1
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Jäger N, Ayyub SA, Peske F, Liedtke D, Bohne J, Hoffmann M, Rodnina MV, Pöhlmann S. The Inhibition of Gag-Pol Expression by the Restriction Factor Shiftless Is Dispensable for the Restriction of HIV-1 Infection. Viruses 2024; 16:583. [PMID: 38675925 PMCID: PMC11055011 DOI: 10.3390/v16040583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
The interferon-induced host cell protein Shiftless (SFL) inhibits -1 programmed ribosomal frameshifting (-1PRF) required for the expression of HIV-1 Gal-Pol and the formation of infectious HIV-1 particles. However, the specific regions in SFL required for antiviral activity and the mechanism by which SFL inhibits -1PRF remain unclear. Employing alanine scanning mutagenesis, we found that basic amino acids in the predicted zinc ribbon motif of SFL are essential for the suppression of Gag-Pol expression but dispensable for anti-HIV-1 activity. We have shown that SFL inhibits the expression of the murine leukemia virus (MLV) Gag-Pol polyprotein and the formation of infectious MLV particles, although Gag-Pol expression of MLV is independent of -1PRF but requires readthrough of a stop codon. These findings indicate that SFL might inhibit HIV-1 infection by more than one mechanism and that SFL might target programmed translational readthrough as well as -1PRF signals, both of which are regulated by mRNA secondary structure elements.
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Affiliation(s)
- Niklas Jäger
- Infection Biology Unit, German Primate Center–Leibniz Institute for Primate Research, 37077 Göttingen, Germany;
- Faculty of Biology and Psychology, University Göttingen, 37073 Göttingen, Germany
| | - Shreya Ahana Ayyub
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; (S.A.A.); (F.P.); (D.L.); (M.V.R.)
| | - Frank Peske
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; (S.A.A.); (F.P.); (D.L.); (M.V.R.)
| | - David Liedtke
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; (S.A.A.); (F.P.); (D.L.); (M.V.R.)
| | - Jens Bohne
- Institute of Virology, Hannover Medical School, 30625 Hannover, Germany;
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center–Leibniz Institute for Primate Research, 37077 Göttingen, Germany;
- Faculty of Biology and Psychology, University Göttingen, 37073 Göttingen, Germany
| | - Marina V. Rodnina
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; (S.A.A.); (F.P.); (D.L.); (M.V.R.)
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center–Leibniz Institute for Primate Research, 37077 Göttingen, Germany;
- Faculty of Biology and Psychology, University Göttingen, 37073 Göttingen, Germany
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2
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Ren G, Gu X, Zhang L, Gong S, Song S, Chen S, Chen Z, Wang X, Li Z, Zhou Y, Li L, Yang J, Lai F, Dang Y. Ribosomal frameshifting at normal codon repeats recodes functional chimeric proteins in human. Nucleic Acids Res 2024; 52:2463-2479. [PMID: 38281188 PMCID: PMC10954444 DOI: 10.1093/nar/gkae035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 01/30/2024] Open
Abstract
Ribosomal frameshifting refers to the process that ribosomes slip into +1 or -1 reading frame, thus produce chimeric trans-frame proteins. In viruses and bacteria, programmed ribosomal frameshifting can produce essential trans-frame proteins for viral replication or regulation of other biological processes. In humans, however, functional trans-frame protein derived from ribosomal frameshifting is scarcely documented. Combining multiple assays, we show that short codon repeats could act as cis-acting elements that stimulate ribosomal frameshifting in humans, abbreviated as CRFS hereafter. Using proteomic analyses, we identified many putative CRFS events from 32 normal human tissues supported by trans-frame peptides positioned at codon repeats. Finally, we show a CRFS-derived trans-frame protein (HDAC1-FS) functions by antagonizing the activities of HDAC1, thus affecting cell migration and apoptosis. These data suggest a novel type of translational recoding associated with codon repeats, which may expand the coding capacity of mRNA and diversify the regulation in human.
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Affiliation(s)
- Guiping Ren
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
| | - Xiaoqian Gu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
| | - Lu Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
| | - Shimin Gong
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
| | - Shuang Song
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
| | - Shunkai Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
| | - Zhenjing Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
| | - Xiaoyan Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
| | - Zhanbiao Li
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
| | - Yingshui Zhou
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
| | - Longxi Li
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
| | - Jiao Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
| | - Fan Lai
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
| | - Yunkun Dang
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
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3
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Bermudez Y, Hatfield D, Muller M. A Balancing Act: The Viral-Host Battle over RNA Binding Proteins. Viruses 2024; 16:474. [PMID: 38543839 PMCID: PMC10974049 DOI: 10.3390/v16030474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/16/2024] [Accepted: 03/18/2024] [Indexed: 04/01/2024] Open
Abstract
A defining feature of a productive viral infection is the co-opting of host cell resources for viral replication. Despite the host repertoire of molecular functions and biological counter measures, viruses still subvert host defenses to take control of cellular factors such as RNA binding proteins (RBPs). RBPs are involved in virtually all steps of mRNA life, forming ribonucleoprotein complexes (mRNPs) in a highly ordered and regulated process to control RNA fate and stability in the cell. As such, the hallmark of the viral takeover of a cell is the reshaping of RNA fate to modulate host gene expression and evade immune responses by altering RBP interactions. Here, we provide an extensive review of work in this area, particularly on the duality of the formation of RNP complexes that can be either pro- or antiviral. Overall, in this review, we highlight the various ways viruses co-opt RBPs to regulate RNA stability and modulate the outcome of infection by gathering novel insights gained from research studies in this field.
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Affiliation(s)
| | | | - Mandy Muller
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA; (Y.B.); (D.H.)
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4
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Karousis ED, Schubert K, Ban N. Coronavirus takeover of host cell translation and intracellular antiviral response: a molecular perspective. EMBO J 2024; 43:151-167. [PMID: 38200146 PMCID: PMC10897431 DOI: 10.1038/s44318-023-00019-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 11/01/2023] [Accepted: 11/24/2023] [Indexed: 01/12/2024] Open
Abstract
Coronaviruses are a group of related RNA viruses that cause respiratory diseases in humans and animals. Understanding the mechanisms of translation regulation during coronaviral infections is critical for developing antiviral therapies and preventing viral spread. Translation of the viral single-stranded RNA genome in the host cell cytoplasm is an essential step in the life cycle of coronaviruses, which affects the cellular mRNA translation landscape in many ways. Here we discuss various viral strategies of translation control, including how members of the Betacoronavirus genus shut down host cell translation and suppress host innate immune functions, as well as the role of the viral non-structural protein 1 (Nsp1) in the process. We also outline the fate of viral RNA, considering stress response mechanisms triggered in infected cells, and describe how unique viral RNA features contribute to programmed ribosomal -1 frameshifting, RNA editing, and translation shutdown evasion.
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Affiliation(s)
- Evangelos D Karousis
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Katharina Schubert
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
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5
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Ito H, Machida K, Hasumi M, Ueyama M, Nagai Y, Imataka H, Taguchi H. Reconstitution of C9orf72 GGGGCC repeat-associated non-AUG translation with purified human translation factors. Sci Rep 2023; 13:22826. [PMID: 38129650 PMCID: PMC10739749 DOI: 10.1038/s41598-023-50188-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/16/2023] [Indexed: 12/23/2023] Open
Abstract
Nucleotide repeat expansion of GGGGCC (G4C2) in the non-coding region of C9orf72 is the most common genetic cause underlying amyotrophic lateral sclerosis and frontotemporal dementia. Transcripts harboring this repeat expansion undergo the translation of dipeptide repeats via a non-canonical process known as repeat-associated non-AUG (RAN) translation. In order to ascertain the essential components required for RAN translation, we successfully recapitulated G4C2-RAN translation using an in vitro reconstituted translation system comprising human factors, namely the human PURE system. Our findings conclusively demonstrate that the presence of fundamental translation factors is sufficient to mediate the elongation from the G4C2 repeat. Furthermore, the initiation mechanism proceeded in a 5' cap-dependent manner, independent of eIF2A or eIF2D. In contrast to cell lysate-mediated RAN translation, where longer G4C2 repeats enhanced translation, we discovered that the expansion of the G4C2 repeats inhibited translation elongation using the human PURE system. These results suggest that the repeat RNA itself functions as a repressor of RAN translation. Taken together, our utilization of a reconstituted RAN translation system employing minimal factors represents a distinctive and potent approach for elucidating the intricacies underlying RAN translation mechanism.
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Grants
- JPMJFS2112 Japan Science and Technology Agency
- JP26116002 Ministry of Education, Culture, Sports, Science and Technology
- JP18H03984 Ministry of Education, Culture, Sports, Science and Technology
- JP21H04763 Ministry of Education, Culture, Sports, Science and Technology
- JP20H05925 Ministry of Education, Culture, Sports, Science and Technology
- 2019-25 Mitsubishi Foundation
- 2019 Uehara Memorial Foundation
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Affiliation(s)
- Hayato Ito
- School of Life Science and Technology, Tokyo Institute of Technology, S2-19, Nagatsuta 4259, Midori-ku, Yokohama, 226-8501, Japan
| | - Kodai Machida
- Graduate School of Engineering, University of Hyogo, Shosha, 2167, Himeji, Hyogo, 671-2280, Japan
| | - Mayuka Hasumi
- School of Life Science and Technology, Tokyo Institute of Technology, S2-19, Nagatsuta 4259, Midori-ku, Yokohama, 226-8501, Japan
| | - Morio Ueyama
- Department of Neurology, Faculty of Medicine, Kindai University, Ohonohigashi 377-2, Osaka-Sayama, 589-8511, Japan
| | - Yoshitaka Nagai
- Department of Neurology, Faculty of Medicine, Kindai University, Ohonohigashi 377-2, Osaka-Sayama, 589-8511, Japan
| | - Hiroaki Imataka
- Graduate School of Engineering, University of Hyogo, Shosha, 2167, Himeji, Hyogo, 671-2280, Japan
| | - Hideki Taguchi
- School of Life Science and Technology, Tokyo Institute of Technology, S2-19, Nagatsuta 4259, Midori-ku, Yokohama, 226-8501, Japan.
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, S2-19, Nagatsuta 4259, Midori-ku, Yokohama, 226-8501, Japan.
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6
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Huang SH, Chen SC, Wu TY, Chen CY, Yu CH. Programmable modulation of ribosomal frameshifting by mRNA targeting CRISPR-Cas12a system. iScience 2023; 26:108492. [PMID: 38125012 PMCID: PMC10730746 DOI: 10.1016/j.isci.2023.108492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/13/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Minus 1 programmed ribosomal frameshifting (-1 PRF) is a conserved translational regulation event essential for critical biological processes, including the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication. Efficient trans-modulation of the structured RNA element crucial to -1 PRF will endow the therapeutic application. Here, we demonstrate that CRISPR RNA can stimulate efficient -1 PRF. Assembled CRISPR-Cas12a, but not CRISPR-Cas9, complex further enhances -1 PRF efficiency through its higher capacity to stall translating ribosomes. We additionally perform CRISPR-Cas12a targeting to impair the SARS-CoV-2 frameshifting pseudoknot structure via a focused screening. We demonstrate that targeting CRISPR-Cas12a results in more than 70% suppression of -1 PRF in vitro and about 50% suppression in mammalian cells. Our results show the expanded function of the CRISPR-Cas12 system in modulating -1 PRF efficiency through stalling ribosomes and deforming frameshifting stimulatory signals, which could serve as a new strategy for future coronavirus pandemics.
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Affiliation(s)
- Shih-Hong Huang
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shih-Cheng Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | | | - Cheng-Yao Chen
- YD BioLabs, Inc., Hsinchu, Taiwan
- School of Medical Laboratory Science and Biotechnology, Taipei Medical University, Taipei, Taiwan
| | - Chien-Hung Yu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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7
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Wang X, Zhang AM. Functional features of a novel interferon-stimulated gene SHFL: a comprehensive review. Front Microbiol 2023; 14:1323231. [PMID: 38149274 PMCID: PMC10750386 DOI: 10.3389/fmicb.2023.1323231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023] Open
Abstract
Various interferon (IFN)-stimulated genes (ISGs), expressed via Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling pathway-stimulated IFNs to increase antiviral effects or regulate immune response, perform different roles in virus-infected cells. In recent years, a novel ISG, SHFL, which is located in the genomic region 19p13.2 and comprises two isoforms, has been studied as a virus-inhibiting agent. Studies have shown that SHFL suppressive effects on human immunodeficiency virus-1 (HIV), Zika virus (ZIKV), dengue virus (DENV), hepatitis C virus (HCV), Japanese encephalitis virus (JEV), porcine epidemic diarrhea virus (PEDV), Human enterovirus A71 (EV-A71) and Kaposi's sarcoma-associated herpes virus (KSHV). SHFL interacts with various viral and host molecules to inhibit viral life circle and activities, such as replication, translation, and ribosomal frameshifting, or regulates host pathways to degrade viral proteins. In this review, we summarized the functional features of SHFL to provide insights to underlying mechanisms of the antiviral effects of SHFL and explored its potential function.
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Affiliation(s)
| | - A-Mei Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
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8
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Kelly JA, Dinman JD. Shiftless Is a Novel Member of the Ribosome Stress Surveillance Machinery That Has Evolved to Play a Role in Innate Immunity and Cancer Surveillance. Viruses 2023; 15:2296. [PMID: 38140537 PMCID: PMC10747187 DOI: 10.3390/v15122296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
A longstanding paradox in molecular biology has centered on the question of how very long proteins are synthesized, despite numerous measurements indicating that ribosomes spontaneously shift reading frame at rates that should preclude their ability completely translate their mRNAs. Shiftless (SFL; C19orf66) was originally identified as an interferon responsive gene encoding an antiviral protein, indicating that it is part of the innate immune response. This activity is due to its ability to bind ribosomes that have been programmed by viral sequence elements to shift reading frame. Curiously, Shiftless is constitutively expressed at low levels in mammalian cells. This study examines the effects of altering Shiftless homeostasis, revealing how it may be used by higher eukaryotes to identify and remove spontaneously frameshifted ribosomes, resolving the apparent limitation on protein length. Data also indicate that Shiftless plays a novel role in the ribosome-associated quality control program. A model is proposed wherein SFL recognizes and arrests frameshifted ribosomes, and depending on SFL protein concentrations, either leads to removal of frameshifted ribosomes while leaving mRNAs intact, or to mRNA degradation. We propose that SFL be added to the growing pantheon of proteins involved in surveilling translational fidelity and controlling gene expression in higher eukaryotes.
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Affiliation(s)
| | - Jonathan D. Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA;
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9
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Hatfield D, Rodriguez W, Mehrmann T, Muller M. The antiviral protein Shiftless blocks p-body formation during KSHV infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.16.567185. [PMID: 38014318 PMCID: PMC10680731 DOI: 10.1101/2023.11.16.567185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
P-bodies (PB) are non-membranous foci involved in determining mRNA fate by affecting translation and mRNA decay. In this study, we identify the anti-viral factor SHFL as a potent disassembly factor of PB. We show that PBs remain sparse in the presence of SHFL even in the context of oxidative stress, a major trigger for PB induction. Mutational approaches revealed that SHFL RNA binding activity is not required for its PB disassembly function. However, we have identified a new region of SHFL which bridges two distant domains as responsible for PB disassembly. Furthermore, we show that SHFL ability to disrupt PB formation is directly linked to its anti-viral activity during KSHV infection. While WT SHFL efficiently restricts KSHV lytic cycle, PB disruption defective mutants no longer lead to reactivation defects. SHFL-mediated PB disassembly also leads to increased expression of key anti-viral cytokines, further expanding SHFL dependent anti-viral state. Taken together, our observations suggest a role of SHFL in PB disassembly, which could have important anti-viral consequences during infection.
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10
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Zhao Y, Sui L, Wu P, Li L, Liu L, Ma B, Wang W, Chi H, Wang ZD, Wei Z, Hou Z, Zhang K, Niu J, Jin N, Li C, Zhao J, Wang G, Liu Q. EGR1 functions as a new host restriction factor for SARS-CoV-2 to inhibit virus replication through the E3 ubiquitin ligase MARCH8. J Virol 2023; 97:e0102823. [PMID: 37772822 PMCID: PMC10653994 DOI: 10.1128/jvi.01028-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/13/2023] [Indexed: 09/30/2023] Open
Abstract
IMPORTANCE Emerging vaccine-breakthrough severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants highlight an urgent need for novel antiviral therapies. Understanding the pathogenesis of coronaviruses is critical for developing antiviral drugs. Here, we demonstrate that the SARS-CoV-2 N protein suppresses interferon (IFN) responses by reducing early growth response gene-1 (EGR1) expression. The overexpression of EGR1 inhibits SARS-CoV-2 replication by promoting IFN-regulated antiviral protein expression, which interacts with and degrades SARS-CoV-2 N protein via the E3 ubiquitin ligase MARCH8 and the cargo receptor NDP52. The MARCH8 mutants without ubiquitin ligase activity are no longer able to degrade SARS-CoV-2 N proteins, indicating that MARCH8 degrades SARS-CoV-2 N proteins dependent on its ubiquitin ligase activity. This study found a novel immune evasion mechanism of SARS-CoV-2 utilized by the N protein, which is helpful for understanding the pathogenesis of SARS-CoV-2 and guiding the design of new prevention strategies against the emerging coronaviruses.
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Affiliation(s)
- Yinghua Zhao
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Liyan Sui
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Ping Wu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Letian Li
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Li Liu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Baohua Ma
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Wenfang Wang
- Department of Pathogenbiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, China
| | - Hongmiao Chi
- Department of Pathogenbiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, China
| | - Ze-Dong Wang
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Zhengkai Wei
- School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Zhijun Hou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Kaiyu Zhang
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Junqi Niu
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Ningyi Jin
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Chang Li
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Jixue Zhao
- Department of Pediatric Surgery, The First Hospital of Jilin University, Changchun, China
| | - Guoqing Wang
- Department of Pathogenbiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, China
| | - Quan Liu
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
- School of Life Sciences and Engineering, Foshan University, Foshan, China
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
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11
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Abstract
Protein synthesis by the ribosome is the final stage of biological information transfer and represents an irreversible commitment to gene expression. Accurate translation of messenger RNA is therefore essential to all life, and spontaneous errors by the translational machinery are highly infrequent (∼1/100,000 codons). Programmed -1 ribosomal frameshifting (-1PRF) is a mechanism in which the elongating ribosome is induced at high frequency to slip backward by one nucleotide at a defined position and to continue translation in the new reading frame. This is exploited as a translational regulation strategy by hundreds of RNA viruses, which rely on -1PRF during genome translation to control the stoichiometry of viral proteins. While early investigations of -1PRF focused on virological and biochemical aspects, the application of X-ray crystallography and cryo-electron microscopy (cryo-EM), and the advent of deep sequencing and single-molecule approaches have revealed unexpected structural diversity and mechanistic complexity. Molecular players from several model systems have now been characterized in detail, both in isolation and, more recently, in the context of the elongating ribosome. Here we provide a summary of recent advances and discuss to what extent a general model for -1PRF remains a useful way of thinking.
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Affiliation(s)
- Chris H Hill
- York Structural Biology Laboratory, York Biomedical Research Institute, Department of Biology, University of York, York, United Kingdom;
| | - Ian Brierley
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom;
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12
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Zhang Y, Feng Y, Liu Y, Liu L, Xia X, Zhang AM. Genetic polymorphisms in the C19orf66 gene influenced HIV-1 infection in a Yunnan population. PeerJ 2023; 11:e16005. [PMID: 37701839 PMCID: PMC10493081 DOI: 10.7717/peerj.16005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 08/09/2023] [Indexed: 09/14/2023] Open
Abstract
Background Due to the deficiencies of vaccines and effective medicine, the human immunodeficiency virus (HIV) infection mechanism should be studied. The C19orf66 gene, one of the interferon-stimulated genes (ISGs), expresses broad-spectra anti-viral activity, including inhibiting HIV replication. Methods In this study, we collect 421 HIV-1 infected patients and 448 controls to genotype three SNPs in the C19orf66 gene. Then, the association between SNPs and biochemical indices/ HIV-1 subtypes are analyzed. Results Genotypes CC and CT of rs12611087 show statistically lower and higher frequencies in HIV-1 infected patients than in controls, respectively. Alleles C and T of rs12611087 play protective and risk roles in Yunnan HIV population, respectively. Biochemical indices analysis shows that HIV-1 infected persons carried genotype TT of rs77076061 express significantly lower CD3+/CD45+ ratio level and higher IBIL level. The epidemic subtypes of HIV-1 patients in this study are CRF 07_BC and CRF 08_BC. Moreover, subtype CRF 08_BC tends to infect persons with genotype CC of rs12611087. Conclusion The genetic polymorphisms of the C19orf66 gene are firstly studied and reported to associate with HIV-1 infection and biochemical indices of patients in Yunnan. Furthermore, subtype CRF 08_BC infection could be influenced by genotypes of SNP in the C19orf66 gene.
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Affiliation(s)
- Yaxiang Zhang
- Kunming University of Science and Technology, Kunming, China
| | - Yue Feng
- Kunming University of Science and Technology, Kunming, China
| | - Yang Liu
- Kunming University of Science and Technology, Kunming, China
| | - Li Liu
- Kunming University of Science and Technology, Kunming, China
| | - Xueshan Xia
- Kunming University of Science and Technology, Kunming, China
- Kunming Medical University, Kunming, China
| | - A-Mei Zhang
- Kunming University of Science and Technology, Kunming, China
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13
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Wei LH, Sun Y, Guo JU. Genome-wide CRISPR screens identify noncanonical translation factor eIF2A as an enhancer of SARS-CoV-2 programmed -1 ribosomal frameshifting. Cell Rep 2023; 42:112987. [PMID: 37581984 DOI: 10.1016/j.celrep.2023.112987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/23/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023] Open
Abstract
Many positive-strand RNA viruses, including all known coronaviruses, employ programmed -1 ribosomal frameshifting (-1 PRF) to regulate the translation of polycistronic viral RNAs. However, only a few host factors have been shown to regulate -1 PRF. Through a genome-wide CRISPR-Cas9 knockout screen, we have identified host factors that either suppress or enhance severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) -1 PRF. Among them, eukaryotic translation initiation factor 2A (eIF2A) specifically and directly enhances -1 PRF independent of changes in initiation. Consistent with the crucial role of efficient -1 PRF in transcriptase/replicase expression, loss of eIF2A reduces SARS-CoV-2 replication in cells. Furthermore, transcriptome-wide analysis shows that eIF2A preferentially binds CG-rich RNA motifs, including a region within 18S ribosomal RNA near the contacts between the SARS-CoV-2 frameshift-stimulatory element (FSE) and the ribosome. Thus, our results indicate a role for eIF2A in modulating the translation of specific RNAs independent of its role during initiation.
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Affiliation(s)
- Lian-Huan Wei
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yu Sun
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Junjie U Guo
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA.
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14
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Zhang Y, Kinast V, Sheldon J, Frericks N, Todt D, Zimmer M, Caliskan N, Brown RJP, Steinmann E, Pietschmann T. Mouse Liver-Expressed Shiftless Is an Evolutionarily Conserved Antiviral Effector Restricting Human and Murine Hepaciviruses. Microbiol Spectr 2023; 11:e0128423. [PMID: 37341610 PMCID: PMC10433982 DOI: 10.1128/spectrum.01284-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/02/2023] [Indexed: 06/22/2023] Open
Abstract
Mice are refractory to infection with human-tropic hepatitis C virus (HCV), although distantly related rodent hepaciviruses (RHV) circulate in wild rodents. To investigate whether liver intrinsic host factors can exhibit broad restriction against these distantly related hepaciviruses, we focused on Shiftless (Shfl), an interferon (IFN)-regulated gene (IRG) which restricts HCV in humans. Unusually, and in contrast to selected classical IRGs, human and mouse SHFL orthologues (hSHFL and mSHFL, respectively) were highly expressed in hepatocytes in the absence of viral infection, weakly induced by IFN, and highly conserved at the amino acid level (>95%). Replication of both HCV and RHV subgenomic replicons was suppressed by ectopic expression of mSHFL in human or rodent hepatoma cell lines. Gene editing of endogenous mShfl in mouse liver tumor cells increased HCV replication and virion production. Colocalization of mSHFL protein with viral double-stranded RNA (dsRNA) intermediates was confirmed and could be ablated by mutational disruption of the SHFL zinc finger domain, concomitant with a loss of antiviral activity. In summary, these data point to an evolutionarily conserved function for this gene in humans and rodents: SHFL is an ancient antiviral effector which targets distantly related hepaciviruses via restriction of viral RNA replication. IMPORTANCE Viruses have evolved ways to evade or blunt innate cellular antiviral mechanisms within their cognate host species. However, these adaptations may fail when viruses infect new species and can therefore limit cross-species transmission. This may also prevent development of animal models for human-pathogenic viruses. HCV shows a narrow species tropism likely due to distinct human host factor usage and innate antiviral defenses limiting infection of nonhuman liver cells. Interferon (IFN)-regulated genes (IRGs) partially inhibit HCV infection of human cells by diverse mechanisms. Here, we show that mouse Shiftless (mSHFL), a protein that interferes with HCV replication factories, inhibits HCV replication and infection in human and mouse liver cells. We further report that the zinc finger domain of SHFL is important for viral restriction. These findings implicate mSHFL as a host factor that impairs HCV infection of mice and provide guidance for development of HCV animal models needed for vaccine development.
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Affiliation(s)
- Yudi Zhang
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Volker Kinast
- Department for Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
- Department of Medical Microbiology and Virology, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Julie Sheldon
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Nicola Frericks
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Daniel Todt
- Department for Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
- European Virus Bioinformatics Center (EVBC), Jena, Germany
| | - Matthias Zimmer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research), Würzburg, Germany
- University of Würzburg, Faculty of Medicine, Würzburg, Germany
| | - Neva Caliskan
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research), Würzburg, Germany
- University of Würzburg, Faculty of Medicine, Würzburg, Germany
| | - Richard J. P. Brown
- Department for Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
- Division of Veterinary Medicine, Paul Ehrlich Institute, Langen, Germany
| | - Eike Steinmann
- Department for Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Thomas Pietschmann
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany
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15
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Tan C, Qin X, Tan Y, Dong X, Chen D, Liang L, Li J, Niu R, Cao K, He Z, Wei G, Huang M, Zhu X. SHFL inhibits enterovirus A71 infection by triggering degradation of viral 3D pol protein via the ubiquitin-proteasome pathway. J Med Virol 2023; 95:e29030. [PMID: 37565734 DOI: 10.1002/jmv.29030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/07/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023]
Abstract
Enterovirus A71 (EV-A71) is a highly contagious virus that poses a major threat to global health, representing the primary etiological agent for hand-foot and mouth disease (HFMD) and neurological complications. It has been established that interferon signaling is critical to establishing a robust antiviral state in host cells, mainly mediated through the antiviral effects of numerous interferon-stimulated genes (ISGs). The host restriction factor SHFL is a novel ISG with broad antiviral activity against various viruses through diverse underlying molecular mechanisms. Although SHFL is widely acknowledged for its broad-spectrum antiviral activity, it remains elusive whether SHFL inhibits EV-A71. In this work, we validated that EV-A71 triggers the upregulation of SHFL both in cell lines and in a mouse model. Knockdown and overexpression of SHFL in EVA71-infected cells suggested that this factor could markedly suppress EV-A71 replication. Our findings further revealed an intriguing mechanism of SHFL that it could interact with the nonstructural proteins 3Dpol of EV-A71 and promoted the degradation of 3Dpol through the ubiquitin-proteasome pathway. Furthermore, the zinc-finger domain and the 36 amino acids (164-199) of SHFL were crucial to the interaction between SHFL and EV-A71 3Dpol . Overall, these findings broadened our understanding of the pivotal roles of SHFL in the interaction between the host and EV-A71.
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Affiliation(s)
- Chahui Tan
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Research Center for Clinical Laboratory Standard, Sun Yat-sen University, Guangzhou, China
- Department of Laboratory Medicine, Changsha Medical University, Changsha, China
| | - Xingliang Qin
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Research Center for Clinical Laboratory Standard, Sun Yat-sen University, Guangzhou, China
| | - Yongyao Tan
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Research Center for Clinical Laboratory Standard, Sun Yat-sen University, Guangzhou, China
| | - Xinhuai Dong
- Shunde Hospital, Medical Research Center, Southern Medical University (The First People's Hospital of Shunde), Foshan, China
| | - Delin Chen
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Research Center for Clinical Laboratory Standard, Sun Yat-sen University, Guangzhou, China
| | - Linyue Liang
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Research Center for Clinical Laboratory Standard, Sun Yat-sen University, Guangzhou, China
| | - Jinling Li
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Research Center for Clinical Laboratory Standard, Sun Yat-sen University, Guangzhou, China
| | - Ruoxi Niu
- Department of Clinical Laboratory Medicine, University-Town Hospital of Chongqing Medical University, Chongqing, China
| | - Kaiyuan Cao
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Research Center for Clinical Laboratory Standard, Sun Yat-sen University, Guangzhou, China
| | - Zhenjian He
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Guohong Wei
- Department of Endocrinology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Mingxing Huang
- Central Laboratory, The Third People's Hospital of Zhuhai, Zhuhai, China
| | - Xun Zhu
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Research Center for Clinical Laboratory Standard, Sun Yat-sen University, Guangzhou, China
- Central Laboratory, The Third People's Hospital of Zhuhai, Zhuhai, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, Guangzhou, China
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16
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Poulis P, Peske F, Rodnina MV. The many faces of ribosome translocation along the mRNA: reading frame maintenance, ribosome frameshifting and translational bypassing. Biol Chem 2023; 404:755-767. [PMID: 37077160 DOI: 10.1515/hsz-2023-0142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 03/22/2023] [Indexed: 04/21/2023]
Abstract
In each round of translation elongation, the ribosome translocates along the mRNA by precisely one codon. Translocation is promoted by elongation factor G (EF-G) in bacteria (eEF2 in eukaryotes) and entails a number of precisely-timed large-scale structural rearrangements. As a rule, the movements of the ribosome, tRNAs, mRNA and EF-G are orchestrated to maintain the exact codon-wise step size. However, signals in the mRNA, as well as environmental cues, can change the timing and dynamics of the key rearrangements leading to recoding of the mRNA into production of trans-frame peptides from the same mRNA. In this review, we discuss recent advances on the mechanics of translocation and reading frame maintenance. Furthermore, we describe the mechanisms and biological relevance of non-canonical translocation pathways, such as hungry and programmed frameshifting and translational bypassing, and their link to disease and infection.
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Affiliation(s)
- Panagiotis Poulis
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
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17
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Liu N, Liu M, Yang J, Dong S, Yue M, Huang P, Xia X, Zhang AM. Association of genetic polymorphisms in the C19orf66 gene and biochemical indices of HBV infected individuals in Yunnan. Front Cell Infect Microbiol 2023; 13:1180366. [PMID: 37293200 PMCID: PMC10245551 DOI: 10.3389/fcimb.2023.1180366] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/24/2023] [Indexed: 06/10/2023] Open
Abstract
Introduction Hepatitis B virus (HBV) infection causes serious liver diseases and is a healthy problem worldwide. Although vaccines are administered to infants after birth, there is no effective medicine for HBV infection. The interferon-stimulated genes (ISGs) are important factors in the host that can aid in restraining the virus, and the C19orf66 gene has a wide-antiviral spectrum. Methods In this study, three SNPs in the C19orf66 gene were sequenced and genotyped, and their potential function were predicted and further verified by dual-luciferase reporter assay. Results Although no significant difference of genotype and allele frequency was observed between HBV patients and the controls, the genotype and allele frequency showed significant difference between HBV patients with HBsAg-positive and HBV patients with HBsAg-negative or controls. Genotype AA (P= 0.009) and AT (P= 0.019) of rs77076061 showed higher and lower frequency in HBV patients with HBsAg-positive than in patients with HBsAg-negative, respectively. Genotype AG of rs1979262 played a risk role in HBV patients with HBsAg-positive (13.22%) than in patients with HBsAg-negative (7.53%, P= 0.036) or controls (8.48%, P= 0.033). The frequency of allele A of rs1979262 was higher in patients with HBsAg-positive (6.61%) than in patients with HBsAg-negative (3.77%, P= 0.042), while it was the opposite for the allele G. Moreover, the associations between genotypes of SNPs in the C19orf66 gene and the ALT, AST, and DBIL level were also identified. The functional assay suggested that the SNPs might influence the C19orf66 expression by changing the connection of transcriptional factors. Conclusion In summary, the association between genetic polymorphisms in the C19orf66 gene and HBV infection/biochemical indices of patients was firstly identified in Yunnan Province.
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Affiliation(s)
- Ni Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Min Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Department of Infectious Disease and Hepatic Disease, First People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Jun Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Clinical Laboratory, The People’s Hospital of Maguan County, Wenshan, Yunnan, China
| | - Shuwei Dong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Ming Yue
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Peng Huang
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Kunming Medical University, Kunming, Yunnan, China
| | - A-Mei Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
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18
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Allan MF, Brivanlou A, Rouskin S. RNA levers and switches controlling viral gene expression. Trends Biochem Sci 2023; 48:391-406. [PMID: 36710231 DOI: 10.1016/j.tibs.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/27/2022] [Accepted: 12/15/2022] [Indexed: 01/29/2023]
Abstract
RNA viruses are diverse and abundant pathogens that are responsible for numerous human diseases. RNA viruses possess relatively compact genomes and have therefore evolved multiple mechanisms to maximize their coding capacities, often by encoding overlapping reading frames. These reading frames are then decoded by mechanisms such as alternative splicing and ribosomal frameshifting to produce multiple distinct proteins. These solutions are enabled by the ability of the RNA genome to fold into 3D structures that can mimic cellular RNAs, hijack host proteins, and expose or occlude regulatory protein-binding motifs to ultimately control key process in the viral life cycle. We highlight recent findings focusing on less conventional mechanisms of gene expression and new discoveries on the role of RNA structures.
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Affiliation(s)
- Matthew F Allan
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Amir Brivanlou
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Silvi Rouskin
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
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19
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Rozman B, Fisher T, Stern-Ginossar N. Translation-A tug of war during viral infection. Mol Cell 2023; 83:481-495. [PMID: 36334591 DOI: 10.1016/j.molcel.2022.10.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/15/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022]
Abstract
Viral reproduction is contingent on viral protein synthesis that relies on the host ribosomes. As such, viruses have evolved remarkable strategies to hijack the host translational apparatus in order to favor viral protein production and to interfere with cellular innate defenses. Here, we describe the approaches viruses use to exploit the translation machinery, focusing on commonalities across diverse viral families, and discuss the functional relevance of this process. We illustrate the complementary strategies host cells utilize to block viral protein production and consider how cells ensure an efficient antiviral response that relies on translation during this tug of war over the ribosome. Finally, we highlight potential roles mRNA modifications and ribosome quality control play in translational regulation and innate immunity. We address these topics in the context of the COVID-19 pandemic and focus on the gaps in our current knowledge of these mechanisms, specifically in viruses with pandemic potential.
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Affiliation(s)
- Batsheva Rozman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tal Fisher
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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20
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Shiftless Restricts Viral Gene Expression and Influences RNA Granule Formation during Kaposi’s Sarcoma-Associated Herpesvirus Lytic Replication. J Virol 2022; 96:e0146922. [PMID: 36326276 PMCID: PMC9682979 DOI: 10.1128/jvi.01469-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the past 5 years, SHFL has emerged as a novel and integral piece of the innate immune response to viral infection. SHFL has been reported to restrict the replication of multiple viruses, including several flaviviruses and the retrovirus HIV-1.
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21
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Champagne J, Mordente K, Nagel R, Agami R. Slippy-Sloppy translation: a tale of programmed and induced-ribosomal frameshifting. Trends Genet 2022; 38:1123-1133. [PMID: 35641342 DOI: 10.1016/j.tig.2022.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 01/24/2023]
Abstract
Programmed ribosomal frameshifting (PRF) is a key mechanism that viruses use to generate essential proteins for replication, and as a means of regulating gene expression. PRF generally involves recoding signals or frameshift stimulators to elevate the occurrence of frameshifting at shift-prone 'slippery' sequences. Given its essential role in viral replication, targeting PRF was envisioned as an attractive tool to block viral infection. However, in contrast to controlled-PRF mechanisms, recent studies have shown that ribosomes of many human cancer cell types are prone to frameshifting upon amino acid shortage; thus, these cells are deemed to be sloppy. The resulting products of a sloppy frameshift at the 'hungry' codons are aberrant proteins the degradation and display of which at the cell surface can trigger T cell activation. In this review, we address recent discoveries in ribosomal frameshifting and their functional consequences for the proteome in human cancer cells.
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Affiliation(s)
- Julien Champagne
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Kelly Mordente
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Remco Nagel
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Reuven Agami
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands; Erasmus MC, Rotterdam University, Rotterdam, The Netherlands.
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22
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Suzuki Y, Murakawa T. Restriction of Flaviviruses by an Interferon-Stimulated Gene SHFL/C19orf66. Int J Mol Sci 2022; 23:ijms232012619. [PMID: 36293480 PMCID: PMC9604422 DOI: 10.3390/ijms232012619] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022] Open
Abstract
Flaviviruses (the genus Flavivirus of the Flaviviridae family) include many arthropod-borne viruses, often causing life-threatening diseases in humans, such as hemorrhaging and encephalitis. Although the flaviviruses have a significant clinical impact, it has become apparent that flavivirus replication is restricted by cellular factors induced by the interferon (IFN) response, which are called IFN-stimulated genes (ISGs). SHFL (shiftless antiviral inhibitor of ribosomal frameshifting) is a novel ISG that inhibits dengue virus (DENV), West Nile virus (WNV), Zika virus (ZIKV), and Japanese encephalitis virus (JEV) infections. Interestingly, SHFL functions as a broad-spectrum antiviral factor exhibiting suppressive activity against various types of RNA and DNA viruses. In this review, we summarize the current understanding of the molecular mechanisms by which SHFL inhibits flavivirus infection and discuss the molecular basis of the inhibitory mechanism using a predicted tertiary structure of SHFL generated by the program AlphaFold2.
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Affiliation(s)
- Youichi Suzuki
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki 569-8686, Japan
- Correspondence: ; Tel.: +81-72-684-7367
| | - Takeshi Murakawa
- Department of Biochemistry, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki 569-8686, Japan
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23
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Romero Romero ML, Landerer C, Poehls J, Toth‐Petroczy A. Phenotypic mutations contribute to protein diversity and shape protein evolution. Protein Sci 2022; 31:e4397. [PMID: 36040266 PMCID: PMC9375231 DOI: 10.1002/pro.4397] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/14/2022] [Accepted: 07/04/2022] [Indexed: 11/16/2022]
Abstract
Errors in DNA replication generate genetic mutations, while errors in transcription and translation lead to phenotypic mutations. Phenotypic mutations are orders of magnitude more frequent than genetic ones, yet they are less understood. Here, we review the types of phenotypic mutations, their quantifications, and their role in protein evolution and disease. The diversity generated by phenotypic mutation can facilitate adaptive evolution. Indeed, phenotypic mutations, such as ribosomal frameshift and stop codon readthrough, sometimes serve to regulate protein expression and function. Phenotypic mutations have often been linked to fitness decrease and diseases. Thus, understanding the protein heterogeneity and phenotypic diversity caused by phenotypic mutations will advance our understanding of protein evolution and have implications on human health and diseases.
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Affiliation(s)
- Maria Luisa Romero Romero
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
- Center for Systems Biology Dresden Dresden Germany
| | - Cedric Landerer
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
- Center for Systems Biology Dresden Dresden Germany
| | - Jonas Poehls
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
- Center for Systems Biology Dresden Dresden Germany
| | - Agnes Toth‐Petroczy
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
- Center for Systems Biology Dresden Dresden Germany
- Cluster of Excellence Physics of Life TU Dresden Dresden Germany
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Abstract
In humans, HIV-1 infection induces innate immune responses mediated mainly by type I interferon (IFN). Type I IFN restricts HIV-1 replication by upregulating the expression of IFN-stimulated genes with diverse anti-HIV properties. In this study, we report that the cell membrane protein otoferlin (OTOF) acts as a type I IFN-induced effector, inhibiting HIV-1 entry in myeloid lineage macrophages and dendritic cells (DCs). OTOF is significantly induced by type I IFN in macrophages and DCs but not in CD4+ T lymphocytes. Silencing OTOF abrogates the IFN-mediated suppression of HIV-1 infection in macrophages and DCs. Moreover, OTOF overexpression exhibits anti-HIV activity in macrophages and CD4+ T cells. Further evidence reveals that OTOF inhibits HIV-1 entry into target cells at the cell membrane. Collectively, OTOF is a downstream molecule induced by type I IFN to inhibit HIV-1 entry in macrophages; it is a new potential agent for the treatment of HIV infection.
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25
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Nafamostat-Mediated Inhibition of SARS-CoV-2 Ribosomal Frameshifting Is Insufficient to Impair Viral Replication in Vero Cells. Comment on Munshi et al. Identifying Inhibitors of −1 Programmed Ribosomal Frameshifting in a Broad Spectrum of Coronaviruses. Viruses 2022, 14, 177. Viruses 2022; 14:v14071526. [PMID: 35891506 PMCID: PMC9324898 DOI: 10.3390/v14071526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 12/21/2022] Open
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26
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Mutagenic Analysis of the HIV Restriction Factor Shiftless. Viruses 2022; 14:v14071454. [PMID: 35891432 PMCID: PMC9324250 DOI: 10.3390/v14071454] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/14/2022] [Accepted: 06/25/2022] [Indexed: 02/01/2023] Open
Abstract
The interferon-induced host cell protein shiftless (SFL) was reported to inhibit human immunodeficiency virus (HIV) infection by blocking the –1 programmed ribosomal frameshifting (–1PRF) required for expression of the Gag-Pol polyprotein. However, it is not clear how SFL inhibits –1PRF. To address this question, we focused on a 36 amino acids comprising region (termed required for antiviral activity (RAA)) that is essential for suppression of –1PRF and HIV infection and is missing from SFL short (SFLS), a splice variant of SFL with unknown function. Here, we confirm that SFL, but not SFLS, inhibits HIV –1PRF and show that inhibition is cell-type-independent. Mutagenic and biochemical analyses demonstrated that the RAA region is required for SFL self-interactions and confirmed that it is necessary for ribosome association and binding to the HIV RNA. Analysis of SFL mutants with six consecutive amino-acids-comprising deletions in the RAA region suggests effects on binding to the HIV RNA, complete inhibition of –1PRF, inhibition of Gag-Pol expression, and antiviral activity. In contrast, these amino acids did not affect SFL expression and were partially dispensable for SFL self-interactions and binding to the ribosome. Collectively, our results support the notion that SFL binds to the ribosome and the HIV RNA in order to block –1PRF and HIV infection, and suggest that the multimerization of SFL may be functionally important.
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Abstract
The constrained nature of viral genomes has allowed a translational sleight of hand known as −1 Programmed Ribosomal Frameshifting (−1 PRF) to flourish. Numerous studies have sought to tease apart the mechanisms and implications of −1PRF utilizing a few techniques. The dual-luciferase assay and ribosomal profiling have driven the PRF field to make great advances; however, the use of these assays means that the full impact of the genomic and cellular context on −1 PRF is often lost. Here, we discuss how the Minimal Frameshifting Element (MFE) and its constraints can hide contextual effects on −1 PRF. We review how sequence elements proximal to the traditionally defined MFE, such as the coronavirus attenuator sequence, can affect the observed rates of −1 PRF. Further, the MFE-based approach fully obscured −1 PRF in Barley yellow dwarf virus and would render the exploration of −1 PRF difficult in Porcine reproductive and respiratory syndrome virus, Encephalomyocarditis virus, Theiler’s murine encephalomyelitis virus, and Sindbis virus. Finally, we examine how the cellular context of tRNA abundance, miRNAs, and immune response elements can affect −1 PRF. The use of MFE was instrumental in establishing the basic foundations of PRF; however, it has become clear that the contextual impact on −1 PRF is no longer the exception so much as it is the rule and argues for new approaches to study −1PRF that embrace context. We therefore urge our field to expand the strategies and methods used to explore −1 PRF.
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28
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Rodriguez W, Muller M. Shiftless, a Critical Piece of the Innate Immune Response to Viral Infection. Viruses 2022; 14:v14061338. [PMID: 35746809 PMCID: PMC9230503 DOI: 10.3390/v14061338] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/08/2022] [Accepted: 06/16/2022] [Indexed: 12/14/2022] Open
Abstract
Since its initial characterization in 2016, the interferon stimulated gene Shiftless (SHFL) has proven to be a critical piece of the innate immune response to viral infection. SHFL expression stringently restricts the replication of multiple DNA, RNA, and retroviruses with an extraordinary diversity of mechanisms that differ from one virus to the next. These inhibitory strategies include the negative regulation of viral RNA stability, translation, and even the manipulation of RNA granule formation during viral infection. Even more surprisingly, SHFL is the first human protein found to directly inhibit the activity of the -1 programmed ribosomal frameshift, a translation recoding strategy utilized across nearly all domains of life and several human viruses. Recent literature has shown that SHFL expression also significantly impacts viral pathogenesis in mouse models, highlighting its in vivo efficacy. To help reconcile the many mechanisms by which SHFL restricts viral replication, we provide here a comprehensive review of this complex ISG, its influence over viral RNA fate, and the implications of its functions on the virus-host arms race for control of the cell.
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29
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The Translational Landscape of SARS-CoV-2-infected Cells Reveals Suppression of Innate Immune Genes. mBio 2022; 13:e0081522. [PMID: 35604092 PMCID: PMC9239271 DOI: 10.1128/mbio.00815-22] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes a number of strategies to modulate viral and host mRNA translation. Here, we used ribosome profiling in SARS-CoV-2-infected model cell lines and primary airway cells grown at an air-liquid interface to gain a deeper understanding of the translationally regulated events in response to virus replication. We found that SARS-CoV-2 mRNAs dominate the cellular mRNA pool but are not more efficiently translated than cellular mRNAs. SARS-CoV-2 utilized a highly efficient ribosomal frameshifting strategy despite notable accumulation of ribosomes within the slippery sequence on the frameshifting element. In a highly permissive cell line model, although SARS-CoV-2 infection induced the transcriptional upregulation of numerous chemokine, cytokine, and interferon-stimulated genes, many of these mRNAs were not translated efficiently. The impact of SARS-CoV-2 on host mRNA translation was more subtle in primary cells, with marked transcriptional and translational upregulation of inflammatory and innate immune responses and downregulation of processes involved in ciliated cell function. Together, these data reveal the key role of mRNA translation in SARS-CoV-2 replication and highlight unique mechanisms for therapeutic development.
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30
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Species-specific KRAB-ZFPs function as repressors of retroviruses by targeting PBS regions. Proc Natl Acad Sci U S A 2022; 119:e2119415119. [PMID: 35259018 PMCID: PMC8931336 DOI: 10.1073/pnas.2119415119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Hosts often target the relatively conserved regions in rapidly mutating retroviruses to inhibit their replication. One of these regions is called a primer binding site (PBS), which has to be complementary to the host tRNA to initiate reverse transcription. By analyzing endogenous retroviral elements, we found that host cells use this sequence as a target in efforts to block the expression of viral elements. A specific type of zinc finger protein targets the PBS in a host genome, which not only inhibits the transcription of endogenous viruses but also inhibits the replication of exogenous retroviruses with the same PBS. Thus, our study sheds light on a strategy for searching for host restriction factors targeting retroviruses. Eukaryotic genomes harbor sequences derived from the chromosomal integration of ancient viruses, such as endogenous retroviruses (ERVs), which comprise 8% of the human genome. Like exogenous retroviruses, ERVs retain many common functional elements, including the corresponding DNA sequences of transfer RNA (tRNA) primer binding sites (PBSs), which are utilized for reverse transcription initiation by exogenous retroviruses. Here, through a medium-scale analysis of PBS loci positioned within ERVs, coupled with chromatin immunoprecipitation sequencing (ChIP-seq) of Kruppel-associated box zinc finger proteins (KRAB-ZFPs), we identified multiple ZFPs that specifically bind to different PBS loci. Among these, we focused on PBS-Lys, which is utilized by HIV-1, and identified its specific binding proteins to be mouse ZFP961 and human ZNF417/ZNF587. We found that these proteins not only repress ERV transcription but also inhibit retrovirus integration and transcription. Disruption of these ZFPs rendered cells more susceptible to HIV-1 infection. Thus, our research provides a methodology for identifying potential host factors that target retroviruses by ERVs.
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31
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Mao D, Yan F, Zhang X, Gao G. TMEM106A inhibits enveloped virus release from cell surface. iScience 2022; 25:103843. [PMID: 35198896 PMCID: PMC8844723 DOI: 10.1016/j.isci.2022.103843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 12/02/2021] [Accepted: 01/27/2022] [Indexed: 12/15/2022] Open
Abstract
Enveloped viruses pose constant threat to hosts from ocean to land. Virion particle release from cell surface is a critical step in the viral life cycle for most enveloped viruses, making it a common antiviral target for the host defense system. Here we report that host factor TMEM106A inhibits the release of enveloped viruses from the cell surface. TMEM106A is a type II transmembrane protein localized on the plasma membrane and can be incorporated into HIV-1 virion particles. Through intermolecular interactions of its C-terminal domains on virion particle and plasma membrane, TMEM106A traps virion particles to the cell surface. HIV-1 Env interacts with TMEM106A to interfere with the intermolecular interactions and partially suppresses its antiviral activity. TMEM106A orthologs from various species displayed potent antiviral activity against multiple enveloped viruses. These results suggest that TMEM106A is an evolutionarily conserved antiviral factor that inhibits the release of enveloped viruses from the cell surface. Type II transmembrane protein TMEM106A can be incorporated into virion particles TMEM106A inhibits enveloped virion release through C-terminal molecular interactions HIV-1 envelope protein interacts with TMEM106A and suppresses its antiviral activity TMEM106A is an evolutionarily conserved antiviral factor against multiple viruses
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Affiliation(s)
- Dexin Mao
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feixiang Yan
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolin Zhang
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Guangxia Gao
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence
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32
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Riegger RJ, Caliskan N. Thinking Outside the Frame: Impacting Genomes Capacity by Programmed Ribosomal Frameshifting. Front Mol Biosci 2022; 9:842261. [PMID: 35281266 PMCID: PMC8915115 DOI: 10.3389/fmolb.2022.842261] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/26/2022] [Indexed: 01/08/2023] Open
Abstract
Translation facilitates the transfer of the genetic information stored in the genome via messenger RNAs to a functional protein and is therefore one of the most fundamental cellular processes. Programmed ribosomal frameshifting is a ubiquitous alternative translation event that is extensively used by viruses to regulate gene expression from overlapping open reading frames in a controlled manner. Recent technical advances in the translation field enabled the identification of precise mechanisms as to how and when ribosomes change the reading frame on mRNAs containing cis-acting signals. Several studies began also to illustrate that trans-acting RNA modulators can adjust the timing and efficiency of frameshifting illuminating that frameshifting can be a dynamically regulated process in cells. Here, we intend to summarize these new findings and emphasize how it fits in our current understanding of PRF mechanisms as previously described.
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Affiliation(s)
- Ricarda J. Riegger
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-Based Infection Research (HIRI), Würzburg, Germany
- Graduate School of Life Sciences (GSLS), University of Würzburg, Würzburg, Germany
| | - Neva Caliskan
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-Based Infection Research (HIRI), Würzburg, Germany
- Medical Faculty, University of Würzburg, Würzburg, Germany
- *Correspondence: Neva Caliskan,
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33
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Wang Y, Wu C, Du Y, Li Z, Li M, Hou P, Shen Z, Chu S, Zheng J, Bai J. Expanding uncapped translation and emerging function of circular RNA in carcinomas and noncarcinomas. Mol Cancer 2022; 21:13. [PMID: 34996480 PMCID: PMC8740365 DOI: 10.1186/s12943-021-01484-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/16/2021] [Indexed: 02/07/2023] Open
Abstract
Circular RNAs (circRNAs) are classified as noncoding RNAs because they are devoid of a 5' end cap and a 3' end poly (A) tail necessary for cap-dependent translation. However, increasing numbers of translated circRNAs identified through high-throughput RNA sequencing overlapping with polysome profiling indicate that this rule is being broken. CircRNAs can be translated in cap-independent mechanism, including IRES (internal ribosome entry site)-initiated pattern, MIRES (m6A internal ribosome entry site) -initiated patterns, and rolling translation mechanism (RCA). CircRNA-encoded proteins harbour diverse functions similar to or different from host proteins. In addition, they are linked to the modulation of human disease including carcinomas and noncarcinomas. CircRNA-related translatomics and proteomics have attracted increasing attention. This review discusses the progress and exclusive characteristics of circRNA translation and highlights the latest mechanisms and regulation of circRNA translatomics. Furthermore, we summarize the extensive functions and mechanisms of circRNA-derived proteins in human diseases, which contribute to a better understanding of intricate noncanonical circRNA translatomics and proteomics and their therapeutic potential in human diseases.
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Affiliation(s)
- Yan Wang
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
- Center of Clinical Oncology, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Department of Pharmacy, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Chunjie Wu
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
- Department of Pharmacy, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yu Du
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
- Department of Pharmacy, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Zhongwei Li
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
| | - Minle Li
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
| | - Pingfu Hou
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
| | - Zhigang Shen
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
| | - Sufang Chu
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
| | - Junnian Zheng
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China.
- Center of Clinical Oncology, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.
| | - Jin Bai
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China.
- Center of Clinical Oncology, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.
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34
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Carmody PJ, Zimmer MH, Kuntz CP, Harrington HR, Duckworth K, Penn W, Mukhopadhyay S, Miller T, Schlebach J. Coordination of -1 programmed ribosomal frameshifting by transcript and nascent chain features revealed by deep mutational scanning. Nucleic Acids Res 2021; 49:12943-12954. [PMID: 34871407 PMCID: PMC8682741 DOI: 10.1093/nar/gkab1172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 10/22/2021] [Accepted: 11/10/2021] [Indexed: 12/17/2022] Open
Abstract
Programmed ribosomal frameshifting (PRF) is a translational recoding mechanism that enables the synthesis of multiple polypeptides from a single transcript. During translation of the alphavirus structural polyprotein, the efficiency of -1PRF is coordinated by a 'slippery' sequence in the transcript, an adjacent RNA stem-loop, and a conformational transition in the nascent polypeptide chain. To characterize each of these effectors, we measured the effects of 4530 mutations on -1PRF by deep mutational scanning. While most mutations within the slip-site and stem-loop reduce the efficiency of -1PRF, the effects of mutations upstream of the slip-site are far more variable. We identify several regions where modifications of the amino acid sequence of the nascent polypeptide impact the efficiency of -1PRF. Molecular dynamics simulations of polyprotein biogenesis suggest the effects of these mutations primarily arise from their impacts on the mechanical forces that are generated by the translocon-mediated cotranslational folding of the nascent polypeptide chain. Finally, we provide evidence suggesting that the coupling between cotranslational folding and -1PRF depends on the translation kinetics upstream of the slip-site. These findings demonstrate how -1PRF is coordinated by features within both the transcript and nascent chain.
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Affiliation(s)
- Patrick J Carmody
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Matthew H Zimmer
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Charles P Kuntz
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | | | - Kate E Duckworth
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Wesley D Penn
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | | | - Thomas F Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Zimmer MM, Kibe A, Rand U, Pekarek L, Ye L, Buck S, Smyth RP, Cicin-Sain L, Caliskan N. The short isoform of the host antiviral protein ZAP acts as an inhibitor of SARS-CoV-2 programmed ribosomal frameshifting. Nat Commun 2021; 12:7193. [PMID: 34893599 PMCID: PMC8664833 DOI: 10.1038/s41467-021-27431-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/18/2021] [Indexed: 12/20/2022] Open
Abstract
Programmed ribosomal frameshifting (PRF) is a fundamental gene expression event in many viruses, including SARS-CoV-2. It allows production of essential viral, structural and replicative enzymes that are encoded in an alternative reading frame. Despite the importance of PRF for the viral life cycle, it is still largely unknown how and to what extent cellular factors alter mechanical properties of frameshift elements and thereby impact virulence. This prompted us to comprehensively dissect the interplay between the SARS-CoV-2 frameshift element and the host proteome. We reveal that the short isoform of the zinc-finger antiviral protein (ZAP-S) is a direct regulator of PRF in SARS-CoV-2 infected cells. ZAP-S overexpression strongly impairs frameshifting and inhibits viral replication. Using in vitro ensemble and single-molecule techniques, we further demonstrate that ZAP-S directly interacts with the SARS-CoV-2 RNA and interferes with the folding of the frameshift RNA element. Together, these data identify ZAP-S as a host-encoded inhibitor of SARS-CoV-2 frameshifting and expand our understanding of RNA-based gene regulation.
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Affiliation(s)
- Matthias M Zimmer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research), Josef-Schneider-Strasse 2, 97080, Würzburg, Germany
| | - Anuja Kibe
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research), Josef-Schneider-Strasse 2, 97080, Würzburg, Germany
| | - Ulfert Rand
- Helmholtz Zentrum für Infektionsforschung, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Lukas Pekarek
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research), Josef-Schneider-Strasse 2, 97080, Würzburg, Germany
| | - Liqing Ye
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research), Josef-Schneider-Strasse 2, 97080, Würzburg, Germany
| | - Stefan Buck
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research), Josef-Schneider-Strasse 2, 97080, Würzburg, Germany
| | - Redmond P Smyth
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research), Josef-Schneider-Strasse 2, 97080, Würzburg, Germany
- Medical Faculty, Julius-Maximilians University Würzburg, 97074, Würzburg, Germany
| | - Luka Cicin-Sain
- Helmholtz Zentrum für Infektionsforschung, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Neva Caliskan
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research), Josef-Schneider-Strasse 2, 97080, Würzburg, Germany.
- Medical Faculty, Julius-Maximilians University Würzburg, 97074, Würzburg, Germany.
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36
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Shiftless inhibits flavivirus replication in vitro and is neuroprotective in a mouse model of Zika virus pathogenesis. Proc Natl Acad Sci U S A 2021; 118:2111266118. [PMID: 34873063 DOI: 10.1073/pnas.2111266118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2021] [Indexed: 12/15/2022] Open
Abstract
Flaviviruses such as Zika virus and West Nile virus have the potential to cause severe neuropathology if they invade the central nervous system. The type I interferon response is well characterized as contributing to control of flavivirus-induced neuropathogenesis. However, the interferon-stimulated gene (ISG) effectors that confer these neuroprotective effects are less well studied. Here, we used an ISG expression screen to identify Shiftless (SHFL, C19orf66) as a potent inhibitor of diverse positive-stranded RNA viruses, including multiple members of the Flaviviridae (Zika, West Nile, dengue, yellow fever, and hepatitis C viruses). In cultured cells, SHFL functions as a viral RNA-binding protein that inhibits viral replication at a step after primary translation of the incoming genome. The murine ortholog, Shfl, is expressed constitutively in multiple tissues, including the central nervous system. In a mouse model of Zika virus infection, Shfl -/- knockout mice exhibit reduced survival, exacerbated neuropathological outcomes, and increased viral replication in the brain and spinal cord. These studies demonstrate that Shfl is an important antiviral effector that contributes to host protection from Zika virus infection and virus-induced neuropathological disease.
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37
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Champagne J, Pataskar A, Blommaert N, Nagel R, Wernaart D, Ramalho S, Kenski J, Bleijerveld OB, Zaal EA, Berkers CR, Altelaar M, Peeper DS, Faller WJ, Agami R. Oncogene-dependent sloppiness in mRNA translation. Mol Cell 2021; 81:4709-4721.e9. [PMID: 34562372 DOI: 10.1016/j.molcel.2021.09.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/13/2021] [Accepted: 08/30/2021] [Indexed: 12/15/2022]
Abstract
mRNA translation is a highly conserved and tightly controlled mechanism for protein synthesis. Despite protein quality control mechanisms, amino acid shortage in melanoma induces aberrant proteins by ribosomal frameshifting. The extent and the underlying mechanisms related to this phenomenon are yet unknown. Here, we show that tryptophan depletion-induced ribosomal frameshifting is a widespread phenomenon in cancer. We termed this event sloppiness and strikingly observed its association with MAPK pathway hyperactivation. Sloppiness is stimulated by RAS activation in primary cells, suppressed by pharmacological inhibition of the oncogenic MAPK pathway in sloppy cells, and restored in cells with acquired resistance to MAPK pathway inhibition. Interestingly, sloppiness causes aberrant peptide presentation at the cell surface, allowing recognition and specific killing of drug-resistant cancer cells by T lymphocytes. Thus, while oncogenes empower cancer progression and aggressiveness, they also expose a vulnerability by provoking the production of aberrant peptides through sloppiness.
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Affiliation(s)
- Julien Champagne
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Abhijeet Pataskar
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Naomi Blommaert
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Remco Nagel
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Demi Wernaart
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Sofia Ramalho
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Juliana Kenski
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Onno B Bleijerveld
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Esther A Zaal
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands; Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University and Netherlands Proteomics Centre, Utrecht, the Netherlands
| | - Celia R Berkers
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands; Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University and Netherlands Proteomics Centre, Utrecht, the Netherlands
| | - Maarten Altelaar
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University and Netherlands Proteomics Centre, Utrecht, the Netherlands
| | - Daniel S Peeper
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - William J Faller
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Reuven Agami
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Erasmus MC, Rotterdam University, Rotterdam, the Netherlands.
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Puray-Chavez M, Lee N, Tenneti K, Wang Y, Vuong HR, Liu Y, Horani A, Huang T, Gunsten SP, Case JB, Yang W, Diamond MS, Brody SL, Dougherty J, Kutluay SB. The translational landscape of SARS-CoV-2 and infected cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.11.03.367516. [PMID: 33173862 PMCID: PMC7654850 DOI: 10.1101/2020.11.03.367516] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
SARS-CoV-2 utilizes a number of strategies to modulate viral and host mRNA translation. Here, we used ribosome profiling in SARS-CoV-2 infected model cell lines and primary airway cells grown at the air-liquid interface to gain a deeper understanding of the translationally regulated events in response to virus replication. We find that SARS-CoV-2 mRNAs dominate the cellular mRNA pool but are not more efficiently translated than cellular mRNAs. SARS-CoV-2 utilized a highly efficient ribosomal frameshifting strategy in comparison to HIV-1, suggesting utilization of distinct structural elements. In the highly permissive cell models, although SARS-CoV-2 infection induced the transcriptional upregulation of numerous chemokines, cytokines and interferon stimulated genes, many of these mRNAs were not translated efficiently. Impact of SARS-CoV-2 on host mRNA translation was more subtle in primary cells, with marked transcriptional and translational upregulation of inflammatory and innate immune responses and downregulation of processes involved in ciliated cell function. Together, these data reveal the key role of mRNA translation in SARS-CoV-2 replication and highlight unique mechanisms for therapeutic development.
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Affiliation(s)
- Maritza Puray-Chavez
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Nakyung Lee
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Kasyap Tenneti
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Yiqing Wang
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Hung R Vuong
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Yating Liu
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Amjad Horani
- Department of Pediatrics, Allergy, Immunology and Pulmonary Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Tao Huang
- Department of Medicine, Pulmonary and Critical Care Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Sean P Gunsten
- Department of Medicine, Pulmonary and Critical Care Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - James B Case
- Department of Medicine, Infectious Disease Division, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Wei Yang
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Michael S Diamond
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Department of Medicine, Infectious Disease Division, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Steven L Brody
- Department of Medicine, Pulmonary and Critical Care Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Joseph Dougherty
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Sebla B Kutluay
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
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Mahajan S, Choudhary S, Kumar P, Tomar S. Antiviral strategies targeting host factors and mechanisms obliging +ssRNA viral pathogens. Bioorg Med Chem 2021; 46:116356. [PMID: 34416512 PMCID: PMC8349405 DOI: 10.1016/j.bmc.2021.116356] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/30/2021] [Accepted: 07/31/2021] [Indexed: 12/21/2022]
Abstract
The ongoing COVID-19 pandemic, periodic recurrence of viral infections, and the emergence of challenging variants has created an urgent need of alternative therapeutic approaches to combat the spread of viral infections, failing to which may pose a greater risk to mankind in future. Resilience against antiviral drugs or fast evolutionary rate of viruses is stressing the scientific community to identify new therapeutic approaches for timely control of disease. Host metabolic pathways are exquisite reservoir of energy to viruses and contribute a diverse array of functions for successful replication and pathogenesis of virus. Targeting the host factors rather than viral enzymes to cease viral infection, has emerged as an alternative antiviral strategy. This approach offers advantage in terms of increased threshold to viral resistance and can provide broad-spectrum antiviral action against different viruses. The article here provides substantial review of literature illuminating the host factors and molecular mechanisms involved in innate/adaptive responses to viral infection, hijacking of signalling pathways by viruses and the intracellular metabolic pathways required for viral replication. Host-targeted drugs acting on the pathways usurped by viruses are also addressed in this study. Host-directed antiviral therapeutics might prove to be a rewarding approach in controlling the unprecedented spread of viral infection, however the probability of cellular side effects or cytotoxicity on host cell should not be ignored at the time of clinical investigations.
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Affiliation(s)
- Supreeti Mahajan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Shweta Choudhary
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand 247667, India.
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Yu D, Zhao Y, Pan J, Yang X, Liang Z, Xie S, Cao R. C19orf66 Inhibits Japanese Encephalitis Virus Replication by Targeting -1 PRF and the NS3 Protein. Virol Sin 2021; 36:1443-1455. [PMID: 34309824 DOI: 10.1007/s12250-021-00423-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 05/18/2021] [Indexed: 12/01/2022] Open
Abstract
The Japanese encephalitis serogroup of the neurogenic Flavivirus has a specific feature that expresses a non-structural protein NS1' produced through a programmed -1 ribosomal frameshifting (-1 PRF). Herein, C19orf66, a novel member of interferon-stimulated gene (ISG) products, exhibited significant activity of antagonizing Japanese encephalitis virus (JEV) infection. Overexpression of C19orf66 in 293T cells significantly inhibited JEV replication, while knock-down of endogenous C19orf66 in HeLa cells and A549 cells significantly increased virus replication. Notably, C19orf66 had an inhibitory effect on frameshift production of JEV NS1'. The inhibition was more significant when C19orf66 and JEV NS1-NS2A were co-expressed in the 293T cells. Both C19orf66-209 and C19orf66-Zincmut did not significantly change the NS1' to NS1 ratio and had weaker antiviral effects than C19orf66. Similarly, C19orf66-209 and C19orf66-Zincmut had no significant effect on the expression of the JEV NS3 protein, whose expression was down-regulated by C19orf66 via the lysosome-dependent pathway. These findings suggest that C19orf66 may possess at least two different mechanisms of antagonizing JEV infection. This study identified C19orf66 as a novel interferon-stimulated gene product that can inhibit JEV replication by targeting -1 PRF and the NS3 protein. The study provides baseline information for the future development of broad-spectrum antiviral agents against JEV.
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Affiliation(s)
- Du Yu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yundi Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Junhui Pan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xingmiao Yang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhenjie Liang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shengda Xie
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruibing Cao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.
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41
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Restriction of SARS-CoV-2 replication by targeting programmed -1 ribosomal frameshifting. Proc Natl Acad Sci U S A 2021; 118:2023051118. [PMID: 34185680 PMCID: PMC8256030 DOI: 10.1073/pnas.2023051118] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A large variety of RNA viruses, including the novel coronavirus SARS-CoV-2, contain specific RNA structures that promote programmed ribosomal frameshifting (PRF) to regulate viral gene expression. From a high-throughput compound screen, we identified a PRF inhibitor for SARS-CoV-2 and found that it substantially impeded viral replication in cultured cells. Interestingly, the compound could target not only SARS-CoV-2 but also other coronaviruses that use similar RNA structures to promote frameshifting. These results suggest targeting PRF is a plausible, effective, and broad-spectrum antiviral strategy for SARS-CoV-2 and other coronaviruses. Translation of open reading frame 1b (ORF1b) in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires a programmed −1 ribosomal frameshift (−1 PRF) promoted by an RNA pseudoknot. The extent to which SARS-CoV-2 replication may be sensitive to changes in −1 PRF efficiency is currently unknown. Through an unbiased, reporter-based high-throughput compound screen, we identified merafloxacin, a fluoroquinolone antibacterial, as a −1 PRF inhibitor for SARS-CoV-2. Frameshift inhibition by merafloxacin is robust to mutations within the pseudoknot region and is similarly effective on −1 PRF of other betacoronaviruses. Consistent with the essential role of −1 PRF in viral gene expression, merafloxacin impedes SARS-CoV-2 replication in Vero E6 cells, thereby providing proof-of-principle for targeting −1 PRF as a plausible and effective antiviral strategy for SARS-CoV-2 and other coronaviruses.
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Lee S, Lee YS, Choi Y, Son A, Park Y, Lee KM, Kim J, Kim JS, Kim VN. The SARS-CoV-2 RNA interactome. Mol Cell 2021; 81:2838-2850.e6. [PMID: 33989516 PMCID: PMC8075806 DOI: 10.1016/j.molcel.2021.04.022] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/26/2021] [Accepted: 04/20/2021] [Indexed: 12/23/2022]
Abstract
SARS-CoV-2 is an RNA virus whose success as a pathogen relies on its abilities to repurpose host RNA-binding proteins (RBPs) and to evade antiviral RBPs. To uncover the SARS-CoV-2 RNA interactome, we here develop a robust ribonucleoprotein (RNP) capture protocol and identify 109 host factors that directly bind to SARS-CoV-2 RNAs. Applying RNP capture on another coronavirus, HCoV-OC43, revealed evolutionarily conserved interactions between coronaviral RNAs and host proteins. Transcriptome analyses and knockdown experiments delineated 17 antiviral RBPs, including ZC3HAV1, TRIM25, PARP12, and SHFL, and 8 proviral RBPs, such as EIF3D and CSDE1, which are responsible for co-opting multiple steps of the mRNA life cycle. This also led to the identification of LARP1, a downstream target of the mTOR signaling pathway, as an antiviral host factor that interacts with the SARS-CoV-2 RNAs. Overall, this study provides a comprehensive list of RBPs regulating coronaviral replication and opens new avenues for therapeutic interventions.
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Affiliation(s)
- Sungyul Lee
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Young-Suk Lee
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Yeon Choi
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Ahyeon Son
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Youngran Park
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Kyung-Min Lee
- International Vaccine Institute, Seoul, Republic of Korea
| | - Jeesoo Kim
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jong-Seo Kim
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.
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Atkins JF, O’Connor KM, Bhatt PR, Loughran G. From Recoding to Peptides for MHC Class I Immune Display: Enriching Viral Expression, Virus Vulnerability and Virus Evasion. Viruses 2021; 13:1251. [PMID: 34199077 PMCID: PMC8310308 DOI: 10.3390/v13071251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/11/2021] [Accepted: 06/19/2021] [Indexed: 01/02/2023] Open
Abstract
Many viruses, especially RNA viruses, utilize programmed ribosomal frameshifting and/or stop codon readthrough in their expression, and in the decoding of a few a UGA is dynamically redefined to specify selenocysteine. This recoding can effectively increase viral coding capacity and generate a set ratio of products with the same N-terminal domain(s) but different C-terminal domains. Recoding can also be regulatory or generate a product with the non-universal 21st directly encoded amino acid. Selection for translation speed in the expression of many viruses at the expense of fidelity creates host immune defensive opportunities. In contrast to host opportunism, certain viruses, including some persistent viruses, utilize recoding or adventitious frameshifting as part of their strategy to evade an immune response or specific drugs. Several instances of recoding in small intensively studied viruses escaped detection for many years and their identification resolved dilemmas. The fundamental importance of ribosome ratcheting is consistent with the initial strong view of invariant triplet decoding which however did not foresee the possibility of transitory anticodon:codon dissociation. Deep level dynamics and structural understanding of recoding is underway, and a high level structure relevant to the frameshifting required for expression of the SARS CoV-2 genome has just been determined.
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Affiliation(s)
- John F. Atkins
- Schools of Biochemistry and Microbiology, University College Cork, T12 XF62 Cork, Ireland; (K.M.O.); (P.R.B.); (G.L.)
| | - Kate M. O’Connor
- Schools of Biochemistry and Microbiology, University College Cork, T12 XF62 Cork, Ireland; (K.M.O.); (P.R.B.); (G.L.)
| | - Pramod R. Bhatt
- Schools of Biochemistry and Microbiology, University College Cork, T12 XF62 Cork, Ireland; (K.M.O.); (P.R.B.); (G.L.)
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Gary Loughran
- Schools of Biochemistry and Microbiology, University College Cork, T12 XF62 Cork, Ireland; (K.M.O.); (P.R.B.); (G.L.)
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Napthine S, Hill CH, Nugent HCM, Brierley I. Modulation of Viral Programmed Ribosomal Frameshifting and Stop Codon Readthrough by the Host Restriction Factor Shiftless. Viruses 2021; 13:v13071230. [PMID: 34202160 PMCID: PMC8310280 DOI: 10.3390/v13071230] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/15/2021] [Accepted: 06/19/2021] [Indexed: 12/18/2022] Open
Abstract
The product of the interferon-stimulated gene C19orf66, Shiftless (SHFL), restricts human immunodeficiency virus replication through downregulation of the efficiency of the viral gag/pol frameshifting signal. In this study, we demonstrate that bacterially expressed, purified SHFL can decrease the efficiency of programmed ribosomal frameshifting in vitro at a variety of sites, including the RNA pseudoknot-dependent signals of the coronaviruses IBV, SARS-CoV and SARS-CoV-2, and the protein-dependent stimulators of the cardioviruses EMCV and TMEV. SHFL also reduced the efficiency of stop-codon readthrough at the murine leukemia virus gag/pol signal. Using size-exclusion chromatography, we confirm the binding of the purified protein to mammalian ribosomes in vitro. Finally, through electrophoretic mobility shift assays and mutational analysis, we show that expressed SHFL has strong RNA binding activity that is necessary for full activity in the inhibition of frameshifting, but shows no clear specificity for stimulatory RNA structures.
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Affiliation(s)
| | | | | | - Ian Brierley
- Correspondence: ; Tel.: +44-12-2333-6914; Fax: +44-12-2333-6926
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Cao C, Cai Z, Xiao X, Rao J, Chen J, Hu N, Yang M, Xing X, Wang Y, Li M, Zhou B, Wang X, Wang J, Xue Y. The architecture of the SARS-CoV-2 RNA genome inside virion. Nat Commun 2021; 12:3917. [PMID: 34168138 PMCID: PMC8225788 DOI: 10.1038/s41467-021-22785-x] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/30/2021] [Indexed: 02/08/2023] Open
Abstract
SARS-CoV-2 carries the largest single-stranded RNA genome and is the causal pathogen of the ongoing COVID-19 pandemic. How the SARS-CoV-2 RNA genome is folded in the virion remains unknown. To fill the knowledge gap and facilitate structure-based drug development, we develop a virion RNA in situ conformation sequencing technology, named vRIC-seq, for probing viral RNA genome structure unbiasedly. Using vRIC-seq data, we reconstruct the tertiary structure of the SARS-CoV-2 genome and reveal a surprisingly "unentangled globule" conformation. We uncover many long-range duplexes and higher-order junctions, both of which are under purifying selections and contribute to the sequential package of the SARS-CoV-2 genome. Unexpectedly, the D614G and the other two accompanying mutations may remodel duplexes into more stable forms. Lastly, the structure-guided design of potent small interfering RNAs can obliterate the SARS-CoV-2 in Vero cells. Overall, our work provides a framework for studying the genome structure, function, and dynamics of emerging deadly RNA viruses.
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Affiliation(s)
- Changchang Cao
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Zhaokui Cai
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xia Xiao
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jian Rao
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Juan Chen
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Naijing Hu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Minnan Yang
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xiaorui Xing
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yongle Wang
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Manman Li
- School of Life Sciences, Henan Normal University, Xinxiang, China
| | - Bing Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Xiangxi Wang
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jianwei Wang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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Vpr counteracts the restriction of LAPTM5 to promote HIV-1 infection in macrophages. Nat Commun 2021; 12:3691. [PMID: 34140527 PMCID: PMC8211709 DOI: 10.1038/s41467-021-24087-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 05/31/2021] [Indexed: 11/09/2022] Open
Abstract
The HIV-1 accessory proteins Vif, Vpu, and Nef can promote infection by overcoming the inhibitory effects of the host cell restriction factors APOBEC3G, Tetherin, and SERINC5, respectively. However, how the HIV-1 accessory protein Vpr enhances infection in macrophages but not in CD4+ T cells remains elusive. Here, we report that Vpr counteracts lysosomal-associated transmembrane protein 5 (LAPTM5), a potent inhibitor of HIV-1 particle infectivity, to enhance HIV-1 infection in macrophages. LAPTM5 transports HIV-1 envelope glycoproteins to lysosomes for degradation, thereby inhibiting virion infectivity. Vpr counteracts the restrictive effects of LAPTM5 by triggering its degradation via DCAF1. In the absence of Vpr, the silencing of LAPTM5 precisely phenocopied the effect of Vpr on HIV-1 infection. In contrast, Vpr did not enhance HIV-1 infection in the absence of LAPTM5. Moreover, LAPTM5 was highly expressed in macrophages but not in CD4+ T lymphocytes. Re-expressing LAPTM5 reconstituted the Vpr-dependent promotion of HIV-1 infection in primary CD4+ T cells, as observed in macrophages. Herein, we demonstrate the molecular mechanism used by Vpr to overcome LAPTM5 restriction in macrophages, providing a potential strategy for anti-HIV/AIDS therapeutics.
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47
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Chang KC, Wen JD. Programmed -1 ribosomal frameshifting from the perspective of the conformational dynamics of mRNA and ribosomes. Comput Struct Biotechnol J 2021; 19:3580-3588. [PMID: 34257837 PMCID: PMC8246090 DOI: 10.1016/j.csbj.2021.06.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 06/11/2021] [Accepted: 06/12/2021] [Indexed: 11/01/2022] Open
Abstract
Programmed -1 ribosomal frameshifting (-1 PRF) is a translation mechanism that regulates the relative expression level of two proteins encoded on the same messenger RNA (mRNA). This regulation is commonly used by viruses such as coronaviruses and retroviruses but rarely by host human cells, and for this reason, it has long been considered as a therapeutic target for antiviral drug development. Understanding the molecular mechanism of -1 PRF is one step toward this goal. Minus-one PRF occurs with a certain efficiency when translating ribosomes encounter the specialized mRNA signal consisting of the frameshifting site and a downstream stimulatory structure, which impedes translocation of the ribosome. The impeded ribosome can still undergo profound conformational changes to proceed with translocation; however, some of these changes may be unique and essential to frameshifting. In addition, most stimulatory structures exhibit conformational dynamics and sufficient mechanical strength, which, when under the action of ribosomes, may in turn further promote -1 PRF efficiency. In this review, we discuss how the dynamic features of ribosomes and mRNA stimulatory structures may influence the occurrence of -1 PRF and propose a hypothetical frameshifting model that recapitulates the role of conformational dynamics.
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Affiliation(s)
- Kai-Chun Chang
- Department of Bioengineering and Therapeutic Sciences, Schools of Medicine and Pharmacy, University of California, San Francisco, CA 94158, United States
| | - Jin-Der Wen
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
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48
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De Lise F, Strazzulli A, Iacono R, Curci N, Di Fenza M, Maurelli L, Moracci M, Cobucci-Ponzano B. Programmed Deviations of Ribosomes From Standard Decoding in Archaea. Front Microbiol 2021; 12:688061. [PMID: 34149676 PMCID: PMC8211752 DOI: 10.3389/fmicb.2021.688061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/04/2021] [Indexed: 11/13/2022] Open
Abstract
Genetic code decoding, initially considered to be universal and immutable, is now known to be flexible. In fact, in specific genes, ribosomes deviate from the standard translational rules in a programmed way, a phenomenon globally termed recoding. Translational recoding, which has been found in all domains of life, includes a group of events occurring during gene translation, namely stop codon readthrough, programmed ± 1 frameshifting, and ribosome bypassing. These events regulate protein expression at translational level and their mechanisms are well known and characterized in viruses, bacteria and eukaryotes. In this review we summarize the current state-of-the-art of recoding in the third domain of life. In Archaea, it was demonstrated and extensively studied that translational recoding regulates the decoding of the 21st and the 22nd amino acids selenocysteine and pyrrolysine, respectively, and only one case of programmed -1 frameshifting has been reported so far in Saccharolobus solfataricus P2. However, further putative events of translational recoding have been hypothesized in other archaeal species, but not extensively studied and confirmed yet. Although this phenomenon could have some implication for the physiology and adaptation of life in extreme environments, this field is still underexplored and genes whose expression could be regulated by recoding are still poorly characterized. The study of these recoding episodes in Archaea is urgently needed.
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Affiliation(s)
- Federica De Lise
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Andrea Strazzulli
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Roberta Iacono
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy
| | - Nicola Curci
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy
| | - Mauro Di Fenza
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Luisa Maurelli
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Marco Moracci
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
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49
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Morita E, Suzuki Y. Membrane-Associated Flavivirus Replication Complex-Its Organization and Regulation. Viruses 2021; 13:v13061060. [PMID: 34205058 PMCID: PMC8228428 DOI: 10.3390/v13061060] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/02/2021] [Accepted: 06/02/2021] [Indexed: 02/07/2023] Open
Abstract
Flavivirus consists of a large number of arthropod-borne viruses, many of which cause life-threatening diseases in humans. A characteristic feature of flavivirus infection is to induce the rearrangement of intracellular membrane structure in the cytoplasm. This unique membranous structure called replication organelle is considered as a microenvironment that provides factors required for the activity of the flaviviral replication complex. The replication organelle serves as a place to coordinate viral RNA amplification, protein translation, and virion assembly and also to protect the viral replication complex from the cellular immune defense system. In this review, we summarize the current understanding of how the formation and function of membrane-associated flaviviral replication organelle are regulated by cellular factors.
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Affiliation(s)
- Eiji Morita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki-shi 036-8561, Japan
- Correspondence: (E.M.); (Y.S.); Tel.: +81-172-39-3586 (E.M.); +81-72-684-7367 (Y.S.)
| | - Youichi Suzuki
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki 569-8686, Japan
- Correspondence: (E.M.); (Y.S.); Tel.: +81-172-39-3586 (E.M.); +81-72-684-7367 (Y.S.)
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50
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Liu Y, Li Z, Zhang M, Zhou H, Wu X, Zhong J, Xiao F, Huang N, Yang X, Zeng R, Yang L, Xia Z, Zhang N. Rolling-translated EGFR variants sustain EGFR signaling and promote glioblastoma tumorigenicity. Neuro Oncol 2021; 23:743-756. [PMID: 33325513 DOI: 10.1093/neuonc/noaa279] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Aberrant epidermal growth factor receptor (EGFR) activation is observed in over 50% of cases of adult glioblastoma (GBM). Nevertheless, EGFR antibodies are ineffective in clinical GBM treatment, suggesting the existence of redundant EGFR activation mechanisms. Whether circular RNA (circRNA) encodes a protein involved in EGFR-driven GBM remains unclear. We reported an unexpected mechanism in which circular EGFR RNA (circ-EGFR) encodes a novel EGFR variant to sustained EGFR activation. METHOD We used RNA-seq, Northern blot, and Sanger sequencing to confirm the existence of circ-EGFR. Antibodies and a liquid chromatograph tandem mass spectrometer were used to identify circ-EGFR protein products. Lentivirus-transfected stable cell lines were used to assess the biological functions of the novel protein in vitro and in vivo. Clinical implications of circ-EGFR were assessed using 97 pathologically diagnosed GBM patient samples. RESULTS The infinite open reading frame (iORF) in circ-EGFR translated repeating amino acid sequences via rolling translation and programmed -1 ribosomal frameshifting (-1PRF) induced out-of-frame stop codon (OSC), forming a polymetric novel protein-complex, which we termed rolling-translated EGFR (rtEGFR). rtEGFR directly interacted with EGFR, maintained EGFR membrane localization and attenuated EGFR endocytosis and degradation. Importantly, circ-EGFR levels correlated with the EGFR signature and predicted the poor prognosis of GBM patients. Deprivation of rtEGFR in brain tumor-initiating cells (BTICs) attenuated tumorigenicity and enhanced the anti-GBM effect. CONCLUSION Our findings identified the endogenous rolling-translated protein and provided strong clinical evidence that targeting rtEGFR could improve the efficiency of EGFR-targeting therapies in GBM.
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Affiliation(s)
- Yi Liu
- Department of Neurosurgery, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangzhou, Guangdong, China
| | - Zhongjun Li
- Department of Neurosurgery, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangzhou, Guangdong, China
| | - Maolei Zhang
- Department of Neurosurgery, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangzhou, Guangdong, China
| | - Huangkai Zhou
- Department of Neurosurgery, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangzhou, Guangdong, China
| | - Xujia Wu
- Department of Neurosurgery, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangzhou, Guangdong, China
| | - Jian Zhong
- Department of Neurosurgery, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangzhou, Guangdong, China
| | - Feizhe Xiao
- Department of Scientific Research Section, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Nunu Huang
- Department of Neurosurgery, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangzhou, Guangdong, China
| | - Xuesong Yang
- Department of Neurosurgery, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangzhou, Guangdong, China
| | - Rong Zeng
- Department of Radiation Oncology, Oncology Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Lixuan Yang
- Department of Neurosurgery, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangzhou, Guangdong, China
| | - Zhibo Xia
- Department of Neurosurgery, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangzhou, Guangdong, China
| | - Nu Zhang
- Department of Neurosurgery, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangzhou, Guangdong, China
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