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Anokhina VS, Miller BL. Targeting Ribosomal Frameshifting as an Antiviral Strategy: From HIV-1 to SARS-CoV-2. Acc Chem Res 2021; 54:3349-3361. [PMID: 34403258 DOI: 10.1021/acs.accounts.1c00316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Treatment of HIV-1 has largely involved targeting viral enzymes using a cocktail of inhibitors. However, resistance to these inhibitors and toxicity in the long term have pushed the field to identify new therapeutic targets. To that end, -1 programmed ribosomal frameshifting (-1 PRF) has gained attention as a potential node for therapeutic intervention. In this process, a ribosome moves one nucleotide backward in the course of translating a mRNA, revealing a new reading frame for protein synthesis. In HIV-1, -1 PRF allows the virus to regulate the ratios of enzymatic and structural proteins as needed for correct viral particle assembly. Two RNA structural elements are central to -1 PRF in HIV: a slippery sequence and a highly conserved stable hairpin called the HIV-1 frameshifting stimulatory signal (FSS). Dysregulation of -1 PRF is deleterious for the virus. Thus, -1 PRF is an attractive target for new antiviral development. It is important to note that HIV-1 is not the only virus exploiting -1 PRF for regulating production of its proteins. Coronaviruses, including the COVID-19 pandemic virus SARS-CoV-2, also rely on -1 PRF. In SARS-CoV-2 and other coronaviruses, -1 PRF is required for synthesis of RNA-dependent RNA polymerase and several other nonstructural proteins. Coronaviruses employ a more complex RNA structural element for regulating -1 PRF called a pseudoknot. The purpose of this Account is primarily to review the development of molecules targeting HIV-1 -1 PRF. These approaches are case studies illustrating how the entire pipeline from screening to the generation of high-affinity leads might be implemented. We consider both target-based and function-based screening, with a particular focus on our group's approach beginning with a resin-bound dynamic combinatorial library (RBDCL) screen. We then used rational design approaches to optimize binding affinity, selectivity, and cellular bioavailability. Our tactic is, to the best of our knowledge, the only study resulting in compounds that bind specifically to the HIV-1 FSS RNA and reduce infectivity of laboratory and drug-resistant strains of HIV-1 in human cells. Lessons learned from strategies targeting -1 PRF HIV-1 might provide solutions in the development of antivirals in areas of unmet medical need. This includes the development of new frameshift-altering therapies for SARS-CoV-2, approaches to which are very recently beginning to appear.
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Affiliation(s)
- Viktoriya S. Anokhina
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642, United States
| | - Benjamin L. Miller
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642, United States
- Department of Dermatology, University of Rochester, Rochester, New York 14642, United States
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Rao S, Hoskins I, Tonn T, Garcia PD, Ozadam H, Sarinay Cenik E, Cenik C. Genes with 5' terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein. RNA (NEW YORK, N.Y.) 2021; 27:1025-1045. [PMID: 34127534 PMCID: PMC8370740 DOI: 10.1261/rna.078661.120] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 06/08/2021] [Indexed: 05/05/2023]
Abstract
Viruses rely on the host translation machinery to synthesize their own proteins. Consequently, they have evolved varied mechanisms to co-opt host translation for their survival. SARS-CoV-2 relies on a nonstructural protein, Nsp1, for shutting down host translation. However, it is currently unknown how viral proteins and host factors critical for viral replication can escape a global shutdown of host translation. Here, using a novel FACS-based assay called MeTAFlow, we report a dose-dependent reduction in both nascent protein synthesis and mRNA abundance in cells expressing Nsp1. We perform RNA-seq and matched ribosome profiling experiments to identify gene-specific changes both at the mRNA expression and translation levels. We discover that a functionally coherent subset of human genes is preferentially translated in the context of Nsp1 expression. These genes include the translation machinery components, RNA binding proteins, and others important for viral pathogenicity. Importantly, we uncovered a remarkable enrichment of 5' terminal oligo-pyrimidine (TOP) tracts among preferentially translated genes. Using reporter assays, we validated that 5' UTRs from TOP transcripts can drive preferential expression in the presence of Nsp1. Finally, we found that LARP1, a key effector protein in the mTOR pathway, may contribute to preferential translation of TOP transcripts in response to Nsp1 expression. Collectively, our study suggests fine-tuning of host gene expression and translation by Nsp1 despite its global repressive effect on host protein synthesis.
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Affiliation(s)
- Shilpa Rao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Ian Hoskins
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Tori Tonn
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - P Daniela Garcia
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Hakan Ozadam
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Elif Sarinay Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
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53
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Roman C, Lewicka A, Koirala D, Li NS, Piccirilli JA. The SARS-CoV-2 Programmed -1 Ribosomal Frameshifting Element Crystal Structure Solved to 2.09 Å Using Chaperone-Assisted RNA Crystallography. ACS Chem Biol 2021; 16:1469-1481. [PMID: 34328734 PMCID: PMC8353986 DOI: 10.1021/acschembio.1c00324] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/19/2021] [Indexed: 12/12/2022]
Abstract
The programmed -1 ribosomal frameshifting element (PFSE) of SARS-CoV-2 is a well conserved structured RNA found in all coronaviruses' genomes. By adopting a pseudoknot structure in the presence of the ribosome, the PFSE promotes a ribosomal frameshifting event near the stop codon of the first open reading frame Orf1a during translation of the polyprotein pp1a. Frameshifting results in continuation of pp1a via a new open reading frame, Orf1b, that produces the longer pp1ab polyprotein. Polyproteins pp1a and pp1ab produce nonstructural proteins NSPs 1-10 and NSPs 1-16, respectively, which contribute vital functions during the viral life cycle and must be present in the proper stoichiometry. Both drugs and sequence alterations that affect the stability of the -1 programmed ribosomal frameshifting element disrupt the stoichiometry of the NSPs produced, which compromise viral replication. For this reason, the -1 programmed frameshifting element is considered a promising drug target. Using chaperone assisted RNA crystallography, we successfully crystallized and solved the three-dimensional structure of the PFSE. We observe a three-stem H-type pseudoknot structure with the three stems stacked in a vertical orientation stabilized by two triple base pairs at the stem 1/stem 2 and stem 1/stem 3 junctions. This structure provides a new conformation of PFSE distinct from the bent conformations inferred from midresolution cryo-EM models and provides a high-resolution framework for mechanistic investigations and structure-based drug design.
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Affiliation(s)
- Christina Roman
- Department
of Biochemistry and Molecular Biology, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Anna Lewicka
- Department
of Biochemistry and Molecular Biology, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Deepak Koirala
- Department
of Chemistry and Biochemistry, University
of Maryland Baltimore County (UMBC), Baltimore, Maryland 21250, United States
| | - Nan-Sheng Li
- Department
of Biochemistry and Molecular Biology, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Joseph A. Piccirilli
- Department
of Biochemistry and Molecular Biology, The
University of Chicago, Chicago, Illinois 60637, United States
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
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A Novel Frameshifting Inhibitor Having Antiviral Activity against Zoonotic Coronaviruses. Viruses 2021; 13:v13081639. [PMID: 34452503 PMCID: PMC8402677 DOI: 10.3390/v13081639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/13/2021] [Accepted: 08/16/2021] [Indexed: 12/12/2022] Open
Abstract
Recent outbreaks of zoonotic coronaviruses, such as Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), have caused tremendous casualties and great economic shock. Although some repurposed drugs have shown potential therapeutic efficacy in clinical trials, specific therapeutic agents targeting coronaviruses have not yet been developed. During coronavirus replication, a replicase gene cluster, including RNA-dependent RNA polymerase (RdRp), is alternatively translated via a process called -1 programmed ribosomal frameshift (−1 PRF) by an RNA pseudoknot structure encoded in viral RNAs. The coronavirus frameshifting has been identified previously as a target for antiviral therapy. In this study, the frameshifting efficiencies of MERS-CoV, SARS-CoV and SARS-CoV-2 were determined using an in vitro −1 PRF assay system. Our group has searched approximately 9689 small molecules to identify potential −1 PRF inhibitors. Herein, we found that a novel compound, 2-(5-acetylthiophen-2yl)furo[2,3-b]quinoline (KCB261770), inhibits the frameshifting of MERS-CoV and effectively suppresses viral propagation in MERS-CoV-infected cells. The inhibitory effects of 87 derivatives of furo[2,3-b]quinolines were also examined showing less prominent inhibitory effect when compared to compound KCB261770. We demonstrated that KCB261770 inhibits the frameshifting without suppressing cap-dependent translation. Furthermore, this compound was able to inhibit the frameshifting, to some extent, of SARS-CoV and SARS-CoV-2. Therefore, the novel compound 2-(5-acetylthiophen-2yl)furo[2,3-b]quinoline may serve as a promising drug candidate to interfere with pan-coronavirus frameshifting.
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Structural dynamics of single SARS-CoV-2 pseudoknot molecules reveal topologically distinct conformers. Nat Commun 2021; 12:4749. [PMID: 34362921 PMCID: PMC8346527 DOI: 10.1038/s41467-021-25085-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 07/21/2021] [Indexed: 11/08/2022] Open
Abstract
The RNA pseudoknot that stimulates programmed ribosomal frameshifting in SARS-CoV-2 is a possible drug target. To understand how it responds to mechanical tension applied by ribosomes, thought to play a key role during frameshifting, we probe its structural dynamics using optical tweezers. We find that it forms multiple structures: two pseudoknotted conformers with different stability and barriers, and alternative stem-loop structures. The pseudoknotted conformers have distinct topologies, one threading the 5′ end through a 3-helix junction to create a knot-like fold, the other with unthreaded 5′ end, consistent with structures observed via cryo-EM and simulations. Refolding of the pseudoknotted conformers starts with stem 1, followed by stem 3 and lastly stem 2; Mg2+ ions are not required, but increase pseudoknot mechanical rigidity and favor formation of the knot-like conformer. These results resolve the SARS-CoV-2 frameshift signal folding mechanism and highlight its conformational heterogeneity, with important implications for structure-based drug-discovery efforts. The RNA pseudoknot of SARS-CoV-2 promotes -1 programmed ribosomal frameshifting. Here the authors use single molecule force spectroscopy to study the folding of this pseudoknot, showing that it forms at least two different pseudoknot conformers with distinct fold topologies.
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56
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Schlick T, Zhu Q, Dey A, Jain S, Yan S, Laederach A. To Knot or Not to Knot: Multiple Conformations of the SARS-CoV-2 Frameshifting RNA Element. J Am Chem Soc 2021; 143:11404-11422. [PMID: 34283611 PMCID: PMC8315264 DOI: 10.1021/jacs.1c03003] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The SARS-CoV-2 frameshifting RNA element (FSE) is an excellent target for therapeutic intervention against Covid-19. This small gene element employs a shifting mechanism to pause and backtrack the ribosome during translation between Open Reading Frames 1a and 1b, which code for viral polyproteins. Any interference with this process has a profound effect on viral replication and propagation. Pinpointing the structures adapted by the FSE and associated structural transformations involved in frameshifting has been a challenge. Using our graph-theory-based modeling tools for representing RNA secondary structures, "RAG" (RNA-As-Graphs), and chemical structure probing experiments, we show that the 3-stem H-type pseudoknot (3_6 dual graph), long assumed to be the dominant structure, has a viable alternative, an HL-type 3-stem pseudoknot (3_3) for longer constructs. In addition, an unknotted 3-way junction RNA (3_5) emerges as a minor conformation. These three conformations share Stems 1 and 3, while the different Stem 2 may be involved in a conformational switch and possibly associations with the ribosome during translation. For full-length genomes, a stem-loop motif (2_2) may compete with these forms. These structural and mechanistic insights advance our understanding of the SARS-CoV-2 frameshifting process and concomitant virus life cycle, and point to three avenues of therapeutic intervention.
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Affiliation(s)
- Tamar Schlick
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, New York 10003, United States
- Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, New York 10012, United States
- New York University-East China Normal University Center for Computational Chemistry, New York University-Shanghai, Shanghai 200062, P. R. China
| | - Qiyao Zhu
- Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, New York 10012, United States
| | - Abhishek Dey
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Swati Jain
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, New York 10003, United States
| | - Shuting Yan
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, New York 10003, United States
| | - Alain Laederach
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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57
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Hsu CF, Chang KC, Chen YL, Hsieh PS, Lee AI, Tu JY, Chen YT, Wen JD. Formation of frameshift-stimulating RNA pseudoknots is facilitated by remodeling of their folding intermediates. Nucleic Acids Res 2021; 49:6941-6957. [PMID: 34161580 PMCID: PMC8266650 DOI: 10.1093/nar/gkab512] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 05/27/2021] [Accepted: 06/04/2021] [Indexed: 12/15/2022] Open
Abstract
Programmed –1 ribosomal frameshifting is an essential regulation mechanism of translation in viruses and bacteria. It is stimulated by mRNA structures inside the coding region. As the structure is unfolded repeatedly by consecutive translating ribosomes, whether it can refold properly each time is important in performing its function. By using single-molecule approaches and molecular dynamics simulations, we found that a frameshift-stimulating RNA pseudoknot folds sequentially through its upstream stem S1 and downstream stem S2. In this pathway, S2 folds from the downstream side and tends to be trapped in intermediates. By masking the last few nucleotides to mimic their gradual emergence from translating ribosomes, S2 can be directed to fold from the upstream region. The results show that the intermediates are greatly suppressed, suggesting that mRNA refolding may be modulated by ribosomes. Moreover, masking the first few nucleotides of S1 favors the folding from S2 and yields native pseudoknots, which are stable enough to retrieve the masked nucleotides. We hypothesize that translating ribosomes can remodel an intermediate mRNA structure into a stable conformation, which may in turn stimulate backward slippage of the ribosome. This supports an interactive model of ribosomal frameshifting and gives an insightful account addressing previous experimental observations.
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Affiliation(s)
- Chiung-Fang Hsu
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Kai-Chun Chang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Lan Chen
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Po-Szu Hsieh
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - An-I Lee
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Jui-Yun Tu
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Yu-Ting Chen
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - 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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58
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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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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: 67] [Impact Index Per Article: 22.3] [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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60
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Fabret C, Namy O. Translational accuracy of a tethered ribosome. Nucleic Acids Res 2021; 49:5308-5318. [PMID: 33950196 PMCID: PMC8136817 DOI: 10.1093/nar/gkab259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/27/2021] [Accepted: 05/04/2021] [Indexed: 01/09/2023] Open
Abstract
Ribosomes are evolutionary conserved ribonucleoprotein complexes that function as two separate subunits in all kingdoms. During translation initiation, the two subunits assemble to form the mature ribosome, which is responsible for translating the messenger RNA. When the ribosome reaches a stop codon, release factors promote translation termination and peptide release, and recycling factors then dissociate the two subunits, ready for use in a new round of translation. A tethered ribosome, called Ribo-T, in which the two subunits are covalently linked to form a single entity, was recently described in Escherichia coli. A hybrid ribosomal RNA (rRNA) consisting of both the small and large subunit rRNA sequences was engineered. The ribosome with inseparable subunits generated in this way was shown to be functional and to sustain cell growth. Here, we investigated the translational properties of Ribo-T. We analyzed its behavior during amino acid misincorporation, -1 or +1 frameshifting, stop codon readthrough, and internal translation initiation. Our data indicate that covalent attachment of the two subunits modifies the properties of the ribosome, altering its ability to initiate and terminate translation correctly.
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Affiliation(s)
- Celine Fabret
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Olivier Namy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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61
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Schlick T, Zhu Q, Dey A, Jain S, Yan S, Laederach A. To knot or not to knot: Multiple conformations of the SARS-CoV-2 frameshifting RNA element. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.31.437955. [PMID: 33821274 PMCID: PMC8020974 DOI: 10.1101/2021.03.31.437955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The SARS-CoV-2 frameshifting RNA element (FSE) is an excellent target for therapeutic intervention against Covid-19. This small gene element employs a shifting mechanism to pause and backtrack the ribosome during translation between Open Reading Frames 1a and 1b, which code for viral polyproteins. Any interference with this process has profound effect on viral replication and propagation. Pinpointing the structures adapted by the FSE and associated structural transformations involved in frameshifting has been a challenge. Using our graph-theory-based modeling tools for representing RNA secondary structures, "RAG" (RNA-As-Graphs), and chemical structure probing experiments, we show that the 3-stem H-type pseudoknot (3_6 dual graph), long assumed to be the dominant structure has a viable alternative, an HL-type 3-stem pseudoknot (3_3) for longer constructs. In addition, an unknotted 3-way junction RNA (3_5) emerges as a minor conformation. These three conformations share Stems 1 and 3, while the different Stem 2 may be involved in a conformational switch and possibly associations with the ribosome during translation. For full-length genomes, a stem-loop motif (2_2) may compete with these forms. These structural and mechanistic insights advance our understanding of the SARS-CoV-2 frameshifting process and concomitant virus life cycle, and point to three avenues of therapeutic intervention.
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Affiliation(s)
- Tamar Schlick
- Department of Chemistry, 100 Washington Square East, Silver Building, New York University, New York, NY 10003 U.S.A
- Courant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, NY 10012 U.S.A
- NYU-ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200062, P.R. China
| | - Qiyao Zhu
- Courant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, NY 10012 U.S.A
| | - Abhishek Dey
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Swati Jain
- Department of Chemistry, 100 Washington Square East, Silver Building, New York University, New York, NY 10003 U.S.A
| | - Shuting Yan
- Department of Chemistry, 100 Washington Square East, Silver Building, New York University, New York, NY 10003 U.S.A
| | - Alain Laederach
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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62
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Malinova I, Zupok A, Massouh A, Schöttler MA, Meyer EH, Yaneva-Roder L, Szymanski W, Rößner M, Ruf S, Bock R, Greiner S. Correction of frameshift mutations in the atpB gene by translational recoding in chloroplasts of Oenothera and tobacco. THE PLANT CELL 2021; 33:1682-1705. [PMID: 33561268 PMCID: PMC8254509 DOI: 10.1093/plcell/koab050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/02/2021] [Indexed: 05/10/2023]
Abstract
Translational recoding, also known as ribosomal frameshifting, is a process that causes ribosome slippage along the messenger RNA, thereby changing the amino acid sequence of the synthesized protein. Whether the chloroplast employs recoding is unknown. I-iota, a plastome mutant of Oenothera (evening primrose), carries a single adenine insertion in an oligoA stretch [11A] of the atpB coding region (encoding the β-subunit of the ATP synthase). The mutation is expected to cause synthesis of a truncated, nonfunctional protein. We report that a full-length AtpB protein is detectable in I-iota leaves, suggesting operation of a recoding mechanism. To characterize the phenomenon, we generated transplastomic tobacco lines in which the atpB reading frame was altered by insertions or deletions in the oligoA motif. We observed that insertion of two adenines was more efficiently corrected than insertion of a single adenine, or deletion of one or two adenines. We further show that homopolymeric composition of the oligoA stretch is essential for recoding, as an additional replacement of AAA lysine codon by AAG resulted in an albino phenotype. Our work provides evidence for the operation of translational recoding in chloroplasts. Recoding enables correction of frameshift mutations and can restore photoautotrophic growth in the presence of a mutation that otherwise would be lethal.
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Affiliation(s)
- Irina Malinova
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Arkadiusz Zupok
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Amid Massouh
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Mark Aurel Schöttler
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Etienne H Meyer
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Liliya Yaneva-Roder
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Witold Szymanski
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Margit Rößner
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Stephanie Ruf
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Stephan Greiner
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
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63
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Wan L, Juszkiewicz S, Blears D, Bajpe PK, Han Z, Faull P, Mitter R, Stewart A, Snijders AP, Hegde RS, Svejstrup JQ. Translation stress and collided ribosomes are co-activators of cGAS. Mol Cell 2021; 81:2808-2822.e10. [PMID: 34111399 PMCID: PMC8260207 DOI: 10.1016/j.molcel.2021.05.018] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 04/23/2021] [Accepted: 05/13/2021] [Indexed: 12/25/2022]
Abstract
The cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway senses cytosolic DNA and induces interferon-stimulated genes (ISGs) to activate the innate immune system. Here, we report the unexpected discovery that cGAS also senses dysfunctional protein production. Purified ribosomes interact directly with cGAS and stimulate its DNA-dependent activity in vitro. Disruption of the ribosome-associated protein quality control (RQC) pathway, which detects and resolves ribosome collision during translation, results in cGAS-dependent ISG expression and causes re-localization of cGAS from the nucleus to the cytosol. Indeed, cGAS preferentially binds collided ribosomes in vitro, and orthogonal perturbations that result in elevated levels of collided ribosomes and RQC activation cause sub-cellular re-localization of cGAS and ribosome binding in vivo as well. Thus, translation stress potently increases DNA-dependent cGAS activation. These findings have implications for the inflammatory response to viral infection and tumorigenesis, both of which substantially reprogram cellular protein synthesis.
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Affiliation(s)
- Li Wan
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Szymon Juszkiewicz
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Daniel Blears
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Cellular and Molecular Medicine, Panum Institute, Blegdamsvej 3B, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Prashanth Kumar Bajpe
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Zhong Han
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Cellular and Molecular Medicine, Panum Institute, Blegdamsvej 3B, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Peter Faull
- Protein Analysis and Proteomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Richard Mitter
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Aengus Stewart
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ambrosius P Snijders
- Protein Analysis and Proteomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ramanujan S Hegde
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Cellular and Molecular Medicine, Panum Institute, Blegdamsvej 3B, University of Copenhagen, 2200 Copenhagen, Denmark.
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64
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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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65
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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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66
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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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67
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Marucci G, Zullino I, Bertuccini L, Camerini S, Cecchetti S, Pietrantoni A, Casella M, Vatta P, Greenwood AD, Fiorillo A, Lalle M. Re-Discovery of Giardiavirus: Genomic and Functional Analysis of Viruses from Giardia duodenalis Isolates. Biomedicines 2021; 9:654. [PMID: 34201207 PMCID: PMC8230311 DOI: 10.3390/biomedicines9060654] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 12/29/2022] Open
Abstract
Giardiasis, caused by the protozoan parasite Giardia duodenalis, is an intestinal diarrheal disease affecting almost one billion people worldwide. A small endosymbiotic dsRNA viruses, G. lamblia virus (GLV), genus Giardiavirus, family Totiviridae, might inhabit human and animal isolates of G. duodenalis. Three GLV genomes have been sequenced so far, and only one was intensively studied; moreover, a positive correlation between GLV and parasite virulence is yet to be proved. To understand the biological significance of GLV infection in Giardia, the characterization of several GLV strains from naturally infected G. duodenalis isolates is necessary. Here we report high-throughput sequencing of four GLVs strains, from Giardia isolates of human and animal origin. We also report on a new, unclassified viral sequence (designed GdRV-2), unrelated to Giardiavirus, encoding and expressing for a single large protein with an RdRp domain homologous to Totiviridae and Botybirnaviridae. The result of our sequencing and proteomic analyses challenge the current knowledge on GLV and strongly suggest that viral capsid protein translation unusually starts with a proline and that translation of the RNA-dependent RNA polymerase (RdRp) occurs via a +1/-2 ribosomal frameshift mechanism. Nucleotide polymorphism, confirmed by mass-spectrometry analysis, was also observed among and between GLV strains. Phylogenetic analysis indicated the occurrence of at least two GLV subtypes which display different phenotypes and transmissibility in experimental infections of a GLV naïve Giardia isolate.
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Affiliation(s)
- Gianluca Marucci
- Unit of Foodborne and Neglected Parasitic Disease, Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (G.M.); (I.Z.); (P.V.)
| | - Ilaria Zullino
- Unit of Foodborne and Neglected Parasitic Disease, Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (G.M.); (I.Z.); (P.V.)
| | - Lucia Bertuccini
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (L.B.); (S.C.); (S.C.); (A.P.); (M.C.)
| | - Serena Camerini
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (L.B.); (S.C.); (S.C.); (A.P.); (M.C.)
| | - Serena Cecchetti
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (L.B.); (S.C.); (S.C.); (A.P.); (M.C.)
| | - Agostina Pietrantoni
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (L.B.); (S.C.); (S.C.); (A.P.); (M.C.)
| | - Marialuisa Casella
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (L.B.); (S.C.); (S.C.); (A.P.); (M.C.)
| | - Paolo Vatta
- Unit of Foodborne and Neglected Parasitic Disease, Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (G.M.); (I.Z.); (P.V.)
| | - Alex D. Greenwood
- Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany;
- Department of Veterinary Medicine, Freie Universität Berlin, 14195 Berlin, Germany
| | - Annarita Fiorillo
- Department of Biochemical Science “A. Rossi-Fanelli”, Sapienza University, 00185 Rome, Italy;
| | - Marco Lalle
- Unit of Foodborne and Neglected Parasitic Disease, Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (G.M.); (I.Z.); (P.V.)
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68
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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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69
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Rao S, Hoskins I, Tonn T, Garcia PD, Ozadam H, Cenik ES, Cenik C. Genes with 5' terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.09.13.295493. [PMID: 32995776 PMCID: PMC7523102 DOI: 10.1101/2020.09.13.295493] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Viruses rely on the host translation machinery to synthesize their own proteins. Consequently, they have evolved varied mechanisms to co-opt host translation for their survival. SARS-CoV-2 relies on a non-structural protein, Nsp1, for shutting down host translation. However, it is currently unknown how viral proteins and host factors critical for viral replication can escape a global shutdown of host translation. Here, using a novel FACS-based assay called MeTAFlow, we report a dose-dependent reduction in both nascent protein synthesis and mRNA abundance in cells expressing Nsp1. We perform RNA-Seq and matched ribosome profiling experiments to identify gene-specific changes both at the mRNA expression and translation level. We discover a functionally-coherent subset of human genes are preferentially translated in the context of Nsp1 expression. These genes include the translation machinery components, RNA binding proteins, and others important for viral pathogenicity. Importantly, we uncovered a remarkable enrichment of 5' terminal oligo-pyrimidine (TOP) tracts among preferentially translated genes. Using reporter assays, we validated that 5' UTRs from TOP transcripts can drive preferential expression in the presence of NSP1. Finally, we found that LARP1, a key effector protein in the mTOR pathway may contribute to preferential translation of TOP transcripts in response to Nsp1 expression. Collectively, our study suggests fine tuning of host gene expression and translation by Nsp1 despite its global repressive effect on host protein synthesis.
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Affiliation(s)
- Shilpa Rao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Ian Hoskins
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Tori Tonn
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - P. Daniela Garcia
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Hakan Ozadam
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Elif Sarinay Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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70
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Unconventional viral gene expression mechanisms as therapeutic targets. Nature 2021; 593:362-371. [PMID: 34012080 DOI: 10.1038/s41586-021-03511-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 03/22/2021] [Indexed: 12/14/2022]
Abstract
Unlike the human genome that comprises mostly noncoding and regulatory sequences, viruses have evolved under the constraints of maintaining a small genome size while expanding the efficiency of their coding and regulatory sequences. As a result, viruses use strategies of transcription and translation in which one or more of the steps in the conventional gene-protein production line are altered. These alternative strategies of viral gene expression (also known as gene recoding) can be uniquely brought about by dedicated viral enzymes or by co-opting host factors (known as host dependencies). Targeting these unique enzymatic activities and host factors exposes vulnerabilities of a virus and provides a paradigm for the design of novel antiviral therapies. In this Review, we describe the types and mechanisms of unconventional gene and protein expression in viruses, and provide a perspective on how future basic mechanistic work could inform translational efforts that are aimed at viral eradication.
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71
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van den Akker GGH, Zacchini F, Housmans BAC, van der Vloet L, Caron MMJ, Montanaro L, Welting TJM. Current Practice in Bicistronic IRES Reporter Use: A Systematic Review. Int J Mol Sci 2021; 22:5193. [PMID: 34068921 PMCID: PMC8156625 DOI: 10.3390/ijms22105193] [Citation(s) in RCA: 9] [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: 03/25/2021] [Revised: 05/05/2021] [Accepted: 05/12/2021] [Indexed: 12/26/2022] Open
Abstract
Bicistronic reporter assays have been instrumental for transgene expression, understanding of internal ribosomal entry site (IRES) translation, and identification of novel cap-independent translational elements (CITE). We observed a large methodological variability in the use of bicistronic reporter assays and data presentation or normalization procedures. Therefore, we systematically searched the literature for bicistronic IRES reporter studies and analyzed methodological details, data visualization, and normalization procedures. Two hundred fifty-seven publications were identified using our search strategy (published 1994-2020). Experimental studies on eukaryotic adherent cell systems and the cell-free translation assay were included for further analysis. We evaluated the following methodological details for 176 full text articles: the bicistronic reporter design, the cell line or type, transfection methods, and time point of analyses post-transfection. For the cell-free translation assay, we focused on methods of in vitro transcription, type of translation lysate, and incubation times and assay temperature. Data can be presented in multiple ways: raw data from individual cistrons, a ratio of the two, or fold changes thereof. In addition, many different control experiments have been suggested when studying IRES-mediated translation. In addition, many different normalization and control experiments have been suggested when studying IRES-mediated translation. Therefore, we also categorized and summarized their use. Our unbiased analyses provide a representative overview of bicistronic IRES reporter use. We identified parameters that were reported inconsistently or incompletely, which could hamper data reproduction and interpretation. On the basis of our analyses, we encourage adhering to a number of practices that should improve transparency of bicistronic reporter data presentation and improve methodological descriptions to facilitate data replication.
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Affiliation(s)
- Guus Gijsbertus Hubert van den Akker
- Department of Orthopedic Surgery, Maastricht University, Medical Center+, 6229 ER Maastricht, The Netherlands; (G.G.H.v.d.A.); (B.A.C.H.); (L.v.d.V.); (M.M.J.C.)
| | - Federico Zacchini
- Department of Experimental, Diagnostic and Specialty Medicine, Bologna University, I-40138 Bologna, Italy; (F.Z.); (L.M.)
- Centro di Ricerca Biomedica Applicata—CRBA, Bologna University, Policlinico di Sant’Orsola, I-40138 Bologna, Italy
| | - Bas Adrianus Catharina Housmans
- Department of Orthopedic Surgery, Maastricht University, Medical Center+, 6229 ER Maastricht, The Netherlands; (G.G.H.v.d.A.); (B.A.C.H.); (L.v.d.V.); (M.M.J.C.)
| | - Laura van der Vloet
- Department of Orthopedic Surgery, Maastricht University, Medical Center+, 6229 ER Maastricht, The Netherlands; (G.G.H.v.d.A.); (B.A.C.H.); (L.v.d.V.); (M.M.J.C.)
| | - Marjolein Maria Johanna Caron
- Department of Orthopedic Surgery, Maastricht University, Medical Center+, 6229 ER Maastricht, The Netherlands; (G.G.H.v.d.A.); (B.A.C.H.); (L.v.d.V.); (M.M.J.C.)
| | - Lorenzo Montanaro
- Department of Experimental, Diagnostic and Specialty Medicine, Bologna University, I-40138 Bologna, Italy; (F.Z.); (L.M.)
- Centro di Ricerca Biomedica Applicata—CRBA, Bologna University, Policlinico di Sant’Orsola, I-40138 Bologna, Italy
- Programma Dipartimentale in Medicina di Laboratorio, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy
| | - Tim Johannes Maria Welting
- Department of Orthopedic Surgery, Maastricht University, Medical Center+, 6229 ER Maastricht, The Netherlands; (G.G.H.v.d.A.); (B.A.C.H.); (L.v.d.V.); (M.M.J.C.)
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72
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Bhatt PR, Scaiola A, Loughran G, Leibundgut M, Kratzel A, Meurs R, Dreos R, O'Connor KM, McMillan A, Bode JW, Thiel V, Gatfield D, Atkins JF, Ban N. Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome. Science 2021; 372:1306-1313. [PMID: 34029205 PMCID: PMC8168617 DOI: 10.1126/science.abf3546] [Citation(s) in RCA: 150] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/24/2021] [Accepted: 05/07/2021] [Indexed: 12/22/2022]
Abstract
Programmed ribosomal frameshifting is a key event during translation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA genome that allows synthesis of the viral RNA-dependent RNA polymerase and downstream proteins. Here, we present the cryo-electron microscopy structure of a translating mammalian ribosome primed for frameshifting on the viral RNA. The viral RNA adopts a pseudoknot structure that lodges at the entry to the ribosomal messenger RNA (mRNA) channel to generate tension in the mRNA and promote frameshifting, whereas the nascent viral polyprotein forms distinct interactions with the ribosomal tunnel. Biochemical experiments validate the structural observations and reveal mechanistic and regulatory features that influence frameshifting efficiency. Finally, we compare compounds previously shown to reduce frameshifting with respect to their ability to inhibit SARS-CoV-2 replication, establishing coronavirus frameshifting as a target for antiviral intervention.
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Affiliation(s)
- Pramod R Bhatt
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.,School of Biochemistry and Cell Biology, University College Cork, Cork T12 XF62, Ireland.,School of Microbiology, University College Cork, Cork T12 K8AF, Ireland
| | - Alain Scaiola
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 XF62, Ireland
| | - Marc Leibundgut
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology, University of Bern, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Romane Meurs
- Center for Integrative Genomics, Génopode, University of Lausanne, 1015 Lausanne, Switzerland
| | - René Dreos
- Center for Integrative Genomics, Génopode, University of Lausanne, 1015 Lausanne, Switzerland
| | - Kate M O'Connor
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 XF62, Ireland
| | - Angus McMillan
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Jeffrey W Bode
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Volker Thiel
- Institute of Virology and Immunology, University of Bern, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - David Gatfield
- Center for Integrative Genomics, Génopode, University of Lausanne, 1015 Lausanne, Switzerland
| | - John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 XF62, Ireland. .,School of Microbiology, University College Cork, Cork T12 K8AF, Ireland.,MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
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73
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Villarreal LP, Witzany G. Social Networking of Quasi-Species Consortia drive Virolution via Persistence. AIMS Microbiol 2021; 7:138-162. [PMID: 34250372 PMCID: PMC8255905 DOI: 10.3934/microbiol.2021010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 04/25/2021] [Indexed: 12/31/2022] Open
Abstract
The emergence of cooperative quasi-species consortia (QS-C) thinking from the more accepted quasispecies equations of Manfred Eigen, provides a conceptual foundation from which concerted action of RNA agents can now be understood. As group membership becomes a basic criteria for the emergence of living systems, we also start to understand why the history and context of social RNA networks become crucial for survival and function. History and context of social RNA networks also lead to the emergence of a natural genetic code. Indeed, this QS-C thinking can also provide us with a transition point between the chemical world of RNA replicators and the living world of RNA agents that actively differentiate self from non-self and generate group identity with membership roles. Importantly the social force of a consortia to solve complex, multilevel problems also depend on using opposing and minority functions. The consortial action of social networks of RNA stem-loops subsequently lead to the evolution of cellular organisms representing a tree of life.
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74
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Identification of polycistronic transcriptional units and non-canonical introns in green algal chloroplasts based on long-read RNA sequencing data. BMC Genomics 2021; 22:298. [PMID: 33892645 PMCID: PMC8063479 DOI: 10.1186/s12864-021-07598-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 04/11/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chloroplasts are important semi-autonomous organelles in plants and algae. Unlike higher plants, the chloroplast genomes of green algal linage have distinct features both in organization and expression. Despite the architecture of chloroplast genome having been extensively studied in higher plants and several model species of algae, little is known about the transcriptional features of green algal chloroplast-encoded genes. RESULTS Based on full-length cDNA (Iso-Seq) sequencing, we identified widely co-transcribed polycistronic transcriptional units (PTUs) in the green alga Caulerpa lentillifera. In addition to clusters of genes from the same pathway, we identified a series of PTUs of up to nine genes whose function in the plastid is not understood. The RNA data further allowed us to confirm widespread expression of fragmented genes and conserved open reading frames, which are both important features in green algal chloroplast genomes. In addition, a newly fragmented gene specific to C. lentillifera was discovered, which may represent a recent gene fragmentation event in the chloroplast genome. With the newly annotated exon-intron boundary information, gene structural annotation was greatly improved across the siphonous green algae lineages. Our data also revealed a type of non-canonical Group II introns, with a deviant secondary structure and intronic ORFs lacking known splicing or mobility domains. These widespread introns have conserved positions in their genes and are excised precisely despite lacking clear consensus intron boundaries. CONCLUSION Our study fills important knowledge gaps in chloroplast genome organization and transcription in green algae, and provides new insights into expression of polycistronic transcripts, freestanding ORFs and fragmented genes in algal chloroplast genomes. Moreover, we revealed an unusual type of Group II intron with distinct features and conserved positions in Bryopsidales. Our data represents interesting additions to knowledge of chloroplast intron structure and highlights clusters of uncharacterized genes that probably play important roles in plastids.
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75
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Transcript Regulation of the Recoded Archaeal α-l-Fucosidase In Vivo. Molecules 2021; 26:molecules26071861. [PMID: 33806142 PMCID: PMC8037382 DOI: 10.3390/molecules26071861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/22/2021] [Accepted: 03/19/2021] [Indexed: 11/17/2022] Open
Abstract
Genetic decoding is flexible, due to programmed deviation of the ribosomes from standard translational rules, globally termed "recoding". In Archaea, recoding has been unequivocally determined only for termination codon readthrough events that regulate the incorporation of the unusual amino acids selenocysteine and pyrrolysine, and for -1 programmed frameshifting that allow the expression of a fully functional α-l-fucosidase in the crenarchaeon Saccharolobus solfataricus, in which several functional interrupted genes have been identified. Increasing evidence suggests that the flexibility of the genetic code decoding could provide an evolutionary advantage in extreme conditions, therefore, the identification and study of interrupted genes in extremophilic Archaea could be important from an astrobiological point of view, providing new information on the origin and evolution of the genetic code and on the limits of life on Earth. In order to shed some light on the mechanism of programmed -1 frameshifting in Archaea, here we report, for the first time, on the analysis of the transcription of this recoded archaeal α-l-fucosidase and of its full-length mutant in different growth conditions in vivo. We found that only the wild type mRNA significantly increased in S. solfataricus after cold shock and in cells grown in minimal medium containing hydrolyzed xyloglucan as carbon source. Our results indicated that the increased level of fucA mRNA cannot be explained by transcript up-regulation alone. A different mechanism related to translation efficiency is discussed.
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76
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Halma MTJ, Ritchie DB, Woodside MT. Conformational Shannon Entropy of mRNA Structures from Force Spectroscopy Measurements Predicts the Efficiency of -1 Programmed Ribosomal Frameshift Stimulation. PHYSICAL REVIEW LETTERS 2021; 126:038102. [PMID: 33543960 DOI: 10.1103/physrevlett.126.038102] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
-1 programmed ribosomal frameshifting (-1 PRF) is stimulated by structures in messenger RNA (mRNA), but the factors determining -1 PRF efficiency are unclear. We show that -1 PRF efficiency varies directly with the conformational heterogeneity of the stimulatory structure, quantified as the Shannon entropy of the state occupancy, for a panel of stimulatory structures with efficiencies from 2% to 80%. The correlation is force dependent and vanishes at forces above those applied by the ribosome. These results support the hypothesis that heterogeneous conformational dynamics are a key factor in stimulating -1 PRF.
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Affiliation(s)
- Matthew T J Halma
- Department of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Dustin B Ritchie
- Department of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Michael T Woodside
- Department of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
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77
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Andreu-Sánchez S, Chen W, Stiller J, Zhang G. Multiple origins of a frameshift insertion in a mitochondrial gene in birds and turtles. Gigascience 2021; 10:giaa161. [PMID: 33463679 PMCID: PMC7814300 DOI: 10.1093/gigascience/giaa161] [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: 04/28/2020] [Revised: 10/05/2020] [Accepted: 12/18/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND During evolutionary history, molecular mechanisms have emerged to cope with deleterious mutations. Frameshift insertions in protein-coding sequences are extremely rare because they disrupt the reading frame. There are a few known examples of their correction through translational frameshifting, a process that enables ribosomes to skip nucleotides during translation to regain proper reading frame. Corrective frameshifting has been proposed to act on the single base pair insertion at position 174 of the mitochondrial NADH dehydrogenase subunit 3 gene (ND3) that has been observed in several turtles and birds. However, the relatively sparse taxonomic representation has hampered our understanding of the evolution of this insertion in vertebrates. RESULTS Here, we analyzed 87,707 ND3 sequences from 10,309 vertebrate taxa to reveal the evolutionary history of this insertion and its common genomic characteristics. We confirmed that the insertion only appears in turtles and birds and reconstructed that it evolved independently in both groups with complex patterns of gains and losses. The insertion was observed in almost all bird orders but was absent in all members of the diverse Passeriformes. We found strong conservation in the nucleotides surrounding the insertion in both turtles and birds, which implies that the insertion enforces structural constraints that could be involved in its correction. CONCLUSIONS Our study demonstrates that frameshifts can be widespread and can be retained for millions of years if they are embedded in a conserved sequence theme.
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Affiliation(s)
- Sergio Andreu-Sánchez
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
- Present Address: University of Groningen, University Medical Center Groningen, Department of Pediatrics, 9700 RB Groningen, Netherlands
| | - Wanjun Chen
- China National Genebank, BGI-Shenzhen, Beishan Industrial Zone, 518083 Shenzhen, China
| | - Josefin Stiller
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Guojie Zhang
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
- China National Genebank, BGI-Shenzhen, Beishan Industrial Zone, 518083 Shenzhen, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu, 650223 Kunming, China
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78
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Gamper H, Li H, Masuda I, Miklos Robkis D, Christian T, Conn AB, Blaha G, Petersson EJ, Gonzalez RL, Hou YM. Insights into genome recoding from the mechanism of a classic +1-frameshifting tRNA. Nat Commun 2021; 12:328. [PMID: 33436566 PMCID: PMC7803779 DOI: 10.1038/s41467-020-20373-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/30/2020] [Indexed: 12/18/2022] Open
Abstract
While genome recoding using quadruplet codons to incorporate non-proteinogenic amino acids is attractive for biotechnology and bioengineering purposes, the mechanism through which such codons are translated is poorly understood. Here we investigate translation of quadruplet codons by a +1-frameshifting tRNA, SufB2, that contains an extra nucleotide in its anticodon loop. Natural post-transcriptional modification of SufB2 in cells prevents it from frameshifting using a quadruplet-pairing mechanism such that it preferentially employs a triplet-slippage mechanism. We show that SufB2 uses triplet anticodon-codon pairing in the 0-frame to initially decode the quadruplet codon, but subsequently shifts to the +1-frame during tRNA-mRNA translocation. SufB2 frameshifting involves perturbation of an essential ribosome conformational change that facilitates tRNA-mRNA movements at a late stage of the translocation reaction. Our results provide a molecular mechanism for SufB2-induced +1 frameshifting and suggest that engineering of a specific ribosome conformational change can improve the efficiency of genome recoding. Genome recoding with quadruplet codons requires a +1-frameshift-suppressor tRNA able to insert an amino acid at quadruplet codons of interest. Here the authors identify the mechanisms resulting in +1 frameshifting and the steps of the elongation cycle in which it occurs.
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Affiliation(s)
- Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Haixing Li
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Isao Masuda
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - D Miklos Robkis
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Thomas Christian
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Adam B Conn
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Gregor Blaha
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia University, New York, NY, 10027, USA.
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA.
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79
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Niblett D, Nelson C, Leung CS, Rexroad G, Cozy J, Zhou J, Lancaster L, Noller HF. Mutations in domain IV of elongation factor EF-G confer -1 frameshifting. RNA (NEW YORK, N.Y.) 2021; 27:40-53. [PMID: 33008838 PMCID: PMC7749637 DOI: 10.1261/rna.077339.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/24/2020] [Indexed: 05/25/2023]
Abstract
A recent crystal structure of a ribosome complex undergoing partial translocation in the absence of elongation factor EF-G showed disruption of codon-anticodon pairing and slippage of the reading frame by -1, directly implicating EF-G in preservation of the translational reading frame. Among mutations identified in a random screen for dominant-lethal mutations of EF-G were a cluster of six that map to the tip of domain IV, which has been shown to contact the codon-anticodon duplex in trapped translocation intermediates. In vitro synthesis of a full-length protein using these mutant EF-Gs revealed dramatically increased -1 frameshifting, providing new evidence for a role for domain IV of EF-G in maintaining the reading frame. These mutations also caused decreased rates of mRNA translocation and rotational movement of the head and body domains of the 30S ribosomal subunit during translocation. Our results are in general agreement with recent findings from Rodnina and coworkers based on in vitro translation of an oligopeptide using EF-Gs containing mutations at two positions in domain IV, who found an inverse correlation between the degree of frameshifting and rates of translocation. Four of our six mutations are substitutions at positions that interact with the translocating tRNA, in each case contacting the RNA backbone of the anticodon loop. We suggest that EF-G helps to preserve the translational reading frame by preventing uncoupled movement of the tRNA through these contacts; a further possibility is that these interactions may stabilize a conformation of the anticodon that favors base-pairing with its codon.
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Affiliation(s)
- Dustin Niblett
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Charlotte Nelson
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Calvin S Leung
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Gillian Rexroad
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Jake Cozy
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Jie Zhou
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Laura Lancaster
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Harry F Noller
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
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80
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Omar SI, Zhao M, Sekar RV, Moghadam SA, Tuszynski JA, Woodside MT. Modeling the structure of the frameshift-stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers. PLoS Comput Biol 2021; 17:e1008603. [PMID: 33465066 PMCID: PMC7845960 DOI: 10.1371/journal.pcbi.1008603] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 01/29/2021] [Accepted: 12/02/2020] [Indexed: 01/26/2023] Open
Abstract
The coronavirus causing the COVID-19 pandemic, SARS-CoV-2, uses -1 programmed ribosomal frameshifting (-1 PRF) to control the relative expression of viral proteins. As modulating -1 PRF can inhibit viral replication, the RNA pseudoknot stimulating -1 PRF may be a fruitful target for therapeutics treating COVID-19. We modeled the unusual 3-stem structure of the stimulatory pseudoknot of SARS-CoV-2 computationally, using multiple blind structural prediction tools followed by μs-long molecular dynamics simulations. The results were compared for consistency with nuclease-protection assays and single-molecule force spectroscopy measurements of the SARS-CoV-1 pseudoknot, to determine the most likely conformations. We found several possible conformations for the SARS-CoV-2 pseudoknot, all having an extended stem 3 but with different packing of stems 1 and 2. Several conformations featured rarely-seen threading of a single strand through junctions formed between two helices. These structural models may help interpret future experiments and support efforts to discover ligands inhibiting -1 PRF in SARS-CoV-2.
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Affiliation(s)
- Sara Ibrahim Omar
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Meng Zhao
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | | | | | - Jack A. Tuszynski
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
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81
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Patel A, Treffers EE, Meier M, Patel TR, Stetefeld J, Snijder EJ, Mark BL. Molecular characterization of the RNA-protein complex directing -2/-1 programmed ribosomal frameshifting during arterivirus replicase expression. J Biol Chem 2020; 295:17904-17921. [PMID: 33127640 PMCID: PMC7939443 DOI: 10.1074/jbc.ra120.016105] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
Programmed ribosomal frameshifting (PRF) is a mechanism used by arteriviruses like porcine reproductive and respiratory syndrome virus (PRRSV) to generate multiple proteins from overlapping reading frames within its RNA genome. PRRSV employs -1 PRF directed by RNA secondary and tertiary structures within its viral genome (canonical PRF), as well as a noncanonical -1 and -2 PRF that are stimulated by the interactions of PRRSV nonstructural protein 1β (nsp1β) and host protein poly(C)-binding protein (PCBP) 1 or 2 with the viral genome. Together, nsp1β and one of the PCBPs act as transactivators that bind a C-rich motif near the shift site to stimulate -1 and -2 PRF, thereby enabling the ribosome to generate two frameshift products that are implicated in viral immune evasion. How nsp1β and PCBP associate with the viral RNA genome remains unclear. Here, we describe the purification of the nsp1β:PCBP2:viral RNA complex on a scale sufficient for structural analysis using small-angle X-ray scattering and stochiometric analysis by analytical ultracentrifugation. The proteins associate with the RNA C-rich motif as a 1:1:1 complex. The monomeric form of nsp1β within the complex differs from previously reported homodimer identified by X-ray crystallography. Functional analysis of the complex via mutational analysis combined with RNA-binding assays and cell-based frameshifting reporter assays reveal a number of key residues within nsp1β and PCBP2 that are involved in complex formation and function. Our results suggest that nsp1β and PCBP2 both interact directly with viral RNA during formation of the complex to coordinate this unusual PRF mechanism.
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Affiliation(s)
- Ankoor Patel
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Emmely E Treffers
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Markus Meier
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Trushar R Patel
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Brian L Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.
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82
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Rastogi M, Pandey N, Shukla A, Singh SK. SARS coronavirus 2: from genome to infectome. Respir Res 2020; 21:318. [PMID: 33261606 PMCID: PMC7706175 DOI: 10.1186/s12931-020-01581-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/22/2020] [Indexed: 02/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) belongs to the group of Betacoronaviruses. The SARS-CoV-2 is closely related to SARS-CoV-1 and probably originated either from bats or pangolins. SARS-CoV-2 is an etiological agent of COVID-19, causing mild to severe respiratory disease which escalates to acute respiratory distress syndrome (ARDS) or multi-organ failure. The virus was first reported from the animal market in Hunan, Hubei province of China in the month of December, 2019, and was rapidly transmitted from animal to human and human-to-human. The human-to-human transmission can occur directly or via droplets generated during coughing and sneezing. Globally, around 53.9 million cases of COVID-19 have been registered with 1.31 million confirmed deaths. The people > 60 years, persons suffering from comorbid conditions and immunocompromised individuals are more susceptible to COVID-19 infection. The virus primarily targets the upper and the lower respiratory tract and quickly disseminates to other organs. SARS-CoV-2 dysregulates immune signaling pathways which generate cytokine storm and leads to the acute respiratory distress syndrome and other multisystemic disorders.
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Affiliation(s)
- Meghana Rastogi
- Molecular Biology Unit, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Neha Pandey
- Molecular Biology Unit, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Astha Shukla
- Molecular Biology Unit, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Sunit K Singh
- Molecular Biology Unit, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India.
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83
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Time-course profiling of bovine alphaherpesvirus 1.1 transcriptome using multiplatform sequencing. Sci Rep 2020; 10:20496. [PMID: 33235226 PMCID: PMC7686369 DOI: 10.1038/s41598-020-77520-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 11/04/2020] [Indexed: 12/11/2022] Open
Abstract
Long-read sequencing (LRS) has become a standard approach for transcriptome analysis in recent years. Bovine alphaherpesvirus 1 (BoHV-1) is an important pathogen of cattle worldwide. This study reports the profiling of the dynamic lytic transcriptome of BoHV-1 using two long-read sequencing (LRS) techniques, the Oxford Nanopore Technologies MinION, and the LoopSeq synthetic LRS methods, using multiple library preparation protocols. In this work, we annotated viral mRNAs and non-coding transcripts, and a large number of transcript isoforms, including transcription start and end sites, as well as splice variants of BoHV-1. Our analysis demonstrated an extremely complex pattern of transcriptional overlaps.
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84
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Rouchka EC, Chariker JH, Chung D. Variant analysis of 1,040 SARS-CoV-2 genomes. PLoS One 2020; 15:e0241535. [PMID: 33152019 PMCID: PMC7643988 DOI: 10.1371/journal.pone.0241535] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/18/2020] [Indexed: 01/02/2023] Open
Abstract
The severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) viral genome is an RNA virus consisting of approximately 30,000 bases. As part of testing efforts, whole genome sequencing of human isolates has resulted in over 1,600 complete genomes publicly available from GenBank. We have performed a comparative analysis of the sequences, in order to detect common mutations within the population. Analysis of variants occurring within the assembled genomes yields 417 variants occurring in at least 1% of the completed genomes, including 229 within the 5' untranslated region (UTR), 152 within the 3'UTR, 2 within intergenic regions and 34 within coding sequences.
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Affiliation(s)
- Eric C. Rouchka
- Department of Computer Science and Engineering, University of Louisville, Louisville, Kentucky, United States of America
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, University of Louisville, Louisville, Kentucky, United States of America
| | - Julia H. Chariker
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, University of Louisville, Louisville, Kentucky, United States of America
- Neuroscience Training Program, University of Louisville, Louisville, Kentucky, United States of America
| | - Donghoon Chung
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, United States of America
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85
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Ramsey J, Rasche H, Maughmer C, Criscione A, Mijalis E, Liu M, Hu JC, Young R, Gill JJ. Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation. PLoS Comput Biol 2020; 16:e1008214. [PMID: 33137082 PMCID: PMC7660901 DOI: 10.1371/journal.pcbi.1008214] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 11/12/2020] [Accepted: 08/02/2020] [Indexed: 01/21/2023] Open
Abstract
In the modern genomic era, scientists without extensive bioinformatic training need to apply high-power computational analyses to critical tasks like phage genome annotation. At the Center for Phage Technology (CPT), we developed a suite of phage-oriented tools housed in open, user-friendly web-based interfaces. A Galaxy platform conducts computationally intensive analyses and Apollo, a collaborative genome annotation editor, visualizes the results of these analyses. The collection includes open source applications such as the BLAST+ suite, InterProScan, and several gene callers, as well as unique tools developed at the CPT that allow maximum user flexibility. We describe in detail programs for finding Shine-Dalgarno sequences, resources used for confident identification of lysis genes such as spanins, and methods used for identifying interrupted genes that contain frameshifts or introns. At the CPT, genome annotation is separated into two robust segments that are facilitated through the automated execution of many tools chained together in an operation called a workflow. First, the structural annotation workflow results in gene and other feature calls. This is followed by a functional annotation workflow that combines sequence comparisons and conserved domain searching, which is contextualized to allow integrated evidence assessment in functional prediction. Finally, we describe a workflow used for comparative genomics. Using this multi-purpose platform enables researchers to easily and accurately annotate an entire phage genome. The portal can be accessed at https://cpt.tamu.edu/galaxy-pub with accompanying user training material.
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Affiliation(s)
- Jolene Ramsey
- Center for Phage Technology, Texas A&M University, College Station, Texas, United States of America
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Helena Rasche
- Center for Phage Technology, Texas A&M University, College Station, Texas, United States of America
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Cory Maughmer
- Center for Phage Technology, Texas A&M University, College Station, Texas, United States of America
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Anthony Criscione
- Center for Phage Technology, Texas A&M University, College Station, Texas, United States of America
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Eleni Mijalis
- Center for Phage Technology, Texas A&M University, College Station, Texas, United States of America
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Mei Liu
- Center for Phage Technology, Texas A&M University, College Station, Texas, United States of America
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - James C. Hu
- Center for Phage Technology, Texas A&M University, College Station, Texas, United States of America
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Ry Young
- Center for Phage Technology, Texas A&M University, College Station, Texas, United States of America
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Jason J. Gill
- Center for Phage Technology, Texas A&M University, College Station, Texas, United States of America
- Department of Animal Science, Texas A&M University, College Station, Texas, United States of America
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86
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Shi X, Tang T, Lin Q, Liu H, Qin Y, Liang X, Cong P, Mo D, Liu X, Chen Y, He Z. Efficient generation of bone morphogenetic protein 15-edited Yorkshire pigs using CRISPR/Cas9†. Biol Reprod 2020; 103:1054-1068. [PMID: 32761111 DOI: 10.1093/biolre/ioaa138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 06/25/2020] [Accepted: 08/06/2020] [Indexed: 12/15/2022] Open
Abstract
Bone morphogenetic protein 15 (BMP15), a member of the transforming growth factor beta superfamily, plays an essential role in ovarian follicular development in mono-ovulatory mammalian species. Studies using a biallelic knockout mouse model revealed that BMP15 potentially has just a minimal impact on female fertility and ovarian follicular development in polyovulatory species. In contrast, our previous study demonstrated that in vivo knockdown of BMP15 significantly affected porcine female fertility, as evidenced by the dysplastic ovaries containing significantly decreased numbers of follicles and an increased number of abnormal follicles. This finding implied that BMP15 plays an important role in the regulation of female fertility and ovarian follicular development in polyovulatory species. To further investigate the regulatory role of BMP15 in porcine ovarian and follicular development, here, we describe the efficient generation of BMP15-edited Yorkshire pigs using CRISPR/Cas9. Using artificial insemination experiments, we found that the biallelically edited gilts were all infertile, regardless of different genotypes. One monoallelically edited gilt #4 (Δ66 bp/WT) was fertile and could deliver offspring with a litter size comparable to that of wild-type gilts. Further analysis established that the infertility of biallelically edited gilts was caused by the arrest of follicular development at preantral stages, with formation of numerous structurally abnormal follicles, resulting in streaky ovaries and the absence of obvious estrous cycles. Our results strongly suggest that the role of BMP15 in nonrodent polyovulatory species may be as important as that in mono-ovulatory species.
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Affiliation(s)
- Xuan Shi
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China
| | - Tao Tang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China
| | - Qiyuan Lin
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China
| | - Hongbo Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China
| | - Yufeng Qin
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China
| | - Xinyu Liang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China
| | - Peiqing Cong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China
| | - Delin Mo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China
| | - Zuyong He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China
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87
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Sun Y, Abriola L, Surovtseva YV, Lindenbach BD, Guo JU. Restriction of SARS-CoV-2 Replication by Targeting Programmed -1 Ribosomal Frameshifting In Vitro. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.10.21.349225. [PMID: 33106809 PMCID: PMC7587830 DOI: 10.1101/2020.10.21.349225] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Translation of open reading frame 1b (ORF1b) in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires programmed -1 ribosomal frameshifting (-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 of SARS-CoV-2. Frameshift inhibition by merafloxacin is robust to mutations within the pseudoknot region and is similarly effective on -1 PRF of other beta coronaviruses. Importantly, frameshift inhibition by merafloxacin substantially impedes SARS-CoV-2 replication in Vero E6 cells, thereby providing the proof of principle of targeting -1 PRF as an effective antiviral strategy for SARS-CoV-2.
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Affiliation(s)
- Yu Sun
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Laura Abriola
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, USA
| | | | - Brett D. Lindenbach
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Junjie U. Guo
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
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88
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Charon J, Marcelino VR, Wetherbee R, Verbruggen H, Holmes EC. Metatranscriptomic Identification of Diverse and Divergent RNA Viruses in Green and Chlorarachniophyte Algae Cultures. Viruses 2020; 12:v12101180. [PMID: 33086653 PMCID: PMC7594059 DOI: 10.3390/v12101180] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022] Open
Abstract
Our knowledge of the diversity and evolution of the virosphere will likely increase dramatically with the study of microbial eukaryotes, including the microalgae within which few RNA viruses have been documented. By combining total RNA sequencing with sequence and structural-based homology detection, we identified 18 novel RNA viruses in cultured samples from two major groups of microbial algae: the chlorophytes and the chlorarachniophytes. Most of the RNA viruses identified in the green algae class Ulvophyceae were related to the Tombusviridae and Amalgaviridae viral families commonly associated with land plants. This suggests that the evolutionary history of these viruses extends to divergence events between algae and land plants. Seven Ostreobium sp-associated viruses exhibited sequence similarity to the mitoviruses most commonly found in fungi, compatible with horizontal virus transfer between algae and fungi. We also document, for the first time, RNA viruses associated with chlorarachniophytes, including the first negative-sense (bunya-like) RNA virus in microalgae, as well as a distant homolog of the plant virus Virgaviridae, potentially signifying viral inheritance from the secondary chloroplast endosymbiosis that marked the origin of the chlorarachniophytes. More broadly, these data suggest that the scarcity of RNA viruses in algae results from limited investigation rather than their absence.
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Affiliation(s)
- Justine Charon
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (J.C.); (V.R.M.)
| | - Vanessa Rossetto Marcelino
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (J.C.); (V.R.M.)
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
| | - Richard Wetherbee
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia; (R.W.); (H.V.)
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia; (R.W.); (H.V.)
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (J.C.); (V.R.M.)
- Correspondence: ; Tel.: +61-2-9351-5591
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89
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Charon J, Marcelino VR, Wetherbee R, Verbruggen H, Holmes EC. Metatranscriptomic Identification of Diverse and Divergent RNA Viruses in Green and Chlorarachniophyte Algae Cultures. Viruses 2020; 12:v12101180. [PMID: 33086653 DOI: 10.1101/2020.06.08.141184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 05/26/2023] Open
Abstract
Our knowledge of the diversity and evolution of the virosphere will likely increase dramatically with the study of microbial eukaryotes, including the microalgae within which few RNA viruses have been documented. By combining total RNA sequencing with sequence and structural-based homology detection, we identified 18 novel RNA viruses in cultured samples from two major groups of microbial algae: the chlorophytes and the chlorarachniophytes. Most of the RNA viruses identified in the green algae class Ulvophyceae were related to the Tombusviridae and Amalgaviridae viral families commonly associated with land plants. This suggests that the evolutionary history of these viruses extends to divergence events between algae and land plants. Seven Ostreobium sp-associated viruses exhibited sequence similarity to the mitoviruses most commonly found in fungi, compatible with horizontal virus transfer between algae and fungi. We also document, for the first time, RNA viruses associated with chlorarachniophytes, including the first negative-sense (bunya-like) RNA virus in microalgae, as well as a distant homolog of the plant virus Virgaviridae, potentially signifying viral inheritance from the secondary chloroplast endosymbiosis that marked the origin of the chlorarachniophytes. More broadly, these data suggest that the scarcity of RNA viruses in algae results from limited investigation rather than their absence.
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Affiliation(s)
- Justine Charon
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Vanessa Rossetto Marcelino
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
| | - Richard Wetherbee
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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90
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Hoffer ED, Hong S, Sunita S, Maehigashi T, Gonzalez RL, Whitford PC, Dunham CM. Structural insights into mRNA reading frame regulation by tRNA modification and slippery codon-anticodon pairing. eLife 2020; 9:51898. [PMID: 33016876 PMCID: PMC7577736 DOI: 10.7554/elife.51898] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/02/2020] [Indexed: 01/10/2023] Open
Abstract
Modifications in the tRNA anticodon loop, adjacent to the three-nucleotide anticodon, influence translation fidelity by stabilizing the tRNA to allow for accurate reading of the mRNA genetic code. One example is the N1-methylguanosine modification at guanine nucleotide 37 (m1G37) located in the anticodon loop andimmediately adjacent to the anticodon nucleotides 34, 35, 36. The absence of m1G37 in tRNAPro causes +1 frameshifting on polynucleotide, slippery codons. Here, we report structures of the bacterial ribosome containing tRNAPro bound to either cognate or slippery codons to determine how the m1G37 modification prevents mRNA frameshifting. The structures reveal that certain codon–anticodon contexts and the lack of m1G37 destabilize interactions of tRNAPro with the P site of the ribosome, causing large conformational changes typically only seen during EF-G-mediated translocation of the mRNA-tRNA pairs. These studies provide molecular insights into how m1G37 stabilizes the interactions of tRNAPro with the ribosome in the context of a slippery mRNA codon.
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Affiliation(s)
- Eric D Hoffer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, United States
| | - Samuel Hong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, United States
| | - S Sunita
- Department of Biochemistry, Emory University School of Medicine, Atlanta, United States
| | - Tatsuya Maehigashi
- Department of Biochemistry, Emory University School of Medicine, Atlanta, United States
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia University, New York, United States
| | - Paul C Whitford
- Department of Physics, Northeastern University, Boston, United States
| | - Christine M Dunham
- Department of Biochemistry, Emory University School of Medicine, Atlanta, United States
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91
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Sidhu-Muñoz RS, Tejedor C, Vizcaíno N. The Three Flagellar Loci of Brucella ovis PA Are Dispensable for Virulence in Cellular Models and Mice. Front Vet Sci 2020; 7:441. [PMID: 32851024 PMCID: PMC7410920 DOI: 10.3389/fvets.2020.00441] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 06/18/2020] [Indexed: 12/22/2022] Open
Abstract
Brucella ovis is a facultative intracellular bacterium that causes a non-zoonotic ovine brucellosis mainly characterized by male genital lesions and is responsible for important economic losses in sheep farming areas. Studies about the virulence mechanisms of Brucella have been mostly performed with smooth (bearing O-polysaccharide in lipopolysaccharide) zoonotic species, and those performed with B. ovis have revealed similarities but also relevant differences. Except for few strains recently isolated from unconventional hosts, Brucella species are non-motile but contain the genes required to assemble a flagellum, which are organized in three main loci of about 18.5, 6.4, and 7.8 kb. Although these loci contain different pseudogenes depending on the non-motile Brucella species, smooth B. melitensis 16M builds a sheathed flagellum under particular culture conditions and requires flagellar genes for virulence. However, nothing is known in this respect regarding other Brucella strains. In this work, we have constructed a panel of B. ovis PA mutants defective in one, two or the three flagellar loci in order to assess their role in virulence of this rough (lacking O-polysaccharide) Brucella species. No relevant differences in growth, outer membrane-related properties or intracellular behavior in cellular models were observed between flagellar mutants and the parental strain, which is in accordance with previous results with B. melitensis 16M single-gene mutants. However, contrary to these B. melitensis mutants, unable to establish a chronic infection in mice, removal of the three flagellar loci in B. ovis did not affect virulence in the mouse model. These results evidence new relevant differences between B. ovis and B. melitensis, two species highly homologous at the DNA level and that cause ovine brucellosis, but that exhibit differences in the zoonotic potential, pathogenicity and tissue tropism.
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Affiliation(s)
- Rebeca S Sidhu-Muñoz
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Carmen Tejedor
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Nieves Vizcaíno
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
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92
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Kelly JA, Olson AN, Neupane K, Munshi S, San Emeterio J, Pollack L, Woodside MT, Dinman JD. Structural and functional conservation of the programmed -1 ribosomal frameshift signal of SARS coronavirus 2 (SARS-CoV-2). J Biol Chem 2020; 295:10741-10748. [PMID: 32571880 PMCID: PMC7397099 DOI: 10.1074/jbc.ac120.013449] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/19/2020] [Indexed: 12/17/2022] Open
Abstract
Approximately 17 years after the severe acute respiratory syndrome coronavirus (SARS-CoV) epidemic, the world is currently facing the COVID-19 pandemic caused by SARS corona virus 2 (SARS-CoV-2). According to the most optimistic projections, it will take more than a year to develop a vaccine, so the best short-term strategy may lie in identifying virus-specific targets for small molecule-based interventions. All coronaviruses utilize a molecular mechanism called programmed -1 ribosomal frameshift (-1 PRF) to control the relative expression of their proteins. Previous analyses of SARS-CoV have revealed that it employs a structurally unique three-stemmed mRNA pseudoknot that stimulates high -1 PRF rates and that it also harbors a -1 PRF attenuation element. Altering -1 PRF activity impairs virus replication, suggesting that this activity may be therapeutically targeted. Here, we comparatively analyzed the SARS-CoV and SARS-CoV-2 frameshift signals. Structural and functional analyses revealed that both elements promote similar -1 PRF rates and that silent coding mutations in the slippery sites and in all three stems of the pseudoknot strongly ablate -1 PRF activity. We noted that the upstream attenuator hairpin activity is also functionally retained in both viruses, despite differences in the primary sequence in this region. Small-angle X-ray scattering analyses indicated that the pseudoknots in SARS-CoV and SARS-CoV-2 have the same conformation. Finally, a small molecule previously shown to bind the SARS-CoV pseudoknot and inhibit -1 PRF was similarly effective against -1 PRF in SARS-CoV-2, suggesting that such frameshift inhibitors may be promising lead compounds to combat the current COVID-19 pandemic.
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Affiliation(s)
- Jamie A Kelly
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Alexandra N Olson
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Krishna Neupane
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Sneha Munshi
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Josue San Emeterio
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, USA
| | | | - Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
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93
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Disome and Trisome Profiling Reveal Genome-wide Targets of Ribosome Quality Control. Mol Cell 2020; 79:588-602.e6. [PMID: 32615089 DOI: 10.1016/j.molcel.2020.06.010] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 04/07/2020] [Accepted: 06/02/2020] [Indexed: 01/18/2023]
Abstract
The ribosome-associated protein quality control (RQC) system that resolves stalled translation events is activated when ribosomes collide and form disome, trisome, or higher-order complexes. However, it is unclear whether this system distinguishes collision complexes formed on defective mRNAs from those with functional roles on endogenous transcripts. Here, we performed disome and trisome footprint profiling in yeast and found collisions were enriched on diverse sequence motifs known to slow translation. When 60S recycling was inhibited, disomes accumulated at stop codons and could move into the 3' UTR to reinitiate translation. The ubiquitin ligase and RQC factor Hel2/ZNF598 generally recognized collisions but did not induce degradation of endogenous transcripts. However, loss of Hel2 triggered the integrated stress response, via phosphorylation of eIF2α, thus linking these pathways. Our results suggest that Hel2 has a role in sensing ribosome collisions on endogenous mRNAs, and such events may be important for cellular homeostasis.
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94
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Pro-Inflammatory Signaling Upregulates a Neurotoxic Conotoxin-Like Protein Encrypted Within Human Endogenous Retrovirus-K. Cells 2020; 9:cells9071584. [PMID: 32629888 PMCID: PMC7407490 DOI: 10.3390/cells9071584] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/20/2020] [Accepted: 06/25/2020] [Indexed: 02/06/2023] Open
Abstract
Motor neuron degeneration and spinal cord demyelination are hallmark pathological events in Amyotrophic Lateral Sclerosis (ALS). Endogenous retrovirus-K (ERVK) expression has an established association with ALS neuropathology, with murine modeling pointing to a role for the ERVK envelope (env) gene in disease processes. Here, we describe a novel viral protein cryptically encoded within the ERVK env transcript, which resembles two distinct cysteine-rich neurotoxic proteins: conotoxin proteins found in marine snails and the Human Immunodeficiency Virus (HIV) Tat protein. Consistent with Nuclear factor-kappa B (NF-κB)-induced retrotransposon expression, the ERVK conotoxin-like protein (CTXLP) is induced by inflammatory signaling. CTXLP is found in the nucleus, impacting innate immune gene expression and NF-κB p65 activity. Using human autopsy specimens from patients with ALS, we further showcase CTXLP expression in degenerating motor cortex and spinal cord tissues, concomitant with inflammation linked pathways, including enhancement of necroptosis marker mixed lineage kinase domain-like (MLKL) protein and oligodendrocyte maturation/myelination inhibitor Nogo-A. These findings identify CTXLP as a novel ERVK protein product, which may act as an effector in ALS neuropathology.
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95
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Penn WD, Harrington HR, Schlebach JP, Mukhopadhyay S. Regulators of Viral Frameshifting: More Than RNA Influences Translation Events. Annu Rev Virol 2020; 7:219-238. [PMID: 32600156 DOI: 10.1146/annurev-virology-012120-101548] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Programmed ribosomal frameshifting (PRF) is a conserved translational recoding mechanism found in all branches of life and viruses. In bacteria, archaea, and eukaryotes PRF is used to downregulate protein production by inducing a premature termination of translation, which triggers messenger RNA (mRNA) decay. In viruses, PRF is used to drive the production of a new protein while downregulating the production of another protein, thus maintaining a stoichiometry optimal for productive infection. Traditionally, PRF motifs have been defined by the characteristics of two cis elements: a slippery heptanucleotide sequence followed by an RNA pseudoknot or stem-loop within the mRNA. Recently, additional cis and new trans elements have been identified that regulate PRF in both host and viral translation. These additional factors suggest PRF is an evolutionarily conserved process whose function and regulation we are just beginning to understand.
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Affiliation(s)
- Wesley D Penn
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Haley R Harrington
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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96
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Kelly JA, Olson AN, Neupane K, Munshi S, Emeterio JS, Pollack L, Woodside MT, Dinman JD. Structural and functional conservation of the programmed -1 ribosomal frameshift signal of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.03.13.991083. [PMID: 32587971 PMCID: PMC7310627 DOI: 10.1101/2020.03.13.991083] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
17 years after the SARS-CoV epidemic, the world is facing the COVID-19 pandemic. COVID-19 is caused by a coronavirus named SARS-CoV-2. Given the most optimistic projections estimating that it will take over a year to develop a vaccine, the best short-term strategy may lie in identifying virus-specific targets for small molecule interventions. All coronaviruses utilize a molecular mechanism called -1 PRF to control the relative expression of their proteins. Prior analyses of SARS-CoV revealed that it employs a structurally unique three-stemmed mRNA pseudoknot to stimulate high rates of -1 PRF, and that it also harbors a -1 PRF attenuation element. Altering -1 PRF activity negatively impacts virus replication, suggesting that this molecular mechanism may be therapeutically targeted. Here we present a comparative analysis of the original SARS-CoV and SARS-CoV-2 frameshift signals. Structural and functional analyses revealed that both elements promote similar rates of -1 PRF and that silent coding mutations in the slippery sites and in all three stems of the pseudoknot strongly ablated -1 PRF activity. The upstream attenuator hairpin activity has also been functionally retained. Small-angle x-ray scattering indicated that the pseudoknots in SARS-CoV and SARS-CoV-2 had the same conformation. Finally, a small molecule previously shown to bind the SARS-CoV pseudoknot and inhibit -1 PRF was similarly effective against -1 PRF in SARS-CoV-2, suggesting that such frameshift inhibitors may provide promising lead compounds to counter the current pandemic.
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Affiliation(s)
- Jamie A. Kelly
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park MD 20742 USA
| | - Alexandra N. Olson
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park MD 20742 USA
| | - Krishna Neupane
- Department of Physics, University of Alberta, Edmonton AB T6G2E1 Canada
| | - Sneha Munshi
- Department of Physics, University of Alberta, Edmonton AB T6G2E1 Canada
| | - Josue San Emeterio
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853 USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853 USA
| | | | - Jonathan D. Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park MD 20742 USA
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97
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O'Loughlin S, Capece MC, Klimova M, Wills NM, Coakley A, Samatova E, O'Connor PBF, Loughran G, Weissman JS, Baranov PV, Rodnina MV, Puglisi JD, Atkins JF. Polysomes Bypass a 50-Nucleotide Coding Gap Less Efficiently Than Monosomes Due to Attenuation of a 5' mRNA Stem-Loop and Enhanced Drop-off. J Mol Biol 2020; 432:4369-4387. [PMID: 32454154 PMCID: PMC7245268 DOI: 10.1016/j.jmb.2020.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 01/03/2023]
Abstract
Efficient translational bypassing of a 50-nt non-coding gap in a phage T4 topoisomerase subunit gene (gp60) requires several recoding signals. Here we investigate the function of the mRNA stem–loop 5′ of the take-off codon, as well as the importance of ribosome loading density on the mRNA for efficient bypassing. We show that polysomes are less efficient at mediating bypassing than monosomes, both in vitro and in vivo, due to their preventing formation of a stem–loop 5′ of the take-off codon and allowing greater peptidyl-tRNA drop off. A ribosome profiling analysis of phage T4-infected Escherichia coli yielded protected mRNA fragments within the normal size range derived from ribosomes stalled at the take-off codon. However, ribosomes at this position also yielded some 53-nucleotide fragments, 16 longer. These were due to protection of the nucleotides that form the 5′ stem–loop. NMR shows that the 5′ stem–loop is highly dynamic. The importance of different nucleotides in the 5′ stem–loop is revealed by mutagenesis studies. These data highlight the significance of the 5′ stem–loop for the 50-nt bypassing and further enhance appreciation of relevance of the extent of ribosome loading for recoding. Monosomes are more efficient than polysome in mediating 50-nt translational bypassing. A 5′ mRNA stem–loop facilitates translational bypassing by monosomes. Ribosome profiling yields an extra-long, 53-nt, protected fragment of mRNA.
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Affiliation(s)
- Sinéad O'Loughlin
- School of Biochemistry, University College Cork, Western Gateway Building, Western Road, Cork, T12 XF62, Ireland; School of Microbiology, University College Cork, Western Gateway Building, Western Road, Cork, T12 YT57, Ireland
| | - Mark C Capece
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-4090, USA
| | - Mariia Klimova
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Norma M Wills
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
| | - Arthur Coakley
- School of Biochemistry, University College Cork, Western Gateway Building, Western Road, Cork, T12 XF62, Ireland
| | - Ekaterina Samatova
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Patrick B F O'Connor
- School of Biochemistry, University College Cork, Western Gateway Building, Western Road, Cork, T12 XF62, Ireland
| | - Gary Loughran
- School of Biochemistry, University College Cork, Western Gateway Building, Western Road, Cork, T12 XF62, Ireland
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Pavel V Baranov
- School of Biochemistry, University College Cork, Western Gateway Building, Western Road, Cork, T12 XF62, Ireland; Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow 117997, Russia
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-4090, USA
| | - John F Atkins
- School of Biochemistry, University College Cork, Western Gateway Building, Western Road, Cork, T12 XF62, Ireland; School of Microbiology, University College Cork, Western Gateway Building, Western Road, Cork, T12 YT57, Ireland; Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA.
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98
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Zarai Y, Zafrir Z, Siridechadilok B, Suphatrakul A, Roopin M, Julander J, Tuller T. Evolutionary selection against short nucleotide sequences in viruses and their related hosts. DNA Res 2020; 27:dsaa008. [PMID: 32339222 PMCID: PMC7320823 DOI: 10.1093/dnares/dsaa008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 04/20/2020] [Indexed: 11/13/2022] Open
Abstract
Viruses are under constant evolutionary pressure to effectively interact with the host intracellular factors, while evading its immune system. Understanding how viruses co-evolve with their hosts is a fundamental topic in molecular evolution and may also aid in developing novel viral based applications such as vaccines, oncologic therapies, and anti-bacterial treatments. Here, based on a novel statistical framework and a large-scale genomic analysis of 2,625 viruses from all classes infecting 439 host organisms from all kingdoms of life, we identify short nucleotide sequences that are under-represented in the coding regions of viruses and their hosts. These sequences cannot be explained by the coding regions' amino acid content, codon, and dinucleotide frequencies. We specifically show that short homooligonucleotide and palindromic sequences tend to be under-represented in many viruses probably due to their effect on gene expression regulation and the interaction with the host immune system. In addition, we show that more sequences tend to be under-represented in dsDNA viruses than in other viral groups. Finally, we demonstrate, based on in vitro and in vivo experiments, how under-represented sequences can be used to attenuated Zika virus strains.
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Affiliation(s)
- Yoram Zarai
- Biomedical Engineering Department, Tel Aviv University, Tel Aviv 69978, Israel
| | - Zohar Zafrir
- Biomedical Engineering Department, Tel Aviv University, Tel Aviv 69978, Israel
- SynVaccine Ltd., Ramat Hachayal, Tel Aviv, Israel
| | | | - Amporn Suphatrakul
- National Center for Genetic Engineering and Biotechnology, Pathumthani 12120, Thailand
| | - Modi Roopin
- Biomedical Engineering Department, Tel Aviv University, Tel Aviv 69978, Israel
- SynVaccine Ltd., Ramat Hachayal, Tel Aviv, Israel
| | - Justin Julander
- Institute for Antiviral Research, Utah State University, Logan, UT, USA
| | - Tamir Tuller
- Biomedical Engineering Department, Tel Aviv University, Tel Aviv 69978, Israel
- SynVaccine Ltd., Ramat Hachayal, Tel Aviv, Israel
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99
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Thulson E, Hartwick EW, Cooper-Sansone A, Williams MAC, Soliman ME, Robinson LK, Kieft JS, Mouzakis KD. An RNA pseudoknot stimulates HTLV-1 pro-pol programmed -1 ribosomal frameshifting. RNA (NEW YORK, N.Y.) 2020; 26:512-528. [PMID: 31980578 PMCID: PMC7075266 DOI: 10.1261/rna.070490.119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
Programmed -1 ribosomal frameshifts (-1 PRFs) are commonly used by viruses to regulate their enzymatic and structural protein levels. Human T-cell leukemia virus type 1 (HTLV-1) is a carcinogenic retrovirus that uses two independent -1 PRFs to express viral enzymes critical to establishing new HTLV-1 infections. How the cis-acting RNA elements in this viral transcript function to induce frameshifting is unknown. The objective of this work was to conclusively define the 3' boundary of and the RNA elements within the HTLV-1 pro-pol frameshift site. We hypothesized that the frameshift site structure was a pseudoknot and that its 3' boundary would be defined by the pseudoknot's 3' end. To test these hypotheses, the in vitro frameshift efficiencies of three HTLV-1 pro-pol frameshift sites with different 3' boundaries were quantified. The results indicated that nucleotides included in the longest construct were essential to highly efficient frameshift stimulation. Interestingly, only this construct could form the putative frameshift site pseudoknot. Next, the secondary structure of this frameshift site was determined. The dominant structure was an H-type pseudoknot which, together with the slippery sequence, stimulated frameshifting to 19.4(±0.3)%. The pseudoknot's critical role in frameshift stimulation was directly revealed by examining the impact of structural changes on HTLV-1 pro-pol -1 PRF. As predicted, mutations that occluded pseudoknot formation drastically reduced the frameshift efficiency. These results are significant because they demonstrate that a pseudoknot is important to HTLV-1 pro-pol -1 PRF and define the frameshift site's 3' boundary.
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Affiliation(s)
- Eliza Thulson
- Department of Chemistry and Biochemistry, Fort Lewis College, Durango, Colorado 81301, USA
| | - Erik W Hartwick
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Andrew Cooper-Sansone
- Department of Chemistry and Biochemistry, Fort Lewis College, Durango, Colorado 81301, USA
| | - Marcus A C Williams
- Department of Chemistry and Biochemistry, Fort Lewis College, Durango, Colorado 81301, USA
| | - Mary E Soliman
- Department of Chemistry and Biochemistry, Loyola Marymount University, Los Angeles, California 90045, USA
| | - Leila K Robinson
- Department of Chemistry and Biochemistry, Loyola Marymount University, Los Angeles, California 90045, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Kathryn D Mouzakis
- Department of Chemistry and Biochemistry, Loyola Marymount University, Los Angeles, California 90045, USA
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100
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Immunohistochemical detection of the pro-apoptotic Bax∆2 protein in human tissues. Histochem Cell Biol 2020; 154:41-53. [PMID: 32200452 DOI: 10.1007/s00418-020-01874-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2020] [Indexed: 12/11/2022]
Abstract
The pro-apoptotic Bax isoform Bax∆2 was originally discovered in cancer patients with a microsatellite guanine deletion (G8 to G7). This deletion leads to an early stop codon; however, when combined with the alternative splicing of exon 2, the reading frame is restored allowing production of a full-length protein (Bax∆2). Unlike the parental Baxα, Bax∆2 triggers apoptosis through a non-mitochondrial pathway and the expression in human tissues was unknown. Here, we analyzed over 1000 tissue microarray samples from 13 different organs using immunohistochemistry. Bax∆2-positive cells were detected in all examined organs at low rates (1-5%) and mainly scattered throughout the connective tissues. Surprisingly, over 70% of normal colon samples scored high for BaxΔ2-positive staining. Only 7% of malignant colon samples scored high, with most high-grade tumors being negative. A similar pattern was observed in most organs examined. We also showed that both Baxα and Bax∆2 can co-exist in the same cells. Genotyping showed that the majority of Bax∆2-positive normal tissues contain no G7 mutation, but an unexpected high rate of G9 was observed. Although the underlying mechanism remains to be explored, the inverse correlation of Bax∆2 expression with tissue malignancy suggests that it may have a clinical implication in cancer development and treatment.
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