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Donnelly CM, Vogel OA, Edwards MR, Taylor PE, Roby JA, Forwood JK, Basler CF. Henipavirus Matrix Protein Employs a Non-Classical Nuclear Localization Signal Binding Mechanism. Viruses 2023; 15:1302. [PMID: 37376602 DOI: 10.3390/v15061302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Nipah virus (NiV) and Hendra virus (HeV) are highly pathogenic species from the Henipavirus genus within the paramyxovirus family and are harbored by Pteropus Flying Fox species. Henipaviruses cause severe respiratory disease, neural symptoms, and encephalitis in various animals and humans, with human mortality rates exceeding 70% in some NiV outbreaks. The henipavirus matrix protein (M), which drives viral assembly and budding of the virion, also performs non-structural functions as a type I interferon antagonist. Interestingly, M also undergoes nuclear trafficking that mediates critical monoubiquitination for downstream cell sorting, membrane association, and budding processes. Based on the NiV and HeV M X-ray crystal structures and cell-based assays, M possesses a putative monopartite nuclear localization signal (NLS) (residues 82KRKKIR87; NLS1 HeV), positioned on an exposed flexible loop and typical of how many NLSs bind importin alpha (IMPα), and a putative bipartite NLS (244RR-10X-KRK258; NLS2 HeV), positioned within an α-helix that is far less typical. Here, we employed X-ray crystallography to determine the binding interface of these M NLSs and IMPα. The interaction of both NLS peptides with IMPα was established, with NLS1 binding the IMPα major binding site, and NLS2 binding as a non-classical NLS to the minor site. Co-immunoprecipitation (co-IP) and immunofluorescence assays (IFA) confirm the critical role of NLS2, and specifically K258. Additionally, localization studies demonstrated a supportive role for NLS1 in M nuclear localization. These studies provide additional insight into the critical mechanisms of M nucleocytoplasmic transport, the study of which can provide a greater understanding of viral pathogenesis and uncover a potential target for novel therapeutics for henipaviral diseases.
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Affiliation(s)
- Camilla M Donnelly
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Olivia A Vogel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Megan R Edwards
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
- School of Population and Public Health, Faculty of Medicine, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Paige E Taylor
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Justin A Roby
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Jade K Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Christopher F Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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2
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Alvisi G, Manaresi E, Cross EM, Hoad M, Akbari N, Pavan S, Ariawan D, Bua G, Petersen GF, Forwood J, Gallinella G. Importin α/β-dependent nuclear transport of human parvovirus B19 nonstructural protein 1 is essential for viral replication. Antiviral Res 2023; 213:105588. [PMID: 36990397 DOI: 10.1016/j.antiviral.2023.105588] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/08/2023] [Accepted: 03/25/2023] [Indexed: 03/30/2023]
Abstract
Human parvovirus B19 (B19V) is a major human pathogen causing a variety of diseases, characterized by a selective tropism to human progenitor cells in bone marrow. In similar fashion to all Parvoviridae members, the B19V ssDNA genome is replicated within the nucleus of infected cells through a process which involves both cellular and viral proteins. Among the latter, a crucial role is played by non-structural protein (NS)1, a multifunctional protein involved in genome replication and transcription, as well as modulation of host gene expression and function. Despite the localization of NS1 within the host cell nucleus during infection, little is known regarding the mechanism of its nuclear transport pathway. In this study we undertake structural, biophysical, and cellular approaches to characterize this process. Quantitative confocal laser scanning microscopy (CLSM), gel mobility shift, fluorescence polarization and crystallographic analysis identified a short sequence of amino acids (GACHAKKPRIT-182) as the classical nuclear localization signal (cNLS) responsible for nuclear import, mediated in an energy and importin (IMP) α/β-dependent fashion. Structure-guided mutagenesis of key residue K177 strongly impaired IMPα binding, nuclear import, and viral gene expression in a minigenome system. Further, treatment with ivermectin, an antiparasitic drug interfering with the IMPα/β dependent nuclear import pathway, inhibited NS1 nuclear accumulation and viral replication in infected UT7/Epo-S1 cells. Thus, NS1 nuclear transport is a potential target of therapeutic intervention against B19V induced disease.
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Affiliation(s)
- Gualtiero Alvisi
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy.
| | - Elisabetta Manaresi
- Department of Pharmacy and Biotechnology, University of Bologna, 40138, Bologna, Italy
| | - Emily M Cross
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650, Australia
| | - Mikayla Hoad
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650, Australia
| | - Nasim Akbari
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | - Silvia Pavan
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | - Daryl Ariawan
- Dementia Research Centre, Macquarie University, Sydney, NSW, 2109, Australia
| | - Gloria Bua
- Department of Pharmacy and Biotechnology, University of Bologna, 40138, Bologna, Italy
| | - Gayle F Petersen
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650, Australia
| | - Jade Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650, Australia
| | - Giorgio Gallinella
- Department of Pharmacy and Biotechnology, University of Bologna, 40138, Bologna, Italy
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Hervouet K, Ferrié M, Ankavay M, Montpellier C, Camuzet C, Alexandre V, Dembélé A, Lecoeur C, Foe AT, Bouquet P, Hot D, Vausselin T, Saliou JM, Salomé-Desnoulez S, Vandeputte A, Marsollier L, Brodin P, Dreux M, Rouillé Y, Dubuisson J, Aliouat-Denis CM, Cocquerel L. An Arginine-Rich Motif in the ORF2 capsid protein regulates the hepatitis E virus lifecycle and interactions with the host cell. PLoS Pathog 2022; 18:e1010798. [PMID: 36007070 PMCID: PMC9451086 DOI: 10.1371/journal.ppat.1010798] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/07/2022] [Accepted: 08/06/2022] [Indexed: 11/18/2022] Open
Abstract
Hepatitis E virus (HEV) infection is the most common cause of acute viral hepatitis worldwide. Hepatitis E is usually asymptomatic and self-limiting but it can become chronic in immunocompromised patients and is associated with increased fulminant hepatic failure and mortality rates in pregnant women. HEV genome encodes three proteins including the ORF2 protein that is the viral capsid protein. Interestingly, HEV produces 3 isoforms of the ORF2 capsid protein which are partitioned in different subcellular compartments and perform distinct functions in the HEV lifecycle. Notably, the infectious ORF2 (ORF2i) protein is the structural component of virions, whereas the genome-free secreted and glycosylated ORF2 proteins likely act as a humoral immune decoy. Here, by using a series of ORF2 capsid protein mutants expressed in the infectious genotype 3 p6 HEV strain as well as chimeras between ORF2 and the CD4 glycoprotein, we demonstrated how an Arginine-Rich Motif (ARM) located in the ORF2 N-terminal region controls the fate and functions of ORF2 isoforms. We showed that the ARM controls ORF2 nuclear translocation likely to promote regulation of host antiviral responses. This motif also regulates the dual topology and functionality of ORF2 signal peptide, leading to the production of either cytosolic infectious ORF2i or reticular non-infectious glycosylated ORF2 forms. It serves as maturation site of glycosylated ORF2 by furin, and promotes ORF2-host cell membrane interactions. The identification of ORF2 ARM as a unique central regulator of the HEV lifecycle uncovers how viruses settle strategies to condense their genetic information and hijack cellular processes.
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Affiliation(s)
- Kévin Hervouet
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Martin Ferrié
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Maliki Ankavay
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
- Division of Gastroenterology and Hepatology, Institute of Microbiology, Lausanne, Switzerland
| | - Claire Montpellier
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Charline Camuzet
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Virginie Alexandre
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Aïcha Dembélé
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Cécile Lecoeur
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Arnold Thomas Foe
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Peggy Bouquet
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR2014 - US41 - PLBS-Plateformes Lilloises de Biologie & Santé, Lille, France
| | - David Hot
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR2014 - US41 - PLBS-Plateformes Lilloises de Biologie & Santé, Lille, France
| | - Thibaut Vausselin
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Jean-Michel Saliou
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR2014 - US41 - PLBS-Plateformes Lilloises de Biologie & Santé, Lille, France
| | - Sophie Salomé-Desnoulez
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR2014 - US41 - PLBS-Plateformes Lilloises de Biologie & Santé, Lille, France
| | - Alexandre Vandeputte
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR2014 - US41 - PLBS-Plateformes Lilloises de Biologie & Santé, Lille, France
| | - Laurent Marsollier
- Université d’Angers, Nantes Université, INSERM, Immunology and New Concepts in ImmunoTherapy, INCIT, UMR 1302, Angers, France
| | - Priscille Brodin
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR2014 - US41 - PLBS-Plateformes Lilloises de Biologie & Santé, Lille, France
| | - Marlène Dreux
- CIRI - Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm-U1111, CNRS-UMR5308, ENS-Lyon, Lyon, France
| | - Yves Rouillé
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Jean Dubuisson
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Cécile-Marie Aliouat-Denis
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Laurence Cocquerel
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
- * E-mail:
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Human Enzyme PADI4 Binds to the Nuclear Carrier Importin α3. Cells 2022; 11:cells11142166. [PMID: 35883608 PMCID: PMC9319256 DOI: 10.3390/cells11142166] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/13/2022] [Accepted: 07/08/2022] [Indexed: 12/18/2022] Open
Abstract
PADI4 is a peptidyl-arginine deiminase (PADI) involved in the conversion of arginine to citrulline. PADI4 is present in macrophages, monocytes, granulocytes, and several cancer cells. It is the only PADI family member observed within both the nucleus and the cytoplasm. PADI4 has a predicted nuclear localization sequence (NLS) comprising residues Pro56 to Ser83, to allow for nuclear translocation. Recent predictors also suggest that the region Arg495 to Ile526 is a possible NLS. To understand how PADI4 is involved in cancer, we studied the ability of intact PADI4 to bind importin α3 (Impα3), a nuclear transport factor that plays tumor-promoting roles in several cancers, and its truncated species (ΔImpα3) without the importin-binding domain (IBB), by using fluorescence, circular dichroism (CD), and isothermal titration calorimetry (ITC). Furthermore, the binding of two peptides, encompassing the first and the second NLS regions, was also studied using the same methods and molecular docking simulations. PADI4 interacted with both importin species, with affinity constants of ~1–5 µM. The isolated peptides also interacted with both importins. The molecular simulations predict that the anchoring of both peptides takes place in the major binding site of Impα3 for the NLS of cargo proteins. These findings suggest that both NLS regions were essentially responsible for the binding of PADI4 to the two importin species. Our data are discussed within the framework of a cell mechanism of nuclear transport that is crucial in cancer.
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Li J, Guo Y, Deng Y, Hu L, Li B, Deng S, Zhong J, Xie L, Shi S, Hong X, Zheng X, Cai M, Li M. Subcellular Localization of Epstein-Barr Virus BLLF2 and Its Underlying Mechanisms. Front Microbiol 2021; 12:672192. [PMID: 34367081 PMCID: PMC8339435 DOI: 10.3389/fmicb.2021.672192] [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: 02/25/2021] [Accepted: 05/24/2021] [Indexed: 11/13/2022] Open
Abstract
Epstein-Barr virus (EBV), the pathogen of several human malignancies, encodes many proteins required to be transported into the nucleus for viral DNA reproduction and nucleocapsids assembly in the lytic replication cycle. Here, fluorescence microscope, mutation analysis, interspecies heterokaryon assays, co-immunoprecipitation assay, RNA interference, and Western blot were performed to explore the nuclear import mechanism of EBV encoded BLLF2 protein. BLLF2 was shown to be a nucleocytoplasmic shuttling protein neither by a chromosomal region maintenance 1 (CRM1)- nor by a transporter associated with antigen processing (TAP)-dependent pathway. Yet, BLLF2's two functional nuclear localization signals (NLSs), NLS1 (16KRQALETVPHPQNRGR31) and NLS2 (44RRPRPPVAKRRRFPR58), were identified, whereas the predicted NES was nonfunctional. Finally, BLLF2 was proven to transport into the nucleus via a Ran-dependent and importin β1-dependent pathway. This mechanism may contribute to a more extensive insight into the assembly and synthesis of EBV virions in the nucleus, thus affording a new direction for the treatment of viruses.
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Affiliation(s)
- Jingjing Li
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China.,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Yingjie Guo
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Yangxi Deng
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Li Hu
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Bolin Li
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Shenyu Deng
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Jiayi Zhong
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Li Xie
- Centralab, Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Shaoxuan Shi
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Xuejun Hong
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Xuelong Zheng
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Mingsheng Cai
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Meili Li
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
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Neira JL, Jiménez-Alesanco A, Rizzuti B, Velazquez-Campoy A. The nuclear localization sequence of the epigenetic factor RYBP binds to human importin α3. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140670. [PMID: 33945888 DOI: 10.1016/j.bbapap.2021.140670] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 11/26/2022]
Abstract
RYBP (Ring1 and YY1 binding protein, UniProt ID: Q8N488) is an epigenetic factor with a key role during embryonic development; it does also show an apoptotic function and an ubiquitin binding activity. RYBP is an intrinsically disordered protein (IDP), with a Zn-finger domain at its N-terminal region, which folds upon binding to DNA. It is predicted that RYBP has a nuclear localization sequence (NLS), comprising residues Asn58 to Lys83, to allow for nuclear translocation. We studied in this work the ability of intact RYBP to bind Impα3 and its truncated species, ΔImpα3, without the importin binding domain (IBB), by using fluorescence and circular dichroism (CD). Furthermore, the binding of the peptide matching the isolated NLS region of RYBP (NLS-RYBP) was also studied using the same methods and isothermal titration calorimetry (ITC), and in silico molecular docking. Moreover, we carried out experiments with NLS-RYBP in the absence or in the presence of NaCl (140 mM). Our results show that RYBP interacted with Impα3 and ΔImpα3, causing protein precipitation. The NLS-RYBP also interacted with both importin species (dissociation constant in the low micromolar range), at low or high ionic strength, as shown by intrinsic fluorescence and ITC. These findings indicate that the NLS region, which was mainly unfolded in isolation in solution, was essentially responsible for the binding of RYBP to each of the importin species. Furthermore, the molecular simulations predict that the anchoring of NLS-RYBP takes place in the major binding site for the NLS of cargo proteins bound to Impα3. Taken together, our findings pinpoint the theoretical predictions of the NLS region in RYBP and, more importantly, suggest that this IDP relies on an importin for its nuclear translocation.
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Affiliation(s)
- José L Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain.
| | - Ana Jiménez-Alesanco
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Bruno Rizzuti
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, 87036 Rende, Italy
| | - Adrián Velazquez-Campoy
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain; Fundación ARAID, Government of Aragón, 50018 Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain
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7
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Neira JL, Rizzuti B, Jiménez-Alesanco A, Abián O, Velázquez-Campoy A, Iovanna JL. The Paralogue of the Intrinsically Disordered Nuclear Protein 1 Has a Nuclear Localization Sequence that Binds to Human Importin α3. Int J Mol Sci 2020; 21:ijms21197428. [PMID: 33050086 PMCID: PMC7583046 DOI: 10.3390/ijms21197428] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 09/28/2020] [Accepted: 10/03/2020] [Indexed: 02/07/2023] Open
Abstract
Numerous carrier proteins intervene in protein transport from the cytoplasm to the nucleus in eukaryotic cells. One of those is importin α, with several human isoforms; among them, importin α3 (Impα3) features a particularly high flexibility. The protein NUPR1L is an intrinsically disordered protein (IDP), evolved as a paralogue of nuclear protein 1 (NUPR1), which is involved in chromatin remodeling and DNA repair. It is predicted that NUPR1L has a nuclear localization sequence (NLS) from residues Arg51 to Gln74, in order to allow for nuclear translocation. We studied in this work the ability of intact NUPR1L to bind Impα3 and its depleted species, ∆Impα3, without the importin binding domain (IBB), using fluorescence, isothermal titration calorimetry (ITC), circular dichroism (CD), nuclear magnetic resonance (NMR), and molecular docking techniques. Furthermore, the binding of the peptide matching the isolated NLS region of NUPR1L (NLS-NUPR1L) was also studied using the same methods. Our results show that NUPR1L was bound to Imp α3 with a low micromolar affinity (~5 μM). Furthermore, a similar affinity value was observed for the binding of NLS-NUPR1L. These findings indicate that the NLS region, which was unfolded in isolation in solution, was essentially responsible for the binding of NUPR1L to both importin species. This result was also confirmed by our in silico modeling. The binding reaction of NLS-NUPR1L to ∆Impα3 showed a larger affinity (i.e., lower dissociation constant) compared with that of Impα3, confirming that the IBB could act as an auto-inhibition region of Impα3. Taken together, our findings pinpoint the theoretical predictions of the NLS region in NUPR1L and, more importantly, suggest that this IDP relies on an importin for its nuclear translocation.
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Affiliation(s)
- José L. Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; (A.J.-A.); (O.A.); (A.V.-C.)
- Correspondence: (J.L.N.); (J.L.I.); Tel.: +34-966-65-8475 (J.L.N.); +33(0)491-82-8803 (J.L.I.)
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, Via P. Bucci, Cubo 31 C, Arcavacata di Rende, 87036 Cosenza, Italy;
| | - Ana Jiménez-Alesanco
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; (A.J.-A.); (O.A.); (A.V.-C.)
| | - Olga Abián
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; (A.J.-A.); (O.A.); (A.V.-C.)
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Instituto Aragonés de Ciencias de la Salud (IACS), 50009 Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; (A.J.-A.); (O.A.); (A.V.-C.)
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Fundacion ARAID, Gobierno de Aragon, 50009 Zaragoza, Spain
| | - Juan L. Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13288 Marseille, France
- Correspondence: (J.L.N.); (J.L.I.); Tel.: +34-966-65-8475 (J.L.N.); +33(0)491-82-8803 (J.L.I.)
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A Phosphorylation-Induced Switch in the Nuclear Localization Sequence of the Intrinsically Disordered NUPR1 Hampers Binding to Importin. Biomolecules 2020; 10:biom10091313. [PMID: 32933064 PMCID: PMC7565984 DOI: 10.3390/biom10091313] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 09/05/2020] [Accepted: 09/09/2020] [Indexed: 12/24/2022] Open
Abstract
Several carrier proteins are involved in protein transport from the cytoplasm to the nucleus in eukaryotic cells. One of those is importin α, of which there are several human isoforms; among them, importin α3 (Impα3) has a high flexibility. The protein NUPR1, a nuclear protein involved in the cell-stress response and cell cycle regulation, is an intrinsically disordered protein (IDP) that has a nuclear localization sequence (NLS) to allow for nuclear translocation. NUPR1 does localize through the whole cell. In this work, we studied the affinity of the isolated wild-type NLS region (residues 54–74) of NUPR1 towards Impα3 and several mutants of the NLS region by using several biophysical techniques and molecular docking approaches. The NLS region of NUPR1 interacted with Impα3, opening the way to model the nuclear translocation of disordered proteins. All the isolated NLS peptides were disordered. They bound to Impα3 with low micromolar affinity (1.7–27 μM). Binding was hampered by removal of either Lys65 or Lys69 residues, indicating that positive charges were important; furthermore, binding decreased when Thr68 was phosphorylated. The peptide phosphorylated at Thr68, as well as four phospho-mimetic peptides (all containing the Thr68Glu mutation), showed the presence of a sequential NN(i,i + 1) nuclear Overhauser effect (NOE) in the 2D-1H-NMR (two-dimensional–proton NMR) spectra, indicating the presence of turn-like conformations. Thus, the phosphorylation of Thr68 modulates the binding of NUPR1 to Impα3 by a conformational, entropy-driven switch from a random-coil conformation to a turn-like structure.
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Comparative study of the interactions between fungal transcription factor nuclear localization sequences with mammalian and fungal importin-alpha. Sci Rep 2020; 10:1458. [PMID: 31996719 PMCID: PMC6989684 DOI: 10.1038/s41598-020-58316-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 01/10/2020] [Indexed: 11/29/2022] Open
Abstract
Importin-α (Impα) is an adaptor protein that binds to cargo proteins (containing Nuclear Localization Sequences - NLSs), for their translocation to the nucleus. The specificities of the Impα/NLS interactions have been studied, since these features could be used as important tools to find potential NLSs in nuclear proteins or even for the development of targets to inhibit nuclear import or to design peptides for drug delivery. Few structural studies have compared different Impα variants from the same organism or Impα of different organisms. Previously, we investigated nuclear transport of transcription factors with Neurospora crassa Impα (NcImpα). Herein, NIT-2 and PAC-3 transcription factors NLSs were studied in complex with Mus musculus Impα (MmImpα). Calorimetric assays demonstrated that the PAC-3 NLS peptide interacts with both Impα proteins with approximately the same affinity. The NIT-2 NLS sequence binds with high affinity to the Impα major binding site from both organisms, but its binding to minor binding sites reveals interesting differences due to the presence of additional interactions of NIT-2-NLS with MmImpα. These findings, together with previous results with Impα from other organisms, indicate that the differential affinity of NLSs to minor binding sites may be also responsible for the selectivity of some cargo proteins recognition and transport.
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10
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Matsuura Y. Structural and biochemical characterization of the recognition of the 53BP1 nuclear localization signal by importin-α. Biochem Biophys Res Commun 2019; 510:236-241. [PMID: 30685087 DOI: 10.1016/j.bbrc.2019.01.075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 01/16/2019] [Indexed: 12/12/2022]
Abstract
53BP1 (TP53-binding protein 1) plays a key role in DNA double-strand break repair by promoting non-homologous end joining (NHEJ) especially during G1 phase of the cell cycle. Nuclear import of 53BP1 is required for proper localization of 53BP1 and maintenance of genome integrity. 53BP1 has a classical bipartite nuclear localization signal (NLS) of sequence 1666-GKRKLITSEEERSPAKRGRKS-1686. Ser1678 within the 53BP1 NLS can be phosphorylated by CDK1/cyclin B, and a phosphomimetic substitution of Ser1678 with aspartate has been shown to negatively regulate nuclear import of 53BP1. Here, the X-ray crystal structures of the nuclear import adaptor importin-α1 bound to the wild-type 53BP1 NLS and the S1678D mutant of 53BP1 NLS are reported at resolutions of 1.9 and 1.7 Å, respectively. In the wild-type structure, not only the two basic clusters of the 53BP1 NLS but also the linker region between the basic clusters made extensive interactions with importin-α1. In the mutant structure, the linker region between the basic clusters in the 53BP1 NLS made fewer interactions with importin-α1 than those observed in the wild-type structure. However, biochemical binding assays using purified proteins showed that the 53BP1 mutation S1678D reduces the binding affinity to importin-α1 only to a modest extent. Implications of these findings for regulatory mechanism of 53BP1 nuclear import are discussed.
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Affiliation(s)
- Yoshiyuki Matsuura
- Division of Biological Science, Graduate School of Science, Nagoya University, Japan; Structural Biology Research Center, Graduate School of Science, Nagoya University, Japan.
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11
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Peng N, Yang X, Zhu C, Zhou L, Yu H, Li M, Lin Y, Wang X, Li Q, She Y, Wang J, Zhao Q, Lu M, Zhu Y, Liu S. MicroRNA-302 Cluster Downregulates Enterovirus 71-Induced Innate Immune Response by Targeting KPNA2. THE JOURNAL OF IMMUNOLOGY 2018; 201:145-156. [PMID: 29777028 DOI: 10.4049/jimmunol.1701692] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 04/25/2018] [Indexed: 12/25/2022]
Abstract
Enterovirus 71 (EV71) induces significantly elevated levels of cytokines and chemokines, leading to local or systemic inflammation and severe complications. As shown in our previous study, microRNA (miR) 302c regulates influenza A virus-induced IFN expression by targeting NF-κB-inducing kinase. However, little is known about the role of the miR-302 cluster in EV71-mediated proinflammatory responses. In this study, we found that the miR-302 cluster controls EV71-induced cytokine expression. Further studies demonstrated that karyopherin α2 (KPNA2) is a direct target of the miR-302 cluster. Interestingly, we also found that EV71 infection upregulates KPNA2 expression by downregulating miR-302 cluster expression. Upon investigating the mechanisms behind this event, we found that KPNA2 intracellularly associates with JNK1/JNK2 and p38, leading to translocation of those transcription factors from the cytosol into the nucleus. In EV71-infected patients, miR-302 cluster expression was downregulated and KPNA2 expression was upregulated compared with controls, and their expression levels were closely correlated. Taken together, our work establishes a link between the miR-302/ KPNA2 axis and EV71-induced cytokine expression and represents a promising target for future antiviral therapy.
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Affiliation(s)
- Nanfang Peng
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xuecheng Yang
- Department of Infectious Diseases, Union Hospital, Wuhan 430030, China
| | - Chengliang Zhu
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
| | - Li Zhou
- Animal Biosafety Level III Laboratory, Center for Animal Experiment, School of Medicine, Wuhan University, Wuhan 430072, China
| | - Haisheng Yu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Mengqi Li
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yong Lin
- Institute of Virology, University Hospital Essen, University of Duisburg-Essen, Essen 45122, Germany
| | - Xueyu Wang
- Institute of Virology, University Hospital Essen, University of Duisburg-Essen, Essen 45122, Germany
| | - Qian Li
- Institute of Virology, University Hospital Essen, University of Duisburg-Essen, Essen 45122, Germany
| | - Yinglong She
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jun Wang
- Center of Clinical Laboratory, The Fifth People's Hospital of Wuxi, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214005, China; and
| | - Qian Zhao
- Basic and Clinical Medicine Institute of Yunnan Province, the First People's Hospital of Yunnan Province, Kunming, Yunnan 650032, China
| | - Mengji Lu
- Institute of Virology, University Hospital Essen, University of Duisburg-Essen, Essen 45122, Germany
| | - Ying Zhu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Shi Liu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China;
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Genome-wide profiling of microRNAs reveals novel insights into the interactions between H9N2 avian influenza virus and avian dendritic cells. Oncogene 2018; 37:4562-4580. [DOI: 10.1038/s41388-018-0279-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 12/30/2017] [Accepted: 01/21/2018] [Indexed: 12/19/2022]
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