Symplekin and Multiple Other Polyadenylation Factors Participate in 3 -End Maturation of Histone Mrnas
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A SARS-Cov-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing
A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing Supplementary Information Supplementary Discussion All SARS-CoV-2 protein and gene functions described in the subnetwork appendices, including the text below and the text found in the individual bait subnetworks, are based on the functions of homologous genes from other coronavirus species. These are mainly from SARS-CoV and MERS-CoV, but when available and applicable other related viruses were used to provide insight into function. The SARS-CoV-2 proteins and genes listed here were designed and researched based on the gene alignments provided by Chan et. al. 1 2020 . Though we are reasonably sure the genes here are well annotated, we want to note that not every protein has been verified to be expressed or functional during SARS-CoV-2 infections, either in vitro or in vivo. In an effort to be as comprehensive and transparent as possible, we are reporting the sub-networks of these functionally unverified proteins along with the other SARS-CoV-2 proteins. In such cases, we have made notes within the text below, and on the corresponding subnetwork figures, and would advise that more caution be taken when examining these proteins and their molecular interactions. Due to practical limits in our sample preparation and data collection process, we were unable to generate data for proteins corresponding to Nsp3, Orf7b, and Nsp16. Therefore these three genes have been left out of the following literature review of the SARS-CoV-2 proteins and the protein-protein interactions (PPIs) identified in this study. -
NUCLEOPROTEINS of CELL NUCLEI by A
344 ZOOLOGY: MIRSK YA ND POLLISTER PROC, N. A. S. NUCLEOPROTEINS OF CELL NUCLEI By A. E. MIRSKY AND A. W. POLLISTER HOSPITAL OF THE ROCKEFELLER INSTITUTE FOR MEDICAL RESEARCH, AND DEPARTMENT OF Z6OLOGY, COLUMBIA UNIVERSITY Communicated August 3, 1942 We have prepared nucleoproteins from a wide variety of animal cells- from mammalian liver, kidney, pancreas, spleen, thymus, brain, from the liver, spleen and blood cells of the dogfish, and from the sperm of the trout, shad, frog and sea urchin. These nucleoproteins are located in the nuclei of the cells from which they are derived. In this paper we shall briefly de- scribe the method of preparation, some properties of the nucleoproteins and the evidence that they are in fact derived from cell nuclei. I. Preparation.-To extract these nucleoproteins from the cell and to separate them from other cellular constituents nothing more drastic is used than neutral sodium chloride solutions of varying concentrations. Before extraction, much cytoplasmic material is removed by thoroughly washing the minced tissue with physiological saline. From liver more than 60 per cent of all the protein present can be removed in this manner with- out destroying the main outlines of cell structure. The washed tissue is then extracted with 1 M NaCl (2 M NaCl is needed for extraction of sea- urchin sperm). As soon as the more concentrated salt solution is added the mixture becomes exceedingly viscous. By centrifugation at high speed (10,000 to 12,000 r. p. m.) a viscous, slightly opalescent supernatant fluid is obtained. The supernatant fluid is viscous because of the nucleoprotein dissolved in it. -
Genes with 5' Terminal Oligopyrimidine Tracts Preferentially Escape Global Suppression of Translation by the SARS-Cov-2 NSP1 Protein
Downloaded from rnajournal.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Genes with 5′ terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein Shilpa Raoa, Ian Hoskinsa, Tori Tonna, P. Daniela Garciaa, Hakan Ozadama, Elif Sarinay Cenika, Can Cenika,1 a Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA 1Corresponding author: [email protected] Key words: SARS-CoV-2, Nsp1, MeTAFlow, translation, ribosome profiling, RNA-Seq, 5′ TOP, Ribo-Seq, gene expression 1 Downloaded from rnajournal.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract Viruses rely on the host translation machinery to synthesize their own proteins. Consequently, they have evolved varied mechanisms to co-opt host translation for their survival. SARS-CoV-2 relies on a non-structural protein, Nsp1, for shutting down host translation. However, it is currently unknown how viral proteins and host factors critical for viral replication can escape a global shutdown of host translation. Here, using a novel FACS-based assay called MeTAFlow, we report a dose-dependent reduction in both nascent protein synthesis and mRNA abundance in cells expressing Nsp1. We perform RNA-Seq and matched ribosome profiling experiments to identify gene-specific changes both at the mRNA expression and translation level. We discover that a functionally-coherent subset of human genes are preferentially translated in the context of Nsp1 expression. These genes include the translation machinery components, RNA binding proteins, and others important for viral pathogenicity. Importantly, we uncovered a remarkable enrichment of 5′ terminal oligo-pyrimidine (TOP) tracts among preferentially translated genes. -
The Role of Nuclear Bodies in Gene Expression and Disease
Biology 2013, 2, 976-1033; doi:10.3390/biology2030976 OPEN ACCESS biology ISSN 2079-7737 www.mdpi.com/journal/biology Review The Role of Nuclear Bodies in Gene Expression and Disease Marie Morimoto and Cornelius F. Boerkoel * Department of Medical Genetics, Child & Family Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-604-875-2157; Fax: +1-604-875-2376. Received: 15 May 2013; in revised form: 13 June 2013 / Accepted: 20 June 2013 / Published: 9 July 2013 Abstract: This review summarizes the current understanding of the role of nuclear bodies in regulating gene expression. The compartmentalization of cellular processes, such as ribosome biogenesis, RNA processing, cellular response to stress, transcription, modification and assembly of spliceosomal snRNPs, histone gene synthesis and nuclear RNA retention, has significant implications for gene regulation. These functional nuclear domains include the nucleolus, nuclear speckle, nuclear stress body, transcription factory, Cajal body, Gemini of Cajal body, histone locus body and paraspeckle. We herein review the roles of nuclear bodies in regulating gene expression and their relation to human health and disease. Keywords: nuclear bodies; transcription; gene expression; genome organization 1. Introduction Gene expression is a multistep process that is vital for the development, adaptation and survival of all living organisms. Regulation of gene expression occurs at the level of transcription, RNA processing, RNA export, translation and protein degradation [1±3]. The nucleus has the ability to modulate gene expression at each of these levels. How the nucleus executes this regulation is gradually being dissected. -
INT6 Interacts with MIF4GD/SLIP1 and Is Necessary for Efficient Histone Mrna Translation
Downloaded from rnajournal.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press INT6 interacts with MIF4GD/SLIP1 and is necessary for efficient histone mRNA translation JULIA NEUSIEDLER,1,3,4 VINCENT MOCQUET,1,3 TARAN LIMOUSIN,2 THEOPHILE OHLMANN,2 CHRISTELLE MORRIS,1 and PIERRE JALINOT1,5 1Laboratoire de Biologie Mole´culaire de la Cellule, Unite´ Mixte de Recherche 5239, Centre National de la Recherche Scientifique, Ecole Normale Supe´rieure de Lyon, 69364 Lyon cedex 07, France 2Virologie Humaine, Unite´ 758, Institut National de la Sante´ et de la Recherche Me´dicale, Ecole Normale Supe´rieure de Lyon, 69364 Lyon cedex 07, France ABSTRACT The INT6/EIF3E protein has been implicated in mouse and human breast carcinogenesis. This subunit of the eIF3 translation initiation factor that includes a PCI domain exhibits specific features such as presence in the nucleus and ability to interact with other important cellular protein complexes like the 26S proteasome and the COP9 signalosome. It has been previously shown that INT6 was not essential for bulk translation, and this protein is considered to regulate expression of specific mRNAs. Based on the results of a two-hybrid screen performed with INT6 as bait, we characterize in this article the MIF4GD/SLIP1 protein as an interactor of this eIF3 subunit. MIF4GD was previously shown to associate with SLBP, which binds the stem–loop located at the 39 end of the histone mRNAs, and to be necessary for efficient translation of these cell cycle–regulated mRNAs that lack a poly(A) tail. In line with the interaction of both proteins, we show using the RNA interference approach that INT6 is also essential to S-phase histone mRNA translation. -
NMR Structure and Dynamics of the RNA-Binding Site for the Histone Mrna Stem-Loop Binding Protein
Downloaded from rnajournal.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press RNA (2002), 8:83–96+ Cambridge University Press+ Printed in the USA+ Copyright © 2002 RNA Society+ DOI: 10+1017+S1355838201013863 NMR structure and dynamics of the RNA-binding site for the histone mRNA stem-loop binding protein ERIC S. DEJONG,1 WILLIAM F. MARZLUFF,2 and EDWARD P. NIKONOWICZ1 1 Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77251-1892, USA 2 Program in Molecular Biology and Biotechnology, Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA ABSTRACT The 39 end of replication-dependent histone mRNAs terminate in a conserved sequence containing a stem-loop. This 26-nt sequence is the binding site for a protein, stem-loop binding protein (SLBP), that is involved in multiple aspects of histone mRNA metabolism and regulation. We have determined the structure of the 26-nt sequence by multidimen- sional NMR spectroscopy. There is a 16-nt stem-loop motif, with a conserved 6-bp stem and a 4-nt loop. The loop is closed by a conserved U•A base pair that terminates the canonical A-form stem. The pyrimidine-rich 4-nt loop, UUUC, is well organized with the three uridines stacking on the helix, and the fourth base extending across the major groove into the solvent. The flanking nucleotides at the base of the hairpin stem do not assume a unique conformation, despite the fact that the 59 flanking nucleotides are a critical component of the SLBP binding site. -
Proteomics Analysis of Cellular Proteins Co-Immunoprecipitated with Nucleoprotein of Influenza a Virus (H7N9)
Article Proteomics Analysis of Cellular Proteins Co-Immunoprecipitated with Nucleoprotein of Influenza A Virus (H7N9) Ningning Sun 1,:, Wanchun Sun 2,:, Shuiming Li 3, Jingbo Yang 1, Longfei Yang 1, Guihua Quan 1, Xiang Gao 1, Zijian Wang 1, Xin Cheng 1, Zehui Li 1, Qisheng Peng 2,* and Ning Liu 1,* Received: 26 August 2015 ; Accepted: 22 October 2015 ; Published: 30 October 2015 Academic Editor: David Sheehan 1 Central Laboratory, Jilin University Second Hospital, Changchun 130041, China; [email protected] (N.S.); [email protected] (J.Y.); [email protected] (L.Y.); [email protected] (G.Q.); [email protected] (X.G.); [email protected] (Z.W.); [email protected] (X.C.); [email protected] (Z.L.) 2 Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun 130062, China; [email protected] 3 College of Life Sciences, Shenzhen University, Shenzhen 518057, China; [email protected] * Correspondence: [email protected] (Q.P.); [email protected] (N.L.); Tel./Fax: +86-431-8879-6510 (Q.P. & N.L.) : These authors contributed equally to this work. Abstract: Avian influenza A viruses are serious veterinary pathogens that normally circulate among avian populations, causing substantial economic impacts. Some strains of avian influenza A viruses, such as H5N1, H9N2, and recently reported H7N9, have been occasionally found to adapt to humans from other species. In order to replicate efficiently in the new host, influenza viruses have to interact with a variety of host factors. In the present study, H7N9 nucleoprotein was transfected into human HEK293T cells, followed by immunoprecipitated and analyzed by proteomics approaches. -
The Interactome Analysis of the Respiratory Syncytial Virus Protein M2-1 Suggests a New Role in Viral Mrna Metabolism Post-Trans
www.nature.com/scientificreports OPEN The Interactome analysis of the Respiratory Syncytial Virus protein M2-1 suggests a new role in viral mRNA metabolism post- transcription Camille Bouillier1, Gina Cosentino1, Thibaut Léger 2, Vincent Rincheval1, Charles-Adrien Richard 3, Aurore Desquesnes1, Delphine Sitterlin1, Sabine Blouquit-Laye1, Jean-Francois Eléouët3, Elyanne Gault1,4 & Marie-Anne Rameix-Welti 1,4* Human respiratory syncytial virus (RSV) is a globally prevalent negative-stranded RNA virus, which can cause life-threatening respiratory infections in young children, elderly people and immunocompromised patients. Its transcription termination factor M2-1 plays an essential role in viral transcription, but the mechanisms underpinning its function are still unclear. We investigated the cellular interactome of M2-1 using green fuorescent protein (GFP)-trap immunoprecipitation on RSV infected cells coupled with mass spectrometry analysis. We identifed 137 potential cellular partners of M2-1, among which many proteins associated with mRNA metabolism, and particularly mRNA maturation, translation and stabilization. Among these, the cytoplasmic polyA-binding protein 1 (PABPC1), a candidate with a major role in both translation and mRNA stabilization, was confrmed to interact with M2-1 using protein complementation assay and specifc immunoprecipitation. PABPC1 was also shown to colocalize with M2-1 from its accumulation in inclusion bodies associated granules (IBAGs) to its liberation in the cytoplasm. Altogether, these results strongly suggest that M2-1 interacts with viral mRNA and mRNA metabolism factors from transcription to translation, and imply that M2-1 may have an additional role in the fate of viral mRNA downstream of transcription. Human respiratory syncytial virus (RSV) is the most common cause of respiratory infection in neonates and infants worldwide. -
The Role and Assembly Mechanism of Nucleoprotein in Influenza a Virus
ARTICLE Received 28 Sep 2012 | Accepted 8 Feb 2013 | Published 12 Mar 2013 DOI: 10.1038/ncomms2589 The role and assembly mechanism of nucleoprotein in influenza A virus ribonucleoprotein complexes Lauren Turrell1, Jon W. Lyall2, Laurence S. Tiley2, Ervin Fodor1 & Frank T. Vreede1 The nucleoprotein of negative-strand RNA viruses forms a major component of the ribonucleoprotein complex that is responsible for viral transcription and replication. However, the precise role of nucleoprotein in viral RNA transcription and replication is not clear. Here we show that nucleoprotein of influenza A virus is entirely dispensable for replication and transcription of short viral RNA-like templates in vivo, suggesting that nucleoprotein repre- sents an elongation factor for the viral RNA polymerase. We also find that the recruitment of nucleoprotein to nascent ribonucleoprotein complexes during replication of full-length viral genes is mediated through nucleoprotein–nucleoprotein homo-oligomerization in a ‘tail loop- first’ orientation and is independent of RNA binding. This work demonstrates that nucleo- protein does not regulate the initiation and termination of transcription and replication by the viral polymerase in vivo, and provides new mechanistic insights into the assembly and regulation of viral ribonucleoprotein complexes. 1 Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK. 2 Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK. Correspondence and requests for materials should be addressed to F.T.V. (email: [email protected]). NATURE COMMUNICATIONS | 4:1591 | DOI: 10.1038/ncomms2589 | www.nature.com/naturecommunications 1 & 2013 Macmillan Publishers Limited. -
Evolutionary Selection of the Nuclear Localization Signal in the Viral Nucleoprotein Leads to Host Adaptation of the Genus Orthobornavirus
viruses Article Evolutionary Selection of the Nuclear Localization Signal in the Viral Nucleoprotein Leads to Host Adaptation of the Genus Orthobornavirus Ryo Komorizono 1,2 , Yukiko Sassa 3, Masayuki Horie 1,4 , Akiko Makino 1,2,* and Keizo Tomonaga 1,2,5,* 1 Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan; [email protected] (R.K.); [email protected] (M.H.) 2 Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto 606-8507, Japan 3 Laboratory of Veterinary Infectious Disease, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan; [email protected] 4 Hakubi Center for Advanced Research, Kyoto University, Kyoto 606-8507, Japan 5 Department of Molecular Virology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan * Correspondence: [email protected] (A.M.); [email protected] (K.T.) Received: 20 October 2020; Accepted: 10 November 2020; Published: 11 November 2020 Abstract: Adaptation of the viral life cycle to host cells is necessary for efficient viral infection and replication. This evolutionary process has contributed to the mechanism for determining the host range of viruses. Orthobornaviruses, members of the family Bornaviridae, are non-segmented, negative-strand RNA viruses, and several genotypes have been isolated from different vertebrate species. Previous studies revealed that some genotypes isolated from avian species can replicate in mammalian cell lines, suggesting the zoonotic potential of avian orthobornaviruses. However, the mechanism by which the host specificity of orthobornaviruses is determined has not yet been identified. -
The SARS-Coronavirus Infection Cycle: a Survey of Viral Membrane Proteins, Their Functional Interactions and Pathogenesis
International Journal of Molecular Sciences Review The SARS-Coronavirus Infection Cycle: A Survey of Viral Membrane Proteins, Their Functional Interactions and Pathogenesis Nicholas A. Wong * and Milton H. Saier, Jr. * Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA * Correspondence: [email protected] (N.A.W.); [email protected] (M.H.S.J.); Tel.: +1-650-763-6784 (N.A.W.); +1-858-534-4084 (M.H.S.J.) Abstract: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a novel epidemic strain of Betacoronavirus that is responsible for the current viral pandemic, coronavirus disease 2019 (COVID- 19), a global health crisis. Other epidemic Betacoronaviruses include the 2003 SARS-CoV-1 and the 2009 Middle East Respiratory Syndrome Coronavirus (MERS-CoV), the genomes of which, particularly that of SARS-CoV-1, are similar to that of the 2019 SARS-CoV-2. In this extensive review, we document the most recent information on Coronavirus proteins, with emphasis on the membrane proteins in the Coronaviridae family. We include information on their structures, functions, and participation in pathogenesis. While the shared proteins among the different coronaviruses may vary in structure and function, they all seem to be multifunctional, a common theme interconnecting these viruses. Many transmembrane proteins encoded within the SARS-CoV-2 genome play important roles in the infection cycle while others have functions yet to be understood. We compare the various structural and nonstructural proteins within the Coronaviridae family to elucidate potential overlaps Citation: Wong, N.A.; Saier, M.H., Jr. -
Fragile X Mental Retardation Protein Stimulates Ribonucleoprotein Assembly of Influenza a Virus
ARTICLE Received 31 Jul 2013 | Accepted 15 Jan 2014 | Published 10 Feb 2014 DOI: 10.1038/ncomms4259 Fragile X mental retardation protein stimulates ribonucleoprotein assembly of influenza A virus Zhuo Zhou1,*, Mengmeng Cao1,*, Yang Guo1,*, Lili Zhao1, Jingfeng Wang1, Xue Jia1, Jianguo Li1, Conghui Wang1, Gu¨lsah Gabriel2, Qinghua Xue1, Yonghong Yi3, Sheng Cui1, Qi Jin1, Jianwei Wang1 & Tao Deng1 The ribonucleoprotein (RNP) of the influenza A virus is responsible for the transcription and replication of viral RNA in the nucleus. These processes require interplay between host factors and RNP components. Here, we report that the Fragile X mental retardation protein (FMRP) targets influenza virus RNA synthesis machinery and facilitates virus replication both in cell culture and in mice. We demonstrate that FMRP transiently associates with viral RNP and stimulates viral RNP assembly through RNA-mediated interaction with the nucleoprotein. Furthermore, the KH2 domain of FMRP mediates its association with the nucleoprotein. A point mutation (I304N) in the KH2 domain, identified from a Fragile X syndrome patient, disrupts the FMRP–nucleoprotein association and abolishes the ability of FMRP to participate in viral RNP assembly. We conclude that FMRP is a critical host factor used by influenza viruses to facilitate viral RNP assembly. Our observation reveals a mechanism of influenza virus RNA synthesis and provides insights into FMRP functions. 1 MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China. 2 Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany. 3 Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, P.R.