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Nam H, Becette O, LeBlanc RM, Oh D, Case DA, Dayie TK. Deleterious effects of carbon-carbon dipolar coupling on RNA NMR dynamics. JOURNAL OF BIOMOLECULAR NMR 2020; 74:321-331. [PMID: 32363430 DOI: 10.1007/s10858-020-00315-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/18/2020] [Indexed: 06/11/2023]
Abstract
Many regulatory RNAs undergo dynamic exchanges that are crucial for their biological functions and NMR spectroscopy is a versatile tool for monitoring dynamic motions of biomolecules. Meaningful information on biomolecular dynamics requires an accurate measurement of relaxation parameters such as longitudinal (R1) rates, transverse (R2) rates and heteronuclear Overhauser effect (hNOE). However, earlier studies have shown that the large 13C-13C interactions complicate analysis of the carbon relaxation parameters. To investigate the effect of 13C-13C interactions on RNA dynamic studies, we performed relaxation measurements on various RNA samples with different labeling patterns and compared these measurements with the computational simulations. For uniformly labeled samples, contributions of the neighboring carbon to R1 measurements were observed. These contributions increased with increasing magnetic field and overall correlation time ([Formula: see text]) for R1 rates, necessitating more careful analysis for uniformly labeled large RNAs. In addition, the hNOE measurements were also affected by the adjacent carbon nuclei. Unlike R1 rates, R1ρ rates showed relatively good agreement between uniformly- and site-selectively labeled samples, suggesting no dramatic effect from their attached carbon, in agreement with previous observations. Overall, having more accurate rate measurements avoids complex analysis and will be a key for interpreting 13C relaxation rates for molecular motion that can provide valuable insights into cellular molecular recognition events.
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Affiliation(s)
- Hyeyeon Nam
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - Owen Becette
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - Regan M LeBlanc
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Daniel Oh
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Theodore K Dayie
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA.
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Callanan J, Stockdale SR, Shkoporov A, Draper LA, Ross RP, Hill C. RNA Phage Biology in a Metagenomic Era. Viruses 2018; 10:E386. [PMID: 30037084 PMCID: PMC6071253 DOI: 10.3390/v10070386] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 12/22/2022] Open
Abstract
The number of novel bacteriophage sequences has expanded significantly as a result of many metagenomic studies of phage populations in diverse environments. Most of these novel sequences bear little or no homology to existing databases (referred to as the "viral dark matter"). Also, these sequences are primarily derived from DNA-encoded bacteriophages (phages) with few RNA phages included. Despite the rapid advancements in high-throughput sequencing, few studies enrich for RNA viruses, i.e., target viral rather than cellular fraction and/or RNA rather than DNA via a reverse transcriptase step, in an attempt to capture the RNA viruses present in a microbial communities. It is timely to compile existing and relevant information about RNA phages to provide an insight into many of their important biological features, which should aid in sequence-based discovery and in their subsequent annotation. Without comprehensive studies, the biological significance of RNA phages has been largely ignored. Future bacteriophage studies should be adapted to ensure they are properly represented in phageomic studies.
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Affiliation(s)
- Julie Callanan
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland.
- School of Microbiology, University College Cork, Cork, T12 YN60, Ireland.
| | - Stephen R Stockdale
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland.
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, P61 C996, Ireland.
| | - Andrey Shkoporov
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland.
| | - Lorraine A Draper
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland.
- School of Microbiology, University College Cork, Cork, T12 YN60, Ireland.
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland.
- School of Microbiology, University College Cork, Cork, T12 YN60, Ireland.
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, P61 C996, Ireland.
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland.
- School of Microbiology, University College Cork, Cork, T12 YN60, Ireland.
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Methyl NMR spectroscopy: Measurement of dynamics in viral RNA-directed RNA polymerases. Methods 2018; 148:100-114. [PMID: 29857193 DOI: 10.1016/j.ymeth.2018.05.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/22/2018] [Accepted: 05/23/2018] [Indexed: 11/23/2022] Open
Abstract
Measurement of nuclear spin relaxation provides a powerful approach to access information about biomolecular conformational dynamics over several orders of magnitude in timescale. In several cases this knowledge in combination with spatial information from three-dimensional structures yields unique insight into protein stability and the kinetics and thermodynamics of their interactions and function. However, due to intrinsic difficulties in studying large systems using solution state nuclear magnetic resonance (NMR) approaches, until recently these measurements were limited to small-to-medium-sized systems. However, the development of a wide range of novel strategies that allow the selective isotope labeling of methyl groups in proteins have allowed the exploitation of the unique relaxation properties of this spin-system. This has in turn enabled the extension of NMR approaches to high molecular weight proteins including a variety of enzymes and their complexes. Here, we recount our experiences in obtaining assignments of the methyl resonances for two representative members of a class of RNA-directed RNA polymerases (RdRps) encoded by bacteriophages of the Cystoviridae family. We demonstrate the utility of these methyl probes, limited in number for one case and more numerous for the other, to investigate the conformational dynamics of RdRps on the fast (ps-ns) and slow (μs-ms) timescales.
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Alphonse S, Itin B, Khayat R, Ghose R. Sequential Protein Expression and Capsid Assembly in Cell: Toward the Study of Multiprotein Viral Capsids Using Solid-State Nuclear Magnetic Resonance Techniques. Biochemistry 2018; 57:1568-1571. [PMID: 29465229 DOI: 10.1021/acs.biochem.8b00003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
While solid-state nuclear magnetic resonance (ssNMR) has emerged as a powerful technique for studying viral capsids, current studies are limited to capsids formed from single proteins or single polyproteins. The ability to selectively label individual protein components within multiprotein viral capsids and the resulting spectral simplification will facilitate the extension of ssNMR techniques to complex viruses. In vitro capsid assembly by combining individually purified, labeled, and unlabeled components in NMR quantities is not a viable option for most viruses. To overcome this barrier, we present a method that utilizes sequential protein expression and in cell assembly of component-specifically labeled viral capsids in amounts suitable for NMR studies. We apply this approach to purify capsids of bacteriophage ϕ6 isotopically labeled on only one of its four constituent protein components, the NTPase P4. Using P4-labeled ϕ6 capsids and the sensitivity enhancement provided by dynamic nuclear polarization, we illustrate the utility of this method to enable ssNMR studies of complex viruses.
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Affiliation(s)
- Sébastien Alphonse
- Department of Chemistry and Biochemistry , The City College of New York , 160 Convent Avenue , New York , New York 10031 , United States
| | - Boris Itin
- New York Structural Biology Center , 89 Convent Avenue , New York , New York 10027 , United States
| | - Reza Khayat
- Department of Chemistry and Biochemistry , The City College of New York , 160 Convent Avenue , New York , New York 10031 , United States.,PhD Programs in Biochemistry and Chemistry , The Graduate Center, City University of New York , New York , New York 10016 , United States
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry , The City College of New York , 160 Convent Avenue , New York , New York 10031 , United States.,PhD Programs in Biochemistry and Chemistry , The Graduate Center, City University of New York , New York , New York 10016 , United States.,PhD Program in Physics , The Graduate Center, City University of New York , New York , New York 10016 , United States
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Affiliation(s)
- Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas, and Universidad Autónoma de Madrid, c/Nicolás Cabrera, 1, Campus de Cantoblanco, 28049 Madrid, Spain.
| | - Raul Andino
- Department of Microbiology and Immunology, University of California at San Francisco, MBGH S572E, Box 2280, 600 16th Street, San Francisco, CA 94158, USA.
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Posthuma CC, Te Velthuis AJW, Snijder EJ. Nidovirus RNA polymerases: Complex enzymes handling exceptional RNA genomes. Virus Res 2017; 234:58-73. [PMID: 28174054 PMCID: PMC7114556 DOI: 10.1016/j.virusres.2017.01.023] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 01/24/2017] [Accepted: 01/26/2017] [Indexed: 12/22/2022]
Abstract
Coronaviruses and arteriviruses are distantly related human and animal pathogens that belong to the order Nidovirales. Nidoviruses are characterized by their polycistronic plus-stranded RNA genome, the production of subgenomic mRNAs and the conservation of a specific array of replicase domains, including key RNA-synthesizing enzymes. Coronaviruses (26-34 kilobases) have the largest known RNA genomes and their replication presumably requires a processive RNA-dependent RNA polymerase (RdRp) and enzymatic functions that suppress the consequences of the typically high error rate of viral RdRps. The arteriviruses have significantly smaller genomes and form an intriguing package with the coronaviruses to analyse viral RdRp evolution and function. The RdRp domain of nidoviruses resides in a cleavage product of the replicase polyprotein named non-structural protein (nsp) 12 in coronaviruses and nsp9 in arteriviruses. In all nidoviruses, the C-terminal RdRp domain is linked to a conserved N-terminal domain, which has been coined NiRAN (nidovirus RdRp-associated nucleotidyl transferase). Although no structural information is available, the functional characterization of the nidovirus RdRp and the larger enzyme complex of which it is part, has progressed significantly over the past decade. In coronaviruses several smaller, non-enzymatic nsps were characterized that direct RdRp function, while a 3'-to-5' exoribonuclease activity in nsp14 was implicated in fidelity. In arteriviruses, the nsp1 subunit was found to maintain the balance between genome replication and subgenomic mRNA production. Understanding RdRp behaviour and interactions during RNA synthesis and subsequent processing will be key to rationalising the evolutionary success of nidoviruses and the development of antiviral strategies.
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Affiliation(s)
- Clara C Posthuma
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Aartjan J W Te Velthuis
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom; Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
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