1
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Shitrit A, Nisnevich V, Rozenshtein N, Kobo H, Phan HV, Tay S, Szpara M, Weitzman MD, Drayman N, Kobiler O. Shared sequence characteristics identified in non-canonical rearrangements of HSV-1 genomes. J Virol 2023; 97:e0095523. [PMID: 37991369 PMCID: PMC10734421 DOI: 10.1128/jvi.00955-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/26/2023] [Indexed: 11/23/2023] Open
Abstract
IMPORTANCE Mutations and genetic rearrangements are the primary driving forces of evolution. Viruses provide valuable model systems for investigating these mechanisms due to their rapid evolutionary rates and vast genetic variability. To investigate genetic rearrangements in the double-stranded DNA genome of herpes simplex virus type 1, the viral population was serially passaged in various cell types. The serial passaging led to formation of defective genomes, resulted from cell-specific non-canonical rearrangements (NCRs). Interestingly, we discovered shared sequence characteristics underlying the formation of these NCRs across all cell types. Moreover, most NCRs identified in clinical samples shared these characteristics. Based on our findings, we propose a model elucidating the formation of NCRs during viral replication within the nucleus of eukaryotic cells.
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Affiliation(s)
- Alina Shitrit
- Department of Clinical Microbiology and Immunology, School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Valerya Nisnevich
- Department of Clinical Microbiology and Immunology, School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nofar Rozenshtein
- Department of Clinical Microbiology and Immunology, School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hila Kobo
- Genomic Research Unit, Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Hoang Van Phan
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, USA
| | - Savaş Tay
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, USA
| | - Moriah Szpara
- Department of Biochemistry and Molecular Biology, Department of Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Matthew D. Weitzman
- Division of Protective Immunity, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nir Drayman
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California, Irvine, California, USA
- Center for Virus Research, University of California, Irvine, California, USA
| | - Oren Kobiler
- Department of Clinical Microbiology and Immunology, School of Medicine, Tel Aviv University, Tel Aviv, Israel
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2
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Kumar M, Michael S, Alvarado-Valverde J, Mészáros B, Sámano‐Sánchez H, Zeke A, Dobson L, Lazar T, Örd M, Nagpal A, Farahi N, Käser M, Kraleti R, Davey N, Pancsa R, Chemes L, Gibson T. The Eukaryotic Linear Motif resource: 2022 release. Nucleic Acids Res 2022; 50:D497-D508. [PMID: 34718738 PMCID: PMC8728146 DOI: 10.1093/nar/gkab975] [Citation(s) in RCA: 98] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 10/27/2021] [Indexed: 02/03/2023] Open
Abstract
Almost twenty years after its initial release, the Eukaryotic Linear Motif (ELM) resource remains an invaluable source of information for the study of motif-mediated protein-protein interactions. ELM provides a comprehensive, regularly updated and well-organised repository of manually curated, experimentally validated short linear motifs (SLiMs). An increasing number of SLiM-mediated interactions are discovered each year and keeping the resource up-to-date continues to be a great challenge. In the current update, 30 novel motif classes have been added and five existing classes have undergone major revisions. The update includes 411 new motif instances mostly focused on cell-cycle regulation, control of the actin cytoskeleton, membrane remodelling and vesicle trafficking pathways, liquid-liquid phase separation and integrin signalling. Many of the newly annotated motif-mediated interactions are targets of pathogenic motif mimicry by viral, bacterial or eukaryotic pathogens, providing invaluable insights into the molecular mechanisms underlying infectious diseases. The current ELM release includes 317 motif classes incorporating 3934 individual motif instances manually curated from 3867 scientific publications. ELM is available at: http://elm.eu.org.
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Affiliation(s)
- Manjeet Kumar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Sushama Michael
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Jesús Alvarado-Valverde
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences
| | - Bálint Mészáros
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Hugo Sámano‐Sánchez
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Zhejiang University School of Medicine, International Campus, Zhejiang University, Haining, China
- Biomedical Sciences, Edinburgh Medical School, The University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - András Zeke
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - Laszlo Dobson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - Tamas Lazar
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Department of Bioengineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Mihkel Örd
- Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Rd, Chelsea, London SW3 6JB, UK
| | - Anurag Nagpal
- Department of Biological Sciences, BITS Pilani, K. K. Birla Goa campus, Zuarinagar, Goa 403726, India
| | - Nazanin Farahi
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Department of Bioengineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Melanie Käser
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Ramya Kraleti
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Justus Liebig University Giessen, Ludwigstraße 23, 35390 Gießen, Germany
| | - Norman E Davey
- Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Rd, Chelsea, London SW3 6JB, UK
| | - Rita Pancsa
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - Lucía B Chemes
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo A. Ugalde”, IIB-UNSAM, IIBIO-CONICET, Universidad Nacional de San Martín, Av. 25 de Mayo y Francia, CP1650 San Martín, Buenos Aires, Argentina
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
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3
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Sorokin II, Vassilenko KS, Terenin IM, Kalinina NO, Agol VI, Dmitriev SE. Non-Canonical Translation Initiation Mechanisms Employed by Eukaryotic Viral mRNAs. Biochemistry (Mosc) 2021; 86:1060-1094. [PMID: 34565312 PMCID: PMC8436584 DOI: 10.1134/s0006297921090042] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/04/2021] [Accepted: 08/04/2021] [Indexed: 12/12/2022]
Abstract
Viruses exploit the translation machinery of an infected cell to synthesize their proteins. Therefore, viral mRNAs have to compete for ribosomes and translation factors with cellular mRNAs. To succeed, eukaryotic viruses adopt multiple strategies. One is to circumvent the need for m7G-cap through alternative instruments for ribosome recruitment. These include internal ribosome entry sites (IRESs), which make translation independent of the free 5' end, or cap-independent translational enhancers (CITEs), which promote initiation at the uncapped 5' end, even if located in 3' untranslated regions (3' UTRs). Even if a virus uses the canonical cap-dependent ribosome recruitment, it can still perturb conventional ribosomal scanning and start codon selection. The pressure for genome compression often gives rise to internal and overlapping open reading frames. Their translation is initiated through specific mechanisms, such as leaky scanning, 43S sliding, shunting, or coupled termination-reinitiation. Deviations from the canonical initiation reduce the dependence of viral mRNAs on translation initiation factors, thereby providing resistance to antiviral mechanisms and cellular stress responses. Moreover, viruses can gain advantage in a competition for the translational machinery by inactivating individual translational factors and/or replacing them with viral counterparts. Certain viruses even create specialized intracellular "translation factories", which spatially isolate the sites of their protein synthesis from cellular antiviral systems, and increase availability of translational components. However, these virus-specific mechanisms may become the Achilles' heel of a viral life cycle. Thus, better understanding of the unconventional mechanisms of viral mRNA translation initiation provides valuable insight for developing new approaches to antiviral therapy.
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Affiliation(s)
- Ivan I Sorokin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Konstantin S Vassilenko
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Ilya M Terenin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Natalia O Kalinina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Vadim I Agol
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Institute of Poliomyelitis, Chumakov Center for Research and Development of Immunobiological Products, Russian Academy of Sciences, Moscow, 108819, Russia
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
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4
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Cieślik M, Bagińska N, Jończyk-Matysiak E, Węgrzyn A, Węgrzyn G, Górski A. Temperate Bacteriophages-The Powerful Indirect Modulators of Eukaryotic Cells and Immune Functions. Viruses 2021; 13:v13061013. [PMID: 34071422 PMCID: PMC8228536 DOI: 10.3390/v13061013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/22/2021] [Accepted: 05/27/2021] [Indexed: 12/11/2022] Open
Abstract
Bacteriophages are natural biological entities that limit the growth and amplification of bacteria. They are important stimulators of evolutionary variability in bacteria, and currently are considered a weapon against antibiotic resistance of bacteria. Nevertheless, apart from their antibacterial activity, phages may act as modulators of mammalian immune responses. In this paper, we focus on temperate phages able to execute the lysogenic development, which may shape animal or human immune response by influencing various processes, including phagocytosis of bacterial invaders and immune modulation of mammalian host cells.
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Affiliation(s)
- Martyna Cieślik
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.C.); (N.B.); (E.J.-M.)
| | - Natalia Bagińska
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.C.); (N.B.); (E.J.-M.)
| | - Ewa Jończyk-Matysiak
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.C.); (N.B.); (E.J.-M.)
| | - Alicja Węgrzyn
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdańsk, Poland;
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland;
| | - Andrzej Górski
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.C.); (N.B.); (E.J.-M.)
- Phage Therapy Unit, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland
- Infant Jesus Hospital, The Medical University of Warsaw, 02-006 Warsaw, Poland
- Correspondence:
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5
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Aylward FO, Moniruzzaman M. ViralRecall-A Flexible Command-Line Tool for the Detection of Giant Virus Signatures in 'Omic Data. Viruses 2021; 13:v13020150. [PMID: 33498458 PMCID: PMC7909515 DOI: 10.3390/v13020150] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/07/2021] [Accepted: 01/18/2021] [Indexed: 01/06/2023] Open
Abstract
Giant viruses are widespread in the biosphere and play important roles in biogeochemical cycling and host genome evolution. Also known as nucleo-cytoplasmic large DNA viruses (NCLDVs), these eukaryotic viruses harbor the largest and most complex viral genomes known. Studies have shown that NCLDVs are frequently abundant in metagenomic datasets, and that sequences derived from these viruses can also be found endogenized in diverse eukaryotic genomes. The accurate detection of sequences derived from NCLDVs is therefore of great importance, but this task is challenging owing to both the high level of sequence divergence between NCLDV families and the extraordinarily high diversity of genes encoded in their genomes, including some encoding for metabolic or translation-related functions that are typically found only in cellular lineages. Here, we present ViralRecall, a bioinformatic tool for the identification of NCLDV signatures in ‘omic data. This tool leverages a library of giant virus orthologous groups (GVOGs) to identify sequences that bear signatures of NCLDVs. We demonstrate that this tool can effectively identify NCLDV sequences with high sensitivity and specificity. Moreover, we show that it can be useful both for removing contaminating sequences in metagenome-assembled viral genomes as well as the identification of eukaryotic genomic loci that derived from NCLDV. ViralRecall is written in Python 3.5 and is freely available on GitHub: https://github.com/faylward/viralrecall.
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6
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Claverie JM. Fundamental Difficulties Prevent the Reconstruction of the Deep Phylogeny of Viruses. Viruses 2020; 12:E1130. [PMID: 33036160 PMCID: PMC7600955 DOI: 10.3390/v12101130] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/01/2020] [Accepted: 10/03/2020] [Indexed: 12/11/2022] Open
Abstract
The extension of virology beyond its traditional medical, veterinary, or agricultural applications, now called environmental virology, has shown that viruses are both the most numerous and diverse biological entities on Earth. In particular, virus isolations from unicellular eukaryotic hosts (heterotrophic and photosynthetic protozoans) revealed numerous viral types previously unexpected in terms of virion structure, gene content, or mode of replication. Complemented by large-scale metagenomic analyses, these discoveries have rekindled interest in the enigma of the origin of viruses, for which a description encompassing all their diversity remains not available. Several laboratories have repeatedly tackled the deep reconstruction of the evolutionary history of viruses, using various methods of molecular phylogeny applied to the few shared "core" genes detected in certain virus groups (e.g., the Nucleocytoviricota). Beyond the practical difficulties of establishing reliable homology relationships from extremely divergent sequences, I present here conceptual arguments highlighting several fundamental limitations plaguing the reconstruction of the deep evolutionary history of viruses, and even more the identification of their unique or multiple origin(s). These arguments also underline the risk of establishing premature high level viral taxonomic classifications. Those limitations are direct consequences of the random mechanisms governing the reductive/retrogressive evolution of all obligate intracellular parasites.
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Affiliation(s)
- Jean-Michel Claverie
- Structural & Genomic Information Laboratory (IGS, UMR 7256), Mediterranean Institute of Microbiology (FR3479), Aix-Marseille University and CNRS, 13288 Marseille, France
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Baxter AA. Stoking the Fire: How Dying Cells Propagate Inflammatory Signalling through Extracellular Vesicle Trafficking. Int J Mol Sci 2020; 21:ijms21197256. [PMID: 33019535 PMCID: PMC7583891 DOI: 10.3390/ijms21197256] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 02/07/2023] Open
Abstract
Communication between dying cells and their environment is a critical process that promotes tissue homeostasis during normal cellular turnover, whilst during disease settings, it can contribute to inflammation through the release of intracellular factors. Extracellular vesicles (EVs) are a heterogeneous class of membrane-bound cell-derived structures that can engage in intercellular communication via the trafficking of bioactive molecules between cells and tissues. In addition to the well-described functions of EVs derived from living cells, the ability of dying cells to release EVs capable of mediating functions on target cells or tissues is also of significant interest. In particular, during inflammatory settings such as acute tissue injury, infection and autoimmunity, the EV-mediated transfer of proinflammatory cargo from dying cells is an important process that can elicit profound proinflammatory effects in recipient cells and tissues. Furthermore, the biogenesis of EVs via unique cell-death-associated pathways has also been recently described, highlighting an emerging niche in EV biology. This review outlines the mechanisms and functions of dying-cell-derived EVs and their ability to drive inflammation during various modes of cell death, whilst reflecting on the challenges and knowledge gaps in investigating this subgenre of extracellular vesicles research.
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Affiliation(s)
- Amy A Baxter
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
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8
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Schulz F, Roux S, Paez-Espino D, Jungbluth S, Walsh DA, Denef VJ, McMahon KD, Konstantinidis KT, Eloe-Fadrosh EA, Kyrpides NC, Woyke T. Giant virus diversity and host interactions through global metagenomics. Nature 2020; 578:432-436. [PMID: 31968354 PMCID: PMC7162819 DOI: 10.1038/s41586-020-1957-x] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 01/09/2020] [Indexed: 12/11/2022]
Abstract
Our current knowledge about nucleocytoplasmic large DNA viruses (NCLDVs) is largely derived from viral isolates that are co-cultivated with protists and algae. Here we reconstructed 2,074 NCLDV genomes from sampling sites across the globe by building on the rapidly increasing amount of publicly available metagenome data. This led to an 11-fold increase in phylogenetic diversity and a parallel 10-fold expansion in functional diversity. Analysis of 58,023 major capsid proteins from large and giant viruses using metagenomic data revealed the global distribution patterns and cosmopolitan nature of these viruses. The discovered viral genomes encoded a wide range of proteins with putative roles in photosynthesis and diverse substrate transport processes, indicating that host reprogramming is probably a common strategy in the NCLDVs. Furthermore, inferences of horizontal gene transfer connected viral lineages to diverse eukaryotic hosts. We anticipate that the global diversity of NCLDVs that we describe here will establish giant viruses-which are associated with most major eukaryotic lineages-as important players in ecosystems across Earth's biomes.
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Affiliation(s)
- Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David Paez-Espino
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sean Jungbluth
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David A Walsh
- Groupe de recherche interuniversitaire en limnologie, Department of Biology, Concordia University, Montréal, Québec, Canada
| | - Vincent J Denef
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Emiley A Eloe-Fadrosh
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nikos C Kyrpides
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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Ressel S, Rosca A, Gordon K, Buck AH. Extracellular RNA in viral-host interactions: Thinking outside the cell. Wiley Interdiscip Rev RNA 2019; 10:e1535. [PMID: 30963709 PMCID: PMC6617787 DOI: 10.1002/wrna.1535] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 03/13/2019] [Accepted: 03/14/2019] [Indexed: 12/15/2022]
Abstract
Small RNAs and their associated RNA interference (RNAi) pathways underpin diverse mechanisms of gene regulation and genome defense across all three kingdoms of life and are integral to virus-host interactions. In plants, fungi and many animals, an ancestral RNAi pathway exists as a host defense mechanism whereby viral double-stranded RNA is processed to small RNAs that enable recognition and degradation of the virus. While this antiviral RNAi pathway is not generally thought to be present in mammals, other RNAi mechanisms can influence infection through both viral- and host-derived small RNAs. Furthermore, a burgeoning body of data suggests that small RNAs in mammals can function in a non-cell autonomous manner to play various roles in cell-to-cell communication and disease through their transport in extracellular vesicles. While vesicular small RNAs have not been proposed as an antiviral defense pathway per se, there is increasing evidence that the export of host- or viral-derived RNAs from infected cells can influence various aspects of the infection process. This review discusses the current knowledge of extracellular RNA functions in viral infection and the technical challenges surrounding this field of research. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA in Disease and Development > RNA in Disease Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action.
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Affiliation(s)
- Sarah Ressel
- Institute of Immunology and Infection Research, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Adelina Rosca
- Department of VirologyCarol Davila University of Medicine and PharmacyBucharestRomania
| | - Katrina Gordon
- Institute of Immunology and Infection Research, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Amy H. Buck
- Institute of Immunology and Infection Research, School of Biological SciencesUniversity of EdinburghEdinburghUK
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10
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Abstract
The Nucleocytoplasmic Large DNA Viruses (NCLDV) of eukaryotes (proposed order "Megavirales") comprise an expansive group of eukaryotic viruses that consists of the families Poxviridae, Asfarviridae, Iridoviridae, Ascoviridae, Phycodnaviridae, Marseilleviridae, Pithoviridae, and Mimiviridae, as well as Pandoraviruses, Molliviruses, and Faustoviruses that so far remain unaccounted by the official virus taxonomy. All these viruses have double-stranded DNA genomes that range in size from about 100 kilobases (kb) to more than 2.5 megabases. The viruses with genomes larger than 500kb are informally considered "giant," and the largest giant viruses surpass numerous bacteria and archaea in both particle and genome size. The discovery of giant viruses has been highly unexpected and has changed the perception of viral size and complexity, and even, arguably, the entire concept of a virus. Given that giant viruses encode multiple proteins that are universal among cellular life forms and are components of the translation system, the quintessential cellular molecular machinery, attempts have been made to incorporate these viruses in the evolutionary tree of cellular life. Moreover, evolutionary scenarios of the origin of giant viruses from a fourth, supposedly extinct domain of cellular life have been proposed. However, despite all the differences in the genome size and gene repertoire, the NCLDV can be confidently defined as monophyletic group, on the strength of the presence of about 40 genes that can be traced back to their last common ancestor. Using several most strongly conserved genes from this ancestral set, a well-resolved phylogenetic tree of the NCLDV was built and employed as the scaffold to reconstruct the history of gene gain and loss throughout the course of the evolution of this group of viruses. This reconstruction reveals extremely dynamic evolution that involved extensive gene gain and loss in many groups of viruses and indicates that giant viruses emerged independently in several clades of the NCLDV. Thus, these giants of the virus world evolved repeatedly from smaller and simpler viruses, rather than from a fourth domain of cellular life, and captured numerous genes, including those for translation system components, from eukaryotes, along with some bacterial genes. Even deeper evolutionary reconstructions reveal apparent links between the NCLDV and smaller viruses of eukaryotes, such as adenoviruses, and ultimately, derive all these viruses from tailless bacteriophages.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States.
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
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Abstract
Prions are proteins that can self-propagate, leading to the misfolding of proteins. In addition to the previously demonstrated pathogenic roles of prions during the development of different mammalian diseases, including neurodegenerative diseases, they have recently been shown to represent an important functional component in many prokaryotic and eukaryotic organisms and bacteriophages, confirming the previously unexplored important regulatory and functional roles. However, an in-depth analysis of these domains in eukaryotic viruses has not been performed. Here, we examined the presence of prion-like proteins in eukaryotic viruses that play a primary role in different ecosystems and that are associated with emerging diseases in humans. We identified relevant functional associations in different viral processes and regularities in their presence at different taxonomic levels. Using the prion-like amino-acid composition computational algorithm, we detected 2679 unique putative prion-like domains within 2,742,160 publicly available viral protein sequences. Our findings indicate that viral prion-like proteins can be found in different viruses of insects, plants, mammals, and humans. The analysis performed here demonstrated common patterns in the distribution of prion-like domains across viral orders and families, and revealed probable functional associations with different steps of viral replication and interaction with host cells. These data allow the identification of the viral prion-like proteins as potential novel regulators of viral infections.
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Affiliation(s)
- George Tetz
- Human Microbiology Institute, New York, NY, 10027, USA.
| | - Victor Tetz
- Human Microbiology Institute, New York, NY, 10027, USA
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12
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Gouw M, Michael S, Sámano-Sánchez H, Kumar M, Zeke A, Lang B, Bely B, Chemes LB, Davey NE, Deng Z, Diella F, Gürth CM, Huber AK, Kleinsorg S, Schlegel LS, Palopoli N, Roey KV, Altenberg B, Reményi A, Dinkel H, Gibson TJ. The eukaryotic linear motif resource - 2018 update. Nucleic Acids Res 2018; 46:D428-D434. [PMID: 29136216 PMCID: PMC5753338 DOI: 10.1093/nar/gkx1077] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 10/17/2017] [Accepted: 10/23/2017] [Indexed: 11/14/2022] Open
Abstract
Short linear motifs (SLiMs) are protein binding modules that play major roles in almost all cellular processes. SLiMs are short, often highly degenerate, difficult to characterize and hard to detect. The eukaryotic linear motif (ELM) resource (elm.eu.org) is dedicated to SLiMs, consisting of a manually curated database of over 275 motif classes and over 3000 motif instances, and a pipeline to discover candidate SLiMs in protein sequences. For 15 years, ELM has been one of the major resources for motif research. In this database update, we present the latest additions to the database including 32 new motif classes, and new features including Uniprot and Reactome integration. Finally, to help provide cellular context, we present some biological insights about SLiMs in the cell cycle, as targets for bacterial pathogenicity and their functionality in the human kinome.
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Affiliation(s)
- Marc Gouw
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Sushama Michael
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Hugo Sámano-Sánchez
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Manjeet Kumar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - András Zeke
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Benjamin Lang
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Benoit Bely
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Lucía B Chemes
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires CP 1405, Argentina
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires CP 2160, Argentina
- Instituto de Investigaciones Biotecnoltógicas, Universidad Nacional de General San Martín, IIB-INTECH-CONICET, San Martín, Buenos Aires CP 1650, Argentina
| | - Norman E Davey
- UCD School of Medicine & Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Ziqi Deng
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Francesca Diella
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | | | | | | | | | - Nicolás Palopoli
- Department of Science and Technology, Universidad Nacional de Quilmes, CONICET, Bernal B1876BXD, Buenos Aires, Argentina
| | - Kim V Roey
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Brigitte Altenberg
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Attila Reményi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Holger Dinkel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Leibniz-Institute on Aging, Fritz Lipmann Institute (FLI), Jena D-07745, Germany
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
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13
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Wang L, Zhao Y, Chen Y, Wang D. The effect of three novel feature extraction methods on the prediction of the subcellular localization of multi-site virus proteins. Bioengineered 2018; 9:196-202. [PMID: 28886267 PMCID: PMC5972939 DOI: 10.1080/21655979.2017.1373536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/05/2017] [Indexed: 11/08/2022] Open
Abstract
Experimental methods play a crucial role in identifying the subcellular localization of proteins and building high-quality databases. However, more efficient, automated computational methods are required to predict the subcellular localization of proteins on a large scale. Various efficient feature extraction methods have been proposed to predict subcellular localization, but challenges remain. In this paper, three novel feature extraction methods are established to improve multi-site prediction. The first novel feature extraction method utilizes repetitive information via moving windows based on a dipeptide pseudo amino acid composition method (R-Dipeptide). The second novel feature extraction method utilizes the impact of each amino acid residue on its following residues based on pseudo amino acids (I-PseAAC). The third novel feature extraction method provides local information about protein sequences that reflects the strength of the physicochemical properties of residues (PseAAC2). The multi-label k-nearest neighbor algorithm (MLKNN) is used to predict the subcellular localization of multi-site virus proteins. The best overall accuracy values of R-Dipeptide, I-PseAAC, and PseAAC2 when applied to dataset S from Virus-mPloc are 59.92%, 59.13%, and 57.94% respectively.
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Affiliation(s)
- Lei Wang
- School of Information Science and Engineering, University of Jinan, Jinan, China
- Shandong Provincial Key Laboratory of Network Based Intelligent Computing, Jinan, China
| | - Yaou Zhao
- School of Information Science and Engineering, University of Jinan, Jinan, China
- Shandong Provincial Key Laboratory of Network Based Intelligent Computing, Jinan, China
| | - Yuehui Chen
- School of Information Science and Engineering, University of Jinan, Jinan, China
- Shandong Provincial Key Laboratory of Network Based Intelligent Computing, Jinan, China
| | - Dong Wang
- School of Information Science and Engineering, University of Jinan, Jinan, China
- Shandong Provincial Key Laboratory of Network Based Intelligent Computing, Jinan, China
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14
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Abstract
Background: Virus discovery using high-throughput next-generation sequencing has become more commonplace. However, although analysis of deep next-generation sequencing data allows us to identity potential pathogens, the entire analytical procedure requires competency in the bioinformatics domain, which includes implementing proper software packages and preparing prerequisite databases. Simple and user-friendly bioinformatics pipelines are urgently required to obtain complete viral genome sequences from metagenomic data. Results: This manuscript presents a pipeline, drVM (detect and reconstruct known viral genomes from metagenomes), for rapid viral read identification, genus-level read partition, read normalization, de novo assembly, sequence annotation, and coverage profiling. The first two procedures and sequence annotation rely on known viral genomes as a reference database. drVM was validated via the analysis of over 300 sequencing runs generated by Illumina and Ion Torrent platforms to provide complete viral genome assemblies for a variety of virus types including DNA viruses, RNA viruses, and retroviruses. drVM is available for free download at: https://sourceforge.net/projects/sb2nhri/files/drVM/ and is also assembled as a Docker container, an Amazon machine image, and a virtual machine to facilitate seamless deployment. Conclusions: drVM was compared with other viral detection tools to demonstrate its merits in terms of viral genome completeness and reduced computation time. This substantiates the platform's potential to produce prompt and accurate viral genome sequences from clinical samples.
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15
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Abstract
Ubiquitin E3 ligases control every aspect of eukaryotic biology by promoting protein ubiquitination and degradation. At the end of a three-enzyme cascade, ubiquitin ligases mediate the transfer of ubiquitin from an E2 ubiquitin-conjugating enzyme to specific substrate proteins. Early investigations of E3s of the RING (really interesting new gene) and HECT (homologous to the E6AP carboxyl terminus) types shed light on their enzymatic activities, general architectures, and substrate degron-binding modes. Recent studies have provided deeper mechanistic insights into their catalysis, activation, and regulation. In this review, we summarize the current progress in structure-function studies of ubiquitin ligases as well as exciting new discoveries of novel classes of E3s and diverse substrate recognition mechanisms. Our increased understanding of ubiquitin ligase function and regulation has provided the rationale for developing E3-targeting therapeutics for the treatment of human diseases.
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Affiliation(s)
- Ning Zheng
- Howard Hughes Medical Institute and Department of Pharmacology, University of Washington, Seattle, Washington 98195; ,
| | - Nitzan Shabek
- Howard Hughes Medical Institute and Department of Pharmacology, University of Washington, Seattle, Washington 98195; ,
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16
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Boltovets RM, Nesterova NV. [SURFACE PLASMON RESONANCE: APPROACHES AND PERSPECTIVES OF APPLICATION FOR VIRUS-SPECIFIC INTERACTIONS INVESTIGATIONS]. Mikrobiol Z 2016; 78:109-124. [PMID: 30653885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In the review the published data on the use of surface plasmon resonance methods for the study of individual viral proteins as well as intact viruses are reviewed. . The principles of the method, its benefits and peculiarities of its use to study viruses are introduced. Particular attention is paid to the requirements to the sensor surface and the methods of its modification, including the formation self assembled monolayers of amphiphilic organic molecules containing functional groups to connect to the surface, creating of the intermediate protective thiocyanate layer between protein and metal, forming of the favorable microenvironment using dextran hydrogels around biomolecules, immobilization of proteins on the surface of the sensor using streptavidin-biotin system, use of protein A Staphylococcus aureus as an sensitive element of the sensory system structure. The approaches to enhance the signal used in virological studies, including the use of labeled antibodies, using competitive analysis for the detection of small molecules, the formation of a complex directly on the sensor surface, and immobilization on the surface of the sensor previously obtained complex receptor-analyte are considered. The conclusion is that the SPR method contains many potential opportunities to study various aspects of the interaction of viruses with specific agents, and changes in the structure of viruses caused by various external factors.
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17
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Abstract
In this article, we provide an overview of translational arrest in eukaryotic cells in response to stress and the tactics used specifically by alphaherpesviruses to overcome translational arrest. One consequence of translational arrest is the formation of cytoplasmic compartments called stress granules (SGs). Many viruses target SGs for disruption and/or modification, including the alphaherpesvirus herpes simplex virus type 2 (HSV-2). Recently, it was discovered that HSV-2 disrupts SG formation early after infection via virion host shutoff protein (vhs), an endoribonuclease that is packaged within the HSV-2 virion. We review this discovery and discuss the insights it has provided into SG biology as well as its potential significance in HSV-2 infection. A model for vhs-mediated disruption of SG formation is presented.
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Affiliation(s)
- Renée L Finnen
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Bruce W Banfield
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
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18
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Abstract
HIV replication requires nuclear export of unspliced and singly spliced viral transcripts. Although a unique RNA structure has been proposed for the Rev-response element (RRE) responsible for viral mRNA export, how it recruits multiple HIV Rev proteins to form an export complex has been unclear. We show here that initial binding of Rev to the RRE triggers RNA tertiary structural changes, enabling further Rev binding and the rapid formation of a viral export complex. Analysis of the Rev-RRE assembly pathway using SHAPE-Seq and small-angle X-ray scattering (SAXS) reveals two major steps of Rev-RRE complex formation, beginning with rapid Rev binding to a pre-organized region presenting multiple Rev binding sites. This step induces long-range remodeling of the RNA to expose a cryptic Rev binding site, enabling rapid assembly of additional Rev proteins into the RNA export complex. This kinetic pathway may help maintain the balance between viral replication and maturation.DOI: http://dx.doi.org/10.7554/eLife.03656.001.
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Affiliation(s)
- Yun Bai
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Akshay Tambe
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Kaihong Zhou
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States Department of Chemistry, University of California, Berkeley, Berkeley, United States Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
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19
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Bilkova E, Forstova J, Abrahamyan L. Coat as a dagger: the use of capsid proteins to perforate membranes during non-enveloped DNA viruses trafficking. Viruses 2014; 6:2899-937. [PMID: 25055856 PMCID: PMC4113798 DOI: 10.3390/v6072899] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 07/09/2014] [Accepted: 07/14/2014] [Indexed: 01/24/2023] Open
Abstract
To get access to the replication site, small non-enveloped DNA viruses have to cross the cell membrane using a limited number of capsid proteins, which also protect the viral genome in the extracellular environment. Most of DNA viruses have to reach the nucleus to replicate. The capsid proteins involved in transmembrane penetration are exposed or released during endosomal trafficking of the virus. Subsequently, the conserved domains of capsid proteins interact with cellular membranes and ensure their efficient permeabilization. This review summarizes our current knowledge concerning the role of capsid proteins of small non-enveloped DNA viruses in intracellular membrane perturbation in the early stages of infection.
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Affiliation(s)
- Eva Bilkova
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicna 5, 12844, Prague 2, Czech Republic.
| | - Jitka Forstova
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicna 5, 12844, Prague 2, Czech Republic.
| | - Levon Abrahamyan
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicna 5, 12844, Prague 2, Czech Republic.
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20
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Krupovic M, Koonin EV. Evolution of eukaryotic single-stranded DNA viruses of the Bidnaviridae family from genes of four other groups of widely different viruses. Sci Rep 2014; 4:5347. [PMID: 24939392 PMCID: PMC4061559 DOI: 10.1038/srep05347] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 05/30/2014] [Indexed: 12/20/2022] Open
Abstract
Single-stranded (ss)DNA viruses are extremely widespread, infect diverse hosts from all three domains of life and include important pathogens. Most ssDNA viruses possess small genomes that replicate by the rolling-circle-like mechanism initiated by a distinct virus-encoded endonuclease. However, viruses of the family Bidnaviridae, instead of the endonuclease, encode a protein-primed type B DNA polymerase (PolB) and hence break this pattern. We investigated the provenance of all bidnavirus genes and uncover an unexpected turbulent evolutionary history of these unique viruses. Our analysis strongly suggests that bidnaviruses evolved from a parvovirus ancestor from which they inherit a jelly-roll capsid protein and a superfamily 3 helicase. The radiation of bidnaviruses from parvoviruses was probably triggered by integration of the ancestral parvovirus genome into a large virus-derived DNA transposon of the Polinton (polintovirus) family resulting in the acquisition of the polintovirus PolB gene along with terminal inverted repeats. Bidnavirus genes for a receptor-binding protein and a potential novel antiviral defense modulator are derived from dsRNA viruses (Reoviridae) and dsDNA viruses (Baculoviridae), respectively. The unusual evolutionary history of bidnaviruses emphasizes the key role of horizontal gene transfer, sometimes between viruses with completely different genomes but occupying the same niche, in the emergence of new viral types.
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Affiliation(s)
- Mart Krupovic
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Department of Microbiology, Paris 75015, France
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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21
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Abstract
Sialic acid linked to glycoproteins and gangliosides is used by many viruses as a receptor for cell entry. These viruses include important human and animal pathogens, such as influenza, parainfluenza, mumps, corona, noro, rota, and DNA tumor viruses. Attachment to sialic acid is mediated by receptor binding proteins that are constituents of viral envelopes or exposed at the surface of non-enveloped viruses. Some of these viruses are also equipped with a neuraminidase or a sialyl-O-acetyl-esterase. These receptor-destroying enzymes promote virus release from infected cells and neutralize sialic acid-containing soluble proteins interfering with cell surface binding of the virus. Variations in the receptor specificity are important determinants for host range, tissue tropism, pathogenicity, and transmissibility of these viruses.
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Affiliation(s)
| | - Philippe Delannoy
- Lille University of Science and Technology, Villeneuve d'Ascq Cedex, France
| | - Mark von Itzstein
- Institute for Glycomics, Griffith University, Southport, Queensland Australia
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22
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Abstract
This chapter describes the protocol for the preparation of recombinant adenoviruses and infection of target cells to transiently express G protein-coupled receptors (GPCRs) or other proteins of interest. Adenoviruses are non-enveloped viruses containing a linear double-stranded DNA genome. Their life cycle does not normally involve integration into the host genome, rather they replicate as episomal -elements in the nucleus of the host cell, and consequently there is no risk of insertional mutagenesis. Up to 30 kb out of the 35 kb of the wild-type adenovirus genome can be replaced by foreign DNA. Adenoviral vectors are very efficient in transducing target cells in vitro and in vivo and can be produced at high titers (>10¹¹/mL). The viral infection has a number of useful features: (1) the efficiency of gene transduction is very high (up to 100% in sensitive cells); (2) the infection is easy and does not physically alter the cell membrane for gene transduction; (3) it is possible to infect cells that are resistant to transfection with plasmids (including nondividing cells); and (4) the viral vectors can be used for infection in vivo (including gene therapy) and can potentially be targeted cell-specifically.
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Affiliation(s)
- Antonio Porcellini
- Department of Physiology and Pharmacology “Vittorio Espèamer”, Piazzale Aldo Moro, Rome, Italy
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23
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Affiliation(s)
- Sandra K Weller
- Department of Molecular, Microbial and Structural Biology, The University of Connecticut Health Center, Farmington, CT, USA.
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24
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Levin A, Hayouka Z, Friedler A, Loyter A. Over-expression of the HIV-1 Rev promotes death of nondividing eukaryotic cells. Virus Genes 2010; 40:341-6. [PMID: 20151187 DOI: 10.1007/s11262-010-0458-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Accepted: 01/30/2010] [Indexed: 10/19/2022]
Abstract
Expression of the human immunodeficiency virus type 1 (HIV-1) Rev protein is essential for completion of the viral life cycle. Rev mediates nuclear export of partially spliced and unspliced viral transcripts and therefore bears a nuclear localization signal (NLS) as well as a nuclear export signal (NES), which allow its nucleocytoplasmic shuttling. Attempts to express the wild-type Rev protein in eukaryotic human cultured cells have encountered difficulties and so far have failed. Here we show that accumulation of Rev, which occurs in nondividing Rev-expressing cells or when such cells reach confluency, results in death of these cells. Cell death was also promoted by addition of a cell permeable peptide bearing the Rev-NES sequence, but not by the Rev-NLS peptide. Our results probably indicate that binding of excess amounts of the Rev protein or the NES peptide to the exportin receptor CRM1 results in cells' death.
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Affiliation(s)
- Aviad Levin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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25
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Abstract
Viruses are adept at evolving or co-opting genomic elements that allow them to maximize their replication potential in the infected host. This evolutionary plasticity makes viruses an invaluable system to identify new mechanisms used not only by viruses but also by vertebrate cells to modulate gene expression. Here, I discuss the identification and characterization of viral mRNA structures and noncoding RNAs that have led to important insights into the molecular mechanisms of eukaryotic cells.
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Affiliation(s)
- Bryan R Cullen
- Department of Molecular Genetics & Microbiology, Center for Virology, Duke University Medical Center, Durham, NC 27710, USA.
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26
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Abstract
Eukaryotic mRNAs are in a dynamic equilibrium between different subcellular locations. Translating mRNAs can be found in polysomes, mRNAs stalled in translation initiation accumulate in stress granules and mRNAs targeted for degradation or translation repression can accumulate in P bodies. Partitioning of mRNAs between polysomes, stress granules, and P bodies affects rates of translation and mRNA degradation. Host proteins within P bodies and stress granules can enhance or limit viral infection, and some viral RNAs and proteins accumulate in P bodies and/or stress granules. Thus, an important interplay among P bodies, stress granules, and viral life cycles is beginning to emerge.
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Affiliation(s)
- Carla J. Beckham
- Department of Cell Biology and Anatomy, The University of Arizona, Tucson, Arizona, 85721-0206, USA
| | - Roy Parker
- Department of Molecular and Cellular Biology and Howard Hughes Medical Institute, The University of Arizona, Tucson, Arizona, 85721-0206, USA
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27
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Filée J, Chandler M. Convergent mechanisms of genome evolution of large and giant DNA viruses. Res Microbiol 2008; 159:325-31. [PMID: 18572389 DOI: 10.1016/j.resmic.2008.04.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Revised: 04/17/2008] [Accepted: 04/17/2008] [Indexed: 11/15/2022]
Abstract
We have taken advantage of the availability of the genome sequences of a collection of large and giant viruses infecting bacteria (T4 family) and eukaryotes (NCLDV group) to assess some of the evolutionary forces which might have shaped their genomes. Despite having apparently different ancestors, these two groups of viruses are affected by convergent evolutionary forces. Both types of virus probably originated from a simple and ancient viral ancestor with a small subset of 30-35 genes encoding replication and structural proteins. The genome size and diversity of the descendants most likely grew progressively by (i) lineage-specific gene duplications, (ii) lateral gene transfers of cellular genes and (iii) accretion of diverse families of mobile genetic elements. These results argue against the hypothesis that giant viruses derive from a regressive cell.
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Affiliation(s)
- Jonathan Filée
- Laboratoire Evolution, Génomes et Spéciation, CNRS UPR 9034, Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France.
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28
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Vesteg M, Krajcovic J. On the origin of eukaryotic cytoskeleton. Riv Biol 2008; 101:109-118. [PMID: 18600633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The origin of eukaryote-specific cytoskeletal proteins is an issue which is closely related to the origin of the domain Eukarya. As nearly all of these proteins are not found in prokaryotes, the prokaryotic origin of eukaryotic cytoskeletal network suggested by most models is questionable. Eukaryotic cytoskeletal proteins might descend from subpopulations of pre-cells co-existing with Bacteria and Archaea prior to the origin of eukaryotes. The pre-karyote (the host for a-proteobacterial ancestors of mitochondria) might have already possessed eukaryotic-like cytoskeleton. A possible role for viruses in the origin of eukaryotic cytoskeletal proteins is discussed. Viruses parasitizing on pre-cells and/or on the pre-karyote might have themselves used several eukaryotic-like cytoskeletal proteins for segregation and packing of their genomes.
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Affiliation(s)
- Matej Vesteg
- Institute of Cell Biology, Faculty of Natural Sciences, Comenius University, Mlynska dolina, 842 15 Bratislava, Slovakia.
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29
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Beutler B, Eidenschenk C, Crozat K, Imler JL, Takeuchi O, Hoffmann JA, Akira S. Genetic analysis of resistance to viral infection. Nat Rev Immunol 2007; 7:753-66. [PMID: 17893693 DOI: 10.1038/nri2174] [Citation(s) in RCA: 150] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
As machines that reprogramme eukaryotic cells to suit their own purposes, viruses present a difficult problem for multicellular hosts, and indeed, have become one of the central pre-occupations of the immune system. Unable to permanently outpace individual viruses in an evolutionary footrace, higher eukaryotes have evolved broadly active mechanisms with which to sense viruses and suppress their proliferation. These mechanisms have recently been elucidated by a combination of forward and reverse genetic methods. Some of these mechanisms are clearly ancient, whereas others are relatively new. All are remarkably adept at discriminating self from non-self, and allow the host to cope with what might seem an impossible predicament.
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Affiliation(s)
- Bruce Beutler
- Department of Genetics, The Scripps Research Institute, IMM-3-1, 10550 N. Torrey Pines Road, La Jolla, California 92037, USA.
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30
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Abstract
Hepatitis C virus (HCV) has been recognized as a major cause of chronic liver diseases worldwide. Molecular studies of the virus became possible with the successful cloning of its genome in 1989. Although much work remains to be done regarding early and late stages of the HCV life cycle, significant progress has been made with respect to the molecular biology of HCV, especially the viral protein processing and the genome replication. This review summarizes our current understanding of genomic organization of HCV, features of the viral protein characteristics, and the viral life cycle.
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Affiliation(s)
- Tetsuro Suzuki
- Department of Virology II, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
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31
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Abstract
There are numerous ways that endocytic cargo molecules may be internalized from the surface of eukaryotic cells. In addition to the classical clathrin-dependent mechanism of endocytosis, several pathways that do not use a clathrin coat are emerging. These pathways transport a diverse array of cargoes and are sometimes hijacked by bacteria and viruses to gain access to the host cell. Here, we review our current understanding of various clathrin-independent mechanisms of endocytosis and propose a classification scheme to help organize the data in this complex and evolving field.
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Affiliation(s)
- Satyajit Mayor
- National Centre for Biological Sciences, UAS-GKVK Campus, Bangalore 560065, India.
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33
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Sherer NM, Lehmann MJ, Jimenez-Soto LF, Horensavitz C, Pypaert M, Mothes W. Retroviruses can establish filopodial bridges for efficient cell-to-cell transmission. Nat Cell Biol 2007; 9:310-5. [PMID: 17293854 PMCID: PMC2628976 DOI: 10.1038/ncb1544] [Citation(s) in RCA: 362] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Accepted: 01/09/2007] [Indexed: 11/08/2022]
Abstract
The spread of retroviruses between cells is estimated to be 2-3 orders of magnitude more efficient when cells can physically interact with each other. The underlying mechanism is largely unknown, but transfer is believed to occur through large-surface interfaces, called virological or infectious synapses. Here, we report the direct visualization of cell-to-cell transmission of retroviruses in living cells. Our results reveal a mechanism of virus transport from infected to non-infected cells, involving thin filopodial bridges. These filopodia originate from non-infected cells and interact, through their tips, with infected cells. A strong association of the viral envelope glycoprotein (Env) in an infected cell with the receptor molecules in a target cell generates a stable bridge. Viruses then move along the outer surface of the filopodial bridge toward the target cell. Our data suggest that retroviruses spread by exploiting an inherent ability of filopodia to transport ligands from cell to cell.
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Affiliation(s)
- Nathan M. Sherer
- Section of Microbial Pathogenesis, Yale University School of Medicine, 295 Congress Ave, New Haven, CT 06536, USA
| | - Maik J. Lehmann
- Section of Microbial Pathogenesis, Yale University School of Medicine, 295 Congress Ave, New Haven, CT 06536, USA
| | - Luisa F. Jimenez-Soto
- Section of Microbial Pathogenesis, Yale University School of Medicine, 295 Congress Ave, New Haven, CT 06536, USA
| | - Christina Horensavitz
- Department of Cell Biology, Yale University School of Medicine, 295 Congress Ave, New Haven, CT 06536, USA
| | - Marc Pypaert
- Department of Cell Biology, Yale University School of Medicine, 295 Congress Ave, New Haven, CT 06536, USA
| | - Walther Mothes
- Section of Microbial Pathogenesis, Yale University School of Medicine, 295 Congress Ave, New Haven, CT 06536, USA
- Correspondence should be addressed to W.M. (e-mail: )
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34
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Abstract
Post-translational modification of proteins and peptides by ubiquitin, a highly evolutionarily conserved 76 residue protein, and ubiquitin-like modifiers has emerged as a major regulatory mechanism in various cellular activities. Eukaryotic viruses are known to modulate protein ubiquitination to their advantage in various ways. At the same time, the evidence for the importance of deubiquitination as a viral target also is growing. This review centers on known viral interactions with protein deubiquitination, on viral enzymes for which deubiquitinating activities were recently demonstrated, and on the roles of viral ubiquitin-like sequences.
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Affiliation(s)
- Holger A Lindner
- Biotechnology Research Institute, National Research Council of Canada, 6100 Avenue Royalmount, Montreal, Quebec, Canada H4P 2R2.
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35
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Abstract
All replication-competent retroviruses contain three main reading frames, gag, pol and env, which are used for the synthesis of structural proteins, enzymes and envelope proteins respectively. Complex retroviruses, such as lentiviruses, also code for regulatory and accessory proteins that have essential roles in viral replication. The concerted expression of these genes ensures the efficient polypeptide production required for the assembly and release of new infectious progeny virions. Retroviral protein synthesis takes place in the cytoplasm and depends exclusively on the translational machinery of the host infected cell. Therefore, not surprisingly, retroviruses have developed RNA structures and strategies to promote robust and efficient expression of viral proteins in a competitive cellular environment.
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Affiliation(s)
- Laurent Balvay
- Ecole Normale Supérieure de Lyon, Unité de Virologie Humaine, IFR 128, Lyon, F-69364 France
- Inserm, U758, Lyon, F-69364 France
| | - Marcelo Lopez Lastra
- Laboratorio de Virología Molecular, Facultad de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Bruno Sargueil
- Centre de Génétique, Moléculaire, CNRS UPR 2167, Avenue de la terrasse, Gif sur Yvette, 91190 France
| | - Jean-Luc Darlix
- Ecole Normale Supérieure de Lyon, Unité de Virologie Humaine, IFR 128, Lyon, F-69364 France
- Inserm, U758, Lyon, F-69364 France
| | - Théophile Ohlmann
- Ecole Normale Supérieure de Lyon, Unité de Virologie Humaine, IFR 128, Lyon, F-69364 France
- Inserm, U758, Lyon, F-69364 France
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36
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Abstract
Advances in genomics have stimulated new hypotheses that DNA viruses were the origin of the eukaryotic cell nucleus, and that they should be considered as living things. The origins of viruses are shrouded in mystery, but advances in genomics and the discovery of highly complex giant DNA viruses have stimulated new hypotheses that DNA viruses were involved in the emergence of the eukaryotic cell nucleus, and that they are worthy of being considered as living organisms.
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Affiliation(s)
- Jean-Michel Claverie
- Structural and Genomic Information Laboratory, CNRS-UPR2589, IBSM, Parc Scientifique de Luminy, 163 Avenue de Luminy, case 934, Marseille 13288, cedex 9, France.
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37
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Abstract
MicroRNAs (miRNAs) are a new class of 18–23 nucleotide long non-coding RNAs that play critical roles in a wide spectrum of biological processes. Recent reports also throw light into the role of microRNAs as critical effectors in the intricate host-pathogen interaction networks. Evidence suggests that both virus and hosts encode microRNAs. The exclusive dependence of viruses on the host cellular machinery for their propagation and survival also make them highly susceptible to the vagaries of the cellular environment like small RNA mediated interference. It also gives the virus an opportunity to fight and/or modulate the host to suite its needs. Thus the range of interactions possible through miRNA-mRNA cross-talk at the host-pathogen interface is large. These interactions can be further fine-tuned in the host by changes in gene expression, mutations and polymorphisms. In the pathogen, the high rate of mutations adds to the complexity of the interaction network. Though evidence regarding microRNA mediated cross-talk in viral infections is just emerging, it offers an immense opportunity not only to understand the intricacies of host-pathogen interactions, and possible explanations to viral tropism, latency and oncogenesis, but also to develop novel biomarkers and therapeutics.
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Affiliation(s)
- Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
| | - Manoj Hariharan
- GN Ramachandran Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
| | - Souvik Maiti
- GN Ramachandran Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
| | - Beena Pillai
- GN Ramachandran Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
| | - Samir K Brahmachari
- GN Ramachandran Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
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38
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Abstract
Over the millennia, pathogens have coevolved with their hosts and acquired the ability to intercept, disrupt, mimic, and usurp numerous signaling pathways of those hosts. The study of host/pathogen interactions thus not only teaches us about the intricate biology of these parasitic invaders but also provides interesting insights into basic cellular processes both at the level of the individual cell and more globally throughout the organism. Host/pathogen relationships also provide insights into the evolutionary forces that shape biological diversity. Here we review a few recent examples of how viruses, bacteria, and parasites manipulate tyrosine kinase-mediated and Rho guanosine triphosphatase-mediated signaling pathways of their hosts to achieve efficient entry, replication, and exit during their infectious cycles.
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Affiliation(s)
- Sylvia Münter
- Department of Parasitology, Hygiene Institute, University of Heidelberg Medical School, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
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39
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Abstract
Cullin RING ubiquitin ligases (CRULs) are found in all eukaryotes and play an essential role in targeting proteins for ubiquitin-mediated destruction, thus regulating a plethora of cellular processes. Viruses manipulate CRULs by redirecting this destruction machinery to eliminate unwanted host cell proteins, thus allowing viruses to slip past host immune barriers. Depending on the host organism, virus-modified CRULs can perform an amazing range of tasks, including the elimination of crucial signal transduction molecules in the human interferon pathway and suppression of virus-induced gene silencing in plants. This Perspective summarizes recent advances in our understanding of how viral proteins manipulate the function of CRULs.
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Affiliation(s)
- Michele Barry
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2H7, Canada
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40
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Kitajima M, Hamazaki H, Miyano-Kurosaki N, Takaku H. Characterization of baculovirus Autographa californica multiple nuclear polyhedrosis virus infection in mammalian cells. Biochem Biophys Res Commun 2006; 343:378-84. [PMID: 16545777 DOI: 10.1016/j.bbrc.2006.02.167] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2006] [Accepted: 02/27/2006] [Indexed: 11/20/2022]
Abstract
The baculovirus Autographa californica multiple nuclear polyhedrosis virus (AcMNPV) is used as a vector in many gene therapy studies. Wild-type AcMNPV infects many mammalian cell types in vitro, but does not replicate. We investigated the dynamics of AcMNPV genomic DNA in infected mammalian cells and used flow cytometric analysis to demonstrate that recombinant baculovirus containing a cytomegalovirus immediate early promoter/enhancer with green fluorescent protein (GFP) expressed high levels of GFP in Huh-7 cells, but not B16, Raw264.7, or YAC-1 cells. The addition of butyrate, a deacetylase inhibitor, markedly enhanced the percentage of GFP-expressing Huh-7 and B16 cells, but not Raw264.7 and YAC-1 cells. The addition of 5-aza-2'-deoxycytidine, a DNA methylation inhibitor, had no enhancing effect. Polymerase chain reaction analysis using AcMNPV-gp64-specific primers indicated that AcMNPV infected not only Huh-7 and B16 cells, but also Raw264.7 and YAC-1 cells in vitro. The genomic DNA was detected in Huh-7 and B16 cells 96 h after infection. Genomic AcMNPV DNA in YAC-1 cells was not transported to the nucleus. Luciferase assay indicated that AcMNPV p35 gene mRNA and p35 promoter activity were clearly expressed only in Huh-7 and B16 cells. These results suggest that viral genomic DNA expression is restricted by different host cell factors, such as degradation, deacetylation, and inhibition of nuclear transport, depending on the mammalian cell type.
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Affiliation(s)
- Masayuki Kitajima
- Department of Life and Environmental Sciences, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
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41
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Friedrich TD, Bedner E, Darzynkiewicz Z, Lehman JM. Distinct patterns of MCM protein binding in nuclei of S phase and rereplicating SV40-infected monkey kidney cells. Cytometry A 2006; 68:10-8. [PMID: 16184610 DOI: 10.1002/cyto.a.20185] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
BACKGROUND Simian Virus 40 (SV40) infection of growth-arrested monkey kidney cells stimulates S phase entry and the continued synthesis of both viral and cellular DNA. Infected cells can attain total DNA contents as high as DNA Index, DI = 5.0-6.0 (10-12C), with host cell DNA representing 70-80% of the total. In this study, SV40-infected and uninfected control cells were compared to determine whether continued DNA replication beyond DI = 2.0 was associated with rebinding of the minichromosome maintenance (MCM) hexamer, the putative replicative helicase, to chromatin. METHOD Laser scanning cytometry was used to measure the total expression per cell and the chromatin/matrix-association of two MCM subunits in relation to DNA content. RESULTS MCM2 and MCM3 proteins that were associated with the chromatin/matrix fraction in G1 phase of both uninfected and SV40-infected cells were gradually released during progression through S phase. However, in SV40-infected cells that progressed beyond DI = 2.0, chromatin/matrix-associated MCM2 and MCM3 remained at the low levels observed at the end of S phase. Rereplication was not preceded by an obvious rebinding of MCM proteins to chromatin, as was observed in G1 phase. CONCLUSIONS The rereplication of host cell DNA in the absence of the reassociation of MCM proteins with chromatin indicates that SV40 infection induces a novel mechanism of licensing cellular DNA replication.
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Affiliation(s)
- Thomas D Friedrich
- Albany Medical College, Center for Immunology and Microbial Diseases, Albany, New York 12208, USA.
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42
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Iyer LM, Balaji S, Koonin EV, Aravind L. Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. Virus Res 2006; 117:156-84. [PMID: 16494962 DOI: 10.1016/j.virusres.2006.01.009] [Citation(s) in RCA: 426] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2005] [Revised: 01/06/2006] [Accepted: 01/09/2006] [Indexed: 11/19/2022]
Abstract
A previous comparative-genomic study of large nuclear and cytoplasmic DNA viruses (NCLDVs) of eukaryotes revealed the monophyletic origin of four viral families: poxviruses, asfarviruses, iridoviruses, and phycodnaviruses [Iyer, L.M., Aravind, L., Koonin, E.V., 2001. Common origin of four diverse families of large eukaryotic DNA viruses. J. Virol. 75 (23), 11720-11734]. Here we update this analysis by including the recently sequenced giant genome of the mimiviruses and several additional genomes of iridoviruses, phycodnaviruses, and poxviruses. The parsimonious reconstruction of the gene complement of the ancestral NCLDV shows that it was a complex virus with at least 41 genes that encoded the replication machinery, up to four RNA polymerase subunits, at least three transcription factors, capping and polyadenylation enzymes, the DNA packaging apparatus, and structural components of an icosahedral capsid and the viral membrane. The phylogeny of the NCLDVs is reconstructed by cladistic analysis of the viral gene complements, and it is shown that the two principal lineages of NCLDVs are comprised of poxviruses grouped with asfarviruses and iridoviruses grouped with phycodnaviruses-mimiviruses. The phycodna-mimivirus grouping was strongly supported by several derived shared characters, which seemed to rule out the previously suggested basal position of the mimivirus [Raoult, D., Audic, S., Robert, C., Abergel, C., Renesto, P., Ogata, H., La Scola, B., Suzan, M., Claverie, J.M. 2004. The 1.2-megabase genome sequence of Mimivirus. Science 306 (5700), 1344-1350]. These results indicate that the divergence of the major NCLDV families occurred at an early stage of evolution, prior to the divergence of the major eukaryotic lineages. It is shown that subsequent evolution of the NCLDV genomes involved lineage-specific expansion of paralogous gene families and acquisition of numerous genes via horizontal gene transfer from the eukaryotic hosts, other viruses, and bacteria (primarily, endosymbionts and parasites). Amongst the expansions, there are multiple families of predicted virus-specific signaling and regulatory domains. Most NCLDVs have also acquired large arrays of genes related to ubiquitin signaling, and the animal viruses in particular have independently evolved several defenses against apoptosis and immune response, including growth factors and potential inhibitors of cytokine signaling. The mimivirus displays an enormous array of genes of bacterial provenance, including a representative of a new class of predicted papain-like peptidases. It is further demonstrated that a significant number of genes found in NCLDVs also have homologs in bacteriophages, although a vertical relationship between the NCLDVs and a particular bacteriophage group could not be established. On the basis of these observations, two alternative scenarios for the origin of the NCLDVs and other groups of large DNA viruses of eukaryotes are considered. One of these scenarios posits an early assembly of an already large DNA virus precursor from which various large DNA viruses diverged through an ongoing process of displacement of the original genes by xenologous or non-orthologous genes from various sources. The second scenario posits convergent emergence, on multiple occasions, of large DNA viruses from small plasmid-like precursors through independent accretion of similar sets of genes due to strong selective pressures imposed by their life cycles and hosts.
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Affiliation(s)
- Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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43
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Forterre P. The origin of viruses and their possible roles in major evolutionary transitions. Virus Res 2006; 117:5-16. [PMID: 16476498 DOI: 10.1016/j.virusres.2006.01.010] [Citation(s) in RCA: 193] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2005] [Revised: 01/04/2006] [Accepted: 01/09/2006] [Indexed: 01/29/2023]
Abstract
Viruses infecting cells from the three domains of life, Archaea, Bacteria and Eukarya, share homologous features, suggesting that viruses originated very early in the evolution of life. The three current hypotheses for virus origin, e.g. the virus first, the escape and the reduction hypotheses are revisited in this new framework. Theoretical considerations suggest that RNA viruses may have originated in the nucleoprotein world by escape or reduction from RNA-cells, whereas DNA viruses (at least some of them) might have evolved directly from RNA viruses. The antiquity of viruses can explain why most viral proteins have no cellular homologues or only distantly related ones. Viral proteins have replaced the ancestral bacterial RNA/DNA polymerases and primase during mitochondrial evolution. It has been suggested that replacement of cellular proteins by viral ones also occurred in early evolution of the DNA replication apparatus and/or that some DNA replication proteins originated directly in the virosphere and were later on transferred to cellular organisms. According to these new hypotheses, viruses played a critical role in major evolutionary transitions, such as the invention of DNA and DNA replication mechanisms, the formation of the three domains of life, or else, the origin of the eukaryotic nucleus.
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Affiliation(s)
- Patrick Forterre
- Institut de Génétique et Microbiologie, CNRS UMR 8621, Université Paris-Sud, 91405 Orsay Cedex, France.
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44
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Abstract
The life cycle of HIV-1 involves a series of steps necessary for the successful infection of human target cells. First the RNA genome enters the cytoplasm after the fusion of the viral membrane and that of the target cell. The RNA genome is then converted to DNA form through the process of reverse transcription. The DNA genome is then integrated into the host cell DNA. Next, viral proteins and more copies of the viral genome are produced. These components assemble to form new virions that are then able to propagate. The cellular proteins involved in HIV-1 entry have been known for more than a decade now and the study of the cellular and viral components involved in HIV-1 entry has led to the development of many therapeutic strategies and drugs designed to block viral replication. Recently, there have been significant advances in the understanding of HIV-1 assembly as a consequence of the identification of the cellular factors that mediate this process. This review will provide a basic outline of the current understanding of HIV-1 entry and exit.
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Affiliation(s)
- Candace Gomez
- University of Illinois at Chicago, College of Medicine, 60612, USA
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45
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46
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Affiliation(s)
- K Dabrowska
- Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
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47
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Abstract
The actin cytoskeleton is harnessed by several pathogenic bacteria that are capable of entering into non-phagocytic cells, the so-called 'invasive bacteria'. Among them, a few also exploit the host actin cytoskeleton to move intra- and inter-cellularly. Our knowledge of the basic mechanisms underlying actin-based motility has dramatically increased and the list of bacteria that are able to move in this way is also increasing including not only Listeria, Shigella and Rickettsia species but also Mycobacterium marinum and Burkholderia pseudomallei. In all cases the central player is the Arp2/3 complex. Vaccinia virus moves intracellularly on microtubules and just after budding, triggers actin polymerization and the formation of protrusions similar to that of adherent enteropathogenic Escherichia coli, that involve the Arp2/3 complex and facilitate its inter-cellular spread.
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Affiliation(s)
- Edith Gouin
- Unité des Interactions Bactéries-cellules, Institut Pasteur, 28 Rue du Docteur Roux, Paris 75015, France
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48
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Abstract
We construct a mathematical model of the within-cell replication of poliovirus, a prototypic RNA virus, and use realistic parameter estimates to describe the increase of copy number of the viral genome. Our initial model is essentially an exponential growth model; we also consider modifications of this model to account for resource utilization. The saturation of viral replication dynamics observed in experimental systems can be explained in terms of heavy resource use by the virus. We then use our models to consider the conditions under which the growth of poliovirus is optimized. Intriguingly, if poliovirus has optimized its replication within cells, the predicted ratio of positive to negative strands is close to what is actually observed. We interpret our findings in terms of the evolution of life-history traits.
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Affiliation(s)
- Roland R Regoes
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA.
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49
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Hattermann K, Müller MA, Nitsche A, Wendt S, Donoso Mantke O, Niedrig M. Susceptibility of different eukaryotic cell lines to SARS-coronavirus. Arch Virol 2005; 150:1023-31. [PMID: 15645376 PMCID: PMC7086824 DOI: 10.1007/s00705-004-0461-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2004] [Accepted: 11/01/2004] [Indexed: 11/02/2022]
Abstract
In order to define and characterize target cells of SARS-coronavirus (SARS-CoV) we studied the susceptibility of 23 different permanent and primary eukaryotic cell lines to SARS-coronavirus. Beneath Vero E6 cells SARS- Coronavirus infection could also be demonstrated in two pig cell lines (POEK, PS) and one human cell line (Huh-7) using the indirect immunofluorescence assay and a newly established quantitative real-time PCR. In all susceptible cell lines mRNA of the Angiotensin-converting enzyme 2 (ACE2), the functional receptor for SARS-CoV infection, could be detected by RT-PCR. Our results show that there is a correlation between the abundance of ACE2 mRNA and SARS-CoV susceptibility.
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Affiliation(s)
- K Hattermann
- Robert Koch-Institut, Center for Biological Safety 1, Berlin, Germany
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50
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Abstract
Protein synthesis is regulated at the translational level by a variety of mechanisms in virus-infected cells. Viruses often induce the shut-off of host translation in order to favour the expression of their own genetic information, but cells possess a number of strategies for counteracting such effects of infection. Important regulatory mechanisms include the phosphorylation of the alpha subunit of polypeptide chain initiation factor eIF2, RNA degradation mediated by the 2'5'-oligoadenylate/RNase L system, control of availability of the cap-binding protein eIF4E by its interaction with the 4E-binding proteins and specific proteolytic cleavage of several key initiation factors. Most of these mechanisms are also utilised in uninfected cells in response to a variety of physiological stresses and during the early stages of apoptosis. Thus, mechanisms of translational control during virus infection can provide models for the cellular stress responses observed in a wide range of other circumstances.
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Affiliation(s)
- Michael J Clemens
- Translational Control Group, Biochemistry and Immunology, Department of Basic Medical Sciences, St. George's Hospital Medical School, Cranmer Terrace, London SW17 0RE, UK.
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