1
|
Bradley D, Garand C, Belda H, Gagnon-Arsenault I, Treeck M, Elowe S, Landry CR. The substrate quality of CK2 target sites has a determinant role on their function and evolution. Cell Syst 2024; 15:544-562.e8. [PMID: 38861992 DOI: 10.1016/j.cels.2024.05.005] [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: 07/03/2023] [Revised: 02/29/2024] [Accepted: 05/20/2024] [Indexed: 06/13/2024]
Abstract
Most biological processes are regulated by signaling modules that bind to short linear motifs. For protein kinases, substrates may have full or only partial matches to the kinase recognition motif, a property known as "substrate quality." However, it is not clear whether differences in substrate quality represent neutral variation or if they have functional consequences. We examine this question for the kinase CK2, which has many fundamental functions. We show that optimal CK2 sites are phosphorylated at maximal stoichiometries and found in many conditions, whereas minimal substrates are more weakly phosphorylated and have regulatory functions. Optimal CK2 sites tend to be more conserved, and substrate quality is often tuned by selection. For intermediate sites, increases or decreases in substrate quality may be deleterious, as we demonstrate for a CK2 substrate at the kinetochore. The results together suggest a strong role for substrate quality in phosphosite function and evolution. A record of this paper's transparent peer review process is included in the supplemental information.
Collapse
Affiliation(s)
- David Bradley
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec City, QC G1V 0A6, Canada; Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec City, QC G1V 0A6, Canada; Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada.
| | - Chantal Garand
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec City, QC G1V 0A6, Canada; Axe de Reproduction, Santé de la mère et de l'enfant, CHU de Québec, Université Laval, Québec City, QC, Canada
| | - Hugo Belda
- Signalling in Host-Pathogen Interaction Laboratory, The Francis Crick Institute, London NW11AT, UK
| | - Isabelle Gagnon-Arsenault
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec City, QC G1V 0A6, Canada; Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec City, QC G1V 0A6, Canada; Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Moritz Treeck
- Signalling in Host-Pathogen Interaction Laboratory, The Francis Crick Institute, London NW11AT, UK; Cell Biology of Host-Pathogen Interaction Laboratory, The Gulbenkian Institute of Science, Oeiras 2780-156, Portugal
| | - Sabine Elowe
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec City, QC G1V 0A6, Canada; Axe de Reproduction, Santé de la mère et de l'enfant, CHU de Québec, Université Laval, Québec City, QC, Canada; Department of Pediatrics, Faculty of Medicine, Université Laval, Québec City, QC, Canada; Centre de Recherche sur le Cancer, CHU de Québec, Université Laval, Québec City, QC, Canada
| | - Christian R Landry
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec City, QC G1V 0A6, Canada; Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec City, QC G1V 0A6, Canada; Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada.
| |
Collapse
|
2
|
Par3 promotes breast cancer invasion and migration through pull tension and protein nanoparticle-induced osmotic pressure. Biomed Pharmacother 2022; 155:113739. [PMID: 36179489 DOI: 10.1016/j.biopha.2022.113739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/13/2022] [Accepted: 09/21/2022] [Indexed: 11/20/2022] Open
Abstract
Cancer cell invasion and metastasis are closely related to intracellular tension. The cell-polarity protein, Par3, is a mechanical transmitter that affects cytoskeletal forces and determines breast cancer aggressiveness. Increased Par3 tension caused by aPKC inactivation is involved in filopodia and lamellipodia formation. Blocking the connection between Par3 and aPKC increases breast cancer aggressiveness both in vitro and in vivo. Meanwhile, aPKC-induced Par3 cytoplasmic translocation results in JAM-A phase separation and microfilament depolymerization, which is associated with increased intracellular protein nanoparticle-induced osmotic pressure. This study demonstrated the effects of aPKC on Par3 tension and osmotic pressure in breast cancer metastasis, and introduced Par3-associated mechanical mechanisms as potential targets for breast cancer treatment.
Collapse
|
3
|
Le LTM, Drakulic S, Nyengaard JR, Golas MM, Sander B. Structural Organization of Human Full-Length PAR3 and the aPKC-PAR6 Complex. Mol Biotechnol 2022; 64:1319-1327. [PMID: 35610404 PMCID: PMC9573856 DOI: 10.1007/s12033-022-00504-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 04/29/2022] [Indexed: 11/24/2022]
Abstract
The tripartite partition defect (PAR) polarity complex, which includes the proteins PAR3, atypical protein kinase C (aPKC), and PAR6, is a major regulator of cellular polarity. It is highly conserved and expressed in various tissues. Its largest component, PAR3, controls protein–protein interactions of the PAR complex with a variety of interaction partners, and PAR3 self-association is critical for the formation of filament-like structures. However, little is known about the structure of the PAR complex. Here, we purified non-filamentous PAR3 and the aPKC–PAR6 complex and characterized them by single-particle electron microscopy (EM). We expressed and purified an oligomerization-deficient form of PAR3, PAR3V13D,D70K, and the active aPKC–PAR6 dimer. For PAR3, engineering at two positions is sufficient to form stable single particles with a maximum dimension of 20 nm. aPKC–PAR6 forms a complex with a maximum dimension of 13.5 nm that contains single copies of aPKC. Thus, the data present a basis for further high-resolution studies of PAR proteins and PAR complex formation.
Collapse
Affiliation(s)
- Le T M Le
- Core Center for Molecular Morphology, Section for Stereology and Microscopy, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
- The Hormel Institute, University of Minnesota, Austin, MN, USA
| | - Srdja Drakulic
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Jens R Nyengaard
- Core Center for Molecular Morphology, Section for Stereology and Microscopy, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Centre for Stochastic Geometry and Advanced Bioimaging, Aarhus University, Wilhelm Meyers Allé 3, Building 1233/1234, 8000, Aarhus C, Denmark
| | - Monika M Golas
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Human Genetics, Faculty of Medicine, University of Augsburg, Stenglinstrasse 2, 86156, Augsburg, Germany
| | - Bjoern Sander
- Centre for Stochastic Geometry and Advanced Bioimaging, Aarhus University, Wilhelm Meyers Allé 3, Building 1233/1234, 8000, Aarhus C, Denmark.
- Institute of Pathology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
| |
Collapse
|
4
|
Shah H, Khan K, Khan N, Badshah Y, Ashraf NM, Shabbir M. Impact of deleterious missense PRKCI variants on structural and functional dynamics of protein. Sci Rep 2022; 12:3781. [PMID: 35260606 PMCID: PMC8904829 DOI: 10.1038/s41598-022-07526-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/08/2022] [Indexed: 11/09/2022] Open
Abstract
Protein kinase C iota (PKCɩ) is a novel protein containing 596 amino acids and is also a member of atypical kinase family. The role of PKCɩ has been explored in neurodegenerative diseases, neuroblastoma, ovarian and pancreatic cancers. Single nucleotide polymorphisms (SNPs) have not been studied in PKCɩ till date. The purpose of the current study is to scrutinize the deleterious missense variants in PKCɩ and determine the effect of these variants on stability and dynamics of the protein. The structure of protein PKCɩ was predicted for the first time and post translational modifications were determined. Genetic variants of PKCɩ were retrieved from ENSEMBL and only missense variants were further analyzed because of its linkage with diseases. The pathogenicity of missense variants, effect on structure and function of protein, association with cancer and conservancy of the protein residues were determined through computational approaches. It is observed that C1 and the pseudo substrate region has the highest number of pathogenic SNPs. Variations in the kinase domain of the protein are predicted to alter overall phosphorylation of the protein. Molecular dynamic simulations predicted noteworthy change in structural and functional dynamics of the protein because of these variants. The study revealed that nine deleterious variants can possibly contribute to malfunctioning of the protein and can be associated with diseases. This can be useful in diagnostics and developing therapeutics for diseases related to these polymorphisms.
Collapse
Affiliation(s)
- Hania Shah
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Khushbukhat Khan
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Naila Khan
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Yasmin Badshah
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Naeem Mahmood Ashraf
- Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat, Pakistan
| | - Maria Shabbir
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan.
| |
Collapse
|
5
|
A genetically-encoded crosslinker screen identifies SERBP1 as a PKCε substrate influencing translation and cell division. Nat Commun 2021; 12:6934. [PMID: 34836941 PMCID: PMC8626422 DOI: 10.1038/s41467-021-27189-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 11/08/2021] [Indexed: 01/09/2023] Open
Abstract
The PKCε-regulated genome protective pathway provides transformed cells a failsafe to successfully complete mitosis. Despite the necessary role for Aurora B in this programme, it is unclear whether its requirement is sufficient or if other PKCε cell cycle targets are involved. To address this, we developed a trapping strategy using UV-photocrosslinkable amino acids encoded in the PKCε kinase domain. The validation of the mRNA binding protein SERBP1 as a PKCε substrate revealed a series of mitotic events controlled by the catalytic form of PKCε. PKCε represses protein translation, altering SERBP1 binding to the 40 S ribosomal subunit and promoting the assembly of ribonucleoprotein granules containing SERBP1, termed M-bodies. Independent of Aurora B, SERBP1 is shown to be necessary for chromosome segregation and successful cell division, correlating with M-body formation. This requirement for SERBP1 demonstrates that Aurora B acts in concert with translational regulation in the PKCε-controlled pathway exerting genome protection.
Collapse
|
6
|
Thompson BJ. Par-3 family proteins in cell polarity & adhesion. FEBS J 2021; 289:596-613. [PMID: 33565714 PMCID: PMC9290619 DOI: 10.1111/febs.15754] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/19/2021] [Accepted: 02/08/2021] [Indexed: 12/27/2022]
Abstract
The Par‐3/Baz family of polarity determinants is highly conserved across metazoans and includes C. elegans PAR‐3, Drosophila Bazooka (Baz), human Par‐3 (PARD3), and human Par‐3‐like (PARD3B). The C. elegans PAR‐3 protein localises to the anterior pole of asymmetrically dividing zygotes with cell division cycle 42 (CDC42), atypical protein kinase C (aPKC), and PAR‐6. The same C. elegans ‘PAR complex’ can also localise in an apical ring in epithelial cells. Drosophila Baz localises to the apical pole of asymmetrically dividing neuroblasts with Cdc42‐aPKC‐Par6, while in epithelial cells localises both in an apical ring with Cdc42‐aPKC‐Par6 and with E‐cadherin at adherens junctions. These apical and junctional localisations have become separated in human PARD3, which is strictly apical in many epithelia, and human PARD3B, which is strictly junctional in many epithelia. We discuss the molecular basis for this fundamental difference in localisation, as well as the possible functions of Par‐3/Baz family proteins as oligomeric clustering agents at the apical domain or at adherens junctions in epithelial stem cells. The evolution of Par‐3 family proteins into distinct apical PARD3 and junctional PARD3B orthologs coincides with the emergence of stratified squamous epithelia in vertebrates, where PARD3B, but not PARD3, is strongly expressed in basal layer stem cells – which lack a typical apical domain. We speculate that PARD3B may contribute to clustering of E‐cadherin, signalling from adherens junctions via Src family kinases or mitotic spindle orientation by adherens junctions in response to mechanical forces.
Collapse
Affiliation(s)
- Barry J Thompson
- ACRF Department of Cancer Biology & Therapeutics, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| |
Collapse
|
7
|
Lippert LG, Ma N, Ritt M, Jain A, Vaidehi N, Sivaramakrishnan S. Kinase inhibitors allosterically disrupt a regulatory interaction to enhance PKCα membrane translocation. J Biol Chem 2021; 296:100339. [PMID: 33508318 PMCID: PMC7949123 DOI: 10.1016/j.jbc.2021.100339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/14/2021] [Accepted: 01/22/2021] [Indexed: 10/28/2022] Open
Abstract
The eukaryotic kinase domain has multiple intrinsically disordered regions whose conformation dictates kinase activity. Small molecule kinase inhibitors (SMKIs) rely on disrupting the active conformations of these disordered regions to inactivate the kinase. While SMKIs are selected for their ability to cause this disruption, the allosteric effects of conformational changes in disordered regions is limited by a lack of dynamic information provided by traditional structural techniques. In this study, we integrated multiscale molecular dynamics simulations with FRET sensors to characterize a novel allosteric mechanism that is selectively triggered by SMKI binding to the protein kinase Cα domain. The indole maleimide inhibitors BimI and sotrastaurin were found to displace the Gly-rich loop (G-loop) that normally shields the ATP-binding site. Displacement of the G-loop interferes with a newly identified, structurally conserved binding pocket for the C1a domain on the N lobe of the kinase domain. This binding pocket, in conjunction with the N-terminal regulatory sequence, masks a diacylglycerol (DAG) binding site on the C1a domain. SMKI-mediated displacement of the G-loop released C1a and exposed the DAG binding site, enhancing protein kinase Cα translocation both to synthetic lipid bilayers and to live cell membranes in the presence of DAG. Inhibitor chemotype determined the extent of the observed allosteric effects on the kinase domain and correlated with the extent of membrane recruitment. Our findings demonstrate the allosteric effects of SMKIs beyond the confines of kinase catalytic conformation and provide an integrated computational-experimental paradigm to investigate parallel mechanisms in other kinases.
Collapse
Affiliation(s)
- Lisa G Lippert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ning Ma
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | - Michael Ritt
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Abhinandan Jain
- The Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California, USA.
| | - Sivaraj Sivaramakrishnan
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, USA.
| |
Collapse
|
8
|
Parker PJ, Brown SJ, Calleja V, Chakravarty P, Cobbaut M, Linch M, Marshall JJT, Martini S, McDonald NQ, Soliman T, Watson L. Equivocal, explicit and emergent actions of PKC isoforms in cancer. Nat Rev Cancer 2021; 21:51-63. [PMID: 33177705 DOI: 10.1038/s41568-020-00310-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/02/2020] [Indexed: 01/02/2023]
Abstract
The maturing mutational landscape of cancer genomes, the development and application of clinical interventions and evolving insights into tumour-associated functions reveal unexpected features of the protein kinase C (PKC) family of serine/threonine protein kinases. These advances include recent work showing gain or loss-of-function mutations relating to driver or bystander roles, how conformational constraints and plasticity impact this class of proteins and how emergent cancer-associated properties may offer opportunities for intervention. The profound impact of the tumour microenvironment, reflected in the efficacy of immune checkpoint interventions, further prompts to incorporate PKC family actions and interventions in this ecosystem, informed by insights into the control of stromal and immune cell functions. Drugging PKC isoforms has offered much promise, but when and how is not obvious.
Collapse
Affiliation(s)
- Peter J Parker
- Protein Phosphorylation Laboratory, Francis Crick Institute, London, UK.
- School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Campus, London, UK.
| | - Sophie J Brown
- Protein Phosphorylation Laboratory, Francis Crick Institute, London, UK
| | - Veronique Calleja
- Protein Phosphorylation Laboratory, Francis Crick Institute, London, UK
| | | | - Mathias Cobbaut
- Protein Phosphorylation Laboratory, Francis Crick Institute, London, UK
| | - Mark Linch
- UCL Cancer Institute, University College London, London, UK
| | | | - Silvia Martini
- Protein Phosphorylation Laboratory, Francis Crick Institute, London, UK
| | - Neil Q McDonald
- Signalling and Structural Biology Laboratory, Francis Crick Institute, London, UK
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, London, UK
| | - Tanya Soliman
- Centre for Cancer Genomics and Computational Biology, Bart's Cancer Institute, London, UK
| | - Lisa Watson
- Protein Phosphorylation Laboratory, Francis Crick Institute, London, UK
| |
Collapse
|
9
|
Kudo Y, Sugimoto M, Arias E, Kasashima H, Cordes T, Linares JF, Duran A, Nakanishi Y, Nakanishi N, L'Hermitte A, Campos A, Senni N, Rooslid T, Roberts LR, Cuervo AM, Metallo CM, Karin M, Diaz-Meco MT, Moscat J. PKCλ/ι Loss Induces Autophagy, Oxidative Phosphorylation, and NRF2 to Promote Liver Cancer Progression. Cancer Cell 2020; 38:247-262.e11. [PMID: 32589943 PMCID: PMC7423690 DOI: 10.1016/j.ccell.2020.05.018] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 03/31/2020] [Accepted: 05/21/2020] [Indexed: 02/07/2023]
Abstract
Oxidative stress plays a critical role in liver tissue damage and in hepatocellular carcinoma (HCC) initiation and progression. However, the mechanisms that regulate autophagy and metabolic reprogramming during reactive oxygen species (ROS) generation, and how ROS promote tumorigenesis, still need to be fully understood. We show that protein kinase C (PKC) λ/ι loss in hepatocytes promotes autophagy and oxidative phosphorylation. This results in ROS generation, which through NRF2 drives HCC through cell-autonomous and non-autonomous mechanisms. Although PKCλ/ι promotes tumorigenesis in oncogene-driven cancer models, emerging evidence demonstrate that it is a tumor suppressor in more complex carcinogenic processes. Consistently, PKCλ/ι levels negatively correlate with HCC histological tumor grade, establishing this kinase as a tumor suppressor in liver cancer.
Collapse
Affiliation(s)
- Yotaro Kudo
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Masayuki Sugimoto
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; Laboratory for Advanced Medicine Research, SHIONOGI & CO., LTD., 3-1-1, Futaba-cho, Toyonaka, 561-0825, Japan
| | - Esperanza Arias
- Departments of Medicine and of Developmental and Molecular Biology and Institute for Aging Studies, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Hiroaki Kasashima
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Thekla Cordes
- Department of Bioengineering, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Juan F Linares
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Angeles Duran
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Yuki Nakanishi
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Naoko Nakanishi
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Antoine L'Hermitte
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Alex Campos
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Nadia Senni
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Tarmo Rooslid
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Lewis R Roberts
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Ana Maria Cuervo
- Departments of Medicine and of Developmental and Molecular Biology and Institute for Aging Studies, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Christian M Metallo
- Department of Bioengineering, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michael Karin
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, Moores Cancer Center, University of California, San Diego, CA 92093-0987, USA
| | - Maria T Diaz-Meco
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Jorge Moscat
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA.
| |
Collapse
|
10
|
Wu X, Cai Q, Feng Z, Zhang M. Liquid-Liquid Phase Separation in Neuronal Development and Synaptic Signaling. Dev Cell 2020; 55:18-29. [PMID: 32726576 DOI: 10.1016/j.devcel.2020.06.012] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/27/2020] [Accepted: 06/09/2020] [Indexed: 01/09/2023]
Abstract
Formation of biomolecular condensates that are not enclosed by membranes via liquid-liquid phase separation (LLPS) is a general strategy that cells adopt to organize membraneless subcellular compartments for diverse functions. Neurons are highly polarized with elaborate branching and functional compartmentalization of their neurites, thus, raising additional demand for the proper subcellular localization of both membraneless and membrane-based organelles. Recent studies have provided evidence that several protein assemblies involved in the establishment of neuronal stem cell (NSC) polarity and in the asymmetric division of NSCs form distinct molecular condensates via LLPS. In synapses of adult neurons, molecular apparatuses controlling presynaptic neurotransmitter release and postsynaptic signaling transmission are also likely formed via LLPS. These molecular condensates, though not enclosed by lipid bilayers, directly associate with plasma membranes or membrane-based organelles, indicating that direct communication between membraneless and membrane-based organelles is a common theme in neurons and other types of cells.
Collapse
Affiliation(s)
- Xiandeng Wu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Qixu Cai
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Zhe Feng
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Mingjie Zhang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
| |
Collapse
|
11
|
Atobe M, Serizawa T, Yamakawa N, Takaba K, Nagano Y, Yamaura T, Tanaka E, Tazumi A, Bito S, Ishiguro M, Kawanishi M. Discovery of 4,6- and 5,7-Disubstituted Isoquinoline Derivatives as a Novel Class of Protein Kinase C ζ Inhibitors with Fragment-Merging Strategy. J Med Chem 2020; 63:7143-7162. [DOI: 10.1021/acs.jmedchem.0c00449] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Masakazu Atobe
- Laboratory for Medicinal Chemistry, Pharmaceutical Research Center, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan
| | - Takayuki Serizawa
- Laboratory for Medicinal Chemistry, Pharmaceutical Research Center, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan
| | - Natsumi Yamakawa
- Laboratory for Medicinal Chemistry, Pharmaceutical Research Center, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan
| | - Kenichiro Takaba
- Laboratory for Medicinal Chemistry, Pharmaceutical Research Center, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan
| | - Yukiko Nagano
- Research Coordination, Pharmaceutical Research Center, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan
| | - Toshiaki Yamaura
- Laboratory for Drug Discovery, Pharmaceutical Research Center, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan
| | - Eiichi Tanaka
- Laboratory for Drug Discovery, Pharmaceutical Research Center, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan
| | - Atsutoshi Tazumi
- Laboratory for Pharmacology, Pharmaceutical Research Center, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan
| | - Shino Bito
- Laboratory for Safety Assessment & ADME, Pharmaceutical Research Center, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni Shizuoka 410-2321, Japan
| | - Masashi Ishiguro
- Laboratory for Safety Assessment & ADME, Pharmaceutical Research Center, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni Shizuoka 410-2321, Japan
| | - Masashi Kawanishi
- Laboratory for Medicinal Chemistry, Pharmaceutical Research Center, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan
| |
Collapse
|
12
|
Liu Z, Yang Y, Gu A, Xu J, Mao Y, Lu H, Hu W, Lei QY, Li Z, Zhang M, Cai Y, Wen W. Par complex cluster formation mediated by phase separation. Nat Commun 2020; 11:2266. [PMID: 32385244 PMCID: PMC7211019 DOI: 10.1038/s41467-020-16135-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 04/16/2020] [Indexed: 02/08/2023] Open
Abstract
The evolutionarily conserved Par3/Par6/aPKC complex regulates the polarity establishment of diverse cell types and distinct polarity-driven functions. However, how the Par complex is concentrated beneath the membrane to initiate cell polarization remains unclear. Here we show that the Par complex exhibits cell cycle-dependent condensation in Drosophila neuroblasts, driven by liquid–liquid phase separation. The open conformation of Par3 undergoes autonomous phase separation likely due to its NTD-mediated oligomerization. Par6, via C-terminal tail binding to Par3 PDZ3, can be enriched to Par3 condensates and in return dramatically promote Par3 phase separation. aPKC can also be concentrated to the Par3N/Par6 condensates as a client. Interestingly, activated aPKC can disperse the Par3/Par6 condensates via phosphorylation of Par3. Perturbations of Par3/Par6 phase separation impair the establishment of apical–basal polarity during neuroblast asymmetric divisions and lead to defective lineage development. We propose that phase separation may be a common mechanism for localized cortical condensation of cell polarity complexes. The evolutionarily conserved complex, the Par proteins, regulates cell polarity. Here, the authors show that in Drosophila neuroblasts, the Par complex exhibits liquid–liquid phase separation dependent on the cell cycle.
Collapse
Affiliation(s)
- Ziheng Liu
- Department of Neurosurgery, Huashan Hospital, the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Ying Yang
- Temasek Life Sciences Laboratory, Department of Biological Sciences, National University of Singapore, Singapore, 117604, Singapore
| | - Aihong Gu
- Department of Neurosurgery, Huashan Hospital, the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Jiawen Xu
- Department of Neurosurgery, Huashan Hospital, the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Haojie Lu
- Department of Neurosurgery, Huashan Hospital, the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Weiguo Hu
- Department of Neurosurgery, Huashan Hospital, the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.,Fudan University Shanghai Cancer Center and Cancer Metabolism Laboratory, Fudan University, Shanghai, 200032, China
| | - Qun-Ying Lei
- Fudan University Shanghai Cancer Center and Cancer Metabolism Laboratory, Fudan University, Shanghai, 200032, China
| | - Zhouhua Li
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Mingjie Zhang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Yu Cai
- Temasek Life Sciences Laboratory, Department of Biological Sciences, National University of Singapore, Singapore, 117604, Singapore.
| | - Wenyu Wen
- Department of Neurosurgery, Huashan Hospital, the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
| |
Collapse
|
13
|
Shank2 Binds to aPKC and Controls Tight Junction Formation with Rap1 Signaling during Establishment of Epithelial Cell Polarity. Cell Rep 2020; 31:107407. [DOI: 10.1016/j.celrep.2020.02.088] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/22/2020] [Accepted: 02/25/2020] [Indexed: 11/19/2022] Open
|
14
|
Holly RW, Jones K, Prehoda KE. A Conserved PDZ-Binding Motif in aPKC Interacts with Par-3 and Mediates Cortical Polarity. Curr Biol 2020; 30:893-898.e5. [PMID: 32084408 DOI: 10.1016/j.cub.2019.12.055] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/20/2019] [Accepted: 12/18/2019] [Indexed: 10/25/2022]
Abstract
Par-3 regulates animal cell polarity by targeting the Par complex proteins Par-6 and atypical protein kinase C (aPKC) to specific cortical sites. Although numerous physical interactions between Par-3 and the Par complex have been identified [1-6], we discovered a novel interaction between Par-3's second PDZ domain and a highly conserved aPKC PDZ-binding motif (PBM) that is required in the context of the full-length, purified Par-6-aPKC complex. We also found that Par-3 is phosphorylated by the full Par complex and phosphorylation induces dissociation of the Par-3 phosphorylation site from aPKC's kinase domain but does not disrupt the Par-3 PDZ2-aPKC PBM interaction. In asymmetrically dividing Drosophila neuroblasts, the aPKC PBM is required for cortical targeting, consistent with its role in mediating a persistent interaction with Par-3. Our results define a physical connection that targets the Par complex to polarized sites on the cell membrane.
Collapse
Affiliation(s)
- Ryan W Holly
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, 1229 University of Oregon, Eugene, OR 97403, USA
| | - Kimberly Jones
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, 1229 University of Oregon, Eugene, OR 97403, USA
| | - Kenneth E Prehoda
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, 1229 University of Oregon, Eugene, OR 97403, USA.
| |
Collapse
|
15
|
Silver JT, Wirtz-Peitz F, Simões S, Pellikka M, Yan D, Binari R, Nishimura T, Li Y, Harris TJC, Perrimon N, Tepass U. Apical polarity proteins recruit the RhoGEF Cysts to promote junctional myosin assembly. J Cell Biol 2019; 218:3397-3414. [PMID: 31409654 PMCID: PMC6781438 DOI: 10.1083/jcb.201807106] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 04/20/2019] [Accepted: 07/29/2019] [Indexed: 12/20/2022] Open
Abstract
Silver et al. show that the RhoGEF Cysts links apical polarity proteins to Rho1 and myosin activation at adherens junctions to support junctional and epithelial integrity in the Drosophila ectoderm. The spatio-temporal regulation of small Rho GTPases is crucial for the dynamic stability of epithelial tissues. However, how RhoGTPase activity is controlled during development remains largely unknown. To explore the regulation of Rho GTPases in vivo, we analyzed the Rho GTPase guanine nucleotide exchange factor (RhoGEF) Cysts, the Drosophila orthologue of mammalian p114RhoGEF, GEF-H1, p190RhoGEF, and AKAP-13. Loss of Cysts causes a phenotype that closely resembles the mutant phenotype of the apical polarity regulator Crumbs. This phenotype can be suppressed by the loss of basolateral polarity proteins, suggesting that Cysts is an integral component of the apical polarity protein network. We demonstrate that Cysts is recruited to the apico-lateral membrane through interactions with the Crumbs complex and Bazooka/Par3. Cysts activates Rho1 at adherens junctions and stabilizes junctional myosin. Junctional myosin depletion is similar in Cysts- and Crumbs-compromised embryos. Together, our findings indicate that Cysts is a downstream effector of the Crumbs complex and links apical polarity proteins to Rho1 and myosin activation at adherens junctions, supporting junctional integrity and epithelial polarity.
Collapse
Affiliation(s)
- Jordan T Silver
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | | | - Sérgio Simões
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Milena Pellikka
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Dong Yan
- Department of Genetics, Harvard Medical School, Boston, MA
| | - Richard Binari
- Department of Genetics, Harvard Medical School, Boston, MA
| | - Takashi Nishimura
- RIKEN Center for Biosystems Dynamics Research, Minatojima-minamimachi, Kobe, Japan
| | - Yan Li
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Tony J C Harris
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, MA .,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA
| | - Ulrich Tepass
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
16
|
Thompson BJ, McDonald NQ. Competitive Inhibition of aPKC by Par-3/Bazooka and Other Substrates. Dev Cell 2019; 49:680. [DOI: 10.1016/j.devcel.2019.05.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
17
|
Spinocerebellar ataxia type 14 caused by a nonsense mutation in the PRKCG gene. Mol Cell Neurosci 2019; 98:46-53. [PMID: 31158466 DOI: 10.1016/j.mcn.2019.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/25/2019] [Accepted: 05/30/2019] [Indexed: 12/15/2022] Open
Abstract
Spinocerebellar ataxia type 14 (SCA14) is an autosomal dominant neurodegenerative disorder characterized by cerebellar ataxia with myoclonus, dystonia, spasticity, and rigidity. Although missense mutations and a deletion mutation have been found in the protein kinase C gamma (PRKCG) gene encoding protein kinase C γ (PKCγ) in SCA14 families, a nonsense mutation has not been reported. The patho-mechanisms underlying SCA14 remain poorly understood. However, gain-of-function mechanisms and loss-of-function mechanisms, but not dominant negative mechanisms, were reported the patho-mechanism of SCA14. We identified the c.226C>T mutation of PRKCG, which caused the p.R76X in PKCγ by whole-exome sequencing in patients presenting cerebellar atrophy with cognitive and hearing impairment. To investigate the patho-mechanism of our case, we studied aggregation formation, cell death, and PKC inhibitory effect by confocal microscopy, western blotting with cleaved caspase 3, and pSer PKC motif antibodies, respectively. PKCγ(R76X)-GFP have aggregations the same as wild-type (WT) PKCγ-GFP. The PKCγ(R76X)-GFP inhibited PKC phosphorylation activity more than GFP alone. It also induced more apoptosis in COS7 and SH-SY5Y cells compared to WT-PKCγ-GFP and GFP. We first reported SCA14 patients with p.R76X in PKCγ who have cerebellar atrophy with cognitive and hearing impairment. Our results suggest that a dominant negative mechanism due to truncated peptides produced by p.R76X may be at least partially responsible for the cerebellar atrophy.
Collapse
|
18
|
Yang Y, Shu C, Li P, Igumenova TI. Structural Basis of Protein Kinase Cα Regulation by the C-Terminal Tail. Biophys J 2019; 114:1590-1603. [PMID: 29642029 DOI: 10.1016/j.bpj.2017.12.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 12/07/2017] [Accepted: 12/21/2017] [Indexed: 10/17/2022] Open
Abstract
Protein kinase C (PKC) isoenzymes are multi-modular proteins activated at the membrane surface to regulate signal transduction processes. When activated by second messengers, PKC undergoes a drastic conformational and spatial transition from the inactive cytosolic state to the activated membrane-bound state. The complete structure of either state of PKC remains elusive. We demonstrate, using NMR spectroscopy, that the isolated Ca2+-sensing membrane-binding C2 domain of the conventional PKCα interacts with a conserved hydrophobic motif of the kinase C-terminal region, and we report a structural model of the complex. Our data suggest that the C-terminal region plays a dual role in regulating the PKC activity: activating, through sensitization of PKC to intracellular Ca2+ oscillations; and auto-inhibitory, through its interaction with a conserved positively charged region of the C2 domain.
Collapse
Affiliation(s)
- Yuan Yang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Chang Shu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Pingwei Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas.
| |
Collapse
|
19
|
Kajimoto T, Caliman AD, Tobias IS, Okada T, Pilo CA, Van AAN, Andrew McCammon J, Nakamura SI, Newton AC. Activation of atypical protein kinase C by sphingosine 1-phosphate revealed by an aPKC-specific activity reporter. Sci Signal 2019; 12:eaat6662. [PMID: 30600259 PMCID: PMC6657501 DOI: 10.1126/scisignal.aat6662] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Atypical protein kinase C (aPKC) isozymes are unique in the PKC superfamily in that they are not regulated by the lipid second messenger diacylglycerol, which has led to speculation about whether a different second messenger acutely controls their function. Here, using a genetically encoded reporter that we designed, aPKC-specific C kinase activity reporter (aCKAR), we found that the lipid mediator sphingosine 1-phosphate (S1P) promoted the cellular activity of aPKC. Intracellular S1P directly bound to the purified kinase domain of aPKC and relieved autoinhibitory constraints, thereby activating the kinase. In silico studies identified potential binding sites on the kinase domain, one of which was validated biochemically. In HeLa cells, S1P-dependent activation of aPKC suppressed apoptosis. Together, our findings identify a previously undescribed molecular mechanism of aPKC regulation, a molecular target for S1P in cell survival regulation, and a tool to further explore the biochemical and biological functions of aPKC.
Collapse
Affiliation(s)
- Taketoshi Kajimoto
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92037, USA.
- Division of Biochemistry, Department of Biochemistry and Molecular Biology, Graduate School of Medicine, Kobe University, Kobe 650-0017, Japan
| | - Alisha D Caliman
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92037, USA
| | - Irene S Tobias
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92037, USA
| | - Taro Okada
- Division of Biochemistry, Department of Biochemistry and Molecular Biology, Graduate School of Medicine, Kobe University, Kobe 650-0017, Japan
| | - Caila A Pilo
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92037, USA
| | - An-Angela N Van
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92037, USA
| | - J Andrew McCammon
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92037, USA
| | - Shun-Ichi Nakamura
- Division of Biochemistry, Department of Biochemistry and Molecular Biology, Graduate School of Medicine, Kobe University, Kobe 650-0017, Japan
| | - Alexandra C Newton
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92037, USA.
| |
Collapse
|
20
|
Okatsu K, Sato Y, Yamano K, Matsuda N, Negishi L, Takahashi A, Yamagata A, Goto-Ito S, Mishima M, Ito Y, Oka T, Tanaka K, Fukai S. Structural insights into ubiquitin phosphorylation by PINK1. Sci Rep 2018; 8:10382. [PMID: 29991771 PMCID: PMC6039469 DOI: 10.1038/s41598-018-28656-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 05/31/2018] [Indexed: 11/09/2022] Open
Abstract
Mutations of PTEN-induced putative kinase 1 (PINK1) and the E3 ubiquitin (Ub) ligase parkin can cause familial parkinsonism. These two proteins are essential for ubiquitylation of damaged mitochondria and subsequent degradation. PINK1 phosphorylates Ser65 of Ub and the Ub-like (UBL) domain of parkin to allosterically relieve the autoinhibition of parkin. To understand the structural mechanism of the Ub/UBL-specific phosphorylation by PINK1, we determined the crystal structure of Tribolium castaneum PINK1 kinase domain (TcPINK1) in complex with a nonhydrolyzable ATP analogue at 2.5 Å resolution. TcPINK1 consists of the N- and C-terminal lobes with the PINK1-specific extension. The ATP analogue is bound in the cleft between the N- and C-terminal lobes. The adenine ring of the ATP analogue is bound to a hydrophobic pocket, whereas the triphosphate group of the ATP analogue and two coordinated Mg ions interact with the catalytic hydrophilic residues. Comparison with protein kinases A and C (PKA and PKC, respectively) unveils a putative Ub/UBL-binding groove, which is wider than the peptide-binding groove of PKA or PKC to accommodate the globular head of Ub or UBL. Further crosslinking analyses suggested a PINK1-interacting surface of Ub. Structure-guided mutational analyses support the findings from the present structural analysis of PINK1.
Collapse
Affiliation(s)
- Kei Okatsu
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Yusuke Sato
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan
| | - Koji Yamano
- Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
| | - Noriyuki Matsuda
- Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan.,PRESTO, Japan Science and Technology Agency, Saitama, 332-0012, Japan
| | - Lumi Negishi
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Akiko Takahashi
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Atsushi Yamagata
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan
| | - Sakurako Goto-Ito
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Masaki Mishima
- Graduate School of Science & Engineering, Tokyo Metropolitan University, Tokyo, 192-0397, Japan
| | - Yutaka Ito
- Graduate School of Science & Engineering, Tokyo Metropolitan University, Tokyo, 192-0397, Japan
| | - Toshihiko Oka
- Department of Life Science, Rikkyo University, Tokyo, 171-8501, Japan
| | - Keiji Tanaka
- Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
| | - Shuya Fukai
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan. .,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan. .,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan.
| |
Collapse
|
21
|
Abstract
Establishing and maintaining cell polarity are dynamic processes that necessitate complicated but highly regulated protein interactions. Phosphorylation is a powerful mechanism for cells to control the function and subcellular localization of a target protein, and multiple kinases have played critical roles in cell polarity. Among them, atypical protein kinase C (aPKC) is likely the most studied kinase in cell polarity and has the largest number of downstream substrates characterized so far. More than half of the polarity proteins that are essential for regulating cell polarity have been identified as aPKC substrates. This review covers mainly studies of aPKC in regulating anterior-posterior polarity in the worm one-cell embryo and apical-basal polarity in epithelial cells and asymmetrically dividing cells (for example,
Drosophila neuroblasts). We will go through aPKC target proteins in cell polarity and discuss various mechanisms by which aPKC phosphorylation controls their subcellular localizations and biological functions. We will also review the recent progress in determining the detailed molecular mechanisms in spatial and temporal control of aPKC subcellular localization and kinase activity during cell polarization.
Collapse
Affiliation(s)
- Yang Hong
- Department of Cell Biology, University of Pittsburgh School of Medicine, S325 BST, 3500 Terrace Street, Pittsburgh, PA 15261, USA
| |
Collapse
|
22
|
Ratnayake WS, Apostolatos CA, Apostolatos AH, Schutte RJ, Huynh MA, Ostrov DA, Acevedo-Duncan M. Oncogenic PKC-ι activates Vimentin during epithelial-mesenchymal transition in melanoma; a study based on PKC-ι and PKC-ζ specific inhibitors. Cell Adh Migr 2018; 12:447-463. [PMID: 29781749 PMCID: PMC6363030 DOI: 10.1080/19336918.2018.1471323] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Melanoma is one of the fastest growing cancers in the United States and is accompanied with a poor prognosis owing to tumors being resistant to most therapies. Atypical protein kinase Cs (aPKC) are involved in malignancy in many cancers. We previously reported that aPKCs play a key role in melanoma's cell motility by regulating cell signaling pathways which induce epithelial-mesenchymal Transition (EMT). We tested three novel inhibitors; [4-(5-amino-4-carbamoylimidazol-1-yl)-2,3-dihydroxycyclopentyl] methyl dihydrogen phosphate (ICA-1T) along with its nucleoside analog 5-amino-1-((1R,2S,3S,4R)-2,3-dihydroxy-4-methylcyclopentyl)-1H-imidazole-4-carboxamide (ICA-1S) which are specific to protein kinase C-iota (PKC-ι) and 8-hydroxy-1,3,6-naphthalenetrisulfonic acid (ζ-Stat) which is specific to PKC-zeta (PKC-ζ) on cell proliferation, apoptosis, migration and invasion of two malignant melanoma cell lines compared to normal melanocytes. Molecular modeling was used to identify potential binding sites for the inhibitors and to predict selectivity. Kinase assay showed >50% inhibition for specified targets beyond 5 μM for all inhibitors. Both ICA-1 and ζ-Stat significantly reduced cell proliferation and induced apoptosis, while ICA-1 also significantly reduced migration and melanoma cell invasion. PKC-ι stimulated EMT via TGFβ/Par6/RhoA pathway and activated Vimentin by phosphorylation at S39. Both ICA-1 and ζ-Stat downregulate TNF-α induced NF-κB translocation to the nucleus there by inducing apoptosis. Results suggest that PKC-ι is involved in melanoma malignancy than PKC-ζ. Inhibitors proved to be effective under in-vitro conditions and need to be tested in-vivo for the validity as effective therapeutics. Overall, results show that aPKCs are essential for melanoma progression and metastasis and that they could be used as effective therapeutic targets for malignant melanoma.
Collapse
Affiliation(s)
| | | | | | - Ryan J Schutte
- b Department of Pathology , Immunology and Laboratory Medicine, University of Florida, College of Medicine , Gainesville , FL , USA
| | - Monica A Huynh
- b Department of Pathology , Immunology and Laboratory Medicine, University of Florida, College of Medicine , Gainesville , FL , USA
| | - David A Ostrov
- b Department of Pathology , Immunology and Laboratory Medicine, University of Florida, College of Medicine , Gainesville , FL , USA
| | | |
Collapse
|
23
|
Miller CJ, Turk BE. Homing in: Mechanisms of Substrate Targeting by Protein Kinases. Trends Biochem Sci 2018; 43:380-394. [PMID: 29544874 DOI: 10.1016/j.tibs.2018.02.009] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 02/08/2018] [Accepted: 02/15/2018] [Indexed: 01/21/2023]
Abstract
Protein phosphorylation is the most common reversible post-translational modification in eukaryotes. Humans have over 500 protein kinases, of which more than a dozen are established targets for anticancer drugs. All kinases share a structurally similar catalytic domain, yet each one is uniquely positioned within signaling networks controlling essentially all aspects of cell behavior. Kinases are distinguished from one another based on their modes of regulation and their substrate repertoires. Coupling specific inputs to the proper signaling outputs requires that kinases phosphorylate a limited number of sites to the exclusion of hundreds of thousands of off-target phosphorylation sites. Here, we review recent progress in understanding mechanisms of kinase substrate specificity and how they function to shape cellular signaling networks.
Collapse
Affiliation(s)
- Chad J Miller
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA.
| |
Collapse
|
24
|
Zhu J, Zhou Q, Shang Y, Li H, Peng M, Ke X, Weng Z, Zhang R, Huang X, Li SS, Feng G, Lu Y, Zhang M. Synaptic Targeting and Function of SAPAPs Mediated by Phosphorylation-Dependent Binding to PSD-95 MAGUKs. Cell Rep 2017; 21:3781-3793. [DOI: 10.1016/j.celrep.2017.11.107] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/13/2017] [Accepted: 11/29/2017] [Indexed: 10/18/2022] Open
|
25
|
Wen W, Zhang M. Protein Complex Assemblies in Epithelial Cell Polarity and Asymmetric Cell Division. J Mol Biol 2017; 430:3504-3520. [PMID: 28963071 DOI: 10.1016/j.jmb.2017.09.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/16/2017] [Accepted: 09/19/2017] [Indexed: 12/24/2022]
Abstract
Asymmetric local concentration of protein complexes on distinct membrane regions is a fundamental property in numerous biological processes and is a hallmark of cell polarity. Evolutionarily conserved core polarity proteins form specific and dynamic networks to regulate the establishment and maintenance of cell polarity, as well as distinct polarity-driven cellular events. This review focuses on the molecular and structural basis governing regulated formation of several sets of core cell polarity regulatory complexes, as well as their functions in epithelial cell polarization and asymmetric cell division.
Collapse
Affiliation(s)
- Wenyu Wen
- Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, Fudan University, Shanghai 200040, China; Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, PR China.
| | - Mingjie Zhang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
| |
Collapse
|
26
|
Soriano EV, Ivanova ME, Fletcher G, Riou P, Knowles PP, Barnouin K, Purkiss A, Kostelecky B, Saiu P, Linch M, Elbediwy A, Kjær S, O'Reilly N, Snijders AP, Parker PJ, Thompson BJ, McDonald NQ. aPKC Inhibition by Par3 CR3 Flanking Regions Controls Substrate Access and Underpins Apical-Junctional Polarization. Dev Cell 2016; 38:384-98. [PMID: 27554858 PMCID: PMC4998004 DOI: 10.1016/j.devcel.2016.07.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 05/24/2016] [Accepted: 07/24/2016] [Indexed: 12/02/2022]
Abstract
Atypical protein kinase C (aPKC) is a key apical-basal polarity determinant and Par complex component. It is recruited by Par3/Baz (Bazooka in Drosophila) into epithelial apical domains through high-affinity interaction. Paradoxically, aPKC also phosphorylates Par3/Baz, provoking its relocalization to adherens junctions (AJs). We show that Par3 conserved region 3 (CR3) forms a tight inhibitory complex with a primed aPKC kinase domain, blocking substrate access. A CR3 motif flanking its PKC consensus site disrupts the aPKC kinase N lobe, separating P-loop/αB/αC contacts. A second CR3 motif provides a high-affinity anchor. Mutation of either motif switches CR3 to an efficient in vitro substrate by exposing its phospho-acceptor site. In vivo, mutation of either CR3 motif alters Par3/Baz localization from apical to AJs. Our results reveal how Par3/Baz CR3 can antagonize aPKC in stable apical Par complexes and suggests that modulation of CR3 inhibitory arms or opposing aPKC pockets would perturb the interaction, promoting Par3/Baz phosphorylation.
Collapse
Affiliation(s)
- Erika V Soriano
- Structural Biology, The Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Marina E Ivanova
- Structural Biology, The Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Georgina Fletcher
- Epithelial Biology, The Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Philippe Riou
- Protein Phosphorylation Laboratories, The Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Philip P Knowles
- Structural Biology, The Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Karin Barnouin
- Protein Analysis, The Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Andrew Purkiss
- Structural Biology, The Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Brenda Kostelecky
- Structural Biology, The Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Peter Saiu
- Structural Biology, The Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Mark Linch
- Protein Phosphorylation Laboratories, The Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Ahmed Elbediwy
- Epithelial Biology, The Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Svend Kjær
- Protein Purification Facilities, The Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Nicola O'Reilly
- Peptide Chemistry, The Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Ambrosius P Snijders
- Protein Analysis, The Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Peter J Parker
- Protein Phosphorylation Laboratories, The Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK; Division of Cancer Studies, King's College London, London SE1 1UL, UK
| | - Barry J Thompson
- Epithelial Biology, The Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK.
| | - Neil Q McDonald
- Structural Biology, The Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK; Institute of Structural and Molecular Biology, School of Biological Science, Birkbeck College, Malet Street, London WC1E 7HX, UK.
| |
Collapse
|
27
|
de Oliveira PSL, Ferraz FAN, Pena DA, Pramio DT, Morais FA, Schechtman D. Revisiting protein kinase-substrate interactions: Toward therapeutic development. Sci Signal 2016; 9:re3. [PMID: 27016527 DOI: 10.1126/scisignal.aad4016] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Despite the efforts of pharmaceutical companies to develop specific kinase modulators, few drugs targeting kinases have been completely successful in the clinic. This is primarily due to the conserved nature of kinases, especially in the catalytic domains. Consequently, many currently available inhibitors lack sufficient selectivity for effective clinical application. Kinases phosphorylate their substrates to modulate their activity. One of the important steps in the catalytic reaction of protein phosphorylation is the correct positioning of the target residue within the catalytic site. This positioning is mediated by several regions in the substrate binding site, which is typically a shallow crevice that has critical subpockets that anchor and orient the substrate. The structural characterization of this protein-protein interaction can aid in the elucidation of the roles of distinct kinases in different cellular processes, the identification of substrates, and the development of specific inhibitors. Because the region of the substrate that is recognized by the kinase can be part of a linear consensus motif or a nonlinear motif, advances in technology beyond simple linear sequence scanning for consensus motifs were needed. Cost-effective bioinformatics tools are already frequently used to predict kinase-substrate interactions for linear consensus motifs, and new tools based on the structural data of these interactions improve the accuracy of these predictions and enable the identification of phosphorylation sites within nonlinear motifs. In this Review, we revisit kinase-substrate interactions and discuss the various approaches that can be used to identify them and analyze their binding structures for targeted drug development.
Collapse
Affiliation(s)
- Paulo Sérgio L de Oliveira
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas 13083-970, Brazil
| | - Felipe Augusto N Ferraz
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas 13083-970, Brazil
| | - Darlene A Pena
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508000, Brazil
| | - Dimitrius T Pramio
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508000, Brazil
| | - Felipe A Morais
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508000, Brazil
| | - Deborah Schechtman
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508000, Brazil.
| |
Collapse
|
28
|
Zhu J, Shang Y, Zhang M. Mechanistic basis of MAGUK-organized complexes in synaptic development and signalling. Nat Rev Neurosci 2016; 17:209-23. [DOI: 10.1038/nrn.2016.18] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
29
|
Molecular Control of Atypical Protein Kinase C: Tipping the Balance between Self-Renewal and Differentiation. J Mol Biol 2016; 428:1455-64. [PMID: 26992354 DOI: 10.1016/j.jmb.2016.03.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/20/2016] [Accepted: 03/03/2016] [Indexed: 01/05/2023]
Abstract
Complex organisms are faced with the challenge of generating and maintaining diverse cell types, ranging from simple epithelia to neurons and motile immune cells [1-3]. To meet this challenge, a complex set of regulatory pathways controls nearly every aspect of cell growth and function, including genetic and epigenetic programming, cytoskeleton dynamics, and protein trafficking. The far reach of cell fate specification pathways makes it particularly catastrophic when they malfunction, both during development and for tissue homeostasis in adult organisms. Furthermore, the therapeutic promise of stem cells derives from their ability to deftly navigate the multitude of pathways that control cell fate [4]. How the molecular components making up these pathways function to specify cell fate is beginning to become clear. Work from diverse systems suggests that the atypical Protein Kinase C (aPKC) is a key regulator of cell fate decisions in metazoans [5-7]. Here, we examine some of the diverse physiological outcomes of aPKC's function in differentiation, along with the molecular pathways that control aPKC and those that are responsive to changes in its catalytic activity.
Collapse
|
30
|
An in cellulo-derived structure of PAK4 in complex with its inhibitor Inka1. Nat Commun 2015; 6:8681. [PMID: 26607847 PMCID: PMC4674680 DOI: 10.1038/ncomms9681] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 09/21/2015] [Indexed: 01/09/2023] Open
Abstract
PAK4 is a metazoan-specific kinase acting downstream of Cdc42. Here we describe the structure of human PAK4 in complex with Inka1, a potent endogenous kinase inhibitor. Using single mammalian cells containing crystals 50 μm in length, we have determined the in cellulo crystal structure at 2.95 Å resolution, which reveals the details of how the PAK4 catalytic domain binds cellular ATP and the Inka1 inhibitor. The crystal lattice consists only of PAK4–PAK4 contacts, which form a hexagonal array with channels of 80 Å in diameter that run the length of the crystal. The crystal accommodates a variety of other proteins when fused to the kinase inhibitor. Inka1–GFP was used to monitor the process crystal formation in living cells. Similar derivatives of Inka1 will allow us to study the effects of PAK4 inhibition in cells and model organisms, to allow better validation of therapeutic agents targeting PAK4. PAK4 is a metazoan-specific kinase, which acts downstream of the cell polarity regulator Cdc42. Here, Baskaran et al. determine the structure of PAK4 bound to the endogenous inhibitor Inka1 from crystals that form spontaneously in mammalian cells overexpressing both proteins.
Collapse
|
31
|
Bailey MJ, Prehoda KE. Establishment of Par-Polarized Cortical Domains via Phosphoregulated Membrane Motifs. Dev Cell 2015; 35:199-210. [PMID: 26481050 DOI: 10.1016/j.devcel.2015.09.016] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 09/03/2015] [Accepted: 09/23/2015] [Indexed: 01/06/2023]
Abstract
The Par polarity complex creates mutually exclusive cortical domains in diverse animal cells. Activity of the atypical protein kinase C (aPKC) is a key output of the Par complex as phosphorylation removes substrates from the Par domain. Here, we investigate how diverse, apparently unrelated Par substrates couple phosphorylation to cortical displacement. Each protein contains a basic and hydrophobic (BH) motif that interacts directly with phospholipids and also overlaps with aPKC phosphorylation sites. Phosphorylation alters the electrostatic character of the sequence, inhibiting interaction with phospholipids and the cell cortex. We searched for overlapping BH and aPKC phosphorylation site motifs (i.e., putative phosphoregulated BH motifs) in several animal proteomes. Candidate proteins with strong PRBH signals associated with the cell cortex but were displaced into the cytoplasm by aPKC. These findings demonstrate a potentially general mechanism for exclusion of proteins from the Par cortical domain in polarized cells.
Collapse
Affiliation(s)
- Matthew J Bailey
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Kenneth E Prehoda
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.
| |
Collapse
|
32
|
Abstract
Protein kinase C (PKC) is a family of Ser/Thr kinases that regulate a multitude of cellular processes through participation in the phosphoinositide signaling pathway. Significant research efforts have been directed at understanding the structure, function, and regulatory modes of the enzyme since its discovery and identification as the first receptor for tumor-promoting phorbol esters. The activation of PKC involves a transition from the cytosolic autoinhibited latent form to the membrane-associated active form. The membrane recruitment step is accompanied by the conformational rearrangement of the enzyme, which relieves autoinhibitory interactions and thereby allows PKC to phosphorylate its targets. The multidomain structure and intrinsic flexibility of PKC present remarkable challenges and opportunities for the biophysical and structural biology studies of this class of enzymes and their interactions with membranes, the major focus of this Current Topic. I will highlight the recent advances in the field, outline the current challenges, and identify areas where biophysics and structural biology approaches can provide insight into the isoenzyme-specific regulation of PKC activity.
Collapse
|
33
|
Bogard AS, Tavalin SJ. Protein Kinase C (PKC)ζ Pseudosubstrate Inhibitor Peptide Promiscuously Binds PKC Family Isoforms and Disrupts Conventional PKC Targeting and Translocation. Mol Pharmacol 2015. [PMID: 26199377 DOI: 10.1124/mol.115.099457] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
PKMζ is generated via an alternative transcriptional start site in the atypical protein kinase C (PKC)ζ isoform, which removes N-terminal regulatory elements, including the inhibitory pseudosubstrate domain, consequently rendering the kinase constitutively active. Persistent PKMζ activity has been proposed as a molecular mechanism for the long-term maintenance of synaptic plasticity underlying some forms of memory. Many studies supporting a role for PKMζ in synaptic plasticity and memory have relied on the PKCζ pseudosubstrate-derived ζ-inhibitory peptide (ZIP). However, recent studies have demonstrated that ZIP-induced impairments to synaptic plasticity and memory occur even in the absence of PKCζ, suggesting that ZIP exerts its actions via additional cellular targets. In this study, we demonstrated that ZIP interacts with conventional and novel PKC, in addition to atypical PKC isoforms. Moreover, when brain abundance of each PKC isoform and affinity for ZIP are taken into account, the signaling capacity of ZIP-responsive pools of conventional and novel PKCs may match or exceed that for atypical PKCs. Pseudosubstrate-derived peptides, like ZIP, are thought to exert their cellular action primarily by inhibiting PKC catalytic activity; however, the ZIP-sensitive catalytic core of PKC is known to participate in the enzyme's subcellular targeting, suggesting an additional mode of ZIP action. Indeed, we have demonstrated that ZIP potently disrupts PKCα interaction with the PKC-targeting protein A-kinase anchoring protein (AKAP) 79 and interferes with ionomycin-induced translocation of conventional PKC to the plasma membrane. Thus, ZIP exhibits broad-spectrum action toward the PKC family of enzymes, and this action may contribute to its unique ability to impair memory.
Collapse
Affiliation(s)
- Amy S Bogard
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Steven J Tavalin
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, Tennessee
| |
Collapse
|
34
|
Co-conserved MAPK features couple D-domain docking groove to distal allosteric sites via the C-terminal flanking tail. PLoS One 2015; 10:e0119636. [PMID: 25799139 PMCID: PMC4370755 DOI: 10.1371/journal.pone.0119636] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 02/02/2015] [Indexed: 11/19/2022] Open
Abstract
Mitogen activated protein kinases (MAPKs) form a closely related family of kinases that control critical pathways associated with cell growth and survival. Although MAPKs have been extensively characterized at the biochemical, cellular, and structural level, an integrated evolutionary understanding of how MAPKs differ from other closely related protein kinases is currently lacking. Here, we perform statistical sequence comparisons of MAPKs and related protein kinases to identify sequence and structural features associated with MAPK functional divergence. We show, for the first time, that virtually all MAPK-distinguishing sequence features, including an unappreciated short insert segment in the β4-β5 loop, physically couple distal functional sites in the kinase domain to the D-domain peptide docking groove via the C-terminal flanking tail (C-tail). The coupling mediated by MAPK-specific residues confers an allosteric regulatory mechanism unique to MAPKs. In particular, the regulatory αC-helix conformation is controlled by a MAPK-conserved salt bridge interaction between an arginine in the αC-helix and an acidic residue in the C-tail. The salt-bridge interaction is modulated in unique ways in individual sub-families to achieve regulatory specificity. Our study is consistent with a model in which the C-tail co-evolved with the D-domain docking site to allosterically control MAPK activity. Our study provides testable mechanistic hypotheses for biochemical characterization of MAPK-conserved residues and new avenues for the design of allosteric MAPK inhibitors.
Collapse
|
35
|
Graybill C, Prehoda KE. Ordered multisite phosphorylation of lethal giant larvae by atypical protein kinase C. Biochemistry 2014; 53:4931-7. [PMID: 25000553 PMCID: PMC4372073 DOI: 10.1021/bi500748w] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In Par complex-mediated cell polarity, phosphorylation by atypical protein kinase C (aPKC) is coupled to substrate cortical displacement. Polarized substrates often contain multiple phosphorylation sites, but the role of multisite phosphorylation in Par-mediated polarity remains unclear. Here, we have dissected the role of the three aPKC phosphorylation sites within the tumor suppressor Lethal giant larvae. Using a cultured Drosophila S2 cell cortical displacement assay, we observed that phosphorylation at any one site causes only partial displacement. Complete displacement requires that all three sites be modified. We undertook a kinetic analysis to determine if aPKC phosphorylates each site equivalently. As the sites are closely spaced, we observed not only differences in the rate of phosphorylation but also interaction between the sites. A complete description of the rates reveals a preferential order of phosphorylation. Our results provide new insights into how multiple phosphorylations and phosphorylation rates could regulate localization behaviors of fate determinants at the cortex.
Collapse
Affiliation(s)
- Chiharu Graybill
- The Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States
| | | |
Collapse
|
36
|
Tang GW, Altman RB. Knowledge-based fragment binding prediction. PLoS Comput Biol 2014; 10:e1003589. [PMID: 24762971 PMCID: PMC3998881 DOI: 10.1371/journal.pcbi.1003589] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 03/11/2014] [Indexed: 11/18/2022] Open
Abstract
Target-based drug discovery must assess many drug-like compounds for potential activity. Focusing on low-molecular-weight compounds (fragments) can dramatically reduce the chemical search space. However, approaches for determining protein-fragment interactions have limitations. Experimental assays are time-consuming, expensive, and not always applicable. At the same time, computational approaches using physics-based methods have limited accuracy. With increasing high-resolution structural data for protein-ligand complexes, there is now an opportunity for data-driven approaches to fragment binding prediction. We present FragFEATURE, a machine learning approach to predict small molecule fragments preferred by a target protein structure. We first create a knowledge base of protein structural environments annotated with the small molecule substructures they bind. These substructures have low-molecular weight and serve as a proxy for fragments. FragFEATURE then compares the structural environments within a target protein to those in the knowledge base to retrieve statistically preferred fragments. It merges information across diverse ligands with shared substructures to generate predictions. Our results demonstrate FragFEATURE's ability to rediscover fragments corresponding to the ligand bound with 74% precision and 82% recall on average. For many protein targets, it identifies high scoring fragments that are substructures of known inhibitors. FragFEATURE thus predicts fragments that can serve as inputs to fragment-based drug design or serve as refinement criteria for creating target-specific compound libraries for experimental or computational screening.
Collapse
Affiliation(s)
- Grace W. Tang
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Russ B. Altman
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
- Department of Genetics, Stanford University, Stanford, California, United States of America
- * E-mail:
| |
Collapse
|
37
|
Xing B, Wang L, Guo D, Huang J, Espenel C, Kreitzer G, Zhang JJ, Guo L, Huang XY. Atypical protein kinase Cλ is critical for growth factor receptor-induced dorsal ruffle turnover and cell migration. J Biol Chem 2013; 288:32827-36. [PMID: 24092753 DOI: 10.1074/jbc.m113.489427] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Gα13, a member of the heterotrimeric G proteins, is critical for actin cytoskeletal reorganization and cell migration. Previously we have shown that Gα13 is essential for both G protein-coupled receptor and receptor tyrosine kinase-induced actin cytoskeletal reorganization such as dynamic dorsal ruffle turnover and cell migration. Ric-8A, a non-receptor guanine nucleotide exchange factor for some heterotrimeric G proteins, is critical for coupling receptor tyrosine kinases to Gα13. Here, we show that PDGF can induce phosphorylation of Ric-8A. Atypical protein kinase Cλ (aPKCλ) is required for Ric-8A phosphorylation. Furthermore, aPKCλ is required for PDGF-induced dorsal ruffle turnover and cell migration as demonstrated by both down-regulation of aPKCλ protein levels in cells by RNA interference and by studies in aPKCλ knock-out cells. Moreover, phosphorylation of Ric-8A modulates its subcellular localization. Hence, aPKCλ is critical for PDGF-induced actin cytoskeletal reorganization and cell migration.
Collapse
Affiliation(s)
- Bowen Xing
- From the College of Life Sciences, Wuhan University, Wuhan 430072, China, and
| | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Linch M, Sanz-Garcia M, Soriano E, Zhang Y, Riou P, Rosse C, Cameron A, Knowles P, Purkiss A, Kjaer S, McDonald NQ, Parker PJ. A cancer-associated mutation in atypical protein kinase Cι occurs in a substrate-specific recruitment motif. Sci Signal 2013; 6:ra82. [PMID: 24045153 DOI: 10.1126/scisignal.2004068] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2024]
Abstract
Atypical protein kinase Cι (PKCι) has roles in cell growth, cellular polarity, and migration, and its abundance is frequently increased in cancer. We identified a protein interaction surface containing a dibasic motif (RIPR) that bound a distinct subset of PKCι substrates including lethal giant larvae 2 (LLGL2) and myosin X, but not other substrates such as Par3. Further characterization demonstrated that Arg471 in this motif was important for binding to LLGL2, whereas Arg474 was critical for interaction with myosin X, indicating that multiple complexes could be formed through this motif. A somatic mutation of the dibasic motif (R471C) was the most frequent mutation of PKCι in human cancer, and the intact dibasic motif was required for normal polarized epithelial morphogenesis in three-dimensional cysts. Thus, the R471C substitution is a change-of-function mutation acting at this substrate-specific recruitment site to selectively disrupt the polarizing activity of PKCι.
Collapse
Affiliation(s)
- Mark Linch
- 1Protein Phosphorylation Laboratory, Cancer Research UK, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Competing molecular interactions of aPKC isoforms regulate neuronal polarity. Proc Natl Acad Sci U S A 2013; 110:14450-5. [PMID: 23940317 DOI: 10.1073/pnas.1301588110] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Atypical protein kinase C (aPKC) isoforms ζ and λ interact with polarity complex protein Par3 and are evolutionarily conserved regulators of cell polarity. Prkcz encodes aPKC-ζ and PKM-ζ, a truncated, neuron-specific alternative transcript, and Prkcl encodes aPKC-λ. Here we show that, in embryonic hippocampal neurons, two aPKC isoforms, aPKC-λ and PKM-ζ, are expressed. The localization of these isoforms is spatially distinct in a polarized neuron. aPKC-λ, as well as Par3, localizes at the presumptive axon, whereas PKM-ζ and Par3 are distributed at non-axon-forming neurites. PKM-ζ competes with aPKC-λ for binding to Par3 and disrupts the aPKC-λ-Par3 complex. Silencing of PKM-ζ or overexpression of aPKC-λ in hippocampal neurons alters neuronal polarity, resulting in neurons with supernumerary axons. In contrast, the overexpression of PKM-ζ prevents axon specification. Our studies suggest a molecular model wherein mutually antagonistic intermolecular competition between aPKC isoforms directs the establishment of neuronal polarity.
Collapse
|
40
|
Chen J, Zhang M. The Par3/Par6/aPKC complex and epithelial cell polarity. Exp Cell Res 2013; 319:1357-64. [PMID: 23535009 DOI: 10.1016/j.yexcr.2013.03.021] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 03/11/2013] [Accepted: 03/16/2013] [Indexed: 12/20/2022]
Abstract
Apical-basal polarity is the basic organizing principle of epithelial cells, and endows epithelial cells to function as defensive barriers and as mediators of vectorial transport of nutrients in and out of organisms. Apical-basal polarity is controlled by a number of conserved polarity factors that regulate cytoskeletal organizations, asymmetric distributions of cellular components, and directional transports across cells. Polarity factors often occupy specific membrane regions in response to the adhesion forces generated by cell-cell and cell-extracellular matrix interactions. Both internal polarity factors and the external extracellular matrices play fundamental roles in epithelial cell polarity establishment and maintenance. This review focuses on recent developments of the Par3/Par6/aPKC complex and its interacting proteins in epithelial cell polarity.
Collapse
Affiliation(s)
- Jia Chen
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | | |
Collapse
|
41
|
Kang JH, Toita R, Kim CW, Katayama Y. Protein kinase C (PKC) isozyme-specific substrates and their design. Biotechnol Adv 2012; 30:1662-72. [DOI: 10.1016/j.biotechadv.2012.07.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 07/17/2012] [Accepted: 07/18/2012] [Indexed: 11/30/2022]
|