1
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Sun Y, He Q, Li J, Yang Z, Ahmad M, Lin Y, Wu D, Zheng L, Li J, Wang B, Chen C, Hu Y, Luo H, Luo Y. A GSTP1-mediated lactic acid signaling promotes tumorigenesis through the PPP oxidative branch. Cell Death Dis 2023; 14:463. [PMID: 37491277 PMCID: PMC10368634 DOI: 10.1038/s41419-023-05998-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/21/2023] [Accepted: 07/13/2023] [Indexed: 07/27/2023]
Abstract
Lactic acidosis is a feature of solid tumors and plays fundamental role(s) rendering cancer cells to adapt to diverse metabolic stresses, but the mechanism underlying its roles in redox homeostasis remains elusive. Here we show that G6PD is phosphorylated at tyrosine 249/322 by the SRC through the formation of a GSTP1-G6PD-SRC complex. Lactic acid attenuates this formation and the phosphorylation of G6PD by non-covalently binding with GSTP1. Furthermore, lactic acid increases the activity of G6PD and facilitates the PPP (NADPH production) through its sensor GSTP1, thereby exhibiting resistance to reactive oxygen species when glucose is scarce. Abrogating a GSTP1-mediated lactic acid signaling showed attenuated tumor growth and reduced resistance to ROS in breast cancer cells. Importantly, positive correlations between immuno-enriched SRC protein and G6PD Y249/322 phosphorylation specifically manifest in ER/PR positive or HER negative types of breast cancer. Taken together, these results suggest that GSTP1 plays a key role in tumor development by functioning as a novel lactate sensor.
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Affiliation(s)
- Yandi Sun
- Cancer Institute, The Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qian He
- Department of Biochemistry & Cancer Medicine, International Institutes of Medicine, the Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, Zhejiang, China
- Department of Biochemistry and Molecular Biology, School of Medicine, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, Zhejiang, China
| | - Jingjia Li
- Department of Biochemistry & Cancer Medicine, International Institutes of Medicine, the Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, Zhejiang, China
- Department of Biochemistry and Molecular Biology, School of Medicine, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, Zhejiang, China
| | - Ze Yang
- Department of Biochemistry & Cancer Medicine, International Institutes of Medicine, the Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, Zhejiang, China
- Department of Biochemistry and Molecular Biology, School of Medicine, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, Zhejiang, China
| | - Mashaal Ahmad
- Department of Biochemistry & Cancer Medicine, International Institutes of Medicine, the Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, Zhejiang, China
- Department of Biochemistry and Molecular Biology, School of Medicine, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, Zhejiang, China
| | - Yindan Lin
- Department of Biochemistry & Cancer Medicine, International Institutes of Medicine, the Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, Zhejiang, China
- Department of Biochemistry and Molecular Biology, School of Medicine, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, Zhejiang, China
| | - Di Wu
- Department of General Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lei Zheng
- Departments of Oncology and Surgery, the Pancreatic Cancer Center of Excellence Program, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jiangtao Li
- Department of General Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ben Wang
- Cancer Institute, The Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chitty Chen
- Department of Research and Development, SysDiagno Biotech, Nanjing, 211800, Jiangsu Province, China
| | - Yue Hu
- Department of Breast Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Heng Luo
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou, China.
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang, Guizhou, China.
| | - Yan Luo
- Department of Biochemistry & Cancer Medicine, International Institutes of Medicine, the Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, Zhejiang, China.
- Department of Biochemistry and Molecular Biology, School of Medicine, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, Zhejiang, China.
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2
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Thüring EM, Hartmann C, Maddumage JC, Javorsky A, Michels BE, Gerke V, Banks L, Humbert PO, Kvansakul M, Ebnet K. Membrane recruitment of the polarity protein Scribble by the cell adhesion receptor TMIGD1. Commun Biol 2023; 6:702. [PMID: 37430142 DOI: 10.1038/s42003-023-05088-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/29/2023] [Indexed: 07/12/2023] Open
Abstract
Scribble (Scrib) is a multidomain polarity protein and member of the leucine-rich repeat and PDZ domain (LAP) protein family. A loss of Scrib expression is associated with disturbed apical-basal polarity and tumor formation. The tumor-suppressive activity of Scrib correlates with its membrane localization. Despite the identification of numerous Scrib-interacting proteins, the mechanisms regulating its membrane recruitment are not fully understood. Here, we identify the cell adhesion receptor TMIGD1 as a membrane anchor of Scrib. TMIGD1 directly interacts with Scrib through a PDZ domain-mediated interaction and recruits Scrib to the lateral membrane domain in epithelial cells. We characterize the association of TMIGD1 with each Scrib PDZ domain and describe the crystal structure of the TMIGD1 C-terminal peptide complexed with PDZ domain 1 of Scrib. Our findings describe a mechanism of Scrib membrane localization and contribute to the understanding of the tumor-suppressive activity of Scrib.
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Affiliation(s)
- Eva-Maria Thüring
- Institute-associated Research Group "Cell adhesion and cell polarity", Institute of Medical Biochemistry, ZMBE, University of Münster, Münster, Germany
| | - Christian Hartmann
- Institute-associated Research Group "Cell adhesion and cell polarity", Institute of Medical Biochemistry, ZMBE, University of Münster, Münster, Germany
| | - Janesha C Maddumage
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Airah Javorsky
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Birgitta E Michels
- Institute-associated Research Group "Cell adhesion and cell polarity", Institute of Medical Biochemistry, ZMBE, University of Münster, Münster, Germany
| | - Volker Gerke
- Institute of Medical Biochemistry, ZMBE, University of Münster, Münster, Germany
| | - Lawrence Banks
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Patrick O Humbert
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Marc Kvansakul
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia.
| | - Klaus Ebnet
- Institute-associated Research Group "Cell adhesion and cell polarity", Institute of Medical Biochemistry, ZMBE, University of Münster, Münster, Germany.
- Cells-in-Motion Interfaculty Center, University of Münster, Münster, Germany.
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3
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Dorgan B, Liu Y, Wang S, Aduse-Opoku J, Whittaker SBM, Roberts MAJ, Lorenz CD, Curtis MA, Garnett JA. Structural Model of a Porphyromonas gingivalis type IX Secretion System Shuttle Complex. J Mol Biol 2022; 434:167871. [PMID: 36404438 DOI: 10.1016/j.jmb.2022.167871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 10/14/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
Porphyromonas gingivalis is a gram-negative oral anaerobic pathogen and is one of the key causative agents of periodontitis. P. gingivalis utilises a range of virulence factors, including the cysteine protease RgpB, to drive pathogenesis and these are exported and attached to the cell surface via the type IX secretion system (T9SS). All cargo proteins possess a conserved C-terminal signal domain (CTD) which is recognised by the T9SS, and the outer membrane β-barrel protein PorV (PG0027/LptO) can interact with cargo proteins as they are exported to the bacterial surface. Using a combination of solution nuclear magnetic resonance (NMR) spectroscopy, biochemical analyses, machine-learning-based modelling and molecular dynamics (MD) simulations, we present a structural model of a PorV:RgpB-CTD complex from P. gingivalis. This is the first structural insight into CTD recognition by the T9SS and shows how the conserved motifs in the CTD are the primary sites that mediate binding. In PorV, interactions with extracellular surface loops are important for binding the CTD, and together these appear to cradle and lock RgpB-CTD in place. This work provides insight into cargo recognition by PorV but may also have important implications for understanding other aspects of type-IX dependent secretion.
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Affiliation(s)
- Ben Dorgan
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK; School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Yichao Liu
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Sunjun Wang
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Joseph Aduse-Opoku
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Sara B-M Whittaker
- Institute of Cancer & Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Mark A J Roberts
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK
| | - Christian D Lorenz
- Biological Physics & Soft Matter Research Group, Department of Physics, King's College London, London, UK
| | - Michael A Curtis
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK.
| | - James A Garnett
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK.
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4
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Russell TM, Richardson DR. The good Samaritan glutathione-S-transferase P1: An evolving relationship in nitric oxide metabolism mediated by the direct interactions between multiple effector molecules. Redox Biol 2022; 59:102568. [PMID: 36563536 PMCID: PMC9800640 DOI: 10.1016/j.redox.2022.102568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/22/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022] Open
Abstract
Glutathione-S-transferases (GSTs) are phase II detoxification isozymes that conjugate glutathione (GSH) to xenobiotics and also suppress redox stress. It was suggested that GSTs have evolved not to enhance their GSH affinity, but to better interact with and metabolize cytotoxic nitric oxide (NO). The interactions between NO and GSTs involve their ability to bind and store NO as dinitrosyl-dithiol iron complexes (DNICs) within cells. Additionally, the association of GSTP1 with inducible nitric oxide synthase (iNOS) results in its inhibition. The function of NO in vasodilation together with studies associating GSTM1 or GSTT1 null genotypes with preeclampsia, additionally suggests an intriguing connection between NO and GSTs. Furthermore, suppression of c-Jun N-terminal kinase (JNK) activity occurs upon increased levels of GSTP1 or NO that decreases transcription of JNK target genes such as c-Jun and c-Fos, which inhibit apoptosis. This latter effect is mediated by the direct association of GSTs with MAPK proteins. GSTP1 can also inhibit nuclear factor kappa B (NF-κB) signaling through its interactions with IKKβ and Iκα, resulting in decreased iNOS expression and the stimulation of apoptosis. It can be suggested that the inhibitory activity of GSTP1 within the JNK and NF-κB pathways may be involved in crosstalk between survival and apoptosis pathways and modulating NO-mediated ROS generation. These studies highlight an innovative role of GSTs in NO metabolism through their interaction with multiple effector proteins, with GSTP1 functioning as a "good Samaritan" within each pathway to promote favorable cellular conditions and NO levels.
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Affiliation(s)
- Tiffany M. Russell
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Des R. Richardson
- Centre for Cancer Cell Biology and Drug Discovery, Griffith Institute for Drug Discovery, Griffith University, Nathan, 4111, Australia,Corresponding author. Centre for Cancer Cell Biology, Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, 4111, Queensland, Australia.
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5
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Yao Y, Wang W, Chen C. Mechanisms of phase-separation-mediated cGAS activation revealed by dcFCCS. PNAS NEXUS 2022; 1:pgac109. [PMID: 36741445 PMCID: PMC9896928 DOI: 10.1093/pnasnexus/pgac109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/02/2022] [Indexed: 02/07/2023]
Abstract
Cyclic GMP-AMP synthase (cGAS), as a DNA sensor, plays an important role in cGAS-STING pathway, which further induces expression of type I interferon as the innate immune response. Previous studies reported that liquid-liquid phase separation (LLPS) driven by cGAS and long DNA is essential to promote catalytic activity of cGAS to produce a second messenger, cyclic GMP-AMP (cGAMP). However, the molecular mechanism of LLPS promoting cGAS activity is still unclear. Here, we applied dual-color fluorescence cross-correlation spectroscopy (dcFCCS), a highly sensitive and quantitative method, to characterize phase separation driven by cGAS and DNA from miscible individual molecule to micronscale. Thus, we captured nanoscale condensates formed by cGAS at close-to-physiological concentration and quantified their sizes, molecular compositions and binding affinities within condensates. Our results pinpointed that interactions between DNA and cGAS at DNA binding sites A, B, and C and the dimerization of cGAS are the fundamental molecular basis to fully activate cGAS in vitro. Due to weak binding constants of these sites, endogenous cGAS cannot form stable interactions at these sites, leading to no activity in the absence of LLPS. Phase separation of cGAS and DNA enriches cGAS and DNA by 2 to 3 orders of magnitude to facilitate these interactions among cGAS and DNA and to promote cGAS activity as an on/off switch. Our discoveries not only shed lights on the molecular mechanisms of phase-separation-mediated cGAS activation, but also guided us to engineer a cGAS fusion, which can be activated by 15 bp short DNA without LLPS.
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Affiliation(s)
- Yirong Yao
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center of Biological Structure, Tsinghua University, Beijing, 100084, China
| | - Wenjuan Wang
- School of Life Sciences, Technology Center for Protein Sciences, Tsinghua University, Beijing, 100084, China
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6
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Hóbor F, Hegedüs Z, Ibarra AA, Petrovicz VL, Bartlett GJ, Sessions RB, Wilson AJ, Edwards TA. Understanding p300-transcription factor interactions using sequence variation and hybridization. RSC Chem Biol 2022; 3:592-603. [PMID: 35656479 PMCID: PMC9092470 DOI: 10.1039/d2cb00026a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/10/2022] [Indexed: 11/21/2022] Open
Abstract
The hypoxic response is central to cell function and plays a significant role in the growth and survival of solid tumours. HIF-1 regulates the hypoxic response by activating over 100...
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Affiliation(s)
- Fruzsina Hóbor
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Zsófia Hegedüs
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H-6720 Szeged Hungary
| | - Amaurys Avila Ibarra
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
| | - Vencel L Petrovicz
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H-6720 Szeged Hungary
| | - Gail J Bartlett
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Richard B Sessions
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
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7
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Kawashima K, Hirota-Tsukimachi M, Toma T, Koga R, Iwamaru K, Kanemaru Y, Yanae M, Ahagon A, Nakamura Y, Anraku K, Tateishi H, Gohda J, Inoue JI, Otsuka M, Fujita M. Development of chimeric receptor activator of nuclear factor-kappa B with glutathione S-transferase in the extracellular domain: Artificial switch in a membrane receptor. Chem Biol Drug Des 2021; 99:573-584. [PMID: 34882966 DOI: 10.1111/cbdd.14002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 11/23/2021] [Accepted: 12/05/2021] [Indexed: 11/26/2022]
Abstract
Various chimeric receptors have been developed and used for biological experiments. In the present study, we constructed three types of chimeric receptor activator of nuclear factor-kappa B (RANK) with the glutathione S-transferase (GST) protein in the extracellular domain, and stimulated them using newly synthesized chemical trimerizers with three glutathiones. Although this stimulation did not activate these proteins, we unexpectedly found that the chimera named RANK-GST-SC, in which GST replaced a major part of the RANK extracellular domain, activated nuclear factor-kappa B (NF-κB) signaling approximately sixfold more strongly than wild-type RANK without the ligand. The dimerization of extracellular GST is considered to function as a switch outside the cell, and signal transduction then occurs. GST has been widely employed as a tag for protein purification; GST-fusion protein can be conveniently captured by glutathione-conjugated beads and easily purified from impurity. The present study is a pioneering example of the novel utility of GST and provides information for the development of new chemical biology systems.
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Affiliation(s)
- Kanako Kawashima
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Mayuko Hirota-Tsukimachi
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Tsugumasa Toma
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Ryoko Koga
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Kana Iwamaru
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yosuke Kanemaru
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Misato Yanae
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Ami Ahagon
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yurine Nakamura
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Kensaku Anraku
- Department of Medical Technology, Kumamoto Health Science University, Kumamoto, Japan
| | - Hiroshi Tateishi
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Jin Gohda
- Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Jun-Ichiro Inoue
- Research Platform Office, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Masami Otsuka
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan.,Science Farm Ltd., Kumamoto, Japan
| | - Mikako Fujita
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
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8
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Bobone S, Pannone L, Biondi B, Solman M, Flex E, Canale VC, Calligari P, De Faveri C, Gandini T, Quercioli A, Torini G, Venditti M, Lauri A, Fasano G, Hoeksma J, Santucci V, Cattani G, Bocedi A, Carpentieri G, Tirelli V, Sanchez M, Peggion C, Formaggio F, den Hertog J, Martinelli S, Bocchinfuso G, Tartaglia M, Stella L. Targeting Oncogenic Src Homology 2 Domain-Containing Phosphatase 2 (SHP2) by Inhibiting Its Protein-Protein Interactions. J Med Chem 2021; 64:15973-15990. [PMID: 34714648 PMCID: PMC8591604 DOI: 10.1021/acs.jmedchem.1c01371] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We developed a new class of inhibitors of protein-protein interactions of the SHP2 phosphatase, which is pivotal in cell signaling and represents a central target in the therapy of cancer and rare diseases. Currently available SHP2 inhibitors target the catalytic site or an allosteric pocket but lack specificity or are ineffective for disease-associated SHP2 mutants. Considering that pathogenic lesions cause signaling hyperactivation due to increased levels of SHP2 association with cognate proteins, we developed peptide-based molecules with nanomolar affinity for the N-terminal Src homology domain of SHP2, good selectivity, stability to degradation, and an affinity for pathogenic variants of SHP2 that is 2-20 times higher than for the wild-type protein. The best peptide reverted the effects of a pathogenic variant (D61G) in zebrafish embryos. Our results provide a novel route for SHP2-targeted therapies and a tool for investigating the role of protein-protein interactions in the function of SHP2.
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Affiliation(s)
- Sara Bobone
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Luca Pannone
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy.,Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Padova 35131, Italy
| | - Maja Solman
- Hubrecht institute-KNAW and University Medical Center Utrecht, Utrecht 3584 CT, The Netherlands
| | - Elisabetta Flex
- Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Viviana Claudia Canale
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Paolo Calligari
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Chiara De Faveri
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Tommaso Gandini
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Andrea Quercioli
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Giuseppe Torini
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Martina Venditti
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Antonella Lauri
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Giulia Fasano
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Jelmer Hoeksma
- Hubrecht institute-KNAW and University Medical Center Utrecht, Utrecht 3584 CT, The Netherlands
| | - Valerio Santucci
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Giada Cattani
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Alessio Bocedi
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Giovanna Carpentieri
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy.,Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Valentina Tirelli
- Centre of Core Facilities, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Massimo Sanchez
- Centre of Core Facilities, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Cristina Peggion
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Fernando Formaggio
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Padova 35131, Italy.,Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Jeroen den Hertog
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Padova 35131, Italy.,Institute of Biology Leiden, Leiden University, Leiden 2333 BE, The Netherlands
| | - Simone Martinelli
- Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Gianfranco Bocchinfuso
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Lorenzo Stella
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
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9
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The N-terminal 5-68 amino acids domain of the minor capsid protein VP1 of human parvovirus B19 enters human erythroid progenitors and inhibits B19 infection. J Virol 2021; 95:JVI.00466-21. [PMID: 33952637 PMCID: PMC8223926 DOI: 10.1128/jvi.00466-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Parvovirus B19 (B19V) infection causes diseases in humans ranging from the mild erythema infectiosum to severe hematological disorders. The unique region of the minor structural protein VP1 (VP1u) of 227 amino acids harbors strong neutralizing epitopes which elicit dominant immune responses in patients. Recent studies have shown that the VP1u selectively binds to and enters B19V permissive cells through an unknown cellular proteinaceous receptor. In the present study, we demonstrated that purified recombinant VP1u effectively inhibits B19V infection of ex vivo expanded primary human erythroid progenitors. Furthermore, we identified the amino acid sequence 5-68 of the VP1 (VP1u5-68aa) is sufficient to confer the inhibition of B19V infection at a level similar to that of the full-length VP1u. In silico structure prediction suggests that the VP1u5-68aa contains three α-helices. Importantly, we found that the inhibition capability of the minimal domain VP1u5-68aa is independent of its dimerization but is likely dependent on the structure of the three predicated α-helices. As VP1u5-68aa outcompetes the full-length VP1u in entering cells, we believe that VP1u5-68aa functions as a receptor-binding ligand during virus entry. Finally, we determined the effective inhibition potency of VP1u5-68aa in B19V infection of human erythroid progenitors, which has a half maximal effective concentration (EC50) of 67 nM, suggesting an anti-viral peptide candidate to combat B19V infection.IMPORTANCEHuman parvovirus B19 infection causes severe hematological disorders, including transient aplastic crisis, pure red cell aplasia, and hydrops fetalis. A productive B19 infection is highly restricted to human erythroid progenitors in human bone marrow and fetal liver. In the current study, we identified that the N-terminal 5-68 amino acids domain of the minor viral capsid protein VP1 enters ex vivo expanded human erythroid progenitors, which is nearly 5 times more efficient than the full-length VP1 unique region (1-227aa). Importantly, purified recombinant 5-68aa of the VP1 has a high efficiency in inhibition of parvovirus B19 infection of human erythroid progenitors, which has a half maximal effective concentration (EC50) of 67 nM and a low cytotoxicity. The N-terminal 5-68 amino acids holds the potential as an effective antiviral of parvovirus B19 caused hematological disorders, as well as a carrier to deliver proteins to human erythroid progenitors.
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10
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Mishra V. Affinity Tags for Protein Purification. Curr Protein Pept Sci 2021; 21:821-830. [PMID: 32504500 DOI: 10.2174/1389203721666200606220109] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 04/09/2020] [Accepted: 05/06/2020] [Indexed: 11/22/2022]
Abstract
The affinity tags are unique proteins/peptides that are attached at the N- or C-terminus of the recombinant proteins. These tags help in protein purification. Additionally, some affinity tags also serve a dual purpose as solubility enhancers for challenging protein targets. By applying a combinatorial approach, carefully chosen affinity tags designed in tandem have proven to be very successful in the purification of single proteins or multi-protein complexes. In this mini-review, the key features of the most commonly used affinity tags are discussed. The affinity tags have been classified into two significant categories, epitope tags, and protein/domain tags. The epitope tags are generally small peptides with high affinity towards a chromatography resin. The protein/domain tags often perform double duty as solubility enhancers as well as aid in affinity purification. Finally, protease-based affinity tag removal strategies after purification are discussed.
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Affiliation(s)
- Vibhor Mishra
- Department of Biology, Indiana University, Bloomington, IN 47405, USA,Howard Hughes Medical Institute, Indiana University, Bloomington, IN 47405, USA
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11
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Ismail A, Lewis E, Sjödin B, Mannervik B. Characterization of Dog Glutathione Transferase P1-1, an Enzyme Relevant to Veterinary Medicine. Int J Mol Sci 2021; 22:ijms22084079. [PMID: 33920860 PMCID: PMC8071248 DOI: 10.3390/ijms22084079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 11/25/2022] Open
Abstract
Glutathione transferases (GSTs) form a family of detoxication enzymes instrumental in the inactivation and elimination of electrophilic mutagenic and carcinogenic compounds. The Pi class GST P1-1 is present in most tissues and is commonly overexpressed in neoplastic cells. GST P1-1 in the dog, Canis lupus familiaris, has merits as a marker for tumors and as a target for enzyme-activated prodrugs. We produced the canine enzyme CluGST P1-1 by heterologous bacterial expression and verified its cross-reactivity with antihuman-GST P1-1 antibodies. The catalytic activity with alternative substrates of biological significance was determined, and the most active substrate found was benzyl isothiocyanate. Among established GST inhibitors, Cibacron Blue showed positive cooperativity with an IC50 value of 43 nM. Dog GST P1-1 catalyzes activation of the prodrug Telcyta, but the activity is significantly lower than that of the human homolog.
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Affiliation(s)
- Aram Ismail
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-10691 Stockholm, Sweden; (A.I.); (B.S.)
| | - Elizabeth Lewis
- College of Liberal Arts & Sciences, University of Illinois Urbana-Champaign, Champaign, IL 61801, USA;
| | - Birgitta Sjödin
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-10691 Stockholm, Sweden; (A.I.); (B.S.)
| | - Bengt Mannervik
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-10691 Stockholm, Sweden; (A.I.); (B.S.)
- Correspondence:
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12
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In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. Proc Natl Acad Sci U S A 2021; 118:2010054118. [PMID: 33443153 PMCID: PMC7817218 DOI: 10.1073/pnas.2010054118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The differentiation of cells depends on a precise control of their internal organization, which is the result of a complex dynamic interplay between the cytoskeleton, molecular motors, signaling molecules, and membranes. For example, in the developing neuron, the protein ADAP1 (ADP-ribosylation factor GTPase-activating protein [ArfGAP] with dual pleckstrin homology [PH] domains 1) has been suggested to control dendrite branching by regulating the small GTPase ARF6. Together with the motor protein KIF13B, ADAP1 is also thought to mediate delivery of the second messenger phosphatidylinositol (3,4,5)-trisphosphate (PIP3) to the axon tip, thus contributing to PIP3 polarity. However, what defines the function of ADAP1 and how its different roles are coordinated are still not clear. Here, we studied ADAP1's functions using in vitro reconstitutions. We found that KIF13B transports ADAP1 along microtubules, but that PIP3 as well as PI(3,4)P2 act as stop signals for this transport instead of being transported. We also demonstrate that these phosphoinositides activate ADAP1's enzymatic activity to catalyze GTP hydrolysis by ARF6. Together, our results support a model for the cellular function of ADAP1, where KIF13B transports ADAP1 until it encounters high PIP3/PI(3,4)P2 concentrations in the plasma membrane. Here, ADAP1 disassociates from the motor to inactivate ARF6, promoting dendrite branching.
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13
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Yang P, Mathieu C, Kolaitis RM, Zhang P, Messing J, Yurtsever U, Yang Z, Wu J, Li Y, Pan Q, Yu J, Martin EW, Mittag T, Kim HJ, Taylor JP. G3BP1 Is a Tunable Switch that Triggers Phase Separation to Assemble Stress Granules. Cell 2020; 181:325-345.e28. [PMID: 32302571 DOI: 10.1016/j.cell.2020.03.046] [Citation(s) in RCA: 581] [Impact Index Per Article: 145.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 10/23/2019] [Accepted: 03/20/2020] [Indexed: 12/18/2022]
Abstract
The mechanisms underlying ribonucleoprotein (RNP) granule assembly, including the basis for establishing and maintaining RNP granules with distinct composition, are unknown. One prominent type of RNP granule is the stress granule (SG), a dynamic and reversible cytoplasmic assembly formed in eukaryotic cells in response to stress. Here, we show that SGs assemble through liquid-liquid phase separation (LLPS) arising from interactions distributed unevenly across a core protein-RNA interaction network. The central node of this network is G3BP1, which functions as a molecular switch that triggers RNA-dependent LLPS in response to a rise in intracellular free RNA concentrations. Moreover, we show that interplay between three distinct intrinsically disordered regions (IDRs) in G3BP1 regulates its intrinsic propensity for LLPS, and this is fine-tuned by phosphorylation within the IDRs. Further regulation of SG assembly arises through positive or negative cooperativity by extrinsic G3BP1-binding factors that strengthen or weaken, respectively, the core SG network.
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Affiliation(s)
- Peiguo Yang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Cécile Mathieu
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Regina-Maria Kolaitis
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Peipei Zhang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - James Messing
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Ugur Yurtsever
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Graduate School of Structure and Dynamics of Living Systems, Université Paris-Saclay, Gif-sur-Yvette, 91190, France
| | - Zemin Yang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jinjun Wu
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yuxin Li
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Qingfei Pan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Erik W Martin
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hong Joo Kim
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - J Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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14
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Uppugunduri CRS, Muthukumaran J, Robin S, Santos-Silva T, Ansari M. In silico and in vitro investigations on the protein-protein interactions of glutathione S-transferases with mitogen-activated protein kinase 8 and apoptosis signal-regulating kinase 1. J Biomol Struct Dyn 2020; 40:1430-1440. [PMID: 32996404 DOI: 10.1080/07391102.2020.1827036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Cytosolic glutathione S-transferase (GST) enzymes participate in several cellular processes in addition to facilitating glutathione conjugation reactions that eliminate endogenous and exogenous toxic compounds, especially electrophiles. GSTs are thought to interact with various kinases, resulting in the modulation of apoptotic processes and cellular proliferation. The present research used a combination of in silico and in vitro studies to investigate protein-protein interactions between the seven most abundant cytosolic GSTs-GST alpha-1 (GST-A1), GST alpha-2 (GST-A2), GST mu-1 (GST-M1), GST mu-2 (GST-M2), GST mu-5 (GST-M5), GST theta-1 (GST-T1) and GST pi-1 (GST-P1)-and Mitogen-activated protein kinase 8 (MAPK8) and Apoptosis signal-regulating kinase 1 (ASK1). MAPK8 and ASK1 were chosen as this study's protein interaction partners because of their predominant role in electrophile or cytokine-induced stress-mediated apoptosis, inflammation and fibrosis. The highest degree of sequence homology or sequence similarity was observed in two GST subgroups: the GST-A1, GST-A2 and GST-P1 isoforms constituted subgroup1; the GST-M1, GST-M2 and GST-M5 isoforms constituted subgroup 2. The GST-T1 isoform diverged from these isoforms. In silico investigations revealed that GST-M1 showed a significantly higher binding affinity to MAPK8, and its complex was more structurally stable than the other isoforms, in the order GST-M1 > GST-M5 > GST-P1 > GST-A2 > GST-A1 > GST-M2 > GST-T1. Similarly, GST-A1, GST-P1 and GST-T1 actively interacted with ASK1, and their structural stability was also better, in the order GST-T1 > GST-A1 > GST-P1 > GST-A2 > GST-M5 > GST-M1 > GST-M2. To validate in silico results, we performed in vitro crosslinking and mass spectroscopy experiments. Results indicated that GST-M1 interacted with GST-T1 to form heterodimers and confirmed the predicted interaction between GST-M1 and MAPK8.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Chakradhara Rao S Uppugunduri
- Onco-Haematology Unit, Department of Paediatrics, Obstetrics and Gynaecology, Geneva University Hospitals, Geneva, Switzerland.,Research Platform on Pediatric Onco-Hematology, Department of Paediatrics, Obstetrics and Gynaecology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Jayaraman Muthukumaran
- UCIBIO-Applied Molecular Biosciences Unit, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.,Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
| | - Shannon Robin
- Research Platform on Pediatric Onco-Hematology, Department of Paediatrics, Obstetrics and Gynaecology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Teresa Santos-Silva
- UCIBIO-Applied Molecular Biosciences Unit, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Marc Ansari
- Onco-Haematology Unit, Department of Paediatrics, Obstetrics and Gynaecology, Geneva University Hospitals, Geneva, Switzerland.,Research Platform on Pediatric Onco-Hematology, Department of Paediatrics, Obstetrics and Gynaecology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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15
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Takahashi H, Dohmae N, Kim KS, Shimuta K, Ohnishi M, Yokoyama S, Yanagisawa T. Genetic incorporation of non-canonical amino acid photocrosslinkers in Neisseria meningitidis: New method provides insights into the physiological function of the function-unknown NMB1345 protein. PLoS One 2020; 15:e0237883. [PMID: 32866169 PMCID: PMC7458321 DOI: 10.1371/journal.pone.0237883] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/04/2020] [Indexed: 02/01/2023] Open
Abstract
Although whole-genome sequencing has provided novel insights into Neisseria meningitidis, many open reading frames have only been annotated as hypothetical proteins with unknown biological functions. Our previous genetic analyses revealed that the hypothetical protein, NMB1345, plays a crucial role in meningococcal infection in human brain microvascular endothelial cells; however, NMB1345 has no homology to any identified protein in databases and its physiological function could not be elucidated using pre-existing methods. Among the many biological technologies to examine transient protein-protein interaction in vivo, one of the developed methods is genetic code expansion with non-canonical amino acids (ncAAs) utilizing a pyrrolysyl-tRNA synthetase/tRNAPyl pair from Methanosarcina species: However, this method has never been applied to assign function-unknown proteins in pathogenic bacteria. In the present study, we developed a new method to genetically incorporate ncAAs-encoded photocrosslinking probes into N. meningitidis by utilizing a pyrrolysyl-tRNA synthetase/tRNAPyl pair and elucidated the biological function(s) of the NMB1345 protein. The results revealed that the NMB1345 protein directly interacts with PilE, a major component of meningococcal pili, and further physicochemical and genetic analyses showed that the interaction between the NMB1345 protein and PilE was important for both functional pilus formation and meningococcal infectious ability in N. meningitidis. The present study using this new methodology for N. meningitidis provides novel insights into meningococcal pathogenesis by assigning the function of a hypothetical protein.
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Affiliation(s)
- Hideyuki Takahashi
- National Institute of Infectious Diseases, Department of Bacteriology I, Shinjuku-ku, Japan
- * E-mail:
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Kwang Sik Kim
- Division of Pediatric Infectious Diseases, Department of Pediatrics, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Ken Shimuta
- National Institute of Infectious Diseases, Department of Bacteriology I, Shinjuku-ku, Japan
| | - Makoto Ohnishi
- National Institute of Infectious Diseases, Department of Bacteriology I, Shinjuku-ku, Japan
| | - Shigeyuki Yokoyama
- RIKEN Structural Biology Laboratory, Yokohama, Japan
- RIKEN Cluster for Science, Technology and Innovation Hub, Yokohama, Japan
| | - Tatsuo Yanagisawa
- RIKEN Structural Biology Laboratory, Yokohama, Japan
- RIKEN Cluster for Science, Technology and Innovation Hub, Yokohama, Japan
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16
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Wacquiez A, Coste F, Kut E, Gaudon V, Trapp S, Castaing B, Marc D. Structure and Sequence Determinants Governing the Interactions of RNAs with Influenza A Virus Non-Structural Protein NS1. Viruses 2020; 12:E947. [PMID: 32867106 PMCID: PMC7552008 DOI: 10.3390/v12090947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/17/2020] [Accepted: 08/25/2020] [Indexed: 11/16/2022] Open
Abstract
The non-structural protein NS1 of influenza A viruses is an RNA-binding protein of which its activities in the infected cell contribute to the success of the viral cycle, notably through interferon antagonism. We have previously shown that NS1 strongly binds RNA aptamers harbouring virus-specific sequence motifs (Marc et al., Nucleic Acids Res. 41, 434-449). Here, we started out investigating the putative role of one particular virus-specific motif through the phenotypic characterization of mutant viruses that were genetically engineered from the parental strain WSN. Unexpectedly, our data did not evidence biological importance of the putative binding of NS1 to this specific motif (UGAUUGAAG) in the 3'-untranslated region of its own mRNA. Next, we sought to identify specificity determinants in the NS1-RNA interaction through interaction assays in vitro with several RNA ligands and through solving by X-ray diffraction the 3D structure of several complexes associating NS1's RBD with RNAs of various affinities. Our data show that the RBD binds the GUAAC motif within double-stranded RNA helices with an apparent specificity that may rely on the sequence-encoded ability of the RNA to bend its axis. On the other hand, we showed that the RBD binds to the virus-specific AGCAAAAG motif when it is exposed in the apical loop of a high-affinity RNA aptamer, probably through a distinct mode of interaction that still requires structural characterization. Our data are consistent with more than one mode of interaction of NS1's RBD with RNAs, recognizing both structure and sequence determinants.
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MESH Headings
- 3' Untranslated Regions
- Animals
- Aptamers, Nucleotide/chemistry
- Aptamers, Nucleotide/metabolism
- Base Sequence
- Cell Line
- Humans
- Influenza A Virus, H1N1 Subtype/chemistry
- Influenza A Virus, H7N1 Subtype/chemistry
- Models, Molecular
- Nucleic Acid Conformation
- Protein Binding
- Protein Domains
- RNA/chemistry
- RNA/metabolism
- RNA, Double-Stranded/chemistry
- RNA, Double-Stranded/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/metabolism
- RNA, Viral/chemistry
- RNA, Viral/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/metabolism
- SELEX Aptamer Technique
- Viral Nonstructural Proteins/chemistry
- Viral Nonstructural Proteins/metabolism
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Affiliation(s)
- Alan Wacquiez
- Equipe 3IMo, UMR1282 Infectiologie et Santé Publique, INRAE, F-37380 Nouzilly, France; (A.W.); (E.K.); (S.T.)
- UMR1282 Infectiologie et Santé Publique, Université de Tours, F-37000 Tours, France
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 02, 45071 Orléans, France; (F.C.); (V.G.)
| | - Franck Coste
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 02, 45071 Orléans, France; (F.C.); (V.G.)
| | - Emmanuel Kut
- Equipe 3IMo, UMR1282 Infectiologie et Santé Publique, INRAE, F-37380 Nouzilly, France; (A.W.); (E.K.); (S.T.)
- UMR1282 Infectiologie et Santé Publique, Université de Tours, F-37000 Tours, France
| | - Virginie Gaudon
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 02, 45071 Orléans, France; (F.C.); (V.G.)
| | - Sascha Trapp
- Equipe 3IMo, UMR1282 Infectiologie et Santé Publique, INRAE, F-37380 Nouzilly, France; (A.W.); (E.K.); (S.T.)
- UMR1282 Infectiologie et Santé Publique, Université de Tours, F-37000 Tours, France
| | - Bertrand Castaing
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 02, 45071 Orléans, France; (F.C.); (V.G.)
| | - Daniel Marc
- Equipe 3IMo, UMR1282 Infectiologie et Santé Publique, INRAE, F-37380 Nouzilly, France; (A.W.); (E.K.); (S.T.)
- UMR1282 Infectiologie et Santé Publique, Université de Tours, F-37000 Tours, France
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17
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Dawn A, Khatri KS, Karmakar S, Deep S. Interaction of TGFβ3 ligand with its receptors type II (TβRII) and type I (TβRI): A unique mechanism of protein-protein association. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140485. [PMID: 32652126 DOI: 10.1016/j.bbapap.2020.140485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/18/2020] [Accepted: 07/01/2020] [Indexed: 11/18/2022]
Abstract
The proper orchestration of transforming growth factor beta (TGFβ) mediated signal transduction depends upon a delicate set of interactions between specific ligands and their receptors. Here we present an in-depth profiling of the binding mechanism of TGFβ3 ligand with its type II and type I receptors (TβRII and TβRI) using isothermal titration calorimetry (ITC). Studies were carried out in acidic pH as it has great physiological relevance for TGFβ3 activity. Our findings reveal an unusual positive enthalpy (∆H) compensated by a large favourable entropy (∆S) during TGFβ3-TβRII interaction. In addition to the hydrophobic effect, we propose that a distinct conformational switch from "closed" to "open" form as experienced by TGFβ3 on binding to TβRII is contributing significantly to the increase in overall entropy of the system. Binding studies of TGFβ3 and TβRII were carried out at different pH values and salt concentrations to gain further insight into the thermodynamics of the interaction. Furthermore, the importance of hydrophobic interactions on the binding affinity of TβRII with TGFβ3 was confirmed by two TβRII variants (interfacial). Finally, a distinct shift from entropy to enthalpy dominated interaction was observed upon recruitment of TβRI to the binary complex forming the ternary complex.
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Affiliation(s)
- Amrita Dawn
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, India
| | - Komal S Khatri
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, India
| | - Sandip Karmakar
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, India
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, India.
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18
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Genetic Polymorphism of GSTP-1 Affects Cyclophosphamide Treatment of Autoimmune Diseases. Molecules 2020; 25:molecules25071542. [PMID: 32231024 PMCID: PMC7180851 DOI: 10.3390/molecules25071542] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/22/2020] [Accepted: 03/25/2020] [Indexed: 11/17/2022] Open
Abstract
Cyclophosphamide is one of the most potent and reliable anti-cancer and immunosuppressive drugs. In our study, 33 individuals with different autoimmune diseases were treated with cyclophosphamide according to standard protocols. The responses to the treatments were determined by measuring the alteration of several typical parameters characterizing the given autoimmune diseases over time. We concluded that about 45% of the patients responded to the treatment. Patients were genotyped for polymorphisms of the CYP3A4, CYP2B6, GSTM1, GSTT1, and GSTP1 genes and disease remission cases were compared to the individual polymorphic genotypes. It was found that the GSTP1 I105V allelic variation significantly associated with the cyclophosphamide treatment-dependent disease-remissions. At the same time the GSH content of the erythrocytes in the patients with I105V allelic variation did not change. It appears that the individuals carrying the Ile105Val SNP in at least one copy had a significantly higher response rate to the treatment. Since this variant of GSTP1 can be characterized by lower conjugation capacity that results in an elongated and higher therapeutic dose of cyclophosphamide, our data suggest that the decreased activity of this variant of GSTP1 can be in the background of the more effective disease treatment.
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19
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Abstract
The mercapturic acid pathway is a major route for the biotransformation of xenobiotic and endobiotic electrophilic compounds and their metabolites. Mercapturic acids (N-acetyl-l-cysteine S-conjugates) are formed by the sequential action of the glutathione transferases, γ-glutamyltransferases, dipeptidases, and cysteine S-conjugate N-acetyltransferase to yield glutathione S-conjugates, l-cysteinylglycine S-conjugates, l-cysteine S-conjugates, and mercapturic acids; these metabolites constitute a "mercapturomic" profile. Aminoacylases catalyze the hydrolysis of mercapturic acids to form cysteine S-conjugates. Several renal transport systems facilitate the urinary elimination of mercapturic acids; urinary mercapturic acids may serve as biomarkers for exposure to chemicals. Although mercapturic acid formation and elimination is a detoxication reaction, l-cysteine S-conjugates may undergo bioactivation by cysteine S-conjugate β-lyase. Moreover, some l-cysteine S-conjugates, particularly l-cysteinyl-leukotrienes, exert significant pathophysiological effects. Finally, some enzymes of the mercapturic acid pathway are described as the so-called "moonlighting proteins," catalytic proteins that exert multiple biochemical or biophysical functions apart from catalysis.
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Affiliation(s)
- Patrick E Hanna
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - M W Anders
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY, USA
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20
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Feldman HC, Vidadala VN, Potter ZE, Papa FR, Backes BJ, Maly DJ. Development of a Chemical Toolset for Studying the Paralog-Specific Function of IRE1. ACS Chem Biol 2019; 14:2595-2605. [PMID: 31609569 PMCID: PMC6925334 DOI: 10.1021/acschembio.9b00482] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The dual kinase endoribonuclease IRE1 is a master regulator of cell fate decisions in cells experiencing endoplasmic reticulum (ER) stress. In mammalian cells, there are two paralogs of IRE1: IRE1α and IRE1β. While IRE1α has been extensively studied, much less is understood about IRE1β and its role in signaling. In addition, whether the regulation of IRE1β's enzymatic activities varies compared to IRE1α is not known. Here, we show that the RNase domain of IRE1β is enzymatically active and capable of cleaving an XBP1 RNA mini-substrate in vitro. Using ATP-competitive inhibitors, we find that, like IRE1α, there is an allosteric relationship between the kinase and RNase domains of IRE1β. This allowed us to develop a novel toolset of both paralog specific and dual-IRE1α/β kinase inhibitors that attenuate RNase activity (KIRAs). Using sequence alignments of IRE1α and IRE1β, we propose a model for paralog-selective inhibition through interactions with nonconserved residues that differentiate the ATP-binding pockets of IRE1α and IRE1β.
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Affiliation(s)
- Hannah C. Feldman
- Department of Chemistry, University of Washington, Seattle, Washington, United States
| | | | - Zachary E. Potter
- Department of Chemistry, University of Washington, Seattle, Washington, United States
| | - Feroz R. Papa
- Department of Medicine, University of California−San Francisco, San Francisco, California, United States
- Lung Biology Center, University of California−San Francisco, San Francisco, California, United States
- Department of Pathology, University of California−San Francisco, San Francisco, California, United States
- Diabetes Center, University of California−San Francisco, San Francisco, California, United States
- California Institute for Quantitative Biosciences, University of California−San Francisco, San Francisco, California, United States
| | - Bradley J. Backes
- Department of Medicine, University of California−San Francisco, San Francisco, California, United States
- Lung Biology Center, University of California−San Francisco, San Francisco, California, United States
| | - Dustin J. Maly
- Department of Chemistry, University of Washington, Seattle, Washington, United States
- Department of Biochemistry, University of Washington, Seattle, Washington, United States
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21
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Smolko CM, Janes KA. An ultrasensitive fiveplex activity assay for cellular kinases. Sci Rep 2019; 9:19409. [PMID: 31857650 PMCID: PMC6923413 DOI: 10.1038/s41598-019-55998-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 09/30/2019] [Indexed: 02/06/2023] Open
Abstract
Protein kinases are enzymes whose abundance, protein-protein interactions, and posttranslational modifications together determine net signaling activity in cells. Large-scale data on cellular kinase activity are limited, because existing assays are cumbersome, poorly sensitive, low throughput, and restricted to measuring one kinase at a time. Here, we surmount the conventional hurdles of activity measurement with a multiplexing approach that leverages the selectivity of individual kinase-substrate pairs. We demonstrate proof of concept by designing an assay that jointly measures activity of five pleiotropic signaling kinases: Akt, IκB kinase (IKK), c-jun N-terminal kinase (JNK), mitogen-activated protein kinase (MAPK)-extracellular regulated kinase kinase (MEK), and MAPK-activated protein kinase-2 (MK2). The assay operates in a 96-well format and specifically measures endogenous kinase activation with coefficients of variation less than 20%. Multiplex tracking of kinase-substrate pairs reduces input requirements by 25-fold, with ~75 µg of cellular extract sufficient for fiveplex activity profiling. We applied the assay to monitor kinase signaling during coxsackievirus B3 infection of two different host-cell types and identified multiple differences in pathway dynamics and coordination that warrant future study. Because the Akt–IKK–JNK–MEK–MK2 pathways regulate many important cellular functions, the fiveplex assay should find applications in inflammation, environmental-stress, and cancer research.
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Affiliation(s)
- Christian M Smolko
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA
| | - Kevin A Janes
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA. .,Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA.
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22
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Nowaczyk-Cieszewska M, Zyla-Uklejewicz D, Noszka M, Jaworski P, Mielke T, Zawilak-Pawlik AM. The role of Helicobacter pylori DnaA domain I in orisome assembly on a bipartite origin of chromosome replication. Mol Microbiol 2019; 113:338-355. [PMID: 31715026 DOI: 10.1111/mmi.14423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 11/08/2019] [Accepted: 11/10/2019] [Indexed: 12/12/2022]
Abstract
The main roles of the DnaA protein are to bind the origin of chromosome replication (oriC), to unwind DNA and to provide a hub for the step-wise assembly of a replisome. DnaA is composed of four domains, with each playing a distinct functional role in the orisome assembly. Out of the four domains, the role of domain I is the least understood and appears to be the most species-specific. To better characterise Helicobacter pylori DnaA domain I, we have constructed a series of DnaA variants and studied their interactions with H. pylori bipartite oriC. We show that domain I is responsible for the stabilisation and organisation of DnaA-oriC complexes and provides cooperativity in DnaA-DNA interactions. Domain I mediates cross-interactions between oriC subcomplexes, which indicates that domain I is important for long-distance DnaA interactions and is essential for orisosme assembly on bipartite origins. HobA, which interacts with domain I, increases the DnaA binding to bipartite oriC; however, it does not stimulate but rather inhibits DNA unwinding. This suggests that HobA helps DnaA to bind oriC, but an unknown factor triggers DNA unwinding. Together, our results indicate that domain I self-interaction is important for the DnaA assembly on bipartite H. pylori oriC.
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Affiliation(s)
- Malgorzata Nowaczyk-Cieszewska
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Dorota Zyla-Uklejewicz
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Mateusz Noszka
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Pawel Jaworski
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Thorsten Mielke
- Microscopy and Cryo-Electron Microscopy Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Anna Magdalena Zawilak-Pawlik
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
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23
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Functional recruitment of dynamin requires multimeric interactions for efficient endocytosis. Nat Commun 2019; 10:4462. [PMID: 31575863 PMCID: PMC6773865 DOI: 10.1038/s41467-019-12434-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 09/10/2019] [Indexed: 02/06/2023] Open
Abstract
During clathrin mediated endocytosis (CME), the concerted action of dynamin and its interacting partners drives membrane scission. Essential interactions occur between the proline/arginine-rich domain of dynamin (dynPRD) and the Src-homology domain 3 (SH3) of various proteins including amphiphysins. Here we show that multiple SH3 domains must bind simultaneously to dynPRD through three adjacent motifs for dynamin’s efficient recruitment and function. First, we show that mutant dynamins modified in a single motif, including the central amphiphysin SH3 (amphSH3) binding motif, partially rescue CME in dynamin triple knock-out cells. However, mutating two motifs largely prevents that ability. Furthermore, we designed divalent dynPRD-derived peptides. These ligands bind multimers of amphSH3 with >100-fold higher affinity than monovalent ones in vitro. Accordingly, dialyzing living cells with these divalent peptides through a patch-clamp pipette blocks CME much more effectively than with monovalent ones. We conclude that dynamin drives vesicle scission via multivalent interactions in cells. During clathrin mediated endocytosis (CME), membrane scission is achieved by the concerted action of dynamin and its interacting partners such as amphiphysins. Here authors show that efficient recruitment and function of dynamin requires simultaneous binding of multiple amphiphysin SH3 domains.
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24
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Abstract
R-SNAREs (soluble N-ethylmaleimide-sensitive factor receptor), Q-SNAREs, and Sec1/Munc18 (SM)-family proteins are essential for membrane fusion in exocytic and endocytic trafficking. The yeast vacuolar tethering/SM complex HOPS (homotypic fusion and vacuole protein sorting) increases the fusion of membranes bearing R-SNARE to those with 3Q-SNAREs far more than it enhances their trans-SNARE pairings. We now report that the fusion of these proteoliposomes is also supported by GST-PX or GST-FYVE, recombinant dimeric proteins which tether by binding the phosphoinositides in both membranes. GST-PX is purely a tether, as it supports fusion without SNARE recognition. GST-PX tethering supports the assembly of new, active SNARE complexes rather than enhancing the function of the fusion-inactive SNARE complexes which had spontaneously formed in the absence of a tether. When SNAREs are more disassembled, as by Sec17, Sec18, and ATP (adenosine triphosphate), HOPS is required, and GST-PX does not suffice. We propose a working model where tethering orients SNARE domains for parallel, active assembly.
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25
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Ershov PV, Mezentsev YV, Kopylov AT, Yablokov EO, Svirid AV, Lushchyk AY, Kaluzhskiy LA, Gilep AA, Usanov SA, Medvedev AE, Ivanov AS. Affinity Isolation and Mass Spectrometry Identification of Prostacyclin Synthase (PTGIS) Subinteractome. BIOLOGY 2019; 8:E49. [PMID: 31226805 PMCID: PMC6628129 DOI: 10.3390/biology8020049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/06/2019] [Accepted: 06/18/2019] [Indexed: 01/04/2023]
Abstract
Prostacyclin synthase (PTGIS; EC 5.3.99.4) catalyzes isomerization of prostaglandin H2 to prostacyclin, a potent vasodilator and inhibitor of platelet aggregation. At present, limited data exist on functional coupling and possible ways of regulating PTGIS due to insufficient information about protein-protein interactions in which this crucial enzyme is involved. The aim of this study is to isolate protein partners for PTGIS from rat tissue lysates. Using CNBr-activated Sepharose 4B with covalently immobilized PTGIS as an affinity sorbent, we confidently identified 58 unique proteins by mass spectrometry (LC-MS/MS). The participation of these proteins in lysate complex formation was characterized by SEC lysate profiling. Several potential members of the PTGIS subinteractome have been validated by surface plasmon resonance (SPR) analysis. SPR revealed that PTGIS interacted with full-length cytochrome P450 2J2 and glutathione S-transferase (GST). In addition, PTGIS was shown to bind synthetic peptides corresponding to sequences of for GSTA1, GSTM1, aldo-keto reductase (AKR1A1), glutaredoxin 3 (GLRX3) and histidine triad nucleotide binding protein 2 (HINT2). Prostacyclin synthase could potentially be involved in functional interactions with identified novel protein partners participating in iron and heme metabolism, oxidative stress, xenobiotic and drugs metabolism, glutathione and prostaglandin metabolism. The possible biological role of the recognized interaction is discussed in the context of PTGIS functioning.
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Affiliation(s)
- Pavel V Ershov
- Department of Proteomic Research and Mass Spectrometry, Institute of Biomedical Chemistry (IBMC), 10 Pogodinskaya str., 119121 Moscow, Russia.
| | - Yuri V Mezentsev
- Department of Proteomic Research and Mass Spectrometry, Institute of Biomedical Chemistry (IBMC), 10 Pogodinskaya str., 119121 Moscow, Russia.
| | - Arthur T Kopylov
- Department of Proteomic Research and Mass Spectrometry, Institute of Biomedical Chemistry (IBMC), 10 Pogodinskaya str., 119121 Moscow, Russia.
| | - Evgeniy O Yablokov
- Department of Proteomic Research and Mass Spectrometry, Institute of Biomedical Chemistry (IBMC), 10 Pogodinskaya str., 119121 Moscow, Russia.
| | - Andrey V Svirid
- Laboratory of Molecular Diagnostics and Biotechnology, Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, 5, bld. 2 V.F. Kuprevich str., 220141 Minsk, Belarus.
| | - Aliaksandr Ya Lushchyk
- Laboratory of Molecular Diagnostics and Biotechnology, Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, 5, bld. 2 V.F. Kuprevich str., 220141 Minsk, Belarus.
| | - Leonid A Kaluzhskiy
- Department of Proteomic Research and Mass Spectrometry, Institute of Biomedical Chemistry (IBMC), 10 Pogodinskaya str., 119121 Moscow, Russia.
| | - Andrei A Gilep
- Laboratory of Molecular Diagnostics and Biotechnology, Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, 5, bld. 2 V.F. Kuprevich str., 220141 Minsk, Belarus.
| | - Sergey A Usanov
- Laboratory of Molecular Diagnostics and Biotechnology, Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, 5, bld. 2 V.F. Kuprevich str., 220141 Minsk, Belarus.
| | - Alexey E Medvedev
- Department of Proteomic Research and Mass Spectrometry, Institute of Biomedical Chemistry (IBMC), 10 Pogodinskaya str., 119121 Moscow, Russia.
| | - Alexis S Ivanov
- Department of Proteomic Research and Mass Spectrometry, Institute of Biomedical Chemistry (IBMC), 10 Pogodinskaya str., 119121 Moscow, Russia.
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26
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Principles and characteristics of biological assemblies in experimentally determined protein structures. Curr Opin Struct Biol 2019; 55:34-49. [PMID: 30965224 DOI: 10.1016/j.sbi.2019.03.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 03/01/2019] [Indexed: 12/27/2022]
Abstract
More than half of all structures in the PDB are assemblies of two or more proteins, including both homooligomers and heterooligomers. Structural information on these assemblies comes from X-ray crystallography, NMR, and cryo-EM spectroscopy. The correct assembly in an X-ray structure is often ambiguous, and computational methods have been developed to identify the most likely biologically relevant assembly based on physical properties of assemblies and sequence conservation in interfaces. Taking advantage of the large number of structures now available, some of the most recent methods have relied on similarity of interfaces and assemblies across structures of homologous proteins.
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27
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Kontur WS, Olmsted CN, Yusko LM, Niles AV, Walters KA, Beebe ET, Vander Meulen KA, Karlen SD, Gall DL, Noguera DR, Donohue TJ. A heterodimeric glutathione S-transferase that stereospecifically breaks lignin's β( R)-aryl ether bond reveals the diversity of bacterial β-etherases. J Biol Chem 2018; 294:1877-1890. [PMID: 30541921 PMCID: PMC6369299 DOI: 10.1074/jbc.ra118.006548] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 12/07/2018] [Indexed: 11/12/2022] Open
Abstract
Lignin is a heterogeneous polymer of aromatic subunits that is a major component of lignocellulosic plant biomass. Understanding how microorganisms deconstruct lignin is important for understanding the global carbon cycle and could aid in developing systems for processing plant biomass into valuable commodities. Sphingomonad bacteria use stereospecific glutathione S-transferases (GSTs) called β-etherases to cleave the β-aryl ether (β-O-4) bond, the most common bond between aromatic subunits in lignin. Previously characterized bacterial β-etherases are homodimers that fall into two distinct GST subclasses: LigE homologues, which cleave the β(R) stereoisomer of the bond, and LigF homologues, which cleave the β(S) stereoisomer. Here, we report on a heterodimeric β-etherase (BaeAB) from the sphingomonad Novosphingobium aromaticivorans that stereospecifically cleaves the β(R)-aryl ether bond of the di-aromatic compound β-(2-methoxyphenoxy)-γ-hydroxypropiovanillone (MPHPV). BaeAB's subunits are phylogenetically distinct from each other and from other β-etherases, although they are evolutionarily related to LigF, despite the fact that BaeAB and LigF cleave different β-aryl ether bond stereoisomers. We identify amino acid residues in BaeAB's BaeA subunit important for substrate binding and catalysis, including an asparagine that is proposed to activate the GSH cofactor. We also show that BaeAB homologues from other sphingomonads can cleave β(R)-MPHPV and that they may be as common in bacteria as LigE homologues. Our results suggest that the ability to cleave the β-aryl ether bond arose independently at least twice in GSTs and that BaeAB homologues may be important for cleaving the β(R)-aryl ether bonds of lignin-derived oligomers in nature.
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Affiliation(s)
- Wayne S Kontur
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and
| | - Charles N Olmsted
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and
| | - Larissa M Yusko
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and
| | - Alyssa V Niles
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and
| | - Kevin A Walters
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and
| | - Emily T Beebe
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and.,the Departments of Biochemistry
| | - Kirk A Vander Meulen
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and.,the Departments of Biochemistry
| | - Steven D Karlen
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and.,the Departments of Biochemistry
| | - Daniel L Gall
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and
| | - Daniel R Noguera
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and.,Civil and Environmental Engineering, and
| | - Timothy J Donohue
- From the Wisconsin Energy Institute, .,the Department of Energy Great Lakes Bioenergy Research Center, and.,Bacteriology, University of Wisconsin, Madison, Wisconsin 53706
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28
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Bojar D, Fuhrer T, Fussenegger M. Purity by design: Reducing impurities in bioproduction by stimulus-controlled global translational downregulation of non-product proteins. Metab Eng 2018; 52:110-123. [PMID: 30468874 DOI: 10.1016/j.ymben.2018.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 11/01/2018] [Accepted: 11/17/2018] [Indexed: 01/22/2023]
Abstract
Capitalizing on the ability of mammalian cells to conduct complex post-translational modifications, most protein therapeutics are currently produced in cell culture systems. Addition of a signal peptide to the product protein enables its accumulation in the cell culture supernatant, but separation of the product from endogenously secreted proteins remains costly and labor-intensive. We considered that global downregulation of translation of non-product proteins would be an efficient strategy to minimize downstream processing requirements. Therefore, taking advantage of the ability of mammalian protein kinase R (PKR) to switch off most cellular translation processes in response to infection by viruses, we fused a caffeine-inducible dimerization domain to the catalytic domain of PKR. Addition of caffeine to this construct results in homodimerization and activation of PKR, effectively rewiring rapid global translational downregulation to the addition of the stimulus in a dose-dependent manner. Then, to protect translation of the target therapeutic, we screened viral and cellular internal ribosomal entry sites (IRESes) known or suspected to be resistant to PKR-induced translational stress. After choosing the best-in-class Seneca valley virus (SVV) IRES, we additionally screened for IRES transactivation factors (ITAFs) as well as for supplementary small molecules to further boost the production titer of the product protein under conditions of global translational downregulation. Importantly, the residual global translation activity of roughly 10% under maximal downregulation is sufficient to maintain cellular viability during a production timeframe of at least five days. Standard industrially used adherent as well as suspension-adapted cell lines transfected with this synthetic biology-inspired Protein Kinase R-Enhanced Protein Production (PREPP) system could produce several medicinally relevant protein therapeutics, such as the blockbuster drug rituximab, in substantial quantities and with significantly higher purity than previous culture technologies. We believe incorporation of such purity-by-design technology in the production process will alleviate downstream processing bottlenecks in future biopharmaceutical manufacturing.
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Affiliation(s)
- Daniel Bojar
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Tobias Fuhrer
- ETH Zurich, Institute of Molecular Systems Biology, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland
| | - Martin Fussenegger
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland; Faculty of Life Science, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland.
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29
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Yuan J, Ng WH, Lam PYP, Wang Y, Xia H, Yap J, Guan SP, Lee ASG, Wang M, Baccarini M, Hu J. The dimer-dependent catalytic activity of RAF family kinases is revealed through characterizing their oncogenic mutants. Oncogene 2018; 37:5719-5734. [PMID: 29930381 PMCID: PMC6202329 DOI: 10.1038/s41388-018-0365-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 05/18/2018] [Accepted: 05/21/2018] [Indexed: 12/19/2022]
Abstract
Although extensively studied for three decades, the molecular mechanisms that regulate the RAF/MEK/ERK kinase cascade remain ambiguous. Recent studies identified the dimerization of RAF as a key event in the activation of this cascade. Here, we show that in-frame deletions in the β3-αC loop activate ARAF as well as BRAF and other oncogenic kinases by enforcing homodimerization. By characterizing these RAF mutants, we find that ARAF has less allosteric and catalytic activity than the other two RAF isoforms, which arises from its non-canonical APE motif. Further, these RAF mutants exhibit a strong oncogenic potential, and a differential inhibitor resistance that correlates with their dimer affinity. Using these unique mutants, we demonstrate that active RAFs, including the BRAF(V600E) mutant, phosphorylate MEK in a dimer-dependent manner. This study characterizes a special category of oncogenic kinase mutations, and elucidates the molecular basis that underlies the differential ability of RAF isoforms to stimulate MEK-ERK pathway. Further, this study reveals a unique catalytic feature of RAF family kinases that can be exploited to control their activities for cancer therapies.
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Affiliation(s)
- Jimin Yuan
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Wan Hwa Ng
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Paula Y P Lam
- Division of Cellular and Molecular Research, Singapore, Singapore.,Cancer and Stem Cell Program, Duke-NUS Medical School, 8 College Road, 169857, Singapore, Singapore
| | - Yu Wang
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Hongping Xia
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Jiajun Yap
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Shou Ping Guan
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Ann S G Lee
- Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Singapore.,Office of Clinical & Academic Faculty Affairs, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.,Department of Physiology, National University of Singapore, 2 Medical Drive, 117597, Singapore, Singapore
| | - Mei Wang
- Cancer and Stem Cell Program, Duke-NUS Medical School, 8 College Road, 169857, Singapore, Singapore
| | - Manuela Baccarini
- Max F. Perutz Laboratories, University of Vienna, Doktor-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Jiancheng Hu
- Division of Cellular and Molecular Research, Singapore, Singapore. .,Cancer and Stem Cell Program, Duke-NUS Medical School, 8 College Road, 169857, Singapore, Singapore.
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30
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Arbildi P, Turell L, López V, Alvarez B, Fernández V. Mechanistic insights into EgGST1, a Mu class glutathione S-transferase from the cestode parasite Echinococcus granulosus. Arch Biochem Biophys 2017; 633:15-22. [DOI: 10.1016/j.abb.2017.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/17/2017] [Accepted: 08/21/2017] [Indexed: 11/26/2022]
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31
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Mantuano E, Azmoon P, Brifault C, Banki MA, Gilder AS, Campana WM, Gonias SL. Tissue-type plasminogen activator regulates macrophage activation and innate immunity. Blood 2017; 130:1364-1374. [PMID: 28684538 PMCID: PMC5600142 DOI: 10.1182/blood-2017-04-780205] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/03/2017] [Indexed: 01/29/2023] Open
Abstract
Tissue-type plasminogen activator (tPA) is the major intravascular activator of fibrinolysis and a ligand for receptors involved in cell signaling. In cultured macrophages, tPA inhibits the response to lipopolysaccharide (LPS) by a pathway that apparently requires low-density lipoprotein receptor-related protein-1 (LRP1). Herein, we show that the mechanism by which tPA neutralizes LPS involves rapid reversal of IκBα phosphorylation. tPA independently induced transient IκBα phosphorylation and extracellular signal-regulated kinase 1/2 (ERK1/2) activation in macrophages; however, these events did not trigger inflammatory mediator expression. The tPA signaling response was distinguished from the signature of signaling events elicited by proinflammatory LRP1 ligands, such as receptor-associated protein (RAP), which included sustained IκBα phosphorylation and activation of all 3 MAP kinases (ERK1/2, c-Jun kinase, and p38 MAP kinase). Enzymatically active and inactive tPA demonstrated similar immune modulatory activity. Intravascular administration of enzymatically inactive tPA in mice blocked the toxicity of LPS. In mice not treated with exogenous tPA, the plasma concentration of endogenous tPA increased 3-fold in response to LPS, to 116 ± 15 pM, but remained below the approximate threshold for eliciting anti-inflammatory cell signaling in macrophages (∼2.0 nM). This threshold is readily achieved in patients when tPA is administered therapeutically for stroke. In addition to LRP1, we demonstrate that the N-methyl-D-aspartic acid receptor (NMDA-R) is expressed by macrophages and essential for anti-inflammatory cell signaling and regulation of cytokine expression by tPA. The NMDA-R and Toll-like receptor-4 were not required for proinflammatory RAP signaling. By mediating the tPA response in macrophages, the NMDA-R provides a pathway by which the fibrinolysis system may regulate innate immunity.
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Affiliation(s)
- Elisabetta Mantuano
- Department of Pathology, University of California, San Diego, La Jolla, CA
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy; and
| | - Pardis Azmoon
- Department of Pathology, University of California, San Diego, La Jolla, CA
| | - Coralie Brifault
- Department of Pathology, University of California, San Diego, La Jolla, CA
| | - Michael A Banki
- Department of Pathology, University of California, San Diego, La Jolla, CA
| | - Andrew S Gilder
- Department of Pathology, University of California, San Diego, La Jolla, CA
| | - Wendy M Campana
- Department of Anesthesiology, University of California, San Diego, La Jolla, CA
| | - Steven L Gonias
- Department of Pathology, University of California, San Diego, La Jolla, CA
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32
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Pettersson JR, Lanni F, Rule GS. Dual Lifetimes for Complexes between Glutathione-S-transferase (hGSTA1-1) and Product-like Ligands Detected by Single-Molecule Fluorescence Imaging. Biochemistry 2017; 56:4073-4083. [PMID: 28677395 DOI: 10.1021/acs.biochem.7b00030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Single-molecule fluorescence techniques were used to characterize the binding of products and inhibitors to human glutathione S-transferase A1-1 (hGSTA1-1). The identification of at least two different bound states for the wild-type enzyme suggests that there are at least two conformations of the protein, consistent with the model that ligand binding promotes closure of the carboxy-terminal helix over the active site. Ligand induced changes in ensemble fluorescence energy transfer support this proposed structural change. The more predominant state in the ensemble of single molecules shows a significantly faster off-rate, suggesting that the carboxy-terminal helix is delocalized in this state, permitting faster exit of the bound ligand. A point mutation (I219A), which is known to interfere with the association of the carboxy-terminal helix with the enzyme, shows increased rates of interconversion between the open and closed state. Kinematic traces of fluorescence from single molecules show that a single molecule readily samples a number of different conformations, each with a characteristic off-rate.
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Affiliation(s)
- John R Pettersson
- Department of Biological Sciences, Carnegie Mellon University , Pittsburgh, Pennsylvania, United States
| | - Frederick Lanni
- Department of Biological Sciences, Carnegie Mellon University , Pittsburgh, Pennsylvania, United States
| | - Gordon S Rule
- Department of Biological Sciences, Carnegie Mellon University , Pittsburgh, Pennsylvania, United States
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Shim J, Huang A, Miller AS. Development of a bioassay as a measure of drozitumab-mediated apoptosis induced by soluble Fc gamma receptors. J Immunol Methods 2017; 448:26-33. [PMID: 28506821 DOI: 10.1016/j.jim.2017.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 05/05/2017] [Accepted: 05/11/2017] [Indexed: 10/19/2022]
Abstract
Drozitumab is an agonistic therapeutic monoclonal antibody (mAb) against the pro-apoptotic death receptor 5 (DR5). In vitro cell killing assays using drozitumab have traditionally required cross-linking with anti-Fc antibody to amplify the pro-apoptotic signal, although drozitumab shows activity in in vivo tumor models without artificial cross-linking. Recently it has been shown that FcγR expressing cells play an important role in the activity of drozitumab by mediating cross-linking in vivo (Wilson et al., 2011). To provide a more biologically relevant alternative to cross-linking with anti-Fc antibody in in vitro bioassays, methods for cross-linking with soluble FcγR extracellular domain (ECD) were developed in this work. FcγR cross-linking methods developed in this work were assessed in solution, bead-bound, and plate-bound assay formats, as well as a cell-based assay format. The assays showed reproducible drozitumab dose-response curves in the concentration range of 5-20,000ng/mL and had acceptable precision and accuracy. The assays are also able to detect degradative changes in drozitumab samples subjected to thermal stress. The data suggest that FcγR cross-linking of drozitumab is a viable alternative to anti-Fc cross-linking of drozitumab to measure effector mediated apoptosis of drozitumab in vitro.
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Affiliation(s)
- Jeongsup Shim
- Biological Technologies-Analytical Development and Quality Control, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Ally Huang
- Biological Technologies-Analytical Development and Quality Control, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Aaron S Miller
- Biological Technologies-Analytical Development and Quality Control, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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Bédard M, Maltais L, Montagne M, Lavigne P. Miz-1 and Max compete to engage c-Myc: implication for the mechanism of inhibition of c-Myc transcriptional activity by Miz-1. Proteins 2016; 85:199-206. [PMID: 27859590 DOI: 10.1002/prot.25214] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 10/20/2016] [Accepted: 11/08/2016] [Indexed: 11/12/2022]
Abstract
c-Myc is a basic helix-loop-helix leucine zipper (b-HLH-LZ) transcription factor deregulated in the majority of human cancers. As a heterodimer with Max, another b-HLH-LZ transcription factor, deregulated and persistent c-Myc accumulates at transcriptionally active promoters and enhancers and amplifies transcription. This leads to the so-called transcriptional addiction of tumor cells. Recent studies have showed that c-Myc transcriptional activities can be reversed by its association with Miz-1, a POZ transcription factor containing 13 classical zinc fingers. Although evidences have led to suggest that c-Myc interacts with both Miz-1 and Max to form a ternary repressive complex, earlier evidences also suggest that Miz-1 and Max may compete to engage c-Myc. In such a scenario, the Miz-1/c-Myc complex would be the entity responsible for the inhibition of c-Myc transcriptional amplification. Considering the implications of the Miz-1/c-Myc interaction, it is highly important to solve this duality. While two potential c-Myc interacting domains (hereafter termed MID) have been identified in Miz-1 by yeast two-hybrid, with the b-HLH-LZ as a bait, the biophysical characterization of these interactions has not been reported so far. Here, we report that the MID located between the 12th and 13th zinc finger of Miz-1 and the b-HLH-LZ of Max compete to form a complex with the b-HLH-LZ of c-Myc. Our results support the notion that the repressive action of Miz-1 on c-Myc does not rely on the formation of a ternary complex. The implications of these observations for the mechanism of inhibition of c-Myc transcriptional activity by Miz-1 are discussed. Proteins 2017; 85:199-206. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Mikaël Bédard
- Département de Biochimie, Institut de Pharmacologie de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, J1H 5N4, Canada.,PROTEO; Regroupement Stratégique sur la Fonction, la Structure et l'Ingénierie des Protéines, Université Laval, Québec, G1V 0A6, Canada.,GRASP; Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Québec, H3G 0B1, Canada
| | - Loïka Maltais
- Département de Biochimie, Institut de Pharmacologie de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, J1H 5N4, Canada.,PROTEO; Regroupement Stratégique sur la Fonction, la Structure et l'Ingénierie des Protéines, Université Laval, Québec, G1V 0A6, Canada.,GRASP; Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Québec, H3G 0B1, Canada
| | - Martin Montagne
- Département de Biochimie, Institut de Pharmacologie de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, J1H 5N4, Canada.,PROTEO; Regroupement Stratégique sur la Fonction, la Structure et l'Ingénierie des Protéines, Université Laval, Québec, G1V 0A6, Canada.,GRASP; Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Québec, H3G 0B1, Canada
| | - Pierre Lavigne
- Département de Biochimie, Institut de Pharmacologie de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, J1H 5N4, Canada.,PROTEO; Regroupement Stratégique sur la Fonction, la Structure et l'Ingénierie des Protéines, Université Laval, Québec, G1V 0A6, Canada.,GRASP; Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Québec, H3G 0B1, Canada
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Sequences in Linker-1 domain of the multidrug resistance associated protein (MRP1 or ABCC1) bind to tubulin and their binding is modulated by phosphorylation. Biochem Biophys Res Commun 2016; 482:1001-1006. [PMID: 27908733 DOI: 10.1016/j.bbrc.2016.11.147] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 11/27/2016] [Indexed: 11/22/2022]
Abstract
The multidrug resistant associated protein 1 (or MRP1, ABCC1) encodes two cytoplasmic linker domains (L0 and L1) composed of highly charged sequences with multiple protein kinase A/C phosphorylation sites. In this report we made use of the scanning peptide approach to identify MRP1 linker L1 (L1MRP1) interacting proteins. Scanning heptapeptides covering L1MRP1 126 amino acids (Ile846- Leu972) were synthesized and used in pull-down assays to isolate proteins from cell extracts (human multidrug resistant SCLC cell line; H69/AR). The results show four high affinity binding sequences in L1MRP1 domain [866FLRTYAST867; 906SAGKQLQRQLSSS912; 925ISRHHNSTA927 and 954AQTGQVKLSVYW959] that bound ∼55 kDa and 110 kDa polypeptides. The latter polypeptides were identified by mass spectrometry as α- and β-tubulin monomers and dimers. Western blotting with monoclonal antibodies to α- and β-tubulin proteins confirmed the mass-spectrometry results. Moreover, using recombinant full-length GST-Linker 1 fusion polypeptide (GST-L1MRP1), we confirmed the peptide scanning approach demonstrating specific binding of tubulin to GST-L1MRP1. Intriguingly, substitutions of serine residues in L1MRP1 by aspartic acid, but not alanine, abolished its binding to tubulin, suggesting that phosphorylation of Ser871, 915, 930, and 961 within L1MRP1 may modulate its binding to tubulin. Taken together, the results of this study suggest possible interaction between MRP1 and tubulin that is modulated by phosphorylation of specific sequences in the L1MRP1 domain.
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Lazarus MB, Levin RS, Shokat KM. Discovery of new substrates of the elongation factor-2 kinase suggests a broader role in the cellular nutrient response. Cell Signal 2016; 29:78-83. [PMID: 27760376 DOI: 10.1016/j.cellsig.2016.10.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 09/25/2016] [Accepted: 10/13/2016] [Indexed: 12/25/2022]
Abstract
Elongation Factor-2 Kinase (eEF2K) in an unusual mammalian enzyme that has one known substrate, elongation factor-2. It belongs to a class of kinases, called alpha kinases, that has little sequence identity to the >500 conventional protein kinases, but performs the same reaction and has similar catalytic residues. The phosphorylation of eEF2 blocks translation elongation, which is thought to be critical to regulating cellular energy usage. Here we report a system for discovering new substrates of alpha kinases and identify the first new substrates of eEF2K including AMPK and alpha4, and determine a sequence motif for the kinase that shows a requirement for threonine residues as the target of phosphorylation. These new substrates suggest that eEF2K has a more diverse role in regulating cellular energy usage that involves multiple pathways and regulatory feedback.
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Affiliation(s)
- Michael B Lazarus
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Rebecca S Levin
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kevan M Shokat
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
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37
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Dissection of molecular assembly dynamics by tracking orientation and position of single molecules in live cells. Proc Natl Acad Sci U S A 2016; 113:E6352-E6361. [PMID: 27679846 DOI: 10.1073/pnas.1607674113] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Regulation of order, such as orientation and conformation, drives the function of most molecular assemblies in living cells but remains difficult to measure accurately through space and time. We built an instantaneous fluorescence polarization microscope, which simultaneously images position and orientation of fluorophores in living cells with single-molecule sensitivity and a time resolution of 100 ms. We developed image acquisition and analysis methods to track single particles that interact with higher-order assemblies of molecules. We tracked the fluctuations in position and orientation of molecules from the level of an ensemble of fluorophores down to single fluorophores. We tested our system in vitro using fluorescently labeled DNA and F-actin, in which the ensemble orientation of polarized fluorescence is known. We then tracked the orientation of sparsely labeled F-actin network at the leading edge of migrating human keratinocytes, revealing the anisotropic distribution of actin filaments relative to the local retrograde flow of the F-actin network. Additionally, we analyzed the position and orientation of septin-GFP molecules incorporated in septin bundles in growing hyphae of a filamentous fungus. Our data indicate that septin-GFP molecules undergo positional fluctuations within ∼350 nm of the binding site and angular fluctuations within ∼30° of the central orientation of the bundle. By reporting position and orientation of molecules while they form dynamic higher-order structures, our approach can provide insights into how micrometer-scale ordered assemblies emerge from nanoscale molecules in living cells.
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38
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McCarthy D, Pulverer W, Weinhaeusel A, Diago OR, Hogan DJ, Ostertag D, Hanna MM. MethylMeter(®): bisulfite-free quantitative and sensitive DNA methylation profiling and mutation detection in FFPE samples. Epigenomics 2016; 8:747-65. [PMID: 27337298 DOI: 10.2217/epi-2016-0004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Development of a sensitive method for DNA methylation profiling and associated mutation detection in clinical samples. MATERIALS & METHODS Formalin-fixed and paraffin-embedded tumors received by clinical laboratories often contain insufficient DNA for analysis with bisulfite or methylation sensitive restriction enzymes-based methods. To increase sensitivity, methyl-CpG DNA capture and Coupled Abscription PCR Signaling detection were combined in a new assay, MethylMeter(®). Gliomas were analyzed for MGMT methylation, glioma CpG island methylator phenotype and IDH1 R132H. RESULTS MethylMeter had 100% assay success rate measuring all five biomarkers in formalin-fixed and paraffin-embedded tissue. MGMT methylation results were supported by survival and mRNA expression data. CONCLUSION MethylMeter is a sensitive and quantitative method for multitarget DNA methylation profiling and associated mutation detection. The MethylMeter-based GliomaSTRAT assay measures methylation of four targets and one mutation to simultaneously grade gliomas and predict their response to temozolomide. This information is clinically valuable in management of gliomas.
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Affiliation(s)
- David McCarthy
- Ribomed Biotechnologies Inc., 3469 Kurtz St., San Diego, CA 92110, USA
| | - Walter Pulverer
- Molecular Diagnostics, Health & Environment Department, Austrian Institute of Technology, Muthgasse 11, 1190 Vienna, Austria
| | - Andreas Weinhaeusel
- Molecular Diagnostics, Health & Environment Department, Austrian Institute of Technology, Muthgasse 11, 1190 Vienna, Austria
| | - Oscar R Diago
- Tocagen Inc., 3030 Bunker Hill Street, Suite 230; San Diego, CA 92109, USA
| | - Daniel J Hogan
- Tocagen Inc., 3030 Bunker Hill Street, Suite 230; San Diego, CA 92109, USA
| | - Derek Ostertag
- Tocagen Inc., 3030 Bunker Hill Street, Suite 230; San Diego, CA 92109, USA
| | - Michelle M Hanna
- Ribomed Biotechnologies Inc., 3469 Kurtz St., San Diego, CA 92110, USA
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39
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Karmakar T, Roy S, Balaram H, Balasubramanian S. Structural and dynamical correlations in PfHGXPRT oligomers: A molecular dynamics simulation study. J Biomol Struct Dyn 2016; 34:1590-605. [PMID: 26441001 DOI: 10.1080/07391102.2015.1085441] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
PfHGXPRT is a key enzyme involved in purine nucleotide salvage pathway of the malarial parasite, Plasmodium falciparum. Atomistic molecular dynamics simulations have been performed on two types of PfHGXPRT dimers (D1 and D3) and its tetramer in their apo and ligand-bound states. A significant event in the catalytic cycle is the dynamics of a gate that provides access for the ligand molecules to the reaction center. The gate is formed by loops II and IV, the former being the most flexible. Large amplitude conformational changes have been observed in active site loop II. Upon complete occupancy of the active site, loop II gets stabilized due to specific interactions between its residues and the ligand molecules. Remote loop, X, is seen to be less fluxional in the D3 dimer than in D1 which is rationalized as due to the greater number of inter-subunit contacts in the former. The presence of ligand molecules in subunits of the tetramer further reduces the flexibility of loop X epitomizing a communication between this region and the active sites in the tetramer. These observations are in accordance with the outcomes of several experimental investigations. Participation of loop X in the oligomerization process has also been discerned. Between the two types of dimers in solution, D1 tetramerizes readily and thus would not be present as free dimers. We conjecture an equilibrium to exist between D3 and the tetramer in solution; upon binding of the ligand molecules to the D3 dimer, this equilibrium shifts toward the tetramer.
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Affiliation(s)
- Tarak Karmakar
- a Chemistry and Physics of Materials Unit , Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore , 560 064 India
| | - Sourav Roy
- b Molecular Biology and Genetics Unit , Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore , 560 064 India
| | - Hemalatha Balaram
- b Molecular Biology and Genetics Unit , Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore , 560 064 India
| | - Sundaram Balasubramanian
- a Chemistry and Physics of Materials Unit , Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore , 560 064 India
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40
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Hiragami-Hamada K, Soeroes S, Nikolov M, Wilkins B, Kreuz S, Chen C, De La Rosa-Velázquez IA, Zenn HM, Kost N, Pohl W, Chernev A, Schwarzer D, Jenuwein T, Lorincz M, Zimmermann B, Walla PJ, Neumann H, Baubec T, Urlaub H, Fischle W. Dynamic and flexible H3K9me3 bridging via HP1β dimerization establishes a plastic state of condensed chromatin. Nat Commun 2016; 7:11310. [PMID: 27090491 PMCID: PMC4838890 DOI: 10.1038/ncomms11310] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 03/13/2016] [Indexed: 12/12/2022] Open
Abstract
Histone H3 trimethylation of lysine 9 (H3K9me3) and proteins of the heterochromatin protein 1 (HP1) family are hallmarks of heterochromatin, a state of compacted DNA essential for genome stability and long-term transcriptional silencing. The mechanisms by which H3K9me3 and HP1 contribute to chromatin condensation have been speculative and controversial. Here we demonstrate that human HP1β is a prototypic HP1 protein exemplifying most basal chromatin binding and effects. These are caused by dimeric and dynamic interaction with highly enriched H3K9me3 and are modulated by various electrostatic interfaces. HP1β bridges condensed chromatin, which we postulate stabilizes the compacted state. In agreement, HP1β genome-wide localization follows H3K9me3-enrichment and artificial bridging of chromatin fibres is sufficient for maintaining cellular heterochromatic conformation. Overall, our findings define a fundamental mechanism for chromatin higher order structural changes caused by HP1 proteins, which might contribute to the plastic nature of condensed chromatin. Heterochromatin protein 1 (HP1), including HP1 α, β and γ, is a family of non-histone chromatin factors thought to be involved in chromatin organization. Here, the authors show that dimeric HP1β interacts dynamically with H3K9me3, a hallmark of heterochromatin, and bridges condensed chromatin.
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Affiliation(s)
- Kyoko Hiragami-Hamada
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
| | - Szabolcs Soeroes
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
| | - Miroslav Nikolov
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany.,Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
| | - Bryan Wilkins
- Applied Synthetic Biology, Institute for Microbiology and Genetics, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Sarah Kreuz
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
| | - Carol Chen
- Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Inti A De La Rosa-Velázquez
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Hans Michael Zenn
- Biaffin GmbH &Co KG, Heinrich-Plett Strasse 40, 34132 Kassel, Germany
| | - Nils Kost
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
| | - Wiebke Pohl
- Biomolecular Spectroscopy and Single-Molecule Detection, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
| | - Aleksandar Chernev
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Thomas Jenuwein
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Matthew Lorincz
- Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | | | - Peter Jomo Walla
- Biomolecular Spectroscopy and Single-Molecule Detection, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany.,Department of Biophysical Chemistry, Technische Universität Braunschweig, Hans-Sommerstr. 10, 38106 Braunschweig, Germany
| | - Heinz Neumann
- Applied Synthetic Biology, Institute for Microbiology and Genetics, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
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41
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Directed evolution of Tau class glutathione transferases reveals a site that regulates catalytic efficiency and masks co-operativity. Biochem J 2015; 473:559-70. [PMID: 26637269 DOI: 10.1042/bj20150930] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 12/04/2015] [Indexed: 12/22/2022]
Abstract
A library of Tau class GSTs (glutathione transferases) was constructed by DNA shuffling using the DNA encoding the Glycine max GSTs GmGSTU2-2, GmGSTU4-4 and GmGSTU10-10. The parental GSTs are >88% identical at the sequence level; however, their specificity varies towards different substrates. The DNA library contained chimaeric structures of alternated segments of the parental sequences and point mutations. Chimaeric GST sequences were expressed in Escherichia coli and their enzymatic activities towards CDNB (1-chloro-2,4-dinitrobenzene) and the herbicide fluorodifen (4-nitrophenyl α,α,α-trifluoro-2-nitro-p-tolyl ether) were determined. A chimaeric clone (Sh14) with enhanced CDNB- and fluorodifen-detoxifying activities, and unusual co-operative kinetics towards CDNB and fluorodifen, but not towards GSH, was identified. The structure of Sh14 was determined at 1.75 Å (1 Å=0.1 nm) resolution in complex with S-(p-nitrobenzyl)-glutathione. Analysis of the Sh14 structure showed that a W114C point mutation is responsible for the altered kinetic properties. This was confirmed by the kinetic properties of the Sh14 C114W mutant. It is suggested that the replacement of the bulky tryptophan residue by a smaller amino acid (cysteine) results in conformational changes of the active-site cavity, leading to enhanced catalytic activity of Sh14. Moreover, the structural changes allow the strengthening of the two salt bridges between Glu(66) and Lys(104) at the dimer interface that triggers an allosteric effect and the communication between the hydrophobic sites.
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42
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Okamura T, Antoun G, Keir ST, Friedman H, Bigner DD, Ali-Osman F. Phosphorylation of Glutathione S-Transferase P1 (GSTP1) by Epidermal Growth Factor Receptor (EGFR) Promotes Formation of the GSTP1-c-Jun N-terminal kinase (JNK) Complex and Suppresses JNK Downstream Signaling and Apoptosis in Brain Tumor Cells. J Biol Chem 2015; 290:30866-78. [PMID: 26429914 DOI: 10.1074/jbc.m115.656140] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Indexed: 11/06/2022] Open
Abstract
Under normal physiologic conditions, the glutathione S-transferase P1 (GSTP1) protein exists intracellularly as a dimer in reversible equilibrium with its monomeric subunits. In the latter form, GSTP1 binds to the mitogen-activated protein kinase, JNK, and inhibits JNK downstream signaling. In tumor cells, which frequently are characterized by constitutively high GSTP1 expression, GSTP1 undergoes phosphorylation by epidermal growth factor receptor (EGFR) at tyrosine residues 3, 7, and 198. Here we report on the effect of this EGFR-dependent GSTP1 tyrosine phosphorylation on the interaction of GSTP1 with JNK, on the regulation of JNK downstream signaling by GSTP1, and on tumor cell survival. Using in vitro and in vivo growing human brain tumors, we show that tyrosine phosphorylation shifts the GSTP1 dimer-monomer equilibrium to the monomeric state and facilitates the formation of the GSTP1-JNK complex, in which JNK is functionally inhibited. Targeted mutagenesis and functional analysis demonstrated that the increased GSTP1 binding to JNK results from phosphorylation of the GSTP1 C-terminal Tyr-198 by EGFR and is associated with a >2.5-fold decrease in JNK downstream signaling and a significant suppression of both spontaneous and drug-induced apoptosis in the tumor cells. The findings define a novel mechanism of regulatory control of JNK signaling that is mediated by the EGFR/GSTP1 cross-talk and provides a survival advantage for tumors with activated EGFR and high GSTP1 expression. The results lay the foundation for a novel strategy of dual EGFR/GSTP1 for treating EGFR+ve, GSTP1 expressing GBMs.
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Affiliation(s)
| | | | - Stephen T Keir
- From the Departments of Neurosurgery and the Preston Robert Tisch Brain Tumor Center
| | - Henry Friedman
- From the Departments of Neurosurgery and the Preston Robert Tisch Brain Tumor Center, Duke Cancer Institute and Duke University School of Medicine, Durham, North Carolina 27710
| | - Darell D Bigner
- From the Departments of Neurosurgery and the Preston Robert Tisch Brain Tumor Center, Duke Cancer Institute and Duke University School of Medicine, Durham, North Carolina 27710 Pathology and
| | - Francis Ali-Osman
- From the Departments of Neurosurgery and the Preston Robert Tisch Brain Tumor Center, Duke Cancer Institute and Duke University School of Medicine, Durham, North Carolina 27710 Pathology and
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43
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Roncalli V, Cieslak MC, Passamaneck Y, Christie AE, Lenz PH. Glutathione S-Transferase (GST) Gene Diversity in the Crustacean Calanus finmarchicus--Contributors to Cellular Detoxification. PLoS One 2015; 10:e0123322. [PMID: 25945801 PMCID: PMC4422733 DOI: 10.1371/journal.pone.0123322] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 02/23/2015] [Indexed: 11/19/2022] Open
Abstract
Detoxification is a fundamental cellular stress defense mechanism, which allows an organism to survive or even thrive in the presence of environmental toxins and/or pollutants. The glutathione S-transferase (GST) superfamily is a set of enzymes involved in the detoxification process. This highly diverse protein superfamily is characterized by multiple gene duplications, with over 40 GST genes reported in some insects. However, less is known about the GST superfamily in marine organisms, including crustaceans. The availability of two de novo transcriptomes for the copepod, Calanus finmarchicus, provided an opportunity for an in depth study of the GST superfamily in a marine crustacean. The transcriptomes were searched for putative GST-encoding transcripts using known GST proteins from three arthropods as queries. The identified transcripts were then translated into proteins, analyzed for structural domains, and annotated using reciprocal BLAST analysis. Mining the two transcriptomes yielded a total of 41 predicted GST proteins belonging to the cytosolic, mitochondrial or microsomal classes. Phylogenetic analysis of the cytosolic GSTs validated their annotation into six different subclasses. The predicted proteins are likely to represent the products of distinct genes, suggesting that the diversity of GSTs in C. finmarchicus exceeds or rivals that described for insects. Analysis of relative gene expression in different developmental stages indicated low levels of GST expression in embryos, and relatively high expression in late copepodites and adult females for several cytosolic GSTs. A diverse diet and complex life history are factors that might be driving the multiplicity of GSTs in C. finmarchicus, as this copepod is commonly exposed to a variety of natural toxins. Hence, diversity in detoxification pathway proteins may well be key to their survival.
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Affiliation(s)
- Vittoria Roncalli
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Matthew C. Cieslak
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Yale Passamaneck
- Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Andrew E. Christie
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Petra H. Lenz
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
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44
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Counts CJ, Ho PS, Donlin MJ, Tavis JE, Chen C. A Functional Interplay between Human Immunodeficiency Virus Type 1 Protease Residues 77 and 93 Involved in Differential Regulation of Precursor Autoprocessing and Mature Protease Activity. PLoS One 2015; 10:e0123561. [PMID: 25893662 PMCID: PMC4404164 DOI: 10.1371/journal.pone.0123561] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 03/04/2015] [Indexed: 11/18/2022] Open
Abstract
HIV-1 protease (PR) is a viral enzyme vital to the production of infectious virions. It is initially synthesized as part of the Gag-Pol polyprotein precursor in the infected cell. The free mature PR is liberated as a result of precursor autoprocessing upon virion release. We previously described a model system to examine autoprocessing in transfected mammalian cells. Here, we report that a covariance analysis of miniprecursor (p6*-PR) sequences derived from drug naïve patients identified a series of amino acid pairs that vary together across independent viral isolates. These covariance pairs were used to build the first topology map of the miniprecursor that suggests high levels of interaction between the p6* peptide and the mature PR. Additionally, several PR-PR covariance pairs are located far from each other (>12 Å Cα to Cα) relative to their positions in the mature PR structure. Biochemical characterization of one such covariance pair (77-93) revealed that each residue shows distinct preference for one of three alkyl amino acids (V, I, and L) and that a polar or charged amino acid at either of these two positions abolishes precursor autoprocessing. The most commonly observed 77V is preferred by the most commonly observed 93I, but the 77I variant is preferred by other 93 variances (L, V, or M) in supporting precursor autoprocessing. Furthermore, the 77I93V covariant enhanced precursor autoprocessing and Gag polyprotein processing but decreased the mature PR activity. Therefore, both covariance and biochemical analyses support a functional association between residues 77 and 93, which are spatially distant from each other in the mature PR structure. Our data also suggests that these covariance pairs differentially regulate precursor autoprocessing and the mature protease activity.
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Affiliation(s)
- Christopher J Counts
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - P Shing Ho
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Maureen J Donlin
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America; Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America; Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America
| | - John E Tavis
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America; Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America
| | - Chaoping Chen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
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45
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Cleavage of BLOC1S1 mRNA by IRE1 Is Sequence Specific, Temporally Separate from XBP1 Splicing, and Dispensable for Cell Viability under Acute Endoplasmic Reticulum Stress. Mol Cell Biol 2015; 35:2186-202. [PMID: 25870107 PMCID: PMC4438243 DOI: 10.1128/mcb.00013-15] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/02/2015] [Indexed: 12/15/2022] Open
Abstract
The unfolded protein response (UPR) remediates endoplasmic reticulum (ER) stress. IRE1, a component of the UPR, senses misfolded protein and cleaves XBP1 mRNA, which is ligated to code for the prosurvival transcription factor. IRE1 also cleaves other mRNAs preceding their degradation, termed regulated IRE1-dependent mRNA decay (RIDD). It has been reported that RIDD may be involved in cell viability under stress and therefore may contribute to cancer cell viability. To investigate RIDD targets that may have functional relevance in cell survival, we identified conserved RIDD targets containing stringent IRE1 RNase target sequences. Using a systematic bioinformatics approach with quantitative-PCR (qPCR) validation, we show that only BLOC1S1 is consistently a RIDD target in all systems tested. Using cancer cell lines, we show that BLOC1S1 is specifically cleaved by IRE1 at guanine 444, but only under conditions of IRE1 hyperactivation. BLOC1S1 cleavage is temporally separate from XBP1 splicing, occurring after depletion of unspliced XBP1. Expression of an uncleavable BLOC1S1 mutant or inhibition of RIDD using an IRE1 RNase inhibitor did not affect cellular recovery from acute ER stress. These data demonstrate that although hyperactivated IRE1 specifically cleaves BLOC1S1, this cleavage event and RIDD as a whole are dispensable for cell viability under acute stress.
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46
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Walkup WG, Kennedy MB. Protein purification using PDZ affinity chromatography. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2015; 80:9.10.1-9.10.37. [PMID: 25829303 PMCID: PMC4435810 DOI: 10.1002/0471140864.ps0910s80] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
PDZ domains function in nature as protein-binding domains within scaffold and membrane-associated proteins. They comprise approximately 90 residues and undergo specific, high-affinity interactions with complementary C-terminal peptide sequences, other PDZ domains, and/or phospholipids. We have previously shown that the specific, strong interactions of PDZ domains with their ligands make them well suited for use in affinity chromatography. This unit provides protocols for the PDZ affinity chromatography procedure that are applicable for the purification of proteins that contain PDZ domains or PDZ domain-binding ligands, either naturally or introduced by genetic engineering. We detail the preparation of affinity resins composed of PDZ domains or PDZ domain peptide ligands coupled to solid supports. These resins can be used to purify proteins containing endogenous or genetically introduced PDZ domains or ligands, eluting the proteins with free PDZ domain peptide ligands.
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Affiliation(s)
- Ward G. Walkup
- Department of Biology and Biological Engineering, California Institute of Technology, 1200 East California Blvd., Mail Code 216-76, Pasadena, California 91125
| | - Mary B. Kennedy
- Department of Biology and Biological Engineering, California Institute of Technology, 1200 East California Blvd., Mail Code 216-76, Pasadena, California 91125
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47
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Zhang YH, Shetty K, Surleac MD, Petrescu AJ, Schatz DG. Mapping and Quantitation of the Interaction between the Recombination Activating Gene Proteins RAG1 and RAG2. J Biol Chem 2015; 290:11802-17. [PMID: 25745109 DOI: 10.1074/jbc.m115.638627] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Indexed: 12/21/2022] Open
Abstract
The RAG endonuclease consists of RAG1, which contains the active site for DNA cleavage, and RAG2, an accessory factor whose interaction with RAG1 is critical for catalytic function. How RAG2 activates RAG1 is not understood. Here, we used biolayer interferometry and pulldown assays to identify regions of RAG1 necessary for interaction with RAG2 and to measure the RAG1-RAG2 binding affinity (KD ∼0.4 μM) (where RAG1 and RAG2 are recombination activating genes 1 or 2). Using the Hermes transposase as a guide, we constructed a 36-kDa "mini" RAG1 capable of interacting robustly with RAG2. Mini-RAG1 consists primarily of the catalytic center and the residues N-terminal to it, but it lacks a zinc finger region in RAG1 previously implicated in binding RAG2. The ability of Mini-RAG1 to interact with RAG2 depends on a predicted α-helix (amino acids 997-1008) near the RAG1 C terminus and a region of RAG1 from amino acids 479 to 559. Two adjacent acidic amino acids in this region (Asp-546 and Glu-547) are important for both the RAG1-RAG2 interaction and recombination activity, with Asp-546 of particular importance. Structural modeling of Mini-RAG1 suggests that Asp-546/Glu-547 lie near the predicted 997-1008 α-helix and components of the active site, raising the possibility that RAG2 binding alters the structure of the RAG1 active site. Quantitative Western blotting allowed us to estimate that mouse thymocytes contain on average ∼1,800 monomers of RAG1 and ∼15,000 molecules of RAG2, implying that nuclear concentrations of RAG1 and RAG2 are below the KD value for their interaction, which could help limit off-target RAG activity.
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Affiliation(s)
- Yu-Hang Zhang
- From the Departments of Immunobiology and Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, Connecticut 06511
| | - Keerthi Shetty
- From the Departments of Immunobiology and Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, Connecticut 06511
| | - Marius D Surleac
- the Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060031 Bucharest, Romania, and
| | - Andrei J Petrescu
- the Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060031 Bucharest, Romania, and
| | - David G Schatz
- From the Departments of Immunobiology and Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, Connecticut 06511, the Howard Hughes Medical Institute, New Haven, Connecticut 06511
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48
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Vander Linden RT, Hemmis CW, Schmitt B, Ndoja A, Whitby FG, Robinson H, Cohen RE, Yao T, Hill CP. Structural basis for the activation and inhibition of the UCH37 deubiquitylase. Mol Cell 2015; 57:901-911. [PMID: 25702872 DOI: 10.1016/j.molcel.2015.01.016] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 12/15/2014] [Accepted: 01/06/2015] [Indexed: 10/24/2022]
Abstract
The UCH37 deubiquitylase functions in two large and very different complexes, the 26S proteasome and the INO80 chromatin remodeler. We have performed biochemical characterization and determined crystal structures of UCH37 in complexes with RPN13 and NFRKB, which mediate its recruitment to the proteasome and INO80, respectively. RPN13 and NFRKB make similar contacts to the UCH37 C-terminal domain but quite different contacts to the catalytic UCH domain. RPN13 can activate UCH37 by disrupting dimerization, although physiologically relevant activation likely results from stabilization of a surface competent for ubiquitin binding and modulation of the active-site crossover loop. In contrast, NFRKB inhibits UCH37 by blocking the ubiquitin-binding site and by disrupting the enzyme active site. These findings reveal remarkable commonality in mechanisms of recruitment, yet very different mechanisms of regulating enzyme activity, and provide a foundation for understanding the roles of UCH37 in the unrelated proteasome and INO80 complexes.
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Affiliation(s)
- Ryan T Vander Linden
- Department of Biochemistry University of Utah School of Medicine, Salt Lake City, UT 84112-5650 USA
| | - Casey W Hemmis
- Department of Biochemistry University of Utah School of Medicine, Salt Lake City, UT 84112-5650 USA
| | - Benjamin Schmitt
- Department of Biochemistry and Molecular Biology Colorado State University, Fort Collins, CO 80523 USA
| | - Ada Ndoja
- Department of Biochemistry and Molecular Biology Colorado State University, Fort Collins, CO 80523 USA
| | - Frank G Whitby
- Department of Biochemistry University of Utah School of Medicine, Salt Lake City, UT 84112-5650 USA
| | - Howard Robinson
- Biology Department Brookhaven National Laboratory, Upton, NY, 11973 USA
| | - Robert E Cohen
- Department of Biochemistry and Molecular Biology Colorado State University, Fort Collins, CO 80523 USA
| | - Tingting Yao
- Department of Biochemistry and Molecular Biology Colorado State University, Fort Collins, CO 80523 USA
| | - Christopher P Hill
- Department of Biochemistry University of Utah School of Medicine, Salt Lake City, UT 84112-5650 USA
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49
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Thom CS, Traxler EA, Khandros E, Nickas JM, Zhou OY, Lazarus JE, Silva APG, Prabhu D, Yao Y, Aribeana C, Fuchs SY, Mackay JP, Holzbaur ELF, Weiss MJ. Trim58 degrades Dynein and regulates terminal erythropoiesis. Dev Cell 2014; 30:688-700. [PMID: 25241935 DOI: 10.1016/j.devcel.2014.07.021] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 04/24/2014] [Accepted: 07/28/2014] [Indexed: 01/23/2023]
Abstract
TRIM58 is an E3 ubiquitin ligase superfamily member implicated by genome-wide association studies to regulate human erythrocyte traits. Here, we show that Trim58 expression is induced during late erythropoiesis and that its depletion by small hairpin RNAs (shRNAs) inhibits the maturation of late-stage nucleated erythroblasts to anucleate reticulocytes. Imaging flow cytometry studies demonstrate that Trim58 regulates polarization and/or extrusion of erythroblast nuclei. In vitro, Trim58 directly binds and ubiquitinates the intermediate chain of the microtubule motor dynein. In cells, Trim58 stimulates proteasome-dependent degradation of the dynein holoprotein complex. During erythropoiesis, Trim58 expression, dynein loss, and enucleation occur concomitantly, and all are inhibited by Trim58 shRNAs. Dynein regulates nuclear positioning and microtubule organization, both of which undergo dramatic changes during erythroblast enucleation. Thus, we propose that Trim58 promotes this process by eliminating dynein. Our findings identify an erythroid-specific regulator of enucleation and elucidate a previously unrecognized mechanism for controlling dynein activity.
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Affiliation(s)
- Christopher S Thom
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elizabeth A Traxler
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eugene Khandros
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jenna M Nickas
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Olivia Y Zhou
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jacob E Lazarus
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Physiology and Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ana P G Silva
- School of Molecular Bioscience, The University of Sydney, Sydney NSW 2006, Australia
| | - Dolly Prabhu
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yu Yao
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Chiaka Aribeana
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Serge Y Fuchs
- Department of Animal Biology and Mari Lowe Comparative Oncology Center, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joel P Mackay
- School of Molecular Bioscience, The University of Sydney, Sydney NSW 2006, Australia
| | - Erika L F Holzbaur
- Department of Physiology and Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mitchell J Weiss
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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50
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Liu X, An BH, Kim MJ, Park JH, Kang YS, Chang M. Human glutathione S-transferase P1-1 functions as an estrogen receptor α signaling modulator. Biochem Biophys Res Commun 2014; 452:840-4. [DOI: 10.1016/j.bbrc.2014.09.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 09/03/2014] [Indexed: 11/17/2022]
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