1
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Andrzejewska-Romanowska A, Gumna J, Tykwińska E, Pachulska-Wieczorek K. Mapping the structural landscape of the yeast Ty3 retrotransposon RNA genome. Nucleic Acids Res 2024:gkae494. [PMID: 38864374 DOI: 10.1093/nar/gkae494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/30/2024] [Accepted: 05/29/2024] [Indexed: 06/13/2024] Open
Abstract
Long terminal repeat (LTR)-retrotransposons are significant contributors to the evolution and diversity of eukaryotic genomes. Their RNA genomes (gRNA) serve as a template for protein synthesis and reverse transcription to a DNA copy, which can integrate into the host genome. Here, we used the SHAPE-MaP strategy to explore Ty3 retrotransposon gRNA structure in yeast and under cell-free conditions. Our study reveals the structural dynamics of Ty3 gRNA and the well-folded core, formed independently of the cellular environment. Based on the detailed map of Ty3 gRNA structure, we characterized the structural context of cis-acting sequences involved in reverse transcription and frameshifting. We also identified a novel functional sequence as a potential initiator for Ty3 gRNA dimerization. Our data indicate that the dimer is maintained by direct interaction between short palindromic sequences at the 5' ends of the two Ty3 gRNAs, resembling the model characteristic for other retroelements like HIV-1 and Ty1. This work points out a range of cell-dependent and -independent Ty3 gRNA structural changes that provide a solid background for studies on RNA structure-function relationships important for retroelement biology.
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Affiliation(s)
- Angelika Andrzejewska-Romanowska
- Department of RNA Structure and Function, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Julita Gumna
- Department of RNA Structure and Function, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Ewa Tykwińska
- Department of RNA Structure and Function, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Katarzyna Pachulska-Wieczorek
- Department of RNA Structure and Function, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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2
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Peterson JM, Becker ST, O'Leary CA, Juneja P, Yang Y, Moss WN. Structure of the SARS-CoV-2 Frameshift Stimulatory Element with an Upstream Multibranch Loop. Biochemistry 2024; 63:1287-1296. [PMID: 38727003 DOI: 10.1021/acs.biochem.3c00716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) frameshift stimulatory element (FSE) is necessary for programmed -1 ribosomal frameshifting (-1 PRF) and optimized viral efficacy. The FSE has an abundance of context-dependent alternate conformations, but two of the structures most crucial to -1 PRF are an attenuator hairpin and a three-stem H-type pseudoknot structure. A crystal structure of the pseudoknot alone features three RNA stems in a helically stacked linear structure, whereas a 6.9 Å cryo-EM structure including the upstream heptameric slippery site resulted in a bend between two stems. Our previous research alluded to an extended upstream multibranch loop that includes both the attenuator hairpin and the slippery site-a conformation not previously modeled. We aim to provide further context to the SARS-CoV-2 FSE via computational and medium resolution cryo-EM approaches, by presenting a 6.1 Å cryo-EM structure featuring a linear pseudoknot structure and a dynamic upstream multibranch loop.
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Affiliation(s)
- Jake M Peterson
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Scott T Becker
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Collin A O'Leary
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Puneet Juneja
- Cryo-EM Facility, Iowa State University, Ames, Iowa 50011, United States
| | - Yang Yang
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Walter N Moss
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
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3
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Sung PY, Phelan JE, Luo D, Kulasegaran-Shylini R, Bohn P, Smyth RP, Roy P. Recruitment of multi-segment genomic RNAs by Bluetongue virus requires a preformed RNA network. Nucleic Acids Res 2024:gkae404. [PMID: 38769067 DOI: 10.1093/nar/gkae404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/22/2024] [Accepted: 05/01/2024] [Indexed: 05/22/2024] Open
Abstract
How do segmented RNA viruses correctly recruit their genome has yet to be clarified. Bluetongue virus is a double-stranded RNA virus with 10 segments of different sizes, but it assembles its genome in single-stranded form through a series of specific RNA-RNA interactions prior to packaging. In this study, we determined the structure of each BTV transcript, individually and in different combinations, using 2'-hydroxyl acylation analysed by primer extension and mutational profiling (SHAPE-MaP). SHAPE-MaP identified RNA structural changes during complex formation and putative RNA-RNA interaction sites. Our data also revealed a core RNA-complex of smaller segments which serves as the foundation ('anchor') for the assembly of a complete network composed of ten ssRNA segments. The same order of core RNA complex formation was identified in cells transfected with viral RNAs. No viral protein was required for these assembly reactions. Further, substitution mutations in the interacting bases within the core assemblies, altered subsequent segment addition and affected virus replication. These data identify a wholly RNA driven reaction that may offer novel opportunities for designed attenuation or antiviral therapeutics.
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Affiliation(s)
- Po-Yu Sung
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Jody E Phelan
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Dongsheng Luo
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Patrick Bohn
- Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
| | - Redmond P Smyth
- Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
- Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Polly Roy
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
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4
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Tipo J, Gottipati K, Choi KH. High-resolution RNA tertiary structures in Zika virus stem-loop A for the development of inhibitory small molecules. RNA (NEW YORK, N.Y.) 2024; 30:609-623. [PMID: 38383158 PMCID: PMC11098461 DOI: 10.1261/rna.079796.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024]
Abstract
Flaviviruses such as Zika (ZIKV) and dengue virus (DENV) are positive-sense RNA viruses belonging to Flaviviridae The flavivirus genome contains a 5' end stem-loop promoter sequence known as stem-loop A (SLA) that is recognized by the flavivirus polymerase NS5 during viral RNA synthesis and 5' guanosine cap methylation. The crystal structures of ZIKV and DENV SLAs show a well-defined fold, consisting of a bottom stem, side loop, and top stem-loop, providing unique interaction sites for small molecule inhibitors to disrupt the promoter function. To facilitate the identification of small molecule binding sites in flavivirus SLA, we determined high-resolution structures of the bottom and top stems of ZIKV SLA, which contain a single U- or G-bulge, respectively. Both bulge nucleotides exhibit multiple orientations, from folded back on the adjacent nucleotide to flipped out of the helix, and are stabilized by stacking or base triple interactions. These structures suggest that even a single unpaired nucleotide can provide flexibility to RNA structures, and its conformation is mainly determined by the stabilizing chemical environment. To facilitate discovery of small molecule inhibitors that interfere with the functions of ZIKV SLA, we screened and identified compounds that bind to the bottom and top stems of ZIKV SLA.
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Affiliation(s)
- Jerricho Tipo
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Keerthi Gottipati
- Department of Biochemistry and Molecular Biology, and Sealy Center for Structural Biology, The University of Texas Medical Branch, Galveston, Texas 77555, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Kyung H Choi
- Department of Biochemistry and Molecular Biology, and Sealy Center for Structural Biology, The University of Texas Medical Branch, Galveston, Texas 77555, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
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5
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Horner SM, Thompson MG. Challenges to mapping and defining m 6A function in viral RNA. RNA (NEW YORK, N.Y.) 2024; 30:482-490. [PMID: 38531643 PMCID: PMC11019751 DOI: 10.1261/rna.079959.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
Viral RNA molecules contain multiple layers of regulatory information. This includes features beyond the primary sequence, such as RNA structures and RNA modifications, including N6-methyladenosine (m6A). Many recent studies have identified the presence and location of m6A in viral RNA and have found diverse regulatory roles for this modification during viral infection. However, to date, viral m6A mapping strategies have limitations that prevent a complete understanding of the function of m6A on individual viral RNA molecules. While m6A sites have been profiled on bulk RNA from many viruses, the resulting m6A maps of viral RNAs described to date present a composite picture of m6A across viral RNA molecules in the infected cell. Thus, for most viruses, it is unknown if unique viral m6A profiles exist throughout infection, nor if they regulate specific viral life cycle stages. Here, we describe several challenges to defining the function of m6A in viral RNA molecules and provide a framework for future studies to help in the understanding of how m6A regulates viral infection.
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Affiliation(s)
- Stacy M Horner
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Matthew G Thompson
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina 27710, USA
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6
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Irving PS, Weeks KM. RNAvigate: efficient exploration of RNA chemical probing datasets. Nucleic Acids Res 2024; 52:2231-2241. [PMID: 38348910 PMCID: PMC10954457 DOI: 10.1093/nar/gkae089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 02/27/2024] Open
Abstract
Chemical probing technologies enable high-throughput examination of diverse structural features of RNA, including local nucleotide flexibility, RNA secondary structure, protein and ligand binding, through-space interaction networks, and multistate structural ensembles. Deep understanding of RNA structure-function relationships typically requires evaluating a system under structure- and function-altering conditions, linking these data with additional information, and visualizing multilayered relationships. Current platforms lack the broad accessibility, flexibility and efficiency needed to iterate on integrative analyses of these diverse, complex data. Here, we share the RNA visualization and graphical analysis toolset RNAvigate, a straightforward and flexible Python library that automatically parses 21 standard file formats (primary sequence annotations, per- and internucleotide data, and secondary and tertiary structures) and outputs 18 plot types. RNAvigate enables efficient exploration of nuanced relationships between multiple layers of RNA structure information and across multiple experimental conditions. Compatibility with Jupyter notebooks enables nonburdensome, reproducible, transparent and organized sharing of multistep analyses and data visualization strategies. RNAvigate simplifies and accelerates discovery and characterization of RNA-centric functions in biology.
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Affiliation(s)
- Patrick S Irving
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
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7
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Xiao L, Fang L, Kool ET. 2'-OH as a universal handle for studying intracellular RNAs. Cell Chem Biol 2024; 31:110-124. [PMID: 37992716 PMCID: PMC10841764 DOI: 10.1016/j.chembiol.2023.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/28/2023] [Accepted: 10/29/2023] [Indexed: 11/24/2023]
Abstract
RNA plays pivotal roles in most cellular processes, serving as both the traditional carrier of genetic information and as a key regulator of cellular functions. The advent of chemical technologies has contributed critically to the analysis of cellular RNA structures, functions, and interactions. Many of these methods and molecules involve the utilization of chemically reactive handles in RNAs, either introduced externally or inherent within the polymer itself. Among these handles, the 2'-hydroxyl (2'-OH) group has emerged as an exceptionally well-suited and general chemical moiety for the modification and profiling of RNAs in intracellular studies. In this review, we provide an overview of the recent advancements in intracellular applications of acylation at the 2'-OH group of RNA. We outline progress made in probing RNA structure and interactomes, controlling RNA function, RNA imaging, and analyzing RNA-small molecule interactions, all achieved in living cells through this simple chemical handle on the biopolymer.
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Affiliation(s)
- Lu Xiao
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Linglan Fang
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA.
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8
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Levintov L, Vashisth H. Structural and computational studies of HIV-1 RNA. RNA Biol 2024; 21:1-32. [PMID: 38100535 PMCID: PMC10730233 DOI: 10.1080/15476286.2023.2289709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Viruses remain a global threat to animals, plants, and humans. The type 1 human immunodeficiency virus (HIV-1) is a member of the retrovirus family and carries an RNA genome, which is reverse transcribed into viral DNA and further integrated into the host-cell DNA for viral replication and proliferation. The RNA structures from the HIV-1 genome provide valuable insights into the mechanisms underlying the viral replication cycle. Moreover, these structures serve as models for designing novel therapeutic approaches. Here, we review structural data on RNA from the HIV-1 genome as well as computational studies based on these structural data. The review is organized according to the type of structured RNA element which contributes to different steps in the viral replication cycle. This is followed by an overview of the HIV-1 transactivation response element (TAR) RNA as a model system for understanding dynamics and interactions in the viral RNA systems. The review concludes with a description of computational studies, highlighting the impact of biomolecular simulations in elucidating the mechanistic details of various steps in the HIV-1's replication cycle.
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Affiliation(s)
- Lev Levintov
- Department of Chemical Engineering & Bioengineering, University of New Hampshire, Durham, USA
| | - Harish Vashisth
- Department of Chemical Engineering & Bioengineering, University of New Hampshire, Durham, USA
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9
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Abram QH, Landry BN, Wang AB, Kothe RF, Hauch HC, Sagan SM. The myriad roles of RNA structure in the flavivirus life cycle. RNA Biol 2024; 21:14-30. [PMID: 38797925 PMCID: PMC11135854 DOI: 10.1080/15476286.2024.2357857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2024] [Indexed: 05/29/2024] Open
Abstract
As positive-sense RNA viruses, the genomes of flaviviruses serve as the template for all stages of the viral life cycle, including translation, replication, and infectious particle production. Yet, they encode just 10 proteins, suggesting that the structure and dynamics of the viral RNA itself helps shepherd the viral genome through these stages. Herein, we highlight advances in our understanding of flavivirus RNA structural elements through the lens of their impact on the viral life cycle. We highlight how RNA structures impact translation, the switch from translation to replication, negative- and positive-strand RNA synthesis, and virion assembly. Consequently, we describe three major themes regarding the roles of RNA structure in flavivirus infections: 1) providing a layer of specificity; 2) increasing the functional capacity; and 3) providing a mechanism to support genome compaction. While the interactions described herein are specific to flaviviruses, these themes appear to extend more broadly across RNA viruses.
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Affiliation(s)
- Quinn H. Abram
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Breanna N. Landry
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Alex B. Wang
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Ronja F. Kothe
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Hannah C.H. Hauch
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Selena M. Sagan
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
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10
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Irving PS, Weeks KM. RNAvigate: Efficient exploration of RNA chemical probing datasets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.25.538311. [PMID: 37162917 PMCID: PMC10168276 DOI: 10.1101/2023.04.25.538311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Chemical probing technologies enable high-throughput examination of diverse structural features of RNA including local nucleotide flexibility, RNA secondary structure, protein- and ligand-binding, through-space interaction networks, and multi-state structural ensembles. Performing these experiments, by themselves, does not directly lead to biological insight. Instead, deep understanding of RNA structure-function relationships typically requires evaluating a system under structure- and function-altering conditions, linking these data with additional information, and visualizing multi-layered relationships. Current platforms lack the broad accessibility, flexibility, and efficiency needed to iterate on integrative analyses of these diverse, complex data. Here, we share the RNA visualization and graphical analysis toolset RNAvigate, a straightforward and flexible Python library. RNAvigate currently automatically parses twenty-one standard file formats (primary sequence annotations, per- and internucleotide data, and secondary and tertiary structures) and outputs eighteen plot types. These features enable efficient exploration of nuanced relationships between chemical probing data, RNA structure, and motif annotations across multiple experimental samples. Compatibility with Jupyter Notebooks enables non-burdensome, reproducible, transparent and organized sharing of multi-step analyses and data visualization strategies. RNAvigate simplifies examination of multi-layered RNA structure information and accelerates discovery and characterization of RNA-centric functions in biology.
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Affiliation(s)
- Patrick S. Irving
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290
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11
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Vilcapoma J, Aliyeva A, Hayden A, Chandrasekaran AR, Zhou L, Punnoose JA, Yang D, Hansen C, Shiu SCC, Russell A, George KS, Wong WP, Halvorsen K. A non-enzymatic test for SARS-CoV-2 RNA using DNA nanoswitches. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.31.23290613. [PMID: 37398235 PMCID: PMC10312858 DOI: 10.1101/2023.05.31.23290613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The emergence of a highly contagious novel coronavirus in 2019 led to an unprecedented need for large scale diagnostic testing. The associated challenges including reagent shortages, cost, deployment delays, and turnaround time have all highlighted the need for an alternative suite of low-cost tests. Here, we demonstrate a diagnostic test for SARS-CoV-2 RNA that provides direct detection of viral RNA and eliminates the need for costly enzymes. We employ DNA nanoswitches that respond to segments of the viral RNA by a change in shape that is readable by gel electrophoresis. A new multi-targeting approach samples 120 different viral regions to improve the limit of detection and provide robust detection of viral variants. We apply our approach to a cohort of clinical samples, positively identifying a subset of samples with high viral loads. Since our method directly detects multiple regions of viral RNA without amplification, it eliminates the risk of amplicon contamination and renders the method less susceptible to false positives. This new tool can benefit the COVID-19 pandemic and future emerging outbreaks, providing a third option between amplification-based RNA detection and protein antigen detection. Ultimately, we believe this tool can be adapted both for low-resource onsite testing as well as for monitoring viral loads in recovering patients.
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Affiliation(s)
- Javier Vilcapoma
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
| | - Asmer Aliyeva
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
| | - Andrew Hayden
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
| | | | - Lifeng Zhou
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
| | | | - Darren Yang
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Clinton Hansen
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Simon Chi-Chin Shiu
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
| | - Alexis Russell
- Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, Albany, NY 12208
| | - Kirsten St. George
- Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, Albany, NY 12208
- Department of Biomedical Science, University at Albany, State University of New York, Albany, NY 12208
| | - Wesley P. Wong
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
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12
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Boerneke MA, Gokhale NS, Horner SM, Weeks KM. Structure-first identification of RNA elements that regulate dengue virus genome architecture and replication. Proc Natl Acad Sci U S A 2023; 120:e2217053120. [PMID: 37011200 PMCID: PMC10104495 DOI: 10.1073/pnas.2217053120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 03/02/2023] [Indexed: 04/05/2023] Open
Abstract
The genomes of RNA viruses encode the information required for replication in host cells both in their linear sequence and in complex higher-order structures. A subset of these RNA genome structures show clear sequence conservation, and have been extensively described for well-characterized viruses. However, the extent to which viral RNA genomes contain functional structural elements-unable to be detected by sequence alone-that nonetheless are critical to viral fitness is largely unknown. Here, we devise a structure-first experimental strategy and use it to identify 22 structure-similar motifs across the coding sequences of the RNA genomes for the four dengue virus serotypes. At least 10 of these motifs modulate viral fitness, revealing a significant unnoticed extent of RNA structure-mediated regulation within viral coding sequences. These viral RNA structures promote a compact global genome architecture, interact with proteins, and regulate the viral replication cycle. These motifs are also thus constrained at the levels of both RNA structure and protein sequence and are potential resistance-refractory targets for antivirals and live-attenuated vaccines. Structure-first identification of conserved RNA structure enables efficient discovery of pervasive RNA-mediated regulation in viral genomes and, likely, other cellular RNAs.
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Affiliation(s)
- Mark A. Boerneke
- Department of Chemistry, University of North Carolina, Chapel Hill, NC27599-3290
| | - Nandan S. Gokhale
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC27710
| | - Stacy M. Horner
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC27710
- Department of Medicine, Duke University Medical Center, Durham, NC27710
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC27599-3290
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13
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Nalewaj M, Szabat M. Examples of Structural Motifs in Viral Genomes and Approaches for RNA Structure Characterization. Int J Mol Sci 2022; 23:ijms232415917. [PMID: 36555559 PMCID: PMC9784701 DOI: 10.3390/ijms232415917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/04/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
The relationship between conserved structural motifs and their biological function in the virus replication cycle is the interest of many researchers around the world. RNA structure is closely related to RNA function. Therefore, technological progress in high-throughput approaches for RNA structure analysis and the development of new ones are very important. In this mini review, we discuss a few perspectives on the structural elements of viral genomes and some methods used for RNA structure prediction and characterization. Based on the recent literature, we describe several examples of studies concerning the viral genomes, especially severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A virus (IAV). Herein, we emphasize that a better understanding of viral genome architecture allows for the discovery of the structure-function relationship, and as a result, the discovery of new potential antiviral therapeutics.
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14
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Xu T, Li LX, Jia Y, Wu Q, Zhu W, Xu Z, Zheng B, Lu X. One microRNA has the potential to target whole viral mRNAs in a given human coronavirus. Front Microbiol 2022; 13:1035044. [PMID: 36439806 PMCID: PMC9686371 DOI: 10.3389/fmicb.2022.1035044] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/24/2022] [Indexed: 09/29/2023] Open
Abstract
MicroRNAs (miRNAs) can repress viral replication by targeting viral messenger RNA (mRNA), which makes them potential antiviral agents. The antiviral effects of miRNAs on infectious viruses have been explored extensively; however, recent studies mainly considered the action modes of miRNAs, neglecting another key factor, the molecular biology of viruses, which may be particularly important in the study of miRNA actions against a given virus. In this paper, the action modes of miRNAs and the molecular biology of viruses are jointly considered for the first time and based on the reported roles of miRNAs on viruses and human coronaviruses (HCoVs) molecular biology, the general and specific interaction modes of miRNAs-HCoVs are systematically reviewed. It was found that HCoVs transcriptome is a nested set of subgenomic mRNAs, sharing the same 5' leader, 3' untranslated region (UTR) and open reading frame (ORF). For a given HCoV, one certain miRNA with a target site in the 5' leader or 3' UTR has the potential to target all viral mRNAs, indicating tremendous antiviral effects against HCoVs. However, for the shared ORFs, some parts are untranslatable attributed to the translation pattern of HCoVs mRNA, and it is unknown whether the base pairing between the untranslated ORFs and miRNAs plays a regulatory effect on the local mRNAs where the untranslated ORFs are located; therefore, the regulatory effects of miRNAs with targets within the shared ORFs are complicated and need to be confirmed. Collectively, miRNAs may bepromising antiviral agents against HCoVs due to their intrinsically nested set of mRNAs, and some gaps are waiting to be filled. In this review, insight is provided into the exploration of miRNAs that can interrupt HCoVs infection.
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Affiliation(s)
- Tielong Xu
- Evidence-Based Medicine Research Center Department, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Long-xue Li
- Laboratory Animal Science and Technology Center, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Yao Jia
- Evidence-Based Medicine Research Center Department, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Qingni Wu
- Evidence-Based Medicine Research Center Department, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Weifeng Zhu
- Evidence-Based Medicine Research Center Department, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Zhou Xu
- Evidence-Based Medicine Research Center Department, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Bin Zheng
- National Institute of Parasitic Diseases Chinese Center for Disease Control and Prevention, and WHO Collaborating Center for Tropical Diseases, Shanghai, China
| | - Xuexin Lu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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15
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Chandler-Bostock R, Bingham RJ, Clark S, Scott AJP, Wroblewski E, Barker A, White SJ, Dykeman EC, Mata CP, Bohon J, Farquhar E, Twarock R, Stockley PG. Genome-regulated Assembly of a ssRNA Virus May Also Prepare It for Infection. J Mol Biol 2022; 434:167797. [PMID: 35998704 DOI: 10.1016/j.jmb.2022.167797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/09/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022]
Abstract
Many single-stranded, positive-sense RNA viruses regulate assembly of their infectious virions by forming multiple, cognate coat protein (CP)-genome contacts at sites termed Packaging Signals (PSs). We have determined the secondary structures of the bacteriophage MS2 ssRNA genome (gRNA) frozen in defined states using constraints from X-ray synchrotron footprinting (XRF). Comparison of the footprints from phage and transcript confirms the presence of multiple PSs in contact with CP dimers in the former. This is also true for a virus-like particle (VLP) assembled around the gRNA in vitro in the absence of the single-copy Maturation Protein (MP) found in phage. Since PS folds are present at many sites across gRNA transcripts, it appears that this genome has evolved to facilitate this mechanism of assembly regulation. There are striking differences between the gRNA-CP contacts seen in phage and the VLP, suggesting that the latter are inappropriate surrogates for aspects of phage structure/function. Roughly 50% of potential PS sites in the gRNA are not in contact with the protein shell of phage. However, many of these sit adjacent to, albeit not in contact with, PS-binding sites on CP dimers. We hypothesize that these act as PSs transiently during assembly but subsequently dissociate. Combining the XRF data with PS locations from an asymmetric cryo-EM reconstruction suggests that the genome positions of such dissociations are non-random and may facilitate infection. The loss of many PS-CP interactions towards the 3' end of the gRNA would allow this part of the genome to transit more easily through the narrow basal body of the pilus extruding machinery. This is the known first step in phage infection. In addition, each PS-CP dissociation event leaves the protein partner trapped in a non-lowest free-energy conformation. This destabilizes the protein shell which must disassemble during infection, further facilitating this stage of the life-cycle.
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Affiliation(s)
| | - Richard J Bingham
- Departments of Mathematics and Biology & York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
| | - Sam Clark
- Departments of Mathematics and Biology & York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
| | - Andrew J P Scott
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Emma Wroblewski
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Amy Barker
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Simon J White
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Eric C Dykeman
- Departments of Mathematics and Biology & York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
| | - Carlos P Mata
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Jen Bohon
- CWRU Center for Synchrotron Biosciences, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Erik Farquhar
- CWRU Center for Synchrotron Biosciences, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Reidun Twarock
- Departments of Mathematics and Biology & York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK.
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
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16
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Xiao L, Fang L, Kool ET. Acylation probing of "generic" RNA libraries reveals critical influence of loop constraints on reactivity. Cell Chem Biol 2022; 29:1341-1352.e8. [PMID: 35662395 PMCID: PMC9391288 DOI: 10.1016/j.chembiol.2022.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/16/2022] [Accepted: 05/12/2022] [Indexed: 01/08/2023]
Abstract
The reactivity of RNA 2'-OH acylation is broadly useful both in probing structure and in preparing conjugates. To date, this reactivity has been analyzed in limited sets of biological RNA sequences, leaving open questions of how reactivity varies inherently without regard to sequence in structured contexts. We constructed and probed "generic" structured RNA libraries using homogeneous loop sequences, employing deep sequencing to carry out a systematic survey of reactivity. We find a wide range of RNA reactivities among single-stranded sequences, with nearest neighbors playing substantial roles. Remarkably, certain small loops are found to be far more reactive on average (up to 4,000-fold) than single-stranded RNAs, due to conformational constraints that enhance reactivity. Among loops, we observe large variations in reactivity based on size, type, and position. The results lend insights into RNA designs for achieving high-efficiency local conjugation and provide new opportunities to refine structure analysis.
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Affiliation(s)
- Lu Xiao
- Department of Chemistry and ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Linglan Fang
- Department of Chemistry and ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Eric T Kool
- Department of Chemistry and ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.
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17
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Yang SL, Ponti RD, Wan Y, Huber RG. Computational and Experimental Approaches to Study the RNA Secondary Structures of RNA Viruses. Viruses 2022; 14:v14081795. [PMID: 36016417 PMCID: PMC9415818 DOI: 10.3390/v14081795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 11/16/2022] Open
Abstract
Most pandemics of recent decades can be traced to RNA viruses, including HIV, SARS, influenza, dengue, Zika, and SARS-CoV-2. These RNA viruses impose considerable social and economic burdens on our society, resulting in a high number of deaths and high treatment costs. As these RNA viruses utilize an RNA genome, which is important for different stages of the viral life cycle, including replication, translation, and packaging, studying how the genome folds is important to understand virus function. In this review, we summarize recent advances in computational and high-throughput RNA structure-mapping approaches and their use in understanding structures within RNA virus genomes. In particular, we focus on the genome structures of the dengue, Zika, and SARS-CoV-2 viruses due to recent significant outbreaks of these viruses around the world.
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Affiliation(s)
- Siwy Ling Yang
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Riccardo Delli Ponti
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
| | - Yue Wan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
- Correspondence: (Y.W.); (R.G.H.)
| | - Roland G. Huber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
- Correspondence: (Y.W.); (R.G.H.)
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18
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Xu B, Zhu Y, Cao C, Chen H, Jin Q, Li G, Ma J, Yang SL, Zhao J, Zhu J, Ding Y, Fang X, Jin Y, Kwok CK, Ren A, Wan Y, Wang Z, Xue Y, Zhang H, Zhang QC, Zhou Y. Recent advances in RNA structurome. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1285-1324. [PMID: 35717434 PMCID: PMC9206424 DOI: 10.1007/s11427-021-2116-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/01/2022] [Indexed: 12/27/2022]
Abstract
RNA structures are essential to support RNA functions and regulation in various biological processes. Recently, a range of novel technologies have been developed to decode genome-wide RNA structures and novel modes of functionality across a wide range of species. In this review, we summarize key strategies for probing the RNA structurome and discuss the pros and cons of representative technologies. In particular, these new technologies have been applied to dissect the structural landscape of the SARS-CoV-2 RNA genome. We also summarize the functionalities of RNA structures discovered in different regulatory layers-including RNA processing, transport, localization, and mRNA translation-across viruses, bacteria, animals, and plants. We review many versatile RNA structural elements in the context of different physiological and pathological processes (e.g., cell differentiation, stress response, and viral replication). Finally, we discuss future prospects for RNA structural studies to map the RNA structurome at higher resolution and at the single-molecule and single-cell level, and to decipher novel modes of RNA structures and functions for innovative applications.
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Affiliation(s)
- Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yanda Zhu
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Changchang Cao
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hao Chen
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Qiongli Jin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Guangnan Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Junfeng Ma
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Siwy Ling Yang
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Jieyu Zhao
- Department of Chemistry, and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Jianghui Zhu
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Chun Kit Kwok
- Department of Chemistry, and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China.
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China.
| | - Yue Wan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore, Singapore.
| | - Zhiye Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
| | - Huakun Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, China.
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
| | - Yu Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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19
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Barnard TR, Wang AB, Sagan SM. A highly sensitive strand-specific multiplex RT-qPCR assay for quantitation of Zika virus replication. J Virol Methods 2022; 307:114556. [PMID: 35654259 DOI: 10.1016/j.jviromet.2022.114556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/25/2022] [Accepted: 05/28/2022] [Indexed: 10/18/2022]
Abstract
Reverse-transcription quantitative polymerase chain reaction (RT-qPCR) is widely used to quantify viral RNA genomes for diagnostics and research, yet conventional RT-qPCR protocols are unable to accurately distinguish between the different viral RNA species that exist during infection. Here we show that false-priming and self-priming occur during reverse transcription with several published Zika virus (ZIKV) primer sets. We developed a RT-qPCR assay using tagged primers and thermostable reverse transcriptase, which greatly reduced the occurrence of nonspecific cDNA products. Furthermore, we optimized the assay for use in multiplex qPCR which allows for simultaneous quantitative detection of positive-strand and negative-strand ZIKV RNA along with an internal control from both human and mosquito cells. Importantly, this assay is sensitive enough to study early stages of virus infection in vitro. Strikingly, using this assay, we detected ZIKV negative-strand RNA as early as 3 h post-infection in mammalian cell culture, at a time point prior to the onset of positive-strand RNA synthesis. Overall, the strand-specific RT-qPCR assay developed herein is a valuable tool to quantify ZIKV RNA and to study viral replication dynamics during infection. The application of these findings has the potential to increase accuracy of RNA detection methods for a variety of viral pathogens.
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Affiliation(s)
- Trisha R Barnard
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Alex B Wang
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Selena M Sagan
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada; Department of Biochemistry, McGill University, Montreal, QC, Canada.
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20
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Powell P, Bhardwaj U, Goss D. Eukaryotic initiation factor 4F promotes a reorientation of eukaryotic initiation factor 3 binding on the 5' and the 3' UTRs of barley yellow dwarf virus mRNA. Nucleic Acids Res 2022; 50:4988-4999. [PMID: 35446425 PMCID: PMC9122605 DOI: 10.1093/nar/gkac284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/06/2022] [Accepted: 04/13/2022] [Indexed: 11/14/2022] Open
Abstract
Viral mRNAs that lack a 5′ m7GTP cap and a 3′ poly-A tail rely on structural elements in their untranslated regions (UTRs) to form unique RNA-protein complexes that regulate viral translation. Recent studies of the barley yellow dwarf virus (BYDV) have revealed eukaryotic initiation factor 3 (eIF3) plays a significant role in facilitating communication between its 5′ and 3′ UTRs by binding both UTRs simultaneously. This report uses in vitro translation assays, fluorescence anisotropy binding assays, and selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) footprinting to identify secondary structures that are selectively interacting with eIF3. SHAPE data also show that eIF3 alters its interaction with BYDV structures when another factor crucial for BYDV translation, eIF4F, is introduced by the 3′ BYDV translational enhancer (BTE). The observed BTE and eIF4F-induced shift of eIF3 position on the 5’ UTR and the translational effects of altering eIF3-binding structures (SLC and SLII) support a new model for BYDV translation initiation that requires the reorientation of eIF3 on BYDV UTRs. This eIF3 function in BYDV translation initiation is both reminiscent of and distinct from eIF3–RNA interactions found in other non-canonically translating mRNAs (e.g. HCV). This characterization of a new role in translation initiation expands the known functionality of eIF3 and may be broadly applicable to other non-canonically translating mRNAs.
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Affiliation(s)
- Paul Powell
- Department of Chemistry, Hunter College, CUNY, New York, NY 10065, USA.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Usha Bhardwaj
- Department of Chemistry, Hunter College, CUNY, New York, NY 10065, USA
| | - Dixie Goss
- Department of Chemistry, Hunter College, CUNY, New York, NY 10065, USA.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA.,Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
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21
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Przanowska RK, Weidmann CA, Saha S, Cichewicz MA, Jensen KN, Przanowski P, Irving PS, Janes KA, Guertin MJ, Weeks KM, Dutta A. Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors. Cell Rep 2022; 38:110361. [PMID: 35172143 PMCID: PMC8937029 DOI: 10.1016/j.celrep.2022.110361] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/03/2021] [Accepted: 01/19/2022] [Indexed: 12/27/2022] Open
Abstract
Many lncRNAs have been discovered using transcriptomic data; however, it is unclear what fraction of lncRNAs is functional and what structural properties affect their phenotype. MUNC lncRNA (also known as DRReRNA) acts as an enhancer RNA for the Myod1 gene in cis and stimulates the expression of other promyogenic genes in trans by recruiting the cohesin complex. Here, experimental probing of the RNA structure revealed that MUNC contains multiple structural domains not detected by prediction algorithms in the absence of experimental information. We show that these specific and structurally distinct domains are required for induction of promyogenic genes, for binding genomic sites and gene expression regulation, and for binding the cohesin complex. Myod1 induction and cohesin interaction comprise only a subset of MUNC phenotype. Our study reveals unexpectedly complex, structure-driven functions for the MUNC lncRNA and emphasizes the importance of experimentally determined structures for understanding structure-function relationships in lncRNAs.
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Affiliation(s)
- Roza K Przanowska
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Biomedical Engineering, University of Virginia School of Engineering, Charlottesville, VA 22908, USA
| | - Chase A Weidmann
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biological Chemistry and Center for RNA Biomedicine, University of Michigan Medical School, Ann Arbor, MI 48103, USA
| | - Shekhar Saha
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Magdalena A Cichewicz
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Kate N Jensen
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Piotr Przanowski
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Biomedical Engineering, University of Virginia School of Engineering, Charlottesville, VA 22908, USA
| | - Patrick S Irving
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kevin A Janes
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Biomedical Engineering, University of Virginia School of Engineering, Charlottesville, VA 22908, USA
| | - Michael J Guertin
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut, Farmington, CT 06030, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Genetics, University of Alabama, Birmingham, AL 35233, USA.
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22
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Identifying proximal RNA interactions from cDNA-encoded crosslinks with ShapeJumper. PLoS Comput Biol 2021; 17:e1009632. [PMID: 34905538 PMCID: PMC8670686 DOI: 10.1371/journal.pcbi.1009632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 11/11/2021] [Indexed: 01/07/2023] Open
Abstract
SHAPE-JuMP is a concise strategy for identifying close-in-space interactions in RNA molecules. Nucleotides in close three-dimensional proximity are crosslinked with a bi-reactive reagent that covalently links the 2'-hydroxyl groups of the ribose moieties. The identities of crosslinked nucleotides are determined using an engineered reverse transcriptase that jumps across crosslinked sites, resulting in a deletion in the cDNA that is detected using massively parallel sequencing. Here we introduce ShapeJumper, a bioinformatics pipeline to process SHAPE-JuMP sequencing data and to accurately identify through-space interactions, as observed in complex JuMP datasets. ShapeJumper identifies proximal interactions with near-nucleotide resolution using an alignment strategy that is optimized to tolerate the unique non-templated reverse-transcription profile of the engineered crosslink-traversing reverse-transcriptase. JuMP-inspired strategies are now poised to replace adapter-ligation for detecting RNA-RNA interactions in most crosslinking experiments.
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23
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Romero-López C, Ramos-Lorente SE, Berzal-Herranz A. In Vitro Methods to Decipher the Structure of Viral RNA Genomes. Pharmaceuticals (Basel) 2021; 14:ph14111192. [PMID: 34832974 PMCID: PMC8620418 DOI: 10.3390/ph14111192] [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: 10/28/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 02/05/2023] Open
Abstract
RNA viruses encode essential information in their genomes as conserved structural elements that are involved in efficient viral protein synthesis, replication, and encapsidation. These elements can also establish complex networks of RNA-RNA interactions, the so-called RNA interactome, to shape the viral genome and control different events during intracellular infection. In recent years, targeting these conserved structural elements has become a promising strategy for the development of new antiviral tools due to their sequence and structural conservation. In this context, RNA-based specific therapeutic strategies, such as the use of siRNAs have been extensively pursued to target the genome of different viruses. Importantly, siRNA-mediated targeting is not a straightforward approach and its efficiency is highly dependent on the structure of the target region. Therefore, the knowledge of the viral structure is critical for the identification of potentially good target sites. Here, we describe detailed protocols used in our laboratory for the in vitro study of the structure of viral RNA genomes. These protocols include DMS (dimethylsulfate) probing, SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) analysis, and HMX (2'-hydroxyl molecular interference). These methodologies involve the use of high-throughput analysis techniques that provide extensive information about the 3D folding of the RNA under study and the structural tuning derived from the interactome activity. They are therefore a good tool for the development of new RNA-based antiviral compounds.
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24
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Li Z, Qian SH, Wang F, Mohamed HI, Yang G, Chen ZX, Wei D. G-quadruplexes in genomes of viruses infecting eukaryotes or prokaryotes are under different selection pressures from hosts. J Genet Genomics 2021; 49:20-29. [PMID: 34601118 DOI: 10.1016/j.jgg.2021.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 08/18/2021] [Accepted: 08/18/2021] [Indexed: 12/12/2022]
Abstract
G-quadruplexes in viral genomes can be applied as the targets of antiviral therapies, which has attracted wide interest. However, it is still not clear whether the pervasive number of such elements in the viral world is the result of natural selection for functionality. In this study, we identified putative quadruplex-forming sequences (PQSs) across the known viral genomes and analyzed the abundance, structural stability, and conservation of viral PQSs. A Viral Putative G-quadruplex Database (ViPGD,http://jsjds.hzau.edu.cn/MBPC/ViPGD/index.php/home/index) was constructed to collect the details of each viral PQS, which provides guidance for selecting the desirable PQS. The PQS with two putative G-tetrads (G2-PQS) was significantly enriched in both eukaryotic viruses and prokaryotic viruses, while the PQSs with three putative G-tetrads (G3-PQS) were only enriched in eukaryotic viruses and depleted in prokaryotic viruses. The structural stability of PQSs in prokaryotic viruses was significantly lower than that in eukaryotic viruses. Conservation analysis showed that the G2-PQS, instead of G3-PQS, was highly conserved within the genus. This suggested that the G2-quadruplex might play an important role in viral biology, and the difference in the occurrence of G-quadruplex between eukaryotic viruses and prokaryotic viruses may result from the different selection pressures from hosts.
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Affiliation(s)
- Zhen Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China; College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Sheng Hu Qian
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Fan Wang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China; International joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China
| | - Hany I Mohamed
- Chemistry Department, Faculty of Science, Benha University, Benha 13518, Egypt
| | - Guangfu Yang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China; International joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China.
| | - Zhen-Xia Chen
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518124, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
| | - Dengguo Wei
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
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25
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Cao C, Cai Z, Xiao X, Rao J, Chen J, Hu N, Yang M, Xing X, Wang Y, Li M, Zhou B, Wang X, Wang J, Xue Y. The architecture of the SARS-CoV-2 RNA genome inside virion. Nat Commun 2021; 12:3917. [PMID: 34168138 PMCID: PMC8225788 DOI: 10.1038/s41467-021-22785-x] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/30/2021] [Indexed: 02/08/2023] Open
Abstract
SARS-CoV-2 carries the largest single-stranded RNA genome and is the causal pathogen of the ongoing COVID-19 pandemic. How the SARS-CoV-2 RNA genome is folded in the virion remains unknown. To fill the knowledge gap and facilitate structure-based drug development, we develop a virion RNA in situ conformation sequencing technology, named vRIC-seq, for probing viral RNA genome structure unbiasedly. Using vRIC-seq data, we reconstruct the tertiary structure of the SARS-CoV-2 genome and reveal a surprisingly "unentangled globule" conformation. We uncover many long-range duplexes and higher-order junctions, both of which are under purifying selections and contribute to the sequential package of the SARS-CoV-2 genome. Unexpectedly, the D614G and the other two accompanying mutations may remodel duplexes into more stable forms. Lastly, the structure-guided design of potent small interfering RNAs can obliterate the SARS-CoV-2 in Vero cells. Overall, our work provides a framework for studying the genome structure, function, and dynamics of emerging deadly RNA viruses.
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Affiliation(s)
- Changchang Cao
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Zhaokui Cai
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xia Xiao
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jian Rao
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Juan Chen
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Naijing Hu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Minnan Yang
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xiaorui Xing
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yongle Wang
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Manman Li
- School of Life Sciences, Henan Normal University, Xinxiang, China
| | - Bing Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Xiangxi Wang
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jianwei Wang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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26
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Marangio P, Law KYT, Sanguinetti G, Granneman S. diffBUM-HMM: a robust statistical modeling approach for detecting RNA flexibility changes in high-throughput structure probing data. Genome Biol 2021; 22:165. [PMID: 34044851 PMCID: PMC8157727 DOI: 10.1186/s13059-021-02379-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 05/10/2021] [Indexed: 11/21/2022] Open
Abstract
Advancing RNA structural probing techniques with next-generation sequencing has generated demands for complementary computational tools to robustly extract RNA structural information amidst sampling noise and variability. We present diffBUM-HMM, a noise-aware model that enables accurate detection of RNA flexibility and conformational changes from high-throughput RNA structure-probing data. diffBUM-HMM is widely compatible, accounting for sampling variation and sequence coverage biases, and displays higher sensitivity than existing methods while robust against false positives. Our analyses of datasets generated with a variety of RNA probing chemistries demonstrate the value of diffBUM-HMM for quantitatively detecting RNA structural changes and RNA-binding protein binding sites.
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Affiliation(s)
- Paolo Marangio
- School of Informatics, The University of Edinburgh, Edinburgh, UK
- SISSA Data Science Excellence Department Initiative, Trieste, Italy
| | - Ka Ying Toby Law
- Centre for Synthetic and Systems Biology, The University of Edinburgh, Edinburgh, UK
| | - Guido Sanguinetti
- Centre for Synthetic and Systems Biology, The University of Edinburgh, Edinburgh, UK.
- School of Informatics, The University of Edinburgh, Edinburgh, UK.
- SISSA Data Science Excellence Department Initiative, Trieste, Italy.
| | - Sander Granneman
- Centre for Synthetic and Systems Biology, The University of Edinburgh, Edinburgh, UK.
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27
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Abstract
RNA lies upstream of nearly all biology and functions as the central conduit of information exchange in all cells. RNA molecules encode information both in their primary sequences and in complex structures that form when an RNA folds back on itself. From the time of discovery of mRNA in the late 1950s until quite recently, we had only a rudimentary understanding of RNA structure across vast regions of most messenger and noncoding RNAs. This deficit is now rapidly being addressed, especially by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry, mutational profiling (MaP), and closely related platform technologies that, collectively, create chemical microscopes for RNA. These technologies make it possible to interrogate RNA structure, quantitatively, at nucleotide resolution, and at large scales, for entire mRNAs, noncoding RNAs, and viral RNA genomes. By applying comprehensive structure probing to diverse problems, we and others are showing that control of biological function mediated by RNA structure is ubiquitous across prokaryotic and eukaryotic organisms.Work over the past decade using SHAPE-based analyses has clarified key principles. First, the method of RNA structure probing matters. SHAPE-MaP, with its direct and one-step readout that probes nearly every nucleotide by reaction at the 2'-hydroxyl, gives a more detailed and accurate readout than alternatives. Second, comprehensive chemical probing is essential. Focusing on fragments of large RNAs or using meta-gene or statistical analyses to compensate for sparse data sets misses critical features and often yields structure models with poor predictive power. Finally, every RNA has its own internal structural personality. There are myriad ways in which RNA structure modulates sequence accessibility, protein binding, translation, splice-site choice, phase separation, and other fundamental biological processes. In essentially every instance where we have applied rigorous and quantitative SHAPE technologies to study RNA structure-function interrelationships, new insights regarding biological regulatory mechanisms have emerged. RNA elements with more complex higher-order structures appear more likely to contain high-information-content clefts and pockets that bind small molecules, broadly informing a vigorous field of RNA-targeted drug discovery.The broad implications of this collective work are twofold. First, it is long past time to abandon depiction of large RNAs as simple noodle-like or gently flowing molecules. Instead, we need to emphasize that nearly all RNAs are punctuated with distinctive internal structures, a subset of which modulate function in profound ways. Second, structure probing should be an integral component of any effort that seeks to understand the functional nexuses and biological roles of large RNAs.
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Affiliation(s)
- Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, United States
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28
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Zhang M, Li K, Bai J, Velema WA, Yu C, van Damme R, Lee WH, Corpuz ML, Chen JF, Lu Z. Optimized photochemistry enables efficient analysis of dynamic RNA structuromes and interactomes in genetic and infectious diseases. Nat Commun 2021; 12:2344. [PMID: 33879794 PMCID: PMC8058046 DOI: 10.1038/s41467-021-22552-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 03/18/2021] [Indexed: 02/02/2023] Open
Abstract
Direct determination of RNA structures and interactions in living cells is critical for understanding their functions in normal physiology and disease states. Here, we present PARIS2, a dramatically improved method for RNA duplex determination in vivo with >4000-fold higher efficiency than previous methods. PARIS2 captures ribosome binding sites on mRNAs, reporting translation status on a transcriptome scale. Applying PARIS2 to the U8 snoRNA mutated in the neurological disorder LCC, we discover a network of dynamic RNA structures and interactions which are destabilized by patient mutations. We report the first whole genome structure of enterovirus D68, an RNA virus that causes polio-like symptoms, revealing highly dynamic conformations altered by antiviral drugs and different pathogenic strains. We also discover a replication-associated asymmetry on the (+) and (-) strands of the viral genome. This study establishes a powerful technology for efficient interrogation of the RNA structurome and interactome in human diseases.
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MESH Headings
- Calcinosis/genetics
- Calcinosis/metabolism
- Central Nervous System Cysts/genetics
- Central Nervous System Cysts/metabolism
- Communicable Diseases/genetics
- Communicable Diseases/metabolism
- Cross-Linking Reagents
- Enterovirus D, Human/genetics
- Furocoumarins
- Genetic Diseases, Inborn/genetics
- Genetic Diseases, Inborn/metabolism
- Genome, Viral
- Humans
- Leukoencephalopathies/genetics
- Leukoencephalopathies/metabolism
- Models, Molecular
- Mutation
- Nucleic Acid Conformation
- Photochemical Processes
- Photochemistry/methods
- RNA/chemistry
- RNA/genetics
- RNA/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
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Affiliation(s)
- Minjie Zhang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Kongpan Li
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Jianhui Bai
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Willem A Velema
- Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Chengqing Yu
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Ryan van Damme
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Wilson H Lee
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Maia L Corpuz
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Jian-Fu Chen
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, USA
| | - Zhipeng Lu
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA.
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29
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Andrzejewska A, Zawadzka M, Gumna J, Garfinkel DJ, Pachulska-Wieczorek K. In vivo structure of the Ty1 retrotransposon RNA genome. Nucleic Acids Res 2021; 49:2878-2893. [PMID: 33621339 PMCID: PMC7969010 DOI: 10.1093/nar/gkab090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/28/2021] [Accepted: 02/02/2021] [Indexed: 12/25/2022] Open
Abstract
Long terminal repeat (LTR)-retrotransposons constitute a significant part of eukaryotic genomes and influence their function and evolution. Like other RNA viruses, LTR-retrotransposons efficiently utilize their RNA genome to interact with host cell machinery during replication. Here, we provide the first genome-wide RNA secondary structure model for a LTR-retrotransposon in living cells. Using SHAPE probing, we explore the secondary structure of the yeast Ty1 retrotransposon RNA genome in its native in vivo state and under defined in vitro conditions. Comparative analyses reveal the strong impact of the cellular environment on folding of Ty1 RNA. In vivo, Ty1 genome RNA is significantly less structured and more dynamic but retains specific well-structured regions harboring functional cis-acting sequences. Ribosomes participate in the unfolding and remodeling of Ty1 RNA, and inhibition of translation initiation stabilizes Ty1 RNA structure. Together, our findings support the dual role of Ty1 genomic RNA as a template for protein synthesis and reverse transcription. This study also contributes to understanding how a complex multifunctional RNA genome folds in vivo, and strengthens the need for studying RNA structure in its natural cellular context.
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Affiliation(s)
- Angelika Andrzejewska
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Małgorzata Zawadzka
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Julita Gumna
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - David J Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Katarzyna Pachulska-Wieczorek
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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30
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Guttinger S. Covid-19 and the need for more history and philosophy of RNA. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2021; 43:42. [PMID: 33759005 PMCID: PMC7986637 DOI: 10.1007/s40656-021-00391-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
RNA is central to the COVID-19 pandemic-it shapes how the SARS Coronavirus 2 (SARS-CoV-2) behaves, and how researchers investigate and fight it. However, RNA has received relatively little attention in the history and philosophy of the life sciences. By analysing RNA biology in more detail, philosophers and historians of science could gain new and powerful tools to assess the current pandemic, and the biological sciences more generally.
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Affiliation(s)
- Stephan Guttinger
- Centre for Philosophy of Natural and Social Science, London School of Economics, Lakatos Building, Houghton Street, London, WC2A 2AE, UK.
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31
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Dicker K, Järvelin AI, Garcia-Moreno M, Castello A. The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity. Semin Cell Dev Biol 2021; 111:108-118. [PMID: 32921578 PMCID: PMC7482619 DOI: 10.1016/j.semcdb.2020.08.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/30/2020] [Accepted: 08/03/2020] [Indexed: 12/14/2022]
Abstract
RNA is a central molecule in RNA virus biology due to its dual function as messenger and genome. However, the small number of proteins encoded by viral genomes is insufficient to enable virus infection. Hence, viruses hijack cellular RNA-binding proteins (RBPs) to aid replication and spread. In this review we discuss the 'knowns' and 'unknowns' regarding the contribution of host RBPs to the formation of viral particles and the initial steps of infection in the newly infected cell. Through comparison of the virion proteomes of ten different human RNA viruses, we confirm that a pool of cellular RBPs are typically incorporated into viral particles. We describe here illustrative examples supporting the important functions of these RBPs in viral particle formation and infectivity and we propose that the role of host RBPs in these steps can be broader than previously anticipated. Understanding how cellular RBPs regulate virus infection can lead to the discovery of novel therapeutic targets against viruses.
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Affiliation(s)
- Kate Dicker
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Aino I Järvelin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Manuel Garcia-Moreno
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK; MRC-University of Glasgow Centre for Virus Research, University of Glasgow, 464 Bearsden Road, Glasgow, G61 1QH, Scotland, UK.
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32
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Manfredonia I, Incarnato D. Structure and regulation of coronavirus genomes: state-of-the-art and novel insights from SARS-CoV-2 studies. Biochem Soc Trans 2021; 49:341-352. [PMID: 33367597 PMCID: PMC7925004 DOI: 10.1042/bst20200670] [Citation(s) in RCA: 27] [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: 11/06/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 12/13/2022]
Abstract
Coronaviruses (CoV) are positive-sense single-stranded RNA viruses, harboring the largest viral RNA genomes known to date. Apart from the primary sequence encoding for all the viral proteins needed for the generation of new viral particles, certain regions of CoV genomes are known to fold into stable structures, controlling several aspects of CoV life cycle, from the regulation of the discontinuous transcription of subgenomic mRNAs, to the packaging of the genome into new virions. Here we review the current knowledge on CoV RNA structures, discussing it in light of the most recent discoveries made possible by analyses of the SARS-CoV-2 genome.
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Affiliation(s)
- Ilaria Manfredonia
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Danny Incarnato
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
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33
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Manfredonia I, Nithin C, Ponce-Salvatierra A, Ghosh P, Wirecki TK, Marinus T, Ogando NS, Snijder E, van Hemert MJ, Bujnicki JM, Incarnato D. Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements. Nucleic Acids Res 2020; 48:12436-12452. [PMID: 33166999 PMCID: PMC7736786 DOI: 10.1093/nar/gkaa1053] [Citation(s) in RCA: 157] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/13/2020] [Accepted: 10/22/2020] [Indexed: 01/25/2023] Open
Abstract
SARS-CoV-2 is a betacoronavirus with a linear single-stranded, positive-sense RNA genome, whose outbreak caused the ongoing COVID-19 pandemic. The ability of coronaviruses to rapidly evolve, adapt, and cross species barriers makes the development of effective and durable therapeutic strategies a challenging and urgent need. As for other RNA viruses, genomic RNA structures are expected to play crucial roles in several steps of the coronavirus replication cycle. Despite this, only a handful of functionally-conserved coronavirus structural RNA elements have been identified to date. Here, we performed RNA structure probing to obtain single-base resolution secondary structure maps of the full SARS-CoV-2 coronavirus genome both in vitro and in living infected cells. Probing data recapitulate the previously described coronavirus RNA elements (5' UTR and s2m), and reveal new structures. Of these, ∼10.2% show significant covariation among SARS-CoV-2 and other coronaviruses, hinting at their functionally-conserved role. Secondary structure-restrained 3D modeling of these segments further allowed for the identification of putative druggable pockets. In addition, we identify a set of single-stranded segments in vivo, showing high sequence conservation, suitable for the development of antisense oligonucleotide therapeutics. Collectively, our work lays the foundation for the development of innovative RNA-targeted therapeutic strategies to fight SARS-related infections.
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Affiliation(s)
- Ilaria Manfredonia
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands
| | - Chandran Nithin
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Almudena Ponce-Salvatierra
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Pritha Ghosh
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Tomasz K Wirecki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Tycho Marinus
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands
| | - Natacha S Ogando
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Martijn J van Hemert
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Danny Incarnato
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands
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34
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Madden EA, Plante KS, Morrison CR, Kutchko KM, Sanders W, Long KM, Taft-Benz S, Cruz Cisneros MC, White AM, Sarkar S, Reynolds G, Vincent HA, Laederach A, Moorman NJ, Heise MT. Using SHAPE-MaP To Model RNA Secondary Structure and Identify 3'UTR Variation in Chikungunya Virus. J Virol 2020; 94:e00701-20. [PMID: 32999019 PMCID: PMC7925192 DOI: 10.1128/jvi.00701-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 09/17/2020] [Indexed: 01/04/2023] Open
Abstract
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus associated with debilitating arthralgia in humans. RNA secondary structure in the viral genome plays an important role in the lifecycle of alphaviruses; however, the specific role of RNA structure in regulating CHIKV replication is poorly understood. Our previous studies found little conservation in RNA secondary structure between alphaviruses, and this structural divergence creates unique functional structures in specific alphavirus genomes. Therefore, to understand the impact of RNA structure on CHIKV biology, we used SHAPE-MaP to inform the modeling of RNA secondary structure throughout the genome of a CHIKV isolate from the 2013 Caribbean outbreak. We then analyzed regions of the genome with high levels of structural specificity to identify potentially functional RNA secondary structures and identified 23 regions within the CHIKV genome with higher than average structural stability, including four previously identified, functionally important CHIKV RNA structures. We also analyzed the RNA flexibility and secondary structures of multiple 3'UTR variants of CHIKV that are known to affect virus replication in mosquito cells. This analysis found several novel RNA structures within these 3'UTR variants. A duplication in the 3'UTR that enhances viral replication in mosquito cells led to an overall increase in the amount of unstructured RNA in the 3'UTR. This analysis demonstrates that the CHIKV genome contains a number of unique, specific RNA secondary structures and provides a strategy for testing these secondary structures for functional importance in CHIKV replication and pathogenesis.IMPORTANCE Chikungunya virus (CHIKV) is a mosquito-borne RNA virus that causes febrile illness and debilitating arthralgia in humans. CHIKV causes explosive outbreaks but there are no approved therapies to treat or prevent CHIKV infection. The CHIKV genome contains functional RNA secondary structures that are essential for proper virus replication. Since RNA secondary structures have only been defined for a small portion of the CHIKV genome, we used a chemical probing method to define the RNA secondary structures of CHIKV genomic RNA. We identified 23 highly specific structured regions of the genome, and confirmed the functional importance of one structure using mutagenesis. Furthermore, we defined the RNA secondary structure of three CHIKV 3'UTR variants that differ in their ability to replicate in mosquito cells. Our study highlights the complexity of the CHIKV genome and describes new systems for designing compensatory mutations to test the functional relevance of viral RNA secondary structures.
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Affiliation(s)
- Emily A Madden
- Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kenneth S Plante
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Clayton R Morrison
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Katrina M Kutchko
- Biology Department, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Bioinformatics and Computational Biology, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Wes Sanders
- Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kristin M Long
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sharon Taft-Benz
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | | | | | - Sanjay Sarkar
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Grace Reynolds
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Heather A Vincent
- Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Alain Laederach
- Biology Department, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nathanial J Moorman
- Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mark T Heise
- Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
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Ehrhardt JE, Weeks KM. Time-Resolved, Single-Molecule, Correlated Chemical Probing of RNA. J Am Chem Soc 2020; 142:18735-18740. [PMID: 33095984 DOI: 10.1021/jacs.0c06221] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Capturing the folding dynamics of large, functionally important RNAs has relied primarily on global measurements of structure or on per-nucleotide chemical probing. These approaches infer, but do not directly measure, through-space structural interactions. Here we introduce trimethyloxonium (TMO) as a chemical probe for RNA. TMO alkylates RNA at high levels in seconds, and thereby enables time-resolved, single-molecule, through-space probing of RNA folding using the RING-MaP correlated chemical probing framework. Time-resolved correlations in the RNase P RNA-a functional RNA with a complex structure stabilized by multiple noncanonical interactions-revealed that a long-range tertiary interaction guides native RNA folding for both secondary and tertiary structure. This unanticipated nonhierarchical folding mechanism was directly validated by examining the consequences of concise disruption of the through-space interaction. Single-molecule, time-resolved RNA structure probing with TMO is poised to reveal a wide range of dynamic RNA folding processes and principles of RNA folding.
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Affiliation(s)
- Jeffrey E Ehrhardt
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, United States
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, United States
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36
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Chkuaseli T, White KA. Activation of viral transcription by stepwise largescale folding of an RNA virus genome. Nucleic Acids Res 2020; 48:9285-9300. [PMID: 32785642 PMCID: PMC7498350 DOI: 10.1093/nar/gkaa675] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/08/2020] [Accepted: 07/31/2020] [Indexed: 12/31/2022] Open
Abstract
The genomes of RNA viruses contain regulatory elements of varying complexity. Many plus-strand RNA viruses employ largescale intra-genomic RNA-RNA interactions as a means to control viral processes. Here, we describe an elaborate RNA structure formed by multiple distant regions in a tombusvirus genome that activates transcription of a viral subgenomic mRNA. The initial step in assembly of this intramolecular RNA complex involves the folding of a large viral RNA domain, which generates a discontinuous binding pocket. Next, a distally-located protracted stem-loop RNA structure docks, via base-pairing, into the binding site and acts as a linchpin that stabilizes the RNA complex and activates transcription. A multi-step RNA folding pathway is proposed in which rate-limiting steps contribute to a delay in transcription of the capsid protein-encoding viral subgenomic mRNA. This study provides an exceptional example of the complexity of genome-scale viral regulation and offers new insights into the assembly schemes utilized by large intra-genomic RNA structures.
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Affiliation(s)
- Tamari Chkuaseli
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
| | - K Andrew White
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
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37
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Arrabito G, Ferrara V, Bonasera A, Pignataro B. Artificial Biosystems by Printing Biology. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1907691. [PMID: 32511894 DOI: 10.1002/smll.201907691] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 05/09/2020] [Indexed: 05/09/2023]
Abstract
The continuous progress of printing technologies over the past 20 years has fueled the development of a plethora of applications in materials sciences, flexible electronics, and biotechnologies. More recently, printing methodologies have started up to explore the world of Artificial Biology, offering new paradigms in the direct assembly of Artificial Biosystems (small condensates, compartments, networks, tissues, and organs) by mimicking the result of the evolution of living systems and also by redesigning natural biological systems, taking inspiration from them. This recent progress is reported in terms of a new field here defined as Printing Biology, resulting from the intersection between the field of printing and the bottom up Synthetic Biology. Printing Biology explores new approaches for the reconfigurable assembly of designed life-like or life-inspired structures. This work presents this emerging field, highlighting its main features, i.e., printing methodologies (from 2D to 3D), molecular ink properties, deposition mechanisms, and finally the applications and future challenges. Printing Biology is expected to show a growing impact on the development of biotechnology and life-inspired fabrication.
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Affiliation(s)
- Giuseppe Arrabito
- Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, Building 17, Palermo, 90128, Italy
| | - Vittorio Ferrara
- Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, Building 17, Palermo, 90128, Italy
- Department of Chemical Sciences, University of Catania, Viale Andrea Doria, 6, Catania, 95125, Italy
| | - Aurelio Bonasera
- Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, Building 17, Palermo, 90128, Italy
| | - Bruno Pignataro
- Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, Building 17, Palermo, 90128, Italy
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38
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Cagliani R, Forni D, Clerici M, Sironi M. Coding potential and sequence conservation of SARS-CoV-2 and related animal viruses. INFECTION GENETICS AND EVOLUTION 2020; 83:104353. [PMID: 32387562 PMCID: PMC7199688 DOI: 10.1016/j.meegid.2020.104353] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/14/2020] [Accepted: 05/02/2020] [Indexed: 12/13/2022]
Abstract
In December 2019, a novel human-infecting coronavirus (SARS-CoV-2) was recognized in China. In a few months, SARS-CoV-2 has caused thousands of disease cases and deaths in several countries. Phylogenetic analyses indicated that SARS-CoV-2 clusters with SARS-CoV in the Sarbecovirus subgenus and viruses related to SARS-CoV-2 were identified from bats and pangolins. Coronaviruses have long and complex genomes with high plasticity in terms of gene content. To date, the coding potential of SARS-CoV-2 remains partially unknown. We thus used available sequences of bat and pangolin viruses to determine the selective events that shaped the genome structure of SARS-CoV-2 and to assess its coding potential. By searching for signals of significantly reduced variability at synonymous sites (dS), we identified six genomic regions, one of these corresponding to the programmed −1 ribosomal frameshift. The most prominent signal of dS reduction was observed within the E gene. A genome-wide analysis of conserved RNA structures indicated that this region harbors a putative functional RNA element that is shared with the SARS-CoV lineage. Additional signals of reduced dS indicated the presence of internal ORFs. Whereas the presence ORF9a (internal to N) was previously proposed by homology with a well characterized protein of SARS-CoV, ORF3h (for hypothetical, within ORF3a) was not previously described. The predicted product of ORF3h has 90% identity with the corresponding predicted product of SARS-CoV and displays features suggestive of a viroporin. Finally, analysis of the putative ORF10 revealed high dN/dS (3.82) in SARS-CoV-2 and related coronaviruses. In the SARS-CoV lineage, the ORF is predicted to encode a truncated protein and is neutrally evolving. These data suggest that ORF10 encodes a functional protein in SARS-CoV-2 and that positive selection is driving its evolution. Experimental analyses will be necessary to validate and characterize the coding and non-coding functional elements we identified. We analyzed the coding region of SARS-CoV-2 and related bat/pangolin viruses. We identified six regions of significantly low variability at sysnonymous sites. One of these corresponds to a conserved RNA structure shared with the SARS-CoV lineage. The dS reduction within ORF3a corresponds to a potential ORF encoding a viroporin. In SARS-CoV-2 and related viruses, the putative 3′ terminal ORF10 has high dN/dS.
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Affiliation(s)
- Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy; Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy.
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Williams GD, Gokhale NS, Horner SM. Regulation of Viral Infection by the RNA Modification N6-Methyladenosine. Annu Rev Virol 2019; 6:235-253. [PMID: 31283446 DOI: 10.1146/annurev-virology-092818-015559] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In recent years, the RNA modification N6-methyladenosine (m6A) has been found to play a role in the life cycles of numerous viruses and also in the cellular response to viral infection. m6A has emerged as a regulator of many fundamental aspects of RNA biology. Here, we highlight recent advances in techniques for the study of m6A, as well as advances in our understanding of the cellular machinery that controls the addition, removal, recognition, and functions of m6A. We then summarize the many newly discovered roles of m6A during viral infection, including how it regulates innate and adaptive immune responses to infection. Overall, the goals of this review are to summarize the roles of m6A on both cellular and viral RNAs and to describe future directions for uncovering new functions of m6A during infection.
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Affiliation(s)
- Graham D Williams
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA; , ,
| | - Nandan S Gokhale
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA; , ,
| | - Stacy M Horner
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA; , , .,Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA
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40
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Abstract
Understanding RNA-mediated functions requires a detailed characterization of the underlying RNA structure. In many cases, structure probing experiments are performed on RNA that has been "refolded" in some way, which may cause the conformation to differ from that of the native RNA. We used SHAPE-MaP (selective 2'-hydroxyl acylation analyzed by primer extension, read out by mutational profiling), to probe the structure of the Dengue virus (DENV) RNA genome after gentle extraction of the native RNA from intact virions (ex virion) and after heat denaturation and refolding. Comparison of mutiple SHAPE-informed structural features revealed that refolded RNA is more highly structured and samples fewer conformations than the ex virion RNA. Regions with similar structural features are generally those with low SHAPE reactivity and low Shannon entropy (lowSS regions), which correspond to elements with high levels of well-determined structure. This high-structure and low-entropy analysis framework, previously shown to make possible discovery of functional RNA structures, is thus now shown to allow de novo identification of structural elements in a refolded RNA that are likely to recapitulate RNA structures in the ex virion RNA state. Regions with less well-defined structures, which occurred more frequently in the more native-like ex virion RNA and may contain RNA switches, are challenging to recapitulate using refolded RNA.
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Affiliation(s)
- Elizabeth A Dethoff
- Department of Chemistry , The University of North Carolina , Chapel Hill , North Carolina 27599-3290 , United States
| | - Kevin M Weeks
- Department of Chemistry , The University of North Carolina , Chapel Hill , North Carolina 27599-3290 , United States
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