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Abou Azar F, Mugabo Y, Yuen S, Del Veliz S, Paré F, Rial SA, Lavoie G, Roux PP, Lim GE. Plakoglobin regulates adipocyte differentiation independently of the Wnt/β-catenin signaling pathway. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119690. [PMID: 38367915 DOI: 10.1016/j.bbamcr.2024.119690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 02/06/2024] [Accepted: 02/11/2024] [Indexed: 02/19/2024]
Abstract
The scaffold protein 14-3-3ζ is an established regulator of adipogenesis and postnatal adiposity. We and others have demonstrated the 14-3-3ζ interactome to be diverse and dynamic, and it can be examined to identify novel regulators of physiological processes, including adipogenesis. In the present study, we sought to determine if factors that influence adipogenesis during the development of obesity could be identified in the 14-3-3ζ interactome found in white adipose tissue of lean or obese TAP-tagged-14-3-3ζ overexpressing mice. Using mass spectrometry, differences in the abundance of novel, as well as established, adipogenic factors within the 14-3-3ζ interactome could be detected in adipose tissues. One novel candidate was revealed to be plakoglobin, the homolog of the known adipogenic inhibitor, β-catenin, and herein, we report that plakoglobin is involved in adipocyte differentiation. Plakoglobin is expressed in murine 3T3-L1 cells and is primarily localized to the nucleus, where its abundance decreases during adipogenesis. Depletion of plakoglobin by siRNA inhibited adipogenesis and reduced PPARγ2 expression, and similarly, plakoglobin depletion in human adipose-derived stem cells also impaired adipogenesis and reduced lipid accumulation post-differentiation. Transcriptional assays indicated that plakoglobin does not participate in Wnt/β-catenin signaling, as its depletion did not affect Wnt3a-mediated transcriptional activity. Taken together, our results establish plakoglobin as a novel regulator of adipogenesis in vitro and highlights the ability of using the 14-3-3ζ interactome to identify potential pro-obesogenic factors.
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Affiliation(s)
- F Abou Azar
- Department of Medicine, Université de Montréal, Montréal, QC, Canada; Cardiometabolic axis, Centre de Recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - Y Mugabo
- Department of Medicine, Université de Montréal, Montréal, QC, Canada; Cardiometabolic axis, Centre de Recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - S Yuen
- Department of Medicine, Université de Montréal, Montréal, QC, Canada; Cardiometabolic axis, Centre de Recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - S Del Veliz
- Department of Medicine, Université de Montréal, Montréal, QC, Canada; Cardiometabolic axis, Centre de Recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - F Paré
- Cardiometabolic axis, Centre de Recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - S A Rial
- Department of Medicine, Université de Montréal, Montréal, QC, Canada; Cardiometabolic axis, Centre de Recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - G Lavoie
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Québec, Canada; Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - P P Roux
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Québec, Canada; Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - G E Lim
- Department of Medicine, Université de Montréal, Montréal, QC, Canada; Cardiometabolic axis, Centre de Recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada.
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Rumpf M, Pautz S, Drebes B, Herberg FW, Müller HAJ. Microtubule-Associated Serine/Threonine (MAST) Kinases in Development and Disease. Int J Mol Sci 2023; 24:11913. [PMID: 37569286 PMCID: PMC10419289 DOI: 10.3390/ijms241511913] [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: 06/28/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023] Open
Abstract
Microtubule-Associated Serine/Threonine (MAST) kinases represent an evolutionary conserved branch of the AGC protein kinase superfamily in the kinome. Since the discovery of the founding member, MAST2, in 1993, three additional family members have been identified in mammals and found to be broadly expressed across various tissues, including the brain, heart, lung, liver, intestine and kidney. The study of MAST kinases is highly relevant for unraveling the molecular basis of a wide range of different human diseases, including breast and liver cancer, myeloma, inflammatory bowel disease, cystic fibrosis and various neuronal disorders. Despite several reports on potential substrates and binding partners of MAST kinases, the molecular mechanisms that would explain their involvement in human diseases remain rather obscure. This review will summarize data on the structure, biochemistry and cell and molecular biology of MAST kinases in the context of biomedical research as well as organismal model systems in order to provide a current profile of this field.
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Affiliation(s)
- Marie Rumpf
- Department of Developmental Genetics, Institute of Biology, University of Kassel, 34321 Kassel, Germany; (M.R.)
| | - Sabine Pautz
- Department of Biochemistry, Institute of Biology, University of Kassel, 34321 Kassel, Germany
| | - Benedikt Drebes
- Department of Developmental Genetics, Institute of Biology, University of Kassel, 34321 Kassel, Germany; (M.R.)
| | - Friedrich W. Herberg
- Department of Biochemistry, Institute of Biology, University of Kassel, 34321 Kassel, Germany
| | - Hans-Arno J. Müller
- Department of Developmental Genetics, Institute of Biology, University of Kassel, 34321 Kassel, Germany; (M.R.)
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Angelotti T. Exploring the eukaryotic Yip and REEP/Yop superfamily of membrane-shaping adapter proteins (MSAPs): A cacophony or harmony of structure and function? Front Mol Biosci 2022; 9:912848. [PMID: 36060263 PMCID: PMC9437294 DOI: 10.3389/fmolb.2022.912848] [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: 04/04/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Polytopic cargo proteins are synthesized and exported along the secretory pathway from the endoplasmic reticulum (ER), through the Golgi apparatus, with eventual insertion into the plasma membrane (PM). While searching for proteins that could enhance cell surface expression of olfactory receptors, a new family of proteins termed “receptor expression-enhancing proteins” or REEPs were identified. These membrane-shaping hairpin proteins serve as adapters, interacting with intracellular transport machinery, to regulate cargo protein trafficking. However, REEPs belong to a larger family of proteins, the Yip (Ypt-interacting protein) family, conserved in yeast and higher eukaryotes. To date, eighteen mammalian Yip family members, divided into four subfamilies (Yipf, REEP, Yif, and PRAF), have been identified. Yeast research has revealed many intriguing aspects of yeast Yip function, functions that have not completely been explored with mammalian Yip family members. This review and analysis will clarify the different Yip family nomenclature that have encumbered prior comparisons between yeast, plants, and eukaryotic family members, to provide a more complete understanding of their interacting proteins, membrane topology, organelle localization, and role as regulators of cargo trafficking and localization. In addition, the biological role of membrane shaping and sensing hairpin and amphipathic helical domains of various Yip proteins and their potential cellular functions will be described. Lastly, this review will discuss the concept of Yip proteins as members of a larger superfamily of membrane-shaping adapter proteins (MSAPs), proteins that both shape membranes via membrane-sensing and hairpin insertion, and well as act as adapters for protein-protein interactions. MSAPs are defined by their localization to specific membranes, ability to alter membrane structure, interactions with other proteins via specific domains, and specific interactions/effects on cargo proteins.
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Interactome Profiling of N-Terminus-Truncated NS1 Protein of Influenza A Virus Reveals Role of 14-3-3γ in Virus Replication. Pathogens 2022; 11:pathogens11070733. [PMID: 35889979 PMCID: PMC9321973 DOI: 10.3390/pathogens11070733] [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: 05/20/2022] [Revised: 06/21/2022] [Accepted: 06/24/2022] [Indexed: 12/03/2022] Open
Abstract
Influenza A virus is transmitted through a respiratory route and has caused several pandemics throughout history. The NS1 protein of influenza A virus, which consists of an N-terminal RNA-binding domain and a C-terminal effector domain, is considered one of the critical virulence factors during influenza A virus infection because the viral protein can downregulate the antiviral response of the host cell and facilitate viral replication. Our previous study identified an N-terminus-truncated NS1 protein that covers the C-terminus effector domain. To comprehensively explore the role of the truncated NS1 in cells, we conducted immunoprecipitation coupled with LC-MS/MS to identify its interacting cellular proteins. There were 46 cellular proteins identified as the components of the truncated NS1 protein complex. As for our previous results for the identification of the full-length NS1-interacting host proteins, we discovered that the truncated NS1 protein interacts with the γ isoform of the 14-3-3 protein family. In addition, we found that the knockdown of 14-3-3γ in host cells reduced the replication of the influenza A/PR8 wild-type virus but not that of the PR8-NS1/1-98 mutant virus, which lacks most of the effector domain of NS1. This research highlights the role of 14-3-3γ, which interacts with the effector domain of NS1 protein, in influenza A viral replication.
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Structural Insight into Terminal Galactose Recognition by Two Non-HBGA Binding GI.3 Noroviruses. J Virol 2022; 96:e0042022. [PMID: 35658530 PMCID: PMC9278146 DOI: 10.1128/jvi.00420-22] [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] [Indexed: 02/05/2023] Open
Abstract
Human noroviruses (huNoVs) cause epidemic acute gastroenteritis using histo-blood group antigens (HBGAs) as host receptors or attachment factors to initiate an infection. While most huNoVs have been shown to bind HBGAs, some known clinical isolates, such as GI.3 DSV and VA115, do not recognize any HBGAs and thus the molecular mechanism behind their infections remains elusive. In this study, we provided both phenotypic and structural evidence to show that huNoV DSV and VA115 recognize a group of glycans with terminal galactoses as ligands. First, through glycan array we found that both DSV and VA115 protruding (P) domain proteins bound two oligosaccharides that share common terminal galactoses. Then, by determination of the crystal structures of DSV/VA115 P proteins in complex with Galα1-3Galβ1-4Glc and/or NA2 N-Glycan, respectively, we showed that the terminal galactose is the main saccharide recognized by the two viral proteins. Our data demonstrated that GI huNoVs can interact with non-HBGA glycans through their conserved galactose binding site, shedding light on the mechanism of huNoV adaptation through recognizing new glycan receptors to facilitate their widespread nature in human population. These findings are also of significance in strategy development for huNoV control and prevention, as well as development of antiviral drugs. IMPORTANCE Human noroviruses (huNoVs) are the most important viral pathogens causing epidemic acute gastroenteritis worldwide. Previous studies indicated that histo-blood group antigens (HBGAs) are critical host-susceptibility factors affecting huNoV host susceptibility, host range, and probably prevalence. However, certain huNoVs, such as GI.3 DSV and VA115, do not recognize any HBGAs. This implies that other unknown host factors might exist and the molecular mechanism underlying their host receptor recognition or attachment remains elusive. In this study, we found that purified capsid protruding domain proteins from two GI.3 huNoVs specifically bind two glycans that contain a common terminal galactose. We solved the crystal structures of the complexes at atomic resolution and validated the vital amino acids involved in glycan recognition. Our findings elucidate the mechanism of GI.3 huNoV-non-HBGA glycan interaction, which explains why GI.3 virus strains could not bind human HBGAs, paving a way to the prevention and treatment of huNoV-associated diseases.
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Abstract
The 14-3-3 family proteins are vital scaffold proteins that ubiquitously expressed in various tissues. They interact with numerous protein targets and mediate many cellular signaling pathways. The 14-3-3 binding motifs are often embedded in intrinsically disordered regions which are closely associated with liquid-liquid phase separation (LLPS). In the past ten years, LLPS has been observed for a variety of proteins and biological processes, indicating that LLPS plays a fundamental role in the formation of membraneless organelles and cellular condensates. While extensive investigations have been performed on 14-3-3 proteins, its involvement in LLPS is overlooked. To date, 14-3-3 proteins have not been reported to undergo LLPS alone or regulate LLPS of their binding partners. To reveal the potential involvement of 14-3-3 proteins in LLPS, in this review, we summarized the LLPS propensity of 14-3-3 binding partners and found that about one half of them may undergo LLPS spontaneously. We further analyzed the phase separation behavior of representative 14-3-3 binders and discussed how 14-3-3 proteins may be involved. By modulating the conformation and valence of interactions and recruiting other molecules, we speculate that 14-3-3 proteins can efficiently regulate the functions of their targets in the context of LLPS. Considering the critical roles of 14-3-3 proteins, there is an urgent need for investigating the involvement of 14-3-3 proteins in the phase separation process of their targets and the underling mechanisms.
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Soini L, Redhead M, Westwood M, Leysen S, Davis J, Ottmann C. Identification of molecular glues of the SLP76/14-3-3 protein-protein interaction. RSC Med Chem 2021; 12:1555-1564. [PMID: 34667951 PMCID: PMC8459327 DOI: 10.1039/d1md00172h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/01/2021] [Indexed: 12/12/2022] Open
Abstract
The stabilisation of protein-protein interactions (PPIs) through molecular glues is a novel and promising approach in drug discovery. In stark contrast to research in protein-protein inhibition the field of stabilisation remains underdeveloped with comparatively few examples of small-molecule stabilisers of PPIs reported to date. At the same time identifying molecular glues has received recent sustained interest, especially in the fields of targeted protein degradation and 14-3-3 PPIs. The hub-protein 14-3-3 has a broad interactome with more than 500 known protein partners which presents a great opportunity for therapeutic intervention. In this study we have developed an HTRF assay suitable for HTS of the 14-3-3/SLP76 PPI and have completed a proof of concept screen against a chemically diverse library of 20 K molecules. The adaptor protein SLP76 has been reported to interact with 14-3-3 proteins downstream of the TCR playing an important role in mediating its own proteasomal degradation. We believe that stabilisation of this PPI could be exploited to potentiate degradation of SLP76 and therefore inhibit TCR signalling. This would represent an interesting alternative to other approaches in the field of targeted protein degradation. Here we disclose 16 novel stabilisers of the 14-3-3/SLP76 PPI across multiple different chemotypes. Based on the early results presented here we would recommend this approach to find molecular glues with broad applicability in the field of 14-3-3 PPIs.
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Affiliation(s)
- Lorenzo Soini
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology Eindhoven The Netherlands .,Department of Chemistry, UCB Celltech Slough UK
| | - Martin Redhead
- Exscientia Ltd, Schrodinger Building, Oxford Science Park Oxford OX44GE UK
| | - Marta Westwood
- Structural Biology, Discovery, Charles River, Chesterford Research Park UK
| | - Seppe Leysen
- Department of Structural Biology and Biophysics, UCB Celltech Slough UK
| | | | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology Eindhoven The Netherlands
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Soini L, Leysen S, Crabbe T, Davis J, Ottmann C. The identification and structural analysis of potential 14-3-3 interaction sites on the bone regulator protein Schnurri-3. Acta Crystallogr F Struct Biol Commun 2021; 77:254-261. [PMID: 34341191 PMCID: PMC8329713 DOI: 10.1107/s2053230x21006658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/25/2021] [Indexed: 11/10/2022] Open
Abstract
14-3-3 proteins regulate many intracellular processes and their ability to bind in subtly different fashions to their numerous partner proteins provides attractive drug-targeting points for a range of diseases. Schnurri-3 is a suppressor of mouse bone formation and a candidate target for novel osteoporosis therapeutics, and thus it is of interest to determine whether it interacts with 14-3-3. In this work, potential 14-3-3 interaction sites on mammalian Schnurri-3 were identified by an in silico analysis of its protein sequence. Using fluorescence polarization, isothermal titration calorimetry and X-ray crystallography, it is shown that synthetic peptides containing either phosphorylated Thr869 or Ser542 can indeed interact with 14-3-3, with the latter capable of forming an interprotein disulfide bond with 14-3-3σ: a hitherto unreported phenomenon.
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Affiliation(s)
- Lorenzo Soini
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Chemistry, UCB Celltech, Slough, United Kingdom
| | - Seppe Leysen
- Department of Structural Biology and Biophysics, UCB Celltech, Slough, United Kingdom
| | - Tom Crabbe
- New Targets, UCB Celltech, Slough, United Kingdom
| | - Jeremy Davis
- Department of Chemistry, UCB Celltech, Slough, United Kingdom
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
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Molecular Analysis of 14-3-3 Genes in Citrus sinensis and Their Responses to Different Stresses. Int J Mol Sci 2021; 22:ijms22020568. [PMID: 33430069 PMCID: PMC7826509 DOI: 10.3390/ijms22020568] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 12/31/2022] Open
Abstract
14-3-3 proteins (14-3-3s) are among the most important phosphorylated molecules playing crucial roles in regulating plant development and defense responses to environmental constraints. No report thus far has documented the gene family of 14-3-3s in Citrus sinensis and their roles in response to stresses. In this study, nine 14-3-3 genes, designated as CitGF14s (CitGF14a through CitGF14i) were identified from the latest C. sinensis genome. Phylogenetic analysis classified them into ε-like and non-ε groups, which were supported by gene structure analysis. The nine CitGF14s were located on five chromosomes, and none had duplication. Publicly available RNA-Seq raw data and microarray databases were mined for 14-3-3 expression profiles in different organs of citrus and in response to biotic and abiotic stresses. RT-qPCR was used for further examining spatial expression patterns of CitGF14s in citrus and their temporal expressions in one-year-old C. sinensis “Xuegan” plants after being exposed to different biotic and abiotic stresses. The nine CitGF14s were expressed in eight different organs with some isoforms displayed tissue-specific expression patterns. Six of the CitGF14s positively responded to citrus canker infection (Xanthomonas axonopodis pv. citri). The CitGF14s showed expressional divergence after phytohormone application and abiotic stress treatments, suggesting that 14-3-3 proteins are ubiquitous regulators in C. sinensis. Using the yeast two-hybrid assay, CitGF14a, b, c, d, g, and h were found to interact with CitGF14i proteins to form a heterodimer, while CitGF14i interacted with itself to form a homodimer. Further analysis of CitGF14s co-expression and potential interactors established a 14-3-3s protein interaction network. The established network identified 14-3-3 genes and several candidate clients which may play an important role in developmental regulation and stress responses in this important fruit crop. This is the first study of 14-3-3s in citrus, and the established network may help further investigation of the roles of 14-3-3s in response to abiotic and biotic constraints.
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Wang X, Ren Y, Li J, Ji Z, Chen F, Wang X. Identification of the 14-3-3 β/α-A protein as a novel maternal peptidoglycan-binding protein that protects embryos of zebrafish against bacterial infections. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 114:103867. [PMID: 32931839 DOI: 10.1016/j.dci.2020.103867] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/02/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
14-3-3 proteins are widespread in animals, but their functions and mechanisms remain poorly defined. Here we clearly demonstrate that 14-3-3 β/α-A is a newly identified PGN-binding protein present abundantly in the eggs/embryos of zebrafish. We also show that recombinant 14-3-3 β/α-A acts as a pattern recognition receptor capable of identifying the bacterial signature molecule PGN, binding the bacteria, and functions as an antibacterial effector molecule directly killing the bacteria. Importantly, microinjection of r14-3-3 β/α-A into early embryos significantly enhanced the resistance of the embryos against pathogenic A. hydrophila challenge, and this enhanced bacterial resistance was markedly reduced by co-injection of anti-14-3-3 β/α-A antibody. Collectively, these results indicate that 14-3-3 β/α-A is a maternal PGN-binding protein that can protect the early embryos of zebrafish against pathogenic attacks, a novel role assigned to 14-3-3 β/α-A proteins. This work also provides new insights into 14-3-3 proteins that are widely distributed in various animals.
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Affiliation(s)
- Xia Wang
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Yiqing Ren
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Jing Li
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China; East China University of Science and Technology, School of Biotechnology, Shanghai, 200237, China
| | - Zhe Ji
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Fushan Chen
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Xiudan Wang
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
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Scalia P, Giordano A, Martini C, Williams SJ. Isoform- and Paralog-Switching in IR-Signaling: When Diabetes Opens the Gates to Cancer. Biomolecules 2020; 10:biom10121617. [PMID: 33266015 PMCID: PMC7761347 DOI: 10.3390/biom10121617] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/21/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
Insulin receptor (IR) and IR-related signaling defects have been shown to trigger insulin-resistance in insulin-dependent cells and ultimately to give rise to type 2 diabetes in mammalian organisms. IR expression is ubiquitous in mammalian tissues, and its over-expression is also a common finding in cancerous cells. This latter finding has been shown to associate with both a relative and absolute increase in IR isoform-A (IR-A) expression, missing 12 aa in its EC subunit corresponding to exon 11. Since IR-A is a high-affinity transducer of Insulin-like Growth Factor-II (IGF-II) signals, a growth factor is often secreted by cancer cells; such event offers a direct molecular link between IR-A/IR-B increased ratio in insulin resistance states (obesity and type 2 diabetes) and the malignant advantage provided by IGF-II to solid tumors. Nonetheless, recent findings on the biological role of isoforms for cellular signaling components suggest that the preferential expression of IR isoform-A may be part of a wider contextual isoform-expression switch in downstream regulatory factors, potentially enhancing IR-dependent oncogenic effects. The present review focuses on the role of isoform- and paralog-dependent variability in the IR and downstream cellular components playing a potential role in the modulation of the IR-A signaling related to the changes induced by insulin-resistance-linked conditions as well as to their relationship with the benign versus malignant transition in underlying solid tumors.
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Affiliation(s)
- Pierluigi Scalia
- Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA 19122, USA; (A.G.); (C.M.); (S.J.W.)
- ISOPROG-Somatolink EPFP Network, Functional Research Unit, Philadelphia, PA 19104, USA and 93100 Caltanissetta, Italy
- Correspondence:
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA 19122, USA; (A.G.); (C.M.); (S.J.W.)
- Department of Medical Biotechnologies, University of Siena, 52100 Siena, Italy
| | - Caroline Martini
- Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA 19122, USA; (A.G.); (C.M.); (S.J.W.)
| | - Stephen J. Williams
- Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA 19122, USA; (A.G.); (C.M.); (S.J.W.)
- ISOPROG-Somatolink EPFP Network, Functional Research Unit, Philadelphia, PA 19104, USA and 93100 Caltanissetta, Italy
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12
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Soini L, Leysen S, Davis J, Westwood M, Ottmann C. The 14-3-3/SLP76 protein-protein interaction in T-cell receptor signalling: a structural and biophysical characterization. FEBS Lett 2020; 595:404-414. [PMID: 33159816 DOI: 10.1002/1873-3468.13993] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/13/2020] [Accepted: 11/01/2020] [Indexed: 12/18/2022]
Abstract
The SH2 domain-containing protein of 76 kDa, SLP76, is an important adaptor protein that coordinates a complex protein network downstream of T-cell receptors (TCR), ultimately regulating the immune response. Upon phosphorylation on Ser376, SLP76 interacts with 14-3-3 adaptor proteins, which leads to its proteolytic degradation. This provides a negative feedback mechanism by which TCR signalling can be controlled. To gain insight into the 14-3-3/SLP76 protein-protein interaction (PPI), we have determined a high-resolution crystal structure of a SLP76 synthetic peptide containing Ser376 with 14-3-3σ. We then characterized its binding to 14-3-3 proteins biophysically by means of fluorescence polarization and isothermal titration calorimetry. Furthermore, we generated two recombinant SLP76 protein constructs and characterized their binding to 14-3-3. Our work lays the foundation for drug design efforts aimed at targeting the 14-3-3/SLP76 interaction and, thereby, TCR signalling.
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Affiliation(s)
- Lorenzo Soini
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands.,Department of Chemistry, UCB Celltech, Slough, UK
| | - Seppe Leysen
- Department of Structural Biology and Biophysics, UCB Celltech, Slough, UK
| | - Jeremy Davis
- Department of Chemistry, UCB Celltech, Slough, UK
| | | | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
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Bouhaddou M, Memon D, Meyer B, White KM, Rezelj VV, Correa Marrero M, Polacco BJ, Melnyk JE, Ulferts S, Kaake RM, Batra J, Richards AL, Stevenson E, Gordon DE, Rojc A, Obernier K, Fabius JM, Soucheray M, Miorin L, Moreno E, Koh C, Tran QD, Hardy A, Robinot R, Vallet T, Nilsson-Payant BE, Hernandez-Armenta C, Dunham A, Weigang S, Knerr J, Modak M, Quintero D, Zhou Y, Dugourd A, Valdeolivas A, Patil T, Li Q, Hüttenhain R, Cakir M, Muralidharan M, Kim M, Jang G, Tutuncuoglu B, Hiatt J, Guo JZ, Xu J, Bouhaddou S, Mathy CJP, Gaulton A, Manners EJ, Félix E, Shi Y, Goff M, Lim JK, McBride T, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, De Wit E, Leach AR, Kortemme T, Shoichet B, Ott M, Saez-Rodriguez J, tenOever BR, Mullins RD, Fischer ER, Kochs G, Grosse R, García-Sastre A, Vignuzzi M, Johnson JR, Shokat KM, Swaney DL, Beltrao P, Krogan NJ. The Global Phosphorylation Landscape of SARS-CoV-2 Infection. Cell 2020; 182:685-712.e19. [PMID: 32645325 PMCID: PMC7321036 DOI: 10.1016/j.cell.2020.06.034] [Citation(s) in RCA: 677] [Impact Index Per Article: 169.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/09/2020] [Accepted: 06/23/2020] [Indexed: 02/07/2023]
Abstract
The causative agent of the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected millions and killed hundreds of thousands of people worldwide, highlighting an urgent need to develop antiviral therapies. Here we present a quantitative mass spectrometry-based phosphoproteomics survey of SARS-CoV-2 infection in Vero E6 cells, revealing dramatic rewiring of phosphorylation on host and viral proteins. SARS-CoV-2 infection promoted casein kinase II (CK2) and p38 MAPK activation, production of diverse cytokines, and shutdown of mitotic kinases, resulting in cell cycle arrest. Infection also stimulated a marked induction of CK2-containing filopodial protrusions possessing budding viral particles. Eighty-seven drugs and compounds were identified by mapping global phosphorylation profiles to dysregulated kinases and pathways. We found pharmacologic inhibition of the p38, CK2, CDK, AXL, and PIKFYVE kinases to possess antiviral efficacy, representing potential COVID-19 therapies.
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Affiliation(s)
- Mehdi Bouhaddou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Danish Memon
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Bjoern Meyer
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris, Cedex 15, France
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Veronica V Rezelj
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris, Cedex 15, France
| | - Miguel Correa Marrero
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Benjamin J Polacco
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James E Melnyk
- QBI COVID-19 Research Group (QCRG), 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; Howard Hughes Medical Institute
| | - Svenja Ulferts
- Institute for Clinical and Experimental Pharmacology and Toxicology, University of Freiburg, Freiburg 79104, Germany
| | - Robyn M Kaake
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jyoti Batra
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alicia L Richards
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Erica Stevenson
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - David E Gordon
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ajda Rojc
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kirsten Obernier
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jacqueline M Fabius
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Margaret Soucheray
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Elena Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Cassandra Koh
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris, Cedex 15, France
| | - Quang Dinh Tran
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris, Cedex 15, France
| | - Alexandra Hardy
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris, Cedex 15, France
| | - Rémy Robinot
- Virus & Immunity Unit, Department of Virology, CNRS UMR 3569, Institut Pasteur, 75724 Paris, Cedex 15, France; Vaccine Research Institute, 94000 Creteil, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris, Cedex 15, France
| | | | - Claudia Hernandez-Armenta
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Alistair Dunham
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sebastian Weigang
- Institute of Virology, Medical Center - University of Freiburg, Freiburg 79104, Germany
| | - Julian Knerr
- Institute for Clinical and Experimental Pharmacology and Toxicology, University of Freiburg, Freiburg 79104, Germany
| | - Maya Modak
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Diego Quintero
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yuan Zhou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Aurelien Dugourd
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg 69120, Germany
| | - Alberto Valdeolivas
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg 69120, Germany
| | - Trupti Patil
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Qiongyu Li
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ruth Hüttenhain
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Merve Cakir
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Monita Muralidharan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Minkyu Kim
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Gwendolyn Jang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Beril Tutuncuoglu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joseph Hiatt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jeffrey Z Guo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jiewei Xu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sophia Bouhaddou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
| | - Christopher J P Mathy
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Anna Gaulton
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Emma J Manners
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Eloy Félix
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ying Shi
- QBI COVID-19 Research Group (QCRG), 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; Howard Hughes Medical Institute
| | - Marisa Goff
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jean K Lim
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | | | | | | | | | | | - Emmie De Wit
- NIH/NIAID/Rocky Mountain Laboratories, Hamilton, MT 59840, USA
| | - Andrew R Leach
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tanja Kortemme
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Brian Shoichet
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Melanie Ott
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg 69120, Germany
| | - Benjamin R tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - R Dyche Mullins
- QBI COVID-19 Research Group (QCRG), 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; Howard Hughes Medical Institute
| | | | - Georg Kochs
- Institute of Virology, Medical Center - University of Freiburg, Freiburg 79104, Germany; Faculty of Medicine, University of Freiburg, Freiburg 79008, Germany
| | - Robert Grosse
- Institute for Clinical and Experimental Pharmacology and Toxicology, University of Freiburg, Freiburg 79104, Germany; Faculty of Medicine, University of Freiburg, Freiburg 79008, Germany; Centre for Integrative Biological Signalling Studies (CIBSS), Freiburg 79104, Germany.
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris, Cedex 15, France.
| | - Jeffery R Johnson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Kevan M Shokat
- QBI COVID-19 Research Group (QCRG), 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; Howard Hughes Medical Institute.
| | - Danielle L Swaney
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Pedro Beltrao
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Nevan J Krogan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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14
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Tugaeva KV, Titterington J, Sotnikov DV, Maksimov EG, Antson AA, Sluchanko NN. Molecular basis for the recognition of steroidogenic acute regulatory protein by the 14‐3‐3 protein family. FEBS J 2020; 287:3944-3966. [DOI: 10.1111/febs.15474] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/26/2020] [Accepted: 07/01/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Kristina V. Tugaeva
- Federal Research Center of Biotechnology of the Russian Academy of Sciences A.N. Bach Institute of Biochemistry Moscow Russia
- Department of Biochemistry School of Biology M.V. Lomonosov Moscow State University Russia
| | - James Titterington
- York Structural Biology Laboratory Department of Chemistry University of York UK
| | - Dmitriy V. Sotnikov
- Federal Research Center of Biotechnology of the Russian Academy of Sciences A.N. Bach Institute of Biochemistry Moscow Russia
| | - Eugene G. Maksimov
- Federal Research Center of Biotechnology of the Russian Academy of Sciences A.N. Bach Institute of Biochemistry Moscow Russia
- Department of Biophysics School of Biology M.V. Lomonosov Moscow State University Russia
| | - Alfred A. Antson
- York Structural Biology Laboratory Department of Chemistry University of York UK
| | - Nikolai N. Sluchanko
- Federal Research Center of Biotechnology of the Russian Academy of Sciences A.N. Bach Institute of Biochemistry Moscow Russia
- Department of Biophysics School of Biology M.V. Lomonosov Moscow State University Russia
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15
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Xu X, Lemmens LJM, den Hamer A, Merkx M, Ottmann C, Brunsveld L. Modular bioengineered kinase sensors via scaffold protein-mediated split-luciferase complementation. Chem Sci 2020; 11:5532-5536. [PMID: 32874496 PMCID: PMC7446724 DOI: 10.1039/d0sc00074d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 05/11/2020] [Indexed: 01/07/2023] Open
Abstract
Phosphorylation is a key regulation event in cellular signaling. To sense the underlying kinase activity, we engineered modular and easy adaptable serine kinase sensors for the exemplary kinases PKA, PKB and CHK1.
Phosphorylation is a key regulation event in cellular signaling. Sensing the underlying kinase activity is of crucial importance for its fundamental understanding and for drug development. For this, modular kinase activity sensing concepts are urgently needed. We engineered modular serine kinase sensors based on complementation of split NanoBiT luciferase on protein assembly platforms generated from the scaffold protein 14-3-3. The bioengineered platforms are modular and easy adaptable as exemplary shown using novel sensors for the kinases PKA, PKB, and CHK1. Two designs were conceptualized, both relying on binding of defined mono- or bivalent kinase recognition motifs to the 14-3-3 platform upon phosphorylation, resulting in reconstitution of active split-luciferase. Especially the design based on double phosphorylation and bivalent 14-3-3 binding exhibits high efficiency for signal amplification (>1000-fold) and sensitivity to specific kinases, including in cellular lysates.
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Affiliation(s)
- Xiaolu Xu
- Laboratory of Chemical Biology , Department of Biomedical Engineering , Institute for Complex Molecular Systems (ICMS) , Eindhoven University of Technology , Den Dolech 2 , 5612AZ , Eindhoven , the Netherlands .
| | - Lenne J M Lemmens
- Laboratory of Chemical Biology , Department of Biomedical Engineering , Institute for Complex Molecular Systems (ICMS) , Eindhoven University of Technology , Den Dolech 2 , 5612AZ , Eindhoven , the Netherlands .
| | - Anniek den Hamer
- Laboratory of Chemical Biology , Department of Biomedical Engineering , Institute for Complex Molecular Systems (ICMS) , Eindhoven University of Technology , Den Dolech 2 , 5612AZ , Eindhoven , the Netherlands .
| | - Maarten Merkx
- Laboratory of Chemical Biology , Department of Biomedical Engineering , Institute for Complex Molecular Systems (ICMS) , Eindhoven University of Technology , Den Dolech 2 , 5612AZ , Eindhoven , the Netherlands .
| | - Christian Ottmann
- Laboratory of Chemical Biology , Department of Biomedical Engineering , Institute for Complex Molecular Systems (ICMS) , Eindhoven University of Technology , Den Dolech 2 , 5612AZ , Eindhoven , the Netherlands .
| | - Luc Brunsveld
- Laboratory of Chemical Biology , Department of Biomedical Engineering , Institute for Complex Molecular Systems (ICMS) , Eindhoven University of Technology , Den Dolech 2 , 5612AZ , Eindhoven , the Netherlands .
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16
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Mei L, Montoya MR, Quanrud GM, Tran M, Villa-Sharma A, Huang M, Genereux JC. Bait Correlation Improves Interactor Identification by Tandem Mass Tag-Affinity Purification-Mass Spectrometry. J Proteome Res 2020; 19:1565-1573. [PMID: 32138514 DOI: 10.1021/acs.jproteome.9b00825] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The quantitative multiplexing capacity of isobaric tandem mass tags (TMT) has increased the throughput of affinity purification mass spectrometry (AP-MS) to characterize protein interaction networks of immunoprecipitated bait proteins. However, variable bait levels between replicates can convolute interactor identification. We compared the Student's t-test and Pearson's R correlation as methods to generate t-statistics and assessed the significance of interactors following TMT-AP-MS. Using a simple linear model of protein recovery in immunoprecipitates to simulate reporter ion ratio distributions, we found that correlation-derived t-statistics protect against bait variance while robustly controlling type I errors (false positives). We experimentally determined the performance of these two approaches for determining t-statistics under two experimental conditions: irreversible prey association to the Hsp40 mutant DNAJB8H31Q followed by stringent washing, and reversible association to 14-3-3ζ with gentle washing. Correlation-derived t-statistics performed at least as well as Student's t-statistics for each sample and with substantial improvement in performance for experiments with high bait-level variance. Deliberately varying bait levels over a large range fails to improve selectivity but does increase the robustness between runs. The use of correlation-derived t-statistics should improve identification of interactors using TMT-AP-MS. Data are available via ProteomeXchange with identifier PXD016613.
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Affiliation(s)
- Liangyong Mei
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Maureen R Montoya
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Guy M Quanrud
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Minh Tran
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Athena Villa-Sharma
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Ming Huang
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
| | - Joseph C Genereux
- Department of Chemistry, University of California, Riverside, California 92521, United States.,Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
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17
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Gigante A, Sijbesma E, Sánchez‐Murcia PA, Hu X, Bier D, Bäcker S, Knauer S, Gago F, Ottmann C, Schmuck C. A Supramolecular Stabilizer of the 14-3-3ζ/ERα Protein-Protein Interaction with a Synergistic Mode of Action. Angew Chem Int Ed Engl 2020; 59:5284-5287. [PMID: 31814236 PMCID: PMC7155037 DOI: 10.1002/anie.201914517] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Indexed: 12/27/2022]
Abstract
We report on a stabilizer of the interaction between 14-3-3ζ and the Estrogen Receptor alpha (ERα). ERα is a driver in the majority of breast cancers and 14-3-3 proteins are negative regulators of this nuclear receptor, making the stabilization of this protein-protein interaction (PPI) an interesting strategy. The stabilizer (1) consists of three symmetric peptidic arms containing an arginine mimetic, previously described as the GCP motif. 1 stabilizes the 14-3-3ζ/ERα interaction synergistically with the natural product Fusicoccin-A and was thus hypothesized to bind to a different site. This is supported by computational analysis of 1 binding to the binary complex of 14-3-3 and an ERα-derived phosphopeptide. Furthermore, 1 shows selectivity towards 14-3-3ζ/ERα interaction over other 14-3-3 client-derived phosphomotifs. These data provide a solid support of a new binding mode for a supramolecular 14-3-3ζ/ERα PPI stabilizer.
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Affiliation(s)
- Alba Gigante
- Department of Organic ChemistryUniversity of Duisburg EssenUniversitätstr. 745141EssenGermany
| | - Eline Sijbesma
- Department of Biomedical EngineeringEindhoven University of TechnologyP.O. Box 5135600 MBEindhovenThe Netherlands
| | - Pedro A. Sánchez‐Murcia
- Departamento de Ciencias BiomédicasUniversidad de Alcalá28805Alcalá de HenaresSpain
- Present address: Institute of Theoretical ChemistryFaculty of ChemistryUniversity of ViennaWähringer Str. 171090ViennaAustria
| | - Xiaoyu Hu
- Department of Organic ChemistryUniversity of Duisburg EssenUniversitätstr. 745141EssenGermany
| | - David Bier
- Department of Organic ChemistryUniversity of Duisburg EssenUniversitätstr. 745141EssenGermany
- Department of Biomedical EngineeringEindhoven University of TechnologyP.O. Box 5135600 MBEindhovenThe Netherlands
| | - Sandra Bäcker
- Centre for Medical BiotechnologyUniversity of Duisburg EssenUniversitätstr. 745141EssenGermany
| | - Shirley Knauer
- Centre for Medical BiotechnologyUniversity of Duisburg EssenUniversitätstr. 745141EssenGermany
| | - Federico Gago
- Departamento de Ciencias BiomédicasUniversidad de Alcalá28805Alcalá de HenaresSpain
| | - Christian Ottmann
- Department of Organic ChemistryUniversity of Duisburg EssenUniversitätstr. 745141EssenGermany
- Department of Biomedical EngineeringEindhoven University of TechnologyP.O. Box 5135600 MBEindhovenThe Netherlands
| | - Carsten Schmuck
- Department of Organic ChemistryUniversity of Duisburg EssenUniversitätstr. 745141EssenGermany
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18
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Gigante A, Sijbesma E, Sánchez‐Murcia PA, Hu X, Bier D, Bäcker S, Knauer S, Gago F, Ottmann C, Schmuck C. A Supramolecular Stabilizer of the 14‐3‐3ζ/ERα Protein‐Protein Interaction with a Synergistic Mode of Action. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Alba Gigante
- Department of Organic ChemistryUniversity of Duisburg Essen Universitätstr. 7 45141 Essen Germany
| | - Eline Sijbesma
- Department of Biomedical EngineeringEindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Pedro A. Sánchez‐Murcia
- Departamento de Ciencias BiomédicasUniversidad de Alcalá 28805 Alcalá de Henares Spain
- Present address: Institute of Theoretical ChemistryFaculty of ChemistryUniversity of Vienna Währinger Str. 17 1090 Vienna Austria
| | - Xiaoyu Hu
- Department of Organic ChemistryUniversity of Duisburg Essen Universitätstr. 7 45141 Essen Germany
| | - David Bier
- Department of Organic ChemistryUniversity of Duisburg Essen Universitätstr. 7 45141 Essen Germany
- Department of Biomedical EngineeringEindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Sandra Bäcker
- Centre for Medical BiotechnologyUniversity of Duisburg Essen Universitätstr. 7 45141 Essen Germany
| | - Shirley Knauer
- Centre for Medical BiotechnologyUniversity of Duisburg Essen Universitätstr. 7 45141 Essen Germany
| | - Federico Gago
- Departamento de Ciencias BiomédicasUniversidad de Alcalá 28805 Alcalá de Henares Spain
| | - Christian Ottmann
- Department of Organic ChemistryUniversity of Duisburg Essen Universitätstr. 7 45141 Essen Germany
- Department of Biomedical EngineeringEindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Carsten Schmuck
- Department of Organic ChemistryUniversity of Duisburg Essen Universitätstr. 7 45141 Essen Germany
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19
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Wolter M, Santo DL, Herman P, Ballone A, Centorrino F, Obsil T, Ottmann C. Interaction of an IκBα Peptide with 14-3-3. ACS OMEGA 2020; 5:5380-5388. [PMID: 32201828 PMCID: PMC7081424 DOI: 10.1021/acsomega.9b04413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 02/19/2020] [Indexed: 06/10/2023]
Abstract
Inflammatory responses mediated by the transcription factor nuclear factor kappa-light-chain enhancer of activated B cells (NF-κB) play key roles in immunity, autoimmune diseases, and cancer. NF-κB is directly regulated through protein-protein interactions, including those with IκB and 14-3-3 proteins. These two important regulatory proteins have been reported to interact with each other, although little is known about this interaction. We analyzed the inhibitor of nuclear factor kappa B α (IκBα)/14-3-3σ interaction via a peptide/protein-based approach. Structural data were acquired via X-ray crystallography, while binding affinities were measured with fluorescence polarization assays and time-resolved tryptophan fluorescence. A high-resolution crystal structure (1.13 Å) of the uncommon 14-3-3 interaction motif of IκBα (IκBαpS63) in a complex with 14-3-3σ was evaluated. This motif harbors a tryptophan that makes this crystal structure the first one with such a residue visible in the electron density at that position. We used this tryptophan to determine the binding affinity of the unlabeled IκBα peptide to 14-3-3 via tryptophan fluorescence decay measurements.
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Affiliation(s)
- Madita Wolter
- Department
of Biomedical Engineering, Laboratory of Chemical Biology and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Domenico Lentini Santo
- Department
of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague 12843, Czech Republic
| | - Petr Herman
- Institute
of Physics, Faculty of Mathematics and Physics, Charles University, Prague 12116, Czech Republic
| | - Alice Ballone
- Department
of Biomedical Engineering, Laboratory of Chemical Biology and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Federica Centorrino
- Department
of Biomedical Engineering, Laboratory of Chemical Biology and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Tomas Obsil
- Department
of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague 12843, Czech Republic
| | - Christian Ottmann
- Department
of Biomedical Engineering, Laboratory of Chemical Biology and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- Department
of Organic Chemistry, University of Duisburg-Essen, 45117 Essen, Germany
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20
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Phospho-peptide binding domains in S. cerevisiae model organism. Biochimie 2019; 163:117-127. [PMID: 31194995 DOI: 10.1016/j.biochi.2019.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 06/06/2019] [Indexed: 02/07/2023]
Abstract
Protein phosphorylation is one of the main mechanisms by which signals are transmitted in eukaryotic cells, and it plays a crucial regulatory role in almost all cellular processes. In yeast, more than half of the proteins are phosphorylated in at least one site, and over 20,000 phosphopeptides have been experimentally verified. However, the functional consequences of these phosphorylation events for most of the identified phosphosites are unknown. A family of protein interaction domains selectively recognises phosphorylated motifs to recruit regulatory proteins and activate signalling pathways. Nine classes of dedicated modules are coded by the yeast genome: 14-3-3, FHA, WD40, BRCT, WW, PBD, and SH2. The recognition specificity relies on a few residues on the target protein and has coevolved with kinase specificity. In the present study, we review the current knowledge concerning yeast phospho-binding domains and their networks. We emphasise the relevance of both positive and negative amino acid selection to orchestrate the highly regulated outcomes of inter- and intra-molecular interactions. Finally, we hypothesise that only a small fraction of yeast phosphorylation events leads to the creation of a docking site on the target molecule, while many have a direct effect on the protein or, as has been proposed, have no function at all.
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21
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Mugabo Y, Lim GE. Scaffold Proteins: From Coordinating Signaling Pathways to Metabolic Regulation. Endocrinology 2018; 159:3615-3630. [PMID: 30204866 PMCID: PMC6180900 DOI: 10.1210/en.2018-00705] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 09/05/2018] [Indexed: 01/13/2023]
Abstract
Among their pleiotropic functions, scaffold proteins are required for the accurate coordination of signaling pathways. It has only been within the past 10 years that their roles in glucose homeostasis and metabolism have emerged. It is well appreciated that changes in the expression or function of signaling effectors, such as receptors or kinases, can influence the development of chronic diseases such as diabetes and obesity. However, little is known regarding whether scaffolds have similar roles in the pathogenesis of metabolic diseases. In general, scaffolds are often underappreciated in the context of metabolism or metabolic diseases. In the present review, we discuss various scaffold proteins and their involvement in signaling pathways related to metabolism and metabolic diseases. The aims of the present review were to highlight the importance of scaffold proteins and to raise awareness of their physiological contributions. A thorough understanding of how scaffolds influence metabolism could aid in the discovery of novel therapeutic approaches to treat chronic conditions, such as diabetes, obesity, and cardiovascular disease, for which the incidence of all continue to increase at alarming rates.
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Affiliation(s)
- Yves Mugabo
- Cardiometabolic Axis, Centre de Recherche de Centre Hospitalier de l’Université de Montréal, Montreal, Quebec, Canada
- Montréal Diabetes Research Centre, Montreal, Quebec, Canada
- Department of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Gareth E Lim
- Cardiometabolic Axis, Centre de Recherche de Centre Hospitalier de l’Université de Montréal, Montreal, Quebec, Canada
- Montréal Diabetes Research Centre, Montreal, Quebec, Canada
- Department of Medicine, Université de Montréal, Montreal, Quebec, Canada
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22
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Haslbeck M, Weinkauf S, Buchner J. Small heat shock proteins: Simplicity meets complexity. J Biol Chem 2018; 294:2121-2132. [PMID: 30385502 DOI: 10.1074/jbc.rev118.002809] [Citation(s) in RCA: 163] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Small heat shock proteins (sHsps) are a ubiquitous and ancient family of ATP-independent molecular chaperones. A key characteristic of sHsps is that they exist in ensembles of iso-energetic oligomeric species differing in size. This property arises from a unique mode of assembly involving several parts of the subunits in a flexible manner. Current evidence suggests that smaller oligomers are more active chaperones. Thus, a shift in the equilibrium of the sHsp ensemble allows regulating the chaperone activity. Different mechanisms have been identified that reversibly change the oligomer equilibrium. The promiscuous interaction with non-native proteins generates complexes that can form aggregate-like structures from which native proteins are restored by ATP-dependent chaperones such as Hsp70 family members. In recent years, this basic paradigm has been expanded, and new roles and new cofactors, as well as variations in structure and regulation of sHsps, have emerged.
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Affiliation(s)
- Martin Haslbeck
- From the Department of Chemie and Center for Integrated Protein Science, Technische Universität München, Lichtenbergstrasse 4, 85 748 Garching, Germany
| | - Sevil Weinkauf
- From the Department of Chemie and Center for Integrated Protein Science, Technische Universität München, Lichtenbergstrasse 4, 85 748 Garching, Germany
| | - Johannes Buchner
- From the Department of Chemie and Center for Integrated Protein Science, Technische Universität München, Lichtenbergstrasse 4, 85 748 Garching, Germany
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23
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Herrera-Uribe J, Jiménez-Marín Á, Lacasta A, Monteagudo PL, Pina-Pedrero S, Rodríguez F, Moreno Á, Garrido JJ. Comparative proteomic analysis reveals different responses in porcine lymph nodes to virulent and attenuated homologous African swine fever virus strains. Vet Res 2018; 49:90. [PMID: 30208957 PMCID: PMC6134756 DOI: 10.1186/s13567-018-0585-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/05/2018] [Indexed: 01/07/2023] Open
Abstract
African swine fever (ASF) is a pathology of pigs against which there is no treatment or vaccine. Understanding the equilibrium between innate and adaptive protective responses and immune pathology might contribute to the development of strategies against ASFV. Here we compare, using a proteomic approach, the course of the in vivo infection caused by two homologous strains: the virulent E75 and the attenuated E75CV1. Our results show a progressive loss of proteins by day 7 post-infection (pi) with E75, reflecting tissue destruction. Many signal pathways were affected by both infections but in different ways and extensions. Cytoskeletal remodelling and clathrin-endocytosis were affected by both isolates, while a greater number of proteins involved on inflammatory and immunological pathways were altered by E75CV1. 14-3-3 mediated signalling, related to immunity and apoptosis, was inhibited by both isolates. The implication of the Rho GTPases by E75CV1 throughout infection is also evident. Early events reflected the lack of E75 recognition by the immune system, an evasion strategy acquired by the virulent strains, and significant changes at 7 days post-infection (dpi), coinciding with the peak of infection and the time of death. The protein signature at day 31 pi with E75CV1 seems to reflect events observed at 1 dpi, including the upregulation of proteosomal subunits and molecules described as autoantigens (vimentin, HSPB1, enolase and lymphocyte cytosolic protein 1), which allow the speculation that auto-antibodies could contribute to chronic ASFV infections. Therefore, the use of proteomics could help understand ASFV pathogenesis and immune protection, opening new avenues for future research.
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Affiliation(s)
- Júber Herrera-Uribe
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Ángeles Jiménez-Marín
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Anna Lacasta
- International Livestock Research Intitute (ILRI), Nairobi, 00100, Kenya.,Centre de Recerca En Sanitat Animal (CReSA), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Paula L Monteagudo
- Centre de Recerca En Sanitat Animal (CReSA), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Sonia Pina-Pedrero
- Centre de Recerca En Sanitat Animal (CReSA), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Fernando Rodríguez
- Centre de Recerca En Sanitat Animal (CReSA), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Ángela Moreno
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain.,Instituto de Agricultura Sostenible, Campus Alameda del Obispo, 14080 CSIC, Córdoba, Spain
| | - Juan J Garrido
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain.
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24
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Mugabo Y, Sadeghi M, Fang NN, Mayor T, Lim GE. Elucidation of the 14-3-3ζ interactome reveals critical roles of RNA-splicing factors during adipogenesis. J Biol Chem 2018. [PMID: 29530978 DOI: 10.1074/jbc.m117.816272] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Adipogenesis involves a complex signaling network requiring strict temporal and spatial organization of effector molecules. Molecular scaffolds, such as 14-3-3 proteins, facilitate such organization, and we have previously identified 14-3-3ζ as an essential scaffold in adipocyte differentiation. The interactome of 14-3-3ζ is large and diverse, and it is possible that novel adipogenic factors may be present within it, but this possibility has not yet been tested. Herein, we generated mouse embryonic fibroblasts from mice overexpressing a tandem affinity purification (TAP) epitope-tagged 14-3-3ζ molecule. After inducing adipogenesis, TAP-14-3-3ζ complexes were purified, followed by MS analysis to determine the 14-3-3ζ interactome. We observed more than 100 proteins that were unique to adipocyte differentiation, 56 of which were novel interacting partners. Among these, we were able to identify previously established regulators of adipogenesis (i.e. Ptrf/Cavin1) within the 14-3-3ζ interactome, confirming the utility of this approach to detect adipogenic factors. We found that proteins related to RNA metabolism, processing, and splicing were enriched in the interactome. Analysis of transcriptomic data revealed that 14-3-3ζ depletion in 3T3-L1 cells affected alternative splicing of mRNA during adipocyte differentiation. siRNA-mediated depletion of RNA-splicing factors within the 14-3-3ζ interactome, that is, of Hnrpf, Hnrpk, Ddx6, and Sfpq, revealed that they have essential roles in adipogenesis and in the alternative splicing of Pparg and the adipogenesis-associated gene Lpin1 In summary, we have identified novel adipogenic factors within the 14-3-3ζ interactome. Further characterization of additional proteins within the 14-3-3ζ interactome may help identify novel targets to block obesity-associated expansion of adipose tissues.
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Affiliation(s)
- Yves Mugabo
- From the Centre Hospitalier de l'Université de Montréal, Montréal, Québec H2X 029, Canada.,the Department of Medicine, Université de Montréal, Montréal, Québec H3T 1J4, Canada, and
| | - Mina Sadeghi
- From the Centre Hospitalier de l'Université de Montréal, Montréal, Québec H2X 029, Canada.,the Department of Medicine, Université de Montréal, Montréal, Québec H3T 1J4, Canada, and
| | - Nancy N Fang
- the Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Thibault Mayor
- the Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Gareth E Lim
- From the Centre Hospitalier de l'Université de Montréal, Montréal, Québec H2X 029, Canada, .,the Department of Medicine, Université de Montréal, Montréal, Québec H3T 1J4, Canada, and
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25
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Stevers LM, Sijbesma E, Botta M, MacKintosh C, Obsil T, Landrieu I, Cau Y, Wilson AJ, Karawajczyk A, Eickhoff J, Davis J, Hann M, O'Mahony G, Doveston RG, Brunsveld L, Ottmann C. Modulators of 14-3-3 Protein-Protein Interactions. J Med Chem 2017; 61:3755-3778. [PMID: 28968506 PMCID: PMC5949722 DOI: 10.1021/acs.jmedchem.7b00574] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Direct
interactions between proteins are essential for the regulation
of their functions in biological pathways. Targeting the complex network
of protein–protein interactions (PPIs) has now been widely
recognized as an attractive means to therapeutically intervene in
disease states. Even though this is a challenging endeavor and PPIs
have long been regarded as “undruggable” targets, the
last two decades have seen an increasing number of successful examples
of PPI modulators, resulting in growing interest in this field. PPI
modulation requires novel approaches and the integrated efforts of
multiple disciplines to be a fruitful strategy. This perspective focuses
on the hub-protein 14-3-3, which has several hundred identified protein
interaction partners, and is therefore involved in a wide range of
cellular processes and diseases. Here, we aim to provide an integrated
overview of the approaches explored for the modulation of 14-3-3 PPIs
and review the examples resulting from these efforts in both inhibiting
and stabilizing specific 14-3-3 protein complexes by small molecules,
peptide mimetics, and natural products.
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Affiliation(s)
- Loes M Stevers
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS) , Eindhoven University of Technology , P.O. Box 513, 5600 MB , Eindhoven , The Netherlands
| | - Eline Sijbesma
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS) , Eindhoven University of Technology , P.O. Box 513, 5600 MB , Eindhoven , The Netherlands
| | - Maurizio Botta
- Department of Biotechnology, Chemistry and Pharmacy , University of Siena , Via Aldo Moro 2 , 53100 Siena , Italy
| | - Carol MacKintosh
- Division of Cell and Developmental Biology, School of Life Sciences , University of Dundee , Dundee DD1 4HN , United Kingdom
| | - Tomas Obsil
- Department of Physical and Macromolecular Chemistry, Faculty of Science , Charles University , Prague 116 36 , Czech Republic
| | | | - Ylenia Cau
- Department of Biotechnology, Chemistry and Pharmacy , University of Siena , Via Aldo Moro 2 , 53100 Siena , Italy
| | - Andrew J Wilson
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , United Kingdom.,Astbury Center For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , United Kingdom
| | | | - Jan Eickhoff
- Lead Discovery Center GmbH , Dortmund 44227 , Germany
| | - Jeremy Davis
- UCB Celltech , 216 Bath Road , Slough SL1 3WE , United Kingdom
| | - Michael Hann
- GlaxoSmithKline , Gunnels Wood Road , Stevenage, Hertfordshire SG1 2NY , United Kingdom
| | - Gavin O'Mahony
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit , AstraZeneca Gothenburg , Pepparedsleden 1 , SE-431 83 Mölndal , Sweden
| | - Richard G Doveston
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS) , Eindhoven University of Technology , P.O. Box 513, 5600 MB , Eindhoven , The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS) , Eindhoven University of Technology , P.O. Box 513, 5600 MB , Eindhoven , The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS) , Eindhoven University of Technology , P.O. Box 513, 5600 MB , Eindhoven , The Netherlands.,Department of Chemistry , University of Duisburg-Essen , Universitätstraße 7 , 45141 Essen , Germany
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26
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Gao WND, Carpentier DCJ, Ewles HA, Lee SA, Smith GL. Vaccinia virus proteins A36 and F12/E2 show strong preferences for different kinesin light chain isoforms. Traffic 2017; 18:505-518. [PMID: 28485852 PMCID: PMC5519951 DOI: 10.1111/tra.12494] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/05/2017] [Accepted: 05/05/2017] [Indexed: 12/27/2022]
Abstract
Vaccinia virus (VACV) utilizes microtubule‐mediated trafficking at several stages of its life cycle, of which virus egress is the most intensely studied. During egress VACV proteins A36, F12 and E2 are involved in kinesin‐1 interactions; however, the roles of these proteins remain poorly understood. A36 forms a direct link between virions and kinesin‐1, yet in its absence VACV egress still occurs on microtubules. During a co‐immunoprecipitation screen to seek an alternative link between virions and kinesin, A36 was found to bind isoform KLC1 rather than KLC2. The F12/E2 complex associates preferentially with the C‐terminal tail of KLC2, to a region that overlaps the binding site of cellular 14‐3‐3 proteins. F12/E2 displaces 14‐3‐3 from KLC and, unlike 14‐3‐3, does not require phosphorylation of KLC for its binding. The region determining the KLC1 specificity of A36 was mapped to the KLC N‐terminal heptad repeat region that is responsible for its association with kinesin heavy chain. Despite these differing binding properties F12/E2 can co‐operatively enhance A36 association with KLC, particularly when using a KLC1‐KLC2 chimaera that resembles several KLC1 spliceforms and can bind A36 and F12/E2 efficiently. This is the first example of a pathogen encoding multiple proteins that co‐operatively associate with kinesin‐1.
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Affiliation(s)
- William N D Gao
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | - Helen A Ewles
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Stacey-Ann Lee
- Department of Pathology, University of Cambridge, Cambridge, UK
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27
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Richens JL, Spencer HL, Butler M, Cantlay F, Vere KA, Bajaj N, Morgan K, O'Shea P. Rationalising the role of Keratin 9 as a biomarker for Alzheimer's disease. Sci Rep 2016; 6:22962. [PMID: 26973255 PMCID: PMC4789650 DOI: 10.1038/srep22962] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 02/19/2016] [Indexed: 02/07/2023] Open
Abstract
Keratin 9 was recently identified as an important component of a biomarker panel which demonstrated a high diagnostic accuracy (87%) for Alzheimer's disease (AD). Understanding how a protein which is predominantly expressed in palmoplantar epidermis is implicated in AD may shed new light on the mechanisms underlying the disease. Here we use immunoassays to examine blood plasma expression patterns of Keratin 9 and its relationship to other AD-associated proteins. We correlate this with the use of an in silico analysis tool VisANT to elucidate possible pathways through which the involvement of Keratin 9 may take place. We identify possible links with Dickkopf-1, a negative regulator of the wnt pathway, and propose that the abnormal expression of Keratin 9 in AD blood and cerebrospinal fluid may be a result of blood brain barrier dysregulation and disruption of the ubiquitin proteasome system. Our findings suggest that dysregulated Keratin 9 expression is a consequence of AD pathology but, as it interacts with a broad range of proteins, it may have other, as yet uncharacterized, downstream effects which could contribute to AD onset and progression.
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Affiliation(s)
- Joanna L Richens
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Hannah L Spencer
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Molly Butler
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Fiona Cantlay
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Kelly-Ann Vere
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Nin Bajaj
- Department of Neurology, Nottingham University Hospitals NHS Trust, Queen's Medical Centre, Nottingham, United Kingdom
| | - Kevin Morgan
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - Paul O'Shea
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
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28
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Tollenaere MAX, Villumsen BH, Blasius M, Nielsen JC, Wagner SA, Bartek J, Beli P, Mailand N, Bekker-Jensen S. p38- and MK2-dependent signalling promotes stress-induced centriolar satellite remodelling via 14-3-3-dependent sequestration of CEP131/AZI1. Nat Commun 2015; 6:10075. [PMID: 26616734 PMCID: PMC4674683 DOI: 10.1038/ncomms10075] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 10/30/2015] [Indexed: 12/26/2022] Open
Abstract
Centriolar satellites (CS) are small granular structures that cluster in the vicinity of centrosomes. CS are highly susceptible to stress stimuli, triggering abrupt displacement of key CS factors. Here we discover a linear p38-MK2-14-3-3 signalling pathway that specifically targets CEP131 to trigger CS remodelling after cell stress. We identify CEP131 as a substrate of the p38 effector kinase MK2 and pinpoint S47 and S78 as critical MK2 phosphorylation sites in CEP131. Ultraviolet-induced phosphorylation of these residues generates direct binding sites for 14-3-3 proteins, which sequester CEP131 in the cytoplasm to block formation of new CS, thereby leading to rapid depletion of these structures. Mutating S47 and S78 in CEP131 is sufficient to abolish stress-induced CS reorganization, demonstrating that CEP131 is the key regulatory target of MK2 and 14-3-3 in these structures. Our findings reveal the molecular mechanism underlying dynamic CS remodelling to modulate centrosome functions on cell stress. Centriolar satellites (CS) dynamically remodel in response to cellular stress. Here the authors describe a mechanism for stress-mediated remodelling, whereby CEP131 is phosphorylated downstream of p38, creating binding sites for 14-3-3 that lead to the sequestration of CEP131 in the cytoplasm and disassembly of CS.
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Affiliation(s)
- Maxim A X Tollenaere
- Ubiquitin Signaling Group, Protein Signaling Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen DK-2200, Denmark
| | - Bine H Villumsen
- Ubiquitin Signaling Group, Protein Signaling Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen DK-2200, Denmark
| | - Melanie Blasius
- Danish Cancer Society Research Center, Strandboulevarden 49, Copenhagen DK-2100, Denmark
| | - Julie C Nielsen
- Ubiquitin Signaling Group, Protein Signaling Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen DK-2200, Denmark
| | - Sebastian A Wagner
- Department of Medicine, Hematology/Oncology, Goethe University Medical School, Theodor-Stern-Kai 7, Frankfurt DE-60590, Germany
| | - Jiri Bartek
- Danish Cancer Society Research Center, Strandboulevarden 49, Copenhagen DK-2100, Denmark.,Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm SE-17176, Sweden
| | - Petra Beli
- Institute of Molecular Biology, Ackermannweg 4, Mainz DE-55128, Germany
| | - Niels Mailand
- Ubiquitin Signaling Group, Protein Signaling Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen DK-2200, Denmark
| | - Simon Bekker-Jensen
- Ubiquitin Signaling Group, Protein Signaling Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen DK-2200, Denmark
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Schaffer BE, Levin RS, Hertz NT, Maures TJ, Schoof ML, Hollstein PE, Benayoun BA, Banko MR, Shaw RJ, Shokat KM, Brunet A. Identification of AMPK Phosphorylation Sites Reveals a Network of Proteins Involved in Cell Invasion and Facilitates Large-Scale Substrate Prediction. Cell Metab 2015; 22:907-21. [PMID: 26456332 PMCID: PMC4635044 DOI: 10.1016/j.cmet.2015.09.009] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 07/28/2015] [Accepted: 09/08/2015] [Indexed: 12/22/2022]
Abstract
AMP-activated protein kinase (AMPK) is a central energy gauge that regulates metabolism and has been increasingly involved in non-metabolic processes and diseases. However, AMPK's direct substrates in non-metabolic contexts are largely unknown. To better understand the AMPK network, we use a chemical genetics screen coupled to a peptide capture approach in whole cells, resulting in identification of direct AMPK phosphorylation sites. Interestingly, the high-confidence AMPK substrates contain many proteins involved in cell motility, adhesion, and invasion. AMPK phosphorylation of the RHOA guanine nucleotide exchange factor NET1A inhibits extracellular matrix degradation, an early step in cell invasion. The identification of direct AMPK phosphorylation sites also facilitates large-scale prediction of AMPK substrates. We provide an AMPK motif matrix and a pipeline to predict additional AMPK substrates from quantitative phosphoproteomics datasets. As AMPK is emerging as a critical node in aging and pathological processes, our study identifies potential targets for therapeutic strategies.
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Affiliation(s)
- Bethany E Schaffer
- Cancer Biology Program, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Rebecca S Levin
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Nicholas T Hertz
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Travis J Maures
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Michael L Schoof
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Pablo E Hollstein
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Max R Banko
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Reuben J Shaw
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Anne Brunet
- Cancer Biology Program, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; Glenn Laboratories for the Biology of Aging, Stanford, CA 94305, USA.
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30
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Abstract
Modulation of protein-protein interactions (PPIs) is becoming increasingly important in drug discovery and chemical biology. While a few years ago this 'target class' was deemed to be largely undruggable an impressing number of publications and success stories now show that targeting PPIs with small, drug-like molecules indeed is a feasible approach. Here, we summarize the current state of small-molecule inhibition and stabilization of PPIs and review the active molecules from a structural and medicinal chemistry angle, especially focusing on the key examples of iNOS, LFA-1 and 14-3-3.
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31
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Carpentier DCJ, Gao WND, Ewles H, Morgan GW, Smith GL. Vaccinia virus protein complex F12/E2 interacts with kinesin light chain isoform 2 to engage the kinesin-1 motor complex. PLoS Pathog 2015; 11:e1004723. [PMID: 25760349 PMCID: PMC4356562 DOI: 10.1371/journal.ppat.1004723] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/01/2015] [Indexed: 11/18/2022] Open
Abstract
During vaccinia virus morphogenesis, intracellular mature virus (IMV) particles are wrapped by a double lipid bilayer to form triple enveloped virions called intracellular enveloped virus (IEV). IEV are then transported to the cell surface where the outer IEV membrane fuses with the cell membrane to expose a double enveloped virion outside the cell. The F12, E2 and A36 proteins are involved in transport of IEVs to the cell surface. Deletion of the F12L or E2L genes causes a severe inhibition of IEV transport and a tiny plaque size. Deletion of the A36R gene leads to a smaller reduction in plaque size and less severe inhibition of IEV egress. The A36 protein is present in the outer membrane of IEVs, and over-expressed fragments of this protein interact with kinesin light chain (KLC). However, no interaction of F12 or E2 with the kinesin complex has been reported hitherto. Here the F12/E2 complex is shown to associate with kinesin-1 through an interaction of E2 with the C-terminal tail of KLC isoform 2, which varies considerably between different KLC isoforms. siRNA-mediated knockdown of KLC isoform 1 increased IEV transport to the cell surface and virus plaque size, suggesting interaction with KLC isoform 1 is somehow inhibitory of IEV transport. In contrast, knockdown of KLC isoform 2 did not affect IEV egress or plaque formation, indicating redundancy in virion egress pathways. Lastly, the enhancement of plaque size resulting from loss of KLC isoform 1 was abrogated by removal of KLC isoforms 1 and 2 simultaneously. These observations suggest redundancy in the mechanisms used for IEV egress, with involvement of KLC isoforms 1 and 2, and provide evidence of interaction of F12/E2 complex with the kinesin-1 complex. Viruses often hijack the cellular transport systems to facilitate their movement within and between cells. Vaccinia virus (VACV), the smallpox vaccine, is very adept at this and exploits cellular transport machinery at several stages during its life cycle. For instance, during transport of new virus particles to the cell surface VACV interacts with a protein motor complex called kinesin-1 that moves cargo on microtubules. However, details of the cellular and viral components needed and the molecular mechanisms involved remain poorly understood. Hitherto, only the VACV protein A36 has been shown to interact with kinesin-1, however viruses lacking A36 still reach the cell surface, albeit at reduced efficiency, indicating other factors are involved. Here we describe an interaction between kinesin-1 and a complex of VACV proteins F12 and E2, which are both needed for virus transport. The F12/E2 complex associates with a subset of kinesin-1 molecules (kinesin light chain isoform 2) with a region thought to be involved in modulation of cargo binding and kinesin-1 motor activity. Further study of this interaction will enhance understanding of the VACV life cycle and of the roles of different kinesin-1 subtypes in cellular processes and the mechanisms that regulate them.
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Affiliation(s)
| | - William N. D. Gao
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Helen Ewles
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Gareth W. Morgan
- Department of Virology, Imperial College London, St. Mary’s Campus, London, United Kingdom
| | - Geoffrey L. Smith
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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32
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Sluchanko NN, Uversky VN. Hidden disorder propensity of the N-terminal segment of universal adapter protein 14-3-3 is manifested in its monomeric form: Novel insights into protein dimerization and multifunctionality. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:492-504. [PMID: 25747569 DOI: 10.1016/j.bbapap.2015.02.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 02/17/2015] [Accepted: 02/24/2015] [Indexed: 11/30/2022]
Abstract
The multiplicity of functions of 14-3-3 proteins, integrated into many cellular interactions and signaling networks, is primarily based upon their dimeric α-helical structure that is capable of binding phosphorylated protein partners as well as displaying a "moonlighting" chaperone-like activity. The structure and functions of 14-3-3 proteins are regulated in different ways, including Ser58 phosphorylation in the interface, which shifts equilibrium towards the formation of protein monomers whose role is poorly understood. While modification of Ser58 induced only partial dissociation, the engineered triple mutation of human 14-3-3ζ located in the first α-helix deeply monomerized the protein, allowing for a structural analysis of the monomeric form. Dimer-incapable 14-3-3 proteins retained binding capacity and specificity towards some phosphopartners, and also demonstrated increased chaperone-like activity on various substrates. Here, we found a substantial propensity of the N-terminal segment (~40 residues) of 14-3-3 proteins to intrinsic disorder, showing remarkable conservation across different isoforms and organisms. We hypothesized that this intrinsic disorder propensity, hidden in the α-helical 14-3-3 dimer, can be manifested upon its dissociation and interrogated novel monomeric 14-3-3ζ carrying both monomerizing and S58E mutations (14-3-3ζmS58E). CD spectroscopy showed that, at physiological temperatures, this protein has ~10-15% reduced helicity relative to the wild type protein, corresponding to roughly 40 residues. Along with the known flexibility of C-terminus, SAXS-based modeling of the 14-3-3ζmS58E structure strongly suggested pliability of its N-terminus. The unraveled disorder propensity of the N-terminal tails of 14-3-3 proteins provides new clues for better understanding of the molecular mechanisms of dimerization and multifunctionality of these universal adapter proteins.
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Affiliation(s)
- Nikolai N Sluchanko
- A. N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky prospect 33, Moscow 119071, Russian Federation.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation; Biology Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russian Federation.
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33
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Madeira F, Tinti M, Murugesan G, Berrett E, Stafford M, Toth R, Cole C, MacKintosh C, Barton GJ. 14-3-3-Pred: improved methods to predict 14-3-3-binding phosphopeptides. Bioinformatics 2015; 31:2276-83. [PMID: 25735772 PMCID: PMC4495292 DOI: 10.1093/bioinformatics/btv133] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/25/2015] [Indexed: 01/19/2023] Open
Abstract
MOTIVATION The 14-3-3 family of phosphoprotein-binding proteins regulates many cellular processes by docking onto pairs of phosphorylated Ser and Thr residues in a constellation of intracellular targets. Therefore, there is a pressing need to develop new prediction methods that use an updated set of 14-3-3-binding motifs for the identification of new 14-3-3 targets and to prioritize the downstream analysis of >2000 potential interactors identified in high-throughput experiments. RESULTS Here, a comprehensive set of 14-3-3-binding targets from the literature was used to develop 14-3-3-binding phosphosite predictors. Position-specific scoring matrix, support vector machines (SVM) and artificial neural network (ANN) classification methods were trained to discriminate experimentally determined 14-3-3-binding motifs from non-binding phosphopeptides. ANN, position-specific scoring matrix and SVM methods showed best performance for a motif window spanning from -6 to +4 around the binding phosphosite, achieving Matthews correlation coefficient of up to 0.60. Blind prediction showed that all three methods outperform two popular 14-3-3-binding site predictors, Scansite and ELM. The new methods were used for prediction of 14-3-3-binding phosphosites in the human proteome. Experimental analysis of high-scoring predictions in the FAM122A and FAM122B proteins confirms the predictions and suggests the new 14-3-3-predictors will be generally useful. AVAILABILITY AND IMPLEMENTATION A standalone prediction web server is available at http://www.compbio.dundee.ac.uk/1433pred. Human candidate 14-3-3-binding phosphosites were integrated in ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome database.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Geoffrey J Barton
- Division of Computational Biology, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
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34
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Li Z, Park HR, Shi Z, Li Z, Pham CD, Du Y, Khuri FR, Zhang Y, Han Q, Fu H. Pro-oncogenic function of HIP-55/Drebrin-like (DBNL) through Ser269/Thr291-phospho-sensor motifs. Oncotarget 2015; 5:3197-209. [PMID: 24912570 PMCID: PMC4102803 DOI: 10.18632/oncotarget.1900] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
HIP-55 (HPK1-interacting protein of 55 kDa, also named DBNL, SH3P7, and mAbp1) is a multidomain adaptor protein that is critical for organ development and the immune response. Here, we report the coupling of HIP-55 to cell growth control through its 14-3-3-binding phospho-Ser/Thr-sensor sites. Using affinity chromatography, we found HIP-55 formed a complex with 14-3-3 proteins, revealing a new node in phospho-Ser/Thr-mediated signaling networks. In addition, we demonstrated that HIP-55 is required for proper cell growth control. Enforced HIP-55 expression promoted proliferation, colony formation, migration, and invasion of lung cancer cells while silencing of HIP-55 reversed these effects. Importantly, HIP-55 was found to be upregulated in lung cancer cell lines and in tumor tissues of lung cancer patients. Upregulated HIP-55 was required to promote the growth of tumors in a xenograft animal model. However, tumors with S269A/T291A-mutated HIP-55, which ablates 14-3-3 binding, exhibited significantly reduced sizes, supporting a vital role of the HIP-55/14-3-3 protein interaction node in transmitting oncogenic signals. Mechanistically, HIP-55-mediated tumorigenesis activity appears to be in part mediated by antagonizing the tumor suppressor function of HPK1. Thus, the HIP-55–mediated oncogenic pathway, through S269/T291, may be exploited for the development of new therapeutic strategies.
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Affiliation(s)
- Zijian Li
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA, 30322, USA
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35
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Gao J, van Kleeff PJM, Oecking C, Li KW, Erban A, Kopka J, Hincha DK, de Boer AH. Light modulated activity of root alkaline/neutral invertase involves the interaction with 14-3-3 proteins. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:785-96. [PMID: 25256212 DOI: 10.1111/tpj.12677] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 09/04/2014] [Accepted: 09/10/2014] [Indexed: 05/17/2023]
Abstract
Alkaline/neutral invertases (A/N-Invs) are now recognized as essential proteins in plant life. They catalyze the irreversible breakdown of sucrose into glucose and fructose and thus supply the cells with energy as well as signaling molecules. In this study we report on a mechanism that affects the activity of the cytosolic invertase AtCINV1 (At-A/N-InvG or AT1G35580). We demonstrate that Ser547 at the extreme C-terminus of the AtCINV1 protein is a substrate of calcium-dependent kinases (CPK3 and 21) and that phosphorylation creates a high-affinity binding site for 14-3-3 proteins. The invertase as such has basal activity, but we provide evidence that interaction with 14-3-3 proteins enhances its activity. The analysis of three quadruple 14-3-3 mutants generated from six T-DNA insertion mutants of the non-epsilon family shows both specificity as well as redundancy for this function of 14-3-3 proteins. The strong reduction in hexose levels in the roots of one 14-3-3 quadruple mutant plant is in line with the activating function of 14-3-3 proteins. The physiological relevance of this mechanism that affects A/N-invertase activity is underscored by the light-induced activation and is another example of the central role of 14-3-3 proteins in mediating dark/light signaling. The nature of the light-induced signal that travels from the shoot to root and the question whether this signal is transmitted via cytosolic Ca(++) changes that activate calcium-dependent kinases, await further study.
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Affiliation(s)
- Jing Gao
- Department of Structural Biology, Faculty of Earth and Life Sciences, Vrije Universiteit, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
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36
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Blasius M, Wagner SA, Choudhary C, Bartek J, Jackson SP. A quantitative 14-3-3 interaction screen connects the nuclear exosome targeting complex to the DNA damage response. Genes Dev 2014; 28:1977-82. [PMID: 25189701 PMCID: PMC4173157 DOI: 10.1101/gad.246272.114] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
RNA metabolism is altered following DNA damage, but the underlying mechanisms are not well understood. Through a 14-3-3 interaction screen for DNA damage-induced protein interactions in human cells, we identified protein complexes connected to RNA biology. These include the nuclear exosome targeting (NEXT) complex that regulates turnover of noncoding RNAs termed promoter upstream transcripts (PROMPTs). We show that the NEXT subunit RBM7 is phosphorylated upon DNA damage by the MAPKAPK2 kinase and establish that this mediates 14-3-3 binding and decreases PROMPT binding. These findings and our observation that cells lacking RBM7 display DNA damage hypersensitivity link PROMPT turnover to the DNA damage response.
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Affiliation(s)
- Melanie Blasius
- The Gurdon Institute, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, United Kingdom; Genome Integrity Unit, Danish Cancer Society Research Centre, 2100 Copenhagen, Denmark
| | - Sebastian A Wagner
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Chunaram Choudhary
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jiri Bartek
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Institute of Molecular and Translational Medicine, Palacky University, 77900 Olomouc, Czech Republic
| | - Stephen P Jackson
- The Gurdon Institute, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, United Kingdom; The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
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Öhman T, Söderholm S, Hintsanen P, Välimäki E, Lietzén N, MacKintosh C, Aittokallio T, Matikainen S, Nyman TA. Phosphoproteomics combined with quantitative 14-3-3-affinity capture identifies SIRT1 and RAI as novel regulators of cytosolic double-stranded RNA recognition pathway. Mol Cell Proteomics 2014; 13:2604-17. [PMID: 24997996 DOI: 10.1074/mcp.m114.038968] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Viral double-stranded RNA (dsRNA) is the most important viral structure recognized by cytosolic pattern-recognition receptors of the innate immune system, and its recognition results in the activation of signaling cascades that stimulate the production of antiviral cytokines and apoptosis of infected cells. 14-3-3 proteins are ubiquitously expressed regulatory molecules that participate in a variety of cellular processes, and 14-3-3 protein-mediated signaling pathways are activated by cytoplasmic dsRNA in human keratinocytes. However, the functional role of 14-3-3 protein-mediated interactions during viral dsRNA stimulation has remained uncharacterized. Here, we used functional proteomics to identify proteins whose phosphorylation and interaction with 14-3-3 is modulated by dsRNA and to characterize the signaling pathways activated during cytosolic dsRNA-induced innate immune response in human HaCaT keratinocytes. Phosphoproteome analysis showed that several MAPK- and immune-response-related signaling pathways were activated after dsRNA stimulation. Interactome analysis identified RelA-associated inhibitor, high-mobility group proteins, and several proteins associated with host responses to viral infection as novel 14-3-3 target proteins. Functional studies showed that RelA-associated inhibitor regulated dsRNA-induced apoptosis and TNF production. Integrated network analyses of proteomic data revealed that sirtuin1 was a central molecule regulated by 14-3-3s during dsRNA stimulation. Further experiments showed that sirtuin 1 negatively regulated dsRNA-induced NFκB transcriptional activity, suppressed expression of antiviral cytokines, and protected cells from apoptosis in dsRNA-stimulated and encephalomyocarditis-virus-infected keratinocytes. In conclusion, our data highlight the importance of 14-3-3 proteins in antiviral responses and identify RelA-associated inhibitor and sirtuin 1 as novel regulators of antiviral innate immune responses.
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Affiliation(s)
- Tiina Öhman
- From the ‡Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland
| | - Sandra Söderholm
- From the ‡Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland; §Finnish Institute of Occupational Health, FI-00250 Helsinki, Finland
| | - Petteri Hintsanen
- ¶Institute for Molecular Medicine Finland (FIMM), FI-00014 University of Helsinki, Helsinki, Finland
| | - Elina Välimäki
- From the ‡Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland; §Finnish Institute of Occupational Health, FI-00250 Helsinki, Finland
| | - Niina Lietzén
- From the ‡Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland
| | - Carol MacKintosh
- **University of Dundee, Dundee, Scotland DD1 5EH, United Kingdom
| | - Tero Aittokallio
- ¶Institute for Molecular Medicine Finland (FIMM), FI-00014 University of Helsinki, Helsinki, Finland
| | - Sampsa Matikainen
- §Finnish Institute of Occupational Health, FI-00250 Helsinki, Finland
| | - Tuula A Nyman
- From the ‡Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland;
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Yoshizaki H, Okuda S. Elucidation of the evolutionary expansion of phosphorylation signaling networks using comparative phosphomotif analysis. BMC Genomics 2014; 15:546. [PMID: 24981518 PMCID: PMC4117960 DOI: 10.1186/1471-2164-15-546] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 06/26/2014] [Indexed: 11/10/2022] Open
Abstract
Background Protein phosphorylation is catalyzed by kinases and is involved in the regulation of a wide range of processes. The phosphosites in protein sequence motifs determine the types of kinases involved. The development of phosphoproteomics has allowed the identification of huge numbers of phosphosites, some of which are not involved in physiological functions. Results We developed a method for extracting phosphosites with important roles in cellular functions and determined 178 phosphomotifs based on the analysis of 34,366 phosphosites. We compared the conservation of serine/threonine/tyrosine residues observed in humans and seven other species. Consequently, we identified 16 phosphomotifs, where the level of conservation increased among species. The highly conserved phosphomotifs in humans and the worm were kinase regulatory sites. The motifs present in the fly were novel phosphomotifs, including zinc finger motifs involved in the regulation of gene expression. Subsequently, we found that this zinc finger motif contributed to subcellular protein localization. The motifs identified in fish allowed us to detect the expansion of phosphorylation signals related to alternative splicing. We also showed that the motifs present in specific species functioned in an additional network that interacted directly with the core signaling network conserved from yeast to humans. Conclusions Our method may facilitate the efficient extraction of novel phosphomotifs with physiological functions, thereby contributing greatly to the analysis of complex phosphorylation signaling cascades. Our study suggests that the phosphorylation networks acquired during evolution have added signaling network modules to the core signaling networks. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-546) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hisayoshi Yoshizaki
- Department of Pathology I, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Ishikawa 920-0293, Japan.
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39
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Kleppe R, Rosati S, Jorge-Finnigan A, Alvira S, Ghorbani S, Haavik J, Valpuesta JM, Heck AJR, Martinez A. Phosphorylation dependence and stoichiometry of the complex formed by tyrosine hydroxylase and 14-3-3γ. Mol Cell Proteomics 2014; 13:2017-30. [PMID: 24947669 PMCID: PMC4125734 DOI: 10.1074/mcp.m113.035709] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phosphorylated tyrosine hydroxylase (TH) can form complexes with 14-3-3 proteins, resulting in enzyme activation and stabilization. Although TH was among the first binding partners identified for these ubiquitous regulatory proteins, the binding stoichiometry and the activation mechanism remain unknown. To address this, we performed native mass spectrometry analyses of human TH (nonphosphorylated or phosphorylated on Ser19 (TH-pS19), Ser40 (TH-pS40), or Ser19 and Ser40 (TH-pS19pS40)) alone and together with 14-3-3γ. Tetrameric TH-pS19 (224 kDa) bound 14-3-3γ (58.3 kDa) with high affinity (Kd = 3.2 nM), generating complexes containing either one (282.4 kDa) or two (340.8 kDa) dimers of 14-3-3. Electron microscopy also revealed one major population of an asymmetric complex, consistent with one TH tetramer and one 14-3-3 dimer, and a minor population of a symmetric complex of one TH tetramer with two 14-3-3 dimers. Lower phosphorylation stoichiometries (0.15–0.54 phosphate/monomer) produced moderate changes in binding kinetics, but native MS detected much less of the symmetric TH:14-3-3γ complex. Interestingly, dephosphorylation of [32P]-TH-pS19 was mono-exponential for low phosphorylation stoichiometries (0.18–0.52), and addition of phosphatase accelerated the dissociation of the TH-pS19:14-3-3γ complex 3- to 4-fold. All together this is consistent with a model in which the pS19 residues in the TH tetramer contribute differently in the association to 14-3-3γ. Complex formation between TH-pS40 and 14-3-3γ was not detected via native MS, and surface plasmon resonance showed that the interaction was very weak. Furthermore, TH-pS19pS40 behaved similarly to TH-pS19 in terms of binding stoichiometry and affinity (Kd = 2.1 nM). However, we found that 14-3-3γ inhibited the phosphorylation rate of TH-pS19 by PKA (3.5-fold) on Ser40. We therefore conclude that Ser40 does not significantly contribute to the binding of 14-3-3γ, and rather has reduced accessibility in the TH:14-3-3γ complex. This adds to our understanding of the fine-tuned physiological regulation of TH, including hierarchical phosphorylation at multiple sites.
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Affiliation(s)
- Rune Kleppe
- From the ‡Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; §K. G. Jebsen Centre for Research on Neuropsychiatric disorders, Jonas Lies vei 91, 5009 Bergen, Norway; ¶Division for Psychiatry, Haukeland University Hospital, Sandviksleitet 1, 5036 Bergen, Norway
| | - Sara Rosati
- **Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; ‡‡Netherland Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Ana Jorge-Finnigan
- From the ‡Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Sara Alvira
- §§Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049 Madrid, Spain
| | - Sadaf Ghorbani
- From the ‡Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Jan Haavik
- From the ‡Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; §K. G. Jebsen Centre for Research on Neuropsychiatric disorders, Jonas Lies vei 91, 5009 Bergen, Norway; ¶Division for Psychiatry, Haukeland University Hospital, Sandviksleitet 1, 5036 Bergen, Norway
| | | | - Albert J R Heck
- **Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; ‡‡Netherland Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands;
| | - Aurora Martinez
- From the ‡Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; §K. G. Jebsen Centre for Research on Neuropsychiatric disorders, Jonas Lies vei 91, 5009 Bergen, Norway;
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Mori M, Vignaroli G, Cau Y, Dinić J, Hill R, Rossi M, Colecchia D, Pešić M, Link W, Chiariello M, Ottmann C, Botta M. Discovery of 14-3-3 Protein-Protein Interaction Inhibitors that Sensitize Multidrug-Resistant Cancer Cells to Doxorubicin and the Akt Inhibitor GSK690693. ChemMedChem 2014; 9:973-83. [DOI: 10.1002/cmdc.201400044] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Indexed: 11/06/2022]
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Phosphosite mapping of HIP-55 protein in mammalian cells. Int J Mol Sci 2014; 15:4903-14. [PMID: 24651461 PMCID: PMC3975430 DOI: 10.3390/ijms15034903] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 02/20/2014] [Accepted: 03/07/2014] [Indexed: 11/16/2022] Open
Abstract
In the present study, hematopoietic progenitor kinase 1 (HPK1)-interacting protein of 55 kDa (HIP-55) protein was over-expressed in HEK293 cells, which was genetically attached with 6x His tag. The protein was purified by nickel-charged resin and was then subjected to tryptic digestion. The phosphorylated peptides within the HIP-55 protein were enriched by TiO2 affinity chromatography, followed by mass spectrometry analysis. Fourteen phosphorylation sites along the primary structure of HIP-55 protein were identified, most of which had not been previously reported. Our results indicate that bio-mass spectrometry coupled with manual interpretation can be used to successfully identify the phosphorylation modification in HIP-55 protein in HEK293 cells.
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Richens JL, Morgan K, O'Shea P. Reverse engineering of Alzheimer's disease based on biomarker pathways analysis. Neurobiol Aging 2014; 35:2029-38. [PMID: 24684789 DOI: 10.1016/j.neurobiolaging.2014.02.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 02/18/2014] [Accepted: 02/26/2014] [Indexed: 12/14/2022]
Abstract
Alzheimer's disease (AD) poses an increasingly profound problem to society, yet progress toward a genuine understanding of the disease remains worryingly slow. Perhaps, the most outstanding problem with the biology of AD is the question of its mechanistic origins, that is, it remains unclear wherein the molecular failures occur that underlie the disease. We demonstrate how molecular biomarkers could help define the nature of AD in terms of the early biochemical events that correlate with disease progression. We use a novel panel of biomolecules that appears in cerebrospinal fluid of AD patients. As changes in the relative abundance of these molecular markers are associated with progression to AD from mild cognitive impairment, we make the assumption that by tracking their origins we can identify the biochemical conditions that predispose their presence and consequently cause the onset of AD. We couple these protein markers with an analysis of a series of genetic factors and together this hypothesis essentially allows us to redefine AD in terms of the molecular pathways that underlie the disease.
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Affiliation(s)
- Joanna L Richens
- Cell Biophysics Group, School of Life Sciences, Faculty of Medicine & Health Sciences, University Park, University of Nottingham, Nottingham, UK
| | - Kevin Morgan
- Humans Genetics Research Group, School of Life Sciences, Faculty of Medicine & Health Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Paul O'Shea
- Cell Biophysics Group, School of Life Sciences, Faculty of Medicine & Health Sciences, University Park, University of Nottingham, Nottingham, UK.
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Tinti M, Madeira F, Murugesan G, Hoxhaj G, Toth R, Mackintosh C. ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bat085. [PMID: 24501395 PMCID: PMC3914767 DOI: 10.1093/database/bat085] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The dimeric 14-3-3 proteins dock onto pairs of phosphorylated Ser and Thr residues on hundreds of proteins, and thereby regulate many events in mammalian cells. To facilitate global analyses of these interactions, we developed a web resource named ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome, which integrates multiple data sets on 14-3-3-binding phosphoproteins. ANIA also pinpoints candidate 14-3-3-binding phosphosites using predictor algorithms, assisted by our recent discovery that the human 14-3-3-interactome is highly enriched in 2R-ohnologues. 2R-ohnologues are proteins in families of two to four, generated by two rounds of whole genome duplication at the origin of the vertebrate animals. ANIA identifies candidate ‘lynchpins’, which are 14-3-3-binding phosphosites that are conserved across members of a given 2R-ohnologue protein family. Other features of ANIA include a link to the catalogue of somatic mutations in cancer database to find cancer polymorphisms that map to 14-3-3-binding phosphosites, which would be expected to interfere with 14-3-3 interactions. We used ANIA to map known and candidate 14-3-3-binding enzymes within the 2R-ohnologue complement of the human kinome. Our projections indicate that 14-3-3s dock onto many more human kinases than has been realized. Guided by ANIA, PAK4, 6 and 7 (p21-activated kinases 4, 6 and 7) were experimentally validated as a 2R-ohnologue family of 14-3-3-binding phosphoproteins. PAK4 binding to 14-3-3 is stimulated by phorbol ester, and involves the ‘lynchpin’ site phosphoSer99 and a major contribution from Ser181. In contrast, PAK6 and PAK7 display strong phorbol ester-independent binding to 14-3-3, with Ser113 critical for the interaction with PAK6. These data point to differential 14-3-3 regulation of PAKs in control of cell morphology. Database URL: https://ania-1433.lifesci.dundee.ac.uk/prediction/webserver/index.py
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Affiliation(s)
- Michele Tinti
- MRC Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK and Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
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44
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REEP1 and REEP2 proteins are preferentially expressed in neuronal and neuronal-like exocytotic tissues. Brain Res 2013; 1545:12-22. [PMID: 24355597 DOI: 10.1016/j.brainres.2013.12.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 11/15/2013] [Accepted: 12/07/2013] [Indexed: 12/19/2022]
Abstract
The six members of the Receptor Expression Enhancing Protein (REEP) family were originally identified based on their ability to enhance heterologous expression of olfactory receptors and other difficult to express G protein-coupled receptors. Interestingly, REEP1 mutations have been linked to neurodegenerative disorders of upper and lower motor neurons, hereditary spastic paraplegia (HSP) and distal hereditary motor neuropathy type V (dHMN-V). The closely related REEP2 isoform has not demonstrated any such disease linkage. Previous research has suggested that REEP1 mRNA is ubiquitously expressed in brain, muscle, endocrine, and multiple other organs, inconsistent with the neurodegenerative phenotype observed in HSP and dHMN-V. To more fully examine REEP1 expression, we developed and characterized a new REEP1 monoclonal antibody for both immunoblotting and immunofluorescent microscopic analysis. Unlike previous RT-PCR studies, immunoblotting demonstrated that REEP1 protein was not ubiquitous; its expression was restricted to neuronal tissues (brain, spinal cord) and testes. Gene expression microarray analysis demonstrated REEP1 and REEP2 mRNA expression in superior cervical and stellate sympathetic ganglia tissue. Furthermore, expression of endogenous REEP1 was confirmed in cultured murine sympathetic ganglion neurons by RT-PCR and immunofluorescent staining, with expression occurring between Day 4 and Day 8 of culture. Lastly, we demonstrated that REEP2 protein expression was also restricted to neuronal tissues (brain and spinal cord) and tissues that exhibit neuronal-like exocytosis (testes, pituitary, and adrenal gland). In addition to sensory tissues, expression of the REEP1/REEP2 subfamily appears to be restricted to neuronal and neuronal-like exocytotic tissues, consistent with neuronally restricted symptoms of REEP1 genetic disorders.
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45
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Kleppe R, Ghorbani S, Martinez A, Haavik J. Modelling cellular signal communication mediated by phosphorylation dependent interaction with 14-3-3 proteins. FEBS Lett 2013; 588:92-8. [DOI: 10.1016/j.febslet.2013.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 11/08/2013] [Accepted: 11/12/2013] [Indexed: 11/25/2022]
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Abstract
Hepatocytes, like other epithelia, are situated at the interface between the organism's exterior and the underlying internal milieu and organize the vectorial exchange of macromolecules between these two spaces. To mediate this function, epithelial cells, including hepatocytes, are polarized with distinct luminal domains that are separated by tight junctions from lateral domains engaged in cell-cell adhesion and from basal domains that interact with the underlying extracellular matrix. Despite these universal principles, hepatocytes distinguish themselves from other nonstriated epithelia by their multipolar organization. Each hepatocyte participates in multiple, narrow lumina, the bile canaliculi, and has multiple basal surfaces that face the endothelial lining. Hepatocytes also differ in the mechanism of luminal protein trafficking from other epithelia studied. They lack polarized protein secretion to the luminal domain and target single-spanning and glycosylphosphatidylinositol-anchored bile canalicular membrane proteins via transcytosis from the basolateral domain. We compare this unique hepatic polarity phenotype with that of the more common columnar epithelial organization and review our current knowledge of the signaling mechanisms and the organization of polarized protein trafficking that govern the establishment and maintenance of hepatic polarity. The serine/threonine kinase LKB1, which is activated by the bile acid taurocholate and, in turn, activates adenosine monophosphate kinase-related kinases including AMPK1/2 and Par1 paralogues has emerged as a key determinant of hepatic polarity. We propose that the absence of a hepatocyte basal lamina and differences in cell-cell adhesion signaling that determine the positioning of tight junctions are two crucial determinants for the distinct hepatic and columnar polarity phenotypes.
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Affiliation(s)
- Aleksandr Treyer
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, New York, USA
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47
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Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system. Nat Methods 2013; 10:1246-53. [PMID: 24162925 DOI: 10.1038/nmeth.2703] [Citation(s) in RCA: 244] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 09/25/2013] [Indexed: 12/22/2022]
Abstract
Protein complexes and protein interaction networks are essential mediators of most biological functions. Complexes supporting transient functions such as signal transduction processes are frequently subject to dynamic remodeling. Currently, the majority of studies on the composition of protein complexes are carried out by affinity purification and mass spectrometry (AP-MS) and present a static view of the system. For a better understanding of inherently dynamic biological processes, methods to reliably quantify temporal changes of protein interaction networks are essential. Here we used affinity purification combined with sequential window acquisition of all theoretical spectra (AP-SWATH) mass spectrometry to study the dynamics of the 14-3-3β scaffold protein interactome after stimulation of the insulin-PI3K-AKT pathway. The consistent and reproducible quantification of 1,967 proteins across all stimulation time points provided insights into the 14-3-3β interactome and its dynamic changes following IGF1 stimulation. We therefore establish AP-SWATH as a tool to quantify dynamic changes in protein-complex interaction networks.
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48
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Welburn JPI. The molecular basis for kinesin functional specificity during mitosis. Cytoskeleton (Hoboken) 2013; 70:476-93. [PMID: 24039047 PMCID: PMC4065354 DOI: 10.1002/cm.21135] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 07/24/2013] [Accepted: 08/21/2013] [Indexed: 12/13/2022]
Abstract
Microtubule-based motor proteins play key roles during mitosis to assemble the bipolar spindle, define the cell division axis, and align and segregate the chromosomes. The majority of mitotic motors are members of the kinesin superfamily. Despite sharing a conserved catalytic core, each kinesin has distinct functions and localization, and is uniquely regulated in time and space. These distinct behaviors and functional specificity are generated by variations in the enzymatic domain as well as the non-conserved regions outside of the kinesin motor domain and the stalk. These flanking regions can directly modulate the properties of the kinesin motor through dimerization or self-interactions, and can associate with extrinsic factors, such as microtubule or DNA binding proteins, to provide additional functional properties. This review discusses the recently identified molecular mechanisms that explain how the control and functional specification of mitotic kinesins is achieved. © 2013 Wiley Periodicals, Inc.
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Affiliation(s)
- Julie P I Welburn
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, Scotland, United Kingdom
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49
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Björk S, Hurt CM, Ho VK, Angelotti T. REEPs are membrane shaping adapter proteins that modulate specific g protein-coupled receptor trafficking by affecting ER cargo capacity. PLoS One 2013; 8:e76366. [PMID: 24098485 PMCID: PMC3788743 DOI: 10.1371/journal.pone.0076366] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 08/29/2013] [Indexed: 12/21/2022] Open
Abstract
Receptor expression enhancing proteins (REEPs) were identified by their ability to enhance cell surface expression of a subset of G protein-coupled receptors (GPCRs), specifically GPCRs that have proven difficult to express in heterologous cell systems. Further analysis revealed that they belong to the Yip (Ypt-interacting protein) family and that some REEP subtypes affect ER structure. Yip family comparisons have established other potential roles for REEPs, including regulation of ER-Golgi transport and processing/neuronal localization of cargo proteins. However, these other potential REEP functions and the mechanism by which they selectively enhance GPCR cell surface expression have not been clarified. By utilizing several REEP family members (REEP1, REEP2, and REEP6) and model GPCRs (α2A and α2C adrenergic receptors), we examined REEP regulation of GPCR plasma membrane expression, intracellular processing, and trafficking. Using a combination of immunolocalization and biochemical methods, we demonstrated that this REEP subset is localized primarily to ER, but not plasma membranes. Single cell analysis demonstrated that these REEPs do not specifically enhance surface expression of all GPCRs, but affect ER cargo capacity of specific GPCRs and thus their surface expression. REEP co-expression with α2 adrenergic receptors (ARs) revealed that this REEP subset interacts with and alter glycosidic processing of α2C, but not α2A ARs, demonstrating selective interaction with cargo proteins. Specifically, these REEPs enhanced expression of and interacted with minimally/non-glycosylated forms of α2C ARs. Most importantly, expression of a mutant REEP1 allele (hereditary spastic paraplegia SPG31) lacking the carboxyl terminus led to loss of this interaction. Thus specific REEP isoforms have additional intracellular functions besides altering ER structure, such as enhancing ER cargo capacity, regulating ER-Golgi processing, and interacting with select cargo proteins. Therefore, some REEPs can be further described as ER membrane shaping adapter proteins.
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Affiliation(s)
- Susann Björk
- Department of Pharmacology, Drug Development and Therapeutics, Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Anesthesia/CCM, Stanford University Medical School, Stanford, California, United States of America
| | - Carl M. Hurt
- Department of Anesthesia/CCM, Stanford University Medical School, Stanford, California, United States of America
| | - Vincent K. Ho
- Department of Anesthesia/CCM, Stanford University Medical School, Stanford, California, United States of America
| | - Timothy Angelotti
- Department of Anesthesia/CCM, Stanford University Medical School, Stanford, California, United States of America
- * E-mail:
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50
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Tinti M, Johnson C, Toth R, Ferrier DEK, Mackintosh C. Evolution of signal multiplexing by 14-3-3-binding 2R-ohnologue protein families in the vertebrates. Open Biol 2013; 2:120103. [PMID: 22870394 PMCID: PMC3411107 DOI: 10.1098/rsob.120103] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 06/29/2012] [Indexed: 01/09/2023] Open
Abstract
14-3-3 proteins regulate cellular responses to stimuli by docking onto pairs of phosphorylated residues on target proteins. The present study shows that the human 14-3-3-binding phosphoproteome is highly enriched in 2R-ohnologues, which are proteins in families of two to four members that were generated by two rounds of whole genome duplication at the origin of the vertebrates. We identify 2R-ohnologue families whose members share a ‘lynchpin’, defined as a 14-3-3-binding phosphosite that is conserved across members of a given family, and aligns with a Ser/Thr residue in pro-orthologues from the invertebrate chordates. For example, the human receptor expression enhancing protein (REEP) 1–4 family has the commonest type of lynchpin motif in current datasets, with a phosphorylatable serine in the –2 position relative to the 14-3-3-binding phosphosite. In contrast, the second 14-3-3-binding sites of REEPs 1–4 differ and are phosphorylated by different kinases, and hence the REEPs display different affinities for 14-3-3 dimers. We suggest a conceptual model for intracellular regulation involving protein families whose evolution into signal multiplexing systems was facilitated by 14-3-3 dimer binding to lynchpins, which gave freedom for other regulatory sites to evolve. While increased signalling complexity was needed for vertebrate life, these systems also generate vulnerability to genetic disorders.
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Affiliation(s)
- Michele Tinti
- MRC Protein Phosphorylation Unit, College of Life Sciences, James Black Centre, University of Dundee, Dow Street, Dundee DD1 5EH , UK
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