1
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Dunuweera AN, Dunuweera SP, Ranganathan K. A Comprehensive Exploration of Bioluminescence Systems, Mechanisms, and Advanced Assays for Versatile Applications. Biochem Res Int 2024; 2024:8273237. [PMID: 38347947 PMCID: PMC10861286 DOI: 10.1155/2024/8273237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/10/2023] [Accepted: 01/21/2024] [Indexed: 02/15/2024] Open
Abstract
Bioluminescence has been a fascinating natural phenomenon of light emission from living creatures. It happens when the enzyme luciferase facilitates the oxidation of luciferin, resulting in the creation of an excited-state species that emits light. Although there are many bioluminescent systems, few have been identified. D-luciferin-dependent systems, coelenterazine-dependent systems, Cypridina luciferin-based systems, tetrapyrrole-based luciferins, bacterial bioluminescent systems, and fungal bioluminescent systems are natural bioluminescent systems. Since different bioluminescence systems, such as various combinations of luciferin-luciferase pair reactions, have different light emission wavelengths, they benefit industrial applications such as drug discovery, protein-protein interactions, in vivo imaging in small animals, and controlling neurons. Due to the expression of luciferase and easy permeation of luciferin into most cells and tissues, bioluminescence assays are applied nowadays with modern technologies in most cell and tissue types. It is a versatile technique in a variety of biomedical research. Furthermore, there are some investigated blue-sky research projects, such as bioluminescent plants and lamps. This review article is mainly based on the theory of diverse bioluminescence systems and their past, present, and future applications.
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Affiliation(s)
| | | | - K. Ranganathan
- Department of Botany, University of Jaffna, Jaffna 40000, Sri Lanka
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2
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Pillay N, Mariotti L, Zaleska M, Inian O, Jessop M, Hibbs S, Desfosses A, Hopkins PCR, Templeton CM, Beuron F, Morris EP, Guettler S. Structural basis of tankyrase activation by polymerization. Nature 2022; 612:162-169. [PMID: 36418402 PMCID: PMC9712121 DOI: 10.1038/s41586-022-05449-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 10/13/2022] [Indexed: 11/25/2022]
Abstract
The poly-ADP-ribosyltransferase tankyrase (TNKS, TNKS2) controls a wide range of disease-relevant cellular processes, including WNT-β-catenin signalling, telomere length maintenance, Hippo signalling, DNA damage repair and glucose homeostasis1,2. This has incentivized the development of tankyrase inhibitors. Notwithstanding, our knowledge of the mechanisms that control tankyrase activity has remained limited. Both catalytic and non-catalytic functions of tankyrase depend on its filamentous polymerization3-5. Here we report the cryo-electron microscopy reconstruction of a filament formed by a minimal active unit of tankyrase, comprising the polymerizing sterile alpha motif (SAM) domain and its adjacent catalytic domain. The SAM domain forms a novel antiparallel double helix, positioning the protruding catalytic domains for recurring head-to-head and tail-to-tail interactions. The head interactions are highly conserved among tankyrases and induce an allosteric switch in the active site within the catalytic domain to promote catalysis. Although the tail interactions have a limited effect on catalysis, they are essential to tankyrase function in WNT-β-catenin signalling. This work reveals a novel SAM domain polymerization mode, illustrates how supramolecular assembly controls catalytic and non-catalytic functions, provides important structural insights into the regulation of a non-DNA-dependent poly-ADP-ribosyltransferase and will guide future efforts to modulate tankyrase and decipher its contribution to disease mechanisms.
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Affiliation(s)
- Nisha Pillay
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Laura Mariotti
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Mariola Zaleska
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Oviya Inian
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Matthew Jessop
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Sam Hibbs
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Ambroise Desfosses
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Paul C R Hopkins
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Catherine M Templeton
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Fabienne Beuron
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
| | - Edward P Morris
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
| | - Sebastian Guettler
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK.
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK.
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3
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Yu P, Liu Z, Yu X, Ye P, Liu H, Xue X, Yang L, Li Z, Wu Y, Fang C, Zhao YJ, Yang F, Luo JH, Jiang LH, Zhang L, Zhang L, Yang W. Direct Gating of the TRPM2 Channel by cADPR via Specific Interactions with the ADPR Binding Pocket. Cell Rep 2020; 27:3684-3695.e4. [PMID: 31216484 DOI: 10.1016/j.celrep.2019.05.067] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 02/05/2019] [Accepted: 05/18/2019] [Indexed: 12/29/2022] Open
Abstract
cADPR is a well-recognized signaling molecule by modulating the RyRs, but considerable debate exists regarding whether cADPR can bind to and gate the TRPM2 channel, which mediates oxidative stress signaling in diverse physiological and pathological processes. Here, we show that purified cADPR evoked TRPM2 channel currents in both whole-cell and cell-free single-channel recordings and specific binding of cADPR to the purified NUDT9-H domain of TRPM2 by surface plasmon resonance. Furthermore, by combining computational modeling with electrophysiological recordings, we show that the TRPM2 channels carrying point mutations at H1346, T1347, L1379, S1391, E1409, and L1484 possess distinct sensitivity profiles for ADPR and cADPR. These results clearly indicate cADPR is a bona fide activator at the TRPM2 channel and clearly delineate the structural basis for cADPR binding, which not only lead to a better understanding in the gating mechanism of TRPM2 channel but also shed light on a cADPR-induced RyRs-independent Ca2+ signaling mechanism.
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Affiliation(s)
- Peilin Yu
- Department of Biophysics, Institute of Neuroscience, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, P.R. China; Department of Toxicology, School of Public Health, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
| | - Zhenming Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, P.R. China
| | - Xiafei Yu
- Department of Biophysics, Institute of Neuroscience, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, P.R. China
| | - Peiwu Ye
- Department of Biophysics, Institute of Neuroscience, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, P.R. China
| | - Huan Liu
- Department of Biophysics, Institute of Neuroscience, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, P.R. China
| | - Xiwen Xue
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, P.R. China
| | - Lixin Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, P.R. China
| | - Zhongtang Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, P.R. China
| | - Yang Wu
- Laboratory of Cytophysiology, State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, P.R. China
| | - Cheng Fang
- Laboratory of Cytophysiology, State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, P.R. China
| | - Yong Juan Zhao
- Laboratory of Cytophysiology, State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, P.R. China
| | - Fan Yang
- Department of Biophysics, Institute of Neuroscience, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, P.R. China; Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
| | - Jian Hong Luo
- Department of Neurobiology, Institute of Neuroscience, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, P.R. China
| | - Lin-Hua Jiang
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; Sino-UK Laboratory of Brain Function and Injury of Henan Province and Department of Physiology and Neurobiology, Xinxiang Medical University, Henan 453003, P.R. China
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, P.R. China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, P.R. China
| | - Wei Yang
- Department of Biophysics, Institute of Neuroscience, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, P.R. China; Department of Neurosurgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China.
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4
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Müller PM, Rademacher J, Bagshaw RD, Wortmann C, Barth C, van Unen J, Alp KM, Giudice G, Eccles RL, Heinrich LE, Pascual-Vargas P, Sanchez-Castro M, Brandenburg L, Mbamalu G, Tucholska M, Spatt L, Czajkowski MT, Welke RW, Zhang S, Nguyen V, Rrustemi T, Trnka P, Freitag K, Larsen B, Popp O, Mertins P, Gingras AC, Roth FP, Colwill K, Bakal C, Pertz O, Pawson T, Petsalaki E, Rocks O. Systems analysis of RhoGEF and RhoGAP regulatory proteins reveals spatially organized RAC1 signalling from integrin adhesions. Nat Cell Biol 2020; 22:498-511. [PMID: 32203420 DOI: 10.1038/s41556-020-0488-x] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 02/18/2020] [Indexed: 02/07/2023]
Abstract
Rho GTPases are central regulators of the cytoskeleton and, in humans, are controlled by 145 multidomain guanine nucleotide exchange factors (RhoGEFs) and GTPase-activating proteins (RhoGAPs). How Rho signalling patterns are established in dynamic cell spaces to control cellular morphogenesis is unclear. Through a family-wide characterization of substrate specificities, interactomes and localization, we reveal at the systems level how RhoGEFs and RhoGAPs contextualize and spatiotemporally control Rho signalling. These proteins are widely autoinhibited to allow local regulation, form complexes to jointly coordinate their networks and provide positional information for signalling. RhoGAPs are more promiscuous than RhoGEFs to confine Rho activity gradients. Our resource enabled us to uncover a multi-RhoGEF complex downstream of G-protein-coupled receptors controlling CDC42-RHOA crosstalk. Moreover, we show that integrin adhesions spatially segregate GEFs and GAPs to shape RAC1 activity zones in response to mechanical cues. This mechanism controls the protrusion and contraction dynamics fundamental to cell motility. Our systems analysis of Rho regulators is key to revealing emergent organization principles of Rho signalling.
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Affiliation(s)
- Paul M Müller
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | | | - Richard D Bagshaw
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | | | - Carolin Barth
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Jakobus van Unen
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Keziban M Alp
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Girolamo Giudice
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Louise E Heinrich
- Institute of Cancer Research, Chester Beatty Laboratories, London, UK
| | | | - Marta Sanchez-Castro
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | | | - Geraldine Mbamalu
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Monika Tucholska
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Lisa Spatt
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Maciej T Czajkowski
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | | | - Sunqu Zhang
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Vivian Nguyen
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | | | - Philipp Trnka
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Kiara Freitag
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Brett Larsen
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Oliver Popp
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Philipp Mertins
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Frederick P Roth
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, Toronto, Ontario, Canada
- Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | - Karen Colwill
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Chris Bakal
- Institute of Cancer Research, Chester Beatty Laboratories, London, UK
| | - Olivier Pertz
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Tony Pawson
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Evangelia Petsalaki
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Oliver Rocks
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.
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5
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Dlugos CP, Picciotto C, Lepa C, Krakow M, Stöber A, Eddy ML, Weide T, Jeibmann A, P Krahn M, Van Marck V, Klingauf J, Ricker A, Wedlich-Söldner R, Pavenstädt H, Klämbt C, George B. Nephrin Signaling Results in Integrin β1 Activation. J Am Soc Nephrol 2019; 30:1006-1019. [PMID: 31097607 DOI: 10.1681/asn.2018040362] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 03/18/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Patients with certain mutations in the gene encoding the slit diaphragm protein Nephrin fail to develop functional slit diaphragms and display severe proteinuria. Many adult-onset glomerulopathies also feature alterations in Nephrin expression and function. Nephrin signals from the podocyte slit diaphragm to the Actin cytoskeleton by recruiting proteins that can interact with C3G, a guanine nucleotide exchange factor of the small GTPase Rap1. Because Rap activity affects formation of focal adhesions, we hypothesized that Nephrin transmits signals to the Integrin receptor complex, which mediates podocyte adhesion to the extracellular matrix. METHODS To investigate Nephrin's role in transmitting signals to the Integrin receptor complex, we conducted genetic studies in Drosophila nephrocytes and validated findings from Drosophila in a cultured human podocyte model. RESULTS Drosophila nephrocytes form a slit diaphragm-like filtration barrier and express the Nephrin ortholog Sticks and stones (Sns). A genetic screen identified c3g as necessary for nephrocyte function. In vivo, nephrocyte-specific gene silencing of sns or c3g compromised nephrocyte filtration and caused nephrocyte diaphragm defects. Nephrocytes with impaired Sns or C3G expression displayed an altered localization of Integrin and the Integrin-associated protein Talin. Furthermore, gene silencing of c3g partly rescued nephrocyte diaphragm defects of an sns overexpression phenotype, pointing to genetic interaction of sns and c3g in nephrocytes. We also found that activated Nephrin recruited phosphorylated C3G and resulted in activation of Integrin β1 in cultured podocytes. CONCLUSIONS Our findings suggest that Nephrin can mediate a signaling pathway that results in activation of Integrin β1 at focal adhesions, which may affect podocyte attachment to the extracellular matrix.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Christian Klämbt
- Neurobiology, Westfälische-Wilhelms University Münster, Münster, Germany
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6
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Hall L, Donovan E, Araya M, Idowa E, Jiminez-Segovia I, Folck A, Wells CD, Kimble-Hill AC. Identification of Specific Lysines and Arginines That Mediate Angiomotin Membrane Association. ACS OMEGA 2019; 4:6726-6736. [PMID: 31179409 PMCID: PMC6547806 DOI: 10.1021/acsomega.9b00165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/28/2019] [Indexed: 05/17/2023]
Abstract
The family of Angiomotin (Amot) proteins regulate several biological pathways associated with cellular differentiation, proliferation, and migration. These adaptor proteins target proteins to the apical membrane, actin fibers, or the nucleus. A major function of the Amot coiled-coil homology (ACCH) domain is to initiate protein interactions with the cellular membrane, particularly those containing phosphatidylinositol lipids. The work presented in this article uses several ACCH domain lysine/arginine mutants to probe the relative importance of individual residues for lipid binding. This identified four lysine and three arginine residues that mediate full lipid binding. Based on these findings, three of these residues were mutated to glutamates in the Angiomotin 80 kDa splice form and were incorporated into human mammary cell lines. Results show that mutating three of these residues in the context of full-length Angiomotin reduced the residence of the protein at the apical membrane. These findings provide new insight into how the ACCH domain mediates lipid binding to enable Amot proteins to control epithelial cell growth.
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Affiliation(s)
- Le’Celia Hall
- Department of Biochemistry
and Molecular Biology, Indiana University
School of Medicine, Room MS 4053, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Emily Donovan
- Department of Biochemistry
and Molecular Biology, Indiana University
School of Medicine, Room MS 4053, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Michael Araya
- Department of Biochemistry
and Molecular Biology, Indiana University
School of Medicine, Room MS 4053, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Eniola Idowa
- Department of Biochemistry
and Molecular Biology, Indiana University
School of Medicine, Room MS 4053, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Ilse Jiminez-Segovia
- Department of Biochemistry
and Molecular Biology, Indiana University
School of Medicine, Room MS 4053, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Anthony Folck
- Department of Biochemistry
and Molecular Biology, Indiana University
School of Medicine, Room MS 4053, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Clark D. Wells
- Department of Biochemistry
and Molecular Biology, Indiana University
School of Medicine, Room MS 4053, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Ann C. Kimble-Hill
- Department of Biochemistry
and Molecular Biology, Indiana University
School of Medicine, Room MS 4053, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
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7
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Peck C, Virtanen P, Johnson D, Kimble-Hill AC. Using the Predicted Structure of the Amot Coiled Coil Homology Domain to Understand Lipid Binding. INDIANA UNIVERSITY JOURNAL OF UNDERGRADUATE RESEARCH 2018; 4:27-46. [PMID: 30957019 PMCID: PMC6448796 DOI: 10.14434/iujur.v4i1.24528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Angiomotins (Amots) are a family of adapter proteins that modulate cellular polarity, differentiation, proliferation, and migration. Amot family members have a characteristic lipid-binding domain, the coiled coil homology (ACCH) domain that selectively targets the protein to membranes, which has been directly linked to its regulatory role in the cell. Several spot blot assays were used to validate the regions of the domain that participate in its membrane association, deformation, and vesicle fusion activity, which indicated the need for a structure to define the mechanism. Therefore, we sought to understand the structure-function relationship of this domain in order to find ways to modulate these signaling pathways. After many failed attempts to crystallize the ACCH domain of each Amot family member for structural analysis, we decided to pursue homologous models that could be refined using small angle x-ray scattering data. Theoretical models were produced using the homology software SWISS-MODEL and threading software I-TASSER and LOMETS, followed by comparison to SAXS data for model selection and refinement. We present a theoretical model of the domain that is driven by alpha helices and short random coil regions. These alpha helical regions form a classic dimer interface followed by two wide spread legs that we predict to be the lipid binding interface.
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8
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Kimble-Hill AC, Petrache HI, Seifert S, Firestone MA. Reorganization of Ternary Lipid Mixtures of Nonphosphorylated Phosphatidylinositol Interacting with Angiomotin. J Phys Chem B 2018; 122:8404-8415. [PMID: 29877706 PMCID: PMC6351316 DOI: 10.1021/acs.jpcb.7b12641] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Phosphatidylinositol (PI) lipids are necessary for many cellular signaling pathways of membrane associated proteins, such as angiomotin (Amot). The Amot family regulates cellular polarity, growth, and migration. Given the low concentration of PI lipids in these membranes, it is likely that such protein-membrane interactions are stabilized by lipid domains or small lipid clusters. By small-angle X-ray scattering, we show that nonphosphorylated PI lipids induce lipid demixing in ternary mixtures of phosphatidylcholine (PC) and phosphatidylethanolamine (PE), likely because of preferential interactions between the head groups of PE and PI. These results were obtained in the presence of buffer containing tris(hydroxymethyl)aminomethane, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, NaCl, ethylenediaminetetraacetic acid, dithiothreitol, and benzamidine at pH 8.0 that in previous work showed an ability to cause PC to phase separate but are necessary to stabilize Amot for in vitro experimentation. Collectively, this provided a framework for determining the effect of Amot on lipid organization. Using fluorescence spectroscopy, we were able to show that the association of Amot with this lipid platform causes significant reorganization of the lipid into a more homogenous structure. This reorganization mechanism could be the basis for Amot membrane association and fusogenic activity previously described in the literature and should be taken into consideration in future protein-membrane interaction studies.
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Affiliation(s)
- Ann C. Kimble-Hill
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, MS 4053, 635 Barnhill Dr., Indianapolis, Indiana 46202, United States
| | - Horia I. Petrache
- Department of Physics, Indiana University Purdue University Indianapolis, LD 154, 402 N. Blackford Street, Indianapolis, Indiana 46202, United States
| | - Soenke Seifert
- X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Millicent A. Firestone
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, MPA-CINT, MS K771, Los Alamos, New Mexico 87545, United States
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9
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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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10
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Bimodal antagonism of PKA signalling by ARHGAP36. Nat Commun 2016; 7:12963. [PMID: 27713425 PMCID: PMC5059767 DOI: 10.1038/ncomms12963] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 08/19/2016] [Indexed: 02/07/2023] Open
Abstract
Protein kinase A is a key mediator of cAMP signalling downstream of G-protein-coupled receptors, a signalling pathway conserved in all eukaryotes. cAMP binding to the regulatory subunits (PKAR) relieves their inhibition of the catalytic subunits (PKAC). Here we report that ARHGAP36 combines two distinct inhibitory mechanisms to antagonise PKA signalling. First, it blocks PKAC activity via a pseudosubstrate motif, akin to the mechanism employed by the protein kinase inhibitor proteins. Second, it targets PKAC for rapid ubiquitin-mediated lysosomal degradation, a pathway usually reserved for transmembrane receptors. ARHGAP36 thus dampens the sensitivity of cells to cAMP. We show that PKA inhibition by ARHGAP36 promotes derepression of the Hedgehog signalling pathway, thereby providing a simple rationale for the upregulation of ARHGAP36 in medulloblastoma. Our work reveals a new layer of PKA regulation that may play an important role in development and disease.
Protein kinase A (PKA) is a key mediator of cyclic AMP signalling. Here, Eccles et al. show that ARHGAP36 antagonizes PKA by acting as a kinase inhibitor and targeting the catalytic subunit for endolysosomal degradation, thus reducing sensitivity of cells to cAMP and promoting Hedgehog signalling.
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11
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Chaudhary VK, Shrivastava N, Verma V, Das S, Kaur C, Grover P, Gupta A. Rapid restriction enzyme-free cloning of PCR products: a high-throughput method applicable for library construction. PLoS One 2014; 9:e111538. [PMID: 25360695 PMCID: PMC4216109 DOI: 10.1371/journal.pone.0111538] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 09/27/2014] [Indexed: 01/05/2023] Open
Abstract
Herein, we describe a novel cloning strategy for PCR-amplified DNA which employs the type IIs restriction endonuclease BsaI to create a linearized vector with four base-long 5′-overhangs, and T4 DNA polymerase treatment of the insert in presence of a single dNTP to create vector-compatible four base-long overhangs. Notably, the insert preparation does not require any restriction enzyme treatment. The BsaI sites in the vector are oriented in such a manner that upon digestion with BsaI, a stuffer sequence along with both BsaI recognition sequences is removed. The sequence of the four base-long overhangs produced by BsaI cleavage were designed to be non-palindromic, non-compatible to each other. Therefore, only ligation of an insert carrying compatible ends allows directional cloning of the insert to the vector to generate a recombinant without recreating the BsaI sites. We also developed rapid protocols for insert preparation and cloning, by which the entire process from PCR to transformation can be completed in 6–8 h and DNA fragments ranging in size from 200 to 2200 bp can be cloned with equal efficiencies. One protocol uses a single tube for insert preparation if amplification is performed using polymerases with low 3′-exonuclease activity. The other protocol is compatible with any thermostable polymerase, including those with high 3′-exonuclease activity, and does not significantly increase the time required for cloning. The suitability of this method for high-throughput cloning was demonstrated by cloning batches of 24 PCR products with nearly 100% efficiency. The cloning strategy is also suitable for high efficiency cloning and was used to construct large libraries comprising more than 108 clones/µg vector. Additionally, based on this strategy, a variety of vectors were constructed for the expression of proteins in E. coli, enabling large number of different clones to be rapidly generated.
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Affiliation(s)
- Vijay K. Chaudhary
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
- * E-mail: (VKC); (AG)
| | - Nimisha Shrivastava
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Vaishali Verma
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Shilpi Das
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Charanpreet Kaur
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Payal Grover
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Amita Gupta
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
- * E-mail: (VKC); (AG)
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12
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Gray EJ, Petsalaki E, James DA, Bagshaw RD, Stacey MM, Rocks O, Gingras AC, Pawson T. Src homology 2 domain containing protein 5 (SH2D5) binds the breakpoint cluster region protein, BCR, and regulates levels of Rac1-GTP. J Biol Chem 2014; 289:35397-408. [PMID: 25331951 DOI: 10.1074/jbc.m114.615112] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SH2D5 is a mammalian-specific, uncharacterized adaptor-like protein that contains an N-terminal phosphotyrosine-binding domain and a C-terminal Src homology 2 (SH2) domain. We show that SH2D5 is highly enriched in adult mouse brain, particularly in Purkinjie cells in the cerebellum and the cornu ammonis of the hippocampus. Despite harboring two potential phosphotyrosine (Tyr(P)) recognition domains, SH2D5 binds minimally to Tyr(P) ligands, consistent with the absence of a conserved Tyr(P)-binding arginine residue in the SH2 domain. Immunoprecipitation coupled to mass spectrometry (IP-MS) from cultured cells revealed a prominent association of SH2D5 with breakpoint cluster region protein, a RacGAP that is also highly expressed in brain. This interaction occurred between the phosphotyrosine-binding domain of SH2D5 and an NxxF motif located within the N-terminal region of the breakpoint cluster region. siRNA-mediated depletion of SH2D5 in a neuroblastoma cell line, B35, induced a cell rounding phenotype correlated with low levels of activated Rac1-GTP, suggesting that SH2D5 affects Rac1-GTP levels. Taken together, our data provide the first characterization of the SH2D5 signaling protein.
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Affiliation(s)
- Elizabeth J Gray
- From the Department of Molecular Genetics, University of Toronto, Ontario M5S1A8, Canada, the Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada,
| | - Evangelia Petsalaki
- the Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada
| | - D Andrew James
- the Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada, Sanofi Pasteur, Toronto, Ontario M2R3T4, Canada, and
| | - Richard D Bagshaw
- the Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada
| | - Melissa M Stacey
- the Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada
| | - Oliver Rocks
- the Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada, the Max Delbrück Center for Molecular Medicine Berlin-Buch, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Anne-Claude Gingras
- From the Department of Molecular Genetics, University of Toronto, Ontario M5S1A8, Canada, the Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada,
| | - Tony Pawson
- From the Department of Molecular Genetics, University of Toronto, Ontario M5S1A8, Canada, the Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada
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13
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Hou J, Wei W, Saund RS, Xiang P, Cunningham TJ, Yi Y, Alder O, Lu DYD, Savory JGA, Krentz NAJ, Montpetit R, Cullum R, Hofs N, Lohnes D, Humphries RK, Yamanaka Y, Duester G, Saijoh Y, Hoodless PA. A regulatory network controls nephrocan expression and midgut patterning. Development 2014; 141:3772-81. [PMID: 25209250 DOI: 10.1242/dev.108274] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Although many regulatory networks involved in defining definitive endoderm have been identified, the mechanisms through which these networks interact to pattern the endoderm are less well understood. To explore the mechanisms involved in midgut patterning, we dissected the transcriptional regulatory elements of nephrocan (Nepn), the earliest known midgut specific gene in mice. We observed that Nepn expression is dramatically reduced in Sox17(-/-) and Raldh2(-/-) embryos compared with wild-type embryos. We further show that Nepn is directly regulated by Sox17 and the retinoic acid (RA) receptor via two enhancer elements located upstream of the gene. Moreover, Nepn expression is modulated by Activin signaling, with high levels inhibiting and low levels enhancing RA-dependent expression. In Foxh1(-/-) embryos in which Nodal signaling is reduced, the Nepn expression domain is expanded into the anterior gut region, confirming that Nodal signaling can modulate its expression in vivo. Together, Sox17 is required for Nepn expression in the definitive endoderm, while RA signaling restricts expression to the midgut region. A balance of Nodal/Activin signaling regulates the anterior boundary of the midgut expression domain.
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Affiliation(s)
- Juan Hou
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Wei Wei
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Ranajeet S Saund
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84132-3401, USA
| | - Ping Xiang
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Thomas J Cunningham
- Development, Aging and Regeneration Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
| | - Yuyin Yi
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada Cell and Developmental Biology Program, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Olivia Alder
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Daphne Y D Lu
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Joanne G A Savory
- Cellular and Molecular Medicine, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Nicole A J Krentz
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Rachel Montpetit
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Rebecca Cullum
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Nicole Hofs
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - David Lohnes
- Cellular and Molecular Medicine, University of Ottawa, Ottawa K1H 8M5, Canada
| | - R Keith Humphries
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada Experimental Medicine, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Yojiro Yamanaka
- Goodman Cancer Research Centre, Department of Human Genetics, McGill University, Montreal, Quebec H2W 1S6, Canada
| | - Gregg Duester
- Development, Aging and Regeneration Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
| | - Yukio Saijoh
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84132-3401, USA
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada Cell and Developmental Biology Program, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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14
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Schulze U, Vollenbröker B, Braun DA, Van Le T, Granado D, Kremerskothen J, Fränzel B, Klosowski R, Barth J, Fufezan C, Wolters DA, Pavenstädt H, Weide T. The Vac14-interaction network is linked to regulators of the endolysosomal and autophagic pathway. Mol Cell Proteomics 2014; 13:1397-411. [PMID: 24578385 DOI: 10.1074/mcp.m113.034108] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The scaffold protein Vac14 acts in a complex with the lipid kinase PIKfyve and its counteracting phosphatase FIG4, regulating the interconversion of phosphatidylinositol-3-phosphate to phosphatidylinositol-3,5-bisphosphate. Dysfunctional Vac14 mutants, a deficiency of one of the Vac14 complex components, or inhibition of PIKfyve enzymatic activity results in the formation of large vacuoles in cells. How these vacuoles are generated and which processes are involved are only poorly understood. Here we show that ectopic overexpression of wild-type Vac14 as well as of the PIKfyve-binding deficient Vac14 L156R mutant causes vacuoles. Vac14-dependent vacuoles and PIKfyve inhibitor-dependent vacuoles resulted in elevated levels of late endosomal, lysosomal, and autophagy-associated proteins. However, only late endosomal marker proteins were bound to the membranes of these enlarged vacuoles. In order to decipher the linkage between the Vac14 complex and regulators of the endolysosomal pathway, a protein affinity approach combined with multidimensional protein identification technology was conducted, and novel molecular links were unraveled. We found and verified the interaction of Rab9 and the Rab7 GAP TBC1D15 with Vac14. The identified Rab-related interaction partners support the theory that the regulation of vesicular transport processes and phosphatidylinositol-modifying enzymes are tightly interconnected.
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Affiliation(s)
- Ulf Schulze
- From the ‡Department of Internal Medicine D, Molecular Nephrology, University Hospital of Muenster, Albert-Schweitzer Campus 1, A14, D-48149 Muenster, Germany
| | - Beate Vollenbröker
- From the ‡Department of Internal Medicine D, Molecular Nephrology, University Hospital of Muenster, Albert-Schweitzer Campus 1, A14, D-48149 Muenster, Germany
| | - Daniela A Braun
- From the ‡Department of Internal Medicine D, Molecular Nephrology, University Hospital of Muenster, Albert-Schweitzer Campus 1, A14, D-48149 Muenster, Germany
| | - Truc Van Le
- From the ‡Department of Internal Medicine D, Molecular Nephrology, University Hospital of Muenster, Albert-Schweitzer Campus 1, A14, D-48149 Muenster, Germany
| | - Daniel Granado
- From the ‡Department of Internal Medicine D, Molecular Nephrology, University Hospital of Muenster, Albert-Schweitzer Campus 1, A14, D-48149 Muenster, Germany
| | - Joachim Kremerskothen
- From the ‡Department of Internal Medicine D, Molecular Nephrology, University Hospital of Muenster, Albert-Schweitzer Campus 1, A14, D-48149 Muenster, Germany
| | - Benjamin Fränzel
- ‖Analytical Chemistry NC4/72, Biomolecular Mass Spectrometry/Proteincenter, Ruhr-University Bochum, Universitätsstr. 150, D-44801 Bochum, Germany
| | - Rafael Klosowski
- ‖Analytical Chemistry NC4/72, Biomolecular Mass Spectrometry/Proteincenter, Ruhr-University Bochum, Universitätsstr. 150, D-44801 Bochum, Germany
| | - Johannes Barth
- ‡‡Institute of Plant Biology and Biotechnology, University of Muenster, Schlossplatz 8, D-48143 Muenster, Germany
| | - Christian Fufezan
- ‡‡Institute of Plant Biology and Biotechnology, University of Muenster, Schlossplatz 8, D-48143 Muenster, Germany
| | - Dirk A Wolters
- ‖Analytical Chemistry NC4/72, Biomolecular Mass Spectrometry/Proteincenter, Ruhr-University Bochum, Universitätsstr. 150, D-44801 Bochum, Germany
| | - Hermann Pavenstädt
- From the ‡Department of Internal Medicine D, Molecular Nephrology, University Hospital of Muenster, Albert-Schweitzer Campus 1, A14, D-48149 Muenster, Germany;
| | - Thomas Weide
- From the ‡Department of Internal Medicine D, Molecular Nephrology, University Hospital of Muenster, Albert-Schweitzer Campus 1, A14, D-48149 Muenster, Germany;
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15
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Knockin’ on pHeaven’s Door: A Fast and Reliable High-Throughput Compatible Zero-Background Cloning Procedure. Mol Biotechnol 2014; 56:449-58. [DOI: 10.1007/s12033-014-9736-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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16
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Luo N, Kumar A, Conwell M, Weinreb RN, Anderson R, Sun Y. Compensatory Role of Inositol 5-Phosphatase INPP5B to OCRL in Primary Cilia Formation in Oculocerebrorenal Syndrome of Lowe. PLoS One 2013; 8:e66727. [PMID: 23805271 PMCID: PMC3689662 DOI: 10.1371/journal.pone.0066727] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 05/10/2013] [Indexed: 12/11/2022] Open
Abstract
Inositol phosphatases are important regulators of cell signaling, polarity, and vesicular trafficking. Mutations in OCRL, an inositol polyphosphate 5-phosphatase, result in Oculocerebrorenal syndrome of Lowe, an X-linked recessive disorder that presents with congenital cataracts, glaucoma, renal dysfunction and mental retardation. INPP5B is a paralog of OCRL and shares similar structural domains. The roles of OCRL and INPP5B in the development of cataracts and glaucoma are not understood. Using ocular tissues, this study finds low levels of INPP5B present in human trabecular meshwork but high levels in murine trabecular meshwork. In contrast, OCRL is localized in the trabecular meshwork and Schlemm's canal endothelial cells in both human and murine eyes. In cultured human retinal pigmented epithelial cells, INPP5B was observed in the primary cilia. A functional role for INPP5B is revealed by defects in cilia formation in cells with silenced expression of INPP5B. This is further supported by the defective cilia formation in zebrafish Kupffer's vesicles and in cilia-dependent melanosome transport assays in inpp5b morphants. Taken together, this study indicates that OCRL and INPP5B are differentially expressed in the human and murine eyes, and play compensatory roles in cilia development.
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Affiliation(s)
- Na Luo
- Glick Eye Institute, Department of Ophthalmology, Department of Biochemistry and Cell Biology, Department of Dermatology, Indiana University Indianapolis, Indiana, United States of America
| | - Akhilesh Kumar
- Glick Eye Institute, Department of Ophthalmology, Department of Biochemistry and Cell Biology, Department of Dermatology, Indiana University Indianapolis, Indiana, United States of America
| | - Michael Conwell
- Glick Eye Institute, Department of Ophthalmology, Department of Biochemistry and Cell Biology, Department of Dermatology, Indiana University Indianapolis, Indiana, United States of America
| | - Robert N. Weinreb
- Department of Ophthalmology, University of California San Diego, San Diego, California, United States of America
| | - Ryan Anderson
- Department of Pediatrics, Indiana University Indianapolis, Indiana,United States of America
| | - Yang Sun
- Glick Eye Institute, Department of Ophthalmology, Department of Biochemistry and Cell Biology, Department of Dermatology, Indiana University Indianapolis, Indiana, United States of America
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17
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Adler JJ, Heller BL, Bringman LR, Ranahan WP, Cocklin RR, Goebl MG, Oh M, Lim HS, Ingham RJ, Wells CD. Amot130 adapts atrophin-1 interacting protein 4 to inhibit yes-associated protein signaling and cell growth. J Biol Chem 2013; 288:15181-93. [PMID: 23564455 DOI: 10.1074/jbc.m112.446534] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The adaptor protein Amot130 scaffolds components of the Hippo pathway to promote the inhibition of cell growth. This study describes how Amot130 through binding and activating the ubiquitin ligase AIP4/Itch achieves these effects. AIP4 is found to bind and ubiquitinate Amot130 at residue Lys-481. This both stabilizes Amot130 and promotes its residence at the plasma membrane. Furthermore, Amot130 is shown to scaffold a complex containing overexpressed AIP4 and the transcriptional co-activator Yes-associated protein (YAP). Consequently, Amot130 promotes the ubiquitination of YAP by AIP4 and prevents AIP4 from binding to large tumor suppressor 1. Amot130 is found to reduce YAP stability. Importantly, Amot130 inhibition of YAP dependent transcription is reversed by AIP4 silencing, whereas Amot130 and AIP4 expression interdependently suppress cell growth. Thus, Amot130 repurposes AIP4 from its previously described role in degrading large tumor suppressor 1 to the inhibition of YAP and cell growth.
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Affiliation(s)
- Jacob J Adler
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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18
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Festa F, Steel J, Bian X, Labaer J. High-throughput cloning and expression library creation for functional proteomics. Proteomics 2013; 13:1381-99. [PMID: 23457047 DOI: 10.1002/pmic.201200456] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 01/11/2013] [Accepted: 01/31/2013] [Indexed: 12/11/2022]
Abstract
The study of protein function usually requires the use of a cloned version of the gene for protein expression and functional assays. This strategy is particularly important when the information available regarding function is limited. The functional characterization of the thousands of newly identified proteins revealed by genomics requires faster methods than traditional single-gene experiments, creating the need for fast, flexible, and reliable cloning systems. These collections of ORF clones can be coupled with high-throughput proteomics platforms, such as protein microarrays and cell-based assays, to answer biological questions. In this tutorial, we provide the background for DNA cloning, discuss the major high-throughput cloning systems (Gateway® Technology, Flexi® Vector Systems, and Creator(TM) DNA Cloning System) and compare them side-by-side. We also report an example of high-throughput cloning study and its application in functional proteomics. This tutorial is part of the International Proteomics Tutorial Programme (IPTP12).
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Affiliation(s)
- Fernanda Festa
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287-6401, USA
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19
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Geertsma ER. FX cloning: a versatile high-throughput cloning system for characterization of enzyme variants. Methods Mol Biol 2013; 978:133-148. [PMID: 23423894 DOI: 10.1007/978-1-62703-293-3_10] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Methods for the cloning of large numbers of open reading frames (ORFs) into expression vectors are of critical importance for diverse disciplines in biology. Here I describe a system termed FX cloning that facilitates the high-throughput generation of expression constructs. FX cloning combines attractive features of established recombination- and single-strand-annealing-based cloning methods that were thus far not unified in one single method. FX cloning allows the straightforward transfer of a sequence-verified ORF to a variety of expression vectors, and it avoids the common but undesirable feature of significantly extending target ORFs with cloning-related sequences. It leaves a minimal seam of only a single amino acid to either side of the protein. Furthermore, FX cloning is highly efficient and economic in its use. The method is based on a class IIS restriction enzyme and negative selection markers. The full procedure takes place in one pot and does not require intermediate purifications. The method has proven to be very robust and suitable for all common pro- and eukaryotic expression systems.
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Affiliation(s)
- Eric R Geertsma
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
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20
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Interaction of cyclin-dependent kinase 12/CrkRS with cyclin K1 is required for the phosphorylation of the C-terminal domain of RNA polymerase II. Mol Cell Biol 2012; 32:4691-704. [PMID: 22988298 DOI: 10.1128/mcb.06267-11] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
CrkRS (Cdc2-related kinase, Arg/Ser), or cyclin-dependent kinase 12 (CKD12), is a serine/threonine kinase believed to coordinate transcription and RNA splicing. While CDK12/CrkRS complexes were known to phosphorylate the C-terminal domain (CTD) of RNA polymerase II (RNA Pol II), the cyclin regulating this activity was not known. Using immunoprecipitation and mass spectrometry, we identified a 65-kDa isoform of cyclin K (cyclin K1) in endogenous CDK12/CrkRS protein complexes. We show that cyclin K1 complexes isolated from mammalian cells contain CDK12/CrkRS but do not contain CDK9, a presumed partner of cyclin K. Analysis of extensive RNA-Seq data shows that the 65-kDa cyclin K1 isoform is the predominantly expressed form across numerous tissue types. We also demonstrate that CDK12/CrkRS is dependent on cyclin K1 for its kinase activity and that small interfering RNA (siRNA) knockdown of CDK12/CrkRS or cyclin K1 has similar effects on the expression of a luciferase reporter gene. Our data suggest that cyclin K1 is the primary cyclin partner for CDK12/CrkRS and that cyclin K1 is required to activate CDK12/CrkRS to phosphorylate the CTD of RNA Pol II. These properties are consistent with a role of CDK12/CrkRS in regulating gene expression through phosphorylation of RNA Pol II.
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21
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Braun P, Gingras AC. History of protein-protein interactions: From egg-white to complex networks. Proteomics 2012; 12:1478-98. [DOI: 10.1002/pmic.201100563] [Citation(s) in RCA: 163] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Pascal Braun
- Department of Plant Systems Biology; Center for Life and Food Sciences Weihenstephan; Technical University Munich; Freising Germany
- Research Unit Protein Science; Helmholtz Centre Munich; Munich Germany
| | - Anne-Claude Gingras
- Samuel Lunenfeld Research Institute at Mount Sinai Hospital; Toronto Ontario Canada
- Department of Molecular Genetics; University of Toronto; Toronto Ontario Canada
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22
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Luo N, West CC, Murga-Zamalloa CA, Sun L, Anderson RM, Wells CD, Weinreb RN, Travers JB, Khanna H, Sun Y. OCRL localizes to the primary cilium: a new role for cilia in Lowe syndrome. Hum Mol Genet 2012; 21:3333-44. [PMID: 22543976 PMCID: PMC3392109 DOI: 10.1093/hmg/dds163] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Oculocerebral renal syndrome of Lowe (OCRL or Lowe syndrome), a severe X-linked congenital disorder characterized by congenital cataracts and glaucoma, mental retardation and kidney dysfunction, is caused by mutations in the OCRL gene. OCRL is a phosphoinositide 5-phosphatase that interacts with small GTPases and is involved in intracellular trafficking. Despite extensive studies, it is unclear how OCRL mutations result in a myriad of phenotypes found in Lowe syndrome. Our results show that OCRL localizes to the primary cilium of retinal pigment epithelial cells, fibroblasts and kidney tubular cells. Lowe syndrome-associated mutations in OCRL result in shortened cilia and this phenotype can be rescued by the introduction of wild-type OCRL; in vivo, knockdown of ocrl in zebrafish embryos results in defective cilia formation in Kupffer vesicles and cilia-dependent phenotypes. Cumulatively, our data provide evidence for a role of OCRL in cilia maintenance and suggest the involvement of ciliary dysfunction in the manifestation of Lowe syndrome.
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Affiliation(s)
- Na Luo
- Department of Ophthalmology, Glick Eye Institute, Indiana University, 1601 W Michigan St., Indianapolis, IN 46202, USA
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23
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Guettler S, LaRose J, Petsalaki E, Gish G, Scotter A, Pawson T, Rottapel R, Sicheri F. Structural basis and sequence rules for substrate recognition by Tankyrase explain the basis for cherubism disease. Cell 2012; 147:1340-54. [PMID: 22153077 DOI: 10.1016/j.cell.2011.10.046] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2011] [Revised: 08/09/2011] [Accepted: 10/18/2011] [Indexed: 01/16/2023]
Abstract
The poly(ADP-ribose)polymerases Tankyrase 1/2 (TNKS/TNKS2) catalyze the covalent linkage of ADP-ribose polymer chains onto target proteins, regulating their ubiquitylation, stability, and function. Dysregulation of substrate recognition by Tankyrases underlies the human disease cherubism. Tankyrases recruit specific motifs (often called RxxPDG "hexapeptides") in their substrates via an N-terminal region of ankyrin repeats. These ankyrin repeats form five domains termed ankyrin repeat clusters (ARCs), each predicted to bind substrate. Here we report crystal structures of a representative ARC of TNKS2 bound to targeting peptides from six substrates. Using a solution-based peptide library screen, we derive a rule-based consensus for Tankyrase substrates common to four functionally conserved ARCs. This 8-residue consensus allows us to rationalize all known Tankyrase substrates and explains the basis for cherubism-causing mutations in the Tankyrase substrate 3BP2. Structural and sequence information allows us to also predict and validate other Tankyrase targets, including Disc1, Striatin, Fat4, RAD54, BCR, and MERIT40.
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Affiliation(s)
- Sebastian Guettler
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
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24
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Bernaudat F, Frelet-Barrand A, Pochon N, Dementin S, Hivin P, Boutigny S, Rioux JB, Salvi D, Seigneurin-Berny D, Richaud P, Joyard J, Pignol D, Sabaty M, Desnos T, Pebay-Peyroula E, Darrouzet E, Vernet T, Rolland N. Heterologous expression of membrane proteins: choosing the appropriate host. PLoS One 2011; 6:e29191. [PMID: 22216205 PMCID: PMC3244453 DOI: 10.1371/journal.pone.0029191] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 11/22/2011] [Indexed: 11/19/2022] Open
Abstract
Background Membrane proteins are the targets of 50% of drugs, although they only represent 1% of total cellular proteins. The first major bottleneck on the route to their functional and structural characterisation is their overexpression; and simply choosing the right system can involve many months of trial and error. This work is intended as a guide to where to start when faced with heterologous expression of a membrane protein. Methodology/Principal Findings The expression of 20 membrane proteins, both peripheral and integral, in three prokaryotic (E. coli, L. lactis, R. sphaeroides) and three eukaryotic (A. thaliana, N. benthamiana, Sf9 insect cells) hosts was tested. The proteins tested were of various origins (bacteria, plants and mammals), functions (transporters, receptors, enzymes) and topologies (between 0 and 13 transmembrane segments). The Gateway system was used to clone all 20 genes into appropriate vectors for the hosts to be tested. Culture conditions were optimised for each host, and specific strategies were tested, such as the use of Mistic fusions in E. coli. 17 of the 20 proteins were produced at adequate yields for functional and, in some cases, structural studies. We have formulated general recommendations to assist with choosing an appropriate system based on our observations of protein behaviour in the different hosts. Conclusions/Significance Most of the methods presented here can be quite easily implemented in other laboratories. The results highlight certain factors that should be considered when selecting an expression host. The decision aide provided should help both newcomers and old-hands to select the best system for their favourite membrane protein.
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Affiliation(s)
- Florent Bernaudat
- Institut de Biologie Structurale Jean-Pierre Ebel, CEA, Grenoble, France.
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25
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Abstract
Eukaryotic gene expression relies on several complex molecular machineries that act in a highly coordinated fashion. These machineries govern all the different steps of mRNA maturation, from gene transcription and pre-mRNA processing in the nucleus to the export of the mRNA to the cytoplasm and its translation. In particular, the pre-mRNA splicing process consists in the joining together of sequences (known as “exons”) that have to be differentiated from their intervening sequences commonly referred to as “introns.” The complex required to perform this process is a very dynamic macromolecular ribonucleoprotein assembly that functions as an enzyme, and is called the “spliceosome.” Because of its flexibility, the splicing process represents one of the main mechanisms of qualitative and quantitative regulation of gene expression in eukaryotic genomes. This flexibility is mainly due to the possibility of alternatively recognizing the various exons that are present in a pre-mRNA molecule and therefore enabling the possibility of obtaining multiple transcripts from the same gene. However, regulation of gene expression by the spliceosome is also achieved through its ability to influence many other gene expression steps that include transcription, mRNA export, mRNA stability, and even protein translation. Therefore, from a biotechnological point of view the splicing process can be exploited to improve production strategies and processes of molecules of interest. In this work, we have aimed to provide an overview on how biotechnology applications may benefit from the introduction of introns within a sequence of interest.
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Affiliation(s)
- Natasa Skoko
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy
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26
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Olhovsky M, Williton K, Dai AY, Pasculescu A, Lee JP, Goudreault M, Wells CD, Park JG, Gingras AC, Linding R, Pawson T, Colwill K. OpenFreezer: a reagent information management software system. Nat Methods 2011; 8:612-3. [PMID: 21799493 DOI: 10.1038/nmeth.1658] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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27
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Colwill K, Gräslund S. A roadmap to generate renewable protein binders to the human proteome. Nat Methods 2011; 8:551-8. [PMID: 21572409 DOI: 10.1038/nmeth.1607] [Citation(s) in RCA: 229] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Accepted: 04/11/2011] [Indexed: 12/16/2022]
Abstract
Despite the wealth of commercially available antibodies to human proteins, research is often hindered by their inconsistent validation, their poor performance and the inadequate coverage of the proteome. These issues could be addressed by systematic, genome-wide efforts to generate and validate renewable protein binders. We report a multicenter study to assess the potential of hybridoma and phage-display technologies in a coordinated large-scale antibody generation and validation effort. We produced over 1,000 antibodies targeting 20 SH2 domain proteins and evaluated them for potency and specificity by enzyme-linked immunosorbent assay (ELISA), protein microarray and surface plasmon resonance (SPR). We also tested selected antibodies in immunoprecipitation, immunoblotting and immunofluorescence assays. Our results show that high-affinity, high-specificity renewable antibodies generated by different technologies can be produced quickly and efficiently. We believe that this work serves as a foundation and template for future larger-scale studies to create renewable protein binders.
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Affiliation(s)
- Karen Colwill
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
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28
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Geertsma ER, Dutzler R. A Versatile and Efficient High-Throughput Cloning Tool for Structural Biology. Biochemistry 2011; 50:3272-8. [DOI: 10.1021/bi200178z] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Eric R. Geertsma
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Raimund Dutzler
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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29
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Ranahan WP, Han Z, Smith-Kinnaman W, Nabinger SC, Heller B, Herbert BS, Chan R, Wells CD. The adaptor protein AMOT promotes the proliferation of mammary epithelial cells via the prolonged activation of the extracellular signal-regulated kinases. Cancer Res 2011; 71:2203-11. [PMID: 21285250 DOI: 10.1158/0008-5472.can-10-1995] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The asymmetric organization of epithelial cells is a basic counter to cellular proliferation. However, the mechanisms whereby pro-growth pathways are modulated by intracellular factors that control cell shape are not well understood. This study demonstrates that the adaptor protein Amot, in addition to its established role in regulating cellular asymmetry, also promotes extracellular signal-regulated kinase 1 and 2 (ERK1/2)-dependent proliferation of mammary cells. Specifically, expression of Amot80, but not a mutant lacking its polarity protein interaction domain, enhances ERK1/2-dependent proliferation of MCF7 cells. Further, expression of Amot80 induces nontransformed MCF10A cells to overgrow as disorganized cellular aggregates in Matrigel. Conversely, Amot expression is required for proliferation of breast cancer cells in specific microenvironmental contexts that require ERK1/2 signaling. Thus, Amot is proposed to coordinate the dysregulation of cell polarity with the induction of neoplastic growth in mammary cells.
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Affiliation(s)
- William P Ranahan
- Department of Biochemistry and Molecular Biology, University of Indiana School of Medicine, Indianapolis, Indiana 46202-5122, USA
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30
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Duning K, Rosenbusch D, Schlüter MA, Tian Y, Kunzelmann K, Meyer N, Schulze U, Markoff A, Pavenstädt H, Weide T. Polycystin-2 activity is controlled by transcriptional coactivator with PDZ binding motif and PALS1-associated tight junction protein. J Biol Chem 2010; 285:33584-8. [PMID: 20833712 DOI: 10.1074/jbc.c110.146381] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is the most frequent monogenic cause of kidney failure, characterized by the development of renal cysts. ADPKD is caused by mutations of the polycystin-1 (PC1) or polycystin-2 (PC2) genes. PC2 encodes a Ca(2+)-permeable cation channel, and its dysfunction has been implicated in cyst development. The transcriptional coactivator with PDZ binding motif (TAZ) is required for the integrity of renal cilia. Its absence results in the development of renal cysts in a knock-out mouse model. TAZ directly interacts with PC2, and it has been suggested that another yet unidentified PDZ domain protein may be involved in the TAZ/PC2 interaction. Here we describe a novel interaction of TAZ with the multi-PDZ-containing PALS1-associated tight junction protein (PATJ). TAZ interacts with both the N-terminal PDZ domains 1-3 and the C-terminal PDZ domains 8-10 of PATJ, suggesting two distinct TAZ binding domains. We also show that the C terminus of PC2 strongly interacts with PDZ domains 8-10 and to a weaker extent with PDZ domains 1-3 of PATJ. Finally, we demonstrate that both TAZ and PATJ impair PC2 channel activity when co-expressed with PC2 in oocytes of Xenopus laevis. These results implicate TAZ and PATJ as novel regulatory elements of the PC2 channel and might thus be involved in ADPKD pathology.
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Affiliation(s)
- Kerstin Duning
- Department of Internal Medicine D, Molecular Nephrology, University Clinics of Münster, University of Münster, D-48149 Münster.
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31
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Dubin M, Nellen W. A versatile set of tagged expression vectors to monitor protein localisation and function in Dictyostelium. Gene 2010; 465:1-8. [PMID: 20600701 DOI: 10.1016/j.gene.2010.06.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2010] [Revised: 06/13/2010] [Accepted: 06/22/2010] [Indexed: 11/29/2022]
Abstract
We describe here a series of vectors for ectopic expression of tagged proteins in Dictyostelium discoideum. These vectors allow the addition of N- or C-terminal tags (GFP, mRFP, 3xFLAG, 3xHA, 6xMYC or TAP) with an optimised polylinker sequence and no additional amino acid residues at the N- or C-terminus of the protein. The expression cassettes were introduced into vectors containing Blasticidin or Geneticin resistance markers and into integrating as well as extrachromosomal plasmids. The vectors are designed as high and low copy versions and thus allow for a limited expression level control. They are also convenient with regard to complementation, co- and super-transformation. Finally the vectors share standardised cloning sites, so that a gene of interest can be easily transferred between vectors as experimental requirements evolve. These vectors were used to study the localisation of several putative RNA processing proteins including EriA and DicerB.
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Affiliation(s)
- Manu Dubin
- Department of Genetics, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany.
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32
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Mead CLR, Kuzyk MA, Moradian A, Wilson GM, Holt RA, Morin GB. Cytosolic protein interactions of the schizophrenia susceptibility gene dysbindin. J Neurochem 2010; 113:1491-503. [PMID: 20236384 DOI: 10.1111/j.1471-4159.2010.06690.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Using immunoprecipitation, mass spectrometry, and western blot analysis we investigated cytosolic protein interactions of the schizophrenia susceptibility gene dysbindin in mammalian cells. We identified novel interactions with members of the exocyst, dynactin and chaperonin containing T-complex protein complexes, and we confirmed interactions reported previously with all members of the biogenesis of lysosome-related organelles complex-1 and the adaptor-related protein complex 3. We report interactions between dysbindin and the exocyst and dynactin complex that confirm a link between two important schizophrenia susceptibility genes: dysbindin and disrupted-in-schizophrenia-1. To expand upon this network of interacting proteins we also investigated protein interactions for members of the exocyst and dynactin complexes in mammalian cells. Our results are consistent with the notion that impairment of aspects of the synaptic vesicle life cycle may be a pathogenic mechanism in schizophrenia.
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Affiliation(s)
- Carri-Lyn R Mead
- Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
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33
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Heller B, Adu-Gyamfi E, Smith-Kinnaman W, Babbey C, Vora M, Xue Y, Bittman R, Stahelin RV, Wells CD. Amot recognizes a juxtanuclear endocytic recycling compartment via a novel lipid binding domain. J Biol Chem 2010; 285:12308-20. [PMID: 20080965 DOI: 10.1074/jbc.m109.096230] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Polarity proteins promote the asymmetric organization of cells by orienting intracellular sorting mechanisms, such as protein trafficking and cytoskeletal assembly. The localization of individual polarity proteins in turn is often determined by association with factors that mediate contact with other cells or the substratum. This arrangement for the Par and Crb apical polarity complexes at the tight junction is disrupted by the adaptor protein Amot. Amot directly binds the scaffolding proteins Patj and Mupp1 and redistributes them and their binding partners from the plasma membrane to endosomes. However, the mechanism by which Amot is targeted to endosomes is unknown. Here, a novel lipid binding domain within Amot is shown to selectively bind with high affinity to membranes containing monophosphorylated phosphatidylinositols and cholesterol. With similar lipid specificity, Amot inserts into and tubulates membranes in vitro and enlarges perinuclear endosomal compartments in cells. Based on the similar distribution of Amot with cholesterol, Rab11, and Arf6, such membrane interactions are identified at juxtanuclear endocytic recycling compartments. Taken together, these findings indicate that Amot is targeted along with associated apical polarity proteins to the endocytic recycling compartment via this novel membrane binding domain.
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Affiliation(s)
- Brigitte Heller
- Department of Biochemistry and Molecular Biology, University of Indiana School ofMedicine, Indianapolis, Indiana 46202, USA
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34
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Wang X, Schwarz TL. The mechanism of Ca2+ -dependent regulation of kinesin-mediated mitochondrial motility. Cell 2009; 136:163-74. [PMID: 19135897 DOI: 10.1016/j.cell.2008.11.046] [Citation(s) in RCA: 659] [Impact Index Per Article: 43.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Revised: 10/14/2008] [Accepted: 11/24/2008] [Indexed: 01/05/2023]
Abstract
Mitochondria are mobile organelles and cells regulate mitochondrial movement in order to meet the changing energy needs of each cellular region. Ca(2+) signaling, which halts both anterograde and retrograde mitochondrial motion, serves as one regulatory input. Anterograde mitochondrial movement is generated by kinesin-1, which interacts with the mitochondrial protein Miro through an adaptor protein, milton. We show that kinesin is present on all axonal mitochondria, including those that are stationary or moving retrograde. We also show that the EF-hand motifs of Miro mediate Ca(2+)-dependent arrest of mitochondria and elucidate the regulatory mechanism. Rather than dissociating kinesin-1 from mitochondria, Ca(2+)-binding permits Miro to interact directly with the motor domain of kinesin-1, preventing motor/microtubule interactions. Thus, kinesin-1 switches from an active state in which it is bound to Miro only via milton, to an inactive state in which direct binding to Miro prevents its interaction with microtubules. Disrupting Ca(2+)-dependent regulation diminishes neuronal resistance to excitotoxicity.
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Affiliation(s)
- Xinnan Wang
- F.M. Kirby Neurobiology Center, Children's Hospital Boston, Boston, MA 02115, USA
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35
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Abstract
Neuronal mitochondria need to be transported and distributed in axons and dendrites in order to ensure an adequate energy supply and provide sufficient Ca(2+) buffering in each portion of these highly extended cells. Errors in mitochondrial transport are implicated in neurodegenerative diseases. Here we present useful tools to analyze axonal transport of mitochondria both in vitro in cultured rat neurons and in vivo in Drosophila larval neurons. These methods enable investigators to take advantage of both systems to study the properties of mitochondrial motility under normal or pathological conditions.
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Affiliation(s)
- Xinnan Wang
- F. M. Kirby Neurobiology Center, Children's Hospital Boston, and Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
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36
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A one pot, one step, precision cloning method with high throughput capability. PLoS One 2008; 3:e3647. [PMID: 18985154 PMCID: PMC2574415 DOI: 10.1371/journal.pone.0003647] [Citation(s) in RCA: 1457] [Impact Index Per Article: 91.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2008] [Accepted: 10/20/2008] [Indexed: 11/19/2022] Open
Abstract
Current cloning technologies based on site-specific recombination are efficient, simple to use, and flexible, but have the drawback of leaving recombination site sequences in the final construct, adding an extra 8 to 13 amino acids to the expressed protein. We have devised a simple and rapid subcloning strategy to transfer any DNA fragment of interest from an entry clone into an expression vector, without this shortcoming. The strategy is based on the use of type IIs restriction enzymes, which cut outside of their recognition sequence. With proper design of the cleavage sites, two fragments cut by type IIs restriction enzymes can be ligated into a product lacking the original restriction site. Based on this property, a cloning strategy called ‘Golden Gate’ cloning was devised that allows to obtain in one tube and one step close to one hundred percent correct recombinant plasmids after just a 5 minute restriction-ligation. This method is therefore as efficient as currently used recombination-based cloning technologies but yields recombinant plasmids that do not contain unwanted sequences in the final construct, thus providing precision for this fundamental process of genetic manipulation.
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37
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Phosphorylated YDXV motifs and Nck SH2/SH3 adaptors act cooperatively to induce actin reorganization. Mol Cell Biol 2008; 28:2035-46. [PMID: 18212058 DOI: 10.1128/mcb.01770-07] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We have analyzed the means by which the Nck family of adaptor proteins couples adhesion proteins to actin reorganization. The nephrin adhesion protein is essential for the formation of actin-based foot processes in glomerular podocytes. The clustering of nephrin induces its tyrosine phosphorylation, Nck recruitment, and sustained localized actin polymerization. Any one of three phosphorylated (p)YDXV motifs on nephrin is sufficient to recruit Nck through its Src homology 2 (SH2) domain and induce localized actin polymerization at these clusters. Similarly, Nck SH3 mutants in which only the second or third SH3 domain is functional can mediate nephrin-induced actin polymerization. However, combining such nephrin and Nck mutants attenuates actin polymerization at nephrin-Nck clusters. We propose that the multiple Nck SH2-binding motifs on nephrin and the multiple SH3 domains of Nck act cooperatively to recruit the high local concentration of effectors at sites of nephrin activation that is required to initiate and maintain actin polymerization in vivo. We also find that YDXV motifs in the Tir protein of enteropathogenic Escherichia coli and nephrin are functionally interchangeable, indicating that Tir reorganizes the actin cytoskeleton by molecular mimicry of nephrin-like signaling. Together, these data identify pYDXV/Nck signaling as a potent and portable mechanism for physiological and pathological actin regulation.
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38
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Lim CS, Seet BT, Ingham RJ, Gish G, Matskova L, Winberg G, Ernberg I, Pawson T. The K15 protein of Kaposi's sarcoma-associated herpesvirus recruits the endocytic regulator intersectin 2 through a selective SH3 domain interaction. Biochemistry 2007; 46:9874-85. [PMID: 17696407 DOI: 10.1021/bi700357s] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Kaposi's sarcoma-associated herpesvirus, also known as human herpesvirus 8, is closely associated with several cancers including Kaposi's sarcoma, primary effusion lymphoma, and multicentric Castleman's disease. The rightmost end of the KSHV genome encodes a protein, K15, with multiple membrane-spanning segments and an intracellular carboxy-terminal tail that contains several conserved motifs with the potential to recruit interaction domains (i.e., SH2, SH3, TRAF) of host cell proteins. K15 has been implicated in downregulating B cell receptor (BCR) signaling through its conserved motifs and may thereby play a role in maintaining viral latency and/or preventing apoptosis of the infected B cells. However, K15's mode of action is largely unknown. We have used mass spectrometry, domain and peptide arrays, and surface plasmon resonance to identify binding partners for a conserved proline-rich sequence (PPLP) in the K15 cytoplasmic tail. We show that the PPLP motif selectively binds the SH3-C domain of an endocytic adaptor protein, Intersectin 2 (ITSN2). This interaction can be observed both in vitro and in cells, where K15 and ITSN2 colocalize to discrete compartments within the B cell. The ability of K15 to associate with ITSN2 suggests a new role for the K15 viral protein in intracellular protein trafficking.
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Affiliation(s)
- Caesar S Lim
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
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39
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Smith MJ, Hardy WR, Murphy JM, Jones N, Pawson T. Screening for PTB domain binding partners and ligand specificity using proteome-derived NPXY peptide arrays. Mol Cell Biol 2006; 26:8461-74. [PMID: 16982700 PMCID: PMC1636785 DOI: 10.1128/mcb.01491-06] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Modular interaction domains that recognize peptide motifs in target proteins can impart selectivity in signaling pathways. Phosphotyrosine binding (PTB) domains are components of cytoplasmic docking proteins that bind cell surface receptors through NPXY motifs. We have employed a library of human proteome-derived NXXY sequences to explore PTB domain specificity and function. SPOTS peptide arrays were used to create a comprehensive matrix of receptor motifs that were probed with a set of 10 diverse PTB domains. This approach confirmed that individual PTB domains have selective and distinct recognition properties and provided a means to explore over 2,500 potential PTB domain-NXXY interactions. The results correlated well with previously known associations between full-length proteins and predicted novel interactions, as well as consensus binding data for specific PTB domains. Using the Ret, MuSK, and ErbB2 receptor tyrosine kinases, we show that interactions of these receptors with PTB domains predicted to bind by the NXXY arrays do occur in cells. Proteome-based peptide arrays can therefore identify networks of receptor interactions with scaffold proteins that may be physiologically relevant.
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Affiliation(s)
- Matthew J Smith
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
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40
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Hartley JL. Cloning technologies for protein expression and purification. Curr Opin Biotechnol 2006; 17:359-66. [PMID: 16839756 DOI: 10.1016/j.copbio.2006.06.011] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2006] [Revised: 05/20/2006] [Accepted: 06/28/2006] [Indexed: 11/25/2022]
Abstract
Detailed knowledge of the biochemistry and structure of individual proteins is fundamental to biomedical research. To further our understanding, however, proteins need to be purified in sufficient quantities, usually from recombinant sources. Although the sequences of genomes are now produced in automated factories purified proteins are not, because their behavior is much more variable. The construction of plasmids and viruses to overexpress proteins for their purification is often tedious. Alternatives to traditional methods that are faster, easier and more flexible are needed and are becoming available.
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Affiliation(s)
- James L Hartley
- Protein Expression Laboratory, Research Technology Program, SAIC-Frederick, Inc, NCI-Frederick, Frederick, MD 21702, USA.
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