1
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Trahan C, Oeffinger M. Single-Step Affinity Purification (ssAP) and Mass Spectrometry of Macromolecular Complexes in the Yeast S. cerevisiae. Methods Mol Biol 2022; 2477:195-223. [PMID: 35524119 DOI: 10.1007/978-1-0716-2257-5_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cellular functions are mostly defined by the dynamic interactions of proteins within macromolecular networks. Deciphering the composition of macromolecular complexes and their dynamic rearrangements is the key to get a comprehensive picture of cellular behavior and to understand biological systems. In the past two decades, affinity purification coupled to mass spectrometry has become a powerful tool to comprehensively study interaction networks and their assemblies. To overcome initial limitations of the approach, in particular, the effect of protein and RNA degradation, loss of transient interactors, and poor overall yield of intact complexes from cell lysates, various modifications to affinity purification protocols have been devised over the years. In this chapter, we describe a rapid single-step affinity purification method for the efficient isolation of dynamic macromolecular complexes. The technique employs cell lysis by cryo-milling, which ensures nondegraded starting material in the submicron range, and magnetic beads, which allow for dense antibody-conjugation and thus rapid complex isolation, while avoiding loss of transient interactions. The method is epitope tag-independent, and overcomes many of the previous limitations to produce large interactomes with almost no contamination. The protocol as described here has been optimized for the yeast S. cerevisiae.
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Affiliation(s)
- Christian Trahan
- RNP Biochemistry Laboratory, Center for Genetic and Neurological Diseases, Institut de recherches cliniques de Montréal, Montréal, QC, Canada
| | - Marlene Oeffinger
- RNP Biochemistry Laboratory, Center for Genetic and Neurological Diseases, Institut de recherches cliniques de Montréal, Montréal, QC, Canada.
- Département de biochimie et médicine moléculaire, Faculté de médecine, Université de Montréal, Montréal, QC, Canada.
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC, Canada.
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2
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Scepanovic G, Hunter MV, Kafri R, Fernandez-Gonzalez R. p38-mediated cell growth and survival drive rapid embryonic wound repair. Cell Rep 2021; 37:109874. [PMID: 34686334 DOI: 10.1016/j.celrep.2021.109874] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 08/02/2021] [Accepted: 09/30/2021] [Indexed: 12/18/2022] Open
Abstract
Embryos repair wounds rapidly, with no inflammation or scarring, in a process that involves polarization of the actomyosin cytoskeleton. Actomyosin polarization results in the assembly of a contractile cable around the wound that drives wound closure. Here, we demonstrate that a contractile actomyosin cable is not sufficient for rapid wound repair in Drosophila embryos. We show that wounding causes activation of the serine/threonine kinase p38 mitogen-activated protein kinase (MAPK) in the cells adjacent to the wound. p38 activation reduces the levels of wound-induced reactive oxygen species in the cells around the wound, limiting wound size. In addition, p38 promotes an increase in volume in the cells around the wound, thus facilitating the collective cell movements that drive rapid wound healing. Our data indicate that p38 regulates cell volumes through the sodium-potassium-chloride cotransporter NKCC1. Our work reveals cell growth and cell survival as cell behaviors critical for embryonic wound repair.
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Affiliation(s)
- Gordana Scepanovic
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada; Ted Rogers Centre for Heart Research, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Miranda Victoria Hunter
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada; Ted Rogers Centre for Heart Research, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Ran Kafri
- Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Rodrigo Fernandez-Gonzalez
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada; Ted Rogers Centre for Heart Research, University of Toronto, Toronto, ON M5G 1M1, Canada; Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada; Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.
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3
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Sun G, Ding XA, Argaw Y, Guo X, Montell DJ. Akt1 and dCIZ1 promote cell survival from apoptotic caspase activation during regeneration and oncogenic overgrowth. Nat Commun 2020; 11:5726. [PMID: 33184261 PMCID: PMC7664998 DOI: 10.1038/s41467-020-19068-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 09/22/2020] [Indexed: 01/07/2023] Open
Abstract
Apoptosis is an ancient and evolutionarily conserved cell suicide program. During apoptosis, executioner caspase enzyme activation has been considered a point of no return. However, emerging evidence suggests that some cells can survive caspase activation following exposure to apoptosis-inducing stresses, raising questions as to the physiological significance and underlying molecular mechanisms of this unexpected phenomenon. Here, we show that, following severe tissue injury, Drosophila wing disc cells that survive executioner caspase activation contribute to tissue regeneration. Through RNAi screening, we identify akt1 and a previously uncharacterized Drosophila gene CG8108, which is homologous to the human gene CIZ1, as essential for survival from the executioner caspase activation. We also show that cells expressing activated oncogenes experience apoptotic caspase activation, and that Akt1 and dCIZ1 are required for their survival and overgrowth. Thus, survival following executioner caspase activation is a normal tissue repair mechanism usurped to promote oncogene-driven overgrowth.
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Affiliation(s)
- Gongping Sun
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Anatomy and Histoembryology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA, 93106, USA.
| | - Xun Austin Ding
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA, 93106, USA
| | - Yewubdar Argaw
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA, 93106, USA
| | - Xiaoran Guo
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA, 93106, USA
| | - Denise J Montell
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA, 93106, USA.
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4
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Phosphoproteomics Meets Chemical Genetics: Approaches for Global Mapping and Deciphering the Phosphoproteome. Int J Mol Sci 2020; 21:ijms21207637. [PMID: 33076458 PMCID: PMC7588962 DOI: 10.3390/ijms21207637] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022] Open
Abstract
Protein kinases are important enzymes involved in the regulation of various cellular processes. To function properly, each protein kinase phosphorylates only a limited number of proteins among the thousands present in the cell. This provides a rapid and dynamic regulatory mechanism that controls biological functions of the proteins. Despite the importance of protein kinases, most of their substrates remain unknown. Recently, the advances in the fields of protein engineering, chemical genetics, and mass spectrometry have boosted studies on identification of bona fide substrates of protein kinases. Among the various methods in protein kinase specific substrate identification, genetically engineered protein kinases and quantitative phosphoproteomics have become promising tools. Herein, we review the current advances in the field of chemical genetics in analog-sensitive protein kinase mutants and highlight selected strategies for identifying protein kinase substrates and studying the dynamic nature of protein phosphorylation.
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5
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Zhang J, Tracy C, Pasare C, Zeng J, Krämer H. Hypersensitivity of Vps33B mutant flies to non-pathogenic infections is dictated by aberrant activation of p38b MAP kinase. Traffic 2020; 21:578-589. [PMID: 32677257 DOI: 10.1111/tra.12756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 07/10/2020] [Accepted: 07/12/2020] [Indexed: 11/29/2022]
Abstract
Loss of the arthrogryposis-renal dysfunction-cholestasis (ARC) syndrome-linked Vps33B protein results in exaggerated inflammatory responses upon activation of receptors of the innate immune system in both vertebrates and flies. However, little is known about the signaling elements downstream of these receptors that are critical for the hypersensitivity of Vps33B mutants. Here, we show that p38b MAP kinase contributes to the enhanced inflammatory responses in flies lacking Vps33B. Loss of p38b mitogen-activated protein kinase (MAPK) reduces enhanced inflammatory responses and prolongs the survival of infected Vps33B deficient flies. The function of p38 MAPK is not limited to its proinflammatory effects downstream of the PGRP-LC receptor as p38 also modulates endosomal trafficking of PGRP-LC and phagocytosis of bacteria. Expression of constitutively active p38b MAPK, but not dominant negative p38b MAPK enhances accumulation of endocytosed PGRP-LC receptors or phagocytosed bacteria within cells. Moreover, p38 MAPK is required for induction of macropinocytosis, an alternate pathway for the downregulation of immune receptors. Together, our data indicate that p38 MAPK activates multiple pathways that can contribute to the dysregulation of innate immune signaling in ARC syndrome.
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Affiliation(s)
- Jian Zhang
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas, USA.,Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangdong Provincial Key Laboratory for Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Guangzhou, China
| | - Charles Tracy
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Chandrashekhar Pasare
- Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, Ohio, USA
| | - Jinsheng Zeng
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangdong Provincial Key Laboratory for Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Guangzhou, China
| | - Helmut Krämer
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas, USA.,Department of Cell Biology, UT Southwestern Medical Center, Dallas, Texas, USA
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Prikas E, Poljak A, Ittner A. Mapping p38α mitogen-activated protein kinase signaling by proximity-dependent labeling. Protein Sci 2020; 29:1196-1210. [PMID: 32189389 DOI: 10.1002/pro.3854] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 03/03/2020] [Accepted: 03/16/2020] [Indexed: 12/15/2022]
Abstract
Mitogen-activated protein (MAP) kinase signaling is central to multiple cellular responses and processes. MAP kinase p38α is the best characterized member of the p38 MAP kinase family. Upstream factors and downstream targets of p38α have been identified in the past by conventional methods such as coimmunoprecipitation. However, a complete picture of its interaction partners and substrates in cells is lacking. Here, we employ a proximity-dependent labeling approach using biotinylation tagging to map the interactome of p38α in cultured 293T cells. Fusing the advanced biotin ligase BioID2 to the N-terminus of p38α, we used mass spectrometry to identify 37 biotin-labeled proteins that putatively interact with p38α. Gene ontology analysis confirms known upstream and downstream factors in the p38 MAP kinase cascade (e.g., MKK3, MAPKAPK2, TAB2, and c-jun). We furthermore identify a cluster of zinc finger (ZnF) domain-containing proteins that is significantly enriched among proximity-labeled interactors and is involved in gene transcription and DNA damage response. Fluorescence imaging and coimmunoprecipitation with overexpressed p38α in cells supports an interaction of p38α with ZnF protein XPA, a key factor in the DNA damage response, that is promoted by UV irradiation. These results define an extensive network of interactions of p38α in cells and new direct molecular targets of MAP kinase p38α in gene regulation and the DNA damage response.
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Affiliation(s)
- Emmanuel Prikas
- Dementia Research Centre, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Anne Poljak
- Mark Wainwright Analytical Centre, University of New South Wales, Sydney, Australia
| | - Arne Ittner
- Dementia Research Centre, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
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7
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Patel PH, Pénalva C, Kardorff M, Roca M, Pavlović B, Thiel A, Teleman AA, Edgar BA. Damage sensing by a Nox-Ask1-MKK3-p38 signaling pathway mediates regeneration in the adult Drosophila midgut. Nat Commun 2019; 10:4365. [PMID: 31554796 PMCID: PMC6761285 DOI: 10.1038/s41467-019-12336-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 08/28/2019] [Indexed: 12/17/2022] Open
Abstract
Epithelia are exposed to diverse types of stress and damage from pathogens and the environment, and respond by regenerating. Yet, the proximal mechanisms that sense epithelial damage remain poorly understood. Here we report that p38 signaling is activated in adult Drosophila midgut enterocytes in response to diverse stresses including pathogenic bacterial infection and chemical and mechanical insult. Two upstream kinases, Ask1 and Licorne (MKK3), are required for p38 activation following infection, oxidative stress, detergent exposure and wounding. Ask1-p38 signaling in enterocytes is required upon infection to promote full intestinal stem cell (ISC) activation and regeneration, partly through Upd3/Jak-Stat signaling. Furthermore, reactive oxygen species (ROS) produced by the NADPH oxidase Nox in enterocytes, are required for p38 activation in enterocytes following infection or wounding, and for ISC activation upon infection or detergent exposure. We propose that Nox-ROS-Ask1-MKK3-p38 signaling in enterocytes integrates multiple different stresses to induce regeneration.
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Affiliation(s)
- Parthive H Patel
- Elizabeth Blackwell Institute for Health Research, University of Bristol, Bristol, BS8 1UH, UK.
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK.
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112, USA.
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
- Center for Molecular Biology, University of Heidelberg (ZMBH), 69120, Heidelberg, Germany.
| | - Clothilde Pénalva
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112, USA
| | - Michael Kardorff
- Center for Molecular Biology, University of Heidelberg (ZMBH), 69120, Heidelberg, Germany
| | - Marianne Roca
- Center for Molecular Biology, University of Heidelberg (ZMBH), 69120, Heidelberg, Germany
| | - Bojana Pavlović
- Center for Molecular Biology, University of Heidelberg (ZMBH), 69120, Heidelberg, Germany
| | - Anja Thiel
- Center for Molecular Biology, University of Heidelberg (ZMBH), 69120, Heidelberg, Germany
| | | | - Bruce A Edgar
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112, USA.
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8
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MKK3 modulates JNK-dependent cell migration and invasion. Cell Death Dis 2019; 10:149. [PMID: 30770795 PMCID: PMC6377636 DOI: 10.1038/s41419-019-1350-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 12/19/2018] [Accepted: 01/07/2019] [Indexed: 01/02/2023]
Abstract
The c-Jun N-terminal kinase (JNK) pathway plays essential roles in regulating a variety of physiological processes including cell migration and invasion. To identify critical factors that regulate JNK-dependent cell migration, we carried out a genetic screen in Drosophila based on the loss-of-cell polarity-triggered cell migration in the wing epithelia, and identified MKK3 licorne (lic) as an essential regulator of JNK-mediated cell migration and invasion. We found that loss of lic suppressed ptc > scrib-IR or ptc > Egr triggered cell migration in the wing epithelia, and Rasv12/lgl−/− induced tumor invasion in the eye discs. In addition, ectopic expression of Lic is sufficient to induce JNK-mediated but p38-independent cell migration, and cooperate with oncogenic Ras to promote tumor invasion. Consistently, Lic is able to activate JNK signaling by phosphorylating JNK, which up-regulates the matrix metalloproteinase MMP1 and integrin, characteristics of epithelial–mesenchymal transition (EMT). Moreover, lic is required for physiological JNK-mediate cell migration in thorax development. Finally, expression of human MKK3 in Drosophila is able to initiate JNK-mediated cell migration, cooperates with oncogenic Ras to trigger tumor invasion, and rescue loss-of-lic induced thorax closure defect. As previous studies suggest that MKK3 specifically phosphorylates and activates p38MAPK, our data provide the first in vivo evidence that MKK3 regulates JNK-dependent cell migration and invasion, a process evolutionarily conserved from flies to human.
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9
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Regulated Intron Removal Integrates Motivational State and Experience. Cell 2017; 169:836-848.e15. [PMID: 28525754 DOI: 10.1016/j.cell.2017.05.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 02/23/2017] [Accepted: 05/01/2017] [Indexed: 11/23/2022]
Abstract
Myriad experiences produce transient memory, yet, contingent on the internal state of the organism and the saliency of the experience, only some memories persist over time. How experience and internal state influence the duration of memory at the molecular level remains unknown. A self-assembled aggregated state of Drosophila Orb2A protein is required specifically for long-lasting memory. We report that in the adult fly brain the mRNA encoding Orb2A protein exists in an unspliced non-protein-coding form. The convergence of experience and internal drive transiently increases the spliced protein-coding Orb2A mRNA. A screen identified pasilla, the fly ortholog of mammalian Nova-1/2, as a mediator of Orb2A mRNA processing. A single-nucleotide substitution in the intronic region that reduces Pasilla binding and intron removal selectively impairs long-term memory. We posit that pasilla-mediated processing of unspliced Orb2A mRNA integrates experience and internal state to control Orb2A protein abundance and long-term memory formation.
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10
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Pimmett VL, Deng H, Haskins JA, Mercier RJ, LaPointe P, Simmonds AJ. The activity of the Drosophila Vestigial protein is modified by Scalloped-dependent phosphorylation. Dev Biol 2017; 425:58-69. [PMID: 28322734 DOI: 10.1016/j.ydbio.2017.03.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 02/01/2017] [Accepted: 03/14/2017] [Indexed: 12/18/2022]
Abstract
The Drosophila vestigial gene is required for proliferation and differentiation of the adult wing and for differentiation of larval and adult muscle identity. Vestigial is part of a multi-protein transcription factor complex, which includes Scalloped, a TEAD-class DNA binding protein. Binding Scalloped is necessary for translocation of Vestigial into the nucleus. We show that Vestigial is extensively post-translationally modified and at least one of these modifications is required for proper function during development. We have shown that there is p38-dependent phosphorylation of Serine 215 in the carboxyl-terminal region of Vestigial. Phosphorylation of Serine 215 occurs in the nucleus and requires the presence of Scalloped. Comparison of a phosphomimetic and non-phosphorylatable mutant forms of Vestigial shows differences in the ability to rescue the wing and muscle phenotypes associated with a null vestigial allele.
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Affiliation(s)
- Virginia L Pimmett
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada T6G2H7
| | - Hua Deng
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada T6G2H7; Howard Hughes Medical Institute, Dept. of Physiology, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Julie A Haskins
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada T6G2H7
| | - Rebecca J Mercier
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada T6G2H7
| | - Paul LaPointe
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada T6G2H7
| | - Andrew J Simmonds
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada T6G2H7
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11
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Huang D, Li X, Sun L, Huang P, Ying H, Wang H, Wu J, Song H. Regulation of Hippo signalling by p38 signalling. J Mol Cell Biol 2016; 8:328-37. [PMID: 27402810 PMCID: PMC4991669 DOI: 10.1093/jmcb/mjw036] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/05/2016] [Indexed: 11/17/2022] Open
Abstract
The Hippo signalling pathway has a crucial role in growth control during development, and its dysregulation contributes to tumorigenesis. Recent studies uncover multiple upstream regulatory inputs into Hippo signalling, which affects phosphorylation of the transcriptional coactivator Yki/YAP/TAZ by Wts/Lats. Here we identify the p38 mitogen-activated protein kinase (MAPK) pathway as a new upstream branch of the Hippo pathway. In Drosophila, overexpression of MAPKK gene licorne (lic), or MAPKKK gene Mekk1, promotes Yki activity and induces Hippo target gene expression. Loss-of-function studies show that lic regulates Hippo signalling in ovary follicle cells and in the wing disc. Epistasis analysis indicates that Mekk1 and lic affect Hippo signalling via p38b and wts. We further demonstrate that the Mekk1-Lic-p38b cascade inhibits Hippo signalling by promoting F-actin accumulation and Jub phosphorylation. In addition, p38 signalling modulates actin filaments and Hippo signalling in parallel to small GTPases Ras, Rac1, and Rho1. Lastly, we show that p38 signalling regulates Hippo signalling in mammalian cell lines. The Lic homologue MKK3 promotes nuclear localization of YAP via the actin cytoskeleton. Upregulation or downregulation of the p38 pathway regulates YAP-mediated transcription. Our work thus reveals a conserved crosstalk between the p38 MAPK pathway and the Hippo pathway in growth regulation.
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Affiliation(s)
- Dashun Huang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science & Technology of China, 96 Jin Zhai Road, Hefei 230031, China Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China Key Laboratory of Food Safety Risk Assessment, Ministry of Health, 37 Guang Qu Road, Beijing 100021, China
| | - Xiaojiao Li
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China Key Laboratory of Food Safety Risk Assessment, Ministry of Health, 37 Guang Qu Road, Beijing 100021, China
| | - Li Sun
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China Key Laboratory of Food Safety Risk Assessment, Ministry of Health, 37 Guang Qu Road, Beijing 100021, China
| | - Ping Huang
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China Key Laboratory of Food Safety Risk Assessment, Ministry of Health, 37 Guang Qu Road, Beijing 100021, China
| | - Hao Ying
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China Key Laboratory of Food Safety Risk Assessment, Ministry of Health, 37 Guang Qu Road, Beijing 100021, China
| | - Hui Wang
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China Key Laboratory of Food Safety Risk Assessment, Ministry of Health, 37 Guang Qu Road, Beijing 100021, China
| | - Jiarui Wu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science & Technology of China, 96 Jin Zhai Road, Hefei 230031, China
| | - Haiyun Song
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China Key Laboratory of Food Safety Risk Assessment, Ministry of Health, 37 Guang Qu Road, Beijing 100021, China
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12
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Trahan C, Aguilar LC, Oeffinger M. Single-Step Affinity Purification (ssAP) and Mass Spectrometry of Macromolecular Complexes in the Yeast S. cerevisiae. Methods Mol Biol 2016; 1361:265-287. [PMID: 26483027 DOI: 10.1007/978-1-4939-3079-1_15] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Cellular functions are mostly defined by the dynamic interactions of proteins within macromolecular networks. Deciphering the composition of macromolecular complexes and their dynamic rearrangements is the key to getting a comprehensive picture of cellular behavior and to understanding biological systems. In the last decade, affinity purification coupled to mass spectrometry has emerged as a powerful tool to comprehensively study interaction networks and their assemblies. However, the study of these interactomes has been hampered by severe methodological limitations. In particular, the affinity purification of intact complexes from cell lysates suffers from protein and RNA degradation, loss of transient interactors, and poor overall yields. In this chapter, we describe a rapid single-step affinity purification method for the efficient isolation of dynamic macromolecular complexes. The technique employs cell lysis by cryo-milling, which ensures nondegraded starting material in the submicron range, and magnetic beads, which allow for dense antibody-conjugation and thus rapid complex isolation, while avoiding loss of transient interactions. The method is epitope tag-independent, and overcomes many of the previous limitations to produce large interactomes with almost no contamination. The protocol described here has been optimized for the yeast S. cerevisiae.
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Affiliation(s)
- Christian Trahan
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, Canada, H2W 1R7
- Département de biochimie et médicine moléculaire, Faculté de médecine, Université de Montréal, Montréal, QC, Canada, H3T 1J4
| | - Lisbeth-Carolina Aguilar
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, Canada, H2W 1R7
| | - Marlene Oeffinger
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, Canada, H2W 1R7.
- Département de biochimie et médicine moléculaire, Faculté de médecine, Université de Montréal, Montréal, QC, Canada, H3T 1J4.
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, Canada, H3A 1A3.
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13
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Chechenova MB, Maes S, Cripps RM. Expression of the Troponin C at 41C Gene in Adult Drosophila Tubular Muscles Depends upon Both Positive and Negative Regulatory Inputs. PLoS One 2015; 10:e0144615. [PMID: 26641463 PMCID: PMC4671713 DOI: 10.1371/journal.pone.0144615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 11/20/2015] [Indexed: 12/05/2022] Open
Abstract
Most animals express multiple isoforms of structural muscle proteins to produce tissues with different physiological properties. In Drosophila, the adult muscles include tubular-type muscles and the fibrillar indirect flight muscles. Regulatory processes specifying tubular muscle fate remain incompletely understood, therefore we chose to analyze the transcriptional regulation of TpnC41C, a Troponin C gene expressed in the tubular jump muscles, but not in the fibrillar flight muscles. We identified a 300-bp promoter fragment of TpnC41C sufficient for the fiber-specific reporter expression. Through an analysis of this regulatory element, we identified two sites necessary for the activation of the enhancer. Mutations in each of these sites resulted in 70% reduction of enhancer activity. One site was characterized as a binding site for Myocyte Enhancer Factor-2. In addition, we identified a repressive element that prevents activation of the enhancer in other muscle fiber types. Mutation of this site increased jump muscle-specific expression of the reporter, but more importantly reporter expression expanded into the indirect flight muscles. Our findings demonstrate that expression of the TpnC41C gene in jump muscles requires integration of multiple positive and negative transcriptional inputs. Identification of the transcriptional regulators binding the cis-elements that we identified will reveal the regulatory pathways controlling muscle fiber differentiation.
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Affiliation(s)
- Maria B Chechenova
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, United States of America
| | - Sara Maes
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, United States of America
| | - Richard M Cripps
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, United States of America
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14
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Deletion of mitogen-activated protein kinase 1 inhibits development and growth of Toxoplasma gondii. Parasitol Res 2015; 115:797-805. [DOI: 10.1007/s00436-015-4807-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 10/23/2015] [Indexed: 01/04/2023]
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15
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Zhan L, Xie Q, Tibbetts RS. Opposing roles of p38 and JNK in a Drosophila model of TDP-43 proteinopathy reveal oxidative stress and innate immunity as pathogenic components of neurodegeneration. Hum Mol Genet 2014; 24:757-72. [PMID: 25281658 DOI: 10.1093/hmg/ddu493] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Pathological aggregation and mutation of the 43-kDa TAR DNA-binding protein (TDP-43) are strongly implicated in the pathogenesis amyotrophic lateral sclerosis and frontotemporal lobar degeneration. TDP-43 neurotoxicity has been extensively modeled in mice, zebrafish, Caenorhabditis elegans and Drosophila, where selective expression of TDP-43 in motoneurons led to paralysis and premature lethality. Through a genetic screen aimed to identify genetic modifiers of TDP-43, we found that the Drosophila dual leucine kinase Wallenda (Wnd) and its downstream kinases JNK and p38 influenced TDP-43 neurotoxicity. Reducing Wnd gene dosage or overexpressing its antagonist highwire partially rescued TDP-43-associated premature lethality. Downstream of Wnd, the JNK and p38 kinases played opposing roles in TDP-43-associated neurodegeneration. LOF alleles of the p38b gene as well as p38 inhibitors diminished TDP-43-associated premature lethality, whereas p38b GOF caused phenotypic worsening. In stark contrast, disruptive alleles of Basket (Bsk), the Drosophila homologue of JNK, exacerbated longevity shortening, whereas overexpression of Bsk extended lifespan. Among possible mechanisms, we found motoneuron-directed expression of TDP-43 elicited oxidative stress and innate immune gene activation that were exacerbated by p38 GOF and Bsk LOF, respectively. A key pathologic role for innate immunity in TDP-43-associated neurodegeneration was further supported by the finding that genetic suppression of the Toll/Dif and Imd/Relish inflammatory pathways dramatically extended lifespan of TDP-43 transgenic flies. We propose that oxidative stress and neuroinflammation are intrinsic components of TDP-43-associated neurodegeneration and that the balance between cytoprotective JNK and cytotoxic p38 signaling dictates phenotypic outcome to TDP-43 expression in Drosophila.
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Affiliation(s)
- Lihong Zhan
- Department of Human Oncology, Program in Molecular and Cellular Pharmacology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Qijing Xie
- Department of Human Oncology, Program in Molecular and Cellular Pharmacology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Randal S Tibbetts
- Department of Human Oncology, Program in Molecular and Cellular Pharmacology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
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16
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Dusik V, Senthilan PR, Mentzel B, Hartlieb H, Wülbeck C, Yoshii T, Raabe T, Helfrich-Förster C. The MAP kinase p38 is part of Drosophila melanogaster's circadian clock. PLoS Genet 2014; 10:e1004565. [PMID: 25144774 PMCID: PMC4140665 DOI: 10.1371/journal.pgen.1004565] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 06/30/2014] [Indexed: 11/18/2022] Open
Abstract
All organisms have to adapt to acute as well as to regularly occurring changes in the environment. To deal with these major challenges organisms evolved two fundamental mechanisms: the p38 mitogen-activated protein kinase (MAPK) pathway, a major stress pathway for signaling stressful events, and circadian clocks to prepare for the daily environmental changes. Both systems respond sensitively to light. Recent studies in vertebrates and fungi indicate that p38 is involved in light-signaling to the circadian clock providing an interesting link between stress-induced and regularly rhythmic adaptations of animals to the environment, but the molecular and cellular mechanisms remained largely unknown. Here, we demonstrate by immunocytochemical means that p38 is expressed in Drosophila melanogaster's clock neurons and that it is activated in a clock-dependent manner. Surprisingly, we found that p38 is most active under darkness and, besides its circadian activation, additionally gets inactivated by light. Moreover, locomotor activity recordings revealed that p38 is essential for a wild-type timing of evening activity and for maintaining ∼ 24 h behavioral rhythms under constant darkness: flies with reduced p38 activity in clock neurons, delayed evening activity and lengthened the period of their free-running rhythms. Furthermore, nuclear translocation of the clock protein Period was significantly delayed on the expression of a dominant-negative form of p38b in Drosophila's most important clock neurons. Western Blots revealed that p38 affects the phosphorylation degree of Period, what is likely the reason for its effects on nuclear entry of Period. In vitro kinase assays confirmed our Western Blot results and point to p38 as a potential "clock kinase" phosphorylating Period. Taken together, our findings indicate that the p38 MAP Kinase is an integral component of the core circadian clock of Drosophila in addition to playing a role in stress-input pathways.
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Affiliation(s)
- Verena Dusik
- Neurobiology and Genetics, Biocenter, University of Würzburg, Würzburg, Germany
| | | | - Benjamin Mentzel
- Institute of Medical Radiation and Cell Research, University of Würzburg, Würzburg, Germany
| | - Heiko Hartlieb
- Neurobiology and Genetics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Corinna Wülbeck
- Institute of Zoology, University of Regensburg, Regensburg, Germany
| | - Taishi Yoshii
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Thomas Raabe
- Institute of Medical Radiation and Cell Research, University of Würzburg, Würzburg, Germany
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17
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In vivo interaction proteomics reveal a novel p38 mitogen-activated protein kinase/Rack1 pathway regulating proteostasis in Drosophila muscle. Mol Cell Biol 2013; 34:474-84. [PMID: 24277934 DOI: 10.1128/mcb.00824-13] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several recent studies suggest that systemic aging in metazoans is differentially affected by functional decline in specific tissues, such as skeletal muscle. In Drosophila, longevity appears to be tightly linked to myoproteostasis, and the formation of misfolded protein aggregates is a hallmark of senescence in aging muscle. Similarly, defective myoproteostasis is described as an important contributor to the pathology of several age-related degenerative muscle diseases in humans, e.g., inclusion body myositis. p38 mitogen-activated protein kinase (MAPK) plays a central role in a conserved signaling pathway activated by a variety of stressful stimuli. Aging p38 MAPK mutant flies display accelerated motor function decline, concomitant with an enhanced accumulation of detergent-insoluble protein aggregates in thoracic muscles. Chemical genetic experiments suggest that p38-mediated regulation of myoproteostasis is not limited to the control of reactive oxygen species production or the protein degradation pathways but also involves upstream turnover pathways, e.g., translation. Using affinity purification and mass spectrometry, we identified Rack1 as a novel substrate of p38 MAPK in aging muscle and showed that the genetic interaction between p38b and Rack1 controls muscle aggregate formation, locomotor function, and longevity. Biochemical analyses of Rack1 in aging and stressed muscle suggest a model whereby p38 MAPK signaling causes a redistribution of Rack1 between a ribosome-bound pool and a putative translational repressor complex.
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18
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Kuzmanov U, Emili A. Protein-protein interaction networks: probing disease mechanisms using model systems. Genome Med 2013; 5:37. [PMID: 23635424 PMCID: PMC3706760 DOI: 10.1186/gm441] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Protein-protein interactions (PPIs) and multi-protein complexes perform central roles in the cellular systems of all living organisms. In humans, disruptions of the normal patterns of PPIs and protein complexes can be causative or indicative of a disease state. Recent developments in the biological applications of mass spectrometry (MS)-based proteomics have expanded the horizon for the application of systematic large-scale mapping of physical interactions to probe disease mechanisms. In this review, we examine the application of MS-based approaches for the experimental analysis of PPI networks and protein complexes, focusing on the different model systems (including human cells) used to study the molecular basis of common diseases such as cancer, cardiomyopathies, diabetes, microbial infections, and genetic and neurodegenerative disorders.
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Affiliation(s)
- Uros Kuzmanov
- Banting and Best Department of Medical Research and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Andrew Emili
- Banting and Best Department of Medical Research and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
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19
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Westermarck J, Ivaska J, Corthals GL. Identification of protein interactions involved in cellular signaling. Mol Cell Proteomics 2013; 12:1752-63. [PMID: 23481661 DOI: 10.1074/mcp.r113.027771] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Protein-protein interactions drive biological processes. They are critical for all intra- and extracellular functions, and the technologies to analyze them are widely applied throughout the various fields of biological sciences. This study takes an in-depth view of some common principles of cellular regulation and provides a detailed account of approaches required to comprehensively map signaling protein-protein interactions in any particular cellular system or condition. We provide a critical review of the benefits and disadvantages of the yeast two-hybrid method and affinity purification coupled with mass spectrometric procedures for identification of signaling protein-protein interactions. In particular, we emphasize the quantitative and qualitative differences between tandem affinity and one-step purification (such as FLAG and Strep tag) methods. Although applicable to all types of interaction studies, a special section is devoted in this review to aspects that should be considered when attempting to identify signaling protein interactions that often are transient and weak by nature. Finally, we discuss shotgun and quantitative information that can be gleaned by MS-coupled methods for analysis of multiprotein complexes.
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Affiliation(s)
- Jukka Westermarck
- Centre for Biotechnology, University of Turku and Åbo Akademi, Turku, Finland
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20
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Xue L, Tao WA. Current technologies to identify protein kinase substrates in high throughput. ACTA ACUST UNITED AC 2013; 8:216-227. [PMID: 25110472 DOI: 10.1007/s11515-013-1257-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Since the discovery of protein phosphorylation as an important modulator of many cellular processes, the involvement of protein kinases in diseases, such as cancer, diabetes, cardiovascular diseases, and central nervous system pathologies, has been extensively documented. Our understanding of many disease pathologies at the molecular level, therefore, requires the comprehensive identification of substrates targeted by protein kinases. In this review, we focus on recent techniques for kinase substrate identification in high throughput, in particular on genetic and proteomic approaches. Each method with its inherent advantages and limitations is discussed.
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Affiliation(s)
- Liang Xue
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA ; Department of Medicinal Chemistry & Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA ; Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA ; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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