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Shirokikh NE, Jensen KB, Thakor N. Editorial: RNA machines. Front Genet 2023; 14:1290420. [PMID: 37829284 PMCID: PMC10565666 DOI: 10.3389/fgene.2023.1290420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 09/18/2023] [Indexed: 10/14/2023] Open
Affiliation(s)
- Nikolay E. Shirokikh
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Kirk Blomquist Jensen
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Nehal Thakor
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada
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2
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Wilkins KC, Venkataramanan S, Floor SN. Lysate and cell-based assays to probe the translational role of RNA helicases. Methods Enzymol 2022; 673:141-168. [DOI: 10.1016/bs.mie.2022.03.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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3
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Komar AA, Merrick WC. A Retrospective on eIF2A-and Not the Alpha Subunit of eIF2. Int J Mol Sci 2020; 21:E2054. [PMID: 32192132 PMCID: PMC7139343 DOI: 10.3390/ijms21062054] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 02/29/2020] [Accepted: 03/13/2020] [Indexed: 12/31/2022] Open
Abstract
Initiation of protein synthesis in eukaryotes is a complex process requiring more than 12 different initiation factors, comprising over 30 polypeptide chains. The functions of many of these factors have been established in great detail; however, the precise role of some of them and their mechanism of action is still not well understood. Eukaryotic initiation factor 2A (eIF2A) is a single chain 65 kDa protein that was initially believed to serve as the functional homologue of prokaryotic IF2, since eIF2A and IF2 catalyze biochemically similar reactions, i.e., they stimulate initiator Met-tRNAi binding to the small ribosomal subunit. However, subsequent identification of a heterotrimeric 126 kDa factor, eIF2 (α,β,γ) showed that this factor, and not eIF2A, was primarily responsible for the binding of Met-tRNAi to 40S subunit in eukaryotes. It was found however, that eIF2A can promote recruitment of Met-tRNAi to 40S/mRNA complexes under conditions of inhibition of eIF2 activity (eIF2α-phosphorylation), or its absence. eIF2A does not function in major steps in the initiation process, but is suggested to act at some minor/alternative initiation events such as re-initiation, internal initiation, or non-AUG initiation, important for translational control of specific mRNAs. This review summarizes our current understanding of the eIF2A structure and function.
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Affiliation(s)
- Anton A. Komar
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA;
| | - William C. Merrick
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA;
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4
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Haberger V, Elgner F, Roos J, Bender D, Hildt E. Regulation of the Transferrin Receptor Recycling in Hepatitis C Virus-Replicating Cells. Front Cell Dev Biol 2020; 8:44. [PMID: 32117974 PMCID: PMC7026371 DOI: 10.3389/fcell.2020.00044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 01/17/2020] [Indexed: 12/11/2022] Open
Abstract
After binding of its ligand transferrin, the transferrin receptor (TfR) is internalized via early endosomes. Ligand and receptor can be recycled. α-Taxilin was identified as an essential factor for TfR recycling. Apart from its role for iron uptake, TfR is a coreceptor for hepatitis C virus (HCV) infection. In HCV-replicating cells, the amount of a-taxilin is decreased. This study aims to investigate the effect of decreased α-taxilin levels in HCV-replicating cells on recycling of TfR, its amount on the cell surface, on iron uptake, and the impact of a disturbed TfR recycling on HCV superinfection exclusion. TfR amount and localization were determined by CLSM and surface biotinylation. α-taxilin expression was modulated by CRISPR-Cas9 knockout, siRNA, and stable or transient overexpression. For analysis of HCV superinfection fluorophor-tagged reporter viruses were used. The amount of α-taxilin is decreased in HCV-infected cells. In accordance to this, the protein amount of TfR is significant lower in HCV-positve cells as compared to the control, while TfR expression is not affected. Due to the impaired recycling, internalized TfR is degraded by the endosomal/lysosomal system. The significant lower number of TfR molecules on the cell surface is reflected by reduced transferrin binding/internalization and strong reduction of intracellular iron level. Overexpression of α-taxilin in HCV-replicating cells rescues TfR recycling, augments TfR on the cell surface, and restores transferrin binding. The block of superinfection in HCV-replicating cells could be overcome by overexpression of α-taxilin. Taken together, the diminished level of α-taxilin in HCV-replicating cells prevents recycling of TfR leading to decreased transferrin binding and iron uptake. Disappearance of TfR from the cell surface could be a factor contributing to the exclusion of superinfection by HCV.
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Affiliation(s)
| | - Fabian Elgner
- Division of Virology, Paul Ehrlich Institute, Langen, Germany
| | - Jessica Roos
- Division of Safety of Medical Products and Devices, Paul Ehrlich Institute, Langen, Germany
| | - Daniela Bender
- Division of Virology, Paul Ehrlich Institute, Langen, Germany
| | - Eberhard Hildt
- Division of Virology, Paul Ehrlich Institute, Langen, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
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5
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Acosta-Reyes F, Neupane R, Frank J, Fernández IS. The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs. EMBO J 2019; 38:e102226. [PMID: 31609474 PMCID: PMC6826211 DOI: 10.15252/embj.2019102226] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 09/02/2019] [Accepted: 09/19/2019] [Indexed: 12/19/2022] Open
Abstract
Colony collapse disorder (CCD) is a multi-faceted syndrome decimating bee populations worldwide, and a group of viruses of the widely distributed Dicistroviridae family have been identified as a causing agent of CCD. This family of viruses employs non-coding RNA sequences, called internal ribosomal entry sites (IRESs), to precisely exploit the host machinery for viral protein production. Using single-particle cryo-electron microscopy (cryo-EM), we have characterized how the IRES of Israeli acute paralysis virus (IAPV) intergenic region captures and redirects translating ribosomes toward viral RNA messages. We reconstituted two in vitro reactions targeting a pre-translocation and a post-translocation state of the IAPV-IRES in the ribosome, allowing us to identify six structures using image processing classification methods. From these, we reconstructed the trajectory of IAPV-IRES from the early small subunit recruitment to the final post-translocated state in the ribosome. An early commitment of IRES/ribosome complexes for global pre-translocation mimicry explains the high efficiency observed for this IRES. Efforts directed toward fighting CCD by targeting the IAPV-IRES using RNA-interference technology are underway, and the structural framework presented here may assist in further refining these approaches.
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Affiliation(s)
- Francisco Acosta-Reyes
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Ritam Neupane
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.,Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.,Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Israel S Fernández
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
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6
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Migration of Small Ribosomal Subunits on the 5' Untranslated Regions of Capped Messenger RNA. Int J Mol Sci 2019; 20:ijms20184464. [PMID: 31510048 PMCID: PMC6769788 DOI: 10.3390/ijms20184464] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/01/2019] [Accepted: 09/05/2019] [Indexed: 12/12/2022] Open
Abstract
Several control mechanisms of eukaryotic gene expression target the initiation step of mRNA translation. The canonical translation initiation pathway begins with cap-dependent attachment of the small ribosomal subunit (SSU) to the messenger ribonucleic acid (mRNA) followed by an energy-dependent, sequential ‘scanning’ of the 5′ untranslated regions (UTRs). Scanning through the 5′UTR requires the adenosine triphosphate (ATP)-dependent RNA helicase eukaryotic initiation factor (eIF) 4A and its efficiency contributes to the specific rate of protein synthesis. Thus, understanding the molecular details of the scanning mechanism remains a priority task for the field. Here, we studied the effects of inhibiting ATP-dependent translation and eIF4A in cell-free translation and reconstituted initiation reactions programmed with capped mRNAs featuring different 5′UTRs. An aptamer that blocks eIF4A in an inactive state away from mRNA inhibited translation of capped mRNA with the moderately structured β-globin sequences in the 5′UTR but not that of an mRNA with a poly(A) sequence as the 5′UTR. By contrast, the nonhydrolysable ATP analogue β,γ-imidoadenosine 5′-triphosphate (AMP-PNP) inhibited translation irrespective of the 5′UTR sequence, suggesting that complexes that contain ATP-binding proteins in their ATP-bound form can obstruct and/or actively block progression of ribosome recruitment and/or scanning on mRNA. Further, using primer extension inhibition to locate SSUs on mRNA (‘toeprinting’), we identify an SSU complex which inhibits primer extension approximately eight nucleotides upstream from the usual toeprinting stop generated by SSUs positioned over the start codon. This ‘−8 nt toeprint’ was seen with mRNA 5′UTRs of different length, sequence and structure potential. Importantly, the ‘−8 nt toeprint’ was strongly stimulated by the presence of the cap on the mRNA, as well as the presence of eIFs 4F, 4A/4B and ATP, implying active scanning. We assembled cell-free translation reactions with capped mRNA featuring an extended 5′UTR and used cycloheximide to arrest elongating ribosomes at the start codon. Impeding scanning through the 5′UTR in this system with elevated magnesium and AMP-PNP (similar to the toeprinting conditions), we visualised assemblies consisting of several SSUs together with one full ribosome by electron microscopy, suggesting direct detection of scanning intermediates. Collectively, our data provide additional biochemical, molecular and physical evidence to underpin the scanning model of translation initiation in eukaryotes.
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Control of Translation at the Initiation Phase During Glucose Starvation in Yeast. Int J Mol Sci 2019; 20:ijms20164043. [PMID: 31430885 PMCID: PMC6720308 DOI: 10.3390/ijms20164043] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/10/2019] [Accepted: 08/15/2019] [Indexed: 12/13/2022] Open
Abstract
Glucose is one of the most important sources of carbon across all life. Glucose starvation is a key stress relevant to all eukaryotic cells. Glucose starvation responses have important implications in diseases, such as diabetes and cancer. In yeast, glucose starvation causes rapid and dramatic effects on the synthesis of proteins (mRNA translation). Response to glucose deficiency targets the initiation phase of translation by different mechanisms and with diverse dynamics. Concomitantly, translationally repressed mRNAs and components of the protein synthesis machinery may enter a variety of cytoplasmic foci, which also form with variable kinetics and may store or degrade mRNA. Much progress has been made in understanding these processes in the last decade, including with the use of high-throughput/omics methods of RNA and RNA:protein detection. This review dissects the current knowledge of yeast reactions to glucose starvation systematized by the stage of translation initiation, with the focus on rapid responses. We provide parallels to mechanisms found in higher eukaryotes, such as metazoans, for the most critical responses, and point out major remaining gaps in knowledge and possible future directions of research on translational responses to glucose starvation.
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Malabirade A, Habier J, Heintz-Buschart A, May P, Godet J, Halder R, Etheridge A, Galas D, Wilmes P, Fritz JV. The RNA Complement of Outer Membrane Vesicles From Salmonella enterica Serovar Typhimurium Under Distinct Culture Conditions. Front Microbiol 2018; 9:2015. [PMID: 30214435 PMCID: PMC6125333 DOI: 10.3389/fmicb.2018.02015] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 08/09/2018] [Indexed: 12/20/2022] Open
Abstract
Bacterial outer membrane vesicles (OMVs), as well as OMV-associated small RNAs, have been demonstrated to play a role in host-pathogen interactions. The presence of larger RNA transcripts in OMVs has been less studied and their potential role in host-pathogen interactions remains largely unknown. Here we analyze RNA from OMVs secreted by Salmonella enterica serovar Typhimurium (S. Typhimurium) cultured under different conditions, which mimic host-pathogen interactions. S. Typhimurium was grown to exponential and stationary growth phases in minimal growth control medium (phosphate-carbon-nitrogen, PCN), as well as in acidic and phosphate-depleted PCN, comparable to the macrophage environment and inducing therefore the expression of Salmonella pathogenicity island 2 (SPI-2) genes. Moreover, Salmonella pathogenicity island 1 (SPI-1), which is required for virulence during the intestinal phase of infection, was induced by culturing S. Typhimurium to the stationary phase in Lysogeny Broth (LB). For each condition, we identified OMV-associated RNAs that are enriched in the extracellular environment relative to the intracellular space. All RNA classes could be observed, but a vast majority of rRNA was exported in all conditions in variable proportions with a notable decrease in LB SPI-1 inducing media. Several mRNAs and ncRNAs were specifically enriched in/on OMVs dependent on the growth conditions. Important to note is that some RNAs showed identical read coverage profiles intracellularly and extracellularly, whereas distinct coverage patterns were observed for other transcripts, suggesting a specific processing or degradation. Moreover, PCR experiments confirmed that distinct RNAs were present in or on OMVs as full-length transcripts (IsrB-1/2; IsrA; ffs; SsrS; CsrC; pSLT035; 10Sa; rnpB; STM0277; sseB; STM0972; STM2606), whereas others seemed to be rather present in a processed or degraded form. Finally, we show by a digestion protection assay that OMVs are able to prevent enzymatic degradation of given full-length transcripts (SsrS, CsrC, 10Sa, and rnpB). In summary, we show that OMV-associated RNA is clearly different in distinct culture conditions and that at least a fraction of the extracellular RNA is associated as a full-length transcripts with OMVs, indicating that some RNAs are protected by OMVs and thereby leaving open the possibility that those might be functionally active.
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Affiliation(s)
- Antoine Malabirade
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Janine Habier
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Anna Heintz-Buschart
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Julien Godet
- UMR CNRS 7021, Laboratoire de BioImagerie et Pathologies, Université de Strasbourg, Strasbourg, France
| | - Rashi Halder
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Alton Etheridge
- Pacific Northwest Research Institute, Seattle, WA, United States
| | - David Galas
- Pacific Northwest Research Institute, Seattle, WA, United States
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Joëlle V Fritz
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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9
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Shirokikh NE, Preiss T. Translation initiation by cap-dependent ribosome recruitment: Recent insights and open questions. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1473. [PMID: 29624880 DOI: 10.1002/wrna.1473] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/02/2018] [Accepted: 02/14/2018] [Indexed: 12/14/2022]
Abstract
Gene expression universally relies on protein synthesis, where ribosomes recognize and decode the messenger RNA template by cycling through translation initiation, elongation, and termination phases. All aspects of translation have been studied for decades using the tools of biochemistry and molecular biology available at the time. Here, we focus on the mechanism of translation initiation in eukaryotes, which is remarkably more complex than prokaryotic initiation and is the target of multiple types of regulatory intervention. The "consensus" model, featuring cap-dependent ribosome entry and scanning of mRNA leader sequences, represents the predominantly utilized initiation pathway across eukaryotes, although several variations of the model and alternative initiation mechanisms are also known. Recent advances in structural biology techniques have enabled remarkable molecular-level insights into the functional states of eukaryotic ribosomes, including a range of ribosomal complexes with different combinations of translation initiation factors that are thought to represent bona fide intermediates of the initiation process. Similarly, high-throughput sequencing-based ribosome profiling or "footprinting" approaches have allowed much progress in understanding the elongation phase of translation, and variants of them are beginning to reveal the remaining mysteries of initiation, as well as aspects of translation termination and ribosomal recycling. A current view on the eukaryotic initiation mechanism is presented here with an emphasis on how recent structural and footprinting results underpin axioms of the consensus model. Along the way, we further outline some contested mechanistic issues and major open questions still to be addressed. This article is categorized under: Translation > Translation Mechanisms Translation > Translation Regulation RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Nikolay E Shirokikh
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
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Nikonov OS, Chernykh ES, Garber MB, Nikonova EY. Enteroviruses: Classification, Diseases They Cause, and Approaches to Development of Antiviral Drugs. BIOCHEMISTRY (MOSCOW) 2018. [PMID: 29523062 PMCID: PMC7087576 DOI: 10.1134/s0006297917130041] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The genus Enterovirus combines a portion of small (+)ssRNA-containing viruses and is divided into 10 species of true enteroviruses and three species of rhinoviruses. These viruses are causative agents of the widest spectrum of severe and deadly epidemic diseases of higher vertebrates, including humans. Their ubiquitous distribution and high pathogenici- ty motivate active search to counteract enterovirus infections. There are no sufficiently effective drugs targeted against enteroviral diseases, thus treatment is reduced to supportive and symptomatic measures. This makes it extremely urgent to develop drugs that directly affect enteroviruses and hinder their development and spread in infected organisms. In this review, we cover the classification of enteroviruses, mention the most common enterovirus infections and their clinical man- ifestations, and consider the current state of development of anti-enteroviral drugs. One of the most promising targets for such antiviral drugs is the viral Internal Ribosome Entry Site (IRES). The classification of these elements of the viral mRNA translation system is also examined.
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Affiliation(s)
- O S Nikonov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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Starck SR, Shastri N. Nowhere to hide: unconventional translation yields cryptic peptides for immune surveillance. Immunol Rev 2017; 272:8-16. [PMID: 27319338 DOI: 10.1111/imr.12434] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Effective immune surveillance by CD8(+) cytotoxic T cells of intracellular microbes and cancer depends on the antigen presentation pathway. This pathway produces an optimal peptide repertoire for presentation by major histocompatibility (MHC) class I molecules (pMHCs I) on the cell surface. We have known for years that the pMHC I repertoire is a reflection of the intracellular protein pool. However, many studies have revealed that pMHCs I present peptides not only from precursors encoded in open-reading frames of mRNA transcripts but also cryptic peptides encoded in apparently 'untranslated' regions. These sources vastly increase the availability of peptides for presentation and immune evasion. Here, we review studies on the composition of the cryptic pMHC I repertoire, the immunological significance of these pMHC I, and the novel translational mechanisms that generate cryptic peptides from unusual sources.
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Affiliation(s)
- Shelley R Starck
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.,NGM Biopharmaceuticals Inc., South San Francisco, CA, USA
| | - Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
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12
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Translation complex profile sequencing to study the in vivo dynamics of mRNA–ribosome interactions during translation initiation, elongation and termination. Nat Protoc 2017; 12:697-731. [DOI: 10.1038/nprot.2016.189] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Bukhari SIA, Vasudevan S. FXR1a-associated microRNP: A driver of specialized non-canonical translation in quiescent conditions. RNA Biol 2016; 14:137-145. [PMID: 27911187 DOI: 10.1080/15476286.2016.1265197] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Eukaryotic protein synthesis is a multifaceted process that requires coordination of a set of translation factors in a particular cellular state. During normal growth and proliferation, cells generally make their proteome via conventional translation that utilizes canonical translation factors. When faced with environmental stress such as growth factor deprivation, or in response to biological cues such as developmental signals, cells can reduce canonical translation. In this situation, cells adapt alternative modes of translation to make specific proteins necessary for required biological functions under these distinct conditions. To date, a number of alternative translation mechanisms have been reported, which include non-canonical, cap dependent translation and cap independent translation such as IRES mediated translation. Here, we discuss one of the alternative modes of translation mediated by a specialized microRNA complex, FXR1a-microRNP that promotes non-canonical, cap dependent translation in quiescent conditions, where canonical translation is reduced due to low mTOR activity.
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Affiliation(s)
- Syed I A Bukhari
- a Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School , Boston , MA , USA
| | - Shobha Vasudevan
- a Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School , Boston , MA , USA
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Makhnovskii PA, Kuzmin IV, Nefedova LN, Kima AI. Functional analysis of Grp and Iris, the gag and env domesticated errantivirus genes, in the Drosophila melanogaster genome. Mol Biol 2016. [DOI: 10.1134/s0026893316020151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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15
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Shier MK, El-Wetidy MS, Ali HH, Al-Qattan MM. Hepatitis c virus genotype 4 replication in the hepatocellular carcinoma cell line HepG2/C3A. Saudi J Gastroenterol 2016; 22:240-8. [PMID: 27184644 PMCID: PMC4898095 DOI: 10.4103/1319-3767.182461] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND/AIMS The lack of a reliable cell culture system allowing persistent in vitro hepatitis C virus (HCV) propagation is still restraining the search for novel antiviral strategies. HepG2 cells transfection with HCV allows for viral replication. However, the replication is weak presumably because of HepG2 lack of miRNA-122, which is essential for viral replication. Other agents such as polyethylene glycol (PEG) and dimethyl sulfoxide (DMSO) have been shown to increase the efficiency of infection with other viruses. This study included comparison of HCV genotype 4 5'UTR and core RNA levels and HCV core protein expression at different time intervals in the absence or presence of PEG and/or DMSO postinfection. MATERIALS AND METHODS We used serum with native HCV particles in infecting HepG2 cells in vitro. HCV replication was assessed by reverse transcriptase polymerase chain reaction for detection of HCV RNA and immunofluorescence and flow cytometry for detection of HCV core protein. RESULTS HCV 5'UTR and core RNA expression was evident at different time intervals after viral infection, especially after cells were treated with PEG. HCV core protein was also evident at different time intervals using both immunofluorescence and flow cytometry. PEG, not DMSO, has increased the HCV core protein expression in the treated cells, similar to its effect on viral RNA expression. CONCLUSIONS These expression profiles suggest that the current model of cultured HepG2 cells allows the study of HCV genotype 4 replication and different stages of the viral life cycle.
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Affiliation(s)
- Medhat K. Shier
- College of Medicine Research Center, King Saud University, Riyadh, Saudi Arabia,Department of Medical Microbiology and Immunology, College of Medicine, Menofia University, Egypt,Address for correspondence: Dr. Medhat K. Shier, College of Medicine Research Center, King Saud University, PO Box 2925 (74), Riyadh - 11461, Saudi Arabia. E-mail:
| | | | - Hebatallah H. Ali
- College of Medicine Research Center, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad M. Al-Qattan
- College of Medicine Research Center, King Saud University, Riyadh, Saudi Arabia,Department of Surgery, College of Medicine, King Saud University, Riyadh, Saudi Arabia
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Komar AA, Hatzoglou M. Exploring Internal Ribosome Entry Sites as Therapeutic Targets. Front Oncol 2015; 5:233. [PMID: 26539410 PMCID: PMC4611151 DOI: 10.3389/fonc.2015.00233] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 10/05/2015] [Indexed: 12/12/2022] Open
Abstract
Initiation of eukaryotic mRNA translation may proceed via several different routes, each requiring a different subset of factors and relying on different and specific interactions between the mRNA and the ribosome. Two modes predominate: (i) so-called cap-dependent initiation, which requires all canonical initiation factors and is responsible for about 95–97% of all initiation events in eukaryotic cells; and (ii) cap-independent internal initiation, which requires a reduced subset of initiation factors and accounts for up to 5% of the remaining initiation events. Internal initiation relies on the presence of so-called internal ribosome entry site (IRES) elements in the 5′ UTRs of some viral and cellular mRNAs. These elements (often possessing complex secondary and tertiary structures) promote efficient interaction of the mRNA with the 40S ribosome and allow for internal ribosome entry. Internal initiation of translation of specific mRNAs may contribute to development of severe disease and pathological states, such as hepatitis C and cancer. Therefore, this cellular mechanism represents an attractive target for pharmacological modulation. The purpose of this review is to provide insight into current strategies used to target viral and cellular IRESs and discuss the physiological consequences (and potential therapeutic implications) of abrogation/modulation of IRES-mediated translation.
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Affiliation(s)
- Anton A Komar
- Department of Biological, Geological and Environmental Sciences, Center for Gene Regulation in Health and Disease, Cleveland State University , Cleveland, OH , USA
| | - Maria Hatzoglou
- Department of Pharmacology, School of Medicine, Case Western Reserve University , Cleveland, OH , USA
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17
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Conformational flexibility of viral RNA switches studied by FRET. Methods 2015; 91:35-39. [PMID: 26381686 DOI: 10.1016/j.ymeth.2015.09.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/10/2015] [Accepted: 09/14/2015] [Indexed: 12/19/2022] Open
Abstract
The function of RNA switches involved in the regulation of transcription and translation relies on their ability to adopt different, structurally well-defined states. A new class of ligand-responsive RNA switches, which we recently discovered in positive strand RNA viruses, are distinct from conventional riboswitches. The viral switches undergo large conformational changes in response to ligand binding while retaining the same secondary structure in their free and ligand-bound forms. Here, we describe FRET experiments to study folding and ligand binding of the viral RNA switches. In addition to reviewing previous approaches involving RNA model constructs which were directly conjugated with fluorescent dyes, we outline the design and application of new modular constructs for FRET experiments, in which dye labeling is achieved by hybridization of a core RNA switch module with universal DNA fluorescent probes. As an example, folding and ligand binding of the RNA switch from the internal ribosome entry site of hepatitis C virus is studied comparatively with conventional and modular FRET constructs.
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Song QQ, Lu MZ, Song J, Chi MM, Sheng LJ, Yu J, Luo XN, Zhang L, Yao HL, Han J. Coxsackievirus B3 2A protease promotes encephalomyocarditis virus replication. Virus Res 2015; 208:22-9. [PMID: 26052084 DOI: 10.1016/j.virusres.2015.05.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/23/2015] [Accepted: 05/25/2015] [Indexed: 01/12/2023]
Abstract
To determine whether 2A protease of the enterovirus genus with type I internal ribosome entry site (IRES) effect on the viral replication of type II IRES, coxsackievirus B3(CVB3)-encoded protease 2A and encephalomyocarditis virus (EMCV) IRES (Type II)-dependent or cap-dependent report gene were transiently co-expressed in eukaryotic cells. We found that CVB3 2A protease not only inhibited translation of cap-dependent reporter genes through the cleavage of eIF4GI, but also conferred high EMCV IRES-dependent translation ability and promoted EMCV replication. Moreover, deletions of short motif (aa13-18 RVVNRH, aa65-70 KNKHYP, or aa88-93 PRRYQSH) resembling the nuclear localization signals (NLS) or COOH-terminal acidic amino acid motif (aa133-147 DIRDLLWLEDDAMEQ) of CVB3 2A protease decreased both its EMCV IRES-dependent translation efficiency and destroy its cleavage on eukaryotic initiation factor 4G (eIF4G) I. Our results may provide better understanding into more effective interventions and treatments for co-infection of viral diseases.
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Affiliation(s)
- Qin-Qin Song
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases (Hangzhou), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Beijing 102206, China
| | - Ming-Zhi Lu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases (Hangzhou), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Beijing 102206, China
| | - Juan Song
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases (Hangzhou), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Beijing 102206, China
| | - Miao-Miao Chi
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases (Hangzhou), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Beijing 102206, China
| | - Lin-Jun Sheng
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases (Hangzhou), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Beijing 102206, China
| | - Jie Yu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases (Hangzhou), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Beijing 102206, China
| | - Xiao-Nuan Luo
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases (Hangzhou), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Beijing 102206, China
| | - Lu Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases (Hangzhou), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Beijing 102206, China
| | - Hai-Lan Yao
- Molecular Immunology Laboratory, Capital Institute of Pediatrics, 2 YaBao Rd, Beijing 100020, China
| | - Jun Han
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases (Hangzhou), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Beijing 102206, China.
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Abstract
Pestiviruses are among the economically most important pathogens of livestock. The biology of these viruses is characterized by unique and interesting features that are both crucial for their success as pathogens and challenging from a scientific point of view. Elucidation of these features at the molecular level has made striking progress during recent years. The analyses revealed that major aspects of pestivirus biology show significant similarity to the biology of human hepatitis C virus (HCV). The detailed molecular analyses conducted for pestiviruses and HCV supported and complemented each other during the last three decades resulting in elucidation of the functions of viral proteins and RNA elements in replication and virus-host interaction. For pestiviruses, the analyses also helped to shed light on the molecular basis of persistent infection, a special strategy these viruses have evolved to be maintained within their host population. The results of these investigations are summarized in this chapter.
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Affiliation(s)
- Norbert Tautz
- Institute for Virology and Cell Biology, University of Lübeck, Lübeck, Germany
| | - Birke Andrea Tews
- Institut für Immunologie, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Gregor Meyers
- Institut für Immunologie, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany.
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Leong SY, Ong BKT, Chu JJH. The role of Misshapen NCK-related kinase (MINK), a novel Ste20 family kinase, in the IRES-mediated protein translation of human enterovirus 71. PLoS Pathog 2015; 11:e1004686. [PMID: 25747578 PMCID: PMC4352056 DOI: 10.1371/journal.ppat.1004686] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 01/16/2015] [Indexed: 11/18/2022] Open
Abstract
Human Enterovirus 71 (EV71) commonly causes Hand, Foot and Mouth Disease in young children, and occasional occurrences of neurological complications can be fatal. In this study, a high-throughput cell-based screening on the serine/threonine kinase siRNA library was performed to identify potential antiviral agents against EV71 replication. Among the hits, Misshapen/NIKs-related kinase (MINK) was selected for detailed analysis due to its strong inhibitory profile and novelty. In the investigation of the stage at which MINK is involved in EV71 replication, virus RNA transfection in MINK siRNA-treated cells continued to cause virus inhibition despite bypassing the normal entry pathway, suggesting its involvement at the post-entry stage. We have also shown that viral RNA and protein expression level was significantly reduced upon MINK silencing, suggesting its involvement in viral protein synthesis which feeds into viral RNA replication process. Through proteomic analysis and infection inhibition assay, we found that the activation of MINK was triggered by early replication events, instead of the binding and entry of the virus. Proteomic analysis on the activation profile of p38 Mitogen-activated Protein Kinase (MAPK) indicated that the phosphorylation of p38 MAPK was stimulated by EV71 infection upon MINK activation. Luciferase reporter assay further revealed that the translation efficiency of the EV71 internal ribosomal entry site (IRES) was reduced after blocking the MINK/p38 MAPK pathway. Further investigation on the effect of MINK silencing on heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) localisation demonstrated that cytoplasmic relocalisation of hnRNP A1 upon EV71 infection may be facilitated via the MINK/p38 MAPK pathway which then positively regulates the translation of viral RNA transcripts. These novel findings hence suggest that MINK plays a functional role in the IRES-mediated translation of EV71 viral RNA and may provide a potential target for the development of specific antiviral strategies against EV71 infection.
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Affiliation(s)
- Shi Yun Leong
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Bryan Kit Teck Ong
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Justin Jang Hann Chu
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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A new role for PGA1 in inhibiting hepatitis C virus-IRES-mediated translation by targeting viral translation factors. Antiviral Res 2015; 117:1-9. [PMID: 25666760 DOI: 10.1016/j.antiviral.2015.01.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 01/26/2015] [Accepted: 01/29/2015] [Indexed: 02/06/2023]
Abstract
Previous studies have demonstrated that cyclopentenone prostaglandins (cyPGs) inhibit the replication of a wide variety of DNA and RNA viruses in different mammalian cell types. We investigated a new role for prostaglandin A1 (PGA1) in the inhibition of hepatitis C virus (HCV)-IRES-mediated translation. PGA1 exhibited dose-dependent inhibitory effects on HCV translation in HCV replicon cells. Furthermore, repetitive PGA1 treatment demonstrated the potential to safely induce the suppression of HCV translation. We also validated a new role for PGA1 in the inhibition of HCV-IRES-mediated translation by targeting cellular translation factors, including the small ribosomal subunit (40S) and eukaryotic initiation factors (eIFs). In pull-down assays, biotinylated PGA1 co-precipitated with the entire HCV IRES RNA/eIF3-40S subunit complex. Moreover, the interactions between PGA1 and the elongation factors and ribosomal subunit were dependent upon HCV IRES RNA binding, and the PGA1/HCV IRES RNA/eIF3-40S subunit complex inhibited HCV-IRES-mediated translation. The novel mechanism revealed in this study may aid in the search for more effective anti-HCV drugs.
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22
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Ozretić P, Bisio A, Musani V, Trnski D, Sabol M, Levanat S, Inga A. Regulation of human PTCH1b expression by different 5' untranslated region cis-regulatory elements. RNA Biol 2015; 12:290-304. [PMID: 25826662 PMCID: PMC4615190 DOI: 10.1080/15476286.2015.1008929] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
PTCH1 gene codes for a 12-pass transmembrane receptor with a negative regulatory role in the Hedgehog-Gli signaling pathway. PTCH1 germline mutations cause Gorlin syndrome, a disorder characterized by developmental abnormalities and tumor susceptibility. The autosomal dominant inheritance, and the evidence for PTCH1 haploinsufficiency, suggests that fine-tuning systems of protein patched homolog 1 (PTC1) levels exist to properly regulate the pathway. Given the role of 5' untranslated region (5'UTR) in protein expression, our aim was to thoroughly explore cis-regulatory elements in the 5'UTR of PTCH1 transcript 1b. The (CGG)n polymorphism was the main potential regulatory element studied so far but with inconsistent results and no clear association between repeat number and disease risk. Using luciferase reporter constructs in human cell lines here we show that the number of CGG repeats has no strong impact on gene expression, both at mRNA and protein levels. We observed variability in the length of 5'UTR and changes in abundance of the associated transcripts after pathway activation. We show that upstream AUG codons (uAUGs) present only in longer 5'UTRs could negatively regulate the amount of PTC1 isoform L (PTC1-L). The existence of an internal ribosome entry site (IRES) observed using different approaches and mapped in the region comprising the CGG repeats, would counteract the effect of the uAUGs and enable synthesis of PTC1-L under stressful conditions, such as during hypoxia. Higher relative translation efficiency of PTCH1b mRNA in HEK 293T cultured hypoxia was observed by polysomal profiling and Western blot analyses. All our results point to an exceptionally complex and so far unexplored role of 5'UTR PTCH1b cis-element features in the regulation of the Hedgehog-Gli signaling pathway.
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Key Words
- 5'UTR
- 5′UTR, 5′ untranslated region
- CGG repeats
- Fluc, Firefly luciferase
- Hedgehog-Gli
- Hh-Gli, Hedgehog-Gli
- IRES
- IRES, internal ribosome entry site
- POL, polysome-associated
- PTC1-L, protein patched homolog 1
- PTCH1
- Rluc, Renilla luciferase
- SUB, subpolysomal
- isoform L PTCH1b, Patched 1 gene, transcript variant 1b
- uAUG
- uAUG, upstream AUG codon
- uORF
- uORF, upstream open reading frame
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Affiliation(s)
- Petar Ozretić
- Laboratory for Hereditary Cancer; Division of Molecular Medicine; Ruđer Bošković Institute; Zagreb, Croatia
| | - Alessandra Bisio
- Laboratory of Transcriptional Networks; Center for Integrative Biology; University of Trento; Mattarello, Trento, Italy
| | - Vesna Musani
- Laboratory for Hereditary Cancer; Division of Molecular Medicine; Ruđer Bošković Institute; Zagreb, Croatia
| | - Diana Trnski
- Laboratory for Hereditary Cancer; Division of Molecular Medicine; Ruđer Bošković Institute; Zagreb, Croatia
| | - Maja Sabol
- Laboratory for Hereditary Cancer; Division of Molecular Medicine; Ruđer Bošković Institute; Zagreb, Croatia
| | - Sonja Levanat
- Laboratory for Hereditary Cancer; Division of Molecular Medicine; Ruđer Bošković Institute; Zagreb, Croatia
- Correspondence to: Sonja Levanat; ; Alberto Inga;
| | - Alberto Inga
- Laboratory of Transcriptional Networks; Center for Integrative Biology; University of Trento; Mattarello, Trento, Italy
- Correspondence to: Sonja Levanat; ; Alberto Inga;
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23
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Haß M, Luttermann C, Meyers G. Feline calicivirus can tolerate gross changes of its minor capsid protein expression levels induced by changing translation reinitiation frequency or use of a separate VP2-coding mRNA. PLoS One 2014; 9:e102254. [PMID: 25007260 PMCID: PMC4090194 DOI: 10.1371/journal.pone.0102254] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 06/16/2014] [Indexed: 12/31/2022] Open
Abstract
Caliciviruses use reinitiation of translation governed by a ‘termination upstream ribosomal binding site’ (TURBS) for expression of their minor capsid protein VP2. Mutation analysis allowed to identify sequences surrounding the translational start/stop site of the feline calicivirus (FCV) that fine tune reinitiation frequency. A selection of these changes was introduced into the infectious FCV cDNA clone to check the influence of altered VP2 levels on virus replication. In addition, full length constructs were established that displayed a conformation, in which VP2 expression occurred under control of a duplicated subgenomic promoter. Viable viruses recovered from such constructs revealed a rather broad range of VP2 expression levels but comparable growth kinetics showing that caliciviruses can tolerate gross changes of the VP2 expression level.
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Affiliation(s)
- Maria Haß
- Institut für Immunologie, Friedrich-Loeffler-Institut, Tübingen, Germany
| | | | - Gregor Meyers
- Institut für Immunologie, Friedrich-Loeffler-Institut, Tübingen, Germany
- * E-mail:
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24
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Abdul Mutalib NE, Mat Isa N, Alitheen NB, Song AAL, Rahim RA. IRES-incorporated lactococcal bicistronic vector for target gene expression in a eukaryotic system. Plasmid 2014; 73:26-33. [PMID: 24780699 DOI: 10.1016/j.plasmid.2014.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 04/11/2014] [Accepted: 04/18/2014] [Indexed: 11/29/2022]
Abstract
Plasmid DNAs isolated from lactic acid bacteria (LAB) such as Lactococcus lactis (L. lactis) has been gaining more interests for its positive prospects in genetic engineering-related applications. In this study, the lactococcal plasmid, pNZ8048 was modified so as to be able to express multiple genes in the eukaryotic system. Therefore, a cassette containing an internal ribosome entry site (IRES) was cloned between VP2 gene of a very virulent infectious bursal disease (vvIBDV) UPM 04190 of Malaysian local isolates and the reporter gene, green fluorescent protein (GFP) into pNZ:CA, a newly constructed derivative of pNZ8048 harboring the cytomegalovirus promoter (Pcmv) and polyadenylation signal. The new bicistronic vector, denoted as pNZ:vig was subjected to in vitro transcription/translation system followed by SDS-PAGE and Western blot analysis to rapidly verify its functionality. Immunoblotting profiles showed the presence of 49 and 29kDa bands that corresponds to the sizes of the VP2 and GFP proteins respectively. This preliminary result shows that the newly constructed lactococcal bicistronic vector can co-express multiple genes in a eukaryotic system via the IRES element thus suggesting its feasibility to be used for transfection of in vitro cell cultures and vaccine delivery.
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Affiliation(s)
- Nur Elina Abdul Mutalib
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
| | - Nurulfiza Mat Isa
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia.
| | - Noorjahan Banu Alitheen
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
| | - Adelene Ai-Lian Song
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
| | - Raha Abdul Rahim
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia; Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
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25
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Brödel AK, Sonnabend A, Roberts LO, Stech M, Wüstenhagen DA, Kubick S. IRES-mediated translation of membrane proteins and glycoproteins in eukaryotic cell-free systems. PLoS One 2013; 8:e82234. [PMID: 24376523 PMCID: PMC3869664 DOI: 10.1371/journal.pone.0082234] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 10/22/2013] [Indexed: 02/04/2023] Open
Abstract
Internal ribosome entry site (IRES) elements found in the 5′ untranslated region of mRNAs enable translation initiation in a cap-independent manner, thereby representing an alternative to cap-dependent translation in cell-free protein expression systems. However, IRES function is largely species-dependent so their utility in cell-free systems from different species is rather limited. A promising approach to overcome these limitations would be the use of IRESs that are able to recruit components of the translation initiation apparatus from diverse origins. Here, we present a solution to this technical problem and describe the ability of a number of viral IRESs to direct efficient protein expression in different eukaryotic cell-free expression systems. The IRES from the intergenic region (IGR) of the Cricket paralysis virus (CrPV) genome was shown to function efficiently in four different cell-free systems based on lysates derived from cultured Sf21, CHO and K562 cells as well as wheat germ. Our results suggest that the CrPV IGR IRES-based expression vector is universally applicable for a broad range of eukaryotic cell lysates. Sf21, CHO and K562 cell-free expression systems are particularly promising platforms for the production of glycoproteins and membrane proteins since they contain endogenous microsomes that facilitate the incorporation of membrane-spanning proteins and the formation of post-translational modifications. We demonstrate the use of the CrPV IGR IRES-based expression vector for the enhanced synthesis of various target proteins including the glycoprotein erythropoietin and the membrane proteins heparin-binding EGF-like growth factor receptor as well as epidermal growth factor receptor in the above mentioned eukaryotic cell-free systems. CrPV IGR IRES-mediated translation will facilitate the development of novel eukaryotic cell-free expression platforms as well as the high-yield synthesis of desired proteins in already established systems.
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Affiliation(s)
- Andreas K. Brödel
- Fraunhofer Institute for Biomedical Engineering (IBMT) Branch Potsdam-Golm, Potsdam, Germany
| | - Andrei Sonnabend
- Fraunhofer Institute for Biomedical Engineering (IBMT) Branch Potsdam-Golm, Potsdam, Germany
| | - Lisa O. Roberts
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Marlitt Stech
- Fraunhofer Institute for Biomedical Engineering (IBMT) Branch Potsdam-Golm, Potsdam, Germany
| | - Doreen A. Wüstenhagen
- Fraunhofer Institute for Biomedical Engineering (IBMT) Branch Potsdam-Golm, Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Biomedical Engineering (IBMT) Branch Potsdam-Golm, Potsdam, Germany
- * E-mail:
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26
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Brödel AK, Sonnabend A, Kubick S. Cell‐free protein expression based on extracts from CHO cells. Biotechnol Bioeng 2013; 111:25-36. [DOI: 10.1002/bit.25013] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 07/08/2013] [Accepted: 07/15/2013] [Indexed: 02/05/2023]
Affiliation(s)
- Andreas K. Brödel
- Fraunhofer Institute for Biomedical Engineering (IBMT)Branch Potsdam‐GolmAm Mühlenberg 1314476PotsdamGermany
| | - Andrei Sonnabend
- Fraunhofer Institute for Biomedical Engineering (IBMT)Branch Potsdam‐GolmAm Mühlenberg 1314476PotsdamGermany
| | - Stefan Kubick
- Fraunhofer Institute for Biomedical Engineering (IBMT)Branch Potsdam‐GolmAm Mühlenberg 1314476PotsdamGermany
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27
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Macarthur KL, Smolic R, Smolic MV, Wu CH, Wu GY. Update on the Development of Anti-Viral Agents Against Hepatitis C. J Clin Transl Hepatol 2013; 1:9-21. [PMID: 26357602 PMCID: PMC4521270 DOI: 10.14218/jcth.2013.007xx] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 05/14/2013] [Accepted: 05/14/2013] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) infects nearly 170 million people worldwide and causes chronic hepatitis, cirrhosis, and hepatocellular carcinoma. The search for a drug regimen that maximizes efficacy and minimizes side effects is quickly evolving. This review will discuss a wide range of drug targets currently in all phases of development for the treatment of HCV. Direct data from agents in phase III/IV clinical trials will be presented, along with reported side-effect profiles. The mechanism of action of all treatments and resistance issues are highlighted. Special attention is given to available trial data supporting interferon-free treatment regimens. HCV has become an increasingly important public health concern, and it is important for physicians to stay up to date on the rapidly growing novel therapeutic options.
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Affiliation(s)
| | | | | | - Catherine H. Wu
- Department of Medicine, Division of Gastroenterology-Hepatology, University of Connecticut Health Center, Farmington, CT, USA
| | - George Y. Wu
- Department of Medicine, Division of Gastroenterology-Hepatology, University of Connecticut Health Center, Farmington, CT, USA
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28
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Recent insights and novel bioinformatics tools to understand the role of microRNAs binding to 5' untranslated region. Int J Mol Sci 2012; 14:480-95. [PMID: 23271365 PMCID: PMC3565276 DOI: 10.3390/ijms14010480] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 12/06/2012] [Accepted: 12/06/2012] [Indexed: 02/02/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression through the binding of the 3′ untranslated region (3′UTR) of specific mRNAs. MiRNAs are post-transcriptional regulators and determine the repression of translation processes or the degradation of mRNA targets. Recently, another kind of miRNA-mediated regulation of translation (repression or activation) involving the binding of miRNA to the 5′UTR of target gene has been reported. The possible interactions and the mechanism of action have been reported in many works that we reviewed here. Moreover, we discussed also the available bioinformatics tools for predicting the miRNA binding sites in the 5′UTR and public databases collecting this information.
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29
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Abstract
Viruses have adapted a broad range of unique mechanisms to modulate the cellular translational machinery to ensure viral translation at the expense of cellular protein synthesis. Many of these promote virus-specific translation by use of molecular tags on viral mRNA such as internal ribosome entry sites (IRES) and genome-linked viral proteins (VPg) that bind translation machinery components in unusual ways and promote RNA circularization. This review describes recent advances in understanding some of the mechanisms in which animal virus mRNAs gain an advantage over cellular transcripts, including new structural and biochemical insights into IRES function and novel proteins that function as alternate met-tRNAimet carriers in translation initiation. Comparisons between animal and plant virus mechanisms that promote translation of viral mRNAs are discussed.
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Affiliation(s)
- Lucas C Reineke
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
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30
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Lessa FA, Raiol T, Brigido MM, Martins Neto DSB, Walter MEMT, Stadler PF. Clustering rfam 10.1: clans, families, and classes. Genes (Basel) 2012; 3:378-90. [PMID: 24704975 PMCID: PMC3899987 DOI: 10.3390/genes3030378] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2012] [Revised: 06/04/2012] [Accepted: 06/15/2012] [Indexed: 11/16/2022] Open
Abstract
The Rfam database contains information about non-coding RNAs emphasizing their secondary structures and organizing them into families of homologous RNA genes or functional RNA elements. Recently, a higher order organization of Rfam in terms of the so-called clans was proposed along with its “decimal release”. In this proposition, some of the families have been assigned to clans based on experimental and computational data in order to find related families. In the present work we investigate an alternative classification for the RNA families based on tree edit distance. The resulting clustering recovers some of the Rfam clans. The majority of clans, however, are not recovered by the structural clustering. Instead, they get dispersed into larger clusters, which correspond roughly to Genes 2012, 3 379 well-described RNA classes such as snoRNAs, miRNAs, and CRISPRs. In conclusion, a structure-based clustering can contribute to the elucidation of the relationships among the Rfam families beyond the realm of clans and classes.
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Affiliation(s)
- Felipe A Lessa
- Department of Computer Science, Institute of Exact Sciences, University of Brasília, Brasília 70910-900, Brazil.
| | - Tainá Raiol
- Department of Cellular Biology, Institute of Biology, University of Brasília, Brasília 70910-900, Brazil.
| | - Marcelo M Brigido
- Department of Cellular Biology, Institute of Biology, University of Brasília, Brasília 70910-900, Brazil.
| | | | - Maria Emília M T Walter
- Department of Computer Science, Institute of Exact Sciences, University of Brasília, Brasília 70910-900, Brazil.
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.
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31
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Synthesis of two SAPAP3 isoforms from a single mRNA is mediated via alternative translational initiation. Sci Rep 2012; 2:484. [PMID: 22761992 PMCID: PMC3387777 DOI: 10.1038/srep00484] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 05/31/2012] [Indexed: 01/01/2023] Open
Abstract
In mammalian neurons, targeting and translation of specific mRNAs in dendrites contribute to synaptic plasticity. After nuclear export, mRNAs designated for dendritic transport are generally assumed to be translationally dormant and activity of individual synapses may locally trigger their extrasomatic translation. We show that the long, GC-rich 5′-untranslated region of dendritic SAPAP3 mRNA restricts translation initiation via a mechanism that involves an upstream open reading frame (uORF). In addition, the uORF enables the use of an alternative translation start site, permitting synthesis of two SAPAP3 isoforms from a single mRNA. While both isoforms progressively accumulate at postsynaptic densities during early rat brain development, their levels relative to each other vary in different adult rat brain areas. Thus, alternative translation initiation events appear to regulate relative expression of distinct SAPAP3 isoforms in different brain regions, which may function to influence synaptic plasticity.
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Structure of a hepatitis C virus RNA domain in complex with a translation inhibitor reveals a binding mode reminiscent of riboswitches. Proc Natl Acad Sci U S A 2012; 109:5223-8. [PMID: 22431596 DOI: 10.1073/pnas.1118699109] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The internal ribosome entry site (IRES) in the hepatitis C virus (HCV) RNA genome is essential for the initiation of viral protein synthesis. IRES domains adopt well-defined folds that are potential targets for antiviral translation inhibitors. We have determined the three-dimensional structure of the IRES subdomain IIa in complex with a benzimidazole translation inhibitor at 2.2 Å resolution. Comparison to the structure of the unbound RNA in conjunction with studies of inhibitor binding to the target in solution demonstrate that the RNA undergoes a dramatic ligand-induced conformational adaptation to form a deep pocket that resembles the substrate binding sites in riboswitches. The presence of a well-defined ligand-binding pocket within the highly conserved IRES subdomain IIa holds promise for the development of unique anti-HCV drugs with a high barrier to resistance.
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Asad S, Ijaz B, Ahmad W, Kausar H, Sarwar MT, Gull S, Shahid I, Khan MK, Hassan S. Development of persistent HCV genotype 3a infection cell culture model in huh-7 cell. Virol J 2012; 9:11. [PMID: 22234052 PMCID: PMC3292816 DOI: 10.1186/1743-422x-9-11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 01/10/2012] [Indexed: 01/06/2023] Open
Abstract
Background Hepatitis C virus (HCV) is one of the major health concerns globally, with genotype 3a as the most prevalent in Pakistan. Lack of efficient HCV genotype 3a small animal models as well as genomic replicons has hampered the complete understanding of its life cycle, pathogenesis and therapeutic options. In this study we aimed to develop a persistent HCV genotype 3a infectious cell culture model. Methods We inoculated Huh-7 cells with HCV genotype 3a serum. Cells and media supernatant were collected at different time periods up to 40th day post infection. Culture media supernatant was also collected to find out its ability to infect naive Huh-7 cells. Results HCV replication was confirmed at both RNA and protein level through Real Time RCR and western blot using HCV core as marker. In order to validate the persistence of our model for HCV genotype 3a replication we inhibited the HCV replication through core specific siRNAs. The HCV RNA was detected intracellularly from the day one post infection up till 40th day, while HCV core protein was detected from the second day up to 40th day consistently. In culture media supernatant HCV RNA was also actively detected conferring its ability to infect the naive Huh-7 cells. Furthermore, core specific siRNA showed significant inhibition at 24th hour post transfection both at RNA and protein level with progressive increase in the expression of core gene after 3rd day. It clearly depicts that the Huh-7 successfully retained the HCV replication after degradation of siRNA. Conclusion Finally, we report that our persistent infection cell culture model consistently replicate HCV genotype 3a for more than 1 month.
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Affiliation(s)
- Sultan Asad
- Applied and Functional Genomics Lab, Centre of Excellence in Molecular Biology, 87-West Canal Bank Road, 53700 Lahore, Pakistan
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Abstract
Given its essential role in the process of hepatitis C virus (HCV) replication, the viral NS3/4A serine protease is arguably the most thoroughly characterized HCV enzyme and the most intensively pursued anti-HCV target for drug development thus far. Recent data have demonstrated promise for the NS3 protease inhibitor boceprevir, which, when added to the standard of care peginterferon and ribavirin, improves sustained virological response while shortening duration of therapy in genotype-1-infected individuals. This review discusses the mechanism of action of boceprevir, its effects on HCV, and its viral resistance.
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Affiliation(s)
- Paul Y Kwo
- Liver Transplantation, Gastroenterology/Hepatology Division, Indiana University School of Medicine, Indianapolis, IN 46202-5121, USA.
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eIF2A mediates translation of hepatitis C viral mRNA under stress conditions. EMBO J 2011; 30:2454-64. [PMID: 21556050 DOI: 10.1038/emboj.2011.146] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 04/13/2011] [Indexed: 02/08/2023] Open
Abstract
Translation of most mRNAs is suppressed under stress conditions. Phosphorylation of the α-subunit of eukaryotic translation initiation factor 2 (eIF2), which delivers initiator tRNA (Met-tRNA(i)) to the P site of the 40S ribosomal subunit, is responsible for such translational suppression. However, translation of hepatitis C viral (HCV) mRNA is refractory to the inhibitory effects of eIF2α phosphorylation, which prevents translation by disrupting formation of the eIF2-GTP-Met-tRNA(i) ternary complex. Here, we report that eIF2A, an alternative initiator tRNA-binding protein, has a key role in the translation of HCV mRNA during HCV infection, in turn promoting eIF2α phosphorylation by activating the eIF2α kinase PKR. Direct interaction of eIF2A with the IIId domain of the HCV internal ribosome entry site (IRES) is required for eIF2A-dependent translation. These data indicate that stress-independent translation of HCV mRNA occurs by recruitment of eIF2A to the HCV IRES via direct interaction with the IIId domain and subsequent loading of Met-tRNA(i) to the P site of the 40S ribosomal subunit.
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Liu G, Yángüez E, Chen Z, Li C. The duck hepatitis virus 5'-UTR possesses HCV-like IRES activity that is independent of eIF4F complex and modulated by downstream coding sequences. Virol J 2011; 8:147. [PMID: 21450110 PMCID: PMC3072930 DOI: 10.1186/1743-422x-8-147] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 03/31/2011] [Indexed: 02/05/2023] Open
Abstract
Duck hepatitis virus (DHV-1) is a worldwide distributed picornavirus that causes acute and fatal disease in young ducklings. Recently, the complete genome of DHV-1 has been determined and comparative sequence analysis has shown that possesses the typical picornavirus organization but exhibits several unique features. For the first time, we provide evidence that the 626-nucleotide-long 5'-UTR of the DHV-1 genome contains an internal ribosome entry site (IRES) element that functions efficiently both in vitro and in mammalian cells. The prediction of the secondary structure of the DHV-1 IRES shows significant similarity to the hepatitis C virus (HCV) IRES. Moreover, similarly to HCV IRES, DHV-1 IRES can direct translation initiation in the absence of a functional eIF4F complex. We also demonstrate that the activity of the DHV-1 IRES is modulated by a viral coding sequence located downstream of the DHV-1 5'-UTR, which enhances DHV-1 IRES activity both in vitro and in vivo. Furthermore, mutational analysis of the predicted pseudo-knot structures at the 3'-end of the putative DHV-1 IRES supported the presence of conserved domains II and III and, as it has been previously described for other picornaviruses, these structures are essential for keeping the normal internal initiation of translation of DHV-1.
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Affiliation(s)
- Guangqing Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China.
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Li B, Zhang J, Li Z, Tan M. Adeno-associated virus serotype 2 mediated transduction and coexpression of the human apoAI and SR-BI gene in HepG2 cells. Mol Biol Rep 2011; 39:25-32. [PMID: 21431865 DOI: 10.1007/s11033-011-0706-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 03/15/2011] [Indexed: 10/18/2022]
Abstract
Cholesterol efflux is the first step in the reverse cholesterol transport (RCT) pathway, removing excess cholesterol from tissues, including the arterial wall, thus preventing the development of atherosclerosis. Adeno-associated virus (rAAV) has demonstrated significant promise as a DNA-delivery vector to treat serious human diseases. In this study, we constructed recombinant adeno-associated viruses coexpressing apoAI and SR-BI successfully, the double gene mRNA and protein were both strongly expressed in transduced HepG2 cells. A novel safe and efficient method of promoting the reverse cholesterol transport (RCT) may be established. These results may provide a new method for gene therapy of Arteriosclerosis.
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Affiliation(s)
- Bingnan Li
- Experimental Hematology Laboratory, Department of Physiology, Xiang-Ya School of Medicine, Central South University, Changsha, 410078, China
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Starck SR, Shastri N. Non-conventional sources of peptides presented by MHC class I. Cell Mol Life Sci 2011; 68:1471-9. [PMID: 21390547 PMCID: PMC3071930 DOI: 10.1007/s00018-011-0655-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 02/17/2011] [Accepted: 02/18/2011] [Indexed: 12/14/2022]
Abstract
Effectiveness of immune surveillance of intracellular viruses and bacteria depends upon a functioning antigen presentation pathway that allows infected cells to reveal the presence of an intracellular pathogen. The antigen presentation pathway uses virtually all endogenous polypeptides as a source to produce antigenic peptides that are eventually chaperoned to the cell surface by MHC class I molecules. Intriguingly, MHC I molecules present peptides encoded not only in the primary open reading frames but also those encoded in alternate reading frames. Here, we review recent studies on the generation of cryptic pMHC I. We focus on the immunological significance of cryptic pMHC I, and the novel translational mechanisms that allow production of these antigenic peptides from unconventional sources.
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Affiliation(s)
- Shelley R. Starck
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, LSA 421, Berkeley, CA 94720-3200 USA
| | - Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, LSA 421, Berkeley, CA 94720-3200 USA
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Structural features of the Seneca Valley virus internal ribosome entry site (IRES) element: a picornavirus with a pestivirus-like IRES. J Virol 2011; 85:4452-61. [PMID: 21325406 DOI: 10.1128/jvi.01107-10] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The RNA genome of Seneca Valley virus (SVV), a recently identified picornavirus, contains an internal ribosome entry site (IRES) element which has structural and functional similarity to that from classical swine fever virus (CSFV) and hepatitis C virus, members of the Flaviviridae. The SVV IRES has an absolute requirement for the presence of a short region of virus-coding sequence to allow it to function either in cells or in rabbit reticulocyte lysate. The IRES activity does not require the translation initiation factor eIF4A or intact eIF4G. The predicted secondary structure indicates that the SVV IRES is more closely related to the CSFV IRES, including the presence of a bipartite IIId domain. Mutagenesis of the SVV IRES, coupled to functional assays, support the core elements of the IRES structure model, but surprisingly, deletion of the conserved IIId(2) domain had no effect on IRES activity, including 40S and eIF3 binding. This is the first example of a picornavirus IRES that is most closely related to the CSFV IRES and suggests the possibility of multiple, independent recombination events between the genomes of the Picornaviridae and Flaviviridae to give rise to similar IRES elements.
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Komar AA, Hatzoglou M. Cellular IRES-mediated translation: the war of ITAFs in pathophysiological states. Cell Cycle 2011; 10:229-40. [PMID: 21220943 DOI: 10.4161/cc.10.2.14472] [Citation(s) in RCA: 297] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Translation of cellular mRNAs via initiation at Internal Ribosome Entry Sites (IRESs) has received increased attention during recent years due to its emerging significance for many physiological and pathological stress conditions in eukaryotic cells. Expression of genes bearing IRES elements in their mRNAs is controlled by multiple molecular mechanisms, with IRES-mediated translation favored under conditions when cap-dependent translation is compromised. In this review, we discuss recent advances in the field and future directions that may bring us closer to understanding the complex mechanisms that guide cellular IRES-mediated expression. We present examples in which the competitive action of IRES-transacting factors (ITAFs) plays a pivotal role in IRES-mediated translation and thereby controls cell-fate decisions leading to either pro-survival stress adaptation or cell death.
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Affiliation(s)
- Anton A Komar
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH, USA.
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Effects of recombinant adeno-associated viral vectors on angiopoiesis and osteogenesis in cultured rabbit bone marrow stem cells via co-expressing hVEGF and hBMP genes: a preliminary study in vitro. Tissue Cell 2011; 42:314-21. [PMID: 20817238 DOI: 10.1016/j.tice.2010.07.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Revised: 06/30/2010] [Accepted: 07/08/2010] [Indexed: 11/24/2022]
Abstract
OBJECTIVE VEGF and BMP play important roles in angiogenesis and osteogenesis. Combining these two factors may be a promising therapeutic strategy for avascular necrosis of the femoral head (ANFH). METHODS Rabbit bone marrow-derived mesenchymal stem cells (BMSCs) were isolated and purified by density gradient centrifugation combined with attachment culture methods. The purity and characteristics of the BMSCs were detected by cell surface antigen identification. The best MOI of BMSCs transfected with rAAV was detected by fluorescent cell counting, and cell viability was determined by MTT assay. Expression of the genes of interest was detected by GFP gene expression, RT-PCR assay, and ELISA assay. The biological activities of VEGF and BMP were detected by angiogenic and osteogenic assays. RESULTS The best MOI of BMSCs transfected with rAAV was 5 x 10(4)v.g./cell. Cell growth curves showed vigorous cell viability. Expressions of the GFP, VEGF165, and BMP(7) genes were detected 1 day post-transfection and peaked 14 days post-transfection. Expression of the genes of interest was sustained over 1 month. VEGF and BMP proteins secreted from BMSCs transfected with rAAV-hVEGF(165)-IRES-hBMP(7) enhanced angiogenesis and osteogenesis in vitro. CONCLUSION Recombinant adeno-associated viral vectors co-expressing the hVEGF(165) and hBMP(7) genes showed efficient gene expression ability. The VEGF(165) and BMP(7) proteins expressed from the vector have efficient biological activity in vitro.
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Matsuda D, Mauro VP. Determinants of initiation codon selection during translation in mammalian cells. PLoS One 2010; 5:e15057. [PMID: 21124832 PMCID: PMC2991327 DOI: 10.1371/journal.pone.0015057] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Accepted: 10/15/2010] [Indexed: 11/24/2022] Open
Abstract
Factors affecting translation of mRNA contribute to the complexity of eukaryotic proteomes. In some cases, translation of a particular mRNA can generate multiple proteins. However, the factors that determine whether ribosomes initiate translation from the first AUG codon in the transcript, from a downstream codon, or from multiple sites are not completely understood. Various mRNA properties, including AUG codon-accessibility and 5′ leader length have been proposed as potential determinants that affect where ribosomes initiate translation. To explore this issue, we performed studies using synthetic mRNAs with two in-frame AUG codons−both in excellent context. Open reading frames initiating at AUG1 and AUG2 encode large and small isoforms of a reporter protein, respectively. Translation of such an mRNA in COS-7 cells was shown to be 5′ cap-dependent and to occur efficiently from both AUG codons. AUG codon-accessibility was modified by using two different elements: an antisense locked nucleic acid oligonucleotide and an exon-junction complex. When either element was used to mask AUG1, the ratio of the proteins synthesized changed, favoring the smaller (AUG2-initiated) protein. In addition, we observed that increased leader length by itself changed the ratio of the proteins and favored initiation at AUG1. These observations demonstrate that initiation codon selection is affected by various factors, including AUG codon-accessibility and 5′ leader length, and is not necessarily determined by the order of AUG codons (5′→3′). The modulation of AUG codon accessibility may provide a powerful means of translation regulation in eukaryotic cells.
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Affiliation(s)
- Daiki Matsuda
- Department of Neurobiology, The Scripps Research Institute and The Skaggs Institute for Chemical Biology, La Jolla, California, United States of America
| | - Vincent P. Mauro
- Department of Neurobiology, The Scripps Research Institute and The Skaggs Institute for Chemical Biology, La Jolla, California, United States of America
- * E-mail:
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Sanz MA, Welnowska E, Redondo N, Carrasco L. Translation driven by picornavirus IRES is hampered from Sindbis virus replicons: rescue by poliovirus 2A protease. J Mol Biol 2010; 402:101-17. [PMID: 20643140 DOI: 10.1016/j.jmb.2010.07.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Revised: 07/06/2010] [Accepted: 07/12/2010] [Indexed: 01/08/2023]
Abstract
Alphavirus replicons are very useful for analyzing different aspects of viral molecular biology. They are also useful tools in the development of new vaccines and highly efficient expression of heterologous genes. We have investigated the translatability of Sindbis virus (SV) subgenomic mRNA bearing different 5'-untranslated regions, including several viral internal ribosome entry sites (IRESs) from picornaviruses, hepatitis C virus, and cricket paralysis virus. Our findings indicate that all these IRES-containing mRNAs are initially translated in culture cells transfected with the corresponding SV replicon but their translation is inhibited in the late phase of SV replication. Notably, co-expression of different poliovirus (PV) non-structural genes reveals that the protease 2A (2A(pro)) is able to increase translation of subgenomic mRNAs containing the PV or encephalomyocarditis virus IRESs but not of those of hepatitis C virus or cricket paralysis virus. A PV 2A(pro) variant deficient in eukaryotic initiation factor (eIF) 4GI cleavage or PV protease 3C, neither of which cleaves eIF4GI, does not increase picornavirus IRES-driven translation, whereas L protease from foot-and-mouth disease virus also rescues translation. These findings suggest that the replicative foci of SV-infected cells where translation takes place are deficient in components necessary to translate IRES-containing mRNAs. In the case of picornavirus IRESs, cleavage of eIF4GI accomplished by PV 2A(pro) or foot-and-mouth disease virus protease L rescues this inhibition. eIF4GI co-localizes with ribosomes both in cells electroporated with SV replicons bearing the picornavirus IRES and in cells co-electroporated with replicons that express PV 2A(pro). These findings support the idea that eIF4GI cleavage is necessary to rescue the translation driven by picornavirus IRESs in baby hamster kidney cells that express SV replicons.
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Affiliation(s)
- Miguel Angel Sanz
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM,C/Nicolás Cabrera, 1,Universidad Autónoma,Cantoblanco, 28049 Madrid,Spain.
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Abstract
IMPORTANCE OF THE FIELD Currently, 170 million people worldwide are affected by the HCV. Chronic HCV infection is amongst the leading causes of chronic liver disease and its complications such as cirrhosis and hepatocellular carcinoma, making it the most common reason for liver transplantation. The current standard of treatment for HCV is pegylated IFN-α plus ribavirin. This treatment, when administered for the standard duration, allows sustained virological response (SVR) in ∼ 50% of patients infected with HCV and about 40% for HCV genotype 1, the most prevalent form of HCV in the US. SVR rates for populations with co-morbidities (patients with chronic renal disease) and certain ethnic backgrounds (African Americans and Hispanics) are lower. Given the high prevalence and relatively low cure rates of current antiviral therapy, the burden of HCV is enormous. AREAS COVERED IN THIS REVIEW Faced with this urgent and growing medical need, research into novel therapeutic compounds for the treatment of HCV is a rapidly growing industry. Several novel compounds are in advanced stages of clinical development, such as HCV protease inhibitors (particularly those against NS3-4A protease), HCV polymerase inhibitors (including both nucleoside and non-nucleoside analogs) and cyclophilin inhibitors. WHAT THE READER WILL GAIN HCV treatment has seen many advances in the last decade and the discovery process has been fraught with both successes and disappointments. Through a process of rigorous research, the current late stage novel HCV therapeutics seem to have overcome some of the obstacles met by their early predecessors and offer the promise of meeting the shortfalls of the current standard of treatment. TAKE HOME MESSAGE Data from clinical trials are encouraging and suggest that combination therapies of these novel agents may have the potential to shorten treatment duration and increase viral clearance when used in conjunction with pegylated IFN-α and ribavirin.
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Affiliation(s)
- Aybike Birerdinc
- Betty and Guy Beatty Center for Integrated Research, Inova Health System, Falls Church, VA, USA
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Lavender CA, Ding F, Dokholyan NV, Weeks KM. Robust and generic RNA modeling using inferred constraints: a structure for the hepatitis C virus IRES pseudoknot domain. Biochemistry 2010; 49:4931-3. [PMID: 20545364 PMCID: PMC2889920 DOI: 10.1021/bi100142y] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
RNA function is dependent on its structure, yet three-dimensional folds for most biologically important RNAs are unknown. We develop a generic discrete molecular dynamics-based modeling system that uses long-range constraints inferred from diverse biochemical or bioinformatic analyses to create statistically significant (p < 0.01) nativelike folds for RNAs of known structure ranging from 45 to 158 nucleotides. We then predict the unknown structure of the hepatitis C virus internal ribosome entry site (IRES) pseudoknot domain. The resulting RNA model rationalizes independent solvent accessibility and cryo-electron microscopy structure information. The pseudoknot domain positions the AUG start codon near the mRNA channel and is tRNA-like, suggesting the IRES employs molecular mimicry as a functional strategy.
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Affiliation(s)
- Christopher A. Lavender
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
| | - Feng Ding
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599-7260
| | - Nikolay V. Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599-7260
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
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Fabian MR, Sonenberg N, Filipowicz W. Regulation of mRNA Translation and Stability by microRNAs. Annu Rev Biochem 2010; 79:351-79. [PMID: 20533884 DOI: 10.1146/annurev-biochem-060308-103103] [Citation(s) in RCA: 2307] [Impact Index Per Article: 164.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Marc Robert Fabian
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, Quebec, H3G 1Y6, Canada;
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, Quebec, H3G 1Y6, Canada;
| | - Witold Filipowicz
- Friedrich Miescher Institute for Biomedical Research, 4002 Basel, Switzerland;
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Abstract
Hepatitis C virus (HCV) causes significant morbidity and mortality worldwide with nearly 3% of the world population infected by this virus. Fortunately, this virus does not establish latency, and hence it may be possible to eradicate it. HCV is strongly associated with liver cirrhosis and hepatocellular carcinoma and is currently treated with pegylated interferon-alpha (peg-IFN-alpha) and ribavirin. Unfortunately, these limited treatment options often produce significant side effects, and currently, complete eradication of virus with combined drug modalities has not yet been achieved for the majority of chronically HCV-infected individuals. Restricted treatment options, lack of a universal cure for HCV and the link between chronic infection, liver cirrhosis and hepatocellular carcinoma necessitate design of novel drugs and treatment options. Understanding the relationship between the immune response, viral clearance and inhibition of viral replication with pharmacology-based design can ultimately allow for complete eradication of HCV. This review focuses upon significant novel preclinical and clinical specifically targeted antiviral therapy (STAT-C) drugs under development, highlights their mechanism of action, and discusses their impact on systemic viral loads and permanent clearance of infection.
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Affiliation(s)
- R F Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Veterans Affairs Medical Center/Emory University School of Medicine, Atlanta, GA, USA.
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Fabian MR, Sundermeier TR, Sonenberg N. Understanding How miRNAs Post-Transcriptionally Regulate Gene Expression. MIRNA REGULATION OF THE TRANSLATIONAL MACHINERY 2010; 50:1-20. [DOI: 10.1007/978-3-642-03103-8_1] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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49
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Malygin AA, Bochkaeva ZV, Bondarenko EI, Kossinova OA, Loktev VB, Shatsky IN, Karpova GG. Binding of the IRES of hepatitis C virus RNA to the 40S ribosomal subunit: Role of p40. Mol Biol 2009. [DOI: 10.1134/s0026893309060120] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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50
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de Miranda JR, Cordoni G, Budge G. The Acute bee paralysis virus-Kashmir bee virus-Israeli acute paralysis virus complex. J Invertebr Pathol 2009; 103 Suppl 1:S30-47. [PMID: 19909972 DOI: 10.1016/j.jip.2009.06.014] [Citation(s) in RCA: 187] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Accepted: 06/30/2009] [Indexed: 10/20/2022]
Abstract
Acute bee paralysis virus (ABPV), Kashmir bee virus (KBV) and Israeli acute paralysis virus (IAPV) are part of a complex of closely related viruses from the Family Dicistroviridae. These viruses have a widespread prevalence in honey bee (Apis mellifera) colonies and a predominantly sub-clinical etiology that contrasts sharply with the extremely virulent pathology encountered at elevated titres, either artificially induced or encountered naturally. These viruses are frequently implicated in honey bee colony losses, especially when the colonies are infested with the parasitic mite Varroa destructor. Here we review the historical and recent literature of this virus complex, covering history and origins; the geographic, host and tissue distribution; pathology and transmission; genetics and variation; diagnostics, and discuss these within the context of the molecular and biological similarities and differences between the viruses. We also briefly discuss three recent developments relating specifically to IAPV, concerning its association with Colony Collapse Disorder, treatment of IAPV infection with siRNA and possible honey bee resistance to IAPV.
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Affiliation(s)
- Joachim R de Miranda
- Department of Ecology, Swedish University of Agricultural Sciences, 750-07 Uppsala, Sweden.
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