1
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Chauveau C, Roby D. Molecular complexity of quantitative immunity in plants: from QTL mapping to functional and systems biology. C R Biol 2024; 347:35-44. [PMID: 38771313 DOI: 10.5802/crbiol.153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/20/2024] [Accepted: 03/28/2024] [Indexed: 05/22/2024]
Abstract
In nature, plants defend themselves against pathogen attack by activating an arsenal of defense mechanisms. During the last decades, work mainly focused on the understanding of qualitative disease resistance mediated by a few genes conferring an almost complete resistance, while quantitative disease resistance (QDR) remains poorly understood despite the fact that it represents the predominant and more durable form of resistance in natural populations and crops. Here, we review our past and present work on the dissection of the complex mechanisms underlying QDR in Arabidopsis thaliana. The strategies, main steps and challenges of our studies related to one atypical QDR gene, RKS1 (Resistance related KinaSe 1), are presented. First, from genetic analyses by QTL (Quantitative Trait Locus) mapping and GWAs (Genome Wide Association studies), the identification, cloning and functional analysis of this gene have been used as a starting point for the exploration of the multiple and coordinated pathways acting together to mount the QDR response dependent on RKS1. Identification of RKS1 protein interactors and complexes was a first step, systems biology and reconstruction of protein networks were then used to decipher the molecular roadmap to the immune responses controlled by RKS1. Finally, exploration of the potential impact of key components of the RKS1-dependent gene network on leaf microbiota offers interesting and challenging perspectives to decipher how the plant immune systems interact with the microbial communities' systems.
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2
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Mühlenbeck H, Tsutsui Y, Lemmon MA, Bender KW, Zipfel C. Allosteric activation of the co-receptor BAK1 by the EFR receptor kinase initiates immune signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.23.554490. [PMID: 37662281 PMCID: PMC10473708 DOI: 10.1101/2023.08.23.554490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Transmembrane signaling by plant receptor kinases (RKs) has long been thought to involve reciprocal trans-phosphorylation of their intracellular kinase domains. The fact that many of these are pseudokinase domains, however, suggests that additional mechanisms must govern RK signaling activation. Non-catalytic (pseudo)kinase signaling mechanisms have been described in metazoans, but information is scarce for plants. Recently, a non-catalytic function was reported for the leucine-rich repeat (LRR)-RK subfamily XIIa member EFR (ELONGATION FACTOR TU RECEPTOR) and phosphorylation-dependent conformational changes were proposed to regulate signaling of RKs with non-RD kinase domains. Here, using EFR as a model, we describe a non-catalytic activation mechanism for LRR-RKs with non-RD kinase domains. EFR is an active kinase, but a kinase-dead variant retains the ability to enhance catalytic activity of its co-receptor kinase BAK1/SERK3 (BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1/SOMATIC EMBRYOGENESIS RECEPTOR KINASE 3). Applying hydrogen-deuterium exchange mass spectrometry (HDX-MS) analysis and designing homology-based intragenic suppressor mutations, we provide evidence that the EFR kinase domain must adopt its active conformation in order to activate BAK1 allosterically, likely by supporting αC-helix positioning in BAK1. Our results suggest a conformational toggle model for signaling, in which BAK1 first phosphorylates EFR in the activation loop to stabilize its active conformation, allowing EFR in turn to allosterically activate BAK1.
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3
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Shi Y, Wu C, Shi J, Gao T, Ma H, Li L, Zhao Y. Protein phosphorylation and kinases: Potential therapeutic targets in necroptosis. Eur J Pharmacol 2024; 970:176508. [PMID: 38493913 DOI: 10.1016/j.ejphar.2024.176508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/05/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
Necroptosis is a pivotal contributor to the pathogenesis of various human diseases, including those affecting the nervous system, cardiovascular system, pulmonary system, and kidneys. Extensive investigations have elucidated the mechanisms and physiological ramifications of necroptosis. Among these, protein phosphorylation emerges as a paramount regulatory process, facilitating the activation or inhibition of specific proteins through the addition of phosphate groups to their corresponding amino acid residues. Currently, the targeting of kinases has gained recognition as a firmly established and efficacious therapeutic approach for diverse diseases, notably cancer. In this comprehensive review, we elucidate the intricate role of phosphorylation in governing key molecular players in the necroptotic pathway. Moreover, we provide an in-depth analysis of recent advancements in the development of kinase inhibitors aimed at modulating necroptosis. Lastly, we deliberate on the prospects and challenges associated with the utilization of kinase inhibitors to modulate necroptotic processes.
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Affiliation(s)
- Yihui Shi
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Chengkun Wu
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Jiayi Shi
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Taotao Gao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Huabin Ma
- Central Laboratory, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
| | - Long Li
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, 315211, China
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4
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Mickus R, Raškevičius V, Sarapinienė I, Mikalayeva V, Prekeris R, Skeberdis VA. Phosphorylation-dependent allosteric regulation of Cx43 gap junction inhibitor potency. Biomed Pharmacother 2024; 174:116550. [PMID: 38593702 DOI: 10.1016/j.biopha.2024.116550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/28/2024] [Accepted: 04/04/2024] [Indexed: 04/11/2024] Open
Abstract
Physiological and pathological processes such as homeostasis, embryogenesis, development, tumorigenesis, and cell movement depend on the intercellular communication through gap junctions (GJIC). Connexin (Cx)-based GJ channels are formed of two apposing hemichannels in the contiguous cells and provide a direct pathway for electrical and metabolic intercellular communication. The main modulators of GJ conductance are transjunctional voltage, intracellular pH, Ca2+, Mg2+, and phosphorylation. Chemical modulators of GJIC are being used in cases of various intercellular communication-dependent diseases. In this study, we used molecular docking, dual whole-cell patch-clamp, and Western blotting to investigate the impact of connexin phosphorylation on GJ chemical gating by α-pinene and other GJ inhibitors (octanol, carbenoxolone, mefloquine, intracellular pH, glycyrrhetinic acid, and sevoflurane) in HeLa cells expressing exogenous Cx43 (full length and truncated at amino acid 258) and other connexins typical of heart and/or nervous system (Cx36, Cx40, Cx45, and Cx47), and in cells expressing endogenous Cx43 (Novikoff and U-87). We found that Ca2+-regulated kinases, such as Ca2+/calmodulin-dependent kinase II, atypical protein kinase C, cyclin-dependent kinase, and Pyk2 kinase may allosterically modulate the potency of α-pinene through phosphorylation of Cx43 C-terminus. The identified new phenomenon was Cx isoform-, inhibitor-, and cell type-dependent. Overall, these results suggest that compounds, the potency of which depends on receptor phosphorylation, might be of particular interest in developing targeted therapies for diseases accompanied by high kinase activity, such as cardiac arrhythmias, epilepsy, stroke, essential tremor, inflammation, and cancer.
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Affiliation(s)
- Rokas Mickus
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas LT-50162, Lithuania
| | - Vytautas Raškevičius
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas LT-50162, Lithuania
| | - Ieva Sarapinienė
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas LT-50162, Lithuania
| | - Valeryia Mikalayeva
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas LT-50162, Lithuania
| | - Rytis Prekeris
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80015, USA
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5
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Sun W, Justice I, Green EM. Defining Biological and Biochemical Functions of Noncanonical SET Domain Proteins. J Mol Biol 2024; 436:168318. [PMID: 37863247 PMCID: PMC10957327 DOI: 10.1016/j.jmb.2023.168318] [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: 09/15/2023] [Accepted: 10/14/2023] [Indexed: 10/22/2023]
Abstract
Within the SET domain superfamily of lysine methyltransferases, there is a well-conserved subfamily, frequently referred to as the Set3 SET domain subfamily, which contain noncanonical SET domains carrying divergent amino acid sequences. These proteins are implicated in diverse biological processes including stress responses, cell differentiation, and development, and their disruption is linked to diseases including cancer and neurodevelopmental disorders. Interestingly, biochemical and structural analysis indicates that they do not possess catalytic methyltransferase activity. At the molecular level, Set3 SET domain proteins appear to play critical roles in the regulation of gene expression, particularly repression and heterochromatin maintenance, and in some cases, via scaffolding other histone modifying activities at chromatin. Here, we explore the common and unique functions among Set3 SET domain subfamily proteins and analyze what is known about the specific contribution of the conserved SET domain to functional roles of these proteins, as well as propose areas of investigation to improve understanding of this important, noncanonical subfamily of proteins.
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Affiliation(s)
- Winny Sun
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, United States
| | - Isabella Justice
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, United States
| | - Erin M Green
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, United States; Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, United States.
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6
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Després PC, Dubé AK, Grenier J, Picard MÈ, Shi R, Landry CR. Compensatory mutations potentiate constructive neutral evolution by gene duplication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.12.579783. [PMID: 38405844 PMCID: PMC10888846 DOI: 10.1101/2024.02.12.579783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Protein functions generally depend on their assembly into complexes. During evolution, some complexes have transitioned from homomers encoded by a single gene to heteromers encoded by duplicate genes. This transition could occur without adaptive evolution through intermolecular compensatory mutations. Here, we experimentally duplicate and evolve an homodimeric enzyme to examine if and how this could happen. We identify hundreds of deleterious mutations that inactivate individual homodimers but produce functional enzymes when co-expressed as duplicated proteins that heterodimerize. The structure of one such heteromer reveals how both losses of function are buffered through the introduction of asymmetry in the complex that allows them to subfunctionalize. Constructive neutral evolution can thus occur by gene duplication followed by only one deleterious mutation per duplicate.
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Affiliation(s)
- Philippe C Després
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives, Université Laval, G1V 0A6, Canada
| | - Alexandre K Dubé
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
| | - Jordan Grenier
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
| | - Marie-Ève Picard
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
| | - Rong Shi
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
| | - Christian R Landry
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
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7
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Mao W, Vandecan NM, Bingham CR, Tsang PK, Ulintz P, Sexton R, Bochar DA, Merajver SD, Soellner MB. Selective and Potent PROTAC Degraders of c-Src Kinase. ACS Chem Biol 2024; 19:110-116. [PMID: 38113191 DOI: 10.1021/acschembio.3c00548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Using dasatinib linked to E3 ligase ligands, we identified a potent and selective dual Csk/c-Src PROTAC degrader. We then replaced dasatinib, the c-Src-directed ligand, with a conformation-selective analogue that stabilizes the αC-helix-out conformation of c-Src. Using the αC-helix-out ligand, we identified a PROTAC that is potent and selective for c-Src. We demonstrated a high degree of catalysis with our c-Src PROTACs. Using our c-Src PROTACs, we identified pharmacological advantages of c-Src degradation compared to inhibition with respect to cancer cell proliferation.
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Affiliation(s)
- Wuxiang Mao
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Nathalie M Vandecan
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Christopher R Bingham
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Pui Ki Tsang
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Peter Ulintz
- Department of Internal Medicine, University of Michigan, 1500 E. Medical Avenue, Ann Arbor, Michigan 48109, United States
| | - Rachel Sexton
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Daniel A Bochar
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Sofia D Merajver
- Department of Internal Medicine, University of Michigan, 1500 E. Medical Avenue, Ann Arbor, Michigan 48109, United States
| | - Matthew B Soellner
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
- Department of Internal Medicine, University of Michigan, 1500 E. Medical Avenue, Ann Arbor, Michigan 48109, United States
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8
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Gormal RS, Martinez-Marmol R, Brooks AJ, Meunier FA. Location, location, location: Protein kinase nanoclustering for optimised signalling output. eLife 2024; 13:e93902. [PMID: 38206309 PMCID: PMC10783869 DOI: 10.7554/elife.93902] [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: 10/24/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Protein kinases (PKs) are proteins at the core of cellular signalling and are thereby responsible for most cellular physiological processes and their regulations. As for all intracellular proteins, PKs are subjected to Brownian thermal energy that tends to homogenise their distribution throughout the volume of the cell. To access their substrates and perform their critical functions, PK localisation is therefore tightly regulated in space and time, relying upon a range of clustering mechanisms. These include post-translational modifications, protein-protein and protein-lipid interactions, as well as liquid-liquid phase separation, allowing spatial restriction and ultimately regulating access to their substrates. In this review, we will focus on key mechanisms mediating PK nanoclustering in physiological and pathophysiological processes. We propose that PK nanoclusters act as a cellular quantal unit of signalling output capable of integration and regulation in space and time. We will specifically outline the various super-resolution microscopy approaches currently used to elucidate the composition and mechanisms driving PK nanoscale clustering and explore the pathological consequences of altered kinase clustering in the context of neurodegenerative disorders, inflammation, and cancer.
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Affiliation(s)
- Rachel S Gormal
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of QueenslandBrisbaneAustralia
| | - Ramon Martinez-Marmol
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of QueenslandBrisbaneAustralia
| | - Andrew J Brooks
- Frazer Institute, The University of QueenslandWoolloongabbaAustralia
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of QueenslandBrisbaneAustralia
- School of Biomedical Sciences, The University of QueenslandSt LuciaAustralia
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9
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Scott KA, Kojima H, Ropek N, Warren CD, Zhang TL, Hogg SJ, Webster C, Zhang X, Rahman J, Melillo B, Cravatt BF, Lyu J, Abdel-Wahab O, Vinogradova EV. Covalent Targeting of Splicing in T Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.572199. [PMID: 38187674 PMCID: PMC10769204 DOI: 10.1101/2023.12.18.572199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Despite significant interest in therapeutic targeting of splicing, few chemical probes are available for the proteins involved in splicing. Here, we show that elaborated stereoisomeric acrylamide chemical probe EV96 and its analogues lead to a selective T cell state-dependent loss of interleukin 2-inducible T cell kinase (ITK) by targeting one of the core splicing factors SF3B1. Mechanistic investigations suggest that the state-dependency stems from a combination of differential protein turnover rates and availability of functional mRNA pools that can be depleted due to extensive alternative splicing. We further introduce a comprehensive list of proteins involved in splicing and leverage both cysteine- and protein-directed activity-based protein profiling (ABPP) data with electrophilic scout fragments to demonstrate covalent ligandability for many classes of splicing factors and splicing regulators in primary human T cells. Taken together, our findings show how chemical perturbation of splicing can lead to immune state-dependent changes in protein expression and provide evidence for the broad potential to target splicing factors with covalent chemistry.
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10
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Black JA, Klinger CM, Lemgruber L, Dacks JB, Mottram JC, McCulloch R. AAK1-like: A putative pseudokinase with potential roles in cargo uptake in bloodstream form Trypanosoma brucei parasites. J Eukaryot Microbiol 2023; 70:e12994. [PMID: 37548427 PMCID: PMC10952953 DOI: 10.1111/jeu.12994] [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: 01/30/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/08/2023]
Abstract
Selection and internalization of cargo via clathrin-mediated endocytosis requires adaptor protein complexes. One complex, AP-2, acts during cargo selection at the plasma membrane. African trypanosomes lack all components of the AP-2 complex, except for a recently identified orthologue of the AP-2-associated protein kinase 1, AAK1. In characterized eukaryotes, AAK1 phosphorylates the μ2 subunit of the AP-2 complex to enhance cargo recognition and uptake into clathrin-coated vesicles. Here, we show that kinetoplastids encode not one, but two AAK1 orthologues: one (AAK1L2) is absent from salivarian trypanosomes, while the other (AAK1L1) lacks important kinase-specific residues in a range of trypanosomes. These AAK1L1 and AAK1L2 novelties reinforce suggestions of functional divergence in endocytic uptake within salivarian trypanosomes. Despite this, we show that AAK1L1 null mutant Trypanosoma brucei, while viable, display slowed proliferation, morphological abnormalities including swelling of the flagellar pocket, and altered cargo uptake. In summary, our data suggest an unconventional role for a putative pseudokinase during endocytosis and/or vesicular trafficking in T. brucei, independent of AP-2.
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Affiliation(s)
- Jennifer A. Black
- The Wellcome Centre for Integrative Parasitology, School of Infection & ImmunityUniversity of GlasgowGlasgowUK
- Department of Cell and Molecular Biology, Ribeirão Preto Medical SchoolUniversity of São PauloSão PauloBrazil
| | - Christen M. Klinger
- The Wellcome Centre for Integrative Parasitology, School of Infection & ImmunityUniversity of GlasgowGlasgowUK
- Division of Infectious Diseases, Department of Medicine, Li Ka Shing Centre for Health, Research InnovationUniversity of AlbertaEdmontonAlbertaCanada
| | - Leandro Lemgruber
- The Wellcome Centre for Integrative Parasitology, School of Infection & ImmunityUniversity of GlasgowGlasgowUK
- Glasgow Imaging Facility, School of Infection & ImmunityUniversity of GlasgowGlasgowUK
| | - Joel B. Dacks
- Department of Cell and Molecular Biology, Ribeirão Preto Medical SchoolUniversity of São PauloSão PauloBrazil
- Institute of Parasitology, Biology CentreCzech Academy of SciencesCeske Budejovice (Budweis)Czech Republic
| | - Jeremy C. Mottram
- York Biomedical Research Institute and Department of BiologyUniversity of YorkYorkUK
| | - Richard McCulloch
- The Wellcome Centre for Integrative Parasitology, School of Infection & ImmunityUniversity of GlasgowGlasgowUK
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11
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Henry SP, Jorgensen WL. Progress on the Pharmacological Targeting of Janus Pseudokinases. J Med Chem 2023; 66:10959-10990. [PMID: 37578217 DOI: 10.1021/acs.jmedchem.3c00926] [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: 08/15/2023]
Abstract
The Janus kinases (JAKs) are key components of the JAK-STAT signaling pathway and are involved in myriad physiological processes. Though they are the molecular targets of many FDA-approved drugs, these drugs manifest adverse effects due in part to their inhibition of the requisite JAK kinase activity. However, the JAKs uniquely possess an integrated pseudokinase domain (JH2) that regulates the adjacent kinase domain (JH1). The therapeutic targeting of JH2 domains has been less thoroughly explored and may present an avenue to modulate the JAKs without the adverse effects associated with targeting the adjacent JH1 domain. The potential of this strategy was recently demonstrated with the FDA approval of the TYK2 JH2 ligand deucravacitinib for treating plaque psoriasis. In this light, the structure and targetability of the JAK pseudokinases are discussed, in conjunction with the state of development of ligands that bind to these domains.
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Affiliation(s)
- Sean P Henry
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - William L Jorgensen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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12
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Torosyan H, Paul MD, Forget A, Lo M, Diwanji D, Pawłowski K, Krogan NJ, Jura N, Verba KA. Structural insights into regulation of the PEAK3 pseudokinase scaffold by 14-3-3. Nat Commun 2023; 14:3543. [PMID: 37336883 PMCID: PMC10279700 DOI: 10.1038/s41467-023-38864-0] [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: 08/24/2022] [Accepted: 05/16/2023] [Indexed: 06/21/2023] Open
Abstract
PEAK pseudokinases are molecular scaffolds which dimerize to regulate cell migration, morphology, and proliferation, as well as cancer progression. The mechanistic role dimerization plays in PEAK scaffolding remains unclear, as there are no structures of PEAKs in complex with their interactors. Here, we report the cryo-EM structure of dimeric PEAK3 in complex with an endogenous 14-3-3 heterodimer. Our structure reveals an asymmetric binding mode between PEAK3 and 14-3-3 stabilized by one pseudokinase domain and the SHED domain of the PEAK3 dimer. The binding interface contains a canonical phosphosite-dependent primary interaction and a unique secondary interaction not observed in previous structures of 14-3-3/client complexes. Additionally, we show that PKD regulates PEAK3/14-3-3 binding, which when prevented leads to PEAK3 nuclear enrichment and distinct protein-protein interactions. Altogether, our data demonstrate that PEAK3 dimerization forms an unusual secondary interface for 14-3-3 binding, facilitating 14-3-3 regulation of PEAK3 localization and interactome diversity.
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Affiliation(s)
- Hayarpi Torosyan
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
- Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Michael D Paul
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Antoine Forget
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Megan Lo
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Devan Diwanji
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
- Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences, 02-787, Warszawa, Poland
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Natalia Jura
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA.
| | - Kliment A Verba
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA.
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13
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Turek I, Nguyen TH, Galea C, Abad I, Freihat L, Manallack DT, Velkov T, Irving H. Mutations in the Vicinity of the IRAK3 Guanylate Cyclase Center Impact Its Subcellular Localization and Ability to Modulate Inflammatory Signaling in Immortalized Cell Lines. Int J Mol Sci 2023; 24:ijms24108572. [PMID: 37239919 DOI: 10.3390/ijms24108572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Interleukin-1 receptor-associated kinase 3 (IRAK3) modulates the magnitude of cellular responses to ligands perceived by interleukin-1 receptors (IL-1Rs) and Toll-like receptors (TLRs), leading to decreases in pro-inflammatory cytokines and suppressed inflammation. The molecular mechanism of IRAK3's action remains unknown. IRAK3 functions as a guanylate cyclase, and its cGMP product suppresses lipopolysaccharide (LPS)-induced nuclear factor kappa-light-chain-enhancer of activated B cell (NFκB) activity. To understand the implications of this phenomenon, we expanded the structure-function analyses of IRAK3 through site-directed mutagenesis of amino acids known or predicted to impact different activities of IRAK3. We verified the capacity of the mutated IRAK3 variants to generate cGMP in vitro and revealed residues in and in the vicinity of its GC catalytic center that impact the LPS-induced NFκB activity in immortalized cell lines in the absence or presence of an exogenous membrane-permeable cGMP analog. Mutant IRAK3 variants with reduced cGMP generating capacity and differential regulation of NFκB activity influence subcellular localization of IRAK3 in HEK293T cells and fail to rescue IRAK3 function in IRAK3 knock-out THP-1 monocytes stimulated with LPS unless the cGMP analog is present. Together, our results shed new light on the mechanism by which IRAK3 and its enzymatic product control the downstream signaling, affecting inflammatory responses in immortalized cell lines.
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Affiliation(s)
- Ilona Turek
- Department of Rural Clinical Sciences, La Trobe Rural Health School, La Trobe University, Bendigo, VIC 3552, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC 3552, Australia
| | - Trang H Nguyen
- Department of Rural Clinical Sciences, La Trobe Rural Health School, La Trobe University, Bendigo, VIC 3552, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC 3552, Australia
| | - Charles Galea
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC 3052, Australia
| | - Isaiah Abad
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC 3052, Australia
| | - Lubna Freihat
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC 3052, Australia
| | - David T Manallack
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC 3052, Australia
| | - Tony Velkov
- Department of Microbiology, Monash University, Wellington Rd, Clayton, VIC 3800, Australia
| | - Helen Irving
- Department of Rural Clinical Sciences, La Trobe Rural Health School, La Trobe University, Bendigo, VIC 3552, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC 3552, Australia
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC 3052, Australia
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14
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Zacharchenko T, Dorendorf T, Locker N, Van Dijk E, Katzemich A, Diederichs K, Bullard B, Mayans O. PK1 from Drosophila obscurin is an inactive pseudokinase with scaffolding properties. Open Biol 2023; 13:220350. [PMID: 37121260 PMCID: PMC10129394 DOI: 10.1098/rsob.220350] [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: 11/25/2022] [Accepted: 03/23/2023] [Indexed: 05/02/2023] Open
Abstract
Obscurins are large filamentous proteins with crucial roles in the assembly, stability and regulation of muscle. Characteristic of these proteins is a tandem of two C-terminal kinase domains, PK1 and PK2, that are separated by a long intrinsically disordered sequence. The significance of this conserved domain arrangement is unknown. Our study of PK1 from Drosophila obscurin shows that this is a pseudokinase with features typical of the CAM-kinase family, but which carries a minimalistic regulatory tail that no longer binds calmodulin or has mechanosensory properties typical of other sarcomeric kinases. PK1 binds ATP with high affinity, but in the absence of magnesium and lacks detectable phosphotransfer activity. It also has a highly diverged active site, strictly conserved across arthropods, that might have evolved to accommodate an unconventional binder. We find that PK1 interacts with PK2, suggesting a functional relation to the latter. These findings lead us to speculate that PK1/PK2 form a pseudokinase/kinase dual system, where PK1 might act as an allosteric regulator of PK2 and where mechanosensing properties, akin to those described for regulatory tails in titin-like kinases, might now reside on the unstructured interkinase segment. We propose that the PK1-interkinase-PK2 region constitutes an integrated functional unit in obscurin proteins.
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Affiliation(s)
- Thomas Zacharchenko
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Till Dorendorf
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Nicolas Locker
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Evert Van Dijk
- Biosynth B.V., Zuidersluisweg 2, 8243 RC Lelystad, The Netherlands
| | | | - Kay Diederichs
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | | | - Olga Mayans
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
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15
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Pon A, Osinski A, Sreelatha A. Redefining pseudokinases: A look at the untapped enzymatic potential of pseudokinases. IUBMB Life 2023; 75:370-376. [PMID: 36602414 PMCID: PMC10050101 DOI: 10.1002/iub.2698] [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: 09/30/2022] [Accepted: 11/19/2022] [Indexed: 01/06/2023]
Abstract
Catalytically inactive kinases, known as pseudokinases, are conserved in all three domains of life. Due to the lack of catalytic residues, pseudokinases are considered to act as allosteric regulators and scaffolding proteins with no enzymatic function. However, since these "dead" kinases are conserved along with their active counterparts, a role for pseudokinases may have been overlooked. In this review, we will discuss the recently characterized pseudokinases Selenoprotein O, Legionella effector SidJ, and the SARS-CoV2 protein nsp12 which catalyze AMPylation, glutamylation, and RNAylation, respectively. These studies provide structural and mechanistic insight into the versatility and diversity of the kinase fold.
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Affiliation(s)
- Alex Pon
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Adam Osinski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Anju Sreelatha
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Center for Mineral Metabolism and Clinical Research, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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16
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Yeh CY, Wang YS, Takahashi Y, Kuusk K, Paul K, Arjus T, Yadlos O, Schroeder JI, Ilves I, Garcia-Sosa AT, Kollist H. MPK12 in stomatal CO 2 signaling: function beyond its kinase activity. THE NEW PHYTOLOGIST 2023. [PMID: 36978283 DOI: 10.1111/nph.18913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/21/2023] [Indexed: 05/24/2023]
Abstract
Protein phosphorylation is a major molecular switch involved in the regulation of stomatal opening and closure. Previous research defined interaction between MAP kinase 12 and Raf-like kinase HT1 as a required step for stomatal movements caused by changes in CO2 concentration. However, whether MPK12 kinase activity is required for regulation of CO2 -induced stomatal responses warrants in-depth investigation. We apply genetic, biochemical, and structural modeling approaches to examining the noncatalytic role of MPK12 in guard cell CO2 signaling that relies on allosteric inhibition of HT1. We show that CO2 /HCO3 - -enhanced MPK12 interaction with HT1 is independent of its kinase activity. By analyzing gas exchange of plant lines expressing various kinase-dead and constitutively active versions of MPK12 in a plant line where MPK12 is deleted, we confirmed that CO2 -dependent stomatal responses rely on MPK12's ability to bind to HT1, but not its kinase activity. We also demonstrate that purified MPK12 and HT1 proteins form a heterodimer in the presence of CO2 /HCO3 - and present structural modeling that explains the MPK12:HT1 interaction interface. These data add to the model that MPK12 kinase-activity-independent interaction with HT1 functions as a molecular switch by which guard cells sense changes in atmospheric CO2 concentration.
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Affiliation(s)
- Chung-Yueh Yeh
- Institute of Technology, University of Tartu, Nooruse 1, Tartu, 50411, Estonia
| | - Yuh-Shuh Wang
- Institute of Technology, University of Tartu, Nooruse 1, Tartu, 50411, Estonia
| | - Yohei Takahashi
- Institute of Transformative Bio-Molecules, Nagoya University, Furocho, Chikusa, Nagoya, Aichi, 464-8601, Japan
| | - Katarina Kuusk
- Institute of Technology, University of Tartu, Nooruse 1, Tartu, 50411, Estonia
| | - Karnelia Paul
- School of Biological Sciences, Cell and Developmental Biology Department, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Triinu Arjus
- Institute of Technology, University of Tartu, Nooruse 1, Tartu, 50411, Estonia
| | - Oleksii Yadlos
- Institute of Technology, University of Tartu, Nooruse 1, Tartu, 50411, Estonia
| | - Julian I Schroeder
- School of Biological Sciences, Cell and Developmental Biology Department, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Ivar Ilves
- Institute of Technology, University of Tartu, Nooruse 1, Tartu, 50411, Estonia
| | | | - Hannes Kollist
- Institute of Technology, University of Tartu, Nooruse 1, Tartu, 50411, Estonia
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17
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Byrne DP, Shrestha S, Daly LA, Marensi V, Ramakrishnan K, Eyers CE, Kannan N, Eyers PA. Evolutionary and cellular analysis of the 'dark' pseudokinase PSKH2. Biochem J 2023; 480:141-160. [PMID: 36520605 PMCID: PMC9988210 DOI: 10.1042/bcj20220474] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
Pseudokinases, so named because they lack one or more conserved canonical amino acids that define their catalytically active relatives, have evolved a variety of biological functions in both prokaryotic and eukaryotic organisms. Human PSKH2 is closely related to the canonical kinase PSKH1, which maps to the CAMK family of protein kinases. Primates encode PSKH2 in the form of a pseudokinase, which is predicted to be catalytically inactive due to loss of the invariant catalytic Asp residue. Although the biological role(s) of vertebrate PSKH2 proteins remains unclear, we previously identified species-level adaptions in PSKH2 that have led to the appearance of kinase or pseudokinase variants in vertebrate genomes alongside a canonical PSKH1 paralog. In this paper we confirm that, as predicted, PSKH2 lacks detectable protein phosphotransferase activity, and exploit structural informatics, biochemistry and cellular proteomics to begin to characterise vertebrate PSKH2 orthologues. AlphaFold 2-based structural analysis predicts functional roles for both the PSKH2 N- and C-regions that flank the pseudokinase domain core, and cellular truncation analysis confirms that the N-terminal domain, which contains a conserved myristoylation site, is required for both stable human PSKH2 expression and localisation to a membrane-rich subcellular fraction containing mitochondrial proteins. Using mass spectrometry-based proteomics, we confirm that human PSKH2 is part of a cellular mitochondrial protein network, and that its expression is regulated through client-status within the HSP90/Cdc37 molecular chaperone system. HSP90 interactions are mediated through binding to the PSKH2 C-terminal tail, leading us to predict that this region might act as both a cis and trans regulatory element, driving outputs linked to the PSKH2 pseudokinase domain that are important for functional signalling.
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Affiliation(s)
- Dominic P. Byrne
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Safal Shrestha
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, U.S.A
| | - Leonard A. Daly
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Vanessa Marensi
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Krithika Ramakrishnan
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Claire E. Eyers
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Natarajan Kannan
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, U.S.A
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, U.S.A
| | - Patrick A. Eyers
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
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18
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Aubol BE, Adams JA. SRPK1 regulates RNA binding in a pre-spliceosomal complex using a catalytic bypass mechanism. FEBS J 2022; 289:7428-7445. [PMID: 35730996 DOI: 10.1111/febs.16560] [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: 02/15/2022] [Revised: 05/10/2022] [Accepted: 06/21/2022] [Indexed: 01/14/2023]
Abstract
Serine-arginine protein kinase 1 (SRPK1) phosphorylates serine-arginine (SR) proteins in the cytoplasm, directing them to the nucleus for splicing function. SRPK1 has also been detected in the nucleus but its function here is still not fully understood. We now demonstrate that nuclear SRPK1 can regulate U1-70K, a protein component of the uridine-rich 1 small nuclear ribonucleoprotein (U1 snRNP) that binds SR proteins and facilitates 5' splice-site selection in precursor mRNA. We found that SRPK1 uses a large, disordered domain to bind U1-70K, regulating the interaction of an exonic splicing enhancer (ESE) to the associated SR protein. Surprisingly, the catalytic activity of SRPK1 is not required for this phenomenon. Instead, SRPK1 associates directly with the N-terminus of U1-70K and alters the regulatory function of the distal C-terminus, modifying interactions between the U1-70K:SR protein complex and the ESE. Disruption of SRPK1 binding to this complex affects the alternative splicing of genes modulated by the C-terminus of U1-70K. Such findings suggest that, in addition to operating as a traditional serine-modifying catalyst, SRPK1 can also bypass this intrinsic activity to regulate RNA contacts in an early pre-spliceosomal complex.
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Affiliation(s)
- Brandon E Aubol
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Joseph A Adams
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
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19
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Hajredini F, Alphonse S, Ghose R. BY-kinases: Protein tyrosine kinases like no other. J Biol Chem 2022; 299:102737. [PMID: 36423682 PMCID: PMC9800525 DOI: 10.1016/j.jbc.2022.102737] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/12/2022] [Accepted: 11/14/2022] [Indexed: 11/23/2022] Open
Abstract
BY-kinases (for bacterial tyrosine kinases) constitute a family of protein tyrosine kinases that are highly conserved in the bacterial kingdom and occur most commonly as essential components of multicomponent assemblies responsible for the biosynthesis, polymerization, and export of complex polysaccharides involved in biofilm or capsule formation. BY-kinase function has been attributed to a cyclic process involving formation of an oligomeric species, its disassembly into constituent monomers, and subsequent reassembly, depending on the overall phosphorylation level of a C-terminal cluster of tyrosine residues. However, the relationship of this process to the active/inactive states of the enzyme and the mechanism of its integration into the polysaccharide production machinery remain unclear. Here, we synthesize the substantial body of biochemical, cell-biological, structural, and computational data, acquired over the nearly 3 decades since the discovery of BY-kinases, to suggest means by which they fulfill their physiological function. We propose a mechanism involving temporal coordination of the assembly/disassembly process with the autokinase activity of the enzyme and its ability to be dephosphorylated by its counteracting phosphatase. We speculate that this temporal control enables BY-kinases to function as molecular timers that coordinate the diverse processes involved in the synthesis, polymerization, and export of complex sugar derivatives. We suggest that BY-kinases, which deploy distinctive catalytic domains resembling P-loop nucleoside triphosphatases, have uniquely adapted this ancient fold to drive functional processes through exquisite spatiotemporal control over protein-protein interactions and conformational changes. It is our hope that the hypotheses proposed here will facilitate future experiments targeting these unique protein kinases.
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Affiliation(s)
- Fatlum Hajredini
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York, USA,PhD Programs in Biochemistry, The Graduate Center of CUNY, New York, New York, USA
| | - Sébastien Alphonse
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York, USA
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York, USA,PhD Programs in Biochemistry, The Graduate Center of CUNY, New York, New York, USA,PhD Programs in Chemistry, The Graduate Center of CUNY, New York, New York, USA,PhD Programs in Physics, The Graduate Center of CUNY, New York, New York, USA,For correspondence: Ranajeet Ghose
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20
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Pseudokinase NRP1 facilitates endocytosis of transferrin in the African trypanosome. Sci Rep 2022; 12:18572. [PMID: 36329148 PMCID: PMC9633767 DOI: 10.1038/s41598-022-22054-x] [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: 05/21/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
Trypanosoma brucei causes human African trypanosomiasis (HAT) and nagana in cattle. During infection of a vertebrate, endocytosis of host transferrin (Tf) is important for viability of the parasite. The majority of proteins involved in trypanosome endocytosis of Tf are unknown. Here we identify pseudokinase NRP1 (Tb427tmp.160.4770) as a regulator of Tf endocytosis. Genetic knockdown of NRP1 inhibited endocytosis of Tf without blocking uptake of bovine serum albumin. Binding of Tf to the flagellar pocket was not affected by knockdown of NRP1. However the quantity of Tf per endosome dropped significantly, consistent with NRP1 promoting robust capture and/or retention of Tf in vesicles. NRP1 is involved in motility of Tf-laden vesicles since distances between endosomes and the kinetoplast were reduced after knockdown of the gene. In search of possible mediators of NRP1 modulation of Tf endocytosis, the gene was knocked down and the phosphoproteome analyzed. Phosphorylation of protein kinases forkhead, NEK6, and MAPK10 was altered, in addition to EpsinR, synaptobrevin and other vesicle-associated proteins predicted to be involved in endocytosis. These candidate proteins may link NRP1 functionally either to protein kinases or to vesicle-associated proteins.
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21
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Sun D, Zhang J, Dong G, He S, Sheng C. Blocking Non-enzymatic Functions by PROTAC-Mediated Targeted Protein Degradation. J Med Chem 2022; 65:14276-14288. [DOI: 10.1021/acs.jmedchem.2c01159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Donghuan Sun
- School of Pharmacy, Second Military Medical University (Naval Medical University), Shanghai 200433, China
| | - Jing Zhang
- Department of Pathology, Changzheng Hospital, Second Military Medical University (Naval Medical University), Shanghai 200003, China
| | - Guoqiang Dong
- School of Pharmacy, Second Military Medical University (Naval Medical University), Shanghai 200433, China
| | - Shipeng He
- Institute of Translational Medicine, Shanghai University, Shanghai 200444, China
| | - Chunquan Sheng
- School of Pharmacy, Second Military Medical University (Naval Medical University), Shanghai 200433, China
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22
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Sheetz JB, Lemmon MA. Looking lively: emerging principles of pseudokinase signaling. Trends Biochem Sci 2022; 47:875-891. [PMID: 35585008 PMCID: PMC9464697 DOI: 10.1016/j.tibs.2022.04.011] [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: 01/28/2022] [Revised: 04/06/2022] [Accepted: 04/21/2022] [Indexed: 10/18/2022]
Abstract
Progress towards understanding catalytically 'dead' protein kinases - pseudokinases - in biology and disease has hastened over the past decade. An especially lively area for structural biology, pseudokinases appear to be strikingly similar to their kinase relatives, despite lacking key catalytic residues. Distinct active- and inactive-like conformation states, which are crucial for regulating bona fide protein kinases, are conserved in pseudokinases and appear to be essential for function. We discuss recent structural data on conformational transitions and nucleotide binding by pseudokinases, from which some common principles emerge. In both pseudokinases and bona fide kinases, a conformational toggle appears to control the ability to interact with signaling effectors. We also discuss how biasing this conformational toggle may provide opportunities to target pseudokinases pharmacologically in disease.
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Affiliation(s)
- Joshua B Sheetz
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06505, USA; Yale Cancer Biology Institute, Yale West Campus, West Haven, CT 06516, USA.
| | - Mark A Lemmon
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06505, USA; Yale Cancer Biology Institute, Yale West Campus, West Haven, CT 06516, USA.
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23
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Breit-McNally C, Laflamme B, Singh RA, Desveaux D, Guttman DS. ZAR1: Guardian of plant kinases. FRONTIERS IN PLANT SCIENCE 2022; 13:981684. [PMID: 36212348 PMCID: PMC9539561 DOI: 10.3389/fpls.2022.981684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/07/2022] [Indexed: 05/25/2023]
Abstract
A key facet of innate immunity in plants entails the recognition of pathogen "effector" virulence proteins by host Nucleotide-Binding Leucine-Rich Repeat Receptors (NLRs). Among characterized NLRs, the broadly conserved ZAR1 NLR is particularly remarkable due to its capacity to recognize at least six distinct families of effectors from at least two bacterial genera. This expanded recognition spectrum is conferred through interactions between ZAR1 and a dynamic network of two families of Receptor-Like Cytoplasmic Kinases (RLCKs): ZED1-Related Kinases (ZRKs) and PBS1-Like Kinases (PBLs). In this review, we survey the history of functional studies on ZAR1, with an emphasis on how the ZAR1-RLCK network functions to trap diverse effectors. We discuss 1) the dynamics of the ZAR1-associated RLCK network; 2) the specificity between ZRKs and PBLs; and 3) the specificity between effectors and the RLCK network. We posit that the shared protein fold of kinases and the switch-like properties of their interactions make them ideal effector sensors, enabling ZAR1 to act as a broad spectrum guardian of host kinases.
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Affiliation(s)
- Clare Breit-McNally
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Bradley Laflamme
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Racquel A. Singh
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Darrell Desveaux
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, Canada
| | - David S. Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, Canada
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24
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Helwer R, Charette JM. The SSU Processome Component Utp25p is a Pseudohelicase. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000606. [PMID: 36212518 PMCID: PMC9539457 DOI: 10.17912/micropub.biology.000606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/19/2022] [Accepted: 09/19/2022] [Indexed: 11/09/2022]
Abstract
RNA helicases are involved in nearly all aspects of RNA metabolism and factor prominently in ribosome assembly. The SSU processome includes 10 helicases and many helicase-cofactors. Together, they mediate the structural rearrangements that occur as part of ribosomal SSU assembly. During the identification of the SSU processome component Utp25/Def, it was noticed that the protein displays some sequence similarity to DEAD-box RNA helicases and is essential for growth. Interestingly, mutational ablation showed that Utp25's DEAD-box motifs are dispensable. Here, we show that the Utp25 AlphaFold prediction displays considerable structural similarity to DEAD-box helicases and is the first fully validated pseudohelicase.
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Affiliation(s)
- Rafe Helwer
- Department of Chemistry, Brandon University, Brandon, Manitoba, Canada.
,
Children’s Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada.
,
CancerCare Manitoba Research Institute, Winnipeg, Manitoba, Canada
| | - J. Michael Charette
- Department of Chemistry, Brandon University, Brandon, Manitoba, Canada.
,
Children’s Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada.
,
CancerCare Manitoba Research Institute, Winnipeg, Manitoba, Canada.
,
Correspondence to: J. Michael Charette (
)
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25
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Liu J, Lu X, Zhang S, Yuan L, Sun Y. Molecular Insights into mRNA Polyadenylation and Deadenylation. Int J Mol Sci 2022; 23:ijms231910985. [PMID: 36232288 PMCID: PMC9570436 DOI: 10.3390/ijms231910985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 11/28/2022] Open
Abstract
Poly(A) tails are present on almost all eukaryotic mRNAs, and play critical roles in mRNA stability, nuclear export, and translation efficiency. The biosynthesis and shortening of a poly(A) tail are regulated by large multiprotein complexes. However, the molecular mechanisms of these protein machineries still remain unclear. Recent studies regarding the structural and biochemical characteristics of those protein complexes have shed light on the potential mechanisms of polyadenylation and deadenylation. This review summarizes the recent structural studies on pre-mRNA 3′-end processing complexes that initiate the polyadenylation and discusses the similarities and differences between yeast and human machineries. Specifically, we highlight recent biochemical efforts in the reconstitution of the active human canonical pre-mRNA 3′-end processing systems, as well as the roles of RBBP6/Mpe1 in activating the entire machinery. We also describe how poly(A) tails are removed by the PAN2-PAN3 and CCR4-NOT deadenylation complexes and discuss the emerging role of the cytoplasmic poly(A)-binding protein (PABPC) in promoting deadenylation. Together, these recent discoveries show that the dynamic features of these machineries play important roles in regulating polyadenylation and deadenylation.
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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.
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Krüger A, Frunzke J. A pseudokinase version of the histidine kinase ChrS promotes high heme tolerance of Corynebacterium glutamicum. Front Microbiol 2022; 13:997448. [PMID: 36160252 PMCID: PMC9491836 DOI: 10.3389/fmicb.2022.997448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/18/2022] [Indexed: 11/21/2022] Open
Abstract
Heme is an essential cofactor for almost all living cells by acting as prosthetic group for various proteins or serving as alternative iron source. However, elevated levels are highly toxic for cells. Several corynebacterial species employ two paralogous, heme-responsive two-component systems (TCS), ChrSA and HrrSA, to cope with heme stress and to maintain intracellular heme homeostasis. Significant cross-talk at the level of phosphorylation between these systems was previously demonstrated. In this study, we have performed a laboratory evolution experiment to adapt Corynebacterium glutamicum to increasing heme levels. Isolated strains showed a highly increased tolerance to heme growing at concentrations of up to 100 μM. The strain featuring the highest heme tolerance harbored a frameshift mutation in the catalytical and ATPase-domain (CA-domain) of the chrS gene, converting it into a catalytically-inactive pseudokinase (ChrS_CA-fs). Reintroduction of the respective mutation in the parental C. glutamicum strain confirmed high heme tolerance and showed a drastic upregulation of hrtBA encoding a heme export system, conserved in Firmicutes and Actinobacteria. The strain encoding the ChrS pseudokinase variant showed significantly higher heme tolerance than a strain lacking chrS. Mutational analysis revealed that induction of hrtBA in the evolved strain is solely mediated via the cross-phosphorylation of the response regulator (RR) ChrA by the kinase HrrS and BACTH assays revealed the formation of heterodimers between HrrS and ChrS. Overall, our results emphasize an important role of the ChrS pseudokinase in high heme tolerance of the evolved C. glutamicum and demonstrate the promiscuity in heme-dependent signaling of the paralogous two-component systems facilitating fast adaptation to changing environmental conditions.
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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.
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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.
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29
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García-Marín J, Rodríguez-Puyol D, Vaquero JJ. Insight into the mechanism of molecular recognition between human Integrin-Linked Kinase and Cpd22 and its implication at atomic level. J Comput Aided Mol Des 2022; 36:575-589. [PMID: 35869378 PMCID: PMC9512720 DOI: 10.1007/s10822-022-00466-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/11/2022] [Indexed: 10/29/2022]
Abstract
AbsractPseudokinases have received increasing attention over the past decade because of their role in different physiological phenomena. Although pseudokinases lack several active-site residues, thereby hindering their catalytic activity, recent discoveries have shown that these proteins can play a role in intracellular signaling thanks to their non-catalytic functions. Integrin-linked kinase (ILK) was discovered more than two decades ago and was subsequently validated as a promising target for neoplastic diseases. Since then, only a few small-molecule inhibitors have been described, with the V-shaped pyrazole Cpd22 being the most interesting and characterized. However, little is known about its detailed mechanism of action at atomic level. In this study, using a combination of computational chemistry methods including PELE calculations, docking, molecular dynamics and experimental surface plasmon resonance, we were able to prove the direct binding of this molecule to ILK, thus providing the basis of its molecular recognition by the protein and the effect over its architecture. Our breakthroughs show that Cpd22 binding stabilizes the ILK domain by binding to the pseudo-active site in a similar way to the ATP, possibly modulating its scaffolding properties as pseudokinase. Moreover, our results explain the experimental observations obtained during Cpd22 development, thus paving the way to the development of new chemical probes and potential drugs.
Graphical abstract
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30
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Riegel K, Vijayarangakannan P, Kechagioglou P, Bogucka K, Rajalingam K. Recent advances in targeting protein kinases and pseudokinases in cancer biology. Front Cell Dev Biol 2022; 10:942500. [PMID: 35938171 PMCID: PMC9354965 DOI: 10.3389/fcell.2022.942500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 06/27/2022] [Indexed: 11/24/2022] Open
Abstract
Kinases still remain the most favorable members of the druggable genome, and there are an increasing number of kinase inhibitors approved by the FDA to treat a variety of cancers. Here, we summarize recent developments in targeting kinases and pseudokinases with some examples. Targeting the cell cycle machinery garnered significant clinical success, however, a large section of the kinome remains understudied. We also review recent developments in the understanding of pseudokinases and discuss approaches on how to effectively target in cancer.
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Affiliation(s)
- Kristina Riegel
- Cell Biology Unit, University Medical Center Mainz, JGU-Mainz, Mainz, Germany
| | | | - Petros Kechagioglou
- Cell Biology Unit, University Medical Center Mainz, JGU-Mainz, Mainz, Germany
| | - Katarzyna Bogucka
- Cell Biology Unit, University Medical Center Mainz, JGU-Mainz, Mainz, Germany
| | - Krishnaraj Rajalingam
- Cell Biology Unit, University Medical Center Mainz, JGU-Mainz, Mainz, Germany
- *Correspondence: Krishnaraj Rajalingam,
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Bogomolovas J, Gravenhorst P, Mayans O. Production and analysis of titin kinase: Exploiting active/inactive kinase homologs in pseudokinase validation. Methods Enzymol 2022; 667:147-181. [PMID: 35525541 DOI: 10.1016/bs.mie.2022.03.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Protein pseudokinases are key regulators of the eukaryotic cell. Understanding their unconventional molecular mechanisms relies on deciphering their putative potential to perform phosphotransfer, their scaffolding properties and the nature of their regulation. Titin pseudokinase (TK) is the defining member of a family of poorly characterized muscle-specific kinases thought to act as sensors and transducers of mechanical signals in the sarcomere. The functional mechanisms of TK remain obscure due to the challenges posed by its production and analysis. Here, we provide guidelines and tailored research approaches for the study of TK, including profiting from its close structure-function relationship to the catalytically active homolog twitchin kinase (TwcK) from C. elegans. We describe a methodological pipeline to produce recombinant TK and TwcK samples; design, prioritize and validate mutated and truncated variants; assess sample stability and perform activity assays. The strategy is exportable to other pseudokinase members of the TK-like kinase family.
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Affiliation(s)
- Julius Bogomolovas
- School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | | | - Olga Mayans
- Department of Biology, University of Konstanz, Konstanz, Germany.
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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.
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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.
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Preuss F, Chatterjee D, Dederer V, Knapp S, Mathea S. Enabling pseudokinases as potential drug targets. Methods Enzymol 2022; 667:663-683. [PMID: 35525558 DOI: 10.1016/bs.mie.2022.03.050] [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
Pseudokinases play significant roles in disease development. Similar to active kinases, their cellular functions can be targeted pharmacologically. But notably, instead of inhibiting an enzymatic activity, drug-like molecules act by stabilizing distinct pseudokinase conformations, by interfering with protein interactions, or by inducing proteasomal degradation. Herein, we describe our approach of enabling particular pseudokinases as potential drug targets. The method starts with obtaining recombinant proteins for assay development and for biochemical evaluation. The next step is to probe the pseudoactive site as a binding pocket for small molecules, providing initial insight into binding modes and even candidate chemotypes. Finally, structural features of pseudokinase:inhibitor complexes are explored. Taken together, we provide detailed method descriptions for essential inhibitor development technologies.
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Affiliation(s)
- Franziska Preuss
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany; Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Deep Chatterjee
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany; Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Verena Dederer
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany; Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Stefan Knapp
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany; Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.
| | - Sebastian Mathea
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany; Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
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34
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Gama Braga L, Garand C, Elowe S. Considerations for studying phosphorylation of the mitotic checkpoint pseudokinase BUBR1. Methods Enzymol 2022; 667:507-534. [PMID: 35525552 DOI: 10.1016/bs.mie.2022.03.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Budding uninhibited by benzimidazole 1-related protein 1 (BUBR1) is a mitotic checkpoint (better known as the spindle assembly checkpoint) protein that forms part of an inhibitory complex required to delay mitosis when errors occur in the attachment between chromosomes and the mitotic spindle. If these errors remain uncorrected, it could result in unequal distribution of genetic material to each of the nascent daughter cells, leading to potentially disastrous consequences at both the cellular and organismal level. In some higher eukaryotes including vertebrates, BUBR1 has a C-terminal kinase fold that is largely thought to be inactive, whereas in many species this domain has been lost through evolution and the truncated protein is known as mitotic arrest deficient 3 (MAD3). Here we present advice and practical considerations for the design of experiments, their analysis and interpretation to study the functions of the vertebrate BUBR1 during mitosis with emphasis on analysis implicating the pseudokinase domain.
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Affiliation(s)
- Luciano Gama Braga
- Biologie Cellulaire et Moléculaire, Faculté de Médicine, Université Laval, Québec, QC, Canada; Centre de Recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe de Reproduction, Santé de la Mère et de l'Enfant, Québec, QC, Canada; PROTEO-Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada; Département de Pédiatire, Faculté de Médicine, Université Laval et le Centre de Recherche sur le Cancer de l'Université Laval, Québec, QC, Canada
| | - Chantal Garand
- Centre de Recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe de Reproduction, Santé de la Mère et de l'Enfant, Québec, QC, Canada; PROTEO-Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
| | - Sabine Elowe
- Biologie Cellulaire et Moléculaire, Faculté de Médicine, Université Laval, Québec, QC, Canada; Centre de Recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe de Reproduction, Santé de la Mère et de l'Enfant, Québec, QC, Canada; PROTEO-Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada; Département de Pédiatire, Faculté de Médicine, Université Laval et le Centre de Recherche sur le Cancer de l'Université Laval, Québec, QC, Canada.
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35
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Sheetz JB, Lemmon MA, Tsutsui Y. Dynamics of protein kinases and pseudokinases by HDX-MS. Methods Enzymol 2022; 667:303-338. [PMID: 35525545 PMCID: PMC9148214 DOI: 10.1016/bs.mie.2022.03.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Dynamics of the protein kinase fold are deeply intertwined with its structure. The past three decades of kinase biophysical studies revealed key dynamic features of the kinase domain and, more recently, how these features may endow catalytically impaired kinases-or pseudokinases-with signaling properties. Hydrogen-deuterium exchange coupled with mass spectrometry (HDX-MS) is proving to be a valuable approach for studies of kinase and pseudokinase domain dynamics. Here, we briefly discuss the methods that have provided insights into protein kinase dynamics, describe how HDX-MS is being used to answer questions in the kinase/pseudokinase field, and provide a detailed protocol for collecting an HDX-MS dataset to study the impacts of small molecule binding to a pseudokinase domain. As more small molecules are discovered that can disrupt pseudokinase conformations, HDX-MS is likely to be a powerful approach for exploring drug-induced changes in pseudokinase dynamics and structure.
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Affiliation(s)
- Joshua B Sheetz
- Department of Pharmacology and Yale Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, United States
| | - Mark A Lemmon
- Department of Pharmacology and Yale Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, United States.
| | - Yuko Tsutsui
- Department of Pharmacology and Yale Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, United States.
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36
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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.
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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.
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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.
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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.
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Jacobsen AV, Murphy JM. CRISPR deletions in cell lines for reconstitution studies of pseudokinase function. Methods Enzymol 2022; 667:229-273. [PMID: 35525543 DOI: 10.1016/bs.mie.2022.03.054] [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
The non-catalytic cousins of protein kinases, the pseudokinases, have grown to prominence as indispensable signaling entities over the past decade, despite their lack of catalytic activity. Because their importance has only been fully embraced recently, many of the 10% of the human kinome categorized as pseudokinases are yet to be attributed biological functions. The advent of CRISPR-Cas9 editing to genetically delete pseudokinases in a cell line of interest has proven invaluable to dissecting many functions and remains the method of choice for gene knockout. Here, using the terminal effector pseudokinase in the necroptosis cell death pathway, MLKL, as an exemplar, we describe a method for genetic knockout of pseudokinases in cultured cells. This method does not retain the CRISPR guide sequence in the edited cells, which eliminates possible interference in subsequent reconstitution studies where mutant forms of the pseudokinase can be reintroduced into cells exogenously for detailed mechanistic characterization.
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Affiliation(s)
- Annette V Jacobsen
- 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.
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Targeting the HER3 pseudokinase domain with small molecule inhibitors. Methods Enzymol 2022; 667:455-505. [PMID: 35525551 DOI: 10.1016/bs.mie.2022.03.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
HER3 is a potent oncogenic growth factor receptor belonging to the human epidermal growth factor (HER/EGFR) family of receptor tyrosine kinases. In contrast to other EGFR family members, HER3 is a pseudokinase, lacking functional kinase activity. As such, efforts to develop small molecule tyrosine kinase inhibitors against this family member have been limited. In response to HER3-specific growth factors such as neuregulin (NRG, also known as heregulin or HRG), HER3 must couple with catalytically active family members, including its preferred partner HER2. Dimerization of the intracellular HER2:HER3 kinase domains is a critical part of the activation mechanism and HER3 plays a specialized role as an allosteric activator of the active HER2 kinase partner. Intriguingly, many pseudokinases retain functionally important nucleotide binding capacity, despite loss of kinase activity. We demonstrated that occupation of the nucleotide pocket of the pseudokinase HER3 retains functional importance for growth factor signaling through oncogenic HER2:HER3 heterodimers. Mutation of the HER3 nucleotide pocket both disrupts signaling and disrupts HER2:HER3 dimerization. Conversely, ATP competitive drugs which bind to HER3, but not HER2, can stabilize HER2:HER3 dimers, induce signaling and promote cell growth in breast cancer models. This indicates a nucleotide-dependent conformational role for the HER3 kinase domain. Critically, our recent proof-of-concept work demonstrated that HER3-directed small molecule inhibitors can also disrupt HER2:HER3 dimerization and signaling, supporting the prospect that HER3 can be a direct drug target despite its lack of intrinsic activity. In this chapter we will describe methods for identifying and validating small molecule inhibitors against the HER3 pseudokinase.
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40
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Karvonen H, Raivola J, Ungureanu D. Cellular thermal shift assay (CETSA) for determining the drug binding affinity using Ba/F3 clones stably expressing receptor pseudokinases. Methods Enzymol 2022; 667:339-363. [PMID: 35525546 DOI: 10.1016/bs.mie.2022.03.038] [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
The majority of drug screening approaches are performed using recombinant proteins, however, drug binding to its target(s) in cells should be also assessed, especially for drugs aimed at modulating intracellular signaling pathways. As a result, the development of a cellular thermal shift assay (CETSA) has become an important tool for determining the binding affinity of drugs to their intracellular targets. Cell lines, such as Ba/F3, are an excellent model system to stably express and study a target protein when this protein is not endogenously expressed or only present at low levels. Together with CETSA, Ba/F3 clones allow study of the transforming properties of the protein in question, its downstream intracellular signaling activation pathways, as well as its drug binding kinetics. This chapter describes in detail the establishment of Ba/F3 clones stably expressing receptor pseudokinases, such as receptor tyrosine kinase-like orphan receptors (ROR1, ROR2) and protein tyrosine kinase 7 (PTK7), and the use thereof to evaluate binding of small molecule inhibitors to their intracellular (pseudo)kinase domain by CETSA.
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Affiliation(s)
- Hanna Karvonen
- Cancer Signaling, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Juuli Raivola
- Applied Tumor Genomics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Daniela Ungureanu
- Cancer Signaling, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Applied Tumor Genomics, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
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Regulatory spine RS3 residue of protein kinases: a lipophilic bystander or a decisive element in the small-molecule kinase inhibitor binding? Biochem Soc Trans 2022; 50:633-648. [PMID: 35226061 PMCID: PMC9022976 DOI: 10.1042/bst20210837] [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: 12/22/2021] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 11/30/2022]
Abstract
In recent years, protein kinases have been one of the most pursued drug targets. These determined efforts have resulted in ever increasing numbers of small-molecule kinase inhibitors reaching to the market, offering novel treatment options for patients with distinct diseases. One essential component related to the activation and normal functionality of a protein kinase is the regulatory spine (R-spine). The R-spine is formed of four conserved residues named as RS1–RS4. One of these residues, RS3, located in the C-terminal part of αC-helix, is usually accessible for the inhibitors from the ATP-binding cavity as its side chain is lining the hydrophobic back pocket in many protein kinases. Although the role of RS3 has been well acknowledged in protein kinase function, this residue has not been actively considered in inhibitor design, even though many small-molecule kinase inhibitors display interactions to this residue. In this minireview, we will cover the current knowledge of RS3, its relationship with the gatekeeper, and the role of RS3 in kinase inhibitor interactions. Finally, we comment on the future perspectives how this residue could be utilized in the kinase inhibitor design.
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Wang Z, Huang W, Zhou K, Ren X, Ding K. Targeting the Non-Catalytic Functions: a New Paradigm for Kinase Drug Discovery? J Med Chem 2022; 65:1735-1748. [PMID: 35000385 DOI: 10.1021/acs.jmedchem.1c01978] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Protein kinases have been highly fruitful targets for cancer drug discovery in the past two decades, while most of these drugs bind to the "adenosine triphosphate (ATP)-site" and inhibit kinase catalytic activity. Recently, accumulated evidence suggests that kinases possess functions beyond catalysis through their scaffolds, and the scaffolding functions could play critical roles in multiple cellular signaling and cell fate controls. Small molecules modulating the noncatalytic functions of kinases are rarely reported but emerge as new promising therapeutic strategies for various diseases. Herein, we summarize the characterized noncatalytic functions of kinases, and highlight the recent progress on developing small-molecule modulators of the noncatalytic functions of kinases. Mechanisms and characteristics of different kinds of modulators are also discussed. It is also speculated that targeting the noncatalytic functions would represent a new direction for kinase-based drug discovery.
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Affiliation(s)
- Zhen Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, #345 Ling Ling Road, Shanghai 200032, People's Republic of China
| | - Weixue Huang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, #345 Ling Ling Road, Shanghai 200032, People's Republic of China
| | - Kaijie Zhou
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, #345 Ling Ling Road, Shanghai 200032, People's Republic of China
| | - Xiaomei Ren
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People's Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, People's Republic of China
| | - Ke Ding
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, #345 Ling Ling Road, Shanghai 200032, People's Republic of China.,International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People's Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, People's Republic of China.,The First Affiliated Hospital (Huaqiao Hospital), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, People's Republic of China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, People's Republic of China
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Ounoughene Y, Fourgous E, Boublik Y, Saland E, Guiraud N, Recher C, Urbach S, Fort P, Sarry JE, Fesquet D, Roche S. SHED-Dependent Oncogenic Signaling of the PEAK3 Pseudo-Kinase. Cancers (Basel) 2021; 13:cancers13246344. [PMID: 34944965 PMCID: PMC8699254 DOI: 10.3390/cancers13246344] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/10/2021] [Accepted: 12/16/2021] [Indexed: 01/09/2023] Open
Abstract
Simple Summary The human kinome is composed of about 50 pseudo-kinases with unclear function, because they are predicted to be catalytically inactive; however, they are shown to play an important role in cancer, similar to active kinases. Understanding how these pseudo-kinases promote tumor formation despite their catalytic inactivity is a great challenge, which may lead to innovative anti-cancer therapies. The PEAK1 and 2 pseudo-kinases have emerged as important components of the protein tyrosine kinase pathway implicated in cancer progression. They can signal using a scaffolding mechanism via a conserved split helical dimerization (SHED) module. In this study, we uncovered a similar SHED-dependent oncogenic activity for PEAK3, a recently discovered new member of this family. We also show that this new signaling mechanism may be implicated in acute myeloid leukemia. Abstract The PEAK1 and Pragmin/PEAK2 pseudo-kinases have emerged as important components of the protein tyrosine kinase pathway implicated in cancer progression. They can signal using a scaffolding mechanism that involves a conserved split helical dimerization (SHED) module. We recently identified PEAK3 as a novel member of this family based on structural homology; however, its signaling mechanism remains unclear. In this study, we found that, although it can self-associate, PEAK3 shows higher evolutionary divergence than PEAK1/2. Moreover, the PEAK3 protein is strongly expressed in human hematopoietic cells and is upregulated in acute myeloid leukemia. Functionally, PEAK3 overexpression in U2OS sarcoma cells enhanced their growth and migratory properties, while its silencing in THP1 leukemic cells reduced these effects. Importantly, an intact SHED module was required for these PEAK3 oncogenic activities. Mechanistically, through a phosphokinase survey, we identified PEAK3 as a novel inducer of AKT signaling, independent of growth-factor stimulation. Then, proteomic analyses revealed that PEAK3 interacts with the signaling proteins GRB2 and ASAP1/2 and the protein kinase PYK2, and that these interactions require the SHED domain. Moreover, PEAK3 activated PYK2, which promoted PEAK3 tyrosine phosphorylation, its association with GRB2 and ASAP1, and AKT signaling. Thus, the PEAK1-3 pseudo-kinases may use a conserved SHED-dependent mechanism to activate specific signaling proteins to promote oncogenesis.
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Affiliation(s)
- Youcef Ounoughene
- CRBM, University Montpellier, CNRS, Equipe Labellisée Ligue Contre le Cancer, F-34000 Montpellier, France; (Y.O.); (E.F.); (Y.B.); (P.F.)
| | - Elise Fourgous
- CRBM, University Montpellier, CNRS, Equipe Labellisée Ligue Contre le Cancer, F-34000 Montpellier, France; (Y.O.); (E.F.); (Y.B.); (P.F.)
| | - Yvan Boublik
- CRBM, University Montpellier, CNRS, Equipe Labellisée Ligue Contre le Cancer, F-34000 Montpellier, France; (Y.O.); (E.F.); (Y.B.); (P.F.)
| | - Estelle Saland
- CRCT, INSERM, CNRS, University of Toulouse, Equipe Labellisée Ligue Contre le Cancer, F-31037 Toulouse, France; (E.S.); (N.G.); (C.R.); (J.-E.S.)
| | - Nathan Guiraud
- CRCT, INSERM, CNRS, University of Toulouse, Equipe Labellisée Ligue Contre le Cancer, F-31037 Toulouse, France; (E.S.); (N.G.); (C.R.); (J.-E.S.)
| | - Christian Recher
- CRCT, INSERM, CNRS, University of Toulouse, Equipe Labellisée Ligue Contre le Cancer, F-31037 Toulouse, France; (E.S.); (N.G.); (C.R.); (J.-E.S.)
| | - Serge Urbach
- IGF, CNRS, INSERM, University Montpellier, F-34000 Montpellier, France;
| | - Philippe Fort
- CRBM, University Montpellier, CNRS, Equipe Labellisée Ligue Contre le Cancer, F-34000 Montpellier, France; (Y.O.); (E.F.); (Y.B.); (P.F.)
| | - Jean-Emmanuel Sarry
- CRCT, INSERM, CNRS, University of Toulouse, Equipe Labellisée Ligue Contre le Cancer, F-31037 Toulouse, France; (E.S.); (N.G.); (C.R.); (J.-E.S.)
| | - Didier Fesquet
- CRBM, University Montpellier, CNRS, Equipe Labellisée Ligue Contre le Cancer, F-34000 Montpellier, France; (Y.O.); (E.F.); (Y.B.); (P.F.)
- Correspondence: (D.F.); (S.R.)
| | - Serge Roche
- CRBM, University Montpellier, CNRS, Equipe Labellisée Ligue Contre le Cancer, F-34000 Montpellier, France; (Y.O.); (E.F.); (Y.B.); (P.F.)
- Correspondence: (D.F.); (S.R.)
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Liang LY, Roy M, Horne CR, Sandow JJ, Surudoi M, Dagley LF, Young SN, Dite T, Babon JJ, Janes PW, Patel O, Murphy JM, Lucet IS. The intracellular domains of the EphB6 and EphA10 receptor tyrosine pseudokinases function as dynamic signalling hubs. Biochem J 2021; 478:3351-3371. [PMID: 34431498 PMCID: PMC8454701 DOI: 10.1042/bcj20210572] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/20/2021] [Accepted: 08/25/2021] [Indexed: 12/25/2022]
Abstract
EphB6 and EphA10 are two poorly characterised pseudokinase members of the Eph receptor family, which collectively serves as mediators of contact-dependent cell-cell communication to transmit extracellular cues into intracellular signals. As per their active counterparts, EphB6 and EphA10 deregulation is strongly linked to proliferative diseases. However, unlike active Eph receptors, whose catalytic activities are thought to initiate an intracellular signalling cascade, EphB6 and EphA10 are classified as catalytically dead, raising the question of how non-catalytic functions contribute to Eph receptor signalling homeostasis. In this study, we have characterised the biochemical properties and topology of the EphB6 and EphA10 intracellular regions comprising the juxtamembrane (JM) region, pseudokinase and SAM domains. Using small-angle X-ray scattering and cross-linking-mass spectrometry, we observed high flexibility within their intracellular regions in solution and a propensity for interaction between the component domains. We identified tyrosine residues in the JM region of EphB6 as EphB4 substrates, which can bind the SH2 domains of signalling effectors, including Abl, Src and Vav3, consistent with cellular roles in recruiting these proteins for downstream signalling. Furthermore, our finding that EphB6 and EphA10 can bind ATP and ATP-competitive small molecules raises the prospect that these pseudokinase domains could be pharmacologically targeted to counter oncogenic signalling.
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Affiliation(s)
- Lung-Yu Liang
- Walter and Eliza Hall Institute or Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Michael Roy
- Walter and Eliza Hall Institute or Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Christopher R. Horne
- Walter and Eliza Hall Institute or Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Jarrod J. Sandow
- Walter and Eliza Hall Institute or Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Minglyanna Surudoi
- Walter and Eliza Hall Institute or Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Laura F. Dagley
- Walter and Eliza Hall Institute or Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Samuel N. Young
- Walter and Eliza Hall Institute or Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Toby Dite
- Walter and Eliza Hall Institute or Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Jeffrey J. Babon
- Walter and Eliza Hall Institute or Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Peter W. Janes
- Tumour Targeting Program, Olivia Newton-John Cancer Research Institute and La Trobe School of Cancer Medicine, Level 5, ONJ Centre, 145 Studley Rd, Heidelberg, Victoria 3084, Australia
| | - Onisha Patel
- Walter and Eliza Hall Institute or Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - James M. Murphy
- Walter and Eliza Hall Institute or Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Isabelle S. Lucet
- Walter and Eliza Hall Institute or Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, Australia
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45
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Serafim RAM, Elkins JM, Zuercher WJ, Laufer SA, Gehringer M. Chemical Probes for Understudied Kinases: Challenges and Opportunities. J Med Chem 2021; 65:1132-1170. [PMID: 34477374 DOI: 10.1021/acs.jmedchem.1c00980] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over 20 years after the approval of the first-in-class protein kinase inhibitor imatinib, the biological function of a significant fraction of the human kinome remains poorly understood while most research continues to be focused on few well-validated targets. Given the strong genetic evidence for involvement of many kinases in health and disease, the understudied fraction of the kinome holds a large and unexplored potential for future therapies. Specific chemical probes are indispensable tools to interrogate biology enabling proper preclinical validation of novel kinase targets. In this Perspective, we highlight recent case studies illustrating the development of high-quality chemical probes for less-studied kinases and their application in target validation. We spotlight emerging techniques and approaches employed in the generation of chemical probes for protein kinases and beyond and discuss the associated challenges and opportunities.
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Affiliation(s)
- Ricardo A M Serafim
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Jonathan M Elkins
- Centre for Medicines Discovery, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - William J Zuercher
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stefan A Laufer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany.,Tübingen Center for Academic Drug Discovery, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
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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.
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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.)
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