1
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Cheng CX, Tan MJA, Chan KWK, Choy MMJ, Roman N, Arnold DDR, Bifani AM, Kong SYZ, Bist P, Nath BK, Swarbrick CMD, Forwood JK, Vasudevan SG. Serotype-Specific Regulation of Dengue Virus NS5 Protein Subcellular Localization. ACS Infect Dis 2024. [PMID: 38811007 DOI: 10.1021/acsinfecdis.4c00054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Dengue virus (DENV) nonstructural protein 5 (NS5), consisting of methyltransferase and RNA-dependent RNA polymerase (RdRp) domains, is critical for viral RNA synthesis within endoplasmic reticulum-derived replication complexes in the cytoplasm. However, a significant proportion of NS5 is localized to the nucleus of infected cells for DENV2, 3, and 4, whereas DENV1 NS5 is localized diffusely in the cytoplasm. We still have an incomplete understanding of how the DENV NS5 subcellular localization is regulated. Within NS5, two putative nuclear localization signal (NLS) sequences have been identified: NLSCentral residing in the palm of the RdRp domain as well as the recently discovered NLSC-term residing in the flexible region at the C-terminal of the RdRp domain. We have previously shown that DENV2 NS5 nuclear localization can be significantly reduced by single-point mutations to the NLSC-term. Here, we present biochemical, virological, and structural data demonstrating that the relative importance of either NLS in NS5 nuclear localization is unique to each of the four DENV serotypes. DENV1 NS5's cytoplasmic localization appears to be due to a functionally weak interaction between its NLSCentral and importin-α (IMPα), while DENV2 NS5 is almost exclusively nuclear through its NLSC-term's strong interaction with IMPα. Both NLSs of DENV3 NS5 appear to contribute to directing its nuclear localization. Lastly, in the case of DENV4, the regulation of its NS5 nuclear localization remains an enigma but appears to be associated with its NLSC-term.
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Affiliation(s)
- Colin Xinru Cheng
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Min Jie Alvin Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Kitti Wing Ki Chan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Milly Ming Ju Choy
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Noelia Roman
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Daniel D R Arnold
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Amanda Makha Bifani
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Sean Yao Zu Kong
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Pradeep Bist
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Babu K Nath
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Crystall M D Swarbrick
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
- Biosecurity Research Program and Training Centre, Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
- Institute for Glycomics, Griffith University, Southport 4222, Australia
| | - Jade K Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
- Biosecurity Research Program and Training Centre, Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Subhash G Vasudevan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
- Department of Microbiology and Immunology, National University of Singapore, Singapore 117545, Singapore
- Institute for Glycomics, Griffith University, Southport 4222, Australia
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2
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Hoad M, Roby JA, Forwood JK. Structural basis for nuclear import of bat adeno-associated virus capsid protein. J Gen Virol 2024; 105:001960. [PMID: 38441555 PMCID: PMC10999750 DOI: 10.1099/jgv.0.001960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 01/22/2024] [Indexed: 03/07/2024] Open
Abstract
Adeno-associated viruses (AAV) are one of the world's most promising gene therapy vectors and as a result, are one of the most intensively studied viral vectors. Despite a wealth of research into these vectors, the precise characterisation of AAVs to translocate into the host cell nucleus remains unclear. Recently we identified the nuclear localization signals of an AAV porcine strain and determined its mechanism of binding to host importin proteins. To expand our understanding of diverse AAV import mechanisms we sought to determine the mechanism in which the Cap protein from a bat-infecting AAV can interact with transport receptor importins for translocation into the nucleus. Using a high-resolution crystal structure and quantitative assays, we were able to not only determine the exact region and residues of the N-terminal domain of the Cap protein which constitute the functional NLS for binding with the importin alpha two protein, but also reveal the differences in binding affinity across the importin-alpha isoforms. Collectively our results allow for a detailed molecular view of the way AAV Cap proteins interact with host proteins for localization into the cell nucleus.
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Affiliation(s)
- Mikayla Hoad
- 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
- Gulbali Institute, 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
- Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
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3
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Moraes IR, de Oliveira HC, Fontes MRM. Structural basis of nuclear transport for NEIL DNA glycosylases mediated by importin-alpha. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140974. [PMID: 38065227 DOI: 10.1016/j.bbapap.2023.140974] [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: 08/29/2023] [Revised: 11/18/2023] [Accepted: 11/30/2023] [Indexed: 01/10/2024]
Abstract
NEIL glycosylases, including NEIL1, NEIL2, and NEIL3, play a crucial role in the base excision DNA repair pathway (BER). The classical importin pathway mediated by importin α/β and cargo proteins containing nuclear localization sequences (NLS) is the most common transport mechanism of DNA repair proteins to the nucleus. Previous studies have identified putative NLSs located at the C-terminus of NEIL3 and NEIL1. Crystallographic, bioinformatics, calorimetric (ITC), and fluorescence assays were used to investigate the interaction between NEIL1 and NEIL3 putative NLSs and importin-α (Impα). Our findings showed that NEIL3 contains a typical cNLS, with medium affinity for the major binding site of Impα. In contrast, crystallographic analysis of NEIL1 NLS revealed its binding to Impα, but with high B-factors and a lack of electron density at the linker region. ITC and fluorescence assays indicated no detectable affinity between NEIL1 NLS and Impα. These data suggest that NEIL1 NLS is a non-classical NLS with low affinity to Impα. Additionally, we compared the binding mode of NEIL3 and NEIL1 with Mus musculus Impα to human isoforms HsImpα1 and HsImpα3, which revealed interesting binding differences for HsImpα3 variant. NEIL3 is a classical medium affinity monopartite NLS, while NEIL1 is likely to be an unclassical low-affinity bipartite NLS. The base excision repair pathway is one of the primary systems involved in repairing DNA. Thus, understanding the mechanisms of nuclear transport of NEIL proteins is crucial for comprehending the role of these proteins in DNA repair and disease development.
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Affiliation(s)
- Ivan R Moraes
- Departamento de Biofísica e Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil
| | - Hamine C de Oliveira
- Departamento de Biofísica e Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil
| | - Marcos R M Fontes
- Departamento de Biofísica e Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil; Instituto de Estudos Avançados do Mar (IEAMar), Universidade Estadual Paulista (UNESP), São Vicente, SP, Brazil.
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4
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Cross EM, Marin O, Ariawan D, Aragão D, Cozza G, Di Iorio E, Forwood JK, Alvisi G. Structural determinants of phosphorylation-dependent nuclear transport of HCMV DNA polymerase processivity factor UL44. FEBS Lett 2024; 598:199-209. [PMID: 38158756 DOI: 10.1002/1873-3468.14797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
Human cytomegalovirus DNA polymerase processivity factor UL44 is transported into the nucleus by importin (IMP) α/β through a classical nuclear localization signal (NLS), and this region is susceptible to cdc2-mediated phosphorylation at position T427. Whilst phosphorylation within and close to the UL44 NLS regulates nuclear transport, the details remain elusive, due to the paucity of structural information regarding the role of negatively charged cargo phosphate groups. We addressed this issue by studying the effect of UL44 T427 phosphorylation on interaction with several IMPα isoforms by biochemical and structural approaches. Phosphorylation decreased UL44/IMPα affinity 10-fold, and a comparative structural analysis of UL44 NLS phosphorylated and non-phosphorylated peptides complexed with mouse IMPα2 revealed the structural rearrangements responsible for phosphorylation-dependent inhibition of UL44 nuclear import.
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Affiliation(s)
- Emily M Cross
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, Australia
- Diamond Light Source, Didcot, UK
| | - Oriano Marin
- Department of Biomedical Sciences, University of Padova, Italy
| | - Daryl Ariawan
- Dementia Research Centre, Macquarie University, Sydney, Australia
| | | | - Giorgio Cozza
- Department of Molecular Medicine, University of Padua, Italy
| | - Enzo Di Iorio
- Department of Molecular Medicine, University of Padua, Italy
| | - Jade K Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, Australia
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5
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Delfing BM, Laracuente XE, Olson A, Foreman KW, Paige M, Kehn-Hall K, Lockhart C, Klimov DK. Binding of viral nuclear localization signal peptides to importin-α nuclear transport protein. Biophys J 2023; 122:3476-3488. [PMID: 37542371 PMCID: PMC10502480 DOI: 10.1016/j.bpj.2023.07.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/23/2023] [Accepted: 07/27/2023] [Indexed: 08/06/2023] Open
Abstract
Using all-atom replica-exchange molecular dynamics simulations, we mapped the mechanisms of binding of the nuclear localization signal (NLS) sequence from Venezuelan equine encephalitis virus (VEEV) capsid protein to importin-α (impα) transport protein. Our objective was to identify the VEEV NLS sequence fragment that confers native, experimentally resolved binding to impα as well as to study associated binding energetics and conformational ensembles. The two selected VEEV NLS peptide fragments, KKPK and KKPKKE, show strikingly different binding mechanisms. The minNLS peptide KKPK binds non-natively and nonspecifically by adopting five diverse conformational clusters with low similarity to the x-ray structure 3VE6 of NLS-impα complex. Despite the prevalence of non-native interactions, the minNLS peptide still largely binds to the impα major NLS binding site. In contrast, the coreNLS peptide KKPKKE binds specifically and natively, adopting a largely homogeneous binding ensemble with a dominant, highly native-like conformational cluster. The coreNLS peptide retains most of native binding interactions, including π-cation contacts and a tryptophan cage. While KKPK binding is governed by a complex multistate free energy landscape featuring transitions between multiple binding poses, the coreNLS peptide free energy map is simple, exhibiting a single dominant native-like bound basin. We argue that the origin of the coreNLS peptide binding specificity is several electrostatic interactions formed by the two C-terminal amino acids, Lys10 and Glu11, with impα. The coreNLS sequence is then sufficient for native binding, but none of the amino acids flanking minNLS, including Lys10 and Glu11, are strictly necessary for the native pose. Our analyses indicate that the VEEV coreNLS sequence is virtually unique among human and viral proteins interacting with impα making it a potential target for VEEV-specific inhibitors.
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Affiliation(s)
- Bryan M Delfing
- School of Systems Biology, George Mason University, Manassas, Virginia
| | | | - Audrey Olson
- School of Systems Biology, George Mason University, Manassas, Virginia
| | - Kenneth W Foreman
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia
| | - Mikell Paige
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia
| | - Kylene Kehn-Hall
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia; Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, Virginia
| | | | - Dmitri K Klimov
- School of Systems Biology, George Mason University, Manassas, Virginia.
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6
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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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7
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Hoad M, Cross EM, Donnelly CM, Sarker S, Roby JA, Forwood JK. Structural Characterization of Porcine Adeno-Associated Virus Capsid Protein with Nuclear Trafficking Protein Importin Alpha Reveals a Bipartite Nuclear Localization Signal. Viruses 2023; 15:v15020315. [PMID: 36851528 PMCID: PMC9964314 DOI: 10.3390/v15020315] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/11/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023] Open
Abstract
Adeno-associated viruses (AAV) are important vectors for gene therapy, and accordingly, many aspects of their cell transduction pathway have been well characterized. However, the specific mechanisms that AAV virions use to enter the host nucleus remain largely unresolved. We therefore aimed to reveal the interactions between the AAV Cap protein and the nuclear transport protein importin alpha (IMPα) at an atomic resolution. Herein we expanded upon our earlier research into the Cap nuclear localization signal (NLS) of a porcine AAV isolate, by examining the influence of upstream basic regions (BRs) towards IMPα binding. Using a high-resolution crystal structure, we identified that the IMPα binding determinants of the porcine AAV Cap comprise a bipartite NLS with an N-terminal BR binding at the minor site of IMPα, and the previously identified NLS motif binding at the major site. Quantitative assays showed a vast difference in binding affinity between the previously determined monopartite NLS, and bipartite NLS described in this study. Our results provide a detailed molecular view of the interaction between AAV capsids and the nuclear import receptor, and support the findings that AAV capsids enter the nucleus by binding the nuclear import adapter IMPα using the classical nuclear localization pathway.
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Affiliation(s)
- Mikayla Hoad
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Emily M. Cross
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Camilla M. Donnelly
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Subir Sarker
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC 3086, 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
- Correspondence:
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8
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Acetylation of the nuclear localization signal in Ku70 diminishes the interaction with importin-α. Biochem Biophys Rep 2022; 33:101418. [PMID: 36620088 PMCID: PMC9811216 DOI: 10.1016/j.bbrep.2022.101418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
Proteins are functionally regulated by various types of posttranslational modifications (PTMs). Ku, a heterodimer complex of Ku70 and Ku80 subunits, participates in DNA repair processes. Ku is distributed not only in the nucleus but also in the cytoplasm, suggesting that the function of Ku is regulated by its subcellular localization. Although Ku70 undergoes PTMs including phosphorylation or acetylation, it remains unknown whether the PTMs of Ku70 affect the subcellular localization of Ku. Using a cell-free pull-down assay technique, we show that Nε-acetylation of lysine residues in the synthetic peptide matched to Ku70's nuclear localization signal (NLS) reduces the peptide's interaction with the nuclear transport factor importin-α. The reduced interaction by acetylation was supported by molecular simulation analysis. In addition, when expressed in the endogenous Ku80-defective Chinese hamster ovary xrs-6 cells, some full-size human Ku70 mutants with substitutions of glutamine, a possible structural mimetic of Nε-acetyl-lysine, for lysine at the specific NLS positions exhibited no nuclear distribution. These findings imply that acetylation of particular lysine residues in the Ku70 NLS regulates nuclear localization of Ku.
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9
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Jin L, Zhang G, Yang G, Dong J. Identification of the Karyopherin Superfamily in Maize and Its Functional Cues in Plant Development. Int J Mol Sci 2022; 23:ijms232214103. [PMID: 36430578 PMCID: PMC9699179 DOI: 10.3390/ijms232214103] [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: 10/05/2022] [Revised: 11/06/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022] Open
Abstract
Appropriate nucleo-cytoplasmic partitioning of proteins is a vital regulatory mechanism in phytohormone signaling and plant development. However, how this is achieved remains incompletely understood. The Karyopherin (KAP) superfamily is critical for separating the biological processes in the nucleus from those in the cytoplasm. The KAP superfamily is divided into Importin α (IMPα) and Importin β (IMPβ) families and includes the core components in mediating nucleocytoplasmic transport. Recent reports suggest the KAPs play crucial regulatory roles in Arabidopsis development and stress response by regulating the nucleo-cytoplasmic transport of members in hormone signaling. However, the KAP members and their associated molecular mechanisms are still poorly understood in maize. Therefore, we first identified seven IMPα and twenty-seven IMPβ genes in the maize genome and described their evolution traits and the recognition rules for substrates with nuclear localization signals (NLSs) or nuclear export signals (NESs) in plants. Next, we searched for the protein interaction partners of the ZmKAPs and selected the ones with Arabidopsis orthologs functioning in auxin biosynthesis, transport, and signaling to predict their potential function. Finally, we found that several ZmKAPs share similar expression patterns with their interacting proteins, implying their function in root development. Overall, this article focuses on the Karyopherin superfamily in maize and starts with this entry point by systematically comprehending the KAP-mediated nucleo-cytoplasmic transport process in plants, and then predicts the function of the ZmKAPs during maize development, with a perspective on a closely associated regulatory mechanism between the nucleo-cytoplasmic transport and the phytohormone network.
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Affiliation(s)
- Lu Jin
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Guobin Zhang
- College of Agronomy, Shandong Agricultural University, Taian 271018, China
| | - Guixiao Yang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Jiaqiang Dong
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
- Correspondence:
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10
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Matsuda A, Mofrad MRK. On the nuclear pore complex and its emerging role in cellular mechanotransduction. APL Bioeng 2022; 6:011504. [PMID: 35308827 PMCID: PMC8916845 DOI: 10.1063/5.0080480] [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: 12/01/2021] [Accepted: 02/21/2022] [Indexed: 12/13/2022] Open
Abstract
The nuclear pore complex (NPC) is a large protein assembly that perforates the nuclear envelope and provides a sole gateway for traffic between the cytoplasm and the nucleus. The NPC controls the nucleocytoplasmic transport by selectively allowing cargoes such as proteins and mRNA to pass through its central channel, thereby playing a vital role in protecting the nuclear component and regulating gene expression and protein synthesis. The selective transport through the NPC originates from its exquisite molecular structure featuring a large scaffold and the intrinsically disordered central channel domain, but the exact mechanism underlying the selective transport remains elusive and is the subject of various, often conflicting, hypotheses. Moreover, recent studies have suggested a new role for the NPC as a mechanosensor, where the NPC changes its channel diameter depending on the nuclear envelope tension, altering the molecular transportability through this nanopore. In this mini-review, we summarize the current understandings of the selective nature of the NPC and discuss its emerging role in cellular mechanotransduction.
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Affiliation(s)
- Atsushi Matsuda
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, California 94720, USA
| | - Mohammad R. K. Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, California 94720, USA
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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11
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Yang SNY, Maher B, Wang C, Wagstaff KM, Fraser JE, Jans DA. High Throughput Screening Targeting the Dengue NS3-NS5 Interface Identifies Antivirals against Dengue, Zika and West Nile Viruses. Cells 2022; 11:730. [PMID: 35203378 PMCID: PMC8870125 DOI: 10.3390/cells11040730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/03/2022] [Accepted: 02/11/2022] [Indexed: 12/04/2022] Open
Abstract
Dengue virus (DENV) threatens almost 70% of the world's population, with no effective therapeutic currently available and controversy surrounding the one approved vaccine. A key factor in dengue viral replication is the interaction between DENV nonstructural proteins (NS) 5 and 3 (NS3) in the infected cell. Here, we perform a proof-of-principle high-throughput screen to identify compounds targeting the NS5-NS3 binding interface. We use a range of approaches to show for the first time that two small molecules-repurposed drugs I-OMe tyrphostin AG538 (I-OMe-AG238) and suramin hexasodium (SHS)-inhibit NS5-NS3 binding at low μM concentration through direct binding to NS5 that impacts thermostability. Importantly, both have strong antiviral activity at low μM concentrations against not only DENV-2, but also Zika virus (ZIKV) and West Nile virus (WNV). This work highlights the NS5-NS3 binding interface as a viable target for the development of anti-flaviviral therapeutics.
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Affiliation(s)
| | | | | | | | | | - David A. Jans
- Nuclear Signalling Laboratory, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Monash, VIC 3800, Australia; (S.N.Y.Y.); (B.M.); (C.W.); (K.M.W.); (J.E.F.)
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12
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Structural and calorimetric studies reveal specific determinants for the binding of a high-affinity NLS to mammalian importin-alpha. Biochem J 2021; 478:2715-2732. [PMID: 34195786 DOI: 10.1042/bcj20210401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/21/2021] [Accepted: 06/25/2021] [Indexed: 11/17/2022]
Abstract
The classical nuclear import pathway is mediated by importin (Impα and Impβ), which recognizes the cargo protein by its nuclear localization sequence (NLS). NLSs have been extensively studied resulting in different proposed consensus; however, recent studies showed that exceptions may occur. This mechanism may be also dependent on specific characteristics of different Impα. Aiming to better understand the importance of specific residues from consensus and adjacent regions of NLSs, we studied different mutations of a high-affinity NLS complexed to Impα by crystallography and calorimetry. We showed that although the consensus sequence allows Lys or Arg residues at the second residue of a monopartite sequence, the presence of Arg is very important to its binding in major and minor sites of Impα. Mutations in the N or C-terminus (position P1 or P6) of the NLS drastically reduces their affinity to the receptor, which is corroborated by the loss of hydrogen bonds and hydrophobic interactions. Surprisingly, a mutation in the far N-terminus of the NLS led to an increase in the affinity for both binding sites, corroborated by the structure with an additional hydrogen bond. The binding of NLSs to the human variant Impα1 revealed that these are similar to those found in structures presented here. For human variant Impα3, the bindings are only relevant for the major site. This study increases understanding of specific issues sparsely addressed in previous studies that are important to the task of predicting NLSs, which will be relevant in the eventual design of synthetic NLSs.
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Hirota K, Matsuda-Imai N, Kiuchi T, Katsuma S. Characterization of nuclear localization signal in Ostrinia furnacalis Masculinizer protein. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2021; 106:e21768. [PMID: 33644912 DOI: 10.1002/arch.21768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 12/29/2020] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
Bombyx mori Masculinizer protein (BmMasc) is essential for both masculinization and dosage compensation in B. mori. We previously identified a bipartite nuclear localization signal (NLS) of BmMasc and two essential residues (lysine at 274 [K274] and arginine at 275 [R275]) implicated in its function. Sequence comparison showed the presence of putative NLSs in lepidopteran Masc proteins, but their functional properties and critical residues are unknown. Here we characterized a putative NLS of Ostrinia furnacalis Masc (OfMasc) using B. mori ovary-derived BmN-4 cell line. Deletion and alanine scanning mutagenesis revealed that a putative NLS is required for nuclear localization of OfMasc. However, mutations at both K227 and R228, which correspond to K274 and R275 of BmMasc, respectively, do not greatly abolish the NLS activity. Additional mutagenesis analysis revealed that triple mutations at K227, R228, and K240 almost completely inhibited OfMasc nuclear localization. These results suggest that lepidopteran Masc proteins possess a common functional NLS, but the critical residues for its activity are different. Moreover, we examined the masculinizing activity of OfMasc derivatives and found that nuclear localization is not required for the masculinizing activity of OfMasc. The results from our studies indicate that lepidopteran Masc proteins function in the cytoplasm to drive masculinizing cascade.
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Affiliation(s)
- Kanako Hirota
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Noriko Matsuda-Imai
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takashi Kiuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Susumu Katsuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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14
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Zhao Z, Tao M, Han W, Fan Z, Imran M, Cao S, Ye J. Nuclear localization of Zika virus NS5 contributes to suppression of type I interferon production and response. J Gen Virol 2021; 102:001376. [PMID: 31859616 PMCID: PMC8515865 DOI: 10.1099/jgv.0.001376] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/28/2019] [Indexed: 12/18/2022] Open
Abstract
Zika virus (ZIKV) is an emerging mosquito-borne flavivirus, which caused an unprecedented epidemic in Latin America. Among all viral non-structural proteins in flavivirus, NS5 is the most highly conserved and has multiple crucial functions, including participating in viral RNA replication and suppressing host innate immunity. Although ZIKV NS5 prominently localizes in the nucleus during infection, its specific nuclear localization signal (NLS), and its role in viral replication and pathogenesis remain controversial. Here, we identified aa 11-90 and aa 370-406 regions that contain NLSs, which are critical for nuclear localization of ZIKV NS5. Further experiments demonstrated that nuclear localization of ZIKV NS5 predominantly participates in suppression of interferon regulatory factor 3 (IRF3)-mediated activation of type I IFN (IFN-I) transcription and inhibition of IFN-I downstream response independent of its effect on signal transducers and activators of transcription 2 (STAT2) degradation. These results suggest that subcellular localization of NS5 is important for its function on innate immune suppression, which provides new insight into ZIKV pathogenesis.
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Affiliation(s)
- Zikai Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Mengying Tao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Wei Han
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Zijing Fan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Muhammad Imran
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Shengbo Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Jing Ye
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, PR China
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15
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Shao M, Lu L, Wang Q, Ma L, Tian X, Li C, Li C, Guo D, Wang Q, Wang W, Wang Y. The multi-faceted role of retinoid X receptor in cardiovascular diseases. Biomed Pharmacother 2021; 137:111264. [PMID: 33761589 DOI: 10.1016/j.biopha.2021.111264] [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] [Received: 11/30/2020] [Revised: 01/04/2021] [Accepted: 01/07/2021] [Indexed: 01/14/2023] Open
Abstract
Retinoid X receptors (RXRs) are members of ligand-dependent transcription factors whose effects on a diversity of cellular processes, including cellular proliferation, the immune response, and lipid and glucose metabolism. Knock out of RXRα causes a hypoplasia of the myocardium which is lethal during fetal life. In addition, the heart maintains a well-orchestrated balances in utilizing fatty acids (FAs) and other substrates to meet the high energy requirements. As the master transcriptional regulators of lipid metabolism, RXRs become particularly important for the energy needs of the heart. Accumulating evidence suggested that RXRs may exert direct beneficial effects in the heart both through heterodimerization with other nuclear receptors (NRs) and homodimerization, thus standing as suitable targets for treating in cardiovascular diseases. Although compounds that target RXRs are promising drugs, their use is limited by toxicity. A better understanding of the structural biology of RXRs in cardiovascular disease should enable the rational design of more selective nuclear receptor modulators to overcome these problems. Here, this review summarizes a brief overview of RXRs structure and versatility of RXR action in the control of cardiovascular diseases. And we also discussed the therapeutic potential of RXR ligand.
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Affiliation(s)
- Mingyan Shao
- School of Life Science, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Linghui Lu
- College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Lin Ma
- School of Life Science, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Xue Tian
- School of Life Science, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Changxiang Li
- College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Chun Li
- Modern Research Center of Traditional Chinese Medicine, School of Traditional Chinese Material Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Dongqing Guo
- School of Life Science, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Qiyan Wang
- School of Life Science, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Wei Wang
- School of Life Science, Beijing University of Chinese Medicine, Beijing, 100029, China.
| | - Yong Wang
- School of Life Science, Beijing University of Chinese Medicine, Beijing, 100029, China; College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China.
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16
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Novel RB1 and MET Gene Mutations in a Case with Bilateral Retinoblastoma Followed by Multiple Metastatic Osteosarcoma. Diagnostics (Basel) 2020; 11:diagnostics11010028. [PMID: 33375764 PMCID: PMC7823920 DOI: 10.3390/diagnostics11010028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 11/17/2022] Open
Abstract
Retinoblastoma (Rb) is a malignant tumor of the developing retina that affects children before the age of five years in association with inherited or early germline mutations of the RB1 gene. The genetic predisposition is also a driver for other primary malignancies, which have become the leading cause of death in retinoblastoma survivors. Other malignancies can occur as a consequence of radiotherapy. We describe a patient with retinoblastoma in which we detected a novel RB1 c.2548C > T, p.(Gln850Ter) and a synchronous MET c.3029C > T, p.(Thr1010Ile) mutation as well. After presenting with bilateral retinoblastoma, the patient developed at least four different manifestations of two independent osteosarcomas. Our goal was to identify all germline and somatic genetic alterations in available tissue samples from different time periods and to reconstruct their clonal relations using next generation sequencing (NGS). We also used structural and functional prediction of the mutant RB and MET proteins to find interactions between the defected proteins with potential causative role in the development of this unique form of retinoblastoma. Both histopathology and NGS findings supported the independent nature of a chondroblastic osteosarcoma of the irradiated facial bone followed by an osteoblastic sarcoma of the leg (tibia).
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17
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Lacasse V, Beaudoin S, Jean S, Leyton JV. A Novel Proteomic Method Reveals NLS Tagging of T-DM1 Contravenes Classical Nuclear Transport in a Model of HER2-Positive Breast Cancer. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 19:99-119. [PMID: 33024794 PMCID: PMC7522293 DOI: 10.1016/j.omtm.2020.08.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 08/27/2020] [Indexed: 11/01/2022]
Abstract
The next breakthrough for protein therapeutics is effective intracellular delivery and accumulation within target cells. Nuclear localization signal (NLS)-tagged therapeutics have been hindered by the lack of efficient nuclear localization due to endosome entrapment. Although development of strategies for tagging therapeutics with technologies capable of increased membrane penetration has resulted in proportional increased potency, nonspecific membrane penetration limits target specificity and, hence, widespread clinical success. There is a long-standing idea that nuclear localization of NLS-tagged agents occurs exclusively via classical nuclear transport. In the present study, we modified the antibody-drug conjugate trastuzumab-emtansine (T-DM1) with a classical NLS linked to cholic acid (cell accumulator [Accum]) that enables modified antibodies to escape endosome entrapment and increase nuclear localization efficiency without abrogating receptor targeting. In parallel, we developed a proteomics-based method to evaluate nuclear transport. Accum-modified T-DM1 significantly enhanced cytotoxic efficacy in the human epidermal growth factor receptor 2 (HER2)-positive SKBR3 breast cancer system. We discovered that efficacy was dependent on the nonclassical importin-7. Our evaluation reveals that when multiple classical NLS tagging occurs, cationic charge build-up as opposed to sequence dominates and becomes a substrate for importin-7. This study results in an effective target cell-specific NLS therapeutic and a general approach to guide future NLS-based development initiatives.
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Affiliation(s)
- Vincent Lacasse
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Centre Hospitalier Universitaire de Sherbrooke (CHUS), Université de Sherbrooke (UdeS), Sherbrooke, QC J1H 5N4, Canada
| | - Simon Beaudoin
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Centre Hospitalier Universitaire de Sherbrooke (CHUS), Université de Sherbrooke (UdeS), Sherbrooke, QC J1H 5N4, Canada
| | - Steve Jean
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, CHUS, UdeS, Sherbrooke, QC J1H 5N4, Canada
| | - Jeffrey V Leyton
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Centre Hospitalier Universitaire de Sherbrooke (CHUS), Université de Sherbrooke (UdeS), Sherbrooke, QC J1H 5N4, Canada.,Sherbrooke Molecular Imaging Centre (CIMS), Centre de Recherche du CHUS, UdeS, Sherbrooke, QC J1H 5N4, Canada
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18
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Lopez-Salas FE, Nadella R, Maldonado-Berny M, Escobedo-Sanchez ML, Fiorentino-Pérez R, Gatica-García B, Fernandez-Parrilla MA, Mario Gil M, Reyes-Corona D, García U, Orozco-Barrios CE, Gutierrez-Castillo ME, Martinez-Fong D. Synthetic Monopartite Peptide That Enables the Nuclear Import of Genes Delivered by the Neurotensin-Polyplex Vector. Mol Pharm 2020; 17:4572-4588. [PMID: 33125243 DOI: 10.1021/acs.molpharmaceut.0c00755] [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: 12/12/2022]
Abstract
Neurotensin (NTS)-polyplex is a multicomponent nonviral vector that enables gene delivery via internalization of the neurotensin type 1 receptor (NTSR1) to dopaminergic neurons and cancer cells. An approach to improving its therapeutic safety is replacing the viral karyophilic component (peptide KPSV40; MAPTKRKGSCPGAAPNKPK), which performs the nuclear import activity, by a shorter synthetic peptide (KPRa; KMAPKKRK). We explored this issue and the mechanism of plasmid DNA translocation through the expression of the green fluorescent protein or red fluorescent protein fused with KPRa and internalization assays and whole-cell patch-clamp configuration experiments in a single cell together with importin α/β pathway blockers. We showed that KPRa electrostatically bound to plasmid DNA increased the transgene expression compared with KPSV40 and enabled nuclear translocation of KPRa-fused red fluorescent proteins and plasmid DNA. Such translocation was blocked with ivermectin or mifepristone, suggesting importin α/β pathway mediation. KPRa also enabled NTS-polyplex-mediated expression of reporter or physiological genes such as human mesencephalic-derived neurotrophic factor (hMANF) in dopaminergic neurons in vivo. KPRa is a synthetic monopartite peptide that showed nuclear import activity in NTS-polyplex vector-mediated gene delivery. KPRa could also improve the transfection of other nonviral vectors used in gene therapy.
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Affiliation(s)
- Francisco E Lopez-Salas
- Programa de Doctorado en Nanociencias y Nanotecnología, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, No. 2508, San Pedro Zacatenco, 07360 Ciudad de México, Mexico
| | - Rasajna Nadella
- Biosciences, IIIT Srikakulam-RGUKT, Etcherla 532402, Srikakulam District, Andhra Pradesh, India
| | - Minerva Maldonado-Berny
- Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, No. 2508, San Pedro Zacatenco, 07360 Ciudad de México, Mexico
| | - Maria L Escobedo-Sanchez
- Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, No. 2508, San Pedro Zacatenco, 07360 Ciudad de México, Mexico
| | - Rosana Fiorentino-Pérez
- Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, No. 2508, San Pedro Zacatenco, 07360 Ciudad de México, Mexico
| | - Bismark Gatica-García
- Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, No. 2508, San Pedro Zacatenco, 07360 Ciudad de México, Mexico
| | - Manuel A Fernandez-Parrilla
- Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, No. 2508, San Pedro Zacatenco, 07360 Ciudad de México, Mexico
| | - Moreno Mario Gil
- Departamento de Farmacología, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, No. 2508, San Pedro Zacatenco, 07360 Ciudad de México, Mexico
| | - David Reyes-Corona
- Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, No. 2508, San Pedro Zacatenco, 07360 Ciudad de México, Mexico
| | - Ubaldo García
- Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, No. 2508, San Pedro Zacatenco, 07360 Ciudad de México, Mexico
| | - Carlos E Orozco-Barrios
- Hospital de Especialidades Dr. Bernardo Sepúlveda, Centro Médico Nacional Siglo XXI, Unidad de Investigaciones Médicas en Enfermedades Neurológicas, CONACyT, Av. Cuauhtémoc 330, Doctores, 06720 Ciudad de México, Mexico
| | - Maria E Gutierrez-Castillo
- Departamento de Biociencias e Ingeniería, Centro Interdisciplinario de Investigaciones y Estudios sobre Medio Ambiente y Desarrollo, Instituto Politécnico Nacional, 30 de junio de 1520 s/n, La Laguna Ticoman, 07340 Ciudad de Mexico, Mexico
| | - Daniel Martinez-Fong
- Programa de Doctorado en Nanociencias y Nanotecnología, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, No. 2508, San Pedro Zacatenco, 07360 Ciudad de México, Mexico.,Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, No. 2508, San Pedro Zacatenco, 07360 Ciudad de México, Mexico
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19
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The structure of importin α and the nuclear localization peptide of ChREBP, and small compound inhibitors of ChREBP-importin α interactions. Biochem J 2020; 477:3253-3269. [PMID: 32776146 PMCID: PMC7489895 DOI: 10.1042/bcj20200520] [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: 06/29/2020] [Revised: 08/06/2020] [Accepted: 08/10/2020] [Indexed: 11/17/2022]
Abstract
The carbohydrate response element binding protein (ChREBP) is a glucose-responsive transcription factor that plays a critical role in glucose-mediated induction of genes involved in hepatic glycolysis and lipogenesis. In response to fluctuating blood glucose levels ChREBP activity is regulated mainly by nucleocytoplasmic shuttling of ChREBP. Under high glucose ChREBP binds to importin α and importin β and translocates into the nucleus to initiate transcription. We have previously shown that the nuclear localization signal site (NLS) for ChREBP is bipartite with the NLS extending from Arg158 to Lys190. Here, we report the 2.5 Å crystal structure of the ChREBP-NLS peptide bound to importin α. The structure revealed that the NLS binding is monopartite, with the amino acid residues K171RRI174 from the ChREBP-NLS interacting with ARM2–ARM5 on importin α. We discovered that importin α also binds to the primary binding site of the 14-3-3 proteins with high affinity, which suggests that both importin α and 14-3-3 are each competing with the other for this broad-binding region (residues 117–196) on ChREBP. We screened a small compound library and identified two novel compounds that inhibit the ChREBP-NLS/importin α interaction, nuclear localization, and transcription activities of ChREBP. These candidate molecules support developing inhibitors of ChREBP that may be useful in treatment of obesity and the associated diseases.
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20
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Oostdyk LT, Wang Z, Zang C, Li H, McConnell MJ, Paschal BM. An epilepsy-associated mutation in the nuclear import receptor KPNA7 reduces nuclear localization signal binding. Sci Rep 2020; 10:4844. [PMID: 32179771 PMCID: PMC7076015 DOI: 10.1038/s41598-020-61369-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 12/24/2019] [Indexed: 12/15/2022] Open
Abstract
KPNA7 is a member of the Importin-α family of nuclear import receptors. KPNA7 forms a complex with Importin-β and facilitates the translocation of signal-containing proteins from the cytoplasm to the nucleus. Exome sequencing of siblings with severe neurodevelopmental defects and clinical features of epilepsy identified two amino acid-altering mutations in KPNA7. Here, we show that the E344Q substitution reduces KPNA7 binding to nuclear localization signals, and that this limits KPNA7 nuclear import activity. The P339A substitution, by contrast, has little effect on KPNA7 binding to nuclear localization signals. Given the neuronal phenotype described in the two patients, we used SILAC labeling, affinity enrichment, and mass spectrometry to identify KPNA7-interacting proteins in human induced pluripotent stem cell-derived neurons. We identified heterogeneous nuclear ribonucleoproteins hnRNP R and hnRNP U as KPNA7-interacting proteins. The E344Q substitution reduced binding and KPNA7-mediated import of these cargoes. The c.1030G > C allele which generates E344Q is within a predicted CTCF binding site, and we found that it reduces CTCF binding by approximately 40-fold. Our data support a role for altered neuronal expression and activity of KPNA7 in a rare type of pediatric epilepsy.
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Affiliation(s)
- Luke T Oostdyk
- Department of Biochemistry & Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.,Center for Cell Signaling, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Zhenjia Wang
- Center for Public Health Genomics and Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Chongzhi Zang
- Center for Public Health Genomics and Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Hui Li
- Department of Biochemistry & Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.,Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Michael J McConnell
- Department of Biochemistry & Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.,Center for Public Health Genomics and Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.,Center for Brain Immunology and Glia, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.,Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Bryce M Paschal
- Department of Biochemistry & Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA. .,Center for Cell Signaling, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
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21
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Yang SNY, Atkinson SC, Wang C, Lee A, Bogoyevitch MA, Borg NA, Jans DA. The broad spectrum antiviral ivermectin targets the host nuclear transport importin α/β1 heterodimer. Antiviral Res 2020; 177:104760. [PMID: 32135219 DOI: 10.1016/j.antiviral.2020.104760] [Citation(s) in RCA: 193] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/28/2020] [Accepted: 02/28/2020] [Indexed: 12/11/2022]
Abstract
Infection by RNA viruses such as human immunodeficiency virus (HIV)-1, influenza, and dengue virus (DENV) represent a major burden for human health worldwide. Although RNA viruses replicate in the infected host cell cytoplasm, the nucleus is central to key stages of the infectious cycle of HIV-1 and influenza, and an important target of DENV nonstructural protein 5 (NS5) in limiting the host antiviral response. We previously identified the small molecule ivermectin as an inhibitor of HIV-1 integrase nuclear entry, subsequently showing ivermectin could inhibit DENV NS5 nuclear import, as well as limit infection by viruses such as HIV-1 and DENV. We show here that ivermectin's broad spectrum antiviral activity relates to its ability to target the host importin (IMP) α/β1 nuclear transport proteins responsible for nuclear entry of cargoes such as integrase and NS5. We establish for the first time that ivermectin can dissociate the preformed IMPα/β1 heterodimer, as well as prevent its formation, through binding to the IMPα armadillo (ARM) repeat domain to impact IMPα thermal stability and α-helicity. We show that ivermectin inhibits NS5-IMPα interaction in a cell context using quantitative bimolecular fluorescence complementation. Finally, we show for the first time that ivermectin can limit infection by the DENV-related West Nile virus at low (μM) concentrations. Since it is FDA approved for parasitic indications, ivermectin merits closer consideration as a broad spectrum antiviral of interest.
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Affiliation(s)
- Sundy N Y Yang
- Nuclear Signalling Laboratory, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic, 3800, Australia
| | - Sarah C Atkinson
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic, 3800, Australia
| | - Chunxiao Wang
- Nuclear Signalling Laboratory, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic, 3800, Australia
| | - Alexander Lee
- Nuclear Signalling Laboratory, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic, 3800, Australia
| | - Marie A Bogoyevitch
- Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Australia
| | - Natalie A Borg
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic, 3800, Australia
| | - David A Jans
- Nuclear Signalling Laboratory, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic, 3800, Australia.
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22
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Sequence-Based Prediction of Fuzzy Protein Interactions. J Mol Biol 2020; 432:2289-2303. [DOI: 10.1016/j.jmb.2020.02.017] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/24/2020] [Accepted: 02/14/2020] [Indexed: 12/31/2022]
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23
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Discovering nuclear targeting signal sequence through protein language learning and multivariate analysis. Anal Biochem 2019; 591:113565. [PMID: 31883904 DOI: 10.1016/j.ab.2019.113565] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 11/24/2022]
Abstract
Nuclear localization signals (NLSs) are peptides that target proteins to the nucleus by binding to carrier proteins in the cytoplasm that transport their cargo across the nuclear membrane. Accurate identification of NLSs can help elucidate the functions of nuclear protein complexes. The currently known NLS predictors are usually specific to certain species or largely dependent on prior knowledge of NLS basic residues. Thus, a more general predictor is highly desired to reduce the potentially high false positives or false negatives in discovering new NLSs. Here, we report a new method, INSP (Identification Nucleus Signal Peptide), to effectively identify NLS mainly based on statistical knowledge and machine learning algorithms. In our NLS machine learning model, we considered the query protein sequence as text and extracted the sequence context features using a natural language model. These word-vector features encode discriminative knowledge of NLS motif frequency and are thus useful for model recognition. The output of the machine learning model will be fused with statistical knowledge of the query sequence to build a final multivariate regression model for NLS peptide identification. The experimental results demonstrate a promising performance of the new INSP approach. INSP is freely available at: www.csbio.sjtu.edu.cn/bioinf/INSP/for academic use.
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24
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Zimmermann MT, Williams MM, Klee EW, Lomberk GA, Urrutia R. Modeling post-translational modifications and cancer-associated mutations that impact the heterochromatin protein 1α-importin α heterodimers. Proteins 2019; 87:904-916. [PMID: 31152607 PMCID: PMC6790107 DOI: 10.1002/prot.25752] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/27/2019] [Indexed: 12/27/2022]
Abstract
Heterochromatin protein 1α (HP1α) is a protein that mediates cancer-associated processes in the cell nucleus. Proteomic experiments, reported here, demonstrate that HP1α complexes with importin α (IMPα), a protein necessary for its nuclear transport. This data is congruent with Simple Linear Motif (SLiM) analyses that identify an IMPα-binding motif within the linker that joins the two globular domains of this protein. Using molecular modeling and dynamics simulations, we develop a model of the IMPα-HP1α complex and investigate the impact of phosphorylation and genomic variants on their interaction. We demonstrate that phosphorylation of the HP1α linker likely regulates its association with IMPα, which has implications for HP1α access to the nucleus, where it functions. Cancer-associated genomic variants do not abolish the interaction of HP1α but instead lead to rearrangements where the variant proteins maintain interaction with IMPα, but with less specificity. Combined, this new mechanistic insight bears biochemical, cell biological, and biomedical relevance.
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Affiliation(s)
- Michael T. Zimmermann
- Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, Genomic Science and Precision Medicine Center (GSPMC)Medical College of WisconsinMilwaukeeWisconsin
- Clinical and Translational Sciences InstituteMedical College of WisconsinMilwaukeeWisconsin
| | - Monique M. Williams
- Department of BiochemistryMayo ClinicRochesterMinnesota
- Division of Biomedical Statistics and InformaticsMayo ClinicRochesterMinnesota
| | - Eric W. Klee
- Department of BiochemistryMayo ClinicRochesterMinnesota
- Division of Biomedical Statistics and InformaticsMayo ClinicRochesterMinnesota
| | - Gwen A. Lomberk
- Division of Research, Department of SurgeryMedical College of WisconsinMilwaukeeWisconsin
- Department of Pharmacology and ToxicologyMedical College of WisconsinMilwaukeeWisconsin
- Genomic Science and Precision Medicine Center (GSPMC)Medical College of WisconsinMilwaukeeWisconsin
| | - Raul Urrutia
- Division of Research, Department of SurgeryMedical College of WisconsinMilwaukeeWisconsin
- Genomic Science and Precision Medicine Center (GSPMC)Medical College of WisconsinMilwaukeeWisconsin
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsin
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25
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Fernandes CAH, Perez AM, Barros AC, Dreyer TR, da Silva MS, Morea EGO, Fontes MRM, Cano MIN. Dual cellular localization of the Leishmania amazonensis Rbp38 (LaRbp38) explains its affinity for telomeric and mitochondrial DNA. Biochimie 2019; 162:15-25. [PMID: 30930281 DOI: 10.1016/j.biochi.2019.03.017] [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: 09/30/2018] [Accepted: 03/26/2019] [Indexed: 10/27/2022]
Abstract
Rbp38 is a protein exclusively found in trypanosomatid parasites, including Leishmania amazonensis, the etiologic agent of tegumentar leishmaniasis in the Americas. The protein was first described as a Leishmania tarentolae mitochondrial RNA binding protein. Later, it was shown that the trypanosomes Rbp38 orthologues were exclusively found in the mitochondria and involved in the stabilization and replication of kinetoplast DNA (kDNA). In contrast, L. amazonensis Rbp38 (LaRbp38), co-purifies with telomerase activity and interacts not only with kDNA but also with telomeric DNA, although shares with its counterparts high sequence identity and a putative N-terminal mitochondrial targeting signal (MTS). To understand how LaRbp38 interacts both with nuclear and kDNA, we have first investigated its subcellular localization. Using hydroxy-urea synchronized L. amazonensis promastigotes we could show that LaRbp38 shuttles from mitochondria to the nucleus at late S and G2 phases. Further, we identified a non-classical nuclear localization signal (NLS) at LaRbp38 C-terminal that binds with importin alpha, a protein involved in the nuclear transport of several proteins. Also, we obtained LaRbp38 truncated forms among which, some of them also showed an affinity for both telomeric DNA and kDNA. Analysis of these truncated forms showed that LaRbp38 DNA-binding region is located between amino acid residues 95-235. Together, our findings strongly suggest that LaRbp38 is multifunctional with dual subcellular localization.
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Affiliation(s)
- Carlos A H Fernandes
- Department of Genetics, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil; Department of Physics and Biophysics, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Arina M Perez
- Department of Genetics, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Andrea C Barros
- Department of Physics and Biophysics, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Thiago R Dreyer
- Department of Physics and Biophysics, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Marcelo S da Silva
- Laboratório Especial de Ciclo Cellular, (LECC), Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, SP, Brazil
| | - Edna Gicela O Morea
- Department of Genetics, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Marcos R M Fontes
- Department of Physics and Biophysics, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Maria Isabel N Cano
- Department of Genetics, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil.
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26
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Anbo H, Sato M, Okoshi A, Fukuchi S. Functional Segments on Intrinsically Disordered Regions in Disease-Related Proteins. Biomolecules 2019; 9:biom9030088. [PMID: 30841624 PMCID: PMC6468909 DOI: 10.3390/biom9030088] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/19/2019] [Accepted: 02/25/2019] [Indexed: 01/05/2023] Open
Abstract
One of the unique characteristics of intrinsically disordered proteins (IPDs) is the existence of functional segments in intrinsically disordered regions (IDRs). A typical function of these segments is binding to partner molecules, such as proteins and DNAs. These segments play important roles in signaling pathways and transcriptional regulation. We conducted bioinformatics analysis to search these functional segments based on IDR predictions and database annotations. We found more than a thousand potential functional IDR segments in disease-related proteins. Large fractions of proteins related to cancers, congenital disorders, digestive system diseases, and reproductive system diseases have these functional IDRs. Some proteins in nervous system diseases have long functional segments in IDRs. The detailed analysis of some of these regions showed that the functional segments are located on experimentally verified IDRs. The proteins with functional IDR segments generally tend to come and go between the cytoplasm and the nucleus. Proteins involved in multiple diseases tend to have more protein-protein interactors, suggesting that hub proteins in the protein-protein interaction networks can have multiple impacts on human diseases.
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Affiliation(s)
- Hiroto Anbo
- Department of Life Science and Informatics, Faculty of Engineering, Maebashi Institute of Technology, 460-1, Kamisadori, Maebashi, Gunma 371-0816, Japan.
| | - Masaya Sato
- Department of Life Science and Informatics, Faculty of Engineering, Maebashi Institute of Technology, 460-1, Kamisadori, Maebashi, Gunma 371-0816, Japan.
| | - Atsushi Okoshi
- Department of Life Science and Informatics, Faculty of Engineering, Maebashi Institute of Technology, 460-1, Kamisadori, Maebashi, Gunma 371-0816, Japan.
| | - Satoshi Fukuchi
- Department of Life Science and Informatics, Faculty of Engineering, Maebashi Institute of Technology, 460-1, Kamisadori, Maebashi, Gunma 371-0816, Japan.
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27
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Canela-Pérez I, López-Villaseñor I, Mendoza L, Cevallos AM, Hernández R. Nuclear localization signals in trypanosomal proteins. Mol Biochem Parasitol 2019; 229:15-23. [PMID: 30772422 DOI: 10.1016/j.molbiopara.2019.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/14/2019] [Accepted: 02/09/2019] [Indexed: 01/04/2023]
Abstract
The nuclear import of proteins in eukaryotic cells is a fundamental biological process. While it has been analysed to different extents in model eukaryotic organisms, this event has rarely been studied in the early divergent protozoa of the order Kinetoplastida. The work presented here represents an overview of nuclear import in these important species of human pathogens. Initially, an in silico study of classical nuclear localization signals within the published nuclear proteomes of Trypanosoma brucei and Trypanosoma cruzi was carried out. The basic amino acids that comprise the monopartite and bipartite classical nuclear localization signals (cNLS) in trypanosomal proteins are similar to the consensus sequences observed for the nuclear proteins of yeasts, animals and plants. In addition, a summarized description of published studies that experimentally address the NLS of nuclear proteins in trypanosomatids is presented, and the clear occurrence of non-classical NLS (NLS that lack the consensus motifs of basic amino acids) in the analysed reports indicate a complex scenario for the types of receptors in these species. In general, the information presented here agrees with the hypothetical appearance of mechanisms for the recognition of nuclear proteins in early eukaryotic evolution.
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Affiliation(s)
- Israel Canela-Pérez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04360, México
| | - Imelda López-Villaseñor
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04360, México
| | - Luis Mendoza
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04360, México
| | - Ana María Cevallos
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04360, México
| | - Roberto Hernández
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04360, México.
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28
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Chen C, Masi RD, Lintermann R, Wirthmueller L. Nuclear Import of Arabidopsis Poly(ADP-Ribose) Polymerase 2 Is Mediated by Importin-α and a Nuclear Localization Sequence Located Between the Predicted SAP Domains. FRONTIERS IN PLANT SCIENCE 2018; 9:1581. [PMID: 30455710 PMCID: PMC6230994 DOI: 10.3389/fpls.2018.01581] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 10/10/2018] [Indexed: 05/17/2023]
Abstract
Proteins of the Poly(ADP-Ribose) Polymerase (PARP) family modify target proteins by covalent attachment of ADP-ribose moieties onto amino acid side chains. In Arabidopsis, PARP proteins contribute to repair of DNA lesions and modulate plant responses to various abiotic and biotic stressors. Arabidopsis PARP1 and PARP2 are nuclear proteins and given that their molecular weights exceed the diffusion limit of nuclear pore complexes, an active import mechanism into the nucleus is likely. Here we use confocal microscopy of fluorescent protein-tagged Arabidopsis PARP2 and PARP2 deletion constructs in combination with site-directed mutagenesis to identify a nuclear localization sequence in PARP2 that is required for nuclear import. We report that in co-immunoprecipitation assays PARP2 interacts with several isoforms of the importin-α group of nuclear transport adapters and that PARP2 binding to IMPORTIN-α2 is mediated by the identified nuclear localization sequence. Our results demonstrate that PARP2 is a cargo protein of the canonical importin-α/β nuclear import pathway.
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Affiliation(s)
| | | | | | - Lennart Wirthmueller
- Department of Plant Biochemistry, Dahlem Centre of Plant Sciences, Institute of Biology, Freie Universität Berlin, Berlin, Germany
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29
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Fuxreiter M. Fold or not to fold upon binding - does it really matter? Curr Opin Struct Biol 2018; 54:19-25. [PMID: 30340123 DOI: 10.1016/j.sbi.2018.09.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 09/20/2018] [Accepted: 09/21/2018] [Indexed: 12/14/2022]
Abstract
Protein interactions are usually determined by well-defined contact patterns. In this scenario, structuring of the interface is a prerequisite, which takes place prior or coupled to binding. Recent data, however, indicate plasticity of the templated folding pathway as well as considerable variations: polymorphism or dynamics in the bound-state. Conformational fluctuations in both cases are modulated by non-native, transient contacts, which complement suboptimal binding motifs to improve affinity. Here I discuss both templated folding and fuzzy binding mechanisms and propose a uniform scheme.
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Affiliation(s)
- Monika Fuxreiter
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Hungary.
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30
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Contribution of the residue at position 4 within classical nuclear localization signals to modulating interaction with importins and nuclear targeting. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:1114-1129. [DOI: 10.1016/j.bbamcr.2018.05.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 05/02/2018] [Accepted: 05/04/2018] [Indexed: 01/08/2023]
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31
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Palopoli N, González Foutel NS, Gibson TJ, Chemes LB. Short linear motif core and flanking regions modulate retinoblastoma protein binding affinity and specificity. Protein Eng Des Sel 2018; 31:69-77. [DOI: 10.1093/protein/gzx068] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 01/10/2018] [Indexed: 12/11/2022] Open
Affiliation(s)
- Nicolás Palopoli
- Department of Science and Technology, Universidad Nacional de Quilmes, CONICET. Roque Sáenz Peña 352. CP (B1876BXD), Bernal, Buenos Aires, Argentina
- Structural Bioinformatics Unit, Fundación Instituto Leloir and IIBBA-CONICET. Av. Patricias Argentinas 435 CP 1405, Buenos Aires, Argentina
| | - Nicolás S González Foutel
- Protein Structure Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET. Av. Patricias Argentinas 435 CP 1405, Buenos Aires, Argentina
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Lucía B Chemes
- Protein Structure Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET. Av. Patricias Argentinas 435 CP 1405, Buenos Aires, Argentina
- Instituto de Investigaciones Biotecnológicas IIB-INTECH, Universidad Nacional de San Martín. Av. 25 de Mayo y Francia CP 1650, San Martín, Buenos Aires, Argentina
- Departamento de Fisiología y Biología Molecular y Celular (DFBMC), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA, Argentina
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32
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Nuclear transport of the Neurospora crassa NIT-2 transcription factor is mediated by importin-α. Biochem J 2017; 474:4091-4104. [DOI: 10.1042/bcj20170654] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The Neurospora crassa NIT-2 transcription factor belongs to the GATA transcription factor family and plays a fundamental role in the regulation of nitrogen metabolism. Because NIT-2 acts by accessing DNA inside the nucleus, understanding the nuclear import process of NIT-2 is necessary to characterize its function. Thus, in the present study, NIT-2 nuclear transport was investigated using a combination of biochemical, cellular, and biophysical methods. A complemented strain that produced an sfGFP–NIT-2 fusion protein was constructed, and nuclear localization assessments were made under conditions that favored protein translocation to the nucleus. Nuclear translocation was also investigated using HeLa cells, which showed that the putative NIT-2 nuclear localization sequence (NLS; 915TISSKRQRRHSKS927) was recognized by importin-α and that subsequent transport occurred via the classical import pathway. The interaction between the N. crassa importin-α (NcImpα) and the NIT-2 NLS was quantified with calorimetric assays, leading to the observation that the peptide bound to two sites with different affinities, which is typical of a monopartite NLS sequence. The crystal structure of the NcImpα/NIT-2 NLS complex was solved and revealed that the NIT-2 peptide binds to NcImpα with the major NLS-binding site playing a primary role. This result contrasts other recent studies that suggested a major role for the minor NLS-binding site in importin-α from the α2 family, indicating that both sites can be used for different cargo proteins according to specific metabolic requirements.
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33
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de Barros AC, Takeda AAS, Dreyer TR, Velazquez-Campoy A, Kobe B, Fontes MRM. DNA mismatch repair proteins MLH1 and PMS2 can be imported to the nucleus by a classical nuclear import pathway. Biochimie 2017; 146:87-96. [PMID: 29175432 DOI: 10.1016/j.biochi.2017.11.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/22/2017] [Indexed: 01/11/2023]
Abstract
MLH1 and PMS2 proteins form the MutLα heterodimer, which plays a major role in DNA mismatch repair (MMR) in humans. Mutations in MMR-related proteins are associated with cancer, especially with colon cancer. The N-terminal region of MutLα comprises the N-termini of PMS2 and MLH1 and, similarly, the C-terminal region of MutLα is composed by the C-termini of PMS2 and MLH1, and the two are connected by linker region. The nuclear localization sequences (NLSs) necessary for the nuclear transport of the two proteins are found in this linker region. However, the exact NLS sequences have been controversial, with different sequences reported, particularly for MLH1. The individual components are not imported efficiently, presumably due to their C-termini masking their NLSs. In order to gain insights into the nuclear transport of these proteins, we solved the crystal structures of importin-α bound to peptides corresponding to the supposed NLSs of MLH1 and PMS2 and performed isothermal titration calorimetry to study their binding affinities. Both putative MLH1 and PMS2 NLSs can bind to importin-α as monopartite NLSs, which is in agreement with some previous studies. However, MLH1-NLS has the highest affinity measured by a natural NLS peptide, suggesting a major role of MLH1 protein in nuclear import compared to PMS2. Finally, the role of MLH1 and PMS2 in the nuclear transport of the MutLα heterodimer is discussed.
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Affiliation(s)
- Andrea C de Barros
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil
| | - Agnes A S Takeda
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil
| | - Thiago R Dreyer
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint-Unit IQFR-CSIC-BIFI, University of Zaragoza, Zaragoza, Spain; Dep. of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza, Spain; Fundacion ARAID, Government of Aragon, Zaragoza, Spain
| | - Boštjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Marcos R M Fontes
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil.
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34
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Wang C, Yang SNY, Smith K, Forwood JK, Jans DA. Nuclear import inhibitor N-(4-hydroxyphenyl) retinamide targets Zika virus (ZIKV) nonstructural protein 5 to inhibit ZIKV infection. Biochem Biophys Res Commun 2017; 493:1555-1559. [PMID: 28988109 DOI: 10.1016/j.bbrc.2017.10.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 10/03/2017] [Indexed: 12/31/2022]
Abstract
In the absence of approved therapeutics, Zika virus (ZIKV)'s recent prolific outbreaks in the Americas, together with impacts on unborn fetuses of infected mothers, make it a pressing human health concern worldwide. Although a key player in viral replication in the infected host cell cytoplasm, ZIKV non-structural protein 5 (NS5) appears to contribute integrally to pathogenesis by localising in the host cell nucleus, in similar fashion to NS5 from Dengue virus (DENV). We show here for the first time that ZIKV NS5 is recognized with high nanomolar affinity by the host cell importin α/β1 heterodimer, and that this interaction can be blocked by the novel DENV NS5 targeting inhibitor N-(4-hydroxyphenyl) retinamide (4-HPR). Importantly, we show that 4-HPR has potent anti-ZIKV activity at low μM concentrations. With an established safety profile for human use, 4-HPR represents an exciting possibility as an anti-ZIKV agent.
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Affiliation(s)
- Chunxiao Wang
- Nuclear Signaling Laboratory, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic. 3800, Australia
| | - Sundy N Y Yang
- Nuclear Signaling Laboratory, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic. 3800, Australia
| | - Kate Smith
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2650, Australia
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2650, Australia
| | - David A Jans
- Nuclear Signaling Laboratory, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic. 3800, Australia.
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35
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Chaston JJ, Stewart AG, Christie M. Structural characterisation of TNRC6A nuclear localisation signal in complex with importin-alpha. PLoS One 2017; 12:e0183587. [PMID: 28837617 PMCID: PMC5570423 DOI: 10.1371/journal.pone.0183587] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 08/06/2017] [Indexed: 12/16/2022] Open
Abstract
The GW182/TNRC6 family of proteins are central scaffolds that link microRNA-associated Argonaute proteins to the cytoplasmic decay machinery for targeted mRNA degradation processes. Although nuclear roles for the GW182/TNRC6 proteins are unknown, recent reports have demonstrated nucleocytoplasmic shuttling activity that utilises the importin-α and importin-β transport receptors for nuclear translocation. Here we describe the structure of mouse importin-α in complex with the TNRC6A nuclear localisation signal peptide. We further show that the interactions observed between TNRC6A and importin-α are conserved between mouse and human complexes. Our results highlight the ability of monopartite cNLS sequences to maximise contacts at the importin-α major binding site, as well as regions outside the main binding cavities.
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Affiliation(s)
- Jessica J. Chaston
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Alastair Gordon Stewart
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Mary Christie
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
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36
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Exploring the Sequence-based Prediction of Folding Initiation Sites in Proteins. Sci Rep 2017; 7:8826. [PMID: 28821744 PMCID: PMC5562875 DOI: 10.1038/s41598-017-08366-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 07/10/2017] [Indexed: 11/23/2022] Open
Abstract
Protein folding is a complex process that can lead to disease when it fails. Especially poorly understood are the very early stages of protein folding, which are likely defined by intrinsic local interactions between amino acids close to each other in the protein sequence. We here present EFoldMine, a method that predicts, from the primary amino acid sequence of a protein, which amino acids are likely involved in early folding events. The method is based on early folding data from hydrogen deuterium exchange (HDX) data from NMR pulsed labelling experiments, and uses backbone and sidechain dynamics as well as secondary structure propensities as features. The EFoldMine predictions give insights into the folding process, as illustrated by a qualitative comparison with independent experimental observations. Furthermore, on a quantitative proteome scale, the predicted early folding residues tend to become the residues that interact the most in the folded structure, and they are often residues that display evolutionary covariation. The connection of the EFoldMine predictions with both folding pathway data and the folded protein structure suggests that the initial statistical behavior of the protein chain with respect to local structure formation has a lasting effect on its subsequent states.
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Hansen S, Kiefer JD, Madhurantakam C, Mittl PRE, Plückthun A. Structures of designed armadillo repeat proteins binding to peptides fused to globular domains. Protein Sci 2017; 26:1942-1952. [PMID: 28691351 DOI: 10.1002/pro.3229] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/02/2017] [Accepted: 07/03/2017] [Indexed: 01/05/2023]
Abstract
Designed armadillo repeat proteins (dArmRP) are α-helical solenoid repeat proteins with an extended peptide binding groove that were engineered to develop a generic modular technology for peptide recognition. In this context, the term "peptide" not only denotes a short unstructured chain of amino acids, but also an unstructured region of a protein, as they occur in termini, loops, or linkers between folded domains. Here we report two crystal structures of dArmRPs, in complex with peptides fused either to the N-terminus of Green Fluorescent Protein or to the C-terminus of a phage lambda protein D. These structures demonstrate that dArmRPs bind unfolded peptides in the intended conformation also when they constitute unstructured parts of folded proteins, which greatly expands possible applications of the dArmRP technology. Nonetheless, the structures do not fully reflect the binding behavior in solution, that is, some binding sites remain unoccupied in the crystal and even unexpected peptide residues appear to be bound. We show how these differences can be explained by restrictions of the crystal lattice or the composition of the crystallization solution. This illustrates that crystal structures have to be interpreted with caution when protein-peptide interactions are characterized, and should always be correlated with measurements in solution.
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Affiliation(s)
- Simon Hansen
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Jonathan D Kiefer
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Chaithanya Madhurantakam
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Peer R E Mittl
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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Marcu O, Dodson EJ, Alam N, Sperber M, Kozakov D, Lensink MF, Schueler-Furman O. FlexPepDock lessons from CAPRI peptide-protein rounds and suggested new criteria for assessment of model quality and utility. Proteins 2017; 85:445-462. [PMID: 28002624 PMCID: PMC6618814 DOI: 10.1002/prot.25230] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/15/2016] [Accepted: 11/23/2016] [Indexed: 12/21/2022]
Abstract
CAPRI rounds 28 and 29 included, for the first time, peptide-receptor targets of three different systems, reflecting increased appreciation of the importance of peptide-protein interactions. The CAPRI rounds allowed us to objectively assess the performance of Rosetta FlexPepDock, one of the first protocols to explicitly include peptide flexibility in docking, accounting for peptide conformational changes upon binding. We discuss here successes and challenges in modeling these targets: we obtain top-performing, high-resolution models of the peptide motif for cases with known binding sites but there is a need for better modeling of flanking regions, as well as better selection criteria, in particular for unknown binding sites. These rounds have also provided us the opportunity to reassess the success criteria, to better reflect the quality of a peptide-protein complex model. Using all models submitted to CAPRI, we analyze the correlation between current classification criteria and the ability to retrieve critical interface features, such as hydrogen bonds and hotspots. We find that loosening the backbone (and ligand) RMSD threshold, together with a restriction on the side chain RMSD measure, allows us to improve the selection of high-accuracy models. We also suggest a new measure to assess interface hydrogen bond recovery, which is not assessed by the current CAPRI criteria. Finally, we find that surprisingly much can be learned from rather inaccurate models about binding hotspots, suggesting that the current status of peptide-protein docking methods, as reflected by the submitted CAPRI models, can already have a significant impact on our understanding of protein interactions. Proteins 2017; 85:445-462. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Orly Marcu
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, the Hebrew University of Jerusalem, Israel
| | - Emma-Joy Dodson
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, the Hebrew University of Jerusalem, Israel
| | - Nawsad Alam
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, the Hebrew University of Jerusalem, Israel
| | - Michal Sperber
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, the Hebrew University of Jerusalem, Israel
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brooks University, Stony Brook, New York, 11794
| | - Marc F Lensink
- University of Lille, CNRS UMR8576 UGSF, Lille, 59000, France
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, the Hebrew University of Jerusalem, Israel
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Loftus KM, Cui H, Coutavas E, King DS, Ceravolo A, Pereiras D, Solmaz SR. Mechanism for G2 phase-specific nuclear export of the kinetochore protein CENP-F. Cell Cycle 2017; 16:1414-1429. [PMID: 28723232 DOI: 10.1080/15384101.2017.1338218] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Centromere protein F (CENP-F) is a component of the kinetochore and a regulator of cell cycle progression. CENP-F recruits the dynein transport machinery and orchestrates several cell cycle-specific transport events, including transport of the nucleus, mitochondria and chromosomes. A key regulatory step for several of these functions is likely the G2 phase-specific export of CENP-F from the nucleus to the cytosol, where the cytoplasmic dynein transport machinery resides; however, the molecular mechanism of this process is elusive. Here, we have identified 3 phosphorylation sites within the bipartite classical nuclear localization signal (cNLS) of CENP-F. These sites are specific for cyclin-dependent kinase 1 (Cdk1), which is active in G2 phase. Phosphomimetic mutations of these residues strongly diminish the interaction of the CENP-F cNLS with its nuclear transport receptor karyopherin α. These mutations also diminish nuclear localization of the CENP-F cNLS in cells. Notably, the cNLS is phosphorylated in the -1 position, which is important to orient the adjacent major motif for binding into its pocket on karyopherin α. We propose that localization of CENP-F is regulated by a cNLS, and a nuclear export pathway, resulting in nuclear localization during most of interphase. In G2 phase, the cNLS is weakened by phosphorylation through Cdk1, likely resulting in nuclear export of CENP-F via the still active nuclear export pathway. Once CENP-F resides in the cytosol, it can engage in pathways that are important for cell cycle progression, kinetochore assembly and the faithful segregation of chromosomes into daughter cells.
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Affiliation(s)
- Kyle M Loftus
- a Department of Chemistry , State University of New York at Binghamton , New York , NY , USA
| | - Heying Cui
- a Department of Chemistry , State University of New York at Binghamton , New York , NY , USA
| | - Elias Coutavas
- b Laboratory of Cell Biology , The Rockefeller University , New York , NY , USA
| | - David S King
- c Howard Hughes Medical Institute, Mass Spectrometry Laboratory , University of California at Berkeley , Berkeley , CA , USA
| | - Amanda Ceravolo
- a Department of Chemistry , State University of New York at Binghamton , New York , NY , USA
| | - Dylan Pereiras
- a Department of Chemistry , State University of New York at Binghamton , New York , NY , USA
| | - Sozanne R Solmaz
- a Department of Chemistry , State University of New York at Binghamton , New York , NY , USA
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Goulding SP, Szumlinski KK, Contet C, MacCoss MJ, Wu CC. A mass spectrometry-based proteomic analysis of Homer2-interacting proteins in the mouse brain. J Proteomics 2017; 166:127-137. [PMID: 28728878 DOI: 10.1016/j.jprot.2017.07.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 07/08/2017] [Accepted: 07/12/2017] [Indexed: 11/26/2022]
Abstract
In the brain, the Homer protein family modulates excitatory signal transduction and receptor plasticity through interactions with other proteins in dendritic spines. Homer proteins are implicated in a variety of psychiatric disorders such as schizophrenia and addiction. Since long Homers serve as scaffolding proteins, identifying their interacting partners is an important first step in understanding their biological function and could help to guide the design of new therapeutic strategies. The present study set out to document Homer2-interacting proteins in the mouse brain using a co-immunoprecipitation-based mass spectrometry approach where Homer2 knockout samples were used to filter out non-specific interactors. We found that in the mouse brain, Homer2 interacts with a limited subset of its previously reported interacting partners (3 out of 31). Importantly, we detected an additional 15 novel Homer2-interacting proteins, most of which are part of the N-methyl-D-aspartate receptor signaling pathway. These results corroborate the central role Homer2 plays in glutamatergic transmission and expand the network of proteins potentially contributing to the behavioral abnormalities associated with altered Homer2 expression. SIGNIFICANCE Long Homer proteins are scaffolding proteins that regulate signal transduction in neurons. Identifying their interacting partners is key to understanding their function. We used co-immunoprecipitation in combination with mass spectrometry to establish the first comprehensive list of Homer2-interacting partners in the mouse brain. The specificity of interactions was evaluated using Homer2 knockout brain tissue as a negative control. The set of proteins that we identified minimally overlaps with previously reported interacting partners of Homer2; however, we identified novel interactors that are part of a signaling cascade activated by glutamatergic transmission, which improves our mechanistic understanding of the role of Homer2 in behavior.
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Affiliation(s)
- Scott P Goulding
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA, United States; Neuroscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, United States; Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States.
| | - Karen K Szumlinski
- Department of Psychological and Brain Sciences, Molecular, Cellular and Developmental Biology, The Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Candice Contet
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA, United States
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States
| | - Christine C Wu
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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Bending-Twisting Motions and Main Interactions in Nucleoplasmin Nuclear Import. PLoS One 2016; 11:e0157162. [PMID: 27258022 PMCID: PMC4892583 DOI: 10.1371/journal.pone.0157162] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 05/25/2016] [Indexed: 01/11/2023] Open
Abstract
Alpha solenoid proteins play a key role in regulating the classical nuclear import pathway, recognizing a target protein and transporting it into the nucleus. Importin-α (Impα) is the solenoid responsible for cargo protein recognition, and it has been extensively studied by X-ray crystallography to understand the binding specificity. To comprehend the main motions of Impα and to extend the information about the critical interactions during carrier-cargo recognition, we surveyed different conformational states based on molecular dynamics (MD) and normal mode (NM) analyses. Our model of study was a crystallographic structure of Impα complexed with the classical nuclear localization sequence (cNLS) from nucleoplasmin (Npl), which was submitted to multiple 100 ns of MD simulations. Representative conformations were selected for calculating the 87 lowest frequencies NMs of vibration, and a displacement approach was applied along each NM. Based on geometric criteria, using the radius of curvature and inter-repeat angles as the reference metrics, the main motions of Impα were described. Moreover, we determined the salt bridges, hydrogen bonds and hydrophobic interactions in the Impα-NplNLS interface. Our results show the bending and twisting motions participating in the recognition of nuclear proteins, allowing the accommodation and adjustment of a classical bipartite NLS sequence. The essential contacts for the nuclear import were also described and were mostly in agreement with previous studies, suggesting that the residues in the cNLS linker region establish important contacts with Impα adjusting the cNLS backbone. The MD simulations combined with NM analysis can be applied to the Impα-NLS system to help understand interactions between Impα and cNLSs and the analysis of non-classic NLSs.
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Sun Y, Xian L, Xing H, Yu J, Yang Z, Yang T, Yang L, Ding P. Factors influencing the nuclear targeting ability of nuclear localization signals. J Drug Target 2016; 24:927-933. [DOI: 10.1080/1061186x.2016.1184273] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Wang S, Lu Y, Yin MX, Wang C, Wu W, Li J, Wu W, Ge L, Hu L, Zhao Y, Zhang L. Importin α1 Mediates Yorkie Nuclear Import via an N-terminal Non-canonical Nuclear Localization Signal. J Biol Chem 2016; 291:7926-37. [PMID: 26887950 DOI: 10.1074/jbc.m115.700823] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Indexed: 01/13/2023] Open
Abstract
The Hippo signaling pathway controls organ size by orchestrating cell proliferation and apoptosis. When the Hippo pathway was inactivated, the transcriptional co-activator Yorkie translocates into the nucleus and forms a complex with transcription factor Scalloped to promote the expression of Hippo pathway target genes. Therefore, the nuclear translocation of Yorkie is a critical step in Hippo signaling. Here, we provide evidence that the N-terminal 1-55 amino acids of Yorkie, especially Arg-15, were essential for its nuclear localization. By mass spectrometry and biochemical analyses, we found that Importin α1 can directly interact with the Yorkie N terminus and drive Yorkie into the nucleus. Further experiments show that the upstream component Hippo can inhibit Importin α1-mediated Yorkie nuclear import. Taken together, we identified a potential nuclear localization signal at the N-terminal end of Yorkie as well as a critical role for Importin α1 in Yorkie nuclear import.
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Affiliation(s)
- Shimin Wang
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China and
| | - Yi Lu
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China and
| | - Meng-Xin Yin
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China and
| | - Chao Wang
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China and
| | - Wei Wu
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China and
| | - Jinhui Li
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China and
| | - Wenqing Wu
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China and
| | - Ling Ge
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China and
| | - Lianxin Hu
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China and
| | - Yun Zhao
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Lei Zhang
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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Wang YP, Du WJ, Huang LP, Wei YW, Wu HL, Feng L, Liu CM. The Pseudorabies Virus DNA Polymerase Accessory Subunit UL42 Directs Nuclear Transport of the Holoenzyme. Front Microbiol 2016; 7:124. [PMID: 26913023 PMCID: PMC4753316 DOI: 10.3389/fmicb.2016.00124] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/25/2016] [Indexed: 01/13/2023] Open
Abstract
Pseudorabies virus (PRV) DNA replication occurs in the nuclei of infected cells and requires the viral DNA polymerase. The PRV DNA polymerase comprises a catalytic subunit, UL30, and an accessory subunit, UL42, that confers processivity to the enzyme. Its nuclear localization is a prerequisite for its enzymatic function in the initiation of viral DNA replication. However, the mechanisms by which the PRV DNA polymerase holoenzyme enters the nucleus have not been determined. In this study, we characterized the nuclear import pathways of the PRV DNA polymerase catalytic and accessory subunits. Immunofluorescence analysis showed that UL42 localizes independently in the nucleus, whereas UL30 alone predominantly localizes in the cytoplasm. Intriguingly, the localization of UL30 was completely shifted to the nucleus when it was coexpressed with UL42, demonstrating that nuclear transport of UL30 occurs in an UL42-dependent manner. Deletion analysis and site-directed mutagenesis of the two proteins showed that UL42 contains a functional and transferable bipartite nuclear localization signal (NLS) at amino acids 354–370 and that K354, R355, and K367 are important for the NLS function, whereas UL30 has no NLS. Coimmunoprecipitation assays verified that UL42 interacts with importins α3 and α4 through its NLS. In vitro nuclear import assays demonstrated that nuclear accumulation of UL42 is a temperature- and energy-dependent process and requires both importins α and β, confirming that UL42 utilizes the importin α/β-mediated pathway for nuclear entry. In an UL42 NLS-null mutant, the UL42/UL30 heterodimer was completely confined to the cytoplasm when UL42 was coexpressed with UL30, indicating that UL30 utilizes the NLS function of UL42 for its translocation into the nucleus. Collectively, these findings suggest that UL42 contains an importin α/β-mediated bipartite NLS that transports the viral DNA polymerase holoenzyme into the nucleus in an in vitro expression system.
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Affiliation(s)
- Yi-Ping Wang
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Wen-Juan Du
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Li-Ping Huang
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Yan-Wu Wei
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Hong-Li Wu
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Li Feng
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Chang-Ming Liu
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
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Barros ACD, Takeda AAS, Dreyer TR, Velazquez-Campoy A, Kobe B, Fontes MRM. Structural and Calorimetric Studies Demonstrate that Xeroderma Pigmentosum Type G (XPG) Can Be Imported to the Nucleus by a Classical Nuclear Import Pathway via a Monopartite NLS Sequence. J Mol Biol 2016; 428:2120-31. [PMID: 26812207 DOI: 10.1016/j.jmb.2016.01.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/08/2016] [Accepted: 01/14/2016] [Indexed: 11/16/2022]
Abstract
Xeroderma pigmentosum type G (XPG) proteins are involved in DNA lesion recognition and promotion of nucleotide excision repair. Specific mutations in these proteins may lead to Cockayne syndrome, in which the patients may display severe developmental retardation and neurological abnormalities. No structural information is available for their spacer region or the C-terminal domain, which are important, respectively, for specific nucleotide excision repair activity and substrate specificity, as well as nuclear translocation. Immunofluorescence studies suggested two specific regions of the XPG C-terminus as potential bipartite nuclear localization sequences, which would be responsible for its translocation to the nucleus by the classical nuclear import pathway mediated by the importin-α (Impα). Thus, in order to test these hypotheses and gain insight into the structural basis for the nuclear import process for the XPG protein, we solved the crystal structures of complexes formed by the Impα and peptides corresponding to both putative nuclear localization signal (NLS) sequences (XPG1 and XPG2) and performed isothermal titration calorimetry assays to determine their binding affinities. Structural experiments confirm the binding of both NLS peptides to Impα but, unexpectedly, they bind to the receptor as monopartite NLSs. The isothermal titration calorimetry assays demonstrated that XPG1 and XPG2 peptides bind to two separate binding sites, but with high affinity to the major NLS-binding site of the Impα, resembling classical monopartite SV40 TAg NLS. The results lead to insights about what distinguishes monopartite and bipartite NLSs, as well as the differential roles of XPG1 and XPG2 NLSs in the nuclear localization of XPG.
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Affiliation(s)
- Andrea C de Barros
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, 18618-970 Brazil
| | - Agnes A S Takeda
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, 18618-970 Brazil
| | - Thiago R Dreyer
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, 18618-970 Brazil
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems, Joint-Unit Institute of Physical Chemistry "Rocasolano"-Consejo Superior de Investigaciones Científicas-Institute of Biocomputation and Physics of Complex Systems, University of Zaragoza, Zaragoza, 50018, Spain; Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza, 50018, Spain; Fundacion Agencia Aragonesa para la Investigación y el Desarrollo, Government of Aragon, Zaragoza, 50018, Spain
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Marcos R M Fontes
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, 18618-970 Brazil.
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Velez G, Lin M, Christensen T, Faubion WA, Lomberk G, Urrutia R. Evidence supporting a critical contribution of intrinsically disordered regions to the biochemical behavior of full-length human HP1γ. J Mol Model 2015; 22:12. [PMID: 26680990 PMCID: PMC4683166 DOI: 10.1007/s00894-015-2874-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Accepted: 11/22/2015] [Indexed: 12/16/2022]
Abstract
HP1γ, a non-histone chromatin protein, has elicited significant attention because of its role in gene silencing, elongation, splicing, DNA repair, cell growth, differentiation, and many other cancer-associated processes, including therapy resistance. These characteristics make it an ideal target for developing small drugs for both mechanistic experimentation and potential therapies. While high-resolution structures of the two globular regions of HP1γ, the chromo- and chromoshadow domains, have been solved, little is currently known about the conformational behavior of the full-length protein. Consequently, in the current study, we use threading, homology-based molecular modeling, molecular mechanics calculations, and molecular dynamics simulations to develop models that allow us to infer properties of full-length HP1γ at an atomic resolution level. HP1γ appears as an elongated molecule in which three Intrinsically Disordered Regions (IDRs, 1, 2, and 3) endow this protein with dynamic flexibility, intermolecular recognition properties, and the ability to integrate signals from various intracellular pathways. Our modeling also suggests that the dynamic flexibility imparted to HP1γ by the three IDRs is important for linking nucleosomes with PXVXL motif-containing proteins, in a chromatin environment. The importance of the IDRs in intermolecular recognition is illustrated by the building and study of both IDR2 HP1γ−importin-α and IDR1 and IDR2 HP1γ−DNA complexes. The ability of the three IDRs for integrating cell signals is demonstrated by combined linear motif analyses and molecular dynamics simulations showing that posttranslational modifications can generate a histone mimetic sequence within the IDR2 of HP1γ, which when bound by the chromodomain can lead to an autoinhibited state. Combined, these data underscore the importance of IDRs 1, 2, and 3 in defining the structural and dynamic properties of HP1γ, discoveries that have both mechanistic and potentially biomedical relevance.
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Affiliation(s)
- Gabriel Velez
- Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street SW, Guggenheim 10, Rochester, MN, 55905, USA.,Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Department of Biophysics, Mayo Clinic, Rochester, MN, USA.,Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Department of Medicine, Mayo Clinic, Rochester, MN, USA.,Medical Scientist Training Program, University of Iowa, Iowa City, IA, USA
| | - Marisa Lin
- Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street SW, Guggenheim 10, Rochester, MN, 55905, USA.,Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Department of Biophysics, Mayo Clinic, Rochester, MN, USA.,Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Trace Christensen
- Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street SW, Guggenheim 10, Rochester, MN, 55905, USA.,Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Department of Biophysics, Mayo Clinic, Rochester, MN, USA.,Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - William A Faubion
- Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street SW, Guggenheim 10, Rochester, MN, 55905, USA.,Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Department of Biophysics, Mayo Clinic, Rochester, MN, USA.,Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Gwen Lomberk
- Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street SW, Guggenheim 10, Rochester, MN, 55905, USA. .,Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Department of Biophysics, Mayo Clinic, Rochester, MN, USA. .,Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Department of Medicine, Mayo Clinic, Rochester, MN, USA.
| | - Raul Urrutia
- Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street SW, Guggenheim 10, Rochester, MN, 55905, USA. .,Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Department of Biophysics, Mayo Clinic, Rochester, MN, USA. .,Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Department of Medicine, Mayo Clinic, Rochester, MN, USA.
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Qiu GH, Xie X, Deng L, Hooi SC. Tumor Suppressor DLEC1 can Stimulate the Proliferation of Cancer Cells When AP-2ɑ2 is Down-Regulated in HCT116. HEPATITIS MONTHLY 2015; 15:e29829. [PMID: 26834787 PMCID: PMC4723729 DOI: 10.5812/hepatmon.29829] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/28/2015] [Accepted: 08/12/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND The molecular mechanisms of tumor suppressor gene DLEC1 are largely unknown. OBJECTIVES In this study, we established DLEC1 over-expression stable clones to study the cellular function of DLEC1 in the colorectal cancer cell line, HCT116. MATERIALS AND METHODS Stable clones with DLEC1 over-expression were first established by the transfection of DLEC1 expression construct pcDNA31DLEC1 in HCT116. On G418 selection, positive stable clones were screened for DLEC1 expression level by conventional reverse transcription-polymerase chain reaction (RT-PCR), and verified by real-time RT-PCR and Western blotting. Subsequently, these stable clones were subjected to colony formation and cell cycle analyses and identification of factors involved in G1 arrest. Lastly, three stable clones, DLEC1-7 (highest DLEC1 expression), DLEC1-3 (lowest expression) and pcDNA31 vector control, were employed to analyze cell proliferation and cell cycle after AP-2α2 knockdown by siRNAs. RESULTS The DLEC1 over-expression was found to reduce the number of colonies in colony formation and to induce G1 arrest in seven clones, and apoptosis in one clone in the cell cycle analysis. Furthermore, regardless of the different cell cycle defects in all eight stable clones, the expression level of transcriptional factor AP-2α2 was found to be elevated. More interestingly, we found that when AP-2α2 was knocked down, DLEC1 over-expression neither suppressed cancer cell growth nor induced G1 arrest, yet, instead promoted cell growth and decreased cells in the G1 fraction. This promotion of cell proliferation and release of G1 cells also seemed to be proportional to DLEC1 expression levels in DLEC1 stable clones. CONCLUSIONS DLEC1 suppresses tumor cell growth the presence of AP-2α2 and stimulates cell proliferation in the down-regulation of AP-2α2 in DLEC1 over-expression stable clones of HTC116.
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Affiliation(s)
- Guo-Hua Qiu
- Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, PR China
- Department of Physiology, Faculty of Medicine, National University of Singapore, Singapore, Republic of Singapore
- Corresponding Authors: Guo-Hua Qiu, Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, Jiangsu 213164, PR China. Tel/Fax: +86-59786330103, E-mail: ; Shing Chuan Hooi, Department of Physiology, Faculty of Medicine, National University of Singapore, Singapore, Republic of Singapore. Tel: +65-65163222, Fax: +65-67788161, E-mail:
| | - Xiaojin Xie
- Department of Physiology, Faculty of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Linhong Deng
- Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, PR China
| | - Shing Chuan Hooi
- Department of Physiology, Faculty of Medicine, National University of Singapore, Singapore, Republic of Singapore
- Corresponding Authors: Guo-Hua Qiu, Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, Jiangsu 213164, PR China. Tel/Fax: +86-59786330103, E-mail: ; Shing Chuan Hooi, Department of Physiology, Faculty of Medicine, National University of Singapore, Singapore, Republic of Singapore. Tel: +65-65163222, Fax: +65-67788161, E-mail:
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Christie M, Chang CW, Róna G, Smith KM, Stewart AG, Takeda AAS, Fontes MRM, Stewart M, Vértessy BG, Forwood JK, Kobe B. Structural Biology and Regulation of Protein Import into the Nucleus. J Mol Biol 2015; 428:2060-90. [PMID: 26523678 DOI: 10.1016/j.jmb.2015.10.023] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 10/16/2015] [Accepted: 10/24/2015] [Indexed: 11/28/2022]
Abstract
Proteins are translated in the cytoplasm, but many need to access the nucleus to perform their functions. Understanding how these nuclear proteins are transported through the nuclear envelope and how the import processes are regulated is therefore an important aspect of understanding cell function. Structural biology has played a key role in understanding the molecular events during the transport processes and their regulation, including the recognition of nuclear targeting signals by the corresponding receptors. Here, we review the structural basis of the principal nuclear import pathways and the molecular basis of their regulation. The pathways involve transport factors that are members of the β-karyopherin family, which can bind cargo directly (e.g., importin-β, transportin-1, transportin-3, importin-13) or through adaptor proteins (e.g., importin-α, snurportin-1, symportin-1), as well as unrelated transport factors such as Hikeshi, involved in the transport of heat-shock proteins, and NTF2, involved in the transport of RanGDP. Solenoid proteins feature prominently in these pathways. Nuclear transport factors recognize nuclear targeting signals on the cargo proteins, including the classical nuclear localization signals, recognized by the adaptor importin-α, and the PY nuclear localization signals, recognized by transportin-1. Post-translational modifications, particularly phosphorylation, constitute key regulatory mechanisms operating in these pathways.
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Affiliation(s)
- Mary Christie
- The Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales Faculty of Medicine, Darlinghurst, NSW 2010, Australia
| | - Chiung-Wen Chang
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gergely Róna
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary; Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest H-1111, Hungary
| | - Kate M Smith
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2650, Australia
| | - Alastair G Stewart
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia
| | - Agnes A S Takeda
- Department of Physics and Biophysics, Institute of Biosciences, Universidade Estadual Paulista, Botucatu, São Paulo 18618-000, Brazil
| | - Marcos R M Fontes
- Department of Physics and Biophysics, Institute of Biosciences, Universidade Estadual Paulista, Botucatu, São Paulo 18618-000, Brazil
| | - Murray Stewart
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Beáta G Vértessy
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary; Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest H-1111, Hungary
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2650, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia.
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Abstract
The Karyopherin-β family of proteins mediates nuclear transport of macromolecules. Nuclear versus cytoplasmic localization of proteins is often suggested by the presence of NLSs (nuclear localization signals) or NESs (nuclear export signals). Import-Karyopherin-βs or Importins bind to NLSs in their protein cargos to transport them through nuclear pore complexes into the nucleus. Until recently, only two classes of NLS had been biochemically and structurally characterized: the classical NLS, which is recognized by the Importin-α/β heterodimer and the PY-NLS (proline-tyrosine NLS), which is recognized by Karyopherin-β2 or Transportin-1. Structures of two other Karyopherin-βs, Kap121 and Transportin-SR2, in complex with their respective cargos were reported for the first time recently, revealing two new distinct classes of NLSs. The present paper briefly describes the classical NLS, reviews recent literature on the PY-NLS and provides in-depth reviews of the two newly discovered classes of NLSs that bind Kap121p and Transportin-SR respectively.
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Róna G, Borsos M, Ellis JJ, Mehdi AM, Christie M, Környei Z, Neubrandt M, Tóth J, Bozóky Z, Buday L, Madarász E, Bodén M, Kobe B, Vértessy BG. Dynamics of re-constitution of the human nuclear proteome after cell division is regulated by NLS-adjacent phosphorylation. Cell Cycle 2015; 13:3551-64. [PMID: 25483092 DOI: 10.4161/15384101.2014.960740] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Phosphorylation by the cyclin-dependent kinase 1 (Cdk1) adjacent to nuclear localization signals (NLSs) is an important mechanism of regulation of nucleocytoplasmic transport. However, no systematic survey has yet been performed in human cells to analyze this regulatory process, and the corresponding cell-cycle dynamics have not yet been investigated. Here, we focused on the human proteome and found that numerous proteins, previously not identified in this context, are associated with Cdk1-dependent phosphorylation sites adjacent to their NLSs. Interestingly, these proteins are involved in key regulatory events of DNA repair, epigenetics, or RNA editing and splicing. This finding indicates that cell-cycle dependent events of genome editing and gene expression profiling may be controlled by nucleocytoplasmic trafficking. For in-depth investigations, we selected a number of these proteins and analyzed how point mutations, expected to modify the phosphorylation ability of the NLS segments, perturb nucleocytoplasmic localization. In each case, we found that mutations mimicking hyper-phosphorylation abolish nuclear import processes. To understand the mechanism underlying these phenomena, we performed a video microscopy-based kinetic analysis to obtain information on cell-cycle dynamics on a model protein, dUTPase. We show that the NLS-adjacent phosphorylation by Cdk1 of human dUTPase, an enzyme essential for genomic integrity, results in dynamic cell cycle-dependent distribution of the protein. Non-phosphorylatable mutants have drastically altered protein re-import characteristics into the nucleus during the G1 phase. Our results suggest a dynamic Cdk1-driven mechanism of regulation of the nuclear proteome composition during the cell cycle.
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Key Words
- Cdc28, cyclin-dependent protein kinase (Cdk) encoded by CDC28
- Cdk1, cyclin-dependent kinase 1
- GO, gene ontology
- NES, nuclear export signal
- NLS, nuclear localization signal
- SNP, single nucleotide polymorphisms
- SV40, Simian virus 40
- UBA1, Ubiquitin-activating enzyme E1
- UNG2, Human Uracil-DNA glycosylase 2
- cNLS, classical nuclear localization signal
- cell cycle
- dNTP, deoxyribonucleotide triphosphate
- dTTP, deoxythymidine triphosphate
- dUMP, deoxyuridine monophosphate
- dUTP, deoxyuridine triphosphate
- dUTPase
- importin
- phosphorylation
- trafficking
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Affiliation(s)
- Gergely Róna
- a Institute of Enzymology; RCNS; Hungarian Academy of Sciences ; Budapest , Hungary
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