1
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Matzel T, Martin MW, Herr A, Wacker A, Richter C, Sreeramulu S, Schwalbe H. NMR characterization and ligand binding site of the stem-loop 2 motif from the Delta variant of SARS-CoV-2. RNA (NEW YORK, N.Y.) 2024; 30:779-794. [PMID: 38565242 PMCID: PMC11182009 DOI: 10.1261/rna.079902.123] [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: 11/27/2023] [Accepted: 03/08/2024] [Indexed: 04/04/2024]
Abstract
The stem-loop 2 motif (s2m) in SARS-CoV-2 (SCoV-2) is located in the 3'-UTR. Although s2m has been reported to display characteristics of a mobile genomic element that might lead to an evolutionary advantage, its function has remained unknown. The secondary structure of the original SCoV-2 RNA sequence (Wuhan-Hu-1) was determined by NMR in late 2020, delineating the base-pairing pattern and revealing substantial differences in secondary structure compared to SARS-CoV-1 (SCoV-1). The existence of a single G29742-A29756 mismatch in the upper stem of s2m leads to its destabilization and impedes a complete NMR analysis. With Delta, a variant of concern has evolved with one mutation compared to the original sequence that replaces G29742 by U29742. We show here that this mutation results in a more defined structure at ambient temperature accompanied by a rise in melting temperature. Consequently, we were able to identify >90% of the relevant NMR resonances using a combination of selective RNA labeling and filtered 2D NOESY as well as 4D NMR experiments. We present a comprehensive NMR analysis of the secondary structure, (sub)nanosecond dynamics, and ribose conformation of s2m Delta based on heteronuclear 13C NOE and T 1 measurements and ribose carbon chemical shift-derived canonical coordinates. We further show that the G29742U mutation in Delta has no influence on the druggability of s2m compared to the Wuhan-Hu-1 sequence. With the assignment at hand, we identify the flexible regions of s2m as the primary site for small molecule binding.
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Affiliation(s)
- Tobias Matzel
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität Frankfurt, 60438 Frankfurt, Germany
| | - Maria Wirtz Martin
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität Frankfurt, 60438 Frankfurt, Germany
| | - Alexander Herr
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität Frankfurt, 60438 Frankfurt, Germany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität Frankfurt, 60438 Frankfurt, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität Frankfurt, 60438 Frankfurt, Germany
| | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität Frankfurt, 60438 Frankfurt, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität Frankfurt, 60438 Frankfurt, Germany
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2
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Kathe NC, Novakovic M, Allain FHT. Buffer choice and pH strongly influence phase separation of SARS-CoV-2 nucleocapsid with RNA. Mol Biol Cell 2024; 35:ar73. [PMID: 38568799 DOI: 10.1091/mbc.e23-12-0500] [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: 04/05/2024] Open
Abstract
The SARS-CoV-2 nucleocapsid (N) protein is crucial for virus replication and genome packaging. N protein forms biomolecular condensates both in vitro and in vivo in a process known as liquid-liquid phase separation (LLPS), but the exact factors regulating LLPS of N protein are not fully understood. Here, we show that pH and buffer choice have a profound impact on LLPS of N protein. The degree of phase separation is highly dependent on the pH of the solution, which is correlated with histidine protonation in N protein. Specifically, we demonstrate that protonation of H356 is essential for LLPS in phosphate buffer. Moreover, electrostatic interactions of buffer molecules with specific amino acid residues are able to alter the net charge of N protein, thus influencing its ability to undergo phase separation in the presence of RNA. Overall, these findings reveal that even subtle changes in amino acid protonation or surface charge caused by the pH and buffer system can strongly influence the LLPS behavior, and point to electrostatic interactions as the main driving forces of N protein phase separation. Further, our findings emphasize the importance of these experimental parameters when studying phase separation of biomolecules, especially in the context of viral infections where the intracellular milieu undergoes drastic changes and intracellular pH normally decreases.
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Affiliation(s)
- Nina C Kathe
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Mihajlo Novakovic
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Frédéric H-T Allain
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
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3
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Cunningham CL, Frye CJ, Makowski JA, Kensinger AH, Shine M, Milback EJ, Lackey PE, Evanseck JD, Mihailescu MR. Effect of the SARS-CoV-2 Delta-associated G15U mutation on the s2m element dimerization and its interactions with miR-1307-3p. RNA (NEW YORK, N.Y.) 2023; 29:1754-1771. [PMID: 37604684 PMCID: PMC10578481 DOI: 10.1261/rna.079627.123] [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: 02/10/2023] [Accepted: 07/30/2023] [Indexed: 08/23/2023]
Abstract
The s2m, a highly conserved 41-nt hairpin structure in the SARS-CoV-2 genome, serves as an attractive therapeutic target that may have important roles in the virus life cycle or interactions with the host. However, the conserved s2m in Delta SARS-CoV-2, a previously dominant variant characterized by high infectivity and disease severity, has received relatively less attention than that of the original SARS-CoV-2 virus. The focus of this work is to identify and define the s2m changes between Delta and SARS-CoV-2 and the subsequent impact of those changes upon the s2m dimerization and interactions with the host microRNA miR-1307-3p. Bioinformatics analysis of the GISAID database targeting the s2m element reveals a >99% correlation of a single nucleotide mutation at the 15th position (G15U) in Delta SARS-CoV-2. Based on 1H NMR spectroscopy assignments comparing the imino proton resonance region of s2m and the s2m G15U at 19°C, we show that the U15-A29 base pair closes, resulting in a stabilization of the upper stem without overall secondary structure deviation. Increased stability of the upper stem did not affect the chaperone activity of the viral N protein, as it was still able to convert the kissing dimers formed by s2m G15U into a stable duplex conformation, consistent with the s2m reference. However, we show that the s2m G15U mutation drastically impacts the binding of host miR-1307-3p. These findings demonstrate that the observed G15U mutation alters the secondary structure of s2m with subsequent impact on viral binding of host miR-1307-3p, with potential consequences on immune responses.
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Affiliation(s)
- Caylee L Cunningham
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
| | - Caleb J Frye
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
| | - Joseph A Makowski
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
| | - Adam H Kensinger
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
| | - Morgan Shine
- Department of Biochemistry and Chemistry, Westminster College, New Wilmington, Pennsylvania 16172, USA
| | - Ella J Milback
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
| | - Patrick E Lackey
- Department of Biochemistry and Chemistry, Westminster College, New Wilmington, Pennsylvania 16172, USA
| | - Jeffrey D Evanseck
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
| | - Mihaela-Rita Mihailescu
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
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4
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Jiang H, Joshi A, Gan T, Janowski AB, Fujii C, Bricker TL, Darling TL, Harastani HH, Seehra K, Chen H, Tahan S, Jung A, Febles B, Blatter JA, Handley SA, Parikh BA, Wang D, Boon ACM. The Highly Conserved Stem-Loop II Motif Is Dispensable for SARS-CoV-2. J Virol 2023; 97:e0063523. [PMID: 37223945 PMCID: PMC10308922 DOI: 10.1128/jvi.00635-23] [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: 04/28/2023] [Accepted: 05/01/2023] [Indexed: 05/25/2023] Open
Abstract
The stem-loop II motif (s2m) is an RNA structural element that is found in the 3' untranslated region (UTR) of many RNA viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Though the motif was discovered over 25 years ago, its functional significance is unknown. In order to understand the importance of s2m, we created viruses with deletions or mutations of the s2m by reverse genetics and also evaluated a clinical isolate harboring a unique s2m deletion. Deletion or mutation of the s2m had no effect on growth in vitro or on growth and viral fitness in Syrian hamsters in vivo. We also compared the secondary structure of the 3' UTR of wild-type and s2m deletion viruses using selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) and dimethyl sulfate mutational profiling and sequencing (DMS-MaPseq). These experiments demonstrate that the s2m forms an independent structure and that its deletion does not alter the overall remaining 3'-UTR RNA structure. Together, these findings suggest that s2m is dispensable for SARS-CoV-2. IMPORTANCE RNA viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), contain functional structures to support virus replication, translation, and evasion of the host antiviral immune response. The 3' untranslated region of early isolates of SARS-CoV-2 contained a stem-loop II motif (s2m), which is an RNA structural element that is found in many RNA viruses. This motif was discovered over 25 years ago, but its functional significance is unknown. We created SARS-CoV-2 with deletions or mutations of the s2m and determined the effect of these changes on viral growth in tissue culture and in rodent models of infection. Deletion or mutation of the s2m element had no effect on growth in vitro or on growth and viral fitness in Syrian hamsters in vivo. We also observed no impact of the deletion on other known RNA structures in the same region of the genome. These experiments demonstrate that s2m is dispensable for SARS-CoV-2.
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Affiliation(s)
- Hongbing Jiang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Astha Joshi
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tianyu Gan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Andrew B. Janowski
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Chika Fujii
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Traci L. Bricker
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tamarand L. Darling
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Houda H. Harastani
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kuljeet Seehra
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Hongwei Chen
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Stephen Tahan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Ana Jung
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Binita Febles
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Joshua A. Blatter
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Scott A. Handley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Bijal A. Parikh
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - David Wang
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Adrianus C. M. Boon
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
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5
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Keep S, Dowgier G, Lulla V, Britton P, Oade M, Freimanis G, Tennakoon C, Jonassen CM, Tengs T, Bickerton E. Deletion of the s2m RNA Structure in the Avian Coronavirus Infectious Bronchitis Virus and Human Astrovirus Results in Sequence Insertions. J Virol 2023; 97:e0003823. [PMID: 36779761 PMCID: PMC10062133 DOI: 10.1128/jvi.00038-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 01/25/2023] [Indexed: 02/14/2023] Open
Abstract
Coronaviruses infect a wide variety of host species, resulting in a range of diseases in both humans and animals. The coronavirus genome consists of a large positive-sense single-stranded molecule of RNA containing many RNA structures. One structure, denoted s2m and consisting of 41 nucleotides, is located within the 3' untranslated region (3' UTR) and is shared between some coronavirus species, including infectious bronchitis virus (IBV), severe acute respiratory syndrome coronavirus (SARS-CoV), and SARS-CoV-2, as well as other pathogens, including human astrovirus. Using a reverse genetic system to generate recombinant viruses, we investigated the requirement of the s2m structure in the replication of IBV, a globally distributed economically important Gammacoronavirus that infects poultry causing respiratory disease. Deletion of three nucleotides predicted to destabilize the canonical structure of the s2m or the deletion of the nucleotides corresponding to s2m impacted viral replication in vitro. In vitro passaging of the recombinant IBV with the s2m sequence deleted resulted in a 36-nucleotide insertion in place of the deletion, which was identified to be composed of a duplication of flanking sequences. A similar result was observed following serial passage of human astrovirus with a deleted s2m sequence. RNA modeling indicated that deletion of the nucleotides corresponding to the s2m impacted other RNA structures present in the IBV 3' UTR. Our results indicated for both IBV and human astrovirus a preference for nucleotide occupation in the genome location corresponding to the s2m, which is independent of the specific s2m sequence. IMPORTANCE Coronaviruses infect many species, including humans and animals, with substantial effects on livestock, particularly with respect to poultry. The coronavirus RNA genome consists of structural elements involved in viral replication whose roles are poorly understood. We investigated the requirement of the RNA structural element s2m in the replication of the Gammacoronavirus infectious bronchitis virus, an economically important viral pathogen of poultry. Using reverse genetics to generate recombinant IBVs with either a disrupted or deleted s2m, we showed that the s2m is not required for viral replication in cell culture; however, replication is decreased in tracheal tissue, suggesting a role for the s2m in the natural host. Passaging of these viruses as well as human astrovirus lacking the s2m sequence demonstrated a preference for nucleotide occupation, independent of the s2m sequence. RNA modeling suggested deletion of the s2m may negatively impact other essential RNA structures.
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Affiliation(s)
- Sarah Keep
- The Pirbright Institute, Woking, United Kingdom
| | | | - Valeria Lulla
- Department of Pathology, University of Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom
| | | | - Michael Oade
- Department of Pathology, University of Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
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6
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Jiang H, Joshi A, Gan T, Janowski AB, Fujii C, Bricker TL, Darling TL, Harastani HH, Seehra K, Chen H, Tahan S, Jung A, Febles B, Blatter JA, Handley SA, Parikh BA, Wang D, Boon ACM. The highly conserved stem-loop II motif is dispensable for SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.532878. [PMID: 36993345 PMCID: PMC10055069 DOI: 10.1101/2023.03.15.532878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The stem-loop II motif (s2m) is a RNA structural element that is found in the 3' untranslated region (UTR) of many RNA viruses including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Though the motif was discovered over twenty-five years ago, its functional significance is unknown. In order to understand the importance of s2m, we created viruses with deletions or mutations of the s2m by reverse genetics and also evaluated a clinical isolate harboring a unique s2m deletion. Deletion or mutation of the s2m had no effect on growth in vitro , or growth and viral fitness in Syrian hamsters in vivo . We also compared the secondary structure of the 3' UTR of wild type and s2m deletion viruses using SHAPE-MaP and DMS-MaPseq. These experiments demonstrate that the s2m forms an independent structure and that its deletion does not alter the overall remaining 3'UTR RNA structure. Together, these findings suggest that s2m is dispensable for SARS-CoV-2. IMPORTANCE RNA viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contain functional structures to support virus replication, translation and evasion of the host antiviral immune response. The 3' untranslated region of early isolates of SARS-CoV-2 contained a stem-loop II motif (s2m), which is a RNA structural element that is found in many RNA viruses. This motif was discovered over twenty-five years ago, but its functional significance is unknown. We created SARS-CoV-2 with deletions or mutations of the s2m and determined the effect of these changes on viral growth in tissue culture and in rodent models of infection. Deletion or mutation of the s2m element had no effect on growth in vitro , or growth and viral fitness in Syrian hamsters in vivo . We also observed no impact of the deletion on other known RNA structures in the same region of the genome. These experiments demonstrate that the s2m is dispensable for SARS-CoV-2.
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Affiliation(s)
- Hongbing Jiang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Astha Joshi
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tianyu Gan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Andrew B Janowski
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Chika Fujii
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Traci L Bricker
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tamarand L Darling
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Houda H. Harastani
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kuljeet Seehra
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Hongwei Chen
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Stephen Tahan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Ana Jung
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Binita Febles
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Joshua A Blatter
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Scott A Handley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Bijal A Parikh
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - David Wang
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Address correspondence to: Adrianus Boon (), Washington University School of Medicine, 660 Euclid Avenue, Campus Box 8051, St Louis MO 63110 USA. or David Wang (), Washington University School of Medicine, 425 S Euclid Avenue, Campus Box 8230, St Louis MO 63110 USA
| | - Adrianus CM Boon
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Lead contact
- Address correspondence to: Adrianus Boon (), Washington University School of Medicine, 660 Euclid Avenue, Campus Box 8051, St Louis MO 63110 USA. or David Wang (), Washington University School of Medicine, 425 S Euclid Avenue, Campus Box 8230, St Louis MO 63110 USA
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7
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Hossain MI, Myers M, Herath D, Aldhumani AH, Boesger H, Hines JV. 4-Aminoquinolines modulate RNA structure and function: Pharmacophore implications of a conformationally restricted polyamine. Biochem Biophys Res Commun 2023; 644:55-61. [PMID: 36630735 PMCID: PMC10473465 DOI: 10.1016/j.bbrc.2022.12.080] [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: 12/16/2022] [Accepted: 12/28/2022] [Indexed: 12/30/2022]
Abstract
RNA structure plays an important role in regulating cellular function and there is a significant emerging interest in targeting RNA for drug discovery. Here we report the identification of 4-aminoquinolines as modulators of RNA structure and function. Aminoquinolines have a broad range of pharmacological activities, but their specific mechanism of action is often not fully understood. Using electrophoretic mobility shift assays and enzymatic probing we identified 4-aminoquinolines that bind the stem-loop II motif (s2m) of SARS-CoV-2 RNA site-specifically and induce dimerization. Using fluorescence-based RNA binding and T-box riboswitch functional assays we identified that hydroxychloroquine binds the T-box riboswitch antiterminator RNA element and inhibits riboswitch function. Based on its structure and riboswitch dose-response activity we identified that the antagonist activity of hydroxychloroquine is consistent with it being a conformationally restricted analog of the polyamine spermidine. Given the known role that polyamines play in RNA function, the identification of an RNA binding ligand with the pharmacophore of a conformationally restricted polyamine has significant implications for further elucidation of RNA structure-function relationships and RNA-targeted drug discovery.
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Affiliation(s)
- Md Ismail Hossain
- Department of Chemistry & Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Mason Myers
- Department of Chemistry & Biochemistry, Ohio University, Athens, OH, 45701, USA; Honors Tutorial College, Ohio University, Athens, OH, 45701, USA
| | - Danushika Herath
- Department of Chemistry & Biochemistry, Ohio University, Athens, OH, 45701, USA; Molecular & Cellular Biology Program, Ohio University, Athens, OH, 45701, USA
| | - Ali H Aldhumani
- Department of Chemistry & Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Hannah Boesger
- Department of Biological Sciences, Ohio University, Athens, OH, 45701, USA; Honors Tutorial College, Ohio University, Athens, OH, 45701, USA
| | - Jennifer V Hines
- Department of Chemistry & Biochemistry, Ohio University, Athens, OH, 45701, USA; Molecular & Cellular Biology Program, Ohio University, Athens, OH, 45701, USA.
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8
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Kensinger AH, Makowski JA, Pellegrene KA, Imperatore JA, Cunningham CL, Frye CJ, Lackey PE, Mihailescu MR, Evanseck JD. Structural, Dynamical, and Entropic Differences between SARS-CoV and SARS-CoV-2 s2m Elements Using Molecular Dynamics Simulations. ACS PHYSICAL CHEMISTRY AU 2023; 3:30-43. [PMID: 36711027 PMCID: PMC9578647 DOI: 10.1021/acsphyschemau.2c00032] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/21/2022] [Accepted: 09/21/2022] [Indexed: 11/05/2022]
Abstract
The functional role of the highly conserved stem-loop II motif (s2m) in SARS-CoV and SARS-CoV-2 in the viral lifecycle remains enigmatic and an intense area of research. Structure and dynamics of the s2m are key to establishing a structure-function connection, yet a full set of atomistic resolution coordinates is not available for SARS-CoV-2 s2m. Our work constructs three-dimensional coordinates consistent with NMR solution phase data for SARS-CoV-2 s2m and provides a comparative analysis with its counterpart SARS-CoV s2m. We employed initial coordinates based on PDB ID 1XJR for SARS-CoV s2m and two models for SARS-CoV-2 s2m: one based on 1XJR in which we introduced the mutations present in SARS-CoV-2 s2m and the second based on the available SARS-CoV-2 NMR NOE data supplemented with knowledge-based methods. For each of the three systems, 3.5 μs molecular dynamics simulations were used to sample the structure and dynamics, and principal component analysis (PCA) reduced the ensembles to hierarchal conformational substates for detailed analysis. Dilute solution simulations of SARS-CoV s2m demonstrate that the GNRA-like terminal pentaloop is rigidly defined by base stacking uniquely positioned for possible kissing dimer formation. However, the SARS-CoV-2 s2m simulation did not retain the reported crystallographic SARS-CoV motifs and the terminal loop expands to a highly dynamic "nonaloop." Increased flexibility and structural disorganization are observed for the larger terminal loop, where an entropic penalty is computed to explain the experimentally observed reduction in kissing complex formation. Overall, both SARS-CoV and SARS-CoV-2 s2m elements have a similarly pronounced L-shape due to different motif interactions. Our study establishes the atomistic three-dimensional structure and uncovers dynamic differences that arise from s2m sequence changes, which sets the stage for the interrogation of different mechanistic pathways of suspected biological function.
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Affiliation(s)
- Adam H. Kensinger
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania15282, United States
| | - Joseph A. Makowski
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania15282, United States
| | - Kendy A. Pellegrene
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania15282, United States
| | - Joshua A. Imperatore
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania15282, United States
| | - Caylee L. Cunningham
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania15282, United States
| | - Caleb J. Frye
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania15282, United States
| | - Patrick E. Lackey
- Department
of Biochemistry and Chemistry, Westminster
College, New Wilmington, Pennsylvania16172, United States
| | - Mihaela Rita Mihailescu
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania15282, United States
| | - Jeffrey D. Evanseck
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania15282, United States
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9
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Frye CJ, Shine M, Makowski JA, Kensinger AH, Cunningham CL, Milback EJ, Evanseck JD, Lackey PE, Mihailescu MR. Bioinformatics analysis of the s2m mutations within the SARS-CoV-2 Omicron lineages. J Med Virol 2023; 95:e28141. [PMID: 36098272 PMCID: PMC9538174 DOI: 10.1002/jmv.28141] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 01/11/2023]
Affiliation(s)
- Caleb J. Frye
- Department of Chemistry & BiochemistryDuquesne UniversityPittsburghPennsylvaniaUSA
| | - Morgan Shine
- Department of Biochemistry & ChemistryWestminster CollegeNew WilmingtonPennsylvaniaUSA
- Present address:
Morgan Shine, Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenConnecticutUSA
| | - Joseph A. Makowski
- Department of Chemistry & BiochemistryDuquesne UniversityPittsburghPennsylvaniaUSA
| | - Adam H. Kensinger
- Department of Chemistry & BiochemistryDuquesne UniversityPittsburghPennsylvaniaUSA
| | - Caylee L. Cunningham
- Department of Chemistry & BiochemistryDuquesne UniversityPittsburghPennsylvaniaUSA
| | - Ella J. Milback
- Department of Chemistry & BiochemistryDuquesne UniversityPittsburghPennsylvaniaUSA
| | - Jeffrey D. Evanseck
- Department of Chemistry & BiochemistryDuquesne UniversityPittsburghPennsylvaniaUSA
| | - Patrick E. Lackey
- Department of Biochemistry & ChemistryWestminster CollegeNew WilmingtonPennsylvaniaUSA
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10
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Host tRNA-Derived RNAs Target the 3'Untranslated Region of SARS-CoV-2. Pathogens 2022; 11:pathogens11121479. [PMID: 36558813 PMCID: PMC9786188 DOI: 10.3390/pathogens11121479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/25/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic revealed a need for new understanding of the mechanisms regulating host-pathogen interactions during viral infection. Transfer RNA-derived RNAs (tDRs), previously called transfer RNA fragments (tRFs), have recently emerged as potential regulators of viral pathogenesis. Many predictive studies using bioinformatic approaches have been conducted providing a repertoire of potential small RNA candidates for further analyses; however, few targets have been validated to directly bind to SARS-CoV-2 sequences. In this study, we used available data sets to identify host tDR expression altered in response to SARS-CoV-2 infection. RNA-interaction-prediction tools were used to identify sequences in the SARS-CoV-2 genome where tDRs could potentially bind. We then developed luciferase assays to confirm direct regulation through a predicted region of SARS-CoV-2 by tDRs. We found that two tDRs were downregulated in both clinical and in vitro cell culture studies of SARS-CoV-2 infection. Binding sites for these two tDRs were present in the 3' untranslated region (3'UTR) of the SARS-CoV-2 reference virus and both sites were altered in Variants of Concern (VOCs) that emerged later in the pandemic. These studies directly confirm the binding of human tDRs to a specific region of the 3'UTR of SARS-CoV-2 providing evidence for a novel mechanism for host-pathogen regulation.
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11
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Lessons Learned and Yet-to-Be Learned on the Importance of RNA Structure in SARS-CoV-2 Replication. Microbiol Mol Biol Rev 2022; 86:e0005721. [PMID: 35862724 PMCID: PMC9491204 DOI: 10.1128/mmbr.00057-21] [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] [Indexed: 11/30/2022] Open
Abstract
SARS-CoV-2, the etiological agent responsible for the COVID-19 pandemic, is a member of the virus family Coronaviridae, known for relatively extensive (~30-kb) RNA genomes that not only encode for numerous proteins but are also capable of forming elaborate structures. As highlighted in this review, these structures perform critical functions in various steps of the viral life cycle, ultimately impacting pathogenesis and transmissibility. We examine these elements in the context of coronavirus evolutionary history and future directions for curbing the spread of SARS-CoV-2 and other potential human coronaviruses. While we focus on structures supported by a variety of biochemical, biophysical, and/or computational methods, we also touch here on recent evidence for novel structures in both protein-coding and noncoding regions of the genome, including an assessment of the potential role for RNA structure in the controversial finding of SARS-CoV-2 integration in “long COVID” patients. This review aims to serve as a consolidation of previous works on coronavirus and more recent investigation of SARS-CoV-2, emphasizing the need for improved understanding of the role of RNA structure in the evolution and adaptation of these human viruses.
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12
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Janowski AB, Jiang H, Fujii C, Owen MC, Bricker TL, Darling TL, Harastani HH, Seehra K, Tahan S, Jung A, Febles B, Blatter JA, Handley SA, Parikh BA, Lulla V, Boon AC, Wang D. The highly conserved stem-loop II motif is important for the lifecycle of astroviruses but dispensable for SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.04.30.486882. [PMID: 35547847 PMCID: PMC9094099 DOI: 10.1101/2022.04.30.486882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The stem-loop II motif (s2m) is an RNA element present in viruses from divergent viral families, including astroviruses and coronaviruses, but its functional significance is unknown. We created deletions or substitutions of the s2m in astrovirus VA1 (VA1), classic human astrovirus 1 (HAstV1) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). For VA1, recombinant virus could not be rescued upon partial deletion of the s2m or substitutions of G-C base pairs. Compensatory substitutions that restored the G-C base-pair enabled recovery of VA1. For HAstV1, a partial deletion of the s2m resulted in decreased viral titers compared to wild-type virus, and reduced activity in a replicon system. In contrast, deletion or mutation of the SARS-CoV-2 s2m had no effect on the ability to rescue the virus, growth in vitro , or growth in Syrian hamsters. Our study demonstrates the importance of the s2m is virus-dependent.
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13
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Li J, Sczepanski JT. Targeting a conserved structural element from the SARS-CoV-2 genome using l-DNA aptamers. RSC Chem Biol 2022; 3:79-84. [PMID: 35128411 PMCID: PMC8729173 DOI: 10.1039/d1cb00172h] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/19/2021] [Indexed: 01/20/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, has resulted in an ongoing global pandemic that has already claimed more than 4 million lives. While most antiviral efforts have focused on essential SARS-CoV-2 proteins, RNA structural elements within the viral genome are also compelling targets. In this study, we identified high-affinity l-DNA aptamers against a SARS-CoV-2 stem-loop II-like motif (s2m), a highly conserved RNA structure with promising diagnostic and therapeutic potential. Optimized l-C1t and l-C3t aptamers bind selectively to s2m RNA with K d values in the nanomolar range, and are capable of differentiating the monomeric s2m stem-loop from the proposed homodimer duplex. This structure-specific mode of recognition also allows l-C1t and l-C3t to discriminate between s2m RNAs from SARS-CoV-2 and SARS-CoV-1, which differ by just two nucleotides. Finally, we show that l-C1t and l-C3t induce dramatic conformational changes in s2m structure upon binding, and thus, have the potential to block protein-s2m interactions. Overall, these results demonstrate the feasibility of targeting SARS-CoV-2 RNA using l-aptamers, which has important implications in the diagnosis and treatment of COVID-19. Moreover, the high affinity and selectivity of l-C1t and l-C3t, coupled with the intrinsic nuclease resistance of l-DNA, present an opportunity for generating new tools and probes for interrogating s2m function in SARS-CoV-2 and related viruses.
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Affiliation(s)
- Jing Li
- Department of Chemistry, Texas A&M University College Station TX USA
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14
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Dantsu Y, Zhang Y, Zhang W. Advances in Therapeutic L-Nucleosides and L-Nucleic Acids with Unusual Handedness. Genes (Basel) 2021; 13:46. [PMID: 35052385 PMCID: PMC8774879 DOI: 10.3390/genes13010046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 12/19/2022] Open
Abstract
Nucleic-acid-based small molecule and oligonucleotide therapies are attractive topics due to their potential for effective target of disease-related modules and specific control of disease gene expression. As the non-naturally occurring biomolecules, modified DNA/RNA nucleoside and oligonucleotide analogues composed of L-(deoxy)riboses, have been designed and applied as innovative therapeutics with superior plasma stability, weakened cytotoxicity, and inexistent immunogenicity. Although all the chiral centers in the backbone are mirror converted from the natural D-nucleic acids, L-nucleic acids are equipped with the same nucleobases (A, G, C and U or T), which are critical to maintain the programmability and form adaptable tertiary structures for target binding. The types of L-nucleic acid drugs are increasingly varied, from chemically modified nucleoside analogues that interact with pathogenic polymerases to nanoparticles containing hundreds of repeating L-nucleotides that circulate durably in vivo. This article mainly reviews three different aspects of L-nucleic acid therapies, including pharmacological L-nucleosides, Spiegelmers as specific target-binding aptamers, and L-nanostructures as effective drug-delivery devices.
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Affiliation(s)
- Yuliya Dantsu
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA; (Y.D.); (Y.Z.)
| | - Ying Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA; (Y.D.); (Y.Z.)
| | - Wen Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA; (Y.D.); (Y.Z.)
- Melvin and Bren Simon Cancer Center, 535 Barnhill Drive, Indianapolis, IN 46202, USA
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15
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Zhang Y, Jin X, Wang H, Miao Y, Yang X, Jiang W, Yin B. Compelling Evidence Suggesting the Codon Usage of SARS-CoV-2 Adapts to Human After the Split From RaTG13. Evol Bioinform Online 2021; 17:11769343211052013. [PMID: 34646060 PMCID: PMC8504689 DOI: 10.1177/11769343211052013] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/17/2021] [Indexed: 11/17/2022] Open
Abstract
SARS-CoV-2 needs to efficiently make use of the resources from hosts in order to survive and propagate. Among the multiple layers of regulatory network, mRNA translation is the rate-limiting step in gene expression. Synonymous codon usage usually conforms with tRNA concentration to allow fast decoding during translation. It is acknowledged that SARS-CoV-2 has adapted to the codon usage of human lungs so that the virus could rapidly proliferate in the lung environment. While this notion seems to nicely explain the adaptation of SARS-CoV-2 to lungs, it is unable to tell why other viruses do not have this advantage. In this study, we retrieve the GTEx RNA-seq data for 30 tissues (belonging to over 17 000 individuals). We calculate the RSCU (relative synonymous codon usage) weighted by gene expression in each human sample, and investigate the correlation of RSCU between the human tissues and SARS-CoV-2 or RaTG13 (the closest coronavirus to SARS-CoV-2). Lung has the highest correlation of RSCU to SARS-CoV-2 among all tissues, suggesting that the lung environment is generally suitable for SARS-CoV-2. Interestingly, for most tissues, SARS-CoV-2 has higher correlations with the human samples compared with the RaTG13-human correlation. This difference is most significant for lungs. In conclusion, the codon usage of SARS-CoV-2 has adapted to human lungs to allow fast decoding and translation. This adaptation probably took place after SARS-CoV-2 split from RaTG13 because RaTG13 is less perfectly correlated with human. This finding depicts the trajectory of adaptive evolution from ancestral sequence to SARS-CoV-2, and also well explains why SARS-CoV-2 rather than other viruses could perfectly adapt to human lung environment.
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Affiliation(s)
- Yanping Zhang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, Shandong, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
| | - Xiaojie Jin
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, Shandong, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
| | - Haiyan Wang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, Shandong, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
| | - Yaoyao Miao
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, Shandong, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
| | - Xiaoping Yang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, Shandong, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
| | - Wenqing Jiang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, Shandong, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
| | - Bin Yin
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, Shandong, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
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