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SARS-CoV-2 ribosomal frameshifting pseudoknot: Improved secondary structure prediction and detection of inter-viral structural similarity

https://doi.org/10.1101/2020.09.15.298604
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Mechanisms and implications of programmed translational frameshifting
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How RNA folds
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Coronaviruses: An Overview of Their Replication and Pathogenesis
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Middle East Respiratory Syndrome
inferredcites →https://doi.org/10.1016/j.bpj.2020.11.1986openalex-snapshot
Modeling the Structure of the Frameshift-Stimulatory Pseudoknot in SARS-CoV-2 Reveals Multiple Possible Conformers
inferredcites →https://doi.org/10.1016/j.cell.2014.04.041openalex-snapshot
Programmed –1 Frameshifting by Kinetic Partitioning during Impeded Translocation
inferredcites →https://doi.org/10.1016/j.cmi.2020.03.026openalex-snapshot
COVID-19, SARS and MERS: are they closely related?
inferredcites →https://doi.org/10.1016/j.genrep.2020.100682openalex-snapshot
Genomic characterization of a novel SARS-CoV-2
inferredcites →https://doi.org/10.1016/j.jmb.2020.09.006openalex-snapshot
Anti-Frameshifting Ligand Active against SARS Coronavirus-2 Is Resistant to Natural Mutations of the Frameshift-Stimulatory Pseudoknot
inferredcites →https://doi.org/10.1016/s0140-6736(19)33221-0openalex-snapshot
Middle East respiratory syndrome
inferredcites →https://doi.org/10.1016/s0140-6736(20)30183-5openalex-snapshot
Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China
inferredcites →https://doi.org/10.1021/ar200098topenalex-snapshot
The Molecular Interactions That Stabilize RNA Tertiary Structure: RNA Motifs, Patterns, and Networks
inferredcites →https://doi.org/10.1021/ja0436749openalex-snapshot
RNA SHAPE Chemistry Reveals Nonhierarchical Interactions Dominate Equilibrium Structural Transitions in tRNAAsp Transcripts
inferredcites →https://doi.org/10.1021/ja1098325openalex-snapshot
Identification of RNA Pseudoknot-Binding Ligand That Inhibits the −1 Ribosomal Frameshifting of SARS-Coronavirus by Structure-Based Virtual Screening
inferredcites →https://doi.org/10.1021/ja410344bopenalex-snapshot
Anti-frameshifting Ligand Reduces the Conformational Plasticity of the SARS Virus Pseudoknot
inferredcites →https://doi.org/10.1038/msb.2011.75openalex-snapshot
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
inferredcites →https://doi.org/10.1038/nature06684openalex-snapshot
The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data
inferredcites →https://doi.org/10.1038/nature10126openalex-snapshot
The ribosome uses two active mechanisms to unwind messenger RNA during translation
inferredcites →https://doi.org/10.1073/pnas.0608668104openalex-snapshot
Correlation between mechanical strength of messenger RNA pseudoknots and ribosomal frameshifting
inferredcites →https://doi.org/10.1073/pnas.0905046106openalex-snapshot
Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of –1 ribosomal frameshifting
inferredcites →https://doi.org/10.1073/pnas.0906625106openalex-snapshot
Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures
inferredcites →https://doi.org/10.1073/pnas.1204114109openalex-snapshot
Programmed −1 frameshifting efficiency correlates with RNA pseudoknot conformational plasticity, not resistance to mechanical unfolding
inferredcites →https://doi.org/10.1073/pnas.1321930111openalex-snapshot
Transactivation of programmed ribosomal frameshifting by a viral protein
inferredcites →https://doi.org/10.1074/jbc.ac120.013449openalex-snapshot
Structural and functional conservation of the programmed −1 ribosomal frameshift signal of SARS coronavirus 2 (SARS-CoV-2)
inferredcites →https://doi.org/10.1093/bioinformatics/btp252openalex-snapshot
PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots
inferredcites →https://doi.org/10.1093/bioinformatics/btv221openalex-snapshot
iFoldRNA v2: folding RNA with constraints
inferredcites →https://doi.org/10.1093/nar/gki329openalex-snapshot
Torsional restraint: a new twist on frameshifting pseudoknots
inferredcites →https://doi.org/10.1093/nar/gkl164openalex-snapshot
BLAST: improvements for better sequence analysis
inferredcites →https://doi.org/10.1093/nar/gks1195openalex-snapshot
GenBank
inferredcites →https://doi.org/10.1093/nar/gks1361openalex-snapshot
RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus
inferredcites →https://doi.org/10.1093/nar/gku1207openalex-snapshot
NCBI Viral Genomes Resource
inferredcites →https://doi.org/10.1093/nar/gkw530openalex-snapshot
Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use
inferredcites →https://doi.org/10.1093/nar/gky314openalex-snapshot
RNApdbee 2.0: multifunctional tool for RNA structure annotation
inferredcites →https://doi.org/10.1093/nar/gky636openalex-snapshot
Translocation kinetics and structural dynamics of ribosomes are modulated by the conformational plasticity of downstream pseudoknots
inferredcites →https://doi.org/10.1093/nar/gkz394openalex-snapshot
Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures
inferredcites →https://doi.org/10.1101/2020.06.26.174193openalex-snapshot
A cytosine-to-uracil change within the programmed -1 ribosomal frameshift signal of SARS-CoV-2 results in structural similarities with the MERS-CoV signal
inferredcites →https://doi.org/10.1126/science.1181085openalex-snapshot
Topology Links RNA Secondary Structure with Global Conformation, Dynamics, and Adaptation
inferredcites →https://doi.org/10.1128/jvi.02480-09openalex-snapshot
Achieving a Golden Mean: Mechanisms by Which Coronaviruses Ensure Synthesis of the Correct Stoichiometric Ratios of Viral Proteins
inferredcites →https://doi.org/10.1136/bmj.m606openalex-snapshot
Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series
inferredcites →https://doi.org/10.1142/9789814295291_0009openalex-snapshot
RNAZ 2.0:
inferredcites →https://doi.org/10.1186/1471-2105-15-147openalex-snapshot
A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures
inferredcites →https://doi.org/10.1186/s12859-015-0718-6openalex-snapshot
New in silico approach to assessing RNA secondary structures with non-canonical base pairs
inferredcites →https://doi.org/10.1261/rna.1689910openalex-snapshot
Improved free energy parameters for RNA pseudoknotted secondary structure prediction
inferredcites →https://doi.org/10.1261/rna.7284905openalex-snapshot
HotKnots: Heuristic prediction of RNA secondary structures including pseudoknots
inferredcites →https://doi.org/10.1261/rna.894608openalex-snapshot
Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms
inferredcites →https://doi.org/10.1371/journal.pbio.0030172openalex-snapshot
A Three-Stemmed mRNA Pseudoknot in the SARS Coronavirus Frameshift Signal
inferredcites →https://doi.org/10.1371/journal.pcbi.1008603openalex-snapshot
Modeling the structure of the frameshift-stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers
inferredcites →https://doi.org/10.2741/4633openalex-snapshot
Procoagulant activity during viral infections
inferredcites →https://doi.org/10.2807/1560-7917.es.2017.22.13.30494openalex-snapshot
GISAID: Global initiative on sharing all influenza data – from vision to reality
inferredcites →https://doi.org/10.3390/ijms20174116openalex-snapshot
3dRNA v2.0: An Updated Web Server for RNA 3D Structure Prediction
inferredcites →https://doi.org/10.3390/v5010279openalex-snapshot
Altering SARS Coronavirus Frameshift Efficiency Affects Genomic and Subgenomic RNA Production
inferredcites →https://doi.org/10.3760/cma.j.issn.0254-6450.2020.02.003openalex-snapshot
[The epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (COVID-19) in China].
inferredcites →https://doi.org/10.46234/ccdcw2020.032openalex-snapshot
The Epidemiological Characteristics of an Outbreak of 2019 Novel Coronavirus Diseases (COVID-19) — China, 2020

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.csbj.2022.11.007openalex-snapshot
Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions
inferred← citeshttps://doi.org/10.1021/jacs.1c03003openalex-snapshot
To Knot or Not to Knot: Multiple Conformations of the SARS-CoV-2 Frameshifting RNA Element
inferred← citeshttps://doi.org/10.3390/ijms232415917openalex-snapshot
Examples of Structural Motifs in Viral Genomes and Approaches for RNA Structure Characterization
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