151
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Cloutier P, Poitras C, Faubert D, Bouchard A, Blanchette M, Gauthier MS, Coulombe B. Upstream ORF-Encoded ASDURF Is a Novel Prefoldin-like Subunit of the PAQosome. J Proteome Res 2019; 19:18-27. [PMID: 31738558 DOI: 10.1021/acs.jproteome.9b00599] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The PAQosome is an 11-subunit chaperone involved in the biogenesis of several human protein complexes. We show that ASDURF, a recently discovered upstream open reading frame (uORF) in the 5' UTR of ASNSD1 mRNA, encodes the 12th subunit of the PAQosome. ASDURF displays significant structural homology to β-prefoldins and assembles with the five known subunits of the prefoldin-like module of the PAQosome to form a heterohexameric prefoldin-like complex. A model of the PAQosome prefoldin-like module is presented. The data presented here provide an example of a eukaryotic uORF-encoded polypeptide whose function is not limited to cis-acting translational regulation of downstream coding sequence and highlights the importance of including alternative ORF products in proteomic studies.
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Affiliation(s)
- Philippe Cloutier
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada
| | - Christian Poitras
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada
| | - Denis Faubert
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada
| | - Annie Bouchard
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada
| | - Mathieu Blanchette
- School of Computer Science , McGill University , 3480 University Street , Montréal , Quebec H3A 0E9 , Canada
| | - Marie-Soleil Gauthier
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada
| | - Benoit Coulombe
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada.,Département de Biochimie et Médecine Moléculaire, Faculté de Médecine , Université de Montréal , 2900 Boulevard Édouart-Montpetit , Montréal , Quebec H3T 1J4 , Canada
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152
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Gingras AC. Connecting proteins: shareable tools for reproducible interaction mapping. Biochem Cell Biol 2019; 98:309-313. [PMID: 31689129 DOI: 10.1139/bcb-2019-0285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Room 992, Toronto, ON M5G 1X5, Canada
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153
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Soares H, Carmona B, Nolasco S, Viseu Melo L. Polarity in Ciliate Models: From Cilia to Cell Architecture. Front Cell Dev Biol 2019; 7:240. [PMID: 31681771 PMCID: PMC6813674 DOI: 10.3389/fcell.2019.00240] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 10/01/2019] [Indexed: 12/21/2022] Open
Abstract
Tetrahymena and Paramecium are highly differentiated unicellular organisms with elaborated cortical patterns showing a regular arrangement of hundreds to thousands of basal bodies in longitudinal rows that extend from the anterior to the posterior region of the cell. Thus both ciliates exhibit a permanent antero–posterior axis and left–right asymmetry. This cell polarity is reflected in the direction of the structures nucleated around each basal body such as the ciliary rootlets. Studies in these ciliates showed that basal bodies assemble two types of cilia, the cortical cilia and the cilia of the oral apparatus, a complex structure specialized in food capture. These two cilia types display structural differences at their tip domain. Basal bodies possessing distinct compositions creating specialized landmarks are also present. Cilia might be expected to express and transmit polarities throughout signaling pathways given their recognized role in signal transduction. This review will focus on how local polarities in basal bodies/cilia are regulated and transmitted through cell division in order to maintain the global polarity and shape of these cells and locally constrain the interpretation of signals by different cilia. We will also discuss ciliates as excellent biological models to study development and morphogenetic mechanisms and their relationship with cilia diversity and function in metazoans.
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Affiliation(s)
- Helena Soares
- Centro de Química e Bioquímica/Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal.,Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Lisbon, Portugal
| | - Bruno Carmona
- Centro de Química e Bioquímica/Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal.,Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Lisbon, Portugal
| | - Sofia Nolasco
- Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Lisbon, Portugal.,CIISA-Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisbon, Portugal
| | - Luís Viseu Melo
- Physics Department and CEFEMA, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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154
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Ko PJ, Woodrow C, Dubreuil MM, Martin BR, Skouta R, Bassik MC, Dixon SJ. A ZDHHC5-GOLGA7 Protein Acyltransferase Complex Promotes Nonapoptotic Cell Death. Cell Chem Biol 2019; 26:1716-1724.e9. [PMID: 31631010 DOI: 10.1016/j.chembiol.2019.09.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/29/2019] [Accepted: 09/26/2019] [Indexed: 12/11/2022]
Abstract
Lethal small molecules are useful probes to discover and characterize novel cell death pathways and biochemical mechanisms. Here we report that the synthetic oxime-containing small molecule caspase-independent lethal 56 (CIL56) induces an unconventional form of nonapoptotic cell death distinct from necroptosis, ferroptosis, and other pathways. CIL56-induced cell death requires a catalytically active protein S-acyltransferase complex comprising the enzyme ZDHHC5 and an accessory subunit GOLGA7. The ZDHHC5-GOLGA7 complex is mutually stabilizing and localizes to the plasma membrane. CIL56 inhibits anterograde protein transport from the Golgi apparatus, which may be lethal in the context of ongoing ZDHHC5-GOLGA7 complex-dependent retrograde protein trafficking from the plasma membrane to internal sites. Other oxime-containing small molecules, structurally distinct from CIL56, may trigger cell death through the same pathway. These results define an unconventional form of nonapoptotic cell death regulated by protein S-acylation.
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Affiliation(s)
- Pin-Joe Ko
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Claire Woodrow
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Michael M Dubreuil
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brent R Martin
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rachid Skouta
- Department of Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Scott J Dixon
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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155
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Lin Z, Yang Z, Xie R, Ji Z, Guan K, Zhang M. Decoding WW domain tandem-mediated target recognitions in tissue growth and cell polarity. eLife 2019; 8:49439. [PMID: 31486770 PMCID: PMC6744271 DOI: 10.7554/elife.49439] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/04/2019] [Indexed: 02/06/2023] Open
Abstract
WW domain tandem-containing proteins such as KIBRA, YAP, and MAGI play critical roles in cell growth and polarity via binding to and positioning target proteins in specific subcellular regions. An immense disparity exists between promiscuity of WW domain-mediated target bindings and specific roles of WW domain proteins in cell growth regulation. Here, we discovered that WW domain tandems of KIBRA and MAGI, but not YAP, bind to specific target proteins with extremely high affinity and exquisite sequence specificity. Via systematic structural biology and biochemistry approaches, we decoded the target binding rules of WW domain tandems from cell growth regulatory proteins and uncovered a list of previously unknown WW tandem binding proteins including β-Dystroglycan, JCAD, and PTPN21. The WW tandem-mediated target recognition mechanisms elucidated here can guide functional studies of WW domain proteins in cell growth and polarity as well as in other cellular processes including neuronal synaptic signaling.
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Affiliation(s)
- Zhijie Lin
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhou Yang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Ruiling Xie
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, United States.,Department of Otolaryngology, Head and Neck Surgery, Peking University First Hospital, Beijing, China
| | - Zeyang Ji
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Kunliang Guan
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, United States
| | - Mingjie Zhang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China.,Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Kowloon, China
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156
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Li N, Lu N, Xie C. The Hippo and Wnt signalling pathways: crosstalk during neoplastic progression in gastrointestinal tissue. FEBS J 2019; 286:3745-3756. [PMID: 31342636 DOI: 10.1111/febs.15017] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 06/24/2019] [Accepted: 07/22/2019] [Indexed: 12/24/2022]
Abstract
The Hippo and Wnt signalling pathways play crucial roles in maintaining tissue homeostasis and organ size by orchestrating cell proliferation, differentiation and apoptosis. These pathways have been frequently found to be dysregulated in human cancers. While the canonical signal transduction of Hippo and Wnt has been well studied, emerging evidence shows that these two signalling pathways contribute to and exhibit overlapping functions in gastrointestinal (GI) tumorigenesis. In fact, the core effectors YAP/TAZ in Hippo signalling pathway cooperate with β-catenin in Wnt signalling pathway to promote GI neoplasia. Here, we provide a brief review to summarize the molecular mechanisms underlying the crosstalk between these two pathways and elucidate their involvement in GI tumorigenesis, particularly focusing on the intestine, stomach and liver.
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Affiliation(s)
- Nianshuang Li
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, China
| | - Nonghua Lu
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, China
| | - Chuan Xie
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, China
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157
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Kück U, Radchenko D, Teichert I. STRIPAK, a highly conserved signaling complex, controls multiple eukaryotic cellular and developmental processes and is linked with human diseases. Biol Chem 2019; 400:1005-1022. [PMID: 31042639 DOI: 10.1515/hsz-2019-0173] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 03/28/2019] [Indexed: 01/17/2023]
Abstract
The striatin-interacting phosphatases and kinases (STRIPAK) complex is evolutionary highly conserved and has been structurally and functionally described in diverse lower and higher eukaryotes. In recent years, this complex has been biochemically characterized better and further analyses in different model systems have shown that it is also involved in numerous cellular and developmental processes in eukaryotic organisms. Further recent results have shown that the STRIPAK complex functions as a macromolecular assembly communicating through physical interaction with other conserved signaling protein complexes to constitute larger dynamic protein networks. Here, we will provide a comprehensive and up-to-date overview of the architecture, function and regulation of the STRIPAK complex and discuss key issues and future perspectives, linked with human diseases, which may form the basis of further research endeavors in this area. In particular, the investigation of bi-directional interactions between STRIPAK and other signaling pathways should elucidate upstream regulators and downstream targets as fundamental parts of a complex cellular network.
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Affiliation(s)
- Ulrich Kück
- Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Daria Radchenko
- Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Ines Teichert
- Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
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158
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Jones PD, Kaiser MA, Ghaderi Najafabadi M, Koplev S, Zhao Y, Douglas G, Kyriakou T, Andrews S, Rajmohan R, Watkins H, Channon KM, Ye S, Yang X, Björkegren JLM, Samani NJ, Webb TR. JCAD, a Gene at the 10p11 Coronary Artery Disease Locus, Regulates Hippo Signaling in Endothelial Cells. Arterioscler Thromb Vasc Biol 2019; 38:1711-1722. [PMID: 29794114 DOI: 10.1161/atvbaha.118.310976] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Objective- A large number of genetic loci have been associated with risk of coronary artery disease (CAD) through genome-wide association studies, however, for most loci the underlying biological mechanism is unknown. Determining the molecular pathways and cellular processes affected by these loci will provide new insights into CAD pathophysiology and may lead to new therapies. The CAD-associated variants at 10p11.23 fall in JCAD, which encodes an endothelial junction protein, however, its molecular function in endothelial cells is not known. In this study, we characterize the molecular role of JCAD (junctional cadherin 5 associated) in endothelial cells. Approach and Results- We show that JCAD knockdown in endothelial cells affects key phenotypes related to atherosclerosis including proliferation, migration, apoptosis, tube formation, and monocyte binding. We demonstrate that JCAD interacts with LATS2 (large tumor suppressor kinase 2) and negatively regulates Hippo signaling leading to increased activity of YAP (yes-associated protein), the transcriptional effector of the pathway. We also show by double siRNA knockdown that the phenotypes caused by JCAD knockdown require LATS2 and that JCAD is involved in transmission of RhoA-mediated signals into the Hippo pathway. In human tissues, we find that the CAD-associated lead variant, rs2487928, is associated with expression of JCAD in arteries, including atherosclerotic arteries. Gene co-expression analyses across disease-relevant tissues corroborate our phenotypic findings and support the link between JCAD and Hippo signaling. Conclusions- Our results show that JCAD negatively regulates Hippo signaling in endothelial cells and we suggest that JCAD contributes to atherosclerosis by mediating YAP activity and contributing to endothelial dysfunction.
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Affiliation(s)
- Peter D Jones
- From the Department of Cardiovascular Sciences (P.D.J., M.A.K., M.G.N., S.A., R.R., S.Y., N.J.S., T.R.W.).,National Institute for Health Research Leicester Cardiovascular Biomedical Research Centre (P.D.J., M.A.K., M.G.N., S.A., R.R., S.Y., N.J.S., T.R.W.), Glenfield Hospital, University of Leicester, United Kingdom
| | - Michael A Kaiser
- From the Department of Cardiovascular Sciences (P.D.J., M.A.K., M.G.N., S.A., R.R., S.Y., N.J.S., T.R.W.).,National Institute for Health Research Leicester Cardiovascular Biomedical Research Centre (P.D.J., M.A.K., M.G.N., S.A., R.R., S.Y., N.J.S., T.R.W.), Glenfield Hospital, University of Leicester, United Kingdom
| | - Maryam Ghaderi Najafabadi
- From the Department of Cardiovascular Sciences (P.D.J., M.A.K., M.G.N., S.A., R.R., S.Y., N.J.S., T.R.W.).,National Institute for Health Research Leicester Cardiovascular Biomedical Research Centre (P.D.J., M.A.K., M.G.N., S.A., R.R., S.Y., N.J.S., T.R.W.), Glenfield Hospital, University of Leicester, United Kingdom
| | - Simon Koplev
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (S.K., J.L.M.B.)
| | - Yuqi Zhao
- Department of Integrative Biology and Physiology, University of California, Los Angeles (Y.Z., X.Y.)
| | - Gillian Douglas
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, British Heart Foundation Centre for Research Excellence (G.D., T.K., H.W., K.M.C.)
| | - Theodosios Kyriakou
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, British Heart Foundation Centre for Research Excellence (G.D., T.K., H.W., K.M.C.).,Wellcome Trust Centre for Human Genetics (T.K.), University of Oxford, United Kingdom
| | - Sarah Andrews
- From the Department of Cardiovascular Sciences (P.D.J., M.A.K., M.G.N., S.A., R.R., S.Y., N.J.S., T.R.W.).,National Institute for Health Research Leicester Cardiovascular Biomedical Research Centre (P.D.J., M.A.K., M.G.N., S.A., R.R., S.Y., N.J.S., T.R.W.), Glenfield Hospital, University of Leicester, United Kingdom
| | - Rathinasabapathy Rajmohan
- National Institute for Health Research Leicester Cardiovascular Biomedical Research Centre (P.D.J., M.A.K., M.G.N., S.A., R.R., S.Y., N.J.S., T.R.W.), Glenfield Hospital, University of Leicester, United Kingdom
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, British Heart Foundation Centre for Research Excellence (G.D., T.K., H.W., K.M.C.)
| | - Keith M Channon
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, British Heart Foundation Centre for Research Excellence (G.D., T.K., H.W., K.M.C.)
| | - Shu Ye
- From the Department of Cardiovascular Sciences (P.D.J., M.A.K., M.G.N., S.A., R.R., S.Y., N.J.S., T.R.W.).,National Institute for Health Research Leicester Cardiovascular Biomedical Research Centre (P.D.J., M.A.K., M.G.N., S.A., R.R., S.Y., N.J.S., T.R.W.), Glenfield Hospital, University of Leicester, United Kingdom
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles (Y.Z., X.Y.)
| | - Johan L M Björkegren
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (S.K., J.L.M.B.).,Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden (J.L.M.B.).,Department of Physiology, Institute of Biomedicine and Translation Medicine, University of Tartu, Estonia (J.LM.B.)
| | - Nilesh J Samani
- From the Department of Cardiovascular Sciences (P.D.J., M.A.K., M.G.N., S.A., R.R., S.Y., N.J.S., T.R.W.).,National Institute for Health Research Leicester Cardiovascular Biomedical Research Centre (P.D.J., M.A.K., M.G.N., S.A., R.R., S.Y., N.J.S., T.R.W.), Glenfield Hospital, University of Leicester, United Kingdom
| | - Tom R Webb
- From the Department of Cardiovascular Sciences (P.D.J., M.A.K., M.G.N., S.A., R.R., S.Y., N.J.S., T.R.W.).,National Institute for Health Research Leicester Cardiovascular Biomedical Research Centre (P.D.J., M.A.K., M.G.N., S.A., R.R., S.Y., N.J.S., T.R.W.), Glenfield Hospital, University of Leicester, United Kingdom
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159
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Klimek C, Jahnke R, Wördehoff J, Kathage B, Stadel D, Behrends C, Hergovich A, Höhfeld J. The Hippo network kinase STK38 contributes to protein homeostasis by inhibiting BAG3-mediated autophagy. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:1556-1566. [PMID: 31326538 PMCID: PMC6692498 DOI: 10.1016/j.bbamcr.2019.07.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 06/18/2019] [Accepted: 07/14/2019] [Indexed: 12/31/2022]
Abstract
Chaperone-assisted selective autophagy (CASA) initiated by the cochaperone Bcl2-associated athanogene 3 (BAG3) represents an important mechanism for the disposal of misfolded and damaged proteins in mammalian cells. Under mechanical stress, the cochaperone cooperates with the small heat shock protein HSPB8 and the cytoskeleton-associated protein SYNPO2 to degrade force-unfolded forms of the actin-crosslinking protein filamin. This is essential for muscle maintenance in flies, fish, mice and men. Here, we identify the serine/threonine protein kinase 38 (STK38), which is part of the Hippo signaling network, as a novel interactor of BAG3. STK38 was previously shown to facilitate cytoskeleton assembly and to promote mitophagy as well as starvation and detachment induced autophagy. Significantly, our study reveals that STK38 exerts an inhibitory activity on BAG3-mediated autophagy. Inhibition relies on a disruption of the functional interplay of BAG3 with HSPB8 and SYNPO2 upon binding of STK38 to the cochaperone. Of note, STK38 attenuates CASA independently of its kinase activity, whereas previously established regulatory functions of STK38 involve target phosphorylation. The ability to exert different modes of regulation on central protein homeostasis (proteostasis) machineries apparently allows STK38 to coordinate the execution of diverse macroautophagy pathways and to balance cytoskeleton assembly and degradation. The Hippo network kinase STK38 interacts with the cochaperone BAG3. STK38 inhibits BAG3-dependent chaperone-assisted selective autophagy (CASA). CASA inhibition does not require the kinase activity of STK38. Hippo network kinases that act upstream of STK38 contribute to CASA regulation. STK38 disrupts interactions of BAG3 with the CASA components HSPB8 and SYNPO2.
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Affiliation(s)
- Christina Klimek
- Institute for Cell Biology, University of Bonn, Ulrich-Haberland-Str. 61a, 53121 Bonn, Germany
| | - Ricarda Jahnke
- Institute for Cell Biology, University of Bonn, Ulrich-Haberland-Str. 61a, 53121 Bonn, Germany
| | - Judith Wördehoff
- Institute for Cell Biology, University of Bonn, Ulrich-Haberland-Str. 61a, 53121 Bonn, Germany
| | - Barbara Kathage
- Institute for Cell Biology, University of Bonn, Ulrich-Haberland-Str. 61a, 53121 Bonn, Germany
| | - Daniela Stadel
- Institute of Biochemistry II, Goethe University Medical School, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Christian Behrends
- Munich Cluster for Systems Neurology, Ludwig-Maximilians-University Munich, Feodor-Lynen Strasse 17, 81377 München, Germany
| | | | - Jörg Höhfeld
- Institute for Cell Biology, University of Bonn, Ulrich-Haberland-Str. 61a, 53121 Bonn, Germany.
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160
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Béganton B, Solassol I, Mangé A, Solassol J. Protein interactions study through proximity-labeling. Expert Rev Proteomics 2019; 16:717-726. [PMID: 31269821 DOI: 10.1080/14789450.2019.1638769] [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] [Indexed: 01/08/2023]
Abstract
Introduction: The proteome is a dynamic system in which protein-protein interactions play a crucial part in shaping the cell phenotype. However, given the current limitations of available technologies to describe the dynamic nature of these interactions, the identification of protein-protein interactions has long been a major challenge in proteomics. In recent years, the development of BioID and APEX, two proximity-tagging technologies, have opened-up new perspectives and have already started to change our conception of protein-protein interactions, and more generally, of the proteome. With a broad range of application encompassing health, these new technologies are currently setting milestones crucial to understand fine cellular mechanisms. Area covered: In this article, we describe both the recent and the more conventional available tools to study protein-protein interactions, compare the advantages and the limitations of these techniques, and discuss the recent advancements led by the proximity tagging techniques to refine our conception of the proteome. Expert opinion: The recent development of proximity labeling techniques emphasizes the growing importance of such technologies to decipher cellular mechanism. Although several challenges still need to be addressed, many fields can benefit from these tools and notably the detection of new therapeutic targets for patient care.
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Affiliation(s)
- Benoît Béganton
- IRCM, INSERM, Univ Montpellier, ICM , Montpellier , France.,Department of Pathology and onco-biology, CHU Montpellier , Montpellier , France
| | - Isabelle Solassol
- Translational Research Unit, Montpellier Cancer Institute , Montpellier , France
| | - Alain Mangé
- IRCM, INSERM, Univ Montpellier, ICM , Montpellier , France
| | - Jérôme Solassol
- IRCM, INSERM, Univ Montpellier, ICM , Montpellier , France.,Department of Pathology and onco-biology, CHU Montpellier , Montpellier , France
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161
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Gundogdu R, Hergovich A. MOB (Mps one Binder) Proteins in the Hippo Pathway and Cancer. Cells 2019; 8:cells8060569. [PMID: 31185650 PMCID: PMC6627106 DOI: 10.3390/cells8060569] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/03/2019] [Accepted: 06/04/2019] [Indexed: 12/22/2022] Open
Abstract
The family of MOBs (monopolar spindle-one-binder proteins) is highly conserved in the eukaryotic kingdom. MOBs represent globular scaffold proteins without any known enzymatic activities. They can act as signal transducers in essential intracellular pathways. MOBs have diverse cancer-associated cellular functions through regulatory interactions with members of the NDR/LATS kinase family. By forming additional complexes with serine/threonine protein kinases of the germinal centre kinase families, other enzymes and scaffolding factors, MOBs appear to be linked to an even broader disease spectrum. Here, we review our current understanding of this emerging protein family, with emphases on post-translational modifications, protein-protein interactions, and cellular processes that are possibly linked to cancer and other diseases. In particular, we summarise the roles of MOBs as core components of the Hippo tissue growth and regeneration pathway.
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Affiliation(s)
- Ramazan Gundogdu
- Vocational School of Health Services, Bingol University, 12000 Bingol, Turkey.
| | - Alexander Hergovich
- UCL Cancer Institute, University College London, WC1E 6BT, London, United Kingdom.
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162
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Lun XK, Szklarczyk D, Gábor A, Dobberstein N, Zanotelli VRT, Saez-Rodriguez J, von Mering C, Bodenmiller B. Analysis of the Human Kinome and Phosphatome by Mass Cytometry Reveals Overexpression-Induced Effects on Cancer-Related Signaling. Mol Cell 2019; 74:1086-1102.e5. [PMID: 31101498 PMCID: PMC6561723 DOI: 10.1016/j.molcel.2019.04.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 02/06/2019] [Accepted: 04/11/2019] [Indexed: 12/24/2022]
Abstract
Kinase and phosphatase overexpression drives tumorigenesis and drug resistance. We previously developed a mass-cytometry-based single-cell proteomics approach that enables quantitative assessment of overexpression effects on cell signaling. Here, we applied this approach in a human kinome- and phosphatome-wide study to assess how 649 individually overexpressed proteins modulated cancer-related signaling in HEK293T cells in an abundance-dependent manner. Based on these data, we expanded the functional classification of human kinases and phosphatases and showed that the overexpression effects include non-catalytic roles. We detected 208 previously unreported signaling relationships. The signaling dynamics analysis indicated that the overexpression of ERK-specific phosphatases sustains proliferative signaling. This suggests a phosphatase-driven mechanism of cancer progression. Moreover, our analysis revealed a drug-resistant mechanism through which overexpression of tyrosine kinases, including SRC, FES, YES1, and BLK, induced MEK-independent ERK activation in melanoma A375 cells. These proteins could predict drug sensitivity to BRAF-MEK concurrent inhibition in cells carrying BRAF mutations.
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Affiliation(s)
- Xiao-Kang Lun
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; Molecular Life Sciences PhD Program, Life Science Zürich Graduate School, ETH Zürich and University of Zürich, 8057 Zürich, Switzerland
| | - Damian Szklarczyk
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland
| | - Attila Gábor
- Joint Research Centre for Computational Biomedicine, Faculty of Medicine, RWTH Aachen University, 52074 Aachen, Germany
| | - Nadine Dobberstein
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland
| | - Vito Riccardo Tomaso Zanotelli
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; Systems Biology PhD Program, Life Science Zürich Graduate School, ETH Zürich and University of Zürich, 8057 Zürich, Switzerland
| | - Julio Saez-Rodriguez
- Joint Research Centre for Computational Biomedicine, Faculty of Medicine, RWTH Aachen University, 52074 Aachen, Germany; European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Hinxton, CB10 1SD Cambridge, UK; Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, BIOQUANT, 69120 Heidelberg, Germany
| | - Christian von Mering
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland
| | - Bernd Bodenmiller
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland.
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163
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Carnes RM, Mobley JA, Crossman DK, Liu H, Korf BR, Kesterson RA, Wallis D. Multi-Omics Profiling for NF1 Target Discovery in Neurofibromin (NF1) Deficient Cells. Proteomics 2019; 19:e1800334. [PMID: 30908848 DOI: 10.1002/pmic.201800334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 02/27/2019] [Indexed: 01/07/2023]
Abstract
Loss of NF1 is an oncogenic driver. In efforts to define pathways responsible for the development of neurofibromas and other cancers, transcriptomic and proteomic changes are evaluated in a non-malignant NF1 null cell line. NF1 null HEK293 cells were created using CRISPR/Cas9 technology and they are compared to parental cells that express neurofibromin. A total of 1222 genes and 132 proteins are found to be differentially expressed. The analysis is integrated to identify eight transcripts/proteins that are differentially regulated in both analyses. Metacore Pathway analysis identifies Neurogenesis NGF/TrkA MAPK-mediated signaling alterations. Next, the data set is compared with other published studies that involve analysis of cells or tumors deficient for NF1 and it is found that 141 genes recur in the sample and others; only thirteen of these genes recur in two or more studies. Genes/proteins of interest are validated via q-RT-PCR or Western blot. It is shown that KRT8 and 14-3-3σ protein levels respond to exogenously introduced mNf1 cDNA. Hence, transcripts/proteins that respond to neurofibromin levels are identified and they can potentially be used as biomarkers.
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Affiliation(s)
- Rachel M Carnes
- Department of Genetics, University of Alabama at Birmingham, 35294, Birmingham, AL, USA
| | - James A Mobley
- Department of Surgery, University of Alabama at Birmingham, 35294, Birmingham, AL, USA
| | - David K Crossman
- Department of Genetics, University of Alabama at Birmingham, 35294, Birmingham, AL, USA
| | - Hui Liu
- Department of Genetics, University of Alabama at Birmingham, 35294, Birmingham, AL, USA
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, 35294, Birmingham, AL, USA
| | - Robert A Kesterson
- Department of Genetics, University of Alabama at Birmingham, 35294, Birmingham, AL, USA
| | - Deeann Wallis
- Department of Genetics, University of Alabama at Birmingham, 35294, Birmingham, AL, USA
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164
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Abstract
Proximity-dependent labeling methods for detecting candidate protein-protein interactions (PPIs) or mapping the protein constituency of subcellular domains have become increasingly utilized by the scientific community. One such method, BioID, allows for the identification of not only strong interactions but also weak and transient associations between a protein of interest (POI) or targeting motif and adjacent proteins. A promiscuous biotin ligase is fused to a POI or targeting motif, expressed in living cells, and induced to biotinylate proximal proteins during a defined labeling period by biotin supplementation. This generates a history of protein-protein associations that occurred with the POI or the protein constituency within a discrete subcellular domain during the labeling period. Biotinylated proteins are subsequently isolated, identified via mass spectrometry, and investigated as candidate interactors with the POI or as constituents within a subcellular domain. The BioID method has been utilized by numerous research groups and is continually being optimized, applied to new models, and modified for use in novel applications. Here we describe a protocol by which a BioID fusion protein can be validated and utilized for BioID pull-downs.
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Affiliation(s)
- Danielle G May
- Enabling Technology Group, Sanford Research, Sioux Falls, SD, USA
| | - Kyle J Roux
- Enabling Technology Group, Sanford Research, Sioux Falls, SD, USA.
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, USA.
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165
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Yamauchi T, Moroishi T. Hippo Pathway in Mammalian Adaptive Immune System. Cells 2019; 8:cells8050398. [PMID: 31052239 PMCID: PMC6563119 DOI: 10.3390/cells8050398] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 04/26/2019] [Accepted: 04/28/2019] [Indexed: 12/11/2022] Open
Abstract
The Hippo pathway was originally identified as an evolutionarily-conserved signaling mechanism that contributes to the control of organ size. It was then rapidly expanded as a key pathway in the regulation of tissue development, regeneration, and cancer pathogenesis. The increasing amount of evidence in recent years has also connected this pathway to the regulation of innate and adaptive immune responses. Notably, the Hippo pathway has been revealed to play a pivotal role in adaptive immune cell lineages, as represented by the patients with T- and B-cell lymphopenia exhibiting defective expressions of the pathway component. The complex regulatory mechanisms of and by the Hippo pathway have also been evident as alternative signal transductions are employed in some immune cell types. In this review article, we summarize the current understanding of the emerging roles of the Hippo pathway in adaptive immune cell development and differentiation. We also highlight the recent findings concerning the dual functions of the Hippo pathway in autoimmunity and anti-cancer immune responses and discuss the key open questions in the interplay between the Hippo pathway and the mammalian immune system.
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Affiliation(s)
- Takayoshi Yamauchi
- Department of Molecular Enzymology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan.
| | - Toshiro Moroishi
- Department of Molecular Enzymology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan.
- Center for Metabolic Regulation of Healthy Aging, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan.
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Kawaguchi 332-0012, Japan.
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166
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Hennigan RF, Fletcher JS, Guard S, Ratner N. Proximity biotinylation identifies a set of conformation-specific interactions between Merlin and cell junction proteins. Sci Signal 2019; 12:12/578/eaau8749. [PMID: 31015291 DOI: 10.1126/scisignal.aau8749] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Neurofibromatosis type 2 is an inherited, neoplastic disease associated with schwannomas, meningiomas, and ependymomas and that is caused by inactivation of the tumor suppressor gene NF2 The NF2 gene product, Merlin, has no intrinsic catalytic activity; its tumor suppressor function is mediated through the proteins with which it interacts. We used proximity biotinylation followed by mass spectrometry and direct binding assays to identify proteins that associated with wild-type and various mutant forms of Merlin in immortalized Schwann cells. We defined a set of 52 proteins in close proximity to wild-type Merlin. Most of the Merlin-proximal proteins were components of cell junctional signaling complexes, suggesting that additional potential interaction partners may exist in adherens junctions, tight junctions, and focal adhesions. With mutant forms of Merlin that cannot bind to phosphatidylinositol 4,5-bisphosphate (PIP2) or that constitutively adopt a closed conformation, we confirmed a critical role for PIP2 binding in Merlin function and identified a large cohort of proteins that specifically interacted with Merlin in the closed conformation. Among these proteins, we identified a previously unreported Merlin-binding protein, apoptosis-stimulated p53 protein 2 (ASPP2, also called Tp53bp2), that bound to closed-conformation Merlin predominately through the FERM domain. Our results demonstrate that Merlin is a component of cell junctional mechanosensing complexes and defines a specific set of proteins through which it acts.
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Affiliation(s)
- Robert F Hennigan
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA.
| | - Jonathan S Fletcher
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Steven Guard
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Nancy Ratner
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
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167
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Zaltsman Y, Masuko S, Bensen JJ, Kiessling LL. Angiomotin Regulates YAP Localization during Neural Differentiation of Human Pluripotent Stem Cells. Stem Cell Reports 2019; 12:869-877. [PMID: 31006631 PMCID: PMC6523060 DOI: 10.1016/j.stemcr.2019.03.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 03/24/2019] [Accepted: 03/25/2019] [Indexed: 12/02/2022] Open
Abstract
Leveraging the extraordinary potential of human pluripotent stem cells (hPSCs) requires an understanding of the mechanisms underlying cell-fate decisions. Substrate elasticity can induce differentiation by signaling through the transcriptional coactivator Yes-associated protein (YAP). Cells cultured on surfaces mimicking brain elasticity exclude YAP from their nuclei and differentiate to neurons. How YAP localization is controlled during neural differentiation has been unclear. We employed CRISPR/Cas9 to tag endogenous YAP in hPSCs and used this fusion protein to identify YAP's interaction partners. This engineered cell line revealed that neural differentiation promotes a change in YAP interactors, including a dramatic increase in angiomotin (AMOT) interaction with YAP. AMOT regulates YAP localization during differentiation. AMOT expression increases during neural differentiation and leads to YAP nuclear exclusion. Our findings that AMOT-dependent regulation of YAP helps direct hPSC fate provide insight into the molecular mechanisms by which the microenvironment can induce neural differentiation. Endogenous tagging reveals YAP interactors in hPSCs AMOT-YAP complex concentration increases during neural differentiation AMOT regulates YAP localization in hPSCs hPSC cytoskeleton influences YAP localization via AMOT
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Affiliation(s)
- Yefim Zaltsman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sayaka Masuko
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joshua J Bensen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Laura L Kiessling
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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168
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Boopathy GTK, Hong W. Role of Hippo Pathway-YAP/TAZ Signaling in Angiogenesis. Front Cell Dev Biol 2019; 7:49. [PMID: 31024911 PMCID: PMC6468149 DOI: 10.3389/fcell.2019.00049] [Citation(s) in RCA: 208] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 03/19/2019] [Indexed: 12/12/2022] Open
Abstract
Angiogenesis is a highly coordinated process of formation of new blood vessels from pre-existing blood vessels. The process of development of the proper vascular network is a complex process that is crucial for the vertebrate development. Several studies have defined essential roles of Hippo pathway-YAP/TAZ in organ size control, tissue regeneration, and self-renewal. Thus Hippo pathway is one of the central components in tissue homeostasis. There are mounting evidences on the eminence of Hippo pathway-YAP/TAZ in angiogenesis in multiple model organisms. Hippo pathway-YAP/TAZ is now demonstrated to regulate endothelial cell proliferation, migration and survival; subsequently regulating vascular sprouting, vascular barrier formation, and vascular remodeling. Major intracellular signaling programs that regulate angiogenesis concomitantly activate YAP/TAZ to regulate key events in angiogenesis. In this review, we provide a brief overview of the recent findings in the Hippo pathway and YAP/TAZ signaling in angiogenesis.
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Affiliation(s)
- Gandhi T K Boopathy
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Wanjin Hong
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
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169
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Mlynarova J, Trentin-Sonoda M, Gaisler da Silva F, Major JL, Salih M, Carneiro-Ramos MS, Tuana BS. SLMAP3 isoform modulates cardiac gene expression and function. PLoS One 2019; 14:e0214669. [PMID: 30934005 PMCID: PMC6443179 DOI: 10.1371/journal.pone.0214669] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 03/18/2019] [Indexed: 12/23/2022] Open
Abstract
The sarcolemmal membrane associated proteins (SLMAPs) belong to the super family of tail anchored membrane proteins which serve diverse roles in biology including cell growth, protein trafficking and ion channel regulation. Mutations in human SLMAP have been linked to Brugada syndrome with putative deficits in trafficking of the sodium channel (Nav1.5) to the cell membrane resulting in aberrant electrical activity and heart function. Three main SLMAP isoforms (SLMAP1 (35 kDa), SLMAP2 (45 kDa), and SLMAP3 (91 kDa)) are expressed in myocardium but their precise role remains to be defined. Here we generated transgenic (Tg) mice with cardiac-specific expression of the SLMAP3 isoform during postnatal development which present with a significant decrease (20%) in fractional shortening and (11%) in cardiac output at 5 weeks of age. There was a lack of any notable cardiac remodeling (hypertrophy, fibrosis or fetal gene activation) in Tg hearts but the electrocardiogram indicated a significant increase (14%) in the PR interval and a decrease (43%) in the R amplitude. Western blot analysis indicated a selective and significant decrease (55%) in protein levels of Nav1.5 while 45% drop in its transcript levels were detectable by qRT-PCR. Significant decreases in the protein and transcript levels of the calcium transport system of the sarcoplasmic reticulum (SERCA2a/PLN) were also evident in Tg hearts. These data reveal a novel role for SLMAP3 in the selective regulation of important ion transport proteins at the level of gene expression and suggest that it may be a unique target in cardiovascular function and disease.
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Affiliation(s)
- Jana Mlynarova
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Mayra Trentin-Sonoda
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Fernanda Gaisler da Silva
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Jennifer L. Major
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Maysoon Salih
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | | | - Balwant S. Tuana
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- * E-mail:
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170
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The Caspase-3 homolog DrICE regulates endocytic trafficking during Drosophila tracheal morphogenesis. Nat Commun 2019; 10:1031. [PMID: 30833576 PMCID: PMC6399233 DOI: 10.1038/s41467-019-09009-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 02/13/2019] [Indexed: 12/30/2022] Open
Abstract
Although well known for its role in apoptosis, the executioner caspase DrICE has a non-apoptotic function that is required for elongation of the epithelial tubes of the Drosophila tracheal system. Here, we show that DrICE acts downstream of the Hippo Network to regulate endocytic trafficking of at least four cell polarity, cell junction and apical extracellular matrix proteins involved in tracheal tube size control: Crumbs, Uninflatable, Kune-Kune and Serpentine. We further show that tracheal cells are competent to undergo apoptosis, even though developmentally-regulated DrICE function rarely kills tracheal cells. Our results reveal a developmental role for caspases, a pool of DrICE that co-localizes with Clathrin, and a mechanism by which the Hippo Network controls endocytic trafficking. Given reports of in vitro regulation of endocytosis by mammalian caspases during apoptosis, we propose that caspase-mediated regulation of endocytic trafficking is an evolutionarily conserved function of caspases that can be deployed during morphogenesis. Caspases are well-known drivers of apoptosis, although recent studies suggest potential non-apoptotic functions. Here, McSharry and Beitel show that the Drosophila executioner caspase DrICE regulates endocytic trafficking of key proteins downstream of Hippo during tracheal morphogenesis.
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171
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Miller CJ, Lou HJ, Simpson C, van de Kooij B, Ha BH, Fisher OS, Pirman NL, Boggon TJ, Rinehart J, Yaffe MB, Linding R, Turk BE. Comprehensive profiling of the STE20 kinase family defines features essential for selective substrate targeting and signaling output. PLoS Biol 2019; 17:e2006540. [PMID: 30897078 PMCID: PMC6445471 DOI: 10.1371/journal.pbio.2006540] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 04/02/2019] [Accepted: 03/14/2019] [Indexed: 12/14/2022] Open
Abstract
Specificity within protein kinase signaling cascades is determined by direct and indirect interactions between kinases and their substrates. While the impact of localization and recruitment on kinase-substrate targeting can be readily assessed, evaluating the relative importance of direct phosphorylation site interactions remains challenging. In this study, we examine the STE20 family of protein serine-threonine kinases to investigate basic mechanisms of substrate targeting. We used peptide arrays to define the phosphorylation site specificity for the majority of STE20 kinases and categorized them into four distinct groups. Using structure-guided mutagenesis, we identified key specificity-determining residues within the kinase catalytic cleft, including an unappreciated role for the kinase β3-αC loop region in controlling specificity. Exchanging key residues between the STE20 kinases p21-activated kinase 4 (PAK4) and Mammalian sterile 20 kinase 4 (MST4) largely interconverted their phosphorylation site preferences. In cells, a reprogrammed PAK4 mutant, engineered to recognize MST substrates, failed to phosphorylate PAK4 substrates or to mediate remodeling of the actin cytoskeleton. In contrast, this mutant could rescue signaling through the Hippo pathway in cells lacking multiple MST kinases. These observations formally demonstrate the importance of catalytic site specificity for directing protein kinase signal transduction pathways. Our findings further suggest that phosphorylation site specificity is both necessary and sufficient to mediate distinct signaling outputs of STE20 kinases and imply broad applicability to other kinase signaling systems.
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Affiliation(s)
- Chad J. Miller
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Craig Simpson
- Biotech Research and Innovation Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bert van de Kooij
- Departments of Biological Engineering and Biology, MIT Center for Precision Cancer Medicine and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Byung Hak Ha
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Oriana S. Fisher
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Natasha L. Pirman
- Department of Cellular and Molecular Physiology and Systems Biology Institute, Yale University, New Haven, Connecticut, United States of America
| | - Titus J. Boggon
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Jesse Rinehart
- Department of Cellular and Molecular Physiology and Systems Biology Institute, Yale University, New Haven, Connecticut, United States of America
| | - Michael B. Yaffe
- Departments of Biological Engineering and Biology, MIT Center for Precision Cancer Medicine and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Rune Linding
- Biotech Research and Innovation Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Benjamin E. Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
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172
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Béganton B, Coyaud E, Mangé A, Solassol J. Approches nouvelles pour l’étude des interactions protéine-protéine. Med Sci (Paris) 2019; 35:223-231. [DOI: 10.1051/medsci/2019035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Le protéome est un système dynamique où les interactions protéine-protéine occupent une place essentielle pour modeler ensemble le phénotype cellulaire. L’identification de ces interactions a toutefois longtemps représenté un obstacle important en protéomique tant les techniques disponibles ne permettaient pas de rendre compte de ces dynamiques d’interactions. Le développement récent du BioID et de l’APEX, deux technologies de marquage de proximité, ouvre aujourd’hui de nouvelles perspectives. Dans cette revue, nous décrivons les outils disponibles pour étudier les interactions protéine-protéine et discutons des progrès récents apportés par les marquages de proximité pour compléter notre vision du protéome et ainsi mieux comprendre les mécanismes cellulaires.
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173
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Architecture, substructures, and dynamic assembly of STRIPAK complexes in Hippo signaling. Cell Discov 2019; 5:3. [PMID: 30622739 PMCID: PMC6323126 DOI: 10.1038/s41421-018-0077-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/08/2018] [Accepted: 12/10/2018] [Indexed: 01/24/2023] Open
Abstract
Striatin-interacting phosphatases and kinases (STRIPAKs) are evolutionarily conserved supramolecular complexes, which have been implicated in the Hippo signaling pathway. Yet the topological structure and dynamic assembly of STRIPAK complexes remain elusive. Here, we report the overall architecture and substructures of a Hippo kinase-containing STRIPAK complex. PP2Aa/c-bound STRN3 directly contacts the Hippo kinase MST2 and also controls the loading of MST2 via two “arms” in a phosphorylation-dependent manner, one arm being STRIP1 and the other SIKE1-SLMAP. A decreased cell density triggered the dissociation of the STRIP1 arm from STRIPAK, reflecting the dynamic assembly of the complex upon sensing upstream signals. Crystallographic studies defined at atomic resolution the interface between STRN3 and SIKE1, and that between SIKE1 and SLMAP. Disrupting the complex assembly abrogated the regulatory effect of STRIPAK towards Hippo signaling. Collectively, our study revealed a “two-arm” assembly of STRIPAK with context-dependent dynamics, offering a framework for further studies on Hippo signaling and biological processes involving MST kinases.
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174
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Amisaki M, Tsuchiya H, Sakabe T, Fujiwara Y, Shiota G. Identification of genes involved in the regulation of TERT in hepatocellular carcinoma. Cancer Sci 2019; 110:550-560. [PMID: 30447097 PMCID: PMC6361581 DOI: 10.1111/cas.13884] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 11/08/2018] [Accepted: 11/15/2018] [Indexed: 02/06/2023] Open
Abstract
Telomerase reverse transcriptase (TERT) promotes immortalization by protecting telomeres in cancer cells. Mutation of the TERT promoter is one of the most common genetic alterations in hepatocellular carcinoma (HCC), indicating that TERT upregulation is a critical event in hepatocarcinogenesis. Regulators of TERT transcription are, therefore, predicted to be plausible targets for HCC treatment. We undertook a genome‐wide shRNA library screen and identified C15orf55 and C7orf43 as regulators of TERT expression in HepG2 cells. Promoter assays showed that C15orf55‐ and C7orf43‐responsive sites exist between base pairs −58 and +36 and −169 and −59 in the TERT promoter, respectively. C15orf55 upregulates TERT expression by binding to two GC motifs in the SP1 binding site of the TERT promoter. C7orf43 upregulates TERT expression through Yes‐associated protein 1. The expression levels of C15orf55 and C7orf43 also correlated with that of TERT, and were significantly increased in both HCC tissues and their adjacent non‐tumor tissues, compared to normal liver tissues from non‐HCC patients. Analysis of 377 HCC patients in The Cancer Genome Atlas dataset showed that overall survival of patients with low levels of C15orf55 and C7orf43 expression in tumor tissues was better compared with patients with high levels of C15orf55 and/or high C7orf43 expression. These results indicate that C15orf55 and C7orf43 are involved in the incidence and progression of HCC by upregulating TERT. In conclusion, we identified C15orf55 and C7orf43 as positive regulators of TERT expression in HCC tissues. These genes are promising targets for HCC treatment.
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Affiliation(s)
- Masataka Amisaki
- Division of Molecular and Genetic Medicine, Graduate School of Medicine, Tottori University, Yonago, Japan.,Division of Surgical Oncology, Department of Surgery, School of Medicine, Tottori University Faculty of Medicine, Yonago, Japan
| | - Hiroyuki Tsuchiya
- Division of Molecular and Genetic Medicine, Graduate School of Medicine, Tottori University, Yonago, Japan
| | - Tomohiko Sakabe
- Division of Organ Pathology, Department of Pathology, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Yoshiyuki Fujiwara
- Division of Surgical Oncology, Department of Surgery, School of Medicine, Tottori University Faculty of Medicine, Yonago, Japan
| | - Goshi Shiota
- Division of Molecular and Genetic Medicine, Graduate School of Medicine, Tottori University, Yonago, Japan
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175
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Abstract
This chapter describes the luciferase assays that are available to monitor YAP/TAZ activity in cell lines and to study their regulation, including the choice for the normalizer, a description of the main YAP-/TAZ-responsive luciferase reporters used so far by the community, and technical notes and experimental considerations on the most appropriate positive controls. Some specific examples are provided to use luciferase assays as the basis to distinguish between Hippo-mediated and phosphorylation-mediated regulatory events and regulatory events that regulate YAP/TAZ independent of these inputs. Finally, typical experimental protocols are outlined briefly for an easier setup of YAP/TAZ luciferase assays.
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Affiliation(s)
- Sirio Dupont
- Department of Molecular Medicine, School of Medicine, University of Padova, Padova, Italy.
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176
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Considerations for Identifying Endogenous Protein Complexes from Tissue via Immunoaffinity Purification and Quantitative Mass Spectrometry. Methods Mol Biol 2019; 1977:115-143. [PMID: 30980326 DOI: 10.1007/978-1-4939-9232-4_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protein complexes perform key roles in nearly all aspects of biology. Identification of the composition of these complexes offers insights into how different cellular processes are carried out. The use of affinity purification coupled to mass spectrometry has become a method of choice for identifying protein-protein interactions, but has been most frequently applied to cell model systems using tagged and overexpressed bait proteins. Although valuable, this approach can create several potential artifacts due to the presence of a tag on a protein and the higher abundance of the protein of interest (bait). The isolation of endogenous proteins using antibodies raised against the proteins of interest instead of an epitope tag offers a means to examine protein interactions in any cellular or animal model system and without the caveats of overexpressed, tagged proteins. Although conceptually simple, the limited use of this approach has been primarily driven by challenges associated with finding adequate antibodies and experimental conditions for effective isolations. In this chapter, we present a protocol for the optimization of lysis conditions, antibody evaluation, affinity purification, and ultimately identification of protein complexes from endogenous immunoaffinity purifications using quantitative mass spectrometry. We also highlight the increased use of targeted mass spectrometry analyses, such as parallel reaction monitoring (PRM) for orthogonal validation of protein isolation and interactions initially identified via data-dependent mass spectrometry analyses.
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177
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Titeca K, Lemmens I, Tavernier J, Eyckerman S. Discovering cellular protein-protein interactions: Technological strategies and opportunities. MASS SPECTROMETRY REVIEWS 2019; 38:79-111. [PMID: 29957823 DOI: 10.1002/mas.21574] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 01/03/2018] [Accepted: 06/04/2018] [Indexed: 05/09/2023]
Abstract
The analysis of protein interaction networks is one of the key challenges in the study of biology. It connects genotypes to phenotypes, and disruption often leads to diseases. Hence, many technologies have been developed to study protein-protein interactions (PPIs) in a cellular context. The expansion of the PPI technology toolbox however complicates the selection of optimal approaches for diverse biological questions. This review gives an overview of the binary and co-complex technologies, with the former evaluating the interaction of two co-expressed genetically tagged proteins, and the latter only needing the expression of a single tagged protein or no tagged proteins at all. Mass spectrometry is crucial for some binary and all co-complex technologies. After the detailed description of the different technologies, the review compares their unique specifications, advantages, disadvantages, and applicability, while highlighting opportunities for further advancements.
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Affiliation(s)
- Kevin Titeca
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Irma Lemmens
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Jan Tavernier
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
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178
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Abstract
Biological activities are mainly executed by proteins and in most of the occasions these activities are accomplished by protein complexes or through protein-protein interactions (PPI). So it is critical to reveal how the protein complexes are organized and demonstrate the PPIs involved in the biological processes. In addition to the traditional biochemical approaches, proximity-dependent labeling (PDL) has recently been proposed to identify the interacting partners of a given protein. PDL requires the fusion expression of the target protein with an enzyme which catalyzes the attachment of a reactive molecule to the interacting partners in a distance-dependent manner. Further analysis of all the proteins that are modified by the reactive molecule discloses the identity of these proteins which are presumed to be interacting partners of the target protein. BioID is one of those representative PDL methods with the most widely applications. The enzyme used in BioID is a biotin ligase BirA which catalyzes the biotinylation of target protein with the presence of biotin. Through streptavidin-mediated pull-down and mass spectrometry analysis, the interacting protein candidates of a given protein can be obtained.
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Affiliation(s)
- Peipei Li
- Faculty of Health Sciences, Cancer Center, University of Macau, Macau, China
| | - Yuan Meng
- Faculty of Health Sciences, Cancer Center, University of Macau, Macau, China
| | - Li Wang
- Faculty of Health Sciences, Cancer Center, University of Macau, Macau, China
| | - Li-Jun Di
- Faculty of Health Sciences, Cancer Center, University of Macau, Macau, China.
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179
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Ohama T. The multiple functions of protein phosphatase 6. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:74-82. [DOI: 10.1016/j.bbamcr.2018.07.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/21/2018] [Accepted: 07/18/2018] [Indexed: 12/26/2022]
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180
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Lahav-Ariel L, Caspi M, Nadar-Ponniah PT, Zelikson N, Hofmann I, Hanson KK, Franke WW, Sklan EH, Avraham KB, Rosin-Arbesfeld R. Striatin is a novel modulator of cell adhesion. FASEB J 2018; 33:4729-4740. [PMID: 30592649 DOI: 10.1096/fj.201801882r] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The adherens junctions (AJs) and tight junctions (TJs) provide critical adhesive contacts between neighboring epithelial cells and are crucial for epithelial adhesion, integrity, and barrier functions in a wide variety of tissues and organisms. The striatin protein family, which are part of the striatin interaction phosphatases and kinases complex, are multidomain scaffolding proteins that play important biologic roles. We have previously shown that striatin colocalizes with the tumor suppressor protein adenomatous polyposis coli in the TJs of epithelial cells. Here we show that striatin affects junction integrity and cell migration, probably through a mechanism that involves the adhesion molecule E-cadherin. Cells engaged in cell-cell adhesion expressed a high MW-modified form of striatin that forms stable associations with detergent-insoluble, membrane-bound cellular fractions. In addition, striatin has recently been suggested to be a target of the poly (ADP-ribose) polymerases Tankyrase 1, and we have found that striatin interacts with Tankyrase 1 and is subsequently poly-ADP-ribosylated. Taken together, our results suggest that striatin is a novel cell-cell junctional protein that functions to maintain correct cell adhesion and may have a role in establishing the relationship between AJs and TJs that is fundamental for epithelial cell-cell adhesion.-Lahav-Ariel, L., Caspi, M., Nadar-Ponniah, P. T., Zelikson, N., Hofmann, I., Hanson, K. K., Franke, W. W., Sklan, E. H., Avraham, K. B., Rosin-Arbesfeld, R. Striatin is a novel modulator of cell adhesion.
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Affiliation(s)
- Lital Lahav-Ariel
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Michal Caspi
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Prathamesh T Nadar-Ponniah
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Natalie Zelikson
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ilse Hofmann
- Division of Vascular Oncology and Metastasis, Center for Molecular Biology-German Cancer Research Center (DKFZ-ZMBH) Alliance, German Cancer Research Center, Heidelberg, Germany.,Department of Vascular Biology and Tumor Angiogenesis (CBTM), Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Kirsten K Hanson
- Department of Biology and South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, Texas, USA; and
| | - Werner W Franke
- Helmholtz Group for Cell Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ella H Sklan
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Rina Rosin-Arbesfeld
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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181
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Getting to know the neighborhood: using proximity-dependent biotinylation to characterize protein complexes and map organelles. Curr Opin Chem Biol 2018; 48:44-54. [PMID: 30458335 DOI: 10.1016/j.cbpa.2018.10.017] [Citation(s) in RCA: 168] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/14/2018] [Accepted: 10/16/2018] [Indexed: 12/12/2022]
Abstract
The use of proximity-dependent biotinylation approaches combined with mass spectrometry (e.g. BioID and APEX) has revolutionized the study of protein-protein interactions and organellar proteomics. These powerful techniques are based on the fusion of an enzyme (e.g. a biotin ligase or peroxidase) to a 'bait' protein of interest, which is then expressed in a relevant biological setting. Addition of enzyme substrate enables covalent biotin labeling of proteins in the vicinity of the bait in vivo. These approaches thus allow for the capture and identification of 'neighborhood' proteins in the context of a living cell, and provide data that are complementary to more established techniques such as fractionation or affinity purification. As compared to standard affinity-based purification approaches, proximity-dependent biotinylation (PDB) can help to: first, identify interactions with and amongst membrane proteins, and other polypeptide classes that are less amenable to study by standard pulldown techniques; second, enrich for transient and/or low affinity interactions that are not readily captured using affinity purification approaches; third, avoid post-lysis artefacts associated with standard biochemical purification experiments and; fourth, provide deep insight into the organization of membrane-less organelles and other subcellular structures that cannot be easily isolated or purified. Given the increasing use of these techniques to answer a variety of different types of biological questions, it is important to understand how best to design PDB-MS experiments, what type of data they generate, and how to analyze and interpret the results.
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182
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Bigenzahn JW, Collu GM, Kartnig F, Pieraks M, Vladimer GI, Heinz LX, Sedlyarov V, Schischlik F, Fauster A, Rebsamen M, Parapatics K, Blomen VA, Müller AC, Winter GE, Kralovics R, Brummelkamp TR, Mlodzik M, Superti-Furga G. LZTR1 is a regulator of RAS ubiquitination and signaling. Science 2018; 362:1171-1177. [PMID: 30442766 DOI: 10.1126/science.aap8210] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 06/26/2018] [Accepted: 10/30/2018] [Indexed: 12/12/2022]
Abstract
In genetic screens aimed at understanding drug resistance mechanisms in chronic myeloid leukemia cells, inactivation of the cullin 3 adapter protein-encoding leucine zipper-like transcription regulator 1 (LZTR1) gene led to enhanced mitogen-activated protein kinase (MAPK) pathway activity and reduced sensitivity to tyrosine kinase inhibitors. Knockdown of the Drosophila LZTR1 ortholog CG3711 resulted in a Ras-dependent gain-of-function phenotype. Endogenous human LZTR1 associates with the main RAS isoforms. Inactivation of LZTR1 led to decreased ubiquitination and enhanced plasma membrane localization of endogenous KRAS (V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog). We propose that LZTR1 acts as a conserved regulator of RAS ubiquitination and MAPK pathway activation. Because LZTR1 disease mutations failed to revert loss-of-function phenotypes, our findings provide a molecular rationale for LZTR1 involvement in a variety of inherited and acquired human disorders.
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Affiliation(s)
- Johannes W Bigenzahn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Giovanna M Collu
- Department of Cell, Developmental, and Regenerative Biology and Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Felix Kartnig
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Melanie Pieraks
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Gregory I Vladimer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Leonhard X Heinz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Vitaly Sedlyarov
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Fiorella Schischlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Astrid Fauster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.,Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - Manuele Rebsamen
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Katja Parapatics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Vincent A Blomen
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Robert Kralovics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Thijn R Brummelkamp
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.,Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands.,Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands.,Cancer Genomics Center (CGC.nl), Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - Marek Mlodzik
- Department of Cell, Developmental, and Regenerative Biology and Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria. .,Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
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183
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Hearn T. ALMS1 and Alström syndrome: a recessive form of metabolic, neurosensory and cardiac deficits. J Mol Med (Berl) 2018; 97:1-17. [PMID: 30421101 PMCID: PMC6327082 DOI: 10.1007/s00109-018-1714-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/25/2018] [Accepted: 10/30/2018] [Indexed: 12/12/2022]
Abstract
Alström syndrome (AS) is characterised by metabolic deficits, retinal dystrophy, sensorineural hearing loss, dilated cardiomyopathy and multi-organ fibrosis. Elucidating the function of the mutated gene, ALMS1, is critical for the development of specific treatments and may uncover pathways relevant to a range of other disorders including common forms of obesity and type 2 diabetes. Interest in ALMS1 is heightened by the recent discovery of its involvement in neonatal cardiomyocyte cell cycle arrest, a process with potential relevance to regenerative medicine. ALMS1 encodes a ~ 0.5 megadalton protein that localises to the base of centrioles. Some studies have suggested a role for this protein in maintaining centriole-nucleated sensory organelles termed primary cilia, and AS is now considered to belong to the growing class of human genetic disorders linked to ciliary dysfunction (ciliopathies). However, mechanistic details are lacking, and recent studies have implicated ALMS1 in several processes including endosomal trafficking, actin organisation, maintenance of centrosome cohesion and transcription. In line with a more complex picture, multiple isoforms of the protein likely exist and non-centrosomal sites of localisation have been reported. This review outlines the evidence for both ciliary and extra-ciliary functions of ALMS1.
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Affiliation(s)
- Tom Hearn
- Institute of Life Science, Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK.
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184
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Oostdyk LT, Shank L, Jividen K, Dworak N, Sherman NE, Paschal BM. Towards improving proximity labeling by the biotin ligase BirA. Methods 2018; 157:66-79. [PMID: 30419333 DOI: 10.1016/j.ymeth.2018.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/26/2018] [Accepted: 11/06/2018] [Indexed: 11/15/2022] Open
Abstract
The discovery and validation of protein-protein interactions provides a knowledge base that is critical for defining protein networks and how they underpin the biology of the cell. Identification of protein interactions that are highly transient, or sensitive to biochemical disruption, can be very difficult. This challenge has been met by proximity labeling methods which generate reactive species that chemically modify neighboring proteins. The most widely used proximity labeling method is BioID, which features a mutant biotin ligase BirA(Arg118Gly), termed BirA*, fused to a protein of interest. Here, we explore how amino acid substitutions at Arg118 affect the biochemical properties of BirA. We found that relative to wild-type BirA, the Arg118Lys substitution both slightly reduced biotin affinity and increased the release of reactive biotinyl-5'-AMP. BioID using a BirA(Arg118Lys)-Lamin A fusion enabled identification of PCNA as a lamina-proximal protein in HEK293T cells, a finding that was validated by immunofluorescence microscopy. Our data expand on the concept that proximity labeling by BirA fused to proteins of interest can be modulated by amino acid substitutions that affect biotin affinity and the release of biotinyl-5'-AMP.
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Affiliation(s)
- Luke T Oostdyk
- Center for Cell Signaling, University of Virginia, Charlottesville, VA 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, VA 22908, USA
| | - Leonard Shank
- Center for Cell Signaling, University of Virginia, Charlottesville, VA 22908, USA
| | - Kasey Jividen
- Center for Cell Signaling, University of Virginia, Charlottesville, VA 22908, USA
| | - Natalia Dworak
- Center for Cell Signaling, University of Virginia, Charlottesville, VA 22908, USA
| | - Nicholas E Sherman
- W.M. Keck Biomedical Mass Spectrometry Laboratory, University of Virginia, VA 22908, USA
| | - Bryce M Paschal
- Center for Cell Signaling, University of Virginia, Charlottesville, VA 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, VA 22908, USA.
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185
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Mojarad BA, Gupta GD, Hasegan M, Goudiam O, Basto R, Gingras AC, Pelletier L. CEP19 cooperates with FOP and CEP350 to drive early steps in the ciliogenesis programme. Open Biol 2018; 7:rsob.170114. [PMID: 28659385 PMCID: PMC5493781 DOI: 10.1098/rsob.170114] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 06/06/2017] [Indexed: 01/12/2023] Open
Abstract
Primary cilia are microtubule-based sensory organelles necessary for efficient transduction of extracellular cues. To initiate cilia formation, ciliary vesicles (CVs) are transported to the vicinity of the centrosome where they dock to the distal end of the mother centriole and fuse to initiate cilium assembly. However, to this date, the early steps in cilia formation remain incompletely understood. Here, we demonstrate functional interplay between CEP19, FOP and CEP350 in ciliogenesis. Using three-dimensional structured-illumination microscopy (3D-SIM) imaging, we mapped the relative spatial distribution of these proteins at the distal end of the mother centriole and show that CEP350/FOP act upstream of CEP19 in their recruitment hierarchy. We demonstrate that CEP19 CRISPR KO cells are severely impaired in their ability to form cilia, analogous to the loss of function of CEP19 binding partners FOP and CEP350. Notably, in the absence of CEP19 microtubule anchoring at centromes is similar in manner to its interaction partners FOP and CEP350. Using GFP-tagged deletion constructs of CEP19, we show that the C-terminus of CEP19 is required for both its localization to centrioles and for its function in ciliogenesis. Critically, this region also mediates the interaction between CEP19 and FOP/CEP350. Interestingly, a morbid-obesity-associated R82* truncated mutant of CEP19 cannot ciliate nor interact with FOP and CEP350, indicative of a putative role for CEP19 in ciliopathies. Finally, analysis of CEP19 KO cells using thin-section electron microscopy revealed marked defects in the docking of CVs to the distal end of the mother centrioles. Together, these data demonstrate a role for the CEP19, FOP and CEP350 module in ciliogenesis and the possible effect of disrupting their functions in ciliopathies.
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Affiliation(s)
- Bahareh A Mojarad
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada M5G 1X5.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Gagan D Gupta
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada M5G 1X5
| | - Monica Hasegan
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada M5G 1X5
| | - Oumou Goudiam
- Institut Curie, PSL Research University, CNRS, UMR144, 12 rue Lhomond, Paris 75005, France
| | - Renata Basto
- Institut Curie, PSL Research University, CNRS, UMR144, 12 rue Lhomond, Paris 75005, France
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada M5G 1X5.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Laurence Pelletier
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada M5G 1X5 .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
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186
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Wu R, Yang H, Wan J, Deng X, Chen L, Hao S, Ma L. Knockdown of the Hippo transducer YAP reduces proliferation and promotes apoptosis in the Jurkat leukemia cell. Mol Med Rep 2018; 18:5379-5388. [PMID: 30320399 PMCID: PMC6236312 DOI: 10.3892/mmr.2018.9556] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 09/10/2018] [Indexed: 12/26/2022] Open
Abstract
Leukemia and lymphoma are common hematological malignancies in children and young adults, which pose a tremendous threat to the survival of these young patients worldwide, despite availability of various effective treatments. The Hippo pathway is a novel-signaling pathway that regulates organ size, cell proliferation, apoptosis and tumorigenesis. The chief component of this pathway is the transducer yes-associated protein (YAP) which is over-expressed in numerous categories of tumors. However, little is known about the effect of YAP in hematological malignancies. In the present study, YAP expression was screened in several leukemia and lymphoma cell lines, and high YAP expression was demonstrated in Jurkat cells. To further unravel its effect on the biological behavior of Jurkat cells, lentivirus transduced short hairpin RNA (shRNA) technique was used to silence YAP. As expected, the YAP-specific shRNA dramatically inhibited YAP expression at the mRNA and protein levels. Reduced leukemia cell proliferation and increased cell apoptosis were demonstrated in YAP knockdown Jurkat cells. It was also demonstrated that YAP knockdown resulted in deregulated expression of a cluster of downstream genes crucial to cell proliferation or apoptosis, including protein kinase B, B-cell lymphoma 2 (BCL2) and BCL2 like protein 1. Consequently, the results of the present study established that suppression of YAP expression serves an important role in Jurkat cell proliferation and apoptosis, which may serve as a potential therapeutic target.
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Affiliation(s)
- Ran Wu
- Department of Hematology, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
| | - Hui Yang
- Department of Hematology, Shanghai 6th People's Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
| | - Jiangbo Wan
- Department of Hematology, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
| | - Xiaohui Deng
- Department of Hematology, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
| | - Linjun Chen
- Department of Hematology, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
| | - Siguo Hao
- Department of Hematology, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
| | - Liyuan Ma
- Department of Hematology, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
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187
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Banerjee SL, Dionne U, Lambert JP, Bisson N. Targeted proteomics analyses of phosphorylation-dependent signalling networks. J Proteomics 2018; 189:39-47. [DOI: 10.1016/j.jprot.2018.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/19/2018] [Accepted: 02/01/2018] [Indexed: 01/18/2023]
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188
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Mana-Capelli S, McCollum D. Angiomotins stimulate LATS kinase autophosphorylation and act as scaffolds that promote Hippo signaling. J Biol Chem 2018; 293:18230-18241. [PMID: 30266805 DOI: 10.1074/jbc.ra118.004187] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 09/17/2018] [Indexed: 01/31/2023] Open
Abstract
The Hippo pathway controls cell proliferation, differentiation, and survival by regulating the Yes-associated protein (YAP) transcriptional coactivator in response to various stimuli, including the mechanical environment. The major YAP regulators are the LATS1/2 kinases, which phosphorylate and inhibit YAP. LATS1/2 are activated by phosphorylation on a hydrophobic motif (HM) outside of the kinase domain by MST1/2 and other kinases. Phosphorylation of the HM motif then triggers autophosphorylation of the kinase in the activation loop to fully activate the kinase, a process facilitated by MOB1. The angiomotin family of proteins (AMOT, AMOTL1, and AMOTL2) bind LATS1/2 and promote its kinase activity and YAP phosphorylation through an unknown mechanism. Here we show that angiomotins increase Hippo signaling through multiple mechanisms. We found that, by binding LATS1/2, SAV1, and YAP, angiomotins function as a scaffold that connects LATS1/2 to both its activator SAV1-MST1 and its target YAP. Deletion of all three angiomotins reduced the association of LATS1 with SAV1-MST1 and decreased MST1/2-mediated LATS1/2-HM phosphorylation. Angiomotin deletion also reduced LATS1/2's ability to associate with and phosphorylate YAP. In addition, we found that angiomotins have an unexpected function along with MOB1 to promote autophosphorylation of LATS1/2 on the activation loop motif independent of HM phosphorylation. These results indicate that angiomotins enhance Hippo signaling by stimulating LATS1/2 autophosphorylation and by connecting LATS1/2 with both its activator SAV1-MST1/2 and its substrate YAP.
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Affiliation(s)
- Sebastian Mana-Capelli
- From the Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Dannel McCollum
- From the Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605.
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189
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Emmer BT, Hesketh GG, Kotnik E, Tang VT, Lascuna PJ, Xiang J, Gingras AC, Chen XW, Ginsburg D. The cargo receptor SURF4 promotes the efficient cellular secretion of PCSK9. eLife 2018; 7:38839. [PMID: 30251625 PMCID: PMC6156083 DOI: 10.7554/elife.38839] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 09/14/2018] [Indexed: 12/17/2022] Open
Abstract
PCSK9 is a secreted protein that regulates plasma cholesterol levels and cardiovascular disease risk. Prior studies suggested the presence of an ER cargo receptor that recruits PCSK9 into the secretory pathway, but its identity has remained elusive. Here, we apply a novel approach that combines proximity-dependent biotinylation and proteomics together with genome-scale CRISPR screening to identify SURF4, a homologue of the yeast cargo receptor Erv29p, as a primary mediator of PCSK9 secretion in HEK293T cells. The functional contribution of SURF4 to PCSK9 secretion was confirmed with multiple independent SURF4-targeting sgRNAs, clonal SURF4-deficient cell lines, and functional rescue with SURF4 cDNA. SURF4 was found to localize to the early secretory pathway where it physically interacts with PCSK9. Deletion of SURF4 resulted in ER accumulation and decreased extracellular secretion of PCSK9. These findings support a model in which SURF4 functions as an ER cargo receptor mediating the efficient cellular secretion of PCSK9.
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Affiliation(s)
- Brian T Emmer
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.,Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
| | - Geoffrey G Hesketh
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | - Emilee Kotnik
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
| | - Vi T Tang
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
| | - Paul J Lascuna
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
| | - Jie Xiang
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
| | - Anne-Claude Gingras
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Xiao-Wei Chen
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan.,State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Center for Life Sciences, Peking University, Beijing, China
| | - David Ginsburg
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.,Life Sciences Institute, University of Michigan, Ann Arbor, Michigan.,Department of Human Genetics, University of Michigan, Ann Arbor, Michigan.,Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, Michigan.,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan
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190
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Meyer K, Kirchner M, Uyar B, Cheng JY, Russo G, Hernandez-Miranda LR, Szymborska A, Zauber H, Rudolph IM, Willnow TE, Akalin A, Haucke V, Gerhardt H, Birchmeier C, Kühn R, Krauss M, Diecke S, Pascual JM, Selbach M. Mutations in Disordered Regions Can Cause Disease by Creating Dileucine Motifs. Cell 2018; 175:239-253.e17. [PMID: 30197081 DOI: 10.1016/j.cell.2018.08.019] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 06/09/2018] [Accepted: 08/08/2018] [Indexed: 01/12/2023]
Abstract
Many disease-causing missense mutations affect intrinsically disordered regions (IDRs) of proteins, but the molecular mechanism of their pathogenicity is enigmatic. Here, we employ a peptide-based proteomic screen to investigate the impact of mutations in IDRs on protein-protein interactions. We find that mutations in disordered cytosolic regions of three transmembrane proteins (GLUT1, ITPR1, and CACNA1H) lead to an increased clathrin binding. All three mutations create dileucine motifs known to mediate clathrin-dependent trafficking. Follow-up experiments on GLUT1 (SLC2A1), the glucose transporter causative of GLUT1 deficiency syndrome, revealed that the mutated protein mislocalizes to intracellular compartments. Mutant GLUT1 interacts with adaptor proteins (APs) in vitro, and knocking down AP-2 reverts the cellular mislocalization and restores glucose transport. A systematic analysis of other known disease-causing variants revealed a significant and specific overrepresentation of gained dileucine motifs in structurally disordered cytosolic domains of transmembrane proteins. Thus, several mutations in disordered regions appear to cause "dileucineopathies."
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Affiliation(s)
- Katrina Meyer
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Marieluise Kirchner
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Bora Uyar
- Bioinformatics Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Jing-Yuan Cheng
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Giulia Russo
- Molecular Pharmacology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Luis R Hernandez-Miranda
- Developmental Biology/Signal Transduction, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Anna Szymborska
- Integrative Vascular Biology Laboratory, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research) partner site, 13347 Berlin, Germany
| | - Henrik Zauber
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Ina-Maria Rudolph
- Molecular Cardiovascular Research, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Thomas E Willnow
- Molecular Cardiovascular Research, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Altuna Akalin
- Bioinformatics Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Volker Haucke
- Molecular Pharmacology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Holger Gerhardt
- Integrative Vascular Biology Laboratory, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research) partner site, 13347 Berlin, Germany; Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Carmen Birchmeier
- Developmental Biology/Signal Transduction, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Ralf Kühn
- Berlin Institute of Health (BIH), 10178 Berlin, Germany; Core Facility Transgenics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Michael Krauss
- Molecular Pharmacology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Sebastian Diecke
- DZHK (German Centre for Cardiovascular Research) partner site, 13347 Berlin, Germany; Berlin Institute of Health (BIH), 10178 Berlin, Germany; Core Facility Pluripotent Stem Cells, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Juan M Pascual
- Department of Neurology and Neurotherapeutics, UT Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX 75390, USA
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany; Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany.
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191
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Radchenko D, Teichert I, Pöggeler S, Kück U. A Hippo Pathway-Related GCK Controls Both Sexual and Vegetative Developmental Processes in the Fungus Sordaria macrospora. Genetics 2018; 210:137-153. [PMID: 30012560 PMCID: PMC6116960 DOI: 10.1534/genetics.118.301261] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 06/25/2018] [Indexed: 11/18/2022] Open
Abstract
The supramolecular striatin-interacting phosphatases and kinases (STRIPAK) complex is conserved from yeast to human, and regulates a variety of key biological processes. In animals, this complex consists of the scaffold protein striatin, the protein phosphatase 2A, and kinases, such as germinal center kinase (GCK) III and GCKIV family members, as well as other associated proteins. The STRIPAK complex was identified as a negative regulator of the Hippo pathway, a large eukaryotic signaling network with a core composed of a GCK and a nuclear Dbf2-related kinase. The signaling architecture of the Hippo core resembles the fungal septation initiation network (SIN) that regulates cytokinesis in fission yeast as well as septation in filamentous fungi. In the filamentous model fungus Sordaria macrospora, core components of the STRIPAK complex have been functionally described and the striatin homolog PRO11 has been shown to interact with the GCK SmKIN3. However, the exact role of SmKIN3 in fungal development has not yet been fully elucidated. Here, we provide comprehensive genetic and functional analysis of SmKIN3 from S. macrospora Using deletion mutants and site-directed mutagenesis, along with phenotypic and phylogenetic analysis, we provide compelling evidence that SmKIN3 is involved in fruiting body formation, hyphal fusion, and septation. Strains carrying the ATP-binding mutant SmKIN3K39R, as well as a double-deletion strain lacking SmKIN3 and the core STRIPAK subunit PRO11, also revealed severe developmental defects. Collectively, this study suggests that SmKIN3 links both the SIN and STRIPAK complex, thereby regulating multiple key cellular processes.
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Affiliation(s)
- Daria Radchenko
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, 44780, Germany
| | - Ines Teichert
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, 44780, Germany
| | - Stefanie Pöggeler
- Genetik Eukaryotischer Mikroorganismen, Institut für Mikrobiologie und Genetik, Universität Göttingen, 37077, Germany
| | - Ulrich Kück
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, 44780, Germany
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192
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Gill MK, Christova T, Zhang YY, Gregorieff A, Zhang L, Narimatsu M, Song S, Xiong S, Couzens AL, Tong J, Krieger JR, Moran MF, Zlotta AR, van der Kwast TH, Gingras AC, Sicheri F, Wrana JL, Attisano L. A feed forward loop enforces YAP/TAZ signaling during tumorigenesis. Nat Commun 2018; 9:3510. [PMID: 30158528 PMCID: PMC6115388 DOI: 10.1038/s41467-018-05939-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 07/30/2018] [Indexed: 12/13/2022] Open
Abstract
In most solid tumors, the Hippo pathway is inactivated through poorly understood mechanisms that result in the activation of the transcriptional regulators, YAP and TAZ. Here, we identify NUAK2 as a YAP/TAZ activator that directly inhibits LATS-mediated phosphorylation of YAP/TAZ and show that NUAK2 induction by YAP/TAZ and AP-1 is required for robust YAP/TAZ signaling. Pharmacological inhibition or loss of NUAK2 reduces the growth of cultured cancer cells and mammary tumors in mice. Moreover, in human patient samples, we show that NUAK2 expression is elevated in aggressive, high-grade bladder cancer and strongly correlates with a YAP/TAZ gene signature. These findings identify a positive feed forward loop in the Hippo pathway that establishes a key role for NUAK2 in enforcing the tumor-promoting activities of YAP/TAZ. Our results thus introduce a new opportunity for cancer therapeutics by delineating NUAK2 as a potential target for re-engaging the Hippo pathway. The Hippo pathway is frequently dysregulated in cancer. Here, the authors identify NUAK2 as negative regulator of the Hippo pathway from a siRNA kinome screen and show that NUAK2 promotes YAP/TAZ nuclear localisation while NUAK2 is a transcriptional target of YAP/TAZ, thus providing a feed forward loop to promote tumorigenesis.
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Affiliation(s)
- Mandeep K Gill
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Tania Christova
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Ying Y Zhang
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Alex Gregorieff
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada.,Department of Pathology, McGill University and Research Institute of the McGill University Health Center, Montreal, H4A 3J1, QC, Canada
| | - Liang Zhang
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada.,Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, 999077, Hong Kong, China.,City University of Hong Kong Shenzhen Research Institute, Shenzhen, Guangdong, 518057, China
| | - Masahiro Narimatsu
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Siyuan Song
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Shawn Xiong
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Amber L Couzens
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Jiefei Tong
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Jonathan R Krieger
- SPARC BioCentre, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Michael F Moran
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Program in Cell Biology, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.,SPARC BioCentre, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Alexandre R Zlotta
- Department of Surgery, Division of Urology, University of Toronto, Mount Sinai Hospital and University Health Network, Toronto, M5G 1X5, ON, Canada
| | - Theodorus H van der Kwast
- Department of Pathology, Toronto General Hospital, University Health Network, Toronto, ON, M5G 2C4, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Frank Sicheri
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Jeffrey L Wrana
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Liliana Attisano
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada. .,Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada.
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193
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Activation mechanisms of the Hippo kinase signaling cascade. Biosci Rep 2018; 38:BSR20171469. [PMID: 30038061 PMCID: PMC6131212 DOI: 10.1042/bsr20171469] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/05/2018] [Accepted: 07/09/2018] [Indexed: 11/21/2022] Open
Abstract
First discovered two decades ago through genetic screens in Drosophila, the Hippo pathway has been shown to be conserved in metazoans and controls organ size and tissue homeostasis through regulating the balance between cell proliferation and apoptosis. Dysregulation of the Hippo pathway leads to aberrant tissue growth and tumorigenesis. Extensive studies in Drosophila and mammals have identified the core components of Hippo signaling, which form a central kinase cascade to ultimately control gene expression. Here, we review recent structural, biochemical, and cellular studies that have revealed intricate phosphorylation-dependent mechanisms in regulating the formation and activation of the core kinase complex in the Hippo pathway. These studies have established the dimerization-mediated activation of the Hippo kinase (mammalian Ste20-like 1 and 2 (MST1/2) in mammals), the dynamic scaffolding and allosteric roles of adaptor proteins in downstream kinase activation, and the importance of multisite linker autophosphorylation by Hippo and MST1/2 in fine-tuning the signaling strength and robustness of the Hippo pathway. We highlight the gaps in our knowledge in this field that will require further mechanistic studies.
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194
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The RASSF6 Tumor Suppressor Protein Regulates Apoptosis and Cell Cycle Progression via Retinoblastoma Protein. Mol Cell Biol 2018; 38:MCB.00046-18. [PMID: 29891515 DOI: 10.1128/mcb.00046-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 06/07/2018] [Indexed: 02/06/2023] Open
Abstract
RASSF6 is a member of the tumor suppressor Ras association domain family (RASSF) proteins. RASSF6 is frequently suppressed in human cancers, and its low expression level is associated with poor prognosis. RASSF6 regulates cell cycle arrest and apoptosis and plays a tumor suppressor role. Mechanistically, RASSF6 blocks MDM2-mediated p53 degradation and enhances p53 expression. However, RASSF6 also induces cell cycle arrest and apoptosis in a p53-negative background, which implies that the tumor suppressor function of RASSF6 does not depend solely on p53. In this study, we revealed that RASSF6 mediates cell cycle arrest and apoptosis via pRb. RASSF6 enhances the interaction between pRb and protein phosphatase. RASSF6 also enhances P16INK4A and P14ARF expression by suppressing BMI1. In this way, RASSF6 increases unphosphorylated pRb and augments the interaction between pRb and E2F1. Moreover, RASSF6 induces TP73 target genes via pRb and E2F1 in a p53-negative background. Finally, we confirmed that RASSF6 depletion induces polyploid cells in p53-negative HCT116 cells. In conclusion, RASSF6 behaves as a tumor suppressor in cancers with loss of function of p53, and pRb is implicated in this function of RASSF6.
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195
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Xiong S, Lorenzen K, Couzens AL, Templeton CM, Rajendran D, Mao DYL, Juang YC, Chiovitti D, Kurinov I, Guettler S, Gingras AC, Sicheri F. Structural Basis for Auto-Inhibition of the NDR1 Kinase Domain by an Atypically Long Activation Segment. Structure 2018; 26:1101-1115.e6. [PMID: 29983373 PMCID: PMC6087429 DOI: 10.1016/j.str.2018.05.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/28/2018] [Accepted: 05/17/2018] [Indexed: 11/27/2022]
Abstract
The human NDR family kinases control diverse aspects of cell growth, and are regulated through phosphorylation and association with scaffolds such as MOB1. Here, we report the crystal structure of the human NDR1 kinase domain in its non-phosphorylated state, revealing a fully resolved atypically long activation segment that blocks substrate binding and stabilizes a non-productive position of helix αC. Consistent with an auto-inhibitory function, mutations within the activation segment of NDR1 dramatically enhance in vitro kinase activity. Interestingly, NDR1 catalytic activity is further potentiated by MOB1 binding, suggesting that regulation through modulation of the activation segment and by MOB1 binding are mechanistically distinct. Lastly, deleting the auto-inhibitory activation segment of NDR1 causes a marked increase in the association with upstream Hippo pathway components and the Furry scaffold. These findings provide a point of departure for future efforts to explore the cellular functions and the mechanism of NDR1.
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MESH Headings
- Adaptor Proteins, Signal Transducing/chemistry
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Amino Acid Sequence
- Binding Sites
- Cell Cycle Proteins
- Cell Line, Tumor
- Cloning, Molecular
- Crystallography, X-Ray
- Epithelial Cells/cytology
- Epithelial Cells/enzymology
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Gene Expression Regulation
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- HEK293 Cells
- Hepatocyte Growth Factor/chemistry
- Hepatocyte Growth Factor/genetics
- Hepatocyte Growth Factor/metabolism
- Humans
- Kinetics
- Microtubule-Associated Proteins/chemistry
- Microtubule-Associated Proteins/genetics
- Microtubule-Associated Proteins/metabolism
- Models, Molecular
- Mutation
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Protein Serine-Threonine Kinases/chemistry
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/metabolism
- Proto-Oncogene Proteins/chemistry
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
- Serine-Threonine Kinase 3
- Signal Transduction
- Substrate Specificity
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Affiliation(s)
- Shawn Xiong
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Kristina Lorenzen
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Amber L Couzens
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Catherine M Templeton
- Divisions of Structural Biology and Cancer Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK
| | - Dushyandi Rajendran
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Daniel Y L Mao
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Yu-Chi Juang
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - David Chiovitti
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Igor Kurinov
- Cornell University, Department of Chemistry and Chemical Biology, NE-CAT, Advanced Photon Source, Bldg. 436E, 9700 S. Cass Avenue, Argonne, IL 60439, USA
| | - Sebastian Guettler
- Divisions of Structural Biology and Cancer Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK.
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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196
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Chen M, Zhang H, Shi Z, Li Y, Zhang X, Gao Z, Zhou L, Ma J, Xu Q, Guan J, Cheng Y, Jiao S, Zhou Z. The MST4-MOB4 complex disrupts the MST1-MOB1 complex in the Hippo-YAP pathway and plays a pro-oncogenic role in pancreatic cancer. J Biol Chem 2018; 293:14455-14469. [PMID: 30072378 DOI: 10.1074/jbc.ra118.003279] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 07/19/2018] [Indexed: 01/07/2023] Open
Abstract
The mammalian STE20-like protein kinase 1 (MST1)-MOB kinase activator 1 (MOB1) complex has been shown to suppress the oncogenic activity of Yes-associated protein (YAP) in the mammalian Hippo pathway, which is involved in the development of multiple tumors, including pancreatic cancer (PC). However, it remains unclear whether other MST-MOB complexes are also involved in regulating Hippo-YAP signaling and have potential roles in PC. Here, we report that mammalian STE20-like kinase 4 (MST4), a distantly related ortholog of the MST1 kinase, forms a complex with MOB4 in a phosphorylation-dependent manner. We found that the overall structure of the MST4-MOB4 complex resembles that of the MST1-MOB1 complex, even though the two complexes exhibited opposite biological functions in PC. In contrast to the tumor-suppressor effect of the MST1-MOB1 complex, the MST4-MOB4 complex promoted growth and migration of PANC-1 cells. Moreover, expression levels of MST4 and MOB4 were elevated in PC and were positively correlated with each other, whereas MST1 expression was down-regulated. Because of divergent evolution of key interface residues, MST4 and MOB4 could disrupt assembly of the MST1-MOB1 complex through alternative pairing and thereby increased YAP activity. Collectively, these findings identify the MST4-MOB4 complex as a noncanonical regulator of the Hippo-YAP pathway with an oncogenic role in PC. Our findings highlight that although MST-MOB complexes display some structural conservation, they functionally diverged during their evolution.
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Affiliation(s)
- Min Chen
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031
| | - Hui Zhang
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031
| | - Zhubing Shi
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031
| | - Yehua Li
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031
| | - Xiaoman Zhang
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031
| | - Ziyang Gao
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031
| | - Li Zhou
- the School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, and
| | - Jian Ma
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031
| | - Qi Xu
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031
| | - Jingmin Guan
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031
| | - Yunfeng Cheng
- the Department of Hematology and Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Shi Jiao
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031,
| | - Zhaocai Zhou
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, .,the School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, and
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197
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Homeostatic Control of Hpo/MST Kinase Activity through Autophosphorylation-Dependent Recruitment of the STRIPAK PP2A Phosphatase Complex. Cell Rep 2018; 21:3612-3623. [PMID: 29262338 DOI: 10.1016/j.celrep.2017.11.076] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/25/2017] [Accepted: 11/21/2017] [Indexed: 12/22/2022] Open
Abstract
The Hippo pathway controls organ size and tissue homeostasis through a kinase cascade leading from the Ste20-like kinase Hpo (MST1/2 in mammals) to the transcriptional coactivator Yki (YAP/TAZ in mammals). Whereas previous studies have uncovered positive and negative regulators of Hpo/MST, how they are integrated to maintain signaling homeostasis remains poorly understood. Here, we identify a self-restricting mechanism whereby autophosphorylation of an unstructured linker in Hpo/MST creates docking sites for the STRIPAK PP2A phosphatase complex to inactivate Hpo/MST. Mutation of the phospho-dependent docking sites in Hpo/MST or deletion of Slmap, the STRIPAK subunit recognizing these docking sites, results in constitutive activation of Hpo/MST in both Drosophila and mammalian cells. In contrast, autophosphorylation of the Hpo/MST linker at distinct sites is known to recruit Mats/MOB1 to facilitate Hippo signaling. Thus, multisite autophosphorylation of Hpo/MST linker provides an evolutionarily conserved built-in molecular platform to maintain signaling homeostasis by coupling antagonistic signaling activities.
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198
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Jacquet K, Banerjee SL, Chartier FJM, Elowe S, Bisson N. Proteomic Analysis of NCK1/2 Adaptors Uncovers Paralog-specific Interactions That Reveal a New Role for NCK2 in Cell Abscission During Cytokinesis. Mol Cell Proteomics 2018; 17:1979-1990. [PMID: 30002203 DOI: 10.1074/mcp.ra118.000689] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 07/11/2018] [Indexed: 12/31/2022] Open
Abstract
Signals from cell surface receptors are often relayed via adaptor proteins. NCK1 and NCK2 are Src-Homology (SH) 2 and 3 domain adaptors that regulate processes requiring a remodeling of the actin cytoskeleton. Evidence from gene inactivation in mouse suggests that NCK1 and NCK2 are functionally redundant, although recent reports support the idea of unique functions for NCK1 and NCK2. We sought to examine this question further by delineating NCK1- and NCK2-specific signaling networks. We used both affinity purification-mass spectrometry and BioID proximity labeling to identify NCK1/2 signaling networks comprised of 98 proteins. Strikingly, we found 30 proteins restricted to NCK1 and 28 proteins specifically associated with NCK2, suggesting differences in their function. We report that Nck2 -/-, but not Nck1 -/- mouse embryo fibroblasts (MEFs) are multinucleated and display extended protrusions reminiscent of intercellular bridges, which correlate with an extended time spent in cytokinesis as well as a failure of a significant proportion of cells to complete abscission. Our data also show that the midbody of NCK2-deficient cells is not only increased in length, but also altered in composition, as judged by the mislocalization of AURKB, PLK1 and ECT2. Finally, we show that NCK2 function during cytokinesis requires its SH2 domain. Taken together, our data delineate the first high-confidence interactome for NCK1/2 adaptors and highlight several proteins specifically associated with either protein. Thus, contrary to what is generally accepted, we demonstrate that NCK1 and NCK2 are not completely redundant, and shed light on a previously uncharacterized function for the NCK2 adaptor protein in cell division.
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Affiliation(s)
- Kévin Jacquet
- From the ‡Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec G1R 2J6, QC, Canada.,§Centre de recherche sur le cancer de l'Université Laval, Québec G1R 2J6, QC, Canada.,¶PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec G1V 0A6, QC, Canada
| | - Sara L Banerjee
- From the ‡Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec G1R 2J6, QC, Canada.,§Centre de recherche sur le cancer de l'Université Laval, Québec G1R 2J6, QC, Canada.,¶PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec G1V 0A6, QC, Canada
| | - François J M Chartier
- From the ‡Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec G1R 2J6, QC, Canada.,§Centre de recherche sur le cancer de l'Université Laval, Québec G1R 2J6, QC, Canada.,¶PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec G1V 0A6, QC, Canada
| | - Sabine Elowe
- §Centre de recherche sur le cancer de l'Université Laval, Québec G1R 2J6, QC, Canada.,¶PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec G1V 0A6, QC, Canada.,‖Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Reproduction, santé de la mère et de l'enfant, Québec G1V 4G2, QC, Canada.,**Department of Pediatrics, Université Laval, Québec, QC, Canada
| | - Nicolas Bisson
- From the ‡Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec G1R 2J6, QC, Canada; .,§Centre de recherche sur le cancer de l'Université Laval, Québec G1R 2J6, QC, Canada.,¶PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec G1V 0A6, QC, Canada.,‡‡Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec G1V 0A6, QC, Canada
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199
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Trepte P, Kruse S, Kostova S, Hoffmann S, Buntru A, Tempelmeier A, Secker C, Diez L, Schulz A, Klockmeier K, Zenkner M, Golusik S, Rau K, Schnoegl S, Garner CC, Wanker EE. LuTHy: a double-readout bioluminescence-based two-hybrid technology for quantitative mapping of protein-protein interactions in mammalian cells. Mol Syst Biol 2018; 14:e8071. [PMID: 29997244 PMCID: PMC6039870 DOI: 10.15252/msb.20178071] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 06/08/2018] [Accepted: 06/15/2018] [Indexed: 12/12/2022] Open
Abstract
Information on protein-protein interactions (PPIs) is of critical importance for studying complex biological systems and developing therapeutic strategies. Here, we present a double-readout bioluminescence-based two-hybrid technology, termed LuTHy, which provides two quantitative scores in one experimental procedure when testing binary interactions. PPIs are first monitored in cells by quantification of bioluminescence resonance energy transfer (BRET) and, following cell lysis, are again quantitatively assessed by luminescence-based co-precipitation (LuC). The double-readout procedure detects interactions with higher sensitivity than traditional single-readout methods and is broadly applicable, for example, for detecting the effects of small molecules or disease-causing mutations on PPIs. Applying LuTHy in a focused screen, we identified 42 interactions for the presynaptic chaperone CSPα, causative to adult-onset neuronal ceroid lipofuscinosis (ANCL), a progressive neurodegenerative disease. Nearly 50% of PPIs were found to be affected when studying the effect of the disease-causing missense mutations L115R and ∆L116 in CSPα with LuTHy. Our study presents a robust, sensitive research tool with high utility for investigating the molecular mechanisms by which disease-associated mutations impair protein activity in biological systems.
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Affiliation(s)
- Philipp Trepte
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Sabrina Kruse
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Simona Kostova
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Sheila Hoffmann
- Synaptopathy, German Center for Neurodegenerative Diseases, Berlin, Germany
| | - Alexander Buntru
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Anne Tempelmeier
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Christopher Secker
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
- Department of Neurology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Lisa Diez
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Aline Schulz
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Konrad Klockmeier
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Martina Zenkner
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Sabrina Golusik
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Kirstin Rau
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Sigrid Schnoegl
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Craig C Garner
- Synaptopathy, German Center for Neurodegenerative Diseases, Berlin, Germany
| | - Erich E Wanker
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
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200
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Samavarchi-Tehrani P, Abdouni H, Samson R, Gingras AC. A Versatile Lentiviral Delivery Toolkit for Proximity-dependent Biotinylation in Diverse Cell Types. Mol Cell Proteomics 2018; 17:2256-2269. [PMID: 29991506 DOI: 10.1074/mcp.tir118.000902] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Indexed: 11/06/2022] Open
Abstract
Proximity-dependent biotinylation strategies have emerged as powerful tools to characterize the subcellular context of proteins in living cells. The popular BioID approach employs an abortive E. coli biotin ligase mutant (R118G; denoted as BirA*), which when fused to a bait protein enables the covalent biotinylation of endogenous proximal polypeptides. This approach has been mainly applied to the study of protein proximity in immortalized mammalian cell lines. To expand the application space of BioID, here we describe a set of lentiviral vectors that enable the inducible expression of BirA*-tagged bait fusion proteins for performing proximity-dependent biotinylation in diverse experimental systems. We benchmark this highly adaptable toolkit across immortalized and primary cell systems, demonstrating the ease, versatility and robustness of the system. We also provide guidelines to perform BioID using these reagents.
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Affiliation(s)
| | - Hala Abdouni
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | - Reuben Samson
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada.,§Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Anne-Claude Gingras
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada; .,§Department of Molecular Genetics, University of Toronto, Toronto, Canada
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