1
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Li Y, Zhang L, Wang L, Li J, Zhao Y, Liu F, Wang Q. Structure and function of type IV IRES in picornaviruses: a systematic review. Front Microbiol 2024; 15:1415698. [PMID: 38855772 PMCID: PMC11157119 DOI: 10.3389/fmicb.2024.1415698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/13/2024] [Indexed: 06/11/2024] Open
Abstract
The Picornaviridae is a family of icosahedral viruses with single-stranded, highly diverse positive-sense RNA genomes. Virions consist of a capsid, without envelope, surrounding a core of RNA genome. A typical genome of picornavirus harbors a well-conserved and highly structured RNA element known as the internal ribosome entry site (IRES), functionally essential for viral replication and protein translation. Based on differences in their structures and mechanisms of action, picornaviral IRESs have been categorized into five types: type I, II, III, IV, and V. Compared with the type IV IRES, the others not only are structurally complicated, but also involve multiple initiation factors for triggering protein translation. The type IV IRES, often referred to as hepatitis C virus (HCV)-like IRES due to its structural resemblance to the HCV IRES, exhibits a simpler and more compact structure than those of the other four. The increasing identification of picornaviruses with the type IV IRES suggests that this IRES type seems to reveal strong retention and adaptation in terms of viral evolution. Here, we systematically reviewed structural features and biological functions of the type IV IRES in picornaviruses. A comprehensive understanding of the roles of type IV IRESs will contribute to elucidating the replication mechanism and pathogenesis of picornaviruses.
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Affiliation(s)
- Yan Li
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
- Qingdao Center for Animal Disease Control and Prevention, Qingdao, China
| | - Lei Zhang
- Shandong New Hope Liuhe Group Co., Ltd., Qingdao, China
| | - Ling Wang
- University Hospital, Qingdao Agricultural University, Qingdao, China
| | - Jing Li
- Market Supervision Administration of Huangdao District, Qingdao, China
| | - Yanwei Zhao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Qianqian Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
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2
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Zagotta WN, Sim BS, Nhim AK, Raza MM, Evans EG, Venkatesh Y, Jones CM, Mehl RA, Petersson EJ, Gordon SE. An improved fluorescent noncanonical amino acid for measuring conformational distributions using time-resolved transition metal ion FRET. eLife 2021; 10:e70236. [PMID: 34623258 PMCID: PMC8500717 DOI: 10.7554/elife.70236] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/09/2021] [Indexed: 11/30/2022] Open
Abstract
With the recent explosion in high-resolution protein structures, one of the next frontiers in biology is elucidating the mechanisms by which conformational rearrangements in proteins are regulated to meet the needs of cells under changing conditions. Rigorously measuring protein energetics and dynamics requires the development of new methods that can resolve structural heterogeneity and conformational distributions. We have previously developed steady-state transition metal ion fluorescence resonance energy transfer (tmFRET) approaches using a fluorescent noncanonical amino acid donor (Anap) and transition metal ion acceptor to probe conformational rearrangements in soluble and membrane proteins. Here, we show that the fluorescent noncanonical amino acid Acd has superior photophysical properties that extend its utility as a donor for tmFRET. Using maltose-binding protein (MBP) expressed in mammalian cells as a model system, we show that Acd is comparable to Anap in steady-state tmFRET experiments and that its long, single-exponential lifetime is better suited for probing conformational distributions using time-resolved FRET. These experiments reveal differences in heterogeneity in the apo and holo conformational states of MBP and produce accurate quantification of the distributions among apo and holo conformational states at subsaturating maltose concentrations. Our new approach using Acd for time-resolved tmFRET sets the stage for measuring the energetics of conformational rearrangements in soluble and membrane proteins in near-native conditions.
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Affiliation(s)
- William N Zagotta
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Brandon S Sim
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Anthony K Nhim
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Marium M Raza
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Eric Gb Evans
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Yarra Venkatesh
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States
| | - Chloe M Jones
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, United States
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States
| | - Sharona E Gordon
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
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3
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Hepatitis C Virus Translation Regulation. Int J Mol Sci 2020; 21:ijms21072328. [PMID: 32230899 PMCID: PMC7178104 DOI: 10.3390/ijms21072328] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/18/2020] [Accepted: 03/25/2020] [Indexed: 12/12/2022] Open
Abstract
Translation of the hepatitis C virus (HCV) RNA genome is regulated by the internal ribosome entry site (IRES), located in the 5’-untranslated region (5′UTR) and part of the core protein coding sequence, and by the 3′UTR. The 5′UTR has some highly conserved structural regions, while others can assume different conformations. The IRES can bind to the ribosomal 40S subunit with high affinity without any other factors. Nevertheless, IRES activity is modulated by additional cis sequences in the viral genome, including the 3′UTR and the cis-acting replication element (CRE). Canonical translation initiation factors (eIFs) are involved in HCV translation initiation, including eIF3, eIF2, eIF1A, eIF5, and eIF5B. Alternatively, under stress conditions and limited eIF2-Met-tRNAiMet availability, alternative initiation factors such as eIF2D, eIF2A, and eIF5B can substitute for eIF2 to allow HCV translation even when cellular mRNA translation is downregulated. In addition, several IRES trans-acting factors (ITAFs) modulate IRES activity by building large networks of RNA-protein and protein–protein interactions, also connecting 5′- and 3′-ends of the viral RNA. Moreover, some ITAFs can act as RNA chaperones that help to position the viral AUG start codon in the ribosomal 40S subunit entry channel. Finally, the liver-specific microRNA-122 (miR-122) stimulates HCV IRES-dependent translation, most likely by stabilizing a certain structure of the IRES that is required for initiation.
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4
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Koirala D, Lewicka A, Koldobskaya Y, Huang H, Piccirilli JA. Synthetic Antibody Binding to a Preorganized RNA Domain of Hepatitis C Virus Internal Ribosome Entry Site Inhibits Translation. ACS Chem Biol 2020; 15:205-216. [PMID: 31765566 DOI: 10.1021/acschembio.9b00785] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Structured RNA elements within the internal ribosome entry site (IRES) of hepatitis C virus (HCV) genome hijack host cell machinery for translation initiation through a cap-independent mechanism. Here, using a phage display selection, we obtained two antibody fragments (Fabs), HCV2 and HCV3, against HCV IRES that bind the RNA with dissociation constants of 32 ± 7 nM and 37 ± 8 nM respectively, specifically recognizing the so-called junction IIIabc (JIIIabc). We used these Fabs as crystallization chaperones and determined the high-resolution crystal structures of JIIIabc-HCV2 and -HCV3 complexes at 1.81 Å and 2.75 Å resolution respectively, revealing an antiparallel four-way junction with the IIIa and IIIc subdomains brought together through tertiary interactions. The RNA conformation observed in the structures supports the structural model for this region derived from cryo-EM data for the HCV IRES-40S ribosome complex, suggesting that the tertiary fold of the RNA preorganizes the domain for interactions with the 40S ribosome. Strikingly, both Fabs and the ribosomal protein eS27 not only interact with a common subset of nucleotides within the JIIIabc but also use physiochemically similar sets of protein residues to do so, suggesting that the RNA surface is well-suited for interactions with proteins, perhaps analogous to the "hot spot" concept elaborated for protein-protein interactions. Using a rabbit reticulocyte lysate-based translation assay with a bicistronic reporter construct, we further demonstrated that Fabs HCV2 and HCV3 specifically inhibit the HCV IRES-directed translation, implicating disruption of the JIIIabc-ribosome interaction as a potential therapeutic strategy against HCV.
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Affiliation(s)
- Deepak Koirala
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Anna Lewicka
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Yelena Koldobskaya
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Hao Huang
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Joseph A. Piccirilli
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
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5
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Bonilla S, Limouse C, Bisaria N, Gebala M, Mabuchi H, Herschlag D. Single-Molecule Fluorescence Reveals Commonalities and Distinctions among Natural and in Vitro-Selected RNA Tertiary Motifs in a Multistep Folding Pathway. J Am Chem Soc 2017; 139:18576-18589. [PMID: 29185740 PMCID: PMC5748328 DOI: 10.1021/jacs.7b08870] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
Decades
of study of the RNA folding problem have revealed that
diverse and complex structured RNAs are built from a common set of
recurring structural motifs, leading to the perspective that a generalizable
model of RNA folding may be developed from understanding of the folding
properties of individual structural motifs. We used single-molecule
fluorescence to dissect the kinetic and thermodynamic properties of
a set of variants of a common tertiary structural motif, the tetraloop/tetraloop-receptor
(TL/TLR). Our results revealed a multistep TL/TLR folding pathway
in which preorganization of the ubiquitous AA-platform submotif precedes
the formation of the docking transition state and tertiary A-minor
hydrogen bond interactions form after the docking transition state.
Differences in ion dependences between TL/TLR variants indicated the
occurrence of sequence-dependent conformational rearrangements prior
to and after the formation of the docking transition state. Nevertheless,
varying the junction connecting the TL/TLR produced a common kinetic
and ionic effect for all variants, suggesting that the global conformational
search and compaction electrostatics are energetically independent
from the formation of the tertiary motif contacts. We also found that in vitro-selected variants, despite their similar stability
at high Mg2+ concentrations, are considerably less stable
than natural variants under near-physiological ionic conditions, and
the occurrence of the TL/TLR sequence variants in Nature correlates
with their thermodynamic stability in isolation. Overall, our findings
are consistent with modular but complex energetic properties of RNA
structural motifs and will aid in the eventual quantitative description
of RNA folding from its secondary and tertiary structural elements.
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Affiliation(s)
- Steve Bonilla
- Department of Chemical Engineering, ‡Department of Applied Physics, §Department of Biochemistry, ∥Department of Chemistry, ⊥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Charles Limouse
- Department of Chemical Engineering, ‡Department of Applied Physics, §Department of Biochemistry, ∥Department of Chemistry, ⊥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Namita Bisaria
- Department of Chemical Engineering, ‡Department of Applied Physics, §Department of Biochemistry, ∥Department of Chemistry, ⊥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Magdalena Gebala
- Department of Chemical Engineering, ‡Department of Applied Physics, §Department of Biochemistry, ∥Department of Chemistry, ⊥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Hideo Mabuchi
- Department of Chemical Engineering, ‡Department of Applied Physics, §Department of Biochemistry, ∥Department of Chemistry, ⊥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Daniel Herschlag
- Department of Chemical Engineering, ‡Department of Applied Physics, §Department of Biochemistry, ∥Department of Chemistry, ⊥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
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6
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Lozano G, Jimenez-Aparicio R, Herrero S, Martinez-Salas E. Fingerprinting the junctions of RNA structure by an open-paddlewheel diruthenium compound. RNA (NEW YORK, N.Y.) 2016; 22:330-8. [PMID: 26759454 PMCID: PMC4748811 DOI: 10.1261/rna.054353.115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/05/2015] [Indexed: 05/17/2023]
Abstract
RNA function is determined by its structural organization. The RNA structure consists of the combination of distinct secondary structure motifs connected by junctions that play an essential role in RNA folding. Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) probing is an established methodology to analyze the secondary structure of long RNA molecules in solution, which provides accurate data about unpaired nucleotides. However, the residues located at the junctions of RNA structures usually remain undetected. Here we report an RNA probing method based on the use of a novel open-paddlewheel diruthenium (OPW-Ru) compound [Ru2Cl2(µ-DPhF)3(DMSO)] (DPhF = N,N'-diphenylformamidinate). This compound has four potential coordination sites in a singular disposition to establish covalent bonds with substrates. As a proof of concept, we have analyzed the reactivity of OPW-Ru toward RNA using two viral internal ribosome entry site (IRES) elements whose function depends on the structural organization of the molecule. Our study suggests that the compound OPW-Ru preferentially attacks at positions located one or two nucleotides away from junctions or bulges of the RNA structure. The OPW-Ru fingerprinting data differ from that obtained by other chemical reagents and provides new information about RNA structure features.
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Affiliation(s)
- Gloria Lozano
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid 28049, Spain
| | - Reyes Jimenez-Aparicio
- Departamento de Química Inorgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Santiago Herrero
- Departamento de Química Inorgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid 28040, Spain
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7
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Lozano G, Fernandez N, Martinez-Salas E. Modeling Three-Dimensional Structural Motifs of Viral IRES. J Mol Biol 2016; 428:767-776. [PMID: 26778619 DOI: 10.1016/j.jmb.2016.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 01/08/2016] [Accepted: 01/08/2016] [Indexed: 01/23/2023]
Abstract
RNA virus genomes are reservoirs of a wide diversity of RNA structural elements. In particular, specific regions of the viral genome have evolved to adopt specialized three-dimensional (3D) structures, which can act in concert with host factors and/or viral proteins to recruit the translation machinery on viral RNA using a mechanism that is independent on the 5' end. This strategy relies on cis-acting RNA sequences designated as internal ribosome entry site (IRES) elements. IRES elements that are found in the genome of different groups of RNA viruses perform the same function despite differing in primary sequence and secondary RNA structure and host factor requirement to recruit the translation machinery internally. Evolutionarily conserved motifs tend to preserve sequences in each group of RNA viruses impacting on RNA structure and RNA-protein interactions important for IRES function. However, due to the lack of sequence homology among genetically distant IRES elements, accurate modeling of 3D IRES structure is currently a challenging task. In addition, as a universal RNA motif unique to IRES elements has not been found, a better understanding of viral IRES structural motifs could greatly assist in the detection of IRES-like motifs hidden in genome sequences. The focus of this review is to describe recent advances in modeling viral IRES tertiary structural motifs and also novel approaches to detect sequences potentially folding as IRES-like motifs.
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Affiliation(s)
- Gloria Lozano
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas Universidad Autónoma de Madrid, Nicolas Cabrera 1, 28049 Madrid, Spain
| | - Noemi Fernandez
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas Universidad Autónoma de Madrid, Nicolas Cabrera 1, 28049 Madrid, Spain
| | - Encarnacion Martinez-Salas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas Universidad Autónoma de Madrid, Nicolas Cabrera 1, 28049 Madrid, Spain.
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8
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Quade N, Boehringer D, Leibundgut M, van den Heuvel J, Ban N. Cryo-EM structure of Hepatitis C virus IRES bound to the human ribosome at 3.9-Å resolution. Nat Commun 2015; 6:7646. [PMID: 26155016 PMCID: PMC4510694 DOI: 10.1038/ncomms8646] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 05/27/2015] [Indexed: 01/10/2023] Open
Abstract
Hepatitis C virus (HCV), a widespread human pathogen, is dependent on a highly structured 5'-untranslated region of its mRNA, referred to as internal ribosome entry site (IRES), for the translation of all of its proteins. The HCV IRES initiates translation by directly binding to the small ribosomal subunit (40S), circumventing the need for many eukaryotic translation initiation factors required for mRNA scanning. Here we present the cryo-EM structure of the human 40S ribosomal subunit in complex with the HCV IRES at 3.9 Å resolution, determined by focused refinement of an 80S ribosome-HCV IRES complex. The structure reveals the molecular details of the interactions between the IRES and the 40S, showing that expansion segment 7 (ES7) of the 18S rRNA acts as a central anchor point for the HCV IRES. The structural data rationalizes previous biochemical and genetic evidence regarding the initiation mechanism of the HCV and other related IRESs.
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Affiliation(s)
- Nick Quade
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zürich, Zürich 8093, Switzerland
| | - Daniel Boehringer
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zürich, Zürich 8093, Switzerland
| | - Marc Leibundgut
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zürich, Zürich 8093, Switzerland
| | - Joop van den Heuvel
- Research Group Recombinant Protein Expression, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig 38124, Germany
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zürich, Zürich 8093, Switzerland
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9
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Khawaja A, Vopalensky V, Pospisek M. Understanding the potential of hepatitis C virus internal ribosome entry site domains to modulate translation initiation via their structure and function. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:211-24. [PMID: 25352252 PMCID: PMC4361049 DOI: 10.1002/wrna.1268] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Revised: 08/31/2014] [Accepted: 09/02/2014] [Indexed: 12/16/2022]
Abstract
Translation initiation in the hepatitis C virus (HCV) occurs through a cap-independent mechanism that involves an internal ribosome entry site (IRES) capable of interacting with and utilizing the eukaryotic translational machinery. In this review, we focus on the structural configuration of the different HCV IRES domains and the impact of IRES primary sequence variations on secondary structure conservation and function. In some cases, multiple mutations, even those scattered across different domains, led to restoration of the translational activity of the HCV IRES, although the individual occurrences of these mutations were found to be deleterious. We propose that such observation may be attributed to probable long-range inter- and/or intra-domain functional interactions. The precise functioning of the HCV IRES requires the specific interaction of its domains with ribosomal subunits and a subset of eukaryotic translation initiation factors (eIFs). The structural conformation, sequence preservation and variability, and translational machinery association with the HCV IRES regions are also thoroughly discussed, along with other factors that can affect and influence the formation of translation initiation complexes. WIREs RNA 2015, 6:211–224. doi: 10.1002/wrna.1268
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Affiliation(s)
- Anas Khawaja
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague 2, Czech Republic
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10
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Interconversion between parallel and antiparallel conformations of a 4H RNA junction in domain 3 of foot-and-mouth disease virus IRES captured by dynamics simulations. Biophys J 2014; 106:447-58. [PMID: 24461020 DOI: 10.1016/j.bpj.2013.12.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 11/23/2013] [Accepted: 12/03/2013] [Indexed: 01/31/2023] Open
Abstract
RNA junctions are common secondary structural elements present in a wide range of RNA species. They play crucial roles in directing the overall folding of RNA molecules as well as in a variety of biological functions. In particular, there has been great interest in the dynamics of RNA junctions, including conformational pathways of fully base-paired 4-way (4H) RNA junctions. In such constructs, all nucleotides participate in one of the four double-stranded stem regions, with no connecting loops. Dynamical aspects of these 4H RNAs are interesting because frequent interchanges between parallel and antiparallel conformations are thought to occur without binding of other factors. Gel electrophoresis and single-molecule fluorescence resonance energy transfer experiments have suggested two possible pathways: one involves a helical rearrangement via disruption of coaxial stacking, and the other occurs by a rotation between the helical axes of coaxially stacked conformers. Employing molecular dynamics simulations, we explore this conformational variability in a 4H junction derived from domain 3 of the foot-and-mouth disease virus internal ribosome entry site (IRES); this junction contains highly conserved motifs for RNA-RNA and RNA-protein interactions, important for IRES activity. Our simulations capture transitions of the 4H junction between parallel and antiparallel conformations. The interconversion is virtually barrier-free and occurs via a rotation between the axes of coaxially stacked helices with a transient perpendicular intermediate. We characterize this transition, with various interhelical orientations, by pseudodihedral angle and interhelical distance measures. The high flexibility of the junction, as also demonstrated experimentally, is suitable for IRES activity. Because foot-and-mouth disease virus IRES structure depends on long-range interactions involving domain 3, the perpendicular intermediate, which maintains coaxial stacking of helices and thereby consensus primary and secondary structure information, may be beneficial for guiding the overall organization of the RNA system in domain 3.
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11
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Abstract
RNA dynamics play a fundamental role in many cellular functions. However, there is no general framework to describe these complex processes, which typically consist of many structural maneuvers that occur over timescales ranging from picoseconds to seconds. Here, we classify RNA dynamics into distinct modes representing transitions between basins on a hierarchical free-energy landscape. These transitions include large-scale secondary-structural transitions at >0.1-s timescales, base-pair/tertiary dynamics at microsecond-to-millisecond timescales, stacking dynamics at timescales ranging from nanoseconds to microseconds, and other "jittering" motions at timescales ranging from picoseconds to nanoseconds. We review various modes within these three different tiers, the different mechanisms by which they are used to regulate function, and how they can be coupled together to achieve greater functional complexity.
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12
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Hepatitis-C-virus-like internal ribosome entry sites displace eIF3 to gain access to the 40S subunit. Nature 2013; 503:539-43. [PMID: 24185006 DOI: 10.1038/nature12658] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 09/13/2013] [Indexed: 12/12/2022]
Abstract
Hepatitis C virus (HCV) and classical swine fever virus (CSFV) messenger RNAs contain related (HCV-like) internal ribosome entry sites (IRESs) that promote 5'-end independent initiation of translation, requiring only a subset of the eukaryotic initiation factors (eIFs) needed for canonical initiation on cellular mRNAs. Initiation on HCV-like IRESs relies on their specific interaction with the 40S subunit, which places the initiation codon into the P site, where it directly base-pairs with eIF2-bound initiator methionyl transfer RNA to form a 48S initiation complex. However, all HCV-like IRESs also specifically interact with eIF3 (refs 2, 5-7, 9-12), but the role of this interaction in IRES-mediated initiation has remained unknown. During canonical initiation, eIF3 binds to the 40S subunit as a component of the 43S pre-initiation complex, and comparison of the ribosomal positions of eIF3 and the HCV IRES revealed that they overlap, so that their rearrangement would be required for formation of ribosomal complexes containing both components. Here we present a cryo-electron microscopy reconstruction of a 40S ribosomal complex containing eIF3 and the CSFV IRES. Remarkably, although the position and interactions of the CSFV IRES with the 40S subunit in this complex are similar to those of the HCV IRES in the 40S-IRES binary complex, eIF3 is completely displaced from its ribosomal position in the 43S complex, and instead interacts through its ribosome-binding surface exclusively with the apical region of domain III of the IRES. Our results suggest a role for the specific interaction of HCV-like IRESs with eIF3 in preventing ribosomal association of eIF3, which could serve two purposes: relieving the competition between the IRES and eIF3 for a common binding site on the 40S subunit, and reducing formation of 43S complexes, thereby favouring translation of viral mRNAs.
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13
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Structure of the full-length HCV IRES in solution. Nat Commun 2013; 4:1612. [PMID: 23511476 DOI: 10.1038/ncomms2611] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 02/15/2013] [Indexed: 01/04/2023] Open
Abstract
The 5'-untranslated region of the hepatitis C virus genome contains an internal ribosome entry site (IRES) that initiates cap-independent translation of the viral RNA. Until now, the structural characterization of the entire (IRES) remained limited to cryo-electron microscopy reconstructions of the (IRES) bound to different cellular partners. Here we report an atomic model of free full-length hepatitis C virus (IRES) refined by selection against small-angle X-ray scattering data that incorporates the known structures of different fragments. We found that an ensemble of conformers reproduces small-angle X-ray scattering data better than a single structure suggesting in combination with molecular dynamics simulations that the hepatitis C virus (IRES) is an articulated molecule made of rigid parts that move relative to each other. Principal component analysis on an ensemble of physically accessible conformers of hepatitis C virus (IRES) revealed dominant collective motions in the molecule, which may underlie the conformational changes occurring in the (IRES) molecule upon formation of the initiation complex.
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14
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Berry KE, Waghray S, Mortimer SA, Bai Y, Doudna JA. Crystal structure of the HCV IRES central domain reveals strategy for start-codon positioning. Structure 2012; 19:1456-66. [PMID: 22000514 DOI: 10.1016/j.str.2011.08.002] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 07/29/2011] [Accepted: 08/02/2011] [Indexed: 01/11/2023]
Abstract
Translation of hepatitis C viral proteins requires an internal ribosome entry site (IRES) located in the 5' untranslated region of the viral mRNA. The core domain of the hepatitis C virus (HCV) IRES contains a four-way helical junction that is integrated within a predicted pseudoknot. This domain is required for positioning the mRNA start codon correctly on the 40S ribosomal subunit during translation initiation. Here, we present the crystal structure of this RNA, revealing a complex double-pseudoknot fold that establishes the alignment of two helical elements on either side of the four-helix junction. The conformation of this core domain constrains the open reading frame's orientation for positioning on the 40S ribosomal subunit. This structure, representing the last major domain of HCV-like IRESs to be determined at near-atomic resolution, provides the basis for a comprehensive cryoelectron microscopy-guided model of the intact HCV IRES and its interaction with 40S ribosomal subunits.
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Affiliation(s)
- Katherine E Berry
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
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15
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Lilley DMJ. Fluorescence Resonance Energy Transfer Studies of Structure and Dynamics in Nucleic Acids. NATO SCIENCE FOR PEACE AND SECURITY SERIES B: PHYSICS AND BIOPHYSICS 2012. [DOI: 10.1007/978-94-007-4923-8_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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16
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Ouellet J, Melcher S, Iqbal A, Ding Y, Lilley DMJ. Structure of the three-way helical junction of the hepatitis C virus IRES element. RNA (NEW YORK, N.Y.) 2010; 16:1597-1609. [PMID: 20581129 PMCID: PMC2905758 DOI: 10.1261/rna.2158410] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Accepted: 05/04/2010] [Indexed: 05/29/2023]
Abstract
The hepatitis C virus internal ribosome entry site (IRES) element contains a three-way junction that is important in the overall RNA conformation, and for its role in the internal initiation of translation. The junction also illustrates some important conformational principles in the folding of three-way helical junctions. It is formally a 3HS(4) junction, with the possibility of two alternative stacking conformers. However, in principle, the junction can also undergo two steps of branch migration that would form 2HS(1)HS(3) and 2HS(2)HS(2) junctions. Comparative gel electrophoresis and ensemble fluorescence resonance energy transfer (FRET) studies show that the junction is induced to fold by the presence of Mg(2+) ions in low micromolar concentrations, and suggest that the structure adopted is based on coaxial stacking of the two helices that do not terminate in a hairpin loop (i.e., helix IIId). Single-molecule FRET studies confirm this conclusion, and indicate that there is no minor conformer present based on an alternative choice of helical stacking partners. Moreover, analysis of single-molecule FRET data at an 8-msec resolution failed to reveal evidence for structural transitions. It seems probable that this junction adopts a single conformation as a unique and stable fold.
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Affiliation(s)
- Jonathan Ouellet
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
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17
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Abstract
Comparative gel electrophoresis provides information on the relative angles subtended between helical arms at a branchpoint in RNA. It is based upon the comparison of electrophoretic mobility in polyacrylamide gels of species containing two long arms, with the remaining one(s) being significantly shorter. Although the method currently lacks a really well-established basis of physical theory, it is very powerful, yet simple to apply. It has had a number of significant successes in RNA, DNA and DNA-protein complexes, and in all cases to date the results have stood the test of time and eventual comparison with crystallographic analysis.
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18
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Analysis of four-way junctions in RNA structures. J Mol Biol 2009; 390:547-59. [PMID: 19445952 DOI: 10.1016/j.jmb.2009.04.084] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Revised: 04/21/2009] [Accepted: 04/30/2009] [Indexed: 11/24/2022]
Abstract
RNA secondary structures can be divided into helical regions composed of canonical Watson-Crick and related base pairs, as well as single-stranded regions such as hairpin loops, internal loops, and junctions. These elements function as building blocks in the design of diverse RNA molecules with various fundamental functions in the cell. To better understand the intricate architecture of three-dimensional (3D) RNAs, we analyze existing RNA four-way junctions in terms of base-pair interactions and 3D configurations. Specifically, we identify nine broad junction families according to coaxial stacking patterns and helical configurations. We find that helices within junctions tend to arrange in roughly parallel and perpendicular patterns and stabilize their conformations using common tertiary motifs such as coaxial stacking, loop-helix interaction, and helix packing interaction. Our analysis also reveals a number of highly conserved base-pair interaction patterns and novel tertiary motifs such as A-minor-coaxial stacking combinations and sarcin/ricin motif variants. Such analyses of RNA building blocks can ultimately help in the difficult task of RNA 3D structure prediction.
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19
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Lilley DMJ. The structure and folding of branched RNA analyzed by fluorescence resonance energy transfer. Methods Enzymol 2009; 469:159-87. [PMID: 20946789 DOI: 10.1016/s0076-6879(09)69008-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Fluorescence resonance energy transfer (FRET) is a spectroscopic means of obtaining distance information over a range up to ~80Å in solution. It is based on the dipolar coupling between the electronic transition moments of a donor and acceptor fluorophore attached at known positions on the RNA species of interest. It can be applied in ensembles of molecules, either by steady-state fluorescence or by lifetime measurements, but it is also very appropriate for single-molecule studies. In addition to the provision of distance information, recent studies have emphasized the orientation dependence of energy transfer.
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Affiliation(s)
- David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, United Kingdom
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20
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Abstract
Electrophoresis in polyacrylamide gels provides a simple yet powerful means of analyzing the relative disposition of helical arms in branched nucleic acids. The electrophoretic mobility of DNA or RNA with a central discontinuity is determined by the angle subtended between the arms radiating from the branchpoint. In a multi-helical branchpoint, comparative gel electrophoresis can provide a relative measure of all the inter-helical angles and thus the shape and symmetry of the molecule. Using the long-short arm approach, the electrophoretic mobility of all the species with two helical arms that are longer than all others is compared. This can be done as a function of conditions, allowing the analysis of ion-dependent folding of branched DNA and RNA species. Notable successes for the technique include the four-way (Holliday) junction in DNA and helical junctions in functionally significant RNA species such as ribozymes. Many of these structures have subsequently been proved correct by crystallography or other methods, up to 10 years later in the case of the Holliday junction. Just as important, the technique has not failed to date. Comparative gel electrophoresis can provide a window on both fast and slow conformational equilibria such as conformer exchange in four-way DNA junctions. But perhaps the biggest test of the approach has been to deduce the structures of complexes of four-way DNA junctions with proteins. Two recent crystallographic structures show that the global structures were correctly deduced by electrophoresis, proving the worth of the method even in these rather complex systems. Comparative gel electrophoresis is a robust method for the analysis of branched nucleic acids and their complexes.
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21
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Lukavsky PJ. Structure and function of HCV IRES domains. Virus Res 2008; 139:166-71. [PMID: 18638512 PMCID: PMC2726286 DOI: 10.1016/j.virusres.2008.06.004] [Citation(s) in RCA: 151] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Accepted: 06/11/2008] [Indexed: 12/16/2022]
Abstract
The HCV IRES is a highly structured RNA which mediates cap-independent translation initiation in higher eukaryotes. This function is encoded in conserved structural motifs in the two major domains of HCV and HCV-like IRESs, which play crucial and distinct roles along the initiation pathway. In this review, I discuss structural features of IRES domains and how these RNA motifs function as RNA-based initiation factors to form 48S initiation complexes and 80S ribosomes with only a subset of canonical, protein-based eukaryotic initiation factors.
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Affiliation(s)
- Peter J Lukavsky
- Laboratory of Molecular Biology, MRC, Hills Road, Cambridge CB2 0QH, UK.
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22
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Fraser CS, Doudna JA. Structural and mechanistic insights into hepatitis C viral translation initiation. Nat Rev Microbiol 2006; 5:29-38. [PMID: 17128284 DOI: 10.1038/nrmicro1558] [Citation(s) in RCA: 159] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hepatitis C virus uses an internal ribosome entry site (IRES) to control viral protein synthesis by directly recruiting ribosomes to the translation-start site in the viral mRNA. Structural insights coupled with biochemical studies have revealed that the IRES substitutes for the activities of translation-initiation factors by binding and inducing conformational changes in the 40S ribosomal subunit. Direct interactions of the IRES with initiation factor eIF3 are also crucial for efficient translation initiation, providing clues to the role of eIF3 in protein synthesis.
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Affiliation(s)
- Christopher S Fraser
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA
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Boehringer D, Thermann R, Ostareck-Lederer A, Lewis JD, Stark H. Structure of the Hepatitis C Virus IRES Bound to the Human 80S Ribosome: Remodeling of the HCV IRES. Structure 2005; 13:1695-706. [PMID: 16271893 DOI: 10.1016/j.str.2005.08.008] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Revised: 07/29/2005] [Accepted: 08/09/2005] [Indexed: 02/05/2023]
Abstract
Initiation of translation of the hepatitis C virus (HCV) polyprotein is driven by an internal ribosome entry site (IRES) RNA that bypasses much of the eukaryotic translation initiation machinery. Here, single-particle electron cryomicroscopy has been used to study the mechanism of HCV IRES-mediated initiation. A HeLa in vitro translation system was used to assemble human IRES-80S ribosome complexes under near physiological conditions; these were stalled before elongation. Domain 2 of the HCV IRES is bound to the tRNA exit site, touching the L1 stalk of the 60S subunit, suggesting a mechanism for the removal of the HCV IRES in the progression to elongation. Domain 3 of the HCV IRES positions the initiation codon in the ribosomal mRNA binding cleft by binding helix 28 at the head of the 40S subunit. The comparison with the previously published binary 40S-HCV IRES complex reveals structural rearrangements in the two pseudoknot structures of the HCV IRES in translation initiation.
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Affiliation(s)
- Daniel Boehringer
- Max Planck Institute for Biophysical Chemistry, 3D Electron Cryomicroscopy, Am Fassberg 11, 37077 Göttingen, Germany
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24
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Pisarev AV, Shirokikh NE, Hellen CUT. Translation initiation by factor-independent binding of eukaryotic ribosomes to internal ribosomal entry sites. C R Biol 2005; 328:589-605. [PMID: 15992743 DOI: 10.1016/j.crvi.2005.02.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2005] [Accepted: 02/16/2005] [Indexed: 02/05/2023]
Abstract
Two exceptional mechanisms of eukaryotic translation initiation have recently been identified that differ fundamentally from the canonical factor-mediated, end-dependent mechanism of ribosomal attachment to mRNA. Instead, ribosomal 40S subunits bind in a factor-independent manner to the internal ribosomal entry site (IRES) in an mRNA. These two mechanisms are exemplified by initiation on the unrelated approximately 300 nt.-long Hepatitis C virus (HCV) IRES and the approximately 200 nt.-long cricket paralysis virus (CrPV) intergenic region (IGR) IRES, respectively. Ribosomal binding involves interaction with multiple non-contiguous sites on these IRESs, and therefore also differs from the factor-independent attachment of prokaryotic ribosomes to mRNA, which involves base-pairing to the linear Shine-Dalgarno sequence. The HCV IRES binds to the solvent side of the 40S subunit, docks a domain of the IRES into the ribosomal exit (E) site and places the initiation codon in the ribosomal peptidyl (P) site. Subsequent binding of eIF3 and the eIF2-GTP/initiator tRNA complex to form a 48S complex is followed by subunit joining to form an 80S ribosome. The CrPV IRES binds to ribosomes in a very different manner, by occupying the ribosomal E and P sites in the intersubunit cavity, thereby excluding initiator tRNA. Ribosomes enter the elongation stage of translation directly, without any involvement of initiator tRNA or initiation factors, following recruitment of aminoacyl-tRNA to the ribosomal aminoacyl (A) site and translocation of it to the P site.
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Affiliation(s)
- Andrey V Pisarev
- Department of Microbiology and Immunology, State University of New York, SUNY, 450 Clarkson Ave., Brooklyn, NY 11203, USA
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25
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Turner B, Melcher SE, Wilson TJ, Norman DG, Lilley DMJ. Induced fit of RNA on binding the L7Ae protein to the kink-turn motif. RNA (NEW YORK, N.Y.) 2005; 11:1192-200. [PMID: 15987806 PMCID: PMC1370803 DOI: 10.1261/rna.2680605] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The kink-turn is a widespread motif in RNA consisting of a three-nucleotide bulge flanked on one side by consecutive A3G mismatches. Important examples are found in the ribosome, U4 RNA, and in snoRNAs involved in RNA modification. The motif is a common protein binding site, and the RNA has been found to adopt a tightly kinked conformation in crystal structures. However, in free solution there is a dynamic exchange between kinked and extended conformations, with the equilibrium driven toward the kinked form by the addition of metal ions. Here we used fluorescence resonance energy transfer (FRET) to show that the L7Ae protein of Archaeoglobus fulgidus binds to RNA containing a kink-turn with nanomolar affinity, and induces folding into the tightly kinked conformation even in the absence of metal ions. Thus this RNA may act as a relatively flexible hinge during RNA folding, until fixed into its ultimate kinked structure by the binding of L7 or related protein.
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Affiliation(s)
- Ben Turner
- Cancer Research-UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, UK
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27
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Liu J, Déclais AC, Lilley DMJ. Electrostatic Interactions and the Folding of the Four-way DNA Junction: Analysis by Selective Methyl Phosphonate Substitution. J Mol Biol 2004; 343:851-64. [PMID: 15476805 DOI: 10.1016/j.jmb.2004.08.079] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2004] [Revised: 08/24/2004] [Accepted: 08/25/2004] [Indexed: 11/16/2022]
Abstract
The structure and dynamics of the four-way (Holliday) junction are strongly dependent on the presence of metal ions. In this study, the importance of phosphate charge in and around the point of strand exchange has been explored by selective replacement with electrically neutral methyl phosphonate groups, guided by crystal structures of the junction in the folded, stacked X conformation. Junction conformation has been analysed by comparative gel electrophoresis and fluorescence resonance energy transfer (FRET). Three of sets of phosphate groups on the exchanging strands have been analysed; those at the point of strand exchange and those to their 3' and 5' sides. The exchanging and 3' phosphate groups form a box of negatively charged groups on the minor groove face of the junction, while the 5' phosphate groups face each other on the major groove side, with their proR oxygen atoms directed at one another. The largest effects are observed on substitution of the exchanging phosphate groups; replacement of both groups leads to the loss of the requirement for addition of metal ions to allow junction folding. When the equivalent phosphate groups on the continuous strands were substituted, a proportion of the junction folded into the alternative conformer so as to bring these phosphate groups onto the exchanging strands. These species did not interconvert, and thus this is likely to result from the alternative diasteromeric forms of the methyl phosphonate group. This shows that some of the conformational effects result from more than purely electrostatic interactions. Smaller but significant effects were observed on substitution of the flanking phosphate groups. All methyl phosphonate substitutions at these positions allowed folding to proceed at a reduced concentration of magnesium ions, with double substitutions more effective than single substitutions. Substitution of 5' phosphates resulted in a greater degree of folding at a given ionic concentration compared to the corresponding 3' phosphate substitutions. These results show that the phosphate groups at the point of strand exchange exert the largest electrostatic effect on junction folding, but a number of phosphate groups in the vicinity of the exchange region contribute to the overall effects.
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Affiliation(s)
- Jia Liu
- Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, UK
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Hohng S, Wilson TJ, Tan E, Clegg RM, Lilley DMJ, Ha T. Conformational flexibility of four-way junctions in RNA. J Mol Biol 2004; 336:69-79. [PMID: 14741204 DOI: 10.1016/j.jmb.2003.12.014] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Helical junctions are common architectural features in RNA. They are particularly important in autonomously folding molecules, as exemplified by the hairpin ribozyme. We have used single-molecule fluorescence spectroscopy to study the dynamic properties of the perfect (4H) four-way helical junction derived from the hairpin ribozyme. In the presence of Mg(2+), the junction samples parallel and antiparallel conformations and both stacking conformers, with a bias towards one antiparallel stacking conformer. There is continual interconversion between the forms, such that there are several transitions per second under physiological conditions. Our data suggest that interconversion proceeds via an open intermediate with reduced cation binding in which coaxial stacking between helices is disrupted. The rate of interconversion becomes slower at higher Mg(2+) concentrations, yet the activation barrier decreases under these conditions, indicating that entropic effects are important. Transitions also occur in the presence of Na(+) only; however, the coaxial stacking appears incomplete under these conditions. The polymorphic and dynamic character of the four-way RNA junction provides a source of structural diversity, from which particular conformations required for biological function might be stabilised by additional RNA interactions or protein binding.
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Affiliation(s)
- Sungchul Hohng
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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29
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Goody TA, Melcher SE, Norman DG, Lilley DMJ. The kink-turn motif in RNA is dimorphic, and metal ion-dependent. RNA (NEW YORK, N.Y.) 2004; 10:254-64. [PMID: 14730024 PMCID: PMC1370537 DOI: 10.1261/rna.5176604] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2003] [Accepted: 10/03/2003] [Indexed: 05/19/2023]
Abstract
The kink-turn (K-turn) is a new motif in RNA structure that was identified by examination of the crystal structures of the ribosome. We examined the structural and dynamic properties of this element in free solution. The K-turn RNA exists in a dynamic equilibrium between a tightly kinked conformation and a more open structure similar to a simple bulge bend. The highly kinked form is stabilized by the noncooperative binding of metal ions, but a significant population of the less-kinked form is present even in the presence of relatively high concentrations of divalent metal ions. The conformation of the tightly kinked population is in excellent agreement with that of the K-turn structures observed in the ribosome by crystallography. The end-to-end FRET efficiency of this species agrees closely with that of the ribosomal K-turn, and the direction of the bend measured by comparative gel electrophoresis also corresponds very well. These results show that the tightly kinked conformation of the K-turn requires stabilization by other factors, possibly by protein binding, for example. The K-turn is therefore unlikely to be of itself a primary organizing feature in RNA.
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Affiliation(s)
- Terry A Goody
- Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, The University of Dundee, Dundee DD1 5EH, UK
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