1
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Gosavi D, Wower I, Beckmann IK, Hofacker IL, Wower J, Wolfinger MT, Sztuba-Solinska J. Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site. RNA Biol 2022; 19:496-506. [PMID: 35380920 PMCID: PMC8986297 DOI: 10.1080/15476286.2022.2058818] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
The internal ribosome entry site (IRES) RNA of bovine viral diarrhoea virus (BVDV), an economically significant Pestivirus, is required for the cap-independent translation of viral genomic RNA. Thus, it is essential for viral replication and pathogenesis. We applied a combination of high-throughput biochemical RNA structure probing (SHAPE-MaP) and in silico modelling approaches to gain insight into the secondary and tertiary structures of BVDV IRES RNA. Our study demonstrated that BVDV IRES RNA in solution forms a modular architecture composed of three distinct structural domains (I-III). Two regions within domain III are represented in tertiary interactions to form an H-type pseudoknot. Computational modelling of the pseudoknot motif provided a fine-grained picture of the tertiary structure and local arrangement of helices in the BVDV IRES. Furthermore, comparative genomics and consensus structure predictions revealed that the pseudoknot is evolutionarily conserved among many Pestivirus species. These studies provide detailed insight into the structural arrangement of BVDV IRES RNA H-type pseudoknot and encompassing motifs that likely contribute to the optimal functionality of viral cap-independent translation element.
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Affiliation(s)
- Devadatta Gosavi
- Department of Biological Sciences, Auburn University, 120 W. Samford Ave, Rouse Life Sciences Building, Auburn, AL, United States
| | - Iwona Wower
- Department of Animal and Dairy Sciences, Auburn University, Auburn, AL, United States
| | - Irene K Beckmann
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Ivo L Hofacker
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria.,Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Jacek Wower
- Department of Animal and Dairy Sciences, Auburn University, Auburn, AL, United States
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria.,Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Joanna Sztuba-Solinska
- Department of Biological Sciences, Auburn University, 120 W. Samford Ave, Rouse Life Sciences Building, Auburn, AL, United States.,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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2
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Johnson PZ, Kasprzak WK, Shapiro BA, Simon AE. Structural characterization of a new subclass of panicum mosaic virus-like 3' cap-independent translation enhancer. Nucleic Acids Res 2022; 50:1601-1619. [PMID: 35104872 PMCID: PMC8860577 DOI: 10.1093/nar/gkac007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 12/29/2021] [Accepted: 01/29/2022] [Indexed: 11/29/2022] Open
Abstract
Canonical eukaryotic mRNA translation requires 5'cap recognition by initiation factor 4E (eIF4E). In contrast, many positive-strand RNA virus genomes lack a 5'cap and promote translation by non-canonical mechanisms. Among plant viruses, PTEs are a major class of cap-independent translation enhancers located in/near the 3'UTR that recruit eIF4E to greatly enhance viral translation. Previous work proposed a single form of PTE characterized by a Y-shaped secondary structure with two terminal stem-loops (SL1 and SL2) atop a supporting stem containing a large, G-rich asymmetric loop that forms an essential pseudoknot (PK) involving C/U residues located between SL1 and SL2. We found that PTEs with less than three consecutive cytidylates available for PK formation have an upstream stem-loop that forms a kissing loop interaction with the apical loop of SL2, important for formation/stabilization of PK. PKs found in both subclasses of PTE assume a specific conformation with a hyperreactive guanylate (G*) in SHAPE structure probing, previously found critical for binding eIF4E. While PTE PKs were proposed to be formed by Watson-Crick base-pairing, alternative chemical probing and 3D modeling indicate that the Watson-Crick faces of G* and an adjacent guanylate have high solvent accessibilities. Thus, PTE PKs are likely composed primarily of non-canonical interactions.
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Affiliation(s)
- Philip Z Johnson
- Department of Cell Biology and Molecular Genetics, University of Maryland - College Park, College Park, MD 20742, USA
| | - Wojciech K Kasprzak
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Bruce A Shapiro
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Anne E Simon
- Department of Cell Biology and Molecular Genetics, University of Maryland - College Park, College Park, MD 20742, USA
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3
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Zhou Y, Li J, Hurst T, Chen SJ. SHAPER: A Web Server for Fast and Accurate SHAPE Reactivity Prediction. Front Mol Biosci 2021; 8:721955. [PMID: 34395533 PMCID: PMC8355595 DOI: 10.3389/fmolb.2021.721955] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/13/2021] [Indexed: 11/13/2022] Open
Abstract
Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) chemical probing serves as a convenient and efficient experiment technique for providing information about RNA local flexibility. The local structural information contained in SHAPE reactivity data can be used as constraints in 2D/3D structure predictions. Here, we present SHAPE predictoR (SHAPER), a web server for fast and accurate SHAPE reactivity prediction. The main purpose of the SHAPER web server is to provide a portal that uses experimental SHAPE data to refine 2D/3D RNA structure selection. Input structures for the SHAPER server can be obtained through experimental or computational modeling. The SHAPER server can accept RNA structures with single or multiple conformations, and the predicted SHAPE profile and correlation with experimental SHAPE data (if provided) for each conformation can be freely downloaded through the web portal. The SHAPER web server is available at http://rna.physics.missouri.edu/shaper/.
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Affiliation(s)
- Yuanzhe Zhou
- Department of Physics and Astronomy, University of Missouri, Columbia, MO, United States
| | - Jun Li
- Department of Physics and Astronomy, University of Missouri, Columbia, MO, United States
| | - Travis Hurst
- Department of Physics and Astronomy, University of Missouri, Columbia, MO, United States
| | - Shi-Jie Chen
- Department of Physics and Astronomy, University of Missouri, Columbia, MO, United States.,Department of Biochemistry, University of Missouri, Columbia, MO, United States.,Institute of Data Sciences and Informatics, University of Missouri, Columbia, MO, United States
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4
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Hurst T, Chen SJ. Sieving RNA 3D Structures with SHAPE and Evaluating Mechanisms Driving Sequence-Dependent Reactivity Bias. J Phys Chem B 2021; 125:1156-1166. [PMID: 33497570 DOI: 10.1021/acs.jpcb.0c11365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemical probing provides local RNA flexibility information at single-nucleotide resolution. In general, SHAPE is thought of as a secondary structure (2D) technology, but we find evidence that robust tertiary structure (3D) information is contained in SHAPE data. Here, we report a new model that achieves a higher correlation between SHAPE data and native RNA 3D structures than the previous 3D structure-SHAPE relationship model. Furthermore, we demonstrate that the new model improves our ability to discern between SHAPE-compatible and -incompatible structures on model decoys. After identifying sequence-dependent bias in SHAPE experiments, we propose a mechanism driving sequence-dependent bias in SHAPE experiments, using replica-exchange umbrella sampling simulations to confirm that the SHAPE sequence bias is largely explained by the stability of the unreacted SHAPE reagent in the binding pocket. Taken together, this work represents multiple practical advances in our mechanistic and predictive understanding of SHAPE technology.
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Affiliation(s)
- Travis Hurst
- Department of Physics, Department of Biochemistry, and Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, United States
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, United States
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5
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Szucs MJ, Nichols PJ, Jones RA, Vicens Q, Kieft JS. A New Subclass of Exoribonuclease-Resistant RNA Found in Multiple Genera of Flaviviridae. mBio 2020; 11:mBio.02352-20. [PMID: 32994331 DOI: 10.1101/2020.06.26.172668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
Viruses have developed innovative strategies to exploit the cellular machinery and overcome the antiviral defenses of the host, often using specifically structured RNA elements. Examples are found in the Flavivirus genus (in the family Flaviviridae), where during flaviviral infection, pathogenic subgenomic flaviviral RNAs (sfRNAs) accumulate in the cell. These sfRNAs are formed when a host cell 5' to 3' exoribonuclease degrades the viral genomic RNA but is blocked by an exoribonuclease-resistant RNA structure (xrRNA) located in the viral genome's 3' untranslated region (UTR). Although known to exist in several Flaviviridae genera, the full distribution and diversity of xrRNAs in this family were unknown. Using the recently solved high-resolution structure of an xrRNA from the divergent flavivirus Tamana bat virus (TABV) as a reference, we used bioinformatic searches to identify xrRNAs in the remaining three genera of Flaviviridae: Pegivirus, Pestivirus, and Hepacivirus We biochemically and structurally characterized several examples, determining that they are genuine xrRNAs with a conserved fold. These new xrRNAs look superficially similar to the previously described xrRNAs but possess structural differences making them distinct from previous classes of xrRNAs. Overall, we have identified the presence of xrRNA in all four genera of Flaviviridae, but not in all species. Our findings thus require adjustments of previous xrRNA classification schemes and expand the previously known distribution of xrRNA in Flaviviridae.IMPORTANCE The members of the Flaviviridae comprise one of the largest families of positive-sense single-stranded RNA (+ssRNA) and are divided into the Flavivirus, Pestivirus, Pegivirus, and Hepacivirus genera. The genus Flavivirus contains many medically relevant viruses such as Zika virus, dengue virus, and Powassan virus. In these, a part of the RNA of the virus twists up into a distinct three-dimensional shape called an exoribonuclease-resistant RNA (xrRNA) that blocks the ability of the cell to "chew up" the viral RNA. Hence, part of the RNA of the virus remains intact, and this protected part is important for viral infection. These xrRNAs were known to occur in flaviviruses, but whether they existed in the other members of the family was not known. In this study, we identified a new subclass of xrRNA found not only in flaviviruses but also in the remaining three genera. The fact that these structured viral RNAs exist throughout the Flaviviridae family suggests they are important parts of the infection strategy of diverse pathogens, which could lead to new avenues of research.
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Affiliation(s)
- Matthew J Szucs
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, USA
| | - Parker J Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, USA
| | - Rachel A Jones
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, USA
| | - Quentin Vicens
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, USA
- RNA BioScience Initiative, University of Colorado Denver School of Medicine, Aurora, Colorado, USA
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6
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Abstract
The members of the Flaviviridae comprise one of the largest families of positive-sense single-stranded RNA (+ssRNA) and are divided into the Flavivirus, Pestivirus, Pegivirus, and Hepacivirus genera. The genus Flavivirus contains many medically relevant viruses such as Zika virus, dengue virus, and Powassan virus. In these, a part of the RNA of the virus twists up into a distinct three-dimensional shape called an exoribonuclease-resistant RNA (xrRNA) that blocks the ability of the cell to “chew up” the viral RNA. Hence, part of the RNA of the virus remains intact, and this protected part is important for viral infection. These xrRNAs were known to occur in flaviviruses, but whether they existed in the other members of the family was not known. In this study, we identified a new subclass of xrRNA found not only in flaviviruses but also in the remaining three genera. The fact that these structured viral RNAs exist throughout the Flaviviridae family suggests they are important parts of the infection strategy of diverse pathogens, which could lead to new avenues of research. Viruses have developed innovative strategies to exploit the cellular machinery and overcome the antiviral defenses of the host, often using specifically structured RNA elements. Examples are found in the Flavivirus genus (in the family Flaviviridae), where during flaviviral infection, pathogenic subgenomic flaviviral RNAs (sfRNAs) accumulate in the cell. These sfRNAs are formed when a host cell 5′ to 3′ exoribonuclease degrades the viral genomic RNA but is blocked by an exoribonuclease-resistant RNA structure (xrRNA) located in the viral genome’s 3′ untranslated region (UTR). Although known to exist in several Flaviviridae genera, the full distribution and diversity of xrRNAs in this family were unknown. Using the recently solved high-resolution structure of an xrRNA from the divergent flavivirus Tamana bat virus (TABV) as a reference, we used bioinformatic searches to identify xrRNAs in the remaining three genera of Flaviviridae: Pegivirus, Pestivirus, and Hepacivirus. We biochemically and structurally characterized several examples, determining that they are genuine xrRNAs with a conserved fold. These new xrRNAs look superficially similar to the previously described xrRNAs but possess structural differences making them distinct from previous classes of xrRNAs. Overall, we have identified the presence of xrRNA in all four genera of Flaviviridae, but not in all species. Our findings thus require adjustments of previous xrRNA classification schemes and expand the previously known distribution of xrRNA in Flaviviridae.
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7
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Abstract
RNA performs and regulates a diverse range of cellular processes, with new functional roles being uncovered at a rapid pace. Interest is growing in how these functions are linked to RNA structures that form in the complex cellular environment. A growing suite of technologies that use advances in RNA structural probes, high-throughput sequencing and new computational approaches to interrogate RNA structure at unprecedented throughput are beginning to provide insights into RNA structures at new spatial, temporal and cellular scales.
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Affiliation(s)
- Eric J Strobel
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Angela M Yu
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Julius B Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.
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8
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Frezza E, Courban A, Allouche D, Sargueil B, Pasquali S. The interplay between molecular flexibility and RNA chemical probing reactivities analyzed at the nucleotide level via an extensive molecular dynamics study. Methods 2019; 162-163:108-127. [PMID: 31145972 DOI: 10.1016/j.ymeth.2019.05.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 05/22/2019] [Accepted: 05/22/2019] [Indexed: 12/20/2022] Open
Abstract
Determination of the tridimensional structure of ribonucleic acid molecules is fundamental for understanding their function in the cell. A common method to investigate RNA structures of large molecules is the use of chemical probes such as SHAPE (2'-hydroxyl acylation analyzed by primer extension) reagents, DMS (dimethyl sulfate) and CMCT (1-cyclohexyl-3-(2-morpholinoethyl) carbodiimide metho-p-toluene sulfate), the reaction of which is dependent on the local structural properties of each nucleotide. In order to understand the interplay between local flexibility, sugar pucker, canonical pairing and chemical reactivity of the probes, we performed all-atom molecular dynamics simulations on a set of RNA molecules for which both tridimensional structure and chemical probing data are available and we analyzed the correlations between geometrical parameters and the chemical reactivity. Our study confirms that SHAPE reactivity is guided by the local flexibility of the different chemical moieties but suggests that a combination of multiple parameters is needed to better understand the implications of the reactivity at the molecular level. This is also the case for DMS and CMCT for which the reactivity appears to be more complex than commonly accepted.
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Affiliation(s)
- Elisa Frezza
- Faculté de Pharmacie de Paris, Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 - CNRS, Université Paris Descartes, 4 Avenue de l'Observatoire 75270 PARIS CEDEX 06, France.
| | - Antoine Courban
- Faculté de Pharmacie de Paris, Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 - CNRS, Université Paris Descartes, 4 Avenue de l'Observatoire 75270 PARIS CEDEX 06, France
| | - Delphine Allouche
- Faculté de Pharmacie de Paris, Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 - CNRS, Université Paris Descartes, 4 Avenue de l'Observatoire 75270 PARIS CEDEX 06, France
| | - Bruno Sargueil
- Faculté de Pharmacie de Paris, Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 - CNRS, Université Paris Descartes, 4 Avenue de l'Observatoire 75270 PARIS CEDEX 06, France.
| | - Samuela Pasquali
- Faculté de Pharmacie de Paris, Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 - CNRS, Université Paris Descartes, 4 Avenue de l'Observatoire 75270 PARIS CEDEX 06, France.
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9
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Kawaguchi R, Kiryu H, Iwakiri J, Sese J. reactIDR: evaluation of the statistical reproducibility of high-throughput structural analyses towards a robust RNA structure prediction. BMC Bioinformatics 2019; 20:130. [PMID: 30925857 PMCID: PMC6439966 DOI: 10.1186/s12859-019-2645-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Background Recently, next-generation sequencing techniques have been applied for the detection of RNA secondary structures, which is referred to as high-throughput RNA structural (HTS) analyses, and many different protocols have been used to detect comprehensive RNA structures at single-nucleotide resolution. However, the existing computational analyses heavily depend on the experimental methodology to generate data, which results in difficulties associated with statistically sound comparisons or combining the results obtained using different HTS methods. Results Here, we introduced a statistical framework, reactIDR, which can be applied to the experimental data obtained using multiple HTS methodologies. Using this approach, nucleotides are classified into three structural categories, loop, stem/background, and unmapped. reactIDR uses the irreproducible discovery rate (IDR) with a hidden Markov model to discriminate between the true and spurious signals obtained in the replicated HTS experiments accurately, and it is able to incorporate an expectation-maximization algorithm and supervised learning for efficient parameter optimization. The results of our analyses of the real-life HTS data showed that reactIDR had the highest accuracy in the classification of ribosomal RNA stem/loop structures when using both individual and integrated HTS datasets, and its results corresponded the best to the three-dimensional structures. Conclusions We have developed a novel software, reactIDR, for the prediction of stem/loop regions from the HTS analysis datasets. For the rRNA structure analyses, reactIDR was shown to have robust accuracy across different datasets by using the reproducibility criterion, suggesting its potential for increasing the value of existing HTS datasets. reactIDR is publicly available at https://github.com/carushi/reactIDR. Electronic supplementary material The online version of this article (10.1186/s12859-019-2645-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Risa Kawaguchi
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, Aomi, Koto-ku, Tokyo, Japan. .,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwanoha, Kashiwa-shi, Chiba, Japan.
| | - Hisanori Kiryu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwanoha, Kashiwa-shi, Chiba, Japan
| | - Junichi Iwakiri
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwanoha, Kashiwa-shi, Chiba, Japan
| | - Jun Sese
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, Aomi, Koto-ku, Tokyo, Japan.,AIST- Tokyo Tech Real World Big-Data Computation Open Innovation Laboratory, Ookayama, Meguro-ku, Tokyo, Japan.,Humanome Lab Inc., Shinjuku-ku, Tokyo, Japan
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10
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Shoffner GM, Wang R, Podell E, Cech TR, Guo F. In Crystallo Selection to Establish New RNA Crystal Contacts. Structure 2018; 26:1275-1283.e3. [PMID: 29910185 DOI: 10.1016/j.str.2018.05.005] [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: 12/01/2017] [Revised: 04/03/2018] [Accepted: 05/10/2018] [Indexed: 11/25/2022]
Abstract
Crystallography is a major technique for determining large RNA structures. Obtaining diffraction-quality crystals has been the bottleneck. Although several RNA crystallization methods have been developed, the field strongly needs additional approaches. Here we invented an in crystallo selection strategy for identifying mutations that enhance a target RNA's crystallizability. The strategy includes constructing an RNA pool containing random mutations, obtaining crystals, and amplifying the sequences enriched by crystallization. We demonstrated a proof-of-principle application to the P4-P6 domain from the Tetrahymena ribozyme. We further determined the structures of four selected mutants. All four establish new crystal lattice contacts while maintaining the native structure. Three mutants achieve this by relocating bulges and one by making a helix more flexible. In crystallo selection provides opportunities to improve crystals of RNAs or RNA-ligand complexes. Our results also suggest that mutants may be rationally designed for crystallization by "walking" a bulge along the RNA chain.
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Affiliation(s)
- Grant M Shoffner
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Ruixuan Wang
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Elaine Podell
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado BioFrontiers Institute, Boulder, CO 80309-0596, USA
| | - Thomas R Cech
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado BioFrontiers Institute, Boulder, CO 80309-0596, USA
| | - Feng Guo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
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11
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Lenz TK, Norris AM, Hud NV, Williams LD. Protein-free ribosomal RNA folds to a near-native state in the presence of Mg2+. RSC Adv 2017. [DOI: 10.1039/c7ra08696b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The assembled bacterial ribosome contains around 50 proteins and many counterions.
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Affiliation(s)
- Timothy K. Lenz
- Department of Chemistry & Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
| | - Ashlyn M. Norris
- Department of Chemistry & Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
| | - Nicholas V. Hud
- Department of Chemistry & Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
| | - Loren Dean Williams
- Department of Chemistry & Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
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12
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Guo S, Kierzek E, Chen G, Zhou YJ, Wong SM. TMV mutants with poly(A) tracts of different lengths demonstrate structural variations in 3'UTR affecting viral RNAs accumulation and symptom expression. Sci Rep 2015; 5:18412. [PMID: 26678425 PMCID: PMC4683447 DOI: 10.1038/srep18412] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/17/2015] [Indexed: 12/13/2022] Open
Abstract
The upstream pseudoknots domain (UPD) of Tobacco mosaic virus (TMV) is located at the 3'-untranslated region (UTR). It plays an important role in virus replication and translation. To determine the importance of UPD and 3'-UTR, and the effects of introduced RNA elements in TMV 3'-UTR, a series of TMV mutants with internal poly(A) tract upstream of UPD was constructed for structural analysis by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE). TMV(24A+UPD) and TMV(42A+UPD) formed a similar structure as that of TMV 3'-UTR, but TMV(62A+UPD) structures altered by the introduced poly(A) tract. In addition, TMV(24A+UPD) had a higher viral RNAs accumulation than TMV in N. benthamiana protoplasts, and induced lethal symptoms in the infected plants. TMV(62A+UPD) showed a drastically reduced accumulation, its coat protein was undetectable in protoplasts, and the inoculated plants remained symptomless. This study analyzed the structures of 3'-UTR of TMV and found that the longer poly(A) tract introduced upstream of UPD reduced viral RNAs accumulation and induced milder symptoms in N. benthamiana. In conclusion, different lengths of the internal poly(A) tract introduced into the TMV 3'UTR lead to structural variations that affect virus accumulation and symptom expression.
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Affiliation(s)
- Song Guo
- Department of Biological Sciences, National University of Singapore, Republic of Singapore
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Yi-Jun Zhou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences; Jiangsu Technical Service Center of Diagnosis and Detection for Plant Virus Diseases, Nanjing 210014, PRC
| | - Sek-Man Wong
- Department of Biological Sciences, National University of Singapore, Republic of Singapore
- Temasek Life Sciences Laboratory, Singapore, Republic of Singapore
- National University of Singapore Research Institute in Suzhou, Jiangsu, PRC
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13
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Aviran S, Pachter L. Rational experiment design for sequencing-based RNA structure mapping. RNA (NEW YORK, N.Y.) 2014; 20:1864-1877. [PMID: 25332375 PMCID: PMC4238353 DOI: 10.1261/rna.043844.113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Accepted: 09/07/2014] [Indexed: 05/30/2023]
Abstract
Structure mapping is a classic experimental approach for determining nucleic acid structure that has gained renewed interest in recent years following advances in chemistry, genomics, and informatics. The approach encompasses numerous techniques that use different means to introduce nucleotide-level modifications in a structure-dependent manner. Modifications are assayed via cDNA fragment analysis, using electrophoresis or next-generation sequencing (NGS). The recent advent of NGS has dramatically increased the throughput, multiplexing capacity, and scope of RNA structure mapping assays, thereby opening new possibilities for genome-scale, de novo, and in vivo studies. From an informatics standpoint, NGS is more informative than prior technologies by virtue of delivering direct molecular measurements in the form of digital sequence counts. Motivated by these new capabilities, we introduce a novel model-based in silico approach for quantitative design of large-scale multiplexed NGS structure mapping assays, which takes advantage of the direct and digital nature of NGS readouts. We use it to characterize the relationship between controllable experimental parameters and the precision of mapping measurements. Our results highlight the complexity of these dependencies and shed light on relevant tradeoffs and pitfalls, which can be difficult to discern by intuition alone. We demonstrate our approach by quantitatively assessing the robustness of SHAPE-Seq measurements, obtained by multiplexing SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) chemistry in conjunction with NGS. We then utilize it to elucidate design considerations in advanced genome-wide approaches for probing the transcriptome, which recently obtained in vivo information using dimethyl sulfate (DMS) chemistry.
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Affiliation(s)
- Sharon Aviran
- Biomedical Engineering Department and Genome Center, University of California at Davis, Davis, California 95616, USA
| | - Lior Pachter
- Center for Computational Biology and Departments of Molecular and Cell Biology and Mathematics, University of California at Berkeley, Berkeley, California 94720, USA
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14
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Górska A, Błaszczyk L, Dutkiewicz M, Ciesiołka J. Length variants of the 5' untranslated region of p53 mRNA and their impact on the efficiency of translation initiation of p53 and its N-truncated isoform ΔNp53. RNA Biol 2014; 10:1726-40. [PMID: 24418891 DOI: 10.4161/rna.26562] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Recently, we have determined the secondary structure of the 5'-terminal region of p53 mRNA that starts from the P1 transcription initiation site and includes two major translation initiation codons responsible for the synthesis of p53 and ΔNp53 isoform. Here, we showed that when this region was extended into 5' direction to the P0 transcription start site, the two characteristic hairpin motifs found in this region were preserved. Moreover, the presence of alternatively spliced intron 2 did not interfere with the formation of the larger hairpin in which the initiation codon for p53 was embedded. The impact of the different variants of p53 5'-terminal region, which start at P0 or P1 site and end with the initiation codon for p53 or ΔNp53, on the translation of luciferase reporter protein was compared. Strikingly, the efficiency of translation performed in rabbit reticulocyte lysate differed by two orders of magnitude. The toe-printing analysis was also applied to investigate the formation of the ribosomal complex on the model mRNA constructs. The relative translation efficiencies in HeLa and MCF-7 cells were similar to those observed in the cell lysate, although some differences were noted in comparison with cell-free conditions. The results were discussed in terms of the role of secondary structure folding of the 5'-terminal region of p53 mRNA in translation and possible modes of p53 and ΔNp53 translation initiation.
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Affiliation(s)
- Agnieszka Górska
- Institute of Bioorganic Chemistry; Polish Academy of Sciences; Noskowskiego 12/14; Poznan, Poland
| | - Leszek Błaszczyk
- Institute of Bioorganic Chemistry; Polish Academy of Sciences; Noskowskiego 12/14; Poznan, Poland
| | - Mariola Dutkiewicz
- Institute of Bioorganic Chemistry; Polish Academy of Sciences; Noskowskiego 12/14; Poznan, Poland
| | - Jerzy Ciesiołka
- Institute of Bioorganic Chemistry; Polish Academy of Sciences; Noskowskiego 12/14; Poznan, Poland
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15
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Evolutionary evidence for alternative structure in RNA sequence co-variation. PLoS Comput Biol 2013; 9:e1003152. [PMID: 23935473 PMCID: PMC3723493 DOI: 10.1371/journal.pcbi.1003152] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 06/05/2013] [Indexed: 02/06/2023] Open
Abstract
Sequence conservation and co-variation of base pairs are hallmarks of structured RNAs. For certain RNAs (e.g. riboswitches), a single sequence must adopt at least two alternative secondary structures to effectively regulate the message. If alternative secondary structures are important to the function of an RNA, we expect to observe evolutionary co-variation supporting multiple conformations. We set out to characterize the evolutionary co-variation supporting alternative conformations in riboswitches to determine the extent to which alternative secondary structures are conserved. We found strong co-variation support for the terminator, P1, and anti-terminator stems in the purine riboswitch by extending alignments to include terminator sequences. When we performed Boltzmann suboptimal sampling on purine riboswitch sequences with terminators we found that these sequences appear to have evolved to favor specific alternative conformations. We extended our analysis of co-variation to classic alignments of group I/II introns, tRNA, and other classes of riboswitches. In a majority of these RNAs, we found evolutionary evidence for alternative conformations that are compatible with the Boltzmann suboptimal ensemble. Our analyses suggest that alternative conformations are selected for and thus likely play functional roles in even the most structured of RNAs. RNA (Ribonucleic Acid) is a messenger of genetic information, master regulator, and catalyst in the cell. To carry out its function, RNA can fold into complex three-dimensional structures. Certain classes of RNAs, called riboswitches, adopt at least two alternative structures to act as a switch. We set out to detect the evolutionary signal for alternative structures in riboswitches as we hypothesize that these RNA sequences must have evolved to allow both conformations. We find that indeed such signals exist when we compare the sequences of riboswitches from multiple species. When we extend this analysis to other RNA regulators in the cell that are not thought of as switches, we detect equivalent evolutionary support for alternative structures. Viewed through the lens of evolutionary structure conservation RNA sequences appear to have adapted to adopt multiple conformations.
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16
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Chen C, Mitra S, Jonikas M, Martin J, Brenowitz M, Laederach A. Understanding the role of three-dimensional topology in determining the folding intermediates of group I introns. Biophys J 2013; 104:1326-37. [PMID: 23528092 DOI: 10.1016/j.bpj.2013.02.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Revised: 01/28/2013] [Accepted: 02/07/2013] [Indexed: 11/30/2022] Open
Abstract
Many RNA molecules exert their biological function only after folding to unique three-dimensional structures. For long, noncoding RNA molecules, the complexity of finding the native topology can be a major impediment to correct folding to the biologically active structure. An RNA molecule may fold to a near-native structure but not be able to continue to the correct structure due to a topological barrier such as crossed strands or incorrectly stacked helices. Achieving the native conformation thus requires unfolding and refolding, resulting in a long-lived intermediate. We investigate the role of topology in the folding of two phylogenetically related catalytic group I introns, the Twort and Azoarcus group I ribozymes. The kinetic models describing the Mg(2+)-mediated folding of these ribozymes were previously determined by time-resolved hydroxyl (∙OH) radical footprinting. Two intermediates formed by parallel intermediates were resolved for each RNA. These data and analytical ultracentrifugation compaction analyses are used herein to constrain coarse-grained models of these folding intermediates as we investigate the role of nonnative topology in dictating the lifetime of the intermediates. Starting from an ensemble of unfolded conformations, we folded the RNA molecules by progressively adding native constraints to subdomains of the RNA defined by the ∙OH time-progress curves to simulate folding through the different kinetic pathways. We find that nonnative topologies (arrangement of helices) occur frequently in the folding simulations despite using only native constraints to drive the reaction, and that the initial conformation, rather than the folding pathway, is the major determinant of whether the RNA adopts nonnative topology during folding. From these analyses we conclude that biases in the initial conformation likely determine the relative flux through parallel RNA folding pathways.
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Affiliation(s)
- Chunxia Chen
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
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17
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Athavale SS, Gossett JJ, Bowman JC, Hud NV, Williams LD, Harvey SC. In vitro secondary structure of the genomic RNA of satellite tobacco mosaic virus. PLoS One 2013; 8:e54384. [PMID: 23349871 PMCID: PMC3551766 DOI: 10.1371/journal.pone.0054384] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 12/11/2012] [Indexed: 12/31/2022] Open
Abstract
Satellite tobacco mosaic virus (STMV) is a T = 1 icosahedral virus with a single-stranded RNA genome. It is widely accepted that the RNA genome plays an important structural role during assembly of the STMV virion. While the encapsidated form of the RNA has been extensively studied, less is known about the structure of the free RNA, aside from a purported tRNA-like structure at the 3' end. Here we use selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) analysis to examine the secondary structure of in vitro transcribed STMV RNA. The predicted secondary structure is unusual in the sense that it is highly extended, which could be significant for protecting the RNA from degradation. The SHAPE data are also consistent with the previously predicted tRNA-like fold at the 3' end of the molecule, which is also known to hinder degradation. Our data are not consistent with the secondary structure proposed for the encapsidated RNA by Schroeder et al., suggesting that, if the Schroeder structure is correct, either the RNA is packaged as it emerges from the replication complex, or the RNA undergoes extensive refolding upon encapsidation. We also consider the alternative, i.e., that the structure of the encapsidated STMV RNA might be the same as the in vitro structure presented here, and we examine how this structure might be organized in the virus. This possibility is not rigorously ruled out by the available data, so it remains open to examination by experiment.
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Affiliation(s)
- Shreyas S. Athavale
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - J. Jared Gossett
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Jessica C. Bowman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Nicholas V. Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Stephen C. Harvey
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
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18
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Sükösd Z, Swenson MS, Kjems J, Heitsch CE. Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions. Nucleic Acids Res 2013; 41:2807-16. [PMID: 23325843 PMCID: PMC3597644 DOI: 10.1093/nar/gks1283] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Recent advances in RNA structure determination include using data from high-throughput probing experiments to improve thermodynamic prediction accuracy. We evaluate the extent and nature of improvements in data-directed predictions for a diverse set of 16S/18S ribosomal sequences using a stochastic model of experimental SHAPE data. The average accuracy for 1000 data-directed predictions always improves over the original minimum free energy (MFE) structure. However, the amount of improvement varies with the sequence, exhibiting a correlation with MFE accuracy. Further analysis of this correlation shows that accurate MFE base pairs are typically preserved in a data-directed prediction, whereas inaccurate ones are not. Thus, the positive predictive value of common base pairs is consistently higher than the directed prediction accuracy. Finally, we confirm sequence dependencies in the directability of thermodynamic predictions and investigate the potential for greater accuracy improvements in the worst performing test sequence.
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Affiliation(s)
- Zsuzsanna Sükösd
- Interdisciplinary Nanoscience Center, Aarhus University, Ny Munkegade 120, Aarhus C DK-8000, Denmark
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19
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Athavale SS, Petrov AS, Hsiao C, Watkins D, Prickett CD, Gossett JJ, Lie L, Bowman JC, O'Neill E, Bernier CR, Hud NV, Wartell RM, Harvey SC, Williams LD. RNA folding and catalysis mediated by iron (II). PLoS One 2012; 7:e38024. [PMID: 22701543 PMCID: PMC3365117 DOI: 10.1371/journal.pone.0038024] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 04/28/2012] [Indexed: 01/06/2023] Open
Abstract
Mg2+ shares a distinctive relationship with RNA, playing important and specific roles in the folding and function of essentially all large RNAs. Here we use theory and experiment to evaluate Fe2+ in the absence of free oxygen as a replacement for Mg2+ in RNA folding and catalysis. We describe both quantum mechanical calculations and experiments that suggest that the roles of Mg2+ in RNA folding and function can indeed be served by Fe2+. The results of quantum mechanical calculations show that the geometry of coordination of Fe2+ by RNA phosphates is similar to that of Mg2+. Chemical footprinting experiments suggest that the conformation of the Tetrahymena thermophila Group I intron P4–P6 domain RNA is conserved between complexes with Fe2+ or Mg2+. The catalytic activities of both the L1 ribozyme ligase, obtained previously by in vitro selection in the presence of Mg2+, and the hammerhead ribozyme are enhanced in the presence of Fe2+ compared to Mg2+. All chemical footprinting and ribozyme assays in the presence of Fe2+ were performed under anaerobic conditions. The primary motivation of this work is to understand RNA in plausible early earth conditions. Life originated during the early Archean Eon, characterized by a non-oxidative atmosphere and abundant soluble Fe2+. The combined biochemical and paleogeological data are consistent with a role for Fe2+ in an RNA World. RNA and Fe2+ could, in principle, support an array of RNA structures and catalytic functions more diverse than RNA with Mg2+ alone.
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Affiliation(s)
- Shreyas S. Athavale
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Anton S. Petrov
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Chiaolong Hsiao
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Derrick Watkins
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Caitlin D. Prickett
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - J. Jared Gossett
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Lively Lie
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Jessica C. Bowman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Eric O'Neill
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Chad R. Bernier
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Nicholas V. Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Roger M. Wartell
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Stephen C. Harvey
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail:
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20
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Chen K, Eargle J, Lai J, Kim H, Abeysirigunawardena S, Mayerle M, Woodson S, Ha T, Luthey-Schulten Z. Assembly of the five-way junction in the ribosomal small subunit using hybrid MD-Gō simulations. J Phys Chem B 2012; 116:6819-31. [PMID: 22458631 DOI: 10.1021/jp212614b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Assembly of the bacterial ribosomal small subunit (SSU) begins with the folding of the five-way junction upon interaction with the primary binding protein S4. This complex contains the largest contiguous molecular signature, which is a conserved feature in all bacterial 16S rRNAs. In a previous study, we used all-atom molecular dynamics simulations to demonstrate that the co-evolving signature in the N-terminus of S4 is intrinsically disordered and capable of accelerating the binding process through a fly casting mechanism. In this paper, comparisons between the all-atom MD simulations and FRET experiments identify multiple metastable conformations of the naked five-way junction without the presence of S4. Furthermore, we capture the simultaneous folding and binding of the five-way junction and r-protein S4 by use of a structure-based Gō potential implemented within the framework of the all-atom molecular dynamics CHARMM force field. Different folding pathways are observed for the refolding of the five-way junction upon partial binding of S4. Our simulations illustrate the complex nature of RNA folding in the presence of a protein binding partner and provide insight into the role of population shift and the induced fit mechanisms in the protein:RNA folding and binding process.
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Affiliation(s)
- Ke Chen
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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21
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McGinnis JL, Dunkle JA, Cate JHD, Weeks KM. The mechanisms of RNA SHAPE chemistry. J Am Chem Soc 2012; 134:6617-24. [PMID: 22475022 DOI: 10.1021/ja2104075] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The biological functions of RNA are ultimately governed by the local environment at each nucleotide. Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry is a powerful approach for measuring nucleotide structure and dynamics in diverse biological environments. SHAPE reagents acylate the 2'-hydroxyl group at flexible nucleotides because unconstrained nucleotides preferentially sample rare conformations that enhance the nucleophilicity of the 2'-hydroxyl. The critical corollary is that some constrained nucleotides must be poised for efficient reaction at the 2'-hydroxyl group. To identify such nucleotides, we performed SHAPE on intact crystals of the Escherichia coli ribosome, monitored the reactivity of 1490 nucleotides in 16S rRNA, and examined those nucleotides that were hyper-reactive toward SHAPE and had well-defined crystallographic conformations. Analysis of these conformations revealed that 2'-hydroxyl reactivity is broadly facilitated by general base catalysis involving multiple RNA functional groups and by two specific orientations of the bridging 3'-phosphate group. Nucleotide analog studies confirmed the contributions of these mechanisms to SHAPE reactivity. These results provide a strong mechanistic explanation for the relationship between SHAPE reactivity and local RNA dynamics and will facilitate interpretation of SHAPE information in the many technologies that make use of this chemistry.
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Affiliation(s)
- Jennifer L McGinnis
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
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22
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Gore KR, Nawale GN, Harikrishna S, Chittoor VG, Pandey SK, Höbartner C, Patankar S, Pradeepkumar PI. Synthesis, gene silencing, and molecular modeling studies of 4'-C-aminomethyl-2'-O-methyl modified small interfering RNAs. J Org Chem 2012; 77:3233-45. [PMID: 22372696 DOI: 10.1021/jo202666m] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The linear syntheses of 4'-C-aminomethyl-2'-O-methyl uridine and cytidine nucleoside phosphoramidites were achieved using glucose as the starting material. The modified RNA building blocks were incorporated into small interfering RNAs (siRNAs) by employing solid phase RNA synthesis. Thermal melting studies showed that the modified siRNA duplexes exhibited slightly lower T(m) (∼1 °C/modification) compared to the unmodified duplex. Molecular dynamics simulations revealed that the 4'-C-aminomethyl-2'-O-methyl modified nucleotides adopt South-type conformation in a siRNA duplex, thereby altering the stacking and hydrogen-bonding interactions. These modified siRNAs were also evaluated for their gene silencing efficiency in HeLa cells using a luciferase-based reporter assay. The results indicate that the modifications are well tolerated in various positions of the passenger strand and at the 3' end of the guide strand but are less tolerated in the seed region of the guide strand. The modified siRNAs exhibited prolonged stability in human serum compared to unmodified siRNA. This work has implications for the use of 4'-C-aminomethyl-2'-O-methyl modified nucleotides to overcome some of the challenges associated with the therapeutic utilities of siRNAs.
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Affiliation(s)
- Kiran R Gore
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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23
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Kladwang W, VanLang CC, Cordero P, Das R. A two-dimensional mutate-and-map strategy for non-coding RNA structure. Nat Chem 2011; 3:954-62. [PMID: 22109276 PMCID: PMC3725140 DOI: 10.1038/nchem.1176] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 09/15/2011] [Indexed: 12/24/2022]
Abstract
Non-coding RNAs fold into precise base-pairing patterns to carry out critical roles in genetic regulation and protein synthesis, but determining RNA structure remains difficult. Here, we show that coupling systematic mutagenesis with high-throughput chemical mapping enables accurate base-pair inference of domains from ribosomal RNA, ribozymes and riboswitches. For a six-RNA benchmark that has challenged previous chemical/computational methods, this 'mutate-and-map' strategy gives secondary structures that are in agreement with crystallography (helix error rates, 2%), including a blind test on a double-glycine riboswitch. Through modelling of partially ordered states, the method enables the first test of an interdomain helix-swap hypothesis for ligand-binding cooperativity in a glycine riboswitch. Finally, the data report on tertiary contacts within non-coding RNAs, and coupling to the Rosetta/FARFAR algorithm gives nucleotide-resolution three-dimensional models (helix root-mean-squared deviation, 5.7 Å) of an adenine riboswitch. These results establish a promising two-dimensional chemical strategy for inferring the secondary and tertiary structures that underlie non-coding RNA behaviour.
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Affiliation(s)
- Wipapat Kladwang
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
| | - Christopher C. VanLang
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA
| | - Pablo Cordero
- Program in Biomedical Informatics, Stanford University, Stanford, California 94305, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
- Program in Biomedical Informatics, Stanford University, Stanford, California 94305, USA
- Department of Physics, Stanford University, Stanford, California 94305, USA
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24
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Vicens Q, Mondragón E, Batey RT. Molecular sensing by the aptamer domain of the FMN riboswitch: a general model for ligand binding by conformational selection. Nucleic Acids Res 2011; 39:8586-98. [PMID: 21745821 PMCID: PMC3201879 DOI: 10.1093/nar/gkr565] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 06/20/2011] [Accepted: 06/21/2011] [Indexed: 12/25/2022] Open
Abstract
Understanding the nature of the free state of riboswitch aptamers is important for illuminating common themes in gene regulation by riboswitches. Prior evidence indicated the flavin mononucleotide (FMN)-binding riboswitch aptamer adopted a 'bound-like' structure in absence of FMN, suggesting only local conformational changes upon ligand binding. In the scope of pinpointing the general nature of such changes at the nucleotide level, we performed SHAPE mapping experiments using the aptamer domain of two phylogenetic variants, both in absence and in presence of FMN. We also solved the crystal structures of one of these domains both free (3.3 Å resolution) and bound to FMN (2.95 Å resolution). Our comparative study reveals that structural rearrangements occurring upon binding are restricted to a few of the joining regions that form the binding pocket in both RNAs. This type of binding event with minimal structural perturbations is reminiscent of binding events by conformational selection encountered in other riboswitches and various RNAs.
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Affiliation(s)
| | | | - Robert T. Batey
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, USA
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25
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Błaszczyk L, Ciesiołka J. Secondary structure and the role in translation initiation of the 5'-terminal region of p53 mRNA. Biochemistry 2011; 50:7080-92. [PMID: 21770379 DOI: 10.1021/bi200659b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The p53 protein is one of the major factors involved in cell cycle control, DNA repair, and induction of apoptosis. We determined the secondary structure of the 5'-terminal region of p53 mRNA that includes two major translation initiation codons AUG1 and AUG2, responsible for the synthesis of p53 and its N-truncated isoform ΔN-p53. It turned out that a part of the coding sequence was involved in the folding of the 5' untranslated region for p53. The most characteristic structural elements in the 5'-terminal region of p53 mRNA were two hairpin motifs. In one of them, the initiation codon AUG1 was embedded while the other hairpin has been earlier shown to bind the Mdm2 protein. Alternative mechanisms of p53 mRNA translation initiation were investigated in vitro using model mRNA templates. The results confirmed that initiation from AUG1 was mostly cap-dependent. The process was stimulated by a cap structure and strongly inhibited by a stable hairpin at the template 5' end. Upon inhibition, the remaining protein fraction was synthesized in a cap-independent process, which was strongly stimulated by the addition of a cap analogue. The translation initiation from AUG2 showed a largely cap-independent character. The 5' cap structure actually decreased initiation from this site which argues against a leaky scanning mechanism but might suggest the presence of an IRES. Moreover, blocking cap-dependent translation from AUG1 by the stable hairpin did not change the level of initiation from AUG2. Upon addition of the cap analogue, translation from this site was even increased.
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Affiliation(s)
- Leszek Błaszczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
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26
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Fernández N, García-Sacristán A, Ramajo J, Briones C, Martínez-Salas E. Structural analysis provides insights into the modular organization of picornavirus IRES. Virology 2010; 409:251-61. [PMID: 21056890 DOI: 10.1016/j.virol.2010.10.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 09/12/2010] [Accepted: 10/08/2010] [Indexed: 10/18/2022]
Abstract
Picornavirus RNA translation is driven by the internal ribosome entry site (IRES) element. The impact of RNA structure on the foot-and-mouth disease virus (FMDV) IRES activity has been analyzed using Selective 2'Hydroxyl Acylation analyzed by Primer Extension (SHAPE) and high throughput analysis of RNA conformation by antisense oligonucleotides printed on microarrays. SHAPE reactivity revealed the self-folding capacity of domain 3 and evidenced a change of RNA structure in a defective GNRA mutant. A modified RNA conformation of this mutant was also evidenced by RNA accessibility to oligonucleotides. Interestingly, comparison of nucleotide reactivity with RNA accessibility revealed that SHAPE reactive nucleotides corresponding to the GNRA motif were not accessible to their respective target oligonucleotides. The differential response was observed both in domain 3 and the entire IRES. Our results demonstrate distant effects of the GNRA motif in the domain 3 RNA conformation, and highlight the modular organization of a picornavirus IRES.
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Affiliation(s)
- Noemí Fernández
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spain
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27
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Low JT, Weeks KM. SHAPE-directed RNA secondary structure prediction. Methods 2010; 52:150-8. [PMID: 20554050 DOI: 10.1016/j.ymeth.2010.06.007] [Citation(s) in RCA: 214] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Indexed: 12/25/2022] Open
Abstract
The diverse functional roles of RNA are determined by its underlying structure. Accurate and comprehensive knowledge of RNA structure would inform a broader understanding of RNA biology and facilitate exploiting RNA as a biotechnological tool and therapeutic target. Determining the pattern of base pairing, or secondary structure, of RNA is a first step in these endeavors. Advances in experimental, computational, and comparative analysis approaches for analyzing secondary structure have yielded accurate structures for many small RNAs, but only a few large (>500 nts) RNAs. In addition, most current methods for determining a secondary structure require considerable effort, analytical expertise, and technical ingenuity. In this review, we outline an efficient strategy for developing accurate secondary structure models for RNAs of arbitrary length. This approach melds structural information obtained using SHAPE chemistry with structure prediction using nearest-neighbor rules and the dynamic programming algorithm implemented in the RNAstructure program. Prediction accuracies reach >or=95% for RNAs on the kilobase scale. This approach facilitates both development of new models and refinement of existing RNA structure models, which we illustrate using the Gag-Pol frameshift element in an HIV-1 M-group genome. Most promisingly, integrated experimental and computational refinement brings closer the ultimate goal of efficiently and accurately establishing the secondary structure for any RNA sequence.
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Affiliation(s)
- Justin T Low
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599-3290, USA
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Quarrier S, Martin JS, Davis-Neulander L, Beauregard A, Laederach A. Evaluation of the information content of RNA structure mapping data for secondary structure prediction. RNA (NEW YORK, N.Y.) 2010; 16:1108-17. [PMID: 20413617 PMCID: PMC2874162 DOI: 10.1261/rna.1988510] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 02/20/2010] [Indexed: 05/21/2023]
Abstract
Structure mapping experiments (using probes such as dimethyl sulfate [DMS], kethoxal, and T1 and V1 RNases) are used to determine the secondary structures of RNA molecules. The process is iterative, combining the results of several probes with constrained minimum free-energy calculations to produce a model of the structure. We aim to evaluate whether particular probes provide more structural information, and specifically, how noise in the data affects the predictions. Our approach involves generating "decoy" RNA structures (using the sFold Boltzmann sampling procedure) and evaluating whether we are able to identify the correct structure from this ensemble of structures. We show that with perfect information, we are always able to identify the optimal structure for five RNAs of known structure. We then collected orthogonal structure mapping data (DMS and RNase T1 digest) under several solution conditions using our high-throughput capillary automated footprinting analysis (CAFA) technique on two group I introns of known structure. Analysis of these data reveals the error rates in the data under optimal (low salt) and suboptimal solution conditions (high MgCl(2)). We show that despite these errors, our computational approach is less sensitive to experimental noise than traditional constraint-based structure prediction algorithms. Finally, we propose a novel approach for visualizing the interaction of chemical and enzymatic mapping data with RNA structure. We project the data onto the first two dimensions of a multidimensional scaling of the sFold-generated decoy structures. We are able to directly visualize the structural information content of structure mapping data and reconcile multiple data sets.
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Affiliation(s)
- Scott Quarrier
- Biomedical Sciences Program, University at Albany, Albany, New York 12208, USA
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Weeks KM. Advances in RNA structure analysis by chemical probing. Curr Opin Struct Biol 2010; 20:295-304. [PMID: 20447823 DOI: 10.1016/j.sbi.2010.04.001] [Citation(s) in RCA: 213] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Revised: 03/18/2010] [Accepted: 04/01/2010] [Indexed: 01/22/2023]
Abstract
RNA is arguably the most versatile biological macromolecule because of its ability both to encode and to manipulate genetic information. The diverse roles of RNA depend on its ability to fold back on itself to form biologically functional structures that bind small molecule and large protein ligands, to change conformation, and to affect the cellular regulatory state. These features of RNA biology can be structurally interrogated using chemical mapping experiments. The usefulness and applications of RNA chemical probing technologies have expanded dramatically over the past five years because of several critical advances. These innovations include new sequence-independent RNA chemistries, algorithmic tools for high-throughput analysis of complex data sets composed of thousands of measurements, new approaches for interpreting chemical probing data for both secondary and tertiary structure prediction, facile methods for following time-dependent processes, and the willingness of individual research groups to tackle increasingly bold problems in RNA structural biology.
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Affiliation(s)
- Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA.
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30
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Montange RK, Mondragón E, van Tyne D, Garst AD, Ceres P, Batey RT. Discrimination between closely related cellular metabolites by the SAM-I riboswitch. J Mol Biol 2009; 396:761-72. [PMID: 20006621 DOI: 10.1016/j.jmb.2009.12.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 11/30/2009] [Accepted: 12/06/2009] [Indexed: 12/17/2022]
Abstract
The SAM-I riboswitch is a cis-acting element of genetic control found in bacterial mRNAs that specifically binds S-adenosylmethionine (SAM). We previously determined the 2.9-A X-ray crystal structure of the effector-binding domain of this RNA element, revealing details of RNA-ligand recognition. To improve this structure, variations were made to the RNA sequence to alter lattice contacts, resulting in a 0.5-A improvement in crystallographic resolution and allowing for a more accurate refinement of the crystallographic model. The basis for SAM specificity was addressed by a structural analysis of the RNA complexed to S-adenosylhomocysteine (SAH) and sinefungin and by measuring the affinity of SAM and SAH for a series of mutants using isothermal titration calorimetry. These data illustrate the importance of two universally conserved base pairs in the RNA that form electrostatic interactions with the positively charged sulfonium group of SAM, thereby providing a basis for discrimination between SAM and SAH.
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Affiliation(s)
- Rebecca K Montange
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Campus Box 215, Boulder, CO 80309-0215, USA
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31
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Abstract
A number of RNAs ranging from small helices to large megadalton ribonucleoprotein complexes have been solved to atomic resolution using X-ray crystallography. As with proteins, RNA crystallography involves a number of screening trials in which the concentration of macromolecule, precipitant, salt, and temperature are varied, an approach known as searching "condition space." In contrast to proteins, the nature of base pairing in nucleic acids creates predictable secondary structure that facilitates the rational design of RNA variants, allowing "sequence space" to be screened in parallel. This chapter reviews RNA-specific techniques and considerations for RNA crystallography and presents a complete workflow used by our laboratory for solving RNA structures starting with initial library construction, methods to investigate and improve RNA crystal quality, and finally phase determination and structure solution.
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Affiliation(s)
- Francis E Reyes
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado, USA
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32
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Simmons K, Martin JS, Shcherbakova I, Laederach A. Rapid quantification and analysis of kinetic •OH radical footprinting data using SAFA. Methods Enzymol 2009; 468:47-66. [PMID: 20946764 DOI: 10.1016/s0076-6879(09)68003-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
The use of highly reactive chemical species to probe the structure and dynamics of nucleic acids is greatly simplified by software that enables rapid quantification of the gel images that result from these experiments. Semiautomated footprinting analysis (SAFA) allows a user to quickly and reproducibly quantify a chemical footprinting gel image through a series of steps that rectify, assign, and integrate the relative band intensities. The output of this procedure is raw band intensities that report on the relative reactivity of each nucleotide with the chemical probe. We describe here how to obtain these raw band intensities using SAFA and the subsequent normalization and analysis procedures required to process these data. In particular, we focus on analyzing time-resolved hydroxyl radical ((•)OH) data, which we use to monitor the kinetics of folding of a large RNA (the L-21 T. thermophila group I intron). Exposing the RNA to bursts of (•)OH radicals at specific time points during the folding process monitors the time progress of the reaction. Specifically, we identify protected (nucleotides that become inaccessible to the (•)OH radical probe when folded) and invariant (nucleotides with constant accessibility to the (•)OH probe) residues that we use for monitoring and normalization of the data. With this analysis, we obtain time-progress curves from which we determine kinetic rates of folding. We also report on a data visualization tool implemented in SAFA that allows users to map data onto a secondary structure diagram.
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Affiliation(s)
- Katrina Simmons
- Developmental Genetics and Bioinformatics, Wadsworth Center, Albany, New York, USA
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33
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Revisiting plus-strand DNA synthesis in retroviruses and long terminal repeat retrotransposons: dynamics of enzyme: substrate interactions. Viruses 2009; 1:657-77. [PMID: 21994564 PMCID: PMC3185511 DOI: 10.3390/v1030657] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Revised: 10/28/2009] [Accepted: 11/04/2009] [Indexed: 11/16/2022] Open
Abstract
Although polypurine tract (PPT)-primed initiation of plus-strand DNA synthesis in retroviruses and LTR-containing retrotransposons can be accurately duplicated, the molecular details underlying this concerted series of events remain largely unknown. Importantly, the PPT 3' terminus must be accommodated by ribonuclease H (RNase H) and DNA polymerase catalytic centers situated at either terminus of the cognate reverse transcriptase (RT), and in the case of the HIV-1 enzyme, ∼70Å apart. Communication between RT and the RNA/DNA hybrid therefore appears necessary to promote these events. The crystal structure of the HIV-1 RT/PPT complex, while informative, positions the RNase H active site several bases pairs from the PPT/U3 junction, and thus provides limited information on cleavage specificity. To fill the gap between biochemical and crystallographic approaches, we review a multidisciplinary approach combining chemical probing, mass spectrometry, NMR spectroscopy and single molecule spectroscopy. Our studies also indicate that nonnucleoside RT inhibitors affect enzyme orientation, suggesting initiation of plus-strand DNA synthesis as a potential therapeutic target.
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34
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Pfingsten JS, Castile AE, Kieft JS. Mechanistic role of structurally dynamic regions in Dicistroviridae IGR IRESs. J Mol Biol 2009; 395:205-17. [PMID: 19878683 DOI: 10.1016/j.jmb.2009.10.047] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 10/15/2009] [Accepted: 10/21/2009] [Indexed: 11/19/2022]
Abstract
Dicistroviridae intergenic region (IGR) internal ribosome entry site(s) (IRES) RNAs drive a cap-independent pathway of translation initiation, recruiting both small and large ribosomal subunits to viral RNA without the use of any canonical translation initiation factors. This ability is conferred by the folded three-dimensional structure of the IRES RNA, which has been solved by X-ray crystallography. Here, we report the chemical probing of Plautia stali intestine virus IGR IRES in the unbound form, in the 40S-subunit-bound form, and in the 80S-ribosome-bound form. The results, when combined with an analysis of crystal structures, suggest that parts of the IRES RNA change structure as the preinitiation complex forms. Using mutagenesis coupled with native gel electrophoresis, preinitiation complex assembly assays, and translation initiation assays, we show that these potentially structurally dynamic elements of the IRES are involved in different steps in the pathway of ribosome recruitment and translation initiation. Like tRNAs, it appears that the IGR IRES undergoes local structural changes that are coordinated with structural changes in the ribosome, and these are critical for the IRES mechanism of action.
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Affiliation(s)
- Jennifer S Pfingsten
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
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35
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Turner KB, Yi-Brunozzi HY, Brinson RG, Marino JP, Fabris D, Le Grice SFJ. SHAMS: combining chemical modification of RNA with mass spectrometry to examine polypurine tract-containing RNA/DNA hybrids. RNA (NEW YORK, N.Y.) 2009; 15:1605-1613. [PMID: 19535461 PMCID: PMC2714758 DOI: 10.1261/rna.1615409] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2009] [Accepted: 04/29/2009] [Indexed: 05/27/2023]
Abstract
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) has gained popularity as a facile method of examining RNA structure both in vitro and in vivo, exploiting accessibility of the ribose 2'-OH to acylation by N-methylisatoic anhydride (NMIA) in unpaired or flexible configurations. Subsequent primer extension terminates at the site of chemical modification, and these products are fractionated by high-resolution gel electrophoresis. When applying SHAPE to investigate structural features associated with the wild-type and analog-substituted polypurine tract (PPT)-containing RNA/DNA hybrids, their size (20-25 base pairs) rendered primer extension impractical. As an alternative method of detection, we reasoned that chemical modification could be combined with tandem mass spectrometry, relying on the mass increment of RNA fragments containing the NMIA adduct (M(r) = 133 Da). Using this approach, we demonstrate both specific modification of the HIV-1 PPT RNA primer and variations in its acylation pattern induced by replacing template nucleotides with a non-hydrogen-bonding thymine isostere. Our selective 2'-hydroxyl acylation analyzed by mass spectrometry strategy (SHAMS) should find utility when examining the structure of small RNA fragments or RNA/DNA hybrids where primer extension cannot be performed.
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Affiliation(s)
- Kevin B Turner
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, Maryland 21250, USA
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36
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Martin JS, Simmons K, Laederach A. Exhaustive Enumeration of Kinetic Model Topologies for the Analysis of Time-Resolved RNA Folding. ALGORITHMS 2009; 2:200-214. [PMID: 19865589 DOI: 10.3390/a2010200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Unlike protein folding, the process by which a large RNA molecule adopts a functionally active conformation remains poorly understood. Chemical mapping techniques, such as Hydroxyl Radical (·OH) footprinting report on local structural changes in an RNA as it folds with single nucleotide resolution. The analysis and interpretation of this kinetic data requires the identification and subsequent optimization of a kinetic model and its parameters. We detail our approach to this problem, specifically focusing on a novel strategy to overcome a factorial explosion in the number of possible models that need to be tested to identify the best fitting model. Previously, smaller systems (less than three intermediates) were computationally tractable using a distributed computing approach. However, for larger systems with three or more intermediates, the problem became computationally intractable. With our new enumeration strategy, we are able to significantly reduce the number of models that need to be tested using non-linear least squares optimization, allowing us to study systems with up to five intermediates. Furthermore, two intermediate systems can now be analyzed on a desktop computer, which eliminates the need for a distributed computing solution for most medium-sized data sets. Our new approach also allows us to study potential degeneracy in kinetic model selection, elucidating the limits of the method when working with large systems. This work establishes clear criteria for determining if experimental ·OH data is sufficient to determine the underlying kinetic model, or if other experimental modalities are required to resolve any degeneracy.
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Affiliation(s)
- Joshua S Martin
- Computational and Structural Biology Department, Wadsworth Center, Albany, NY 12208, USA
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37
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Laederach A, Das R, Vicens Q, Pearlman SM, Brenowitz M, Herschlag D, Altman RB. Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments. Nat Protoc 2008; 3:1395-401. [PMID: 18772866 DOI: 10.1038/nprot.2008.134] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We have developed protocols for rapidly quantifying the band intensities from nucleic acid chemical mapping gels at single-nucleotide resolution. These protocols are implemented in the software SAFA (semi-automated footprinting analysis) that can be downloaded without charge from http://safa.stanford.edu. The protocols implemented in SAFA have five steps: (i) lane identification, (ii) gel rectification, (iii) band assignment, (iv) model fitting and (v) band-intensity normalization. SAFA enables the rapid quantitation of gel images containing thousands of discrete bands, thereby eliminating a bottleneck to the analysis of chemical mapping experiments. An experienced user of the software can quantify a gel image in approximately 20 min. Although SAFA was developed to analyze hydroxyl radical (*OH) footprints, it effectively quantifies the gel images obtained with other types of chemical mapping probes. We also present a series of tutorial movies that illustrate the best practices and different steps in the SAFA analysis as a supplement to this protocol.
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Affiliation(s)
- Alain Laederach
- Department of Developmental Genetics and Bioinformatics, Wadsworth Center, Albany, New York 12208, USA.
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38
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Edwards AL, Batey RT. A structural basis for the recognition of 2'-deoxyguanosine by the purine riboswitch. J Mol Biol 2008; 385:938-48. [PMID: 19007790 DOI: 10.1016/j.jmb.2008.10.074] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Revised: 10/16/2008] [Accepted: 10/26/2008] [Indexed: 12/21/2022]
Abstract
Riboswitches are noncoding RNA elements that are commonly found in the 5'-untranslated region of bacterial mRNA. Binding of a small-molecule metabolite to the riboswitch aptamer domain guides the folding of the downstream sequence into one of two mutually exclusive secondary structures that directs gene expression. The purine riboswitch family, which regulates aspects of purine biosynthesis and transport, contains three distinct classes that specifically recognize guanine/hypoxanthine, adenine, or 2'-deoxyguanosine (dG). Structural analysis of the guanine and adenine classes revealed a binding pocket that almost completely buries the nucleobase within the core of the folded RNA. Thus, it is somewhat surprising that this family of RNA elements also recognizes dG. We have used a combination of structural and biochemical techniques to understand how the guanine riboswitch could be converted into a dG binder and the structural basis for dG recognition. These studies reveal that a limited number of sequence changes to a guanine-sensing RNA are required to cause a specificity switch from guanine to 2'-deoxyguanosine, and to impart an altered structure for accommodating the additional deoxyribose sugar moiety.
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Affiliation(s)
- Andrea L Edwards
- Department of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, CO 80309, USA
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39
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Vasa SM, Guex N, Wilkinson KA, Weeks KM, Giddings MC. ShapeFinder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis. RNA (NEW YORK, N.Y.) 2008; 14:1979-90. [PMID: 18772246 PMCID: PMC2553743 DOI: 10.1261/rna.1166808] [Citation(s) in RCA: 168] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Analysis of the long-range architecture of RNA is a challenging experimental and computational problem. Local nucleotide flexibility, which directly reports underlying base pairing and tertiary interactions in an RNA, can be comprehensively assessed at single nucleotide resolution using high-throughput selective 2'-hydroxyl acylation analyzed by primer extension (hSHAPE). hSHAPE resolves structure-sensitive chemical modification information by high-resolution capillary electrophoresis and typically yields quantitative nucleotide flexibility information for 300-650 nucleotides (nt) per experiment. The electropherograms generated in hSHAPE experiments provide a wealth of structural information; however, significant algorithmic analysis steps are required to generate quantitative and interpretable data. We have developed a set of software tools called ShapeFinder to make possible rapid analysis of raw sequencer data from hSHAPE, and most other classes of nucleic acid reactivity experiments. The algorithms in ShapeFinder (1) convert measured fluorescence intensity to quantitative cDNA fragment amounts, (2) correct for signal decay over read lengths extending to 600 nts or more, (3) align reactivity data to the known RNA sequence, and (4) quantify per nucleotide reactivities using whole-channel Gaussian integration. The algorithms and user interface tools implemented in ShapeFinder create new opportunities for tackling ambitious problems involving high-throughput analysis of structure-function relationships in large RNAs.
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Affiliation(s)
- Suzy M Vasa
- Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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40
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Gherghe CM, Mortimer SA, Krahn JM, Thompson NL, Weeks KM. Slow conformational dynamics at C2'-endo nucleotides in RNA. J Am Chem Soc 2008; 130:8884-5. [PMID: 18558680 PMCID: PMC4501255 DOI: 10.1021/ja802691e] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RNA molecules undergo local conformational dynamics on timescales spanning picoseconds to minutes. Slower local motions have the greater potential to govern RNA folding, ligand recognition, and ribonucleoprotein assembly reactions but are difficult to detect in large RNAs with complex structures. RNA SHAPE chemistry employs acylation of the ribose 2'-hydroxyl position to measure local nucleotide flexibility in RNA and is well-characterized by a mechanism in which each nucleotide samples unreactive (closed) and reactive (open) states. We monitor RNA conformational dynamics over distinct time domains by varying the electrophilicity of the acylating reagent. Select C2'-endo nucleotides are nonreactive toward fast reagents but reactive toward slower SHAPE reagents in both model RNAs and in a large RNA with a tertiary fold. We conclude, first, that the C2'-endo conformation by itself does not govern SHAPE reactivity. However, some C2'-endo nucleotides undergo extraordinarily slow conformational changes, on the order of 10(-4) s(-1). Due to their distinctive local dynamics, C2'-endo nucleotides have the potential to function as rate-determining molecular switches and are likely to play central, currently unexplored, roles in RNA folding and function.
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Affiliation(s)
- Costin M. Gherghe
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
| | - Stefanie A. Mortimer
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
| | - Joseph M. Krahn
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
| | - Nancy L. Thompson
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
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High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. PLoS Biol 2008; 6:e96. [PMID: 18447581 PMCID: PMC2689691 DOI: 10.1371/journal.pbio.0060096] [Citation(s) in RCA: 322] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Accepted: 03/05/2008] [Indexed: 02/04/2023] Open
Abstract
Replication and pathogenesis of the human immunodeficiency virus (HIV) is tightly linked to the structure of its RNA genome, but genome structure in infectious virions is poorly understood. We invent high-throughput SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) technology, which uses many of the same tools as DNA sequencing, to quantify RNA backbone flexibility at single-nucleotide resolution and from which robust structural information can be immediately derived. We analyze the structure of HIV-1 genomic RNA in four biologically instructive states, including the authentic viral genome inside native particles. Remarkably, given the large number of plausible local structures, the first 10% of the HIV-1 genome exists in a single, predominant conformation in all four states. We also discover that noncoding regions functioning in a regulatory role have significantly lower (p-value < 0.0001) SHAPE reactivities, and hence more structure, than do viral coding regions that function as the template for protein synthesis. By directly monitoring protein binding inside virions, we identify the RNA recognition motif for the viral nucleocapsid protein. Seven structurally homologous binding sites occur in a well-defined domain in the genome, consistent with a role in directing specific packaging of genomic RNA into nascent virions. In addition, we identify two distinct motifs that are targets for the duplex destabilizing activity of this same protein. The nucleocapsid protein destabilizes local HIV-1 RNA structure in ways likely to facilitate initial movement both of the retroviral reverse transcriptase from its tRNA primer and of the ribosome in coding regions. Each of the three nucleocapsid interaction motifs falls in a specific genome domain, indicating that local protein interactions can be organized by the long-range architecture of an RNA. High-throughput SHAPE reveals a comprehensive view of HIV-1 RNA genome structure, and further application of this technology will make possible newly informative analysis of any RNA in a cellular transcriptome. The function of the RNA genome of the human immunodeficiency virus (HIV) is determined both by its sequence and by its ability to fold back on itself to form specific higher-order structures. In order to describe physical structures in a region of the HIV RNA genome known to play multiple, critical roles in viral replication and pathogenesis, we invent a high-throughput, quantitative, and comprehensive structure-mapping approach that locates flexible (unpaired) nucleotides within a folded RNA, assaying hundreds of nucleotides at a time. We find that the first 10% of the HIV-1 genome has a single predominant structure and that regulatory motifs have significantly greater structure than do protein-coding segments. The HIV genome interacts with numerous proteins, including multiple copies of the nucleocapsid protein. We directly map RNA–protein interactions inside virions and discover that the nucleocapsid prottein interacts with viral RNA in at least three distinct ways, depending on the context within the overall genome structure. Further application of the high-throughput RNA-structure analysis tools described here will make it possible to address diverse structure–function relationships in intact cellular and viral RNAs. Development of novel, quantitative, high-throughput RNA structure analysis tools allows the outline of structure-function relationships for the first 10% of an HIV genome, discovery of structural differences between regulatory and coding regions, and analysis of protein-RNA interactions inside authentic virions.
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42
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Mitra S, Shcherbakova IV, Altman RB, Brenowitz M, Laederach A. High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis. Nucleic Acids Res 2008; 36:e63. [PMID: 18477638 PMCID: PMC2441812 DOI: 10.1093/nar/gkn267] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The use of capillary electrophoresis with fluorescently labeled nucleic acids revolutionized DNA sequencing, effectively fueling the genomic revolution. We present an application of this technology for the high-throughput structural analysis of nucleic acids by chemical and enzymatic mapping (‘footprinting’). We achieve the throughput and data quality necessary for genomic-scale structural analysis by combining fluorophore labeling of nucleic acids with novel quantitation algorithms. We implemented these algorithms in the CAFA (capillary automated footprinting analysis) open-source software that is downloadable gratis from https://simtk.org/home/cafa. The accuracy, throughput and reproducibility of CAFA analysis are demonstrated using hydroxyl radical footprinting of RNA. The versatility of CAFA is illustrated by dimethyl sulfate mapping of RNA secondary structure and DNase I mapping of a protein binding to a specific sequence of DNA. Our experimental and computational approach facilitates the acquisition of high-throughput chemical probing data for solution structural analysis of nucleic acids.
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Affiliation(s)
- Somdeb Mitra
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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43
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Structural inference of native and partially folded RNA by high-throughput contact mapping. Proc Natl Acad Sci U S A 2008; 105:4144-9. [PMID: 18322008 DOI: 10.1073/pnas.0709032105] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The biological behaviors of ribozymes, riboswitches, and numerous other functional RNA molecules are critically dependent on their tertiary folding and their ability to sample multiple functional states. The conformational heterogeneity and partially folded nature of most of these states has rendered their characterization by high-resolution structural approaches difficult or even intractable. Here we introduce a method to rapidly infer the tertiary helical arrangements of large RNA molecules in their native and non-native solution states. Multiplexed hydroxyl radical (.OH) cleavage analysis (MOHCA) enables the high-throughput detection of numerous pairs of contacting residues via random incorporation of radical cleavage agents followed by two-dimensional gel electrophoresis. We validated this technology by recapitulating the unfolded and native states of a well studied model RNA, the P4-P6 domain of the Tetrahymena ribozyme, at subhelical resolution. We then applied MOHCA to a recently discovered third state of the P4-P6 RNA that is stabilized by high concentrations of monovalent salt and whose partial order precludes conventional techniques for structure determination. The three-dimensional portrait of a compact, non-native RNA state reveals a well ordered subset of native tertiary contacts, in contrast to the dynamic but otherwise similar molten globule states of proteins. With its applicability to nearly any solution state, we expect MOHCA to be a powerful tool for illuminating the many functional structures of large RNA molecules and RNA/protein complexes.
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Ying BW, Fourmy D, Yoshizawa S. Substitution of the use of radioactivity by fluorescence for biochemical studies of RNA. RNA (NEW YORK, N.Y.) 2007; 13:2042-50. [PMID: 17848413 PMCID: PMC2040085 DOI: 10.1261/rna.637907] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
We present here the use of fluorescent methodologies for structural and functional studies of RNA in place of radioactivity. The methods are highly sensitive and quantitative with the use of an infrared fluorescence imaging system. IRD-700 and IRD-800 labels are used for fluorescence detection. Chemical probing methods are largely used for mapping RNA secondary structure and to monitor ligand interactions and conformational changes involving individual bases of RNA. The new fluorescent primer extension methodology allows simple and fast chemical probing of RNA with high sensitivity. IRD-700 and IRD-800 labeled primers can also be used to monitor protein-RNA interactions by fluorescent mobility shift assays. The speed and ease of these approaches are advantages over prior methods that used hazardous radioisotopes. Structural and biochemical investigations of RNA should benefit from the use of these fluorescent methodologies.
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Affiliation(s)
- Bei-Wen Ying
- Laboratoire de Chimie et Biologie Structurales, Gif-sur-Yvette, France
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Dorman N. Citations. Biotechniques 2007. [DOI: 10.2144/000112481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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