7554/elife.95980] [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: 01/10/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Tuberculosis is a major global health problem and is one of the top 10 causes of death worldwide. There is a pressing need for new treatments that circumvent emerging antibiotic resistance. Mycobacterium tuberculosis parasitises macrophages, reprogramming them to establish a niche in which to proliferate, therefore macrophage manipulation is a potential host-directed therapy if druggable molecular targets could be identified. The pseudokinase Tribbles1 (Trib1) regulates multiple innate immune processes and inflammatory profiles making it a potential drug target in infections. Trib1 controls macrophage function, cytokine production, and macrophage polarisation. Despite wide-ranging effects on leukocyte biology, data exploring the roles of Tribbles in infection in vivo are limited. Here, we identify that human Tribbles1 is expressed in monocytes and is upregulated at the transcript level after stimulation with mycobacterial antigen. To investigate the mechanistic roles of Tribbles in the host response to mycobacteria in vivo, we used a zebrafish Mycobacterium marinum (Mm) infection tuberculosis model. Zebrafish Tribbles family members were characterised and shown to have substantial mRNA and protein sequence homology to their human orthologues. trib1 overexpression was host-protective against Mm infection, reducing burden by approximately 50%. Conversely, trib1 knockdown/knockout exhibited increased infection. Mechanistically, trib1 overexpression significantly increased the levels of proinflammatory factors il-1β and nitric oxide. The host-protective effect of trib1 was found to be dependent on the E3 ubiquitin kinase Cop1. These findings highlight the importance of Trib1 and Cop1 as immune regulators during infection in vivo and suggest that enhancing macrophage TRIB1 levels may provide a tractable therapeutic intervention to improve bacterial infection outcomes in tuberculosis.
Collapse
Affiliation(s)
- Ffion R Hammond
- The Bateson Centre, School of Medicine and Population Health, Faculty of Health, University of SheffieldSheffieldUnited Kingdom
| | - Amy Lewis
- The Bateson Centre, School of Medicine and Population Health, Faculty of Health, University of SheffieldSheffieldUnited Kingdom
| | - Gabriele Pollara
- Division of Infection & Immunity, University College LondonLondonUnited Kingdom
| | - Gillian S Tomlinson
- Division of Infection & Immunity, University College LondonLondonUnited Kingdom
| | - Mahdad Noursadeghi
- Division of Infection & Immunity, University College LondonLondonUnited Kingdom
| | - Endre Kiss-Toth
- The Bateson Centre, School of Medicine and Population Health, Faculty of Health, University of SheffieldSheffieldUnited Kingdom
| | - Philip M Elks
- The Bateson Centre, School of Medicine and Population Health, Faculty of Health, University of SheffieldSheffieldUnited Kingdom
| |
Collapse
|
2
|
Santana FR, Linossi EM, Jura N. Trapping Tribbles: Nanobody-assisted structure of the TRIB2 pseudokinase. Structure 2022; 30:1465-1467. [DOI: 10.1016/j.str.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
3
|
TRIB3 Modulates PPARγ-Mediated Growth Inhibition by Interfering with the MLL Complex in Breast Cancer Cells. Int J Mol Sci 2022; 23:ijms231810535. [PMID: 36142452 PMCID: PMC9503934 DOI: 10.3390/ijms231810535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 12/03/2022] Open
Abstract
Aberrant expression or activity of proteins are amongst the best understood mechanisms that can drive cancer initiation and progression, as well as therapy resistance. TRIB3, a member of the Tribbles family of pseudokinases, is often dysregulated in cancer and has been associated with breast cancer initiation and metastasis formation. However, the underlying mechanisms by which TRIB3 contributes to these events are unclear. In this study, we demonstrate that TRIB3 regulates the expression of PPARγ, a transcription factor that has gained attention as a potential drug target in breast cancer for its antiproliferative actions. Proteomics and phosphoproteomics analyses together with classical biochemical assays indicate that TRIB3 interferes with the MLL complex and reduces MLL-mediated H3K4 trimethylation of the PPARG locus, thereby reducing PPARγ mRNA expression. Consequently, the overexpression of TRIB3 blunts the antiproliferative effect of PPARγ ligands in breast cancer cells, while reduced TRIB3 expression gives the opposite effect. In conclusion, our data implicate TRIB3 in epigenetic gene regulation and suggest that expression levels of this pseudokinase may serve as a predictor of successful experimental treatments with PPARγ ligands in breast cancer.
Collapse
|
4
|
Jamieson SA, Pudjihartono M, Horne CR, Viloria JS, Dunlop JL, McMillan HD, Day RC, Keeshan K, Murphy JM, Mace PD. Nanobodies identify an activated state of the TRIB2 pseudokinase. Structure 2022; 30:1518-1529.e5. [PMID: 36108635 DOI: 10.1016/j.str.2022.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/02/2022] [Accepted: 08/19/2022] [Indexed: 12/23/2022]
Abstract
Tribbles proteins (TRIB1-3) are pseudokinases that recruit substrates to the COP1 ubiquitin ligase. TRIB2 was the first Tribbles ortholog to be implicated as a myeloid leukemia oncogene, because it recruits the C/EBPα transcription factor for ubiquitination by COP1. Here we report identification of nanobodies that bind the TRIB2 pseudokinase domain with low nanomolar affinity. A crystal structure of the TRIB2-Nb4.103 complex identified the nanobody to bind the N-terminal lobe of TRIB2, enabling specific recognition of TRIB2 in an activated conformation that is similar to the C/EBPα-bound state of TRIB1. Characterization in solution revealed that Nb4.103 can stabilize a TRIB2 pseudokinase domain dimer in a face-to-face manner. Conversely, a distinct nanobody (Nb4.101) binds through a similar epitope but does not readily promote dimerization. In combination, this study identifies features of TRIB2 that could be exploited for the development of inhibitors and nanobody tools for future investigation of TRIB2 function.
Collapse
Affiliation(s)
- Sam A Jamieson
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Michael Pudjihartono
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Christopher R Horne
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | | | - Jessica L Dunlop
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Hamish D McMillan
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Robert C Day
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Karen Keeshan
- Paul O'Gorman Leukaemia Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, Scotland
| | - 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 3010, Australia
| | - Peter D Mace
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand.
| |
Collapse
|
5
|
Lal R, Ritchie J, Richmond L, Keeshan K. Detecting endogenous TRIB2 protein expression by flow cytometry and Western blotting. Methods Enzymol 2022; 667:59-77. [PMID: 35525555 DOI: 10.1016/bs.mie.2022.03.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Protein kinases catalyze the transfer of a phosphate group thereby activating proteins and initiating signaling cascades. Their cousins, the pseudokinases, are enzymatically nonactive counterparts of protein kinases that can be considered zombie enzymes. Interestingly, pseudokinases, which constitute about 10% of the human kinome, have been implicated in many cancers, despite their sequences predicting a lack of catalytic activity. Owing to recent research, it has been demonstrated that dysregulation of many pseudokinases triggers changes in cell signaling, proliferation, and drug resistance. This review is aimed at describing methods that can be used for detection of Tribbles family of pseudokinases, specifically TRIB2. We describe intracellular staining by flow cytometry and Western blotting techniques for the detection of endogenous TRIB2 protein.
Collapse
Affiliation(s)
- Ridhima Lal
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, SC, United Kingdom
| | - Jake Ritchie
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, SC, United Kingdom
| | - Laura Richmond
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, SC, United Kingdom
| | - Karen Keeshan
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, SC, United Kingdom.
| |
Collapse
|
6
|
Harris JA, Fairweather E, Byrne DP, Eyers PA. Analysis of human Tribbles 2 (TRIB2) pseudokinase. Methods Enzymol 2022; 667:79-99. [PMID: 35525562 DOI: 10.1016/bs.mie.2022.03.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Human Tribbles 2 (TRIB2) is a cancer-associated pseudokinase with a broad human protein interactome, including the well-studied AKT, C/EBPα and MAPK modules. Several lines of evidence indicate that human TRIB2 promotes cell survival and drug-resistance in solid tumors and blood cancers and is therefore of interest as a potential therapeutic target, although its physiological functions remain relatively poorly understood. The unique TRIB2 pseudokinase domain lacks the canonical 'DFG' motif, and subsequently possesses very low affinity for ATP in both the presence and absence of metal ions. However, TRIB2 also contains a unique cysteine-rich αC-helix, which interacts with a conserved peptide motif in its own carboxyl-terminal tail. This regulatory flanking region drives regulated interactions with distinct E3 ubiquitin ligases that serve to control the stability and turnover of TRIB2 client proteins. TRIB2 is also a low-affinity target of several known small-molecule protein kinase inhibitors, which were originally identified using purified recombinant TRIB2 proteins and a thermal shift assay. In this chapter, we discuss laboratory-based procedures for purification, stabilization and analysis of human TRIB2, including screening procedures that can be used for the identification of both reversible and covalent small molecule ligands.
Collapse
Affiliation(s)
- John A Harris
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Emma Fairweather
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Dominic P Byrne
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Patrick A Eyers
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom.
| |
Collapse
|
7
|
Fitzgibbon C, Meng Y, Murphy JM. Co-expression of recombinant RIPK3:MLKL complexes using the baculovirus-insect cell system. Methods Enzymol 2022; 667:183-227. [PMID: 35525542 DOI: 10.1016/bs.mie.2022.03.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pseudokinase domains are found throughout the kingdoms of life and serve myriad roles in cell signaling. These domains, which resemble protein kinases but are catalytically-deficient, have been described principally as protein interaction domains. Broadly, pseudokinases have been reported to function as: allosteric regulators of conventional enzymes; scaffolds to nucleate assembly and/or localization of signaling complexes; molecular switches; or competitors of signaling complex assembly. From detailed structural and biochemical studies of individual pseudokinases, a picture of how they mediate protein interactions is beginning to emerge. Many such studies have relied on recombinant protein production in insect cells, where endogenous chaperones and modifying enzymes favor bona fide folding of pseudokinases. Here, we describe methods for co-expression of pseudokinases and their interactors in insect cells, as exemplified by the MLKL pseudokinase, which is the terminal effector in the necroptosis cell death pathway, and its upstream regulator kinase RIPK3. These methods are broadly applicable to co-expression of other pseudokinases with their interaction partners from bacmids using the baculovirus-insect cell expression system.
Collapse
Affiliation(s)
- Cheree Fitzgibbon
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Yanxiang Meng
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
| |
Collapse
|
8
|
Hernández-Quiles M, Baak R, Borgman A, den Haan S, Sobrevals Alcaraz P, van Es R, Kiss-Toth E, Vos H, Kalkhoven E. Comprehensive Profiling of Mammalian Tribbles Interactomes Implicates TRIB3 in Gene Repression. Cancers (Basel) 2021; 13:6318. [PMID: 34944947 PMCID: PMC8699236 DOI: 10.3390/cancers13246318] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 12/30/2022] Open
Abstract
The three human Tribbles (TRIB) pseudokinases have been implicated in a plethora of signaling and metabolic processes linked to cancer initiation and progression and can potentially be used as biomarkers of disease and prognosis. While their modes of action reported so far center around protein-protein interactions, the comprehensive profiling of TRIB interactomes has not been reported yet. Here, we have developed a robust mass spectrometry (MS)-based proteomics approach to characterize Tribbles' interactomes and report a comprehensive assessment and comparison of the TRIB1, -2 and -3 interactomes, as well as domain-specific interactions for TRIB3. Interestingly, TRIB3, which is predominantly localized in the nucleus, interacts with multiple transcriptional regulators, including proteins involved in gene repression. Indeed, we found that TRIB3 repressed gene transcription when tethered to DNA in breast cancer cells. Taken together, our comprehensive proteomic assessment reveals previously unknown interacting partners and functions of Tribbles proteins that expand our understanding of this family of proteins. In addition, our findings show that MS-based proteomics provides a powerful tool to unravel novel pseudokinase biology.
Collapse
Affiliation(s)
- Miguel Hernández-Quiles
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.H.-Q.); (R.B.); (A.B.); (S.d.H.)
| | - Rosalie Baak
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.H.-Q.); (R.B.); (A.B.); (S.d.H.)
| | - Anouska Borgman
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.H.-Q.); (R.B.); (A.B.); (S.d.H.)
| | - Suzanne den Haan
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.H.-Q.); (R.B.); (A.B.); (S.d.H.)
| | - Paula Sobrevals Alcaraz
- Oncode Institute and Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (P.S.A.); (R.v.E.); (H.V.)
| | - Robert van Es
- Oncode Institute and Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (P.S.A.); (R.v.E.); (H.V.)
| | - Endre Kiss-Toth
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2TN, UK;
| | - Harmjan Vos
- Oncode Institute and Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (P.S.A.); (R.v.E.); (H.V.)
| | - Eric Kalkhoven
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.H.-Q.); (R.B.); (A.B.); (S.d.H.)
| |
Collapse
|
9
|
Zahid S, Basharat S, Fakhar M, Rashid S. Molecular dynamics and structural analysis of the binding of COP1 E3 ubiquitin ligase to β-catenin and TRIB pseudokinases. Proteins 2021; 90:993-1004. [PMID: 34881468 DOI: 10.1002/prot.26292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 11/14/2021] [Accepted: 12/02/2021] [Indexed: 12/30/2022]
Abstract
Tribbles pseudokinases, Tribbles homolog 1 (TRIB1), Tribbles homolog 2 (TRIB2), and Tribbles homolog 3 (TRIB3), bind to constitutive photomorphogenesis protein 1 (COP1) E3 ligase to mediate the regulation of β-catenin expression. The interaction mechanism between COP1 E3 ligase and β-catenin has not been addressed to date. Based on the functional presence of TRIBs in wingless-related integration site (WNT) signaling, we analyzed their interaction patterns with β-catenin and COP1. Here, through in silico approaches, we ascribe the COP1 binding pattern against TRIBs and β-catenin. TRIB1 (355-DQIVPEY-361), TRIB2 (326-DQLVPDV-332), and TRIB3 (333-AQVVPDG-339) peptides revealed a shallow binding pocket at the COP1 interface to accommodate the V-P sequence motif. Reinvigoration of the comparative binding pattern and subtle structural analysis via docking, molecular dynamics simulations, molecular mechanics Poisson-Boltzmann surface area, topological, and tunnel analysis revealed that both β-catenin phosphodegron (DSGXXS) and TRIB (D/E/AQXVPD/E) motifs occupied a common COP1 binding site. Current study suggests a structural paradigm of TRIB homologs bearing a conserved motif that may compete with β-catenin phosphodegron signature for binding to WD40 domain of COP1. Thorough understanding of the structural basis for TRIB-mediated regulation of WNT/β-catenin signaling may help in devising more promising therapeutic strategy for liver and colorectal cancers.
Collapse
Affiliation(s)
- Sana Zahid
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Saba Basharat
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Fakhar
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sajid Rashid
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| |
Collapse
|
10
|
Pan H, Liu Q, Zhang F, Wang X, Wang S, Shi X. High STK40 Expression as an Independent Prognostic Biomarker and Correlated with Immune Infiltrates in Low-Grade Gliomas. Int J Gen Med 2021; 14:6389-6400. [PMID: 34675607 DOI: 10.2147/ijgm.s335821] [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: 08/24/2021] [Accepted: 09/22/2021] [Indexed: 11/23/2022] Open
Abstract
Background Expression of STK40 is observed in some cancer types, while its role in low-grade gliomas (LGG) is unclear. The present study aimed to demonstrate the relationship between STK40 and LGG based on The Cancer Genome Atlas (TCGA) database and bioinformatics analysis. Methods Kruskal-Wallis test, Wilcoxon sign-rank test, and logistic regression were used to evaluate the relationship between clinicopathological features and STK40 expression. Kaplan-Meier method and Cox regression analysis were used to evaluate prognostic factors. Gene set enrichment analysis (GSEA) and immuno-infiltration analysis were used to determine the significant involvement of STK40 in function. Results High STK40 expression in LGG was associated with WHO grade (P<0.001), IDH status (P<0.001), primary therapy outcome (P=0.027), 1p/19q codeletion (P<0.001) and histological type (P<0.001). High STK40 expression predicted a poorer overall survival (OS) (HR: 3.07; 95% CI: 2.09-4.51; P<0.001), progression-free survival (PFS) (HR:2.11; 95% CI: 1.59-2.81; P<0.001) and disease specific survival (DSS) (HR: 3.27; 95% CI: 2.17-4.92; P<0.001). STK40 expression (HR: 2.284; 95% CI: 1.125-4.637; P=0.022) was independently correlated with OS in LGG patients. GSEA demonstrated that pathways including cell cycle mitotic, neutrophil degranulation, signaling by Rho GTPases, signaling by interleukins, M phase, PI3K-Akt signaling pathway and naba secreted factors were differentially enriched in STK40 high expression phenotype. Immune infiltration analysis showed that STK40 expression was correlated with some types of immune infiltrating cells. Conclusion STK40 expression was significantly correlated with poor survival and immune infiltration in LGG, and it may be a promising prognostic biomarker in LGG.
Collapse
Affiliation(s)
- Heyue Pan
- Department of Neurology, The Third People's Hospital of Huai'an, Huai'an, Jiangsu, 223001, People's Republic of China
| | - Qirui Liu
- Department of Neurology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221000, People's Republic of China
| | - Fuchi Zhang
- Department of Neurology, The Third People's Hospital of Huai'an, Huai'an, Jiangsu, 223001, People's Republic of China
| | - Xiaohua Wang
- Department of Neurology, The Third People's Hospital of Huai'an, Huai'an, Jiangsu, 223001, People's Republic of China
| | - Shouyong Wang
- Department of Neurology, The Third People's Hospital of Huai'an, Huai'an, Jiangsu, 223001, People's Republic of China
| | - Xiangsong Shi
- Department of Neurology, The Third People's Hospital of Huai'an, Huai'an, Jiangsu, 223001, People's Republic of China
| |
Collapse
|
11
|
Yu LY, Tseng TJ, Lin HC, Hsu CL, Lu TX, Tsai CJ, Lin YC, Chu I, Peng CT, Chen HJ, Tsai FC. Synthetic dysmobility screen unveils an integrated STK40-YAP-MAPK system driving cell migration. SCIENCE ADVANCES 2021; 7:eabg2106. [PMID: 34321207 PMCID: PMC8318371 DOI: 10.1126/sciadv.abg2106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 06/10/2021] [Indexed: 05/05/2023]
Abstract
Integrating signals is essential for cell survival, leading to the concept of synthetic lethality. However, how signaling is integrated to control cell migration remains unclear. By conducting a "two-hit" screen, we revealed the synergistic reduction of cell migration when serine-threonine kinase 40 (STK40) and mitogen-activated protein kinase (MAPK) were simultaneously suppressed. Single-cell analyses showed that STK40 knockdown reduced cell motility and coordination by strengthening focal adhesion (FA) complexes. Furthermore, STK40 knockdown reduced the stability of yes-associated protein (YAP) and subsequently decreased YAP transported into the nucleus, while MAPK inhibition further weakened YAP activities in the nucleus to disturb FA remodeling. Together, we unveiled an integrated STK40-YAP-MAPK system regulating cell migration and introduced "synthetic dysmobility" as a novel strategy to collaboratively control cell migration.
Collapse
Affiliation(s)
- Ling-Yea Yu
- Department of Pharmacology, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Ting-Jen Tseng
- Department of Pharmacology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Hsuan-Chao Lin
- Department of Immunology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chi-Lin Hsu
- Department of Pharmacology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ting-Xuan Lu
- Department of Pharmacology, National Taiwan University College of Medicine, Taipei, Taiwan
- Ph.D. Program in Biological Sciences, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Chia-Jung Tsai
- Department of Pharmacology, National Taiwan University College of Medicine, Taipei, Taiwan
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Japan
| | - Yu-Chiao Lin
- Department of Pharmacology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - I Chu
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Tzu Peng
- Department of Pharmacology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Hou-Jen Chen
- Department of Pharmacology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Feng-Chiao Tsai
- Department of Pharmacology, National Taiwan University College of Medicine, Taipei, Taiwan.
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| |
Collapse
|
12
|
McMillan HD, Keeshan K, Dunbier AK, Mace PD. Structure vs. Function of TRIB1-Myeloid Neoplasms and Beyond. Cancers (Basel) 2021; 13:3060. [PMID: 34205360 PMCID: PMC8235551 DOI: 10.3390/cancers13123060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 12/31/2022] Open
Abstract
The Tribbles family of proteins-comprising TRIB1, TRIB2, TRIB3 and more distantly related STK40-play important, but distinct, roles in differentiation, development and oncogenesis. Of the four Tribbles proteins, TRIB1 has been most well characterised structurally and plays roles in diverse cancer types. The most well-understood role of TRIB1 is in acute myeloid leukaemia, where it can regulate C/EBP transcription factors and kinase pathways. Structure-function studies have uncovered conformational switching of TRIB1 from an inactive to an active state when it binds to C/EBPα. This conformational switching is centred on the active site of TRIB1, which appears to be accessible to small-molecule inhibitors in spite of its inability to bind ATP. Beyond myeloid neoplasms, TRIB1 plays diverse roles in signalling pathways with well-established roles in tumour progression. Thus, TRIB1 can affect both development and chemoresistance in leukaemia; glioma; and breast, lung and prostate cancers. The pervasive roles of TRIB1 and other Tribbles proteins across breast, prostate, lung and other cancer types, combined with small-molecule susceptibility shown by mechanistic studies, suggests an exciting potential for Tribbles as direct targets of small molecules or biomarkers to predict treatment response.
Collapse
Affiliation(s)
- Hamish D McMillan
- Biochemistry Department, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; (H.D.M.); (A.K.D.)
| | - Karen Keeshan
- Paul O’Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Scotland G12 0YN, UK;
| | - Anita K Dunbier
- Biochemistry Department, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; (H.D.M.); (A.K.D.)
| | - Peter D Mace
- Biochemistry Department, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; (H.D.M.); (A.K.D.)
| |
Collapse
|
13
|
Mace PD, Murphy JM. There's more to death than life: Noncatalytic functions in kinase and pseudokinase signaling. J Biol Chem 2021; 296:100705. [PMID: 33895136 PMCID: PMC8141879 DOI: 10.1016/j.jbc.2021.100705] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 12/11/2022] Open
Abstract
Protein kinases are present in all domains of life and play diverse roles in cellular signaling. Whereas the impact of substrate phosphorylation by protein kinases has long been appreciated, it is becoming increasingly clear that protein kinases also play other, noncatalytic, functions. Here, we review recent developments in understanding the noncatalytic functions of protein kinases. Many noncatalytic activities are best exemplified by protein kinases that are devoid of enzymatic activity altogether-known as pseudokinases. These dead proteins illustrate that, beyond conventional notions of kinase function, catalytic activity can be dispensable for biological function. Through key examples we illustrate diverse mechanisms of noncatalytic kinase activity: as allosteric modulators; protein-based switches; scaffolds for complex assembly; and as competitive inhibitors in signaling pathways. In common, these noncatalytic mechanisms exploit the nature of the protein kinase fold as a versatile protein-protein interaction module. Many examples are also intrinsically linked to the ability of the protein kinase to switch between multiple states, a function shared with catalytic protein kinases. Finally, we consider the contemporary landscape of small molecules to modulate noncatalytic functions of protein kinases, which, although challenging, has significant potential given the scope of noncatalytic protein kinase function in health and disease.
Collapse
Affiliation(s)
- Peter D Mace
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.
| | - James M Murphy
- Inflammation Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
| |
Collapse
|
14
|
Preuss F, Chatterjee D, Mathea S, Shrestha S, St-Germain J, Saha M, Kannan N, Raught B, Rottapel R, Knapp S. Nucleotide Binding, Evolutionary Insights, and Interaction Partners of the Pseudokinase Unc-51-like Kinase 4. Structure 2020; 28:1184-1196.e6. [PMID: 32814032 DOI: 10.1016/j.str.2020.07.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/17/2020] [Accepted: 07/29/2020] [Indexed: 01/11/2023]
Abstract
Unc-51-like kinase 4 (ULK4) is a pseudokinase that has been linked to the development of several diseases. Even though sequence motifs required for ATP binding in kinases are lacking, ULK4 still tightly binds ATP and the presence of the co-factor is required for structural stability of ULK4. Here, we present a high-resolution structure of a ULK4-ATPγS complex revealing a highly unusual ATP binding mode in which the lack of the canonical VAIK motif lysine is compensated by K39, located N-terminal to αC. Evolutionary analysis suggests that degradation of active site motifs in metazoan ULK4 has co-occurred with an ULK4-specific activation loop, which stabilizes the C helix. In addition, cellular interaction studies using BioID and biochemical validation data revealed high confidence interactors of the pseudokinase and armadillo repeat domains. Many of the identified ULK4 interaction partners were centrosomal and tubulin-associated proteins and several active kinases suggesting interesting regulatory roles for ULK4.
Collapse
Affiliation(s)
- Franziska Preuss
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Structural Genomics Consortium, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Deep Chatterjee
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Structural Genomics Consortium, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Sebastian Mathea
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Structural Genomics Consortium, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Safal Shrestha
- Institute of Bioinformatics & Department of Biochemistry and Molecular Biology, University of Georgia, 120 Green Street, Athens, GA 30602-7229, USA
| | - Jonathan St-Germain
- Princess Margaret Cancer Centre, University Health Network, Toronto M5G 2C4, Canada
| | - Manipa Saha
- Princess Margaret Cancer Centre, University Health Network, Toronto M5G 2C4, Canada
| | - Natarajan Kannan
- Institute of Bioinformatics & Department of Biochemistry and Molecular Biology, University of Georgia, 120 Green Street, Athens, GA 30602-7229, USA
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto M5G 2C4, Canada
| | - Robert Rottapel
- Princess Margaret Cancer Centre, University Health Network, Toronto M5G 2C4, Canada; Departments of Medicine, Immunology and Medical Biophysics, University of Toronto, Toronto M5G 1L7, Canada; Division of Rheumatology, St. Michael's Hospital, Toronto M5B 1W8, Canada
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Structural Genomics Consortium, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany; German Cancer Consortium (DKTK) and Frankfurt Cancer Institute (FCI), 60596 Frankfurt am Main, Germany.
| |
Collapse
|
15
|
Kahle N, Sheerin DJ, Fischbach P, Koch LA, Schwenk P, Lambert D, Rodriguez R, Kerner K, Hoecker U, Zurbriggen MD, Hiltbrunner A. COLD REGULATED 27 and 28 are targets of CONSTITUTIVELY PHOTOMORPHOGENIC 1 and negatively affect phytochrome B signalling. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1038-1053. [PMID: 32890447 DOI: 10.1111/tpj.14979] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 07/31/2020] [Accepted: 08/10/2020] [Indexed: 05/23/2023]
Abstract
Phytochromes are red/far-red light receptors in plants involved in the regulation of growth and development. Phytochromes can sense the light environment and contribute to measuring day length; thereby, they allow plants to respond and adapt to changes in the ambient environment. Two well-characterized signalling pathways act downstream of phytochromes and link light perception to the regulation of gene expression. The CONSTITUTIVELY PHOTOMORPHOGENIC 1/SUPPRESSOR OF PHYA-105 (COP1/SPA) E3 ubiquitin ligase complex and the PHYTOCHROME INTERACTING FACTORs (PIFs) are key components of these pathways and repress light responses in the dark. In light-grown seedlings, phytochromes inhibit COP1/SPA and PIF activity and thereby promote light signalling. In a yeast-two-hybrid screen for proteins binding to light-activated phytochromes, we identified COLD-REGULATED GENE 27 (COR27). COR27 and its homologue COR28 bind to phyA and phyB, the two primary phytochromes in seed plants. COR27 and COR28 have been described previously with regard to a function in the regulation of freezing tolerance, flowering and the circadian clock. Here, we show that COR27 and COR28 repress early seedling development in blue, far-red and in particular red light. COR27 and COR28 contain a conserved Val-Pro (VP)-peptide motif, which mediates binding to the COP1/SPA complex. COR27 and COR28 are targeted for degradation by COP1/SPA and mutant versions with a VP to AA amino acid substitution in the VP-peptide motif are stabilized. Overall, our data suggest that COR27 and COR28 accumulate in light but act as negative regulators of light signalling during early seedling development, thereby preventing an exaggerated response to light.
Collapse
Affiliation(s)
- Nikolai Kahle
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - David J Sheerin
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - Patrick Fischbach
- Institute of Synthetic Biology and CEPLAS, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Leonie-Alexa Koch
- Institute of Synthetic Biology and CEPLAS, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Philipp Schwenk
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, 79104, Germany
| | - Dorothee Lambert
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - Ryan Rodriguez
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - Konstantin Kerner
- Institute for Plant Sciences, University of Cologne, Cologne, 50674, Germany
| | - Ute Hoecker
- Institute for Plant Sciences, University of Cologne, Cologne, 50674, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Andreas Hiltbrunner
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
| |
Collapse
|
16
|
Shrestha S, Byrne DP, Harris JA, Kannan N, Eyers PA. Cataloguing the dead: breathing new life into pseudokinase research. FEBS J 2020; 287:4150-4169. [PMID: 32053275 PMCID: PMC7586955 DOI: 10.1111/febs.15246] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/22/2020] [Accepted: 02/11/2020] [Indexed: 12/22/2022]
Abstract
Pseudoenzymes are present within many, but not all, known enzyme families and lack one or more conserved canonical amino acids that help define their catalytically active counterparts. Recent findings in the pseudokinase field confirm that evolutionary repurposing of the structurally defined bilobal protein kinase fold permits distinct biological functions to emerge, many of which rely on conformational switching, as opposed to canonical catalysis. In this analysis, we evaluate progress in evaluating several members of the 'dark' pseudokinome that are pertinent to help drive this expanding field. Initially, we discuss how adaptions in erythropoietin-producing hepatocellular carcinoma (Eph) receptor tyrosine kinase domains resulted in two vertebrate pseudokinases, EphA10 and EphB6, in which co-evolving sequences generate new motifs that are likely to be important for both nucleotide binding and catalysis-independent signalling. Secondly, we discuss how conformationally flexible Tribbles pseudokinases, which have radiated in the complex vertebrates, control fundamental aspects of cell signalling that may be targetable with covalent small molecules. Finally, we show how species-level adaptions in the duplicated canonical kinase protein serine kinase histone (PSKH)1 sequence have led to the appearance of the pseudokinase PSKH2, whose physiological role remains mysterious. In conclusion, we show how the patterns we discover are selectively conserved within specific pseudokinases, and that when they are modelled alongside closely related canonical kinases, many are found to be located in functionally important regions of the conserved kinase fold. Interrogation of these patterns will be useful for future evaluation of these, and other, members of the unstudied human kinome.
Collapse
Affiliation(s)
- Safal Shrestha
- Institute of BioinformaticsUniversity of GeorgiaAthensGAUSA
- Department of Biochemistry & Molecular BiologyUniversity of GeorgiaAthensGAUSA
| | - Dominic P. Byrne
- Department of BiochemistryInstitute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - John A. Harris
- Department of BiochemistryInstitute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Natarajan Kannan
- Institute of BioinformaticsUniversity of GeorgiaAthensGAUSA
- Department of Biochemistry & Molecular BiologyUniversity of GeorgiaAthensGAUSA
| | - Patrick A. Eyers
- Department of BiochemistryInstitute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
| |
Collapse
|
17
|
Ndoja A, Reja R, Lee SH, Webster JD, Ngu H, Rose CM, Kirkpatrick DS, Modrusan Z, Chen YJJ, Dugger DL, Gandham V, Xie L, Newton K, Dixit VM. Ubiquitin Ligase COP1 Suppresses Neuroinflammation by Degrading c/EBPβ in Microglia. Cell 2020; 182:1156-1169.e12. [PMID: 32795415 DOI: 10.1016/j.cell.2020.07.011] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/09/2020] [Accepted: 07/10/2020] [Indexed: 12/21/2022]
Abstract
Dysregulated microglia are intimately involved in neurodegeneration, including Alzheimer's disease (AD) pathogenesis, but the mechanisms controlling pathogenic microglial gene expression remain poorly understood. The transcription factor CCAAT/enhancer binding protein beta (c/EBPβ) regulates pro-inflammatory genes in microglia and is upregulated in AD. We show expression of c/EBPβ in microglia is regulated post-translationally by the ubiquitin ligase COP1 (also called RFWD2). In the absence of COP1, c/EBPβ accumulates rapidly and drives a potent pro-inflammatory and neurodegeneration-related gene program, evidenced by increased neurotoxicity in microglia-neuronal co-cultures. Antibody blocking studies reveal that neurotoxicity is almost entirely attributable to complement. Remarkably, loss of a single allele of Cebpb prevented the pro-inflammatory phenotype. COP1-deficient microglia markedly accelerated tau-mediated neurodegeneration in a mouse model where activated microglia play a deleterious role. Thus, COP1 is an important suppressor of pathogenic c/EBPβ-dependent gene expression programs in microglia.
Collapse
Affiliation(s)
- Ada Ndoja
- Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA
| | - Rohit Reja
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Seung-Hye Lee
- Department of Neuroscience, Genentech, South San Francisco, CA 94080, USA
| | - Joshua D Webster
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Hai Ngu
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Christopher M Rose
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA 94080, USA
| | - Donald S Kirkpatrick
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA 94080, USA
| | - Zora Modrusan
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA 94080, USA
| | - Ying-Jiun Jasmine Chen
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA 94080, USA
| | - Debra L Dugger
- Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA
| | - Vineela Gandham
- Department of Biomedical Imaging, Genentech, South San Francisco, CA 94080, USA
| | - Luke Xie
- Department of Biomedical Imaging, Genentech, South San Francisco, CA 94080, USA
| | - Kim Newton
- Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA.
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA.
| |
Collapse
|
18
|
Ponnu J. Molecular mechanisms suppressing COP1/SPA E3 ubiquitin ligase activity in blue light. PHYSIOLOGIA PLANTARUM 2020; 169:418-429. [PMID: 32248530 DOI: 10.1111/ppl.13103] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/19/2020] [Accepted: 03/27/2020] [Indexed: 05/23/2023]
Abstract
Arabidopsis CONSTITUTIVE PHOTOMORPHOGENIC1/SUPPRESSOR OF PHYA-105 (COP1/SPA) is an E3 ubiquitin ligase complex that prevents photomorphogenesis in darkness by ubiquitinating and subsequently degrading light-responsive transcription factors. Upon light perception, photoreceptors directly interact with the COP1/SPA complex to suppress its activity. In blue light (450-500 nm of visible spectrum), COP1/SPA activity is inhibited by the cryptochrome photoreceptors (CRY1 and CRY2), FKF1 from the ZEITLUPE family as well as phytochrome A. Together, these photoreceptors regulate vital aspects of plant growth and development from seedling stage to the induction of flowering. This review presents and discusses the recent advances in blue light-mediated suppression of COP1/SPA activity.
Collapse
Affiliation(s)
- Jathish Ponnu
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, 50674 Cologne, Germany
| |
Collapse
|
19
|
Song Y, Liu Y, Pan S, Xie S, Wang ZW, Zhu X. Role of the COP1 protein in cancer development and therapy. Semin Cancer Biol 2020; 67:43-52. [PMID: 32027978 DOI: 10.1016/j.semcancer.2020.02.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 01/29/2020] [Accepted: 02/01/2020] [Indexed: 12/31/2022]
Abstract
COP1, an E3 ubiquitin ligase, has been demonstrated to play a vital role in the regulation of cell proliferation, apoptosis and DNA repair. Accumulated evidence has revealed that COP1 is involved in carcinogenesis via targeting its substrates, including p53, c-Jun, ETS, β-catenin, STAT3, MTA1, p27, 14-3-3σ, and C/EBPα, for ubiquitination and degradation. COP1 can play tumor suppressive and oncogenic roles in human malignancies, urging us to summarize the functions of COP1 in tumorigenesis. In this review, we describe the structure of COP1 and its known substrates. Moreover, we dissect the function of COP1 by physiological (mouse models), pathological (human tumor specimens) and biochemical (ubiquitin substrates) Evidence. Furthermore, we discuss COP1 as a potential therapeutic target for cancer therapy.
Collapse
Affiliation(s)
- Yizuo Song
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Yi Liu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Shuya Pan
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Shangdan Xie
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Zhi-Wei Wang
- Center of Scientific Research, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China; Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
| | - Xueqiong Zhu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China.
| |
Collapse
|
20
|
Abstract
Pseudokinases are members of the protein kinase superfamily but signal primarily through noncatalytic mechanisms. Many pseudokinases contribute to the pathologies of human diseases, yet they remain largely unexplored as drug targets owing to challenges associated with modulation of their biological functions. Our understanding of the structure and physiological roles of pseudokinases has improved substantially over the past decade, revealing intriguing similarities between pseudokinases and their catalytically active counterparts. Pseudokinases often adopt conformations that are analogous to those seen in catalytically active kinases and, in some cases, can also bind metal cations and/or nucleotides. Several clinically approved kinase inhibitors have been shown to influence the noncatalytic functions of active kinases, providing hope that similar properties in pseudokinases could be pharmacologically regulated. In this Review, we discuss known roles of pseudokinases in disease, their unique structural features and the progress that has been made towards developing pseudokinase-directed therapeutics.
Collapse
|
21
|
Richmond L, Keeshan K. Pseudokinases: a tribble-edged sword. FEBS J 2019; 287:4170-4182. [PMID: 31621188 DOI: 10.1111/febs.15096] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/29/2019] [Accepted: 10/14/2019] [Indexed: 12/20/2022]
Abstract
Advances in the understanding of the Tribbles family of pseudokinases (TRIB1, TRIB2 and TRIB3) reveal these proteins as potentially valuable biomarkers of disease diagnosis, prognosis, prediction and clinical strategy. In their role as signalling mediators and scaffolding proteins, TRIBs lead to changes in protein stability and activity, which impact on diverse cellular processes such as proliferation, differentiation, cell cycle and cell death. We review the role of TRIB proteins as promising therapeutic targets, with an emphasis on their role in cancer, and as biomarkers, with potential application across diverse pathological processes.
Collapse
Affiliation(s)
- Laura Richmond
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, UK
| | - Karen Keeshan
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, UK
| |
Collapse
|
22
|
Lau K, Podolec R, Chappuis R, Ulm R, Hothorn M. Plant photoreceptors and their signaling components compete for COP1 binding via VP peptide motifs. EMBO J 2019; 38:e102140. [PMID: 31304983 PMCID: PMC6745501 DOI: 10.15252/embj.2019102140] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/29/2019] [Accepted: 06/07/2019] [Indexed: 12/31/2022] Open
Abstract
Plants sense different parts of the sun's light spectrum using distinct photoreceptors, which signal through the E3 ubiquitin ligase COP1. Here, we analyze why many COP1‐interacting transcription factors and photoreceptors harbor sequence‐divergent Val‐Pro (VP) motifs that bind COP1 with different binding affinities. Crystal structures of the VP motifs of the UV‐B photoreceptor UVR8 and the transcription factor HY5 in complex with COP1, quantitative binding assays, and reverse genetic experiments together suggest that UVR8 and HY5 compete for COP1. Photoactivation of UVR8 leads to high‐affinity cooperative binding of its VP motif and its photosensing core to COP1, preventing COP1 binding to its substrate HY5. UVR8–VP motif chimeras suggest that UV‐B signaling specificity resides in the UVR8 photoreceptor core. Different COP1–VP peptide motif complexes highlight sequence fingerprints required for COP1 targeting. The blue‐light photoreceptors CRY1 and CRY2 also compete with transcription factors for COP1 binding using similar VP motifs. Thus, our work reveals that different photoreceptors and their signaling components compete for COP1 via a conserved mechanism to control different light signaling cascades.
Collapse
Affiliation(s)
- Kelvin Lau
- Department of Botany and Plant Biology, Section of Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Roman Podolec
- Department of Botany and Plant Biology, Section of Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Richard Chappuis
- Department of Botany and Plant Biology, Section of Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Roman Ulm
- Department of Botany and Plant Biology, Section of Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Michael Hothorn
- Department of Botany and Plant Biology, Section of Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| |
Collapse
|
23
|
Hu J, Li S, Sun X, Fang Z, Wang L, Xiao F, Shao M, Ge L, Tang F, Gu J, Yu H, Guo Y, Guo X, Liao B, Jin Y. Stk40 deletion elevates c-JUN protein level and impairs mesoderm differentiation. J Biol Chem 2019; 294:9959-9972. [PMID: 31092598 DOI: 10.1074/jbc.ra119.007840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/07/2019] [Indexed: 11/06/2022] Open
Abstract
Mesoderm development is a finely tuned process initiated by the differentiation of pluripotent epiblast cells. Serine/threonine kinase 40 (STK40) controls the development of several mesoderm-derived cell types, its overexpression induces differentiation of mouse embryonic stem cells (mESCs) toward the extraembryonic endoderm, and Stk40 knockout (KO) results in multiple organ failure and is lethal at the perinatal stage in mice. However, molecular mechanisms underlying the physiological functions of STK40 in mesoderm differentiation remain elusive. Here, we report that Stk40 ablation impairs mesoderm differentiation both in vitro and in vivo Mechanistically, STK40 interacts with both the E3 ubiquitin ligase mammalian constitutive photomorphogenesis protein 1 (COP1) and the transcriptional regulator proto-oncogene c-Jun (c-JUN), promoting c-JUN protein degradation. Consequently, Stk40 knockout leads to c-JUN protein accumulation, which, in turn, apparently suppresses WNT signaling activity and impairs the mesoderm differentiation process. Overall, this study reveals that STK40, together with COP1, represents a previously unknown regulatory axis that modulates the c-JUN protein level within an appropriate range during mesoderm differentiation from mESCs. Our findings provide critical insights into the molecular mechanisms regulating the c-JUN protein level and may have potential implications for managing cellular disorders arising from c-JUN dysfunction.
Collapse
Affiliation(s)
- Jing Hu
- From the Basic Clinical Research Center, Renji Hospital and Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China
| | - Shuang Li
- From the Basic Clinical Research Center, Renji Hospital and Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China
| | - Xiaozhi Sun
- From the Basic Clinical Research Center, Renji Hospital and Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China
| | - Zhuoqing Fang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200032, China
| | - Lina Wang
- From the Basic Clinical Research Center, Renji Hospital and Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China
| | - Feng Xiao
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200032, China
| | - Min Shao
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200032, China
| | - Laixiang Ge
- From the Basic Clinical Research Center, Renji Hospital and Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China
| | - Fan Tang
- From the Basic Clinical Research Center, Renji Hospital and Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China
| | - Junjie Gu
- From the Basic Clinical Research Center, Renji Hospital and Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China
| | - Hongyao Yu
- From the Basic Clinical Research Center, Renji Hospital and Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China
| | - Yueshuai Guo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Bing Liao
- From the Basic Clinical Research Center, Renji Hospital and Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China,
| | - Ying Jin
- From the Basic Clinical Research Center, Renji Hospital and Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China, .,CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200032, China.,School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China, and
| |
Collapse
|
24
|
Kung JE, Jura N. The pseudokinase TRIB1 toggles an intramolecular switch to regulate COP1 nuclear export. EMBO J 2019; 38:e99708. [PMID: 30692133 PMCID: PMC6376274 DOI: 10.15252/embj.201899708] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 12/18/2018] [Accepted: 12/20/2018] [Indexed: 01/17/2023] Open
Abstract
COP1 is a highly conserved ubiquitin ligase that regulates diverse cellular processes in plants and metazoans. Tribbles pseudokinases, which only exist in metazoans, act as scaffolds that interact with COP1 and its substrates to facilitate ubiquitination. Here, we report that, in addition to this scaffolding role, TRIB1 promotes nuclear localization of COP1 by disrupting an intramolecular interaction between the WD40 domain and a previously uncharacterized regulatory site within COP1. This site, which we have termed the pseudosubstrate latch (PSL), resembles the consensus COP1-binding motif present in known COP1 substrates. Our findings support a model in which binding of the PSL to the WD40 domain stabilizes a conformation of COP1 that is conducive to CRM1-mediated nuclear export, and TRIB1 displaces this intramolecular interaction to induce nuclear retention of COP1. Coevolution of Tribbles and the PSL in metazoans further underscores the importance of this role of Tribbles in regulating COP1 function.
Collapse
Affiliation(s)
- Jennifer E Kung
- Cardiovascular Research Institute, University of California-San Francisco, San Francisco, CA, USA
| | - Natalia Jura
- Cardiovascular Research Institute, University of California-San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, CA, USA
| |
Collapse
|
25
|
Adelmant G, Garg BK, Tavares M, Card JD, Marto JA. Tandem Affinity Purification and Mass Spectrometry (TAP-MS) for the Analysis of Protein Complexes. ACTA ACUST UNITED AC 2019; 96:e84. [PMID: 30706993 DOI: 10.1002/cpps.84] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Affinity purification followed by mass spectrometry has become the technique of choice to identify binding partners in biochemical complexes isolated from a physiologic cellular context. In this report we detail our protocol for tandem affinity purification (TAP) primarily based on the use of the FLAG and HA peptide epitopes, with a particular emphasis on factors affecting yield and specificity, as well as steps to implement an automated version of the TAP procedure. © 2019 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Guillaume Adelmant
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Brijesh K Garg
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Maria Tavares
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Joseph D Card
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jarrod A Marto
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
26
|
Jamieson SA, Ruan Z, Burgess AE, Curry JR, McMillan HD, Brewster JL, Dunbier AK, Axtman AD, Kannan N, Mace PD. Substrate binding allosterically relieves autoinhibition of the pseudokinase TRIB1. Sci Signal 2018; 11:11/549/eaau0597. [PMID: 30254053 DOI: 10.1126/scisignal.aau0597] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The Tribbles family of pseudokinases recruits substrates to the ubiquitin ligase COP1 to facilitate ubiquitylation. CCAAT/enhancer-binding protein (C/EBP) family transcription factors are crucial Tribbles substrates in adipocyte and myeloid cell development. We found that the TRIB1 pseudokinase was able to recruit various C/EBP family members and that the binding of C/EBPβ was attenuated by phosphorylation. To explain the mechanism of C/EBP recruitment, we solved the crystal structure of TRIB1 in complex with C/EBPα, which revealed that TRIB1 underwent a substantial conformational change relative to its substrate-free structure and bound C/EBPα in a pseudosubstrate-like manner. Crystallographic analysis and molecular dynamics and subsequent biochemical assays showed that C/EBP binding triggered allosteric changes that link substrate recruitment to COP1 binding. These findings offer a view of pseudokinase regulation with striking parallels to bona fide kinase regulation-by means of the activation loop and αC helix-and raise the possibility of small molecules targeting either the activation "loop-in" or "loop-out" conformations of Tribbles pseudokinases.
Collapse
Affiliation(s)
- Sam A Jamieson
- Biochemistry Department, School of Biomedical Sciences, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin 9054, New Zealand
| | - Zheng Ruan
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Abigail E Burgess
- Biochemistry Department, School of Biomedical Sciences, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin 9054, New Zealand
| | - Jack R Curry
- Biochemistry Department, School of Biomedical Sciences, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin 9054, New Zealand
| | - Hamish D McMillan
- Biochemistry Department, School of Biomedical Sciences, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin 9054, New Zealand
| | - Jodi L Brewster
- Biochemistry Department, School of Biomedical Sciences, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin 9054, New Zealand
| | - Anita K Dunbier
- Biochemistry Department, School of Biomedical Sciences, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin 9054, New Zealand
| | - Alison D Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.,Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Peter D Mace
- Biochemistry Department, School of Biomedical Sciences, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin 9054, New Zealand.
| |
Collapse
|
27
|
Foulkes DM, Byrne DP, Yeung W, Shrestha S, Bailey FP, Ferries S, Eyers CE, Keeshan K, Wells C, Drewry DH, Zuercher WJ, Kannan N, Eyers PA. Covalent inhibitors of EGFR family protein kinases induce degradation of human Tribbles 2 (TRIB2) pseudokinase in cancer cells. Sci Signal 2018; 11:11/549/eaat7951. [PMID: 30254057 DOI: 10.1126/scisignal.aat7951] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A major challenge associated with biochemical and cellular analysis of pseudokinases is a lack of target-validated small-molecule compounds with which to probe function. Tribbles 2 (TRIB2) is a cancer-associated pseudokinase with a diverse interactome, including the canonical AKT signaling module. There is substantial evidence that human TRIB2 promotes survival and drug resistance in solid tumors and blood cancers and therefore is of interest as a therapeutic target. The unusual TRIB2 pseudokinase domain contains a unique cysteine-rich C-helix and interacts with a conserved peptide motif in its own carboxyl-terminal tail, which also supports its interaction with E3 ubiquitin ligases. We found that TRIB2 is a target of previously described small-molecule protein kinase inhibitors, which were originally designed to inhibit the canonical kinase domains of epidermal growth factor receptor tyrosine kinase family members. Using a thermal shift assay, we discovered TRIB2-binding compounds within the Published Kinase Inhibitor Set (PKIS) and used a drug repurposing approach to classify compounds that either stabilized or destabilized TRIB2 in vitro. TRIB2 destabilizing agents, including the covalent drug afatinib, led to rapid TRIB2 degradation in human AML cancer cells, eliciting tractable effects on signaling and survival. Our data reveal new drug leads for the development of TRIB2-degrading compounds, which will also be invaluable for unraveling the cellular mechanisms of TRIB2-based signaling. Our study highlights that small molecule-induced protein down-regulation through drug "off-targets" might be relevant for other inhibitors that serendipitously target pseudokinases.
Collapse
Affiliation(s)
- Daniel M Foulkes
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Dominic P Byrne
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Wayland Yeung
- Institute of Bioinformatics and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Safal Shrestha
- Institute of Bioinformatics and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Fiona P Bailey
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Samantha Ferries
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.,Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Claire E Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.,Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Karen Keeshan
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Scotland, UK
| | - Carrow Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David H Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - William J Zuercher
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natarajan Kannan
- Institute of Bioinformatics and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| |
Collapse
|
28
|
Salomé M, Hopcroft L, Keeshan K. Inverse and correlative relationships between TRIBBLES genes indicate non-redundant functions during normal and malignant hemopoiesis. Exp Hematol 2018; 66:63-78.e13. [PMID: 30031847 DOI: 10.1016/j.exphem.2018.07.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/11/2018] [Accepted: 07/12/2018] [Indexed: 01/31/2023]
Abstract
TRIBBLES pseudokinases (TRIB1, TRIB2, and TRIB3) are important regulators of normal and malignant hemopoiesis. The relative abundance of each TRIBBLES family member may be important for distinct oncogenic or tumor suppressor functions. We map the expression profiles of TRIB1, TRIB2, and TRIB3 in human and murine hemopoietic stem, progenitor and mature cells, and in human leukemia datasets. Our data show that TRIB1-TRIB2 have an inverse expression relationship in normal hemopoiesis, whereas TRIB1-TRIB3 have a positive correlation. We reveal that TRIB3 expression is high in the dormant hemopoietic stem cell (HSC) population, implicating a novel role for TRIB3 in stem cell quiescence. These analyses support a non-redundant role for each TRIBBLES member during normal hemopoietic differentiation. We show that TRIB1-TRIB2 display a significant negative correlation in myelodysplastic syndrome and acute myeloid leukemia (AML) subtypes, but not in acute lymphoid leukemia. This inverse relationship is specific to certain subtypes of AML. A positive correlation exists in different leukemia subtypes between TRIB1-TRIB3. The TRIB1-TRIB2 and TRIB1-TRIB3 correlations are consistent with a correlative relationship with C/EBP transcription factor family members. Our results have implications for the development of strategies to therapeutically target these genes in different types of leukemia.
Collapse
Affiliation(s)
- Mara Salomé
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Scotland, UK
| | - Lisa Hopcroft
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Scotland, UK
| | - Karen Keeshan
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Scotland, UK.
| |
Collapse
|
29
|
Arndt L, Dokas J, Gericke M, Kutzner CE, Müller S, Jeromin F, Thiery J, Burkhardt R. Tribbles homolog 1 deficiency modulates function and polarization of murine bone marrow-derived macrophages. J Biol Chem 2018; 293:11527-11536. [PMID: 29899113 DOI: 10.1074/jbc.ra117.000703] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 05/23/2018] [Indexed: 01/12/2023] Open
Abstract
Macrophages are essential for innate immunity and inflammatory responses and differentiate into various functional phenotypes. Tribbles homolog 1 (Trib1), a member of the mammalian Tribbles homolog pseudokinase family, has been implicated in regulation of cell differentiation, proliferation, and metabolism, but its role in macrophage biology has not been fully elucidated. Here, we investigated the consequences of Trib1 deficiency on macrophage functions and M1/M2 polarization. Bone marrow-derived macrophages (BMDMs) from Trib1-deficient (Trib1-/-) mice exhibited elevated phagocytic capacity, correlating with up-regulation of several scavenger receptors. Concomitantly, uptake of modified low-density lipoprotein was increased in Trib1-/- BMDMs. Trib1-/- macrophages also exhibited diminished migration in the presence of the chemokine MCP-1, associated with reduced expression of the MCP-1 receptor Ccr2 Furthermore, Trib1 deficiency attenuated the response of BMDMs to both M1 and M2 stimuli; induction of the M1-marker genes Il6, Il1b, and Nos2 upon LPS/IFNγ stimulation and of the M2-marker genes Cd206, Fizz1, and Arg1 upon IL-4 stimulation was reduced. Functionally, Trib1 deficiency decreased secretion of proinflammatory cytokines (IL-6, TNFα, IL-1β, and CXCL1) and reduced nitric oxide and reactive oxygen species production in M1-polarized macrophages. Supporting the attenuated M2 phenotype, IL-4-stimulated Trib1-/- macrophages secreted less IL-10 and TGFβ. Mechanistically, Trib1-/- BMDMs displayed lower levels of Janus kinase 1 (JAK1), resulting in reduced activation of LPS/IFNγ-mediated STAT1 signaling. Likewise, decreased levels of JAK1 along with lower activation of STAT6 and STAT3 were observed in M2-polarized Trib1-/- BMDMs. Our findings suggest that Trib1 extensively controls macrophage M1/M2 polarization via the JAK/STAT signaling pathway.
Collapse
Affiliation(s)
- Lilli Arndt
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, 04103 Leipzig, Germany
| | - Janine Dokas
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, 04103 Leipzig, Germany
| | - Martin Gericke
- Institute of Anatomy, University of Leipzig, 04103 Leipzig, Germany
| | - Carl Elias Kutzner
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, 04103 Leipzig, Germany
| | - Silvana Müller
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, 04103 Leipzig, Germany
| | - Franziska Jeromin
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, 04103 Leipzig, Germany
| | - Joachim Thiery
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, 04103 Leipzig, Germany; LIFE-Leipzig Research Center for Civilization Diseases, University of Leipzig, 04103 Leipzig, Germany
| | - Ralph Burkhardt
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, 04103 Leipzig, Germany; LIFE-Leipzig Research Center for Civilization Diseases, University of Leipzig, 04103 Leipzig, Germany.
| |
Collapse
|
30
|
Maubant S, Tahtouh T, Brisson A, Maire V, Némati F, Tesson B, Ye M, Rigaill G, Noizet M, Dumont A, Gentien D, Marty-Prouvost B, de Koning L, Mahmood SF, Decaudin D, Cruzalegui F, Tucker GC, Roman-Roman S, Dubois T. LRP5 regulates the expression of STK40, a new potential target in triple-negative breast cancers. Oncotarget 2018; 9:22586-22604. [PMID: 29854300 PMCID: PMC5978250 DOI: 10.18632/oncotarget.25187] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/04/2018] [Indexed: 12/21/2022] Open
Abstract
Triple-negative breast cancers (TNBCs) account for a large proportion of breast cancer deaths, due to the high rate of recurrence from residual, resistant tumor cells. New treatments are needed, to bypass chemoresistance and improve survival. The WNT pathway, which is activated in TNBCs, has been identified as an attractive pathway for treatment targeting. We analyzed expression of the WNT coreceptors LRP5 and LRP6 in human breast cancer samples. As previously described, LRP6 was overexpressed in TNBCs. However, we also showed, for the first time, that LRP5 was overexpressed in TNBCs too. The knockdown of LRP5 or LRP6 decreased tumorigenesis in vitro and in vivo, identifying both receptors as potential treatment targets in TNBC. The apoptotic effect of LRP5 knockdown was more robust than that of LRP6 depletion. We analyzed and compared the transcriptomes of cells depleted of LRP5 or LRP6, to identify genes specifically deregulated by LRP5 potentially implicated in cell death. We identified serine/threonine kinase 40 (STK40) as one of two genes specifically downregulated soon after LRP5 depletion. STK40 was found to be overexpressed in TNBCs, relative to other breast cancer subtypes, and in various other tumor types. STK40 depletion decreased cell viability and colony formation, and induced the apoptosis of TNBC cells. In addition, STK40 knockdown impaired growth in an anchorage-independent manner in vitro and slowed tumor growth in vivo. These findings identify the largely uncharacterized putative protein kinase STK40 as a novel candidate treatment target for TNBC.
Collapse
Affiliation(s)
- Sylvie Maubant
- Institut Curie, PSL Research University, Translational Research Department, Breast Cancer Biology Group, Paris, France
| | - Tania Tahtouh
- Institut Curie, PSL Research University, Translational Research Department, Breast Cancer Biology Group, Paris, France
| | - Amélie Brisson
- Institut Curie, PSL Research University, Translational Research Department, Breast Cancer Biology Group, Paris, France
| | - Virginie Maire
- Institut Curie, PSL Research University, Translational Research Department, Breast Cancer Biology Group, Paris, France
| | - Fariba Némati
- Institut Curie, PSL Research University, Translational Research Department, Preclinical Investigation Laboratory, Paris, France
| | - Bruno Tesson
- Institut Curie, PSL Research University, Translational Research Department, Breast Cancer Biology Group, Paris, France.,Institut Curie, PSL Research University, INSERM U900, Paris, France
| | - Mengliang Ye
- Institut Curie, PSL Research University, Translational Research Department, Breast Cancer Biology Group, Paris, France
| | - Guillem Rigaill
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR 1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Orsay, France.,Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Université d'Evry Val d'Essonne, UMR CNRS 8071, ENSIIE, USC INRA, Évry, France
| | - Maïté Noizet
- Institut Curie, PSL Research University, Translational Research Department, Breast Cancer Biology Group, Paris, France
| | - Aurélie Dumont
- Institut Curie, PSL Research University, Translational Research Department, Breast Cancer Biology Group, Paris, France
| | - David Gentien
- Institut Curie, PSL Research University, Translational Research Department, Genomics Platform, Paris, France
| | - Bérengère Marty-Prouvost
- Institut Curie, PSL Research University, Translational Research Department, Breast Cancer Biology Group, Paris, France
| | - Leanne de Koning
- Institut Curie, PSL Research University, Translational Research Department, Reverse-Phase Protein Array Platform, Paris, France
| | - Sardar Faisal Mahmood
- Institut Curie, PSL Research University, Translational Research Department, Breast Cancer Biology Group, Paris, France
| | - Didier Decaudin
- Institut Curie, PSL Research University, Translational Research Department, Preclinical Investigation Laboratory, Paris, France
| | - Francisco Cruzalegui
- Oncology Research and Development Unit, Institut de Recherches SERVIER, Croissy-Sur-Seine, France
| | - Gordon C Tucker
- Oncology Research and Development Unit, Institut de Recherches SERVIER, Croissy-Sur-Seine, France
| | - Sergio Roman-Roman
- Institut Curie, PSL Research University, Translational Research Department, Paris, France
| | - Thierry Dubois
- Institut Curie, PSL Research University, Translational Research Department, Breast Cancer Biology Group, Paris, France
| |
Collapse
|
31
|
The secret life of kinases: insights into non-catalytic signalling functions from pseudokinases. Biochem Soc Trans 2017; 45:665-681. [PMID: 28620028 DOI: 10.1042/bst20160331] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/08/2017] [Accepted: 03/09/2017] [Indexed: 12/31/2022]
Abstract
Over the past decade, our understanding of the mechanisms by which pseudokinases, which comprise ∼10% of the human and mouse kinomes, mediate signal transduction has advanced rapidly with increasing structural, biochemical, cellular and genetic studies. Pseudokinases are the catalytically defective counterparts of conventional, active protein kinases and have been attributed functions as protein interaction domains acting variously as allosteric modulators of conventional protein kinases and other enzymes, as regulators of protein trafficking or localisation, as hubs to nucleate assembly of signalling complexes, and as transmembrane effectors of such functions. Here, by categorising mammalian pseudokinases based on their known functions, we illustrate the mechanistic diversity among these proteins, which can be viewed as a window into understanding the non-catalytic functions that can be exerted by conventional protein kinases.
Collapse
|
32
|
Murphy JM, Mace PD, Eyers PA. Live and let die: insights into pseudoenzyme mechanisms from structure. Curr Opin Struct Biol 2017; 47:95-104. [PMID: 28787627 DOI: 10.1016/j.sbi.2017.07.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/30/2017] [Accepted: 07/20/2017] [Indexed: 12/22/2022]
Abstract
Pseudoenzymes were first described more than 50 years ago, when it was recognised that a subset of proteins that are structurally homologous to active enzymes lack amino acids necessary for catalytic activity. Recently, interest in pseudoenzymes has surged as it has become apparent that they constitute ∼10% of proteomes and perform essential metabolic and signalling functions that can be experimentally distinguished from catalytic outputs of enzymes. Here, we highlight recent structural studies of pseudoenzymes, which have revealed the molecular basis for roles as allosteric regulators of conventional enzymes, as molecular switches and integrators, as hubs for assembling protein complexes, and as competitors of substrate availability and holoenzyme assembly. As structural studies continue to illuminate pseudoenzyme molecular mechanisms, we anticipate that our knowledge of the breadth of their biological functions will expand in parallel.
Collapse
Affiliation(s)
- James M Murphy
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia.
| | - Peter D Mace
- Biochemistry Department, School of Biomedical Sciences, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
| | - Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK.
| |
Collapse
|