4.7 Review

Examples of Structural Motifs in Viral Genomes and Approaches for RNA Structure Characterization

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Review Biochemistry & Molecular Biology

From cells to atoms: Cryo-EM as an essential tool to investigate pathogen biology, host-pathogen interaction, and drug discovery

Doulin C. Shepherd et al.

Summary: Electron cryo-microscopy (cryo-EM) has become a powerful tool in structural biology and cell biology, bridging the resolution gap between the two fields. It has revolutionized our understanding of pathogen biology, host-pathogen interaction, and structure-based drug discovery. The unique ability of cryo-EM to provide information at various spatial resolution scales has led to significant advancements in these areas.

MOLECULAR MICROBIOLOGY (2022)

Article Biochemistry & Molecular Biology

Length-Dependent Deep Learning Model for RNA Secondary Structure Prediction

Kangkun Mao et al.

Summary: Deep learning methods have shown better performance than traditional methods in RNA secondary structure prediction, but there is still room for improvement. This is because the length and secondary structures of RNAs vary significantly. Existing deep learning models can't learn very different secondary structures since they are length-independent. In this study, we propose a length-dependent model that further trains the length-independent model using transfer learning for different length ranges of RNAs. The benchmarking results demonstrate that the length-dependent model outperforms the usual length-independent model.

MOLECULES (2022)

Article Virology

Secondary Structure of Subgenomic RNA M of SARS-CoV-2

Marta Soszynska-Jozwiak et al.

Summary: This study investigates the structure of a subgenomic RNA of SARS-CoV-2 and identifies its important functions. The findings of this study enhance our understanding of virus biology and could be utilized in the development of new therapeutics.

VIRUSES-BASEL (2022)

Article Biochemistry & Molecular Biology

RNAspider: a webserver to analyze entanglements in RNA 3D structures

Kamil Luwanski et al.

Summary: Advancements in experimental and computational techniques have allowed for the exploration of large and complex RNA 3D structures, leading to the discovery of previously unstudied properties and motifs. RNAspider is a web server that automatically identifies, classifies, and visualizes entanglements in RNA tertiary structures.

NUCLEIC ACIDS RESEARCH (2022)

Article Biochemistry & Molecular Biology

Programmable antivirals targeting critical conserved viral RNA secondary structures from influenza A virus and SARS-CoV-2

Rachel J. Hagey et al.

Summary: By targeting conserved RNA secondary structures, researchers have discovered a potential therapeutic approach that can effectively treat multiple viruses and has shown good efficacy and resistance in experiments. These findings are important for antiviral prophylaxis and post-exposure therapy.

NATURE MEDICINE (2022)

Article Genetics & Heredity

Prediction and analysis of functional RNA structures within the integrative genomics viewer

Warren B. Rouse et al.

Summary: In recent years, there has been a surge of interest in RNA secondary structure due to its implications in biological functions and therapeutics. To enhance the study of RNA secondary structure, we have integrated the functional secondary structure prediction tool ScanFold into IGV. By comparing predicted structures with published data, functional inferences can be made and potential drug targets can be discovered.

NAR GENOMICS AND BIOINFORMATICS (2022)

Article Biochemical Research Methods

Discovery of G-quadruplex-forming sequences in SARS-CoV-2

Danyang Ji et al.

Summary: Researchers have identified potential G-quadruplex-forming sequences in the SARS-CoV-2 RNA genome and other Coronaviridae family members, with some confirmed to form RNA G-quadruplex structures in vitro. These structures were found to interact with viral helicase (nsp13), suggesting a potential target for inhibiting the virus.

BRIEFINGS IN BIOINFORMATICS (2021)

Article Biochemistry & Molecular Biology

Structure-based virtual screening and molecular dynamics simulation of SARS-CoV-2 Guanine-N7 methyltransferase (nsp14) for identifying antiviral inhibitors against COVID-19

Chandrabose Selvaraj et al.

Summary: This study focuses on screening for antiviral inhibitors targeting guanine-N7 methyltransferase (N7-MTase), a key drug target in the first methylation step of the SARS-CoV-2 RNA capping mechanism. Compounds binding the substrate-binding site can disrupt enzyme catalysis and hinder 5'-end cap formation, crucial for mimicking host RNA and evading host immune responses. Our research suggests potential compounds from the Traditional Chinese Medicine (TCM) database through a combination of computational approaches.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2021)

Review Biotechnology & Applied Microbiology

Genetics and genomics of SARS-CoV-2: A review of the literature with the special focus on genetic diversity and SARS-CoV-2 genome detection

Azadeh Rahimi et al.

Summary: The study examined the genetic characteristics of SARS-CoV-2, including genetic diversity, mutations, diagnostic methods, and vaccination strategies, and discussed the unanswered questions and uncertainties in these areas.

GENOMICS (2021)

Article Biology

Structural plasticity of mumps virus nucleocapsids with cryo-EM structures

Hong Shan et al.

Summary: The study describes high-resolution structures of the Nucleoprotein in two different oligomeric states and four different higher-order helical structures. The structural rearrangements required to transition between the different helical assemblies obtained are highlighted, providing a basis for the structural plasticity among different MuV nucleocapsids.

COMMUNICATIONS BIOLOGY (2021)

Article Biochemistry & Molecular Biology

RASP: an atlas of transcriptome-wide RNA secondary structure probing data

Pan Li et al.

Summary: RASP is a comprehensive RNA structure probing database that collects 161 deduplicated transcriptome-wide RNA secondary structure probing datasets from 38 papers, covering 18 species and 18 experimental methods. It specifically curates up-to-date datasets for the RNA genome of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, providing a user-friendly interface for querying, browsing, and visualizing RNA structure profiles based on experimental data.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms

Nicholas C. Huston et al.

Summary: This study utilized a novel approach to determine the secondary structure of the SARS-CoV-2 RNA genome, revealing well-folded RNA structures in infected cells. The research also identified unique aspects of the SARS-CoV-2 genome architecture and conserved features across beta-coronaviruses. The presented native, secondary structure of SARS-CoV-2 serves as a roadmap for focused studies on the viral life cycle, primer design, and identification of RNA drug targets against COVID-19.

MOLECULAR CELL (2021)

Article Biochemistry & Molecular Biology

Universal and strain specific structure features of segment 8 genomic RNA of influenza A virus-application of 4-thiouridine photocrosslinking

Marta Soszynska-Jozwiak et al.

Summary: In this study, RNA secondary structures of influenza A virus were determined using chemical mapping and 4-thiouridine (4sU) crosslinking, revealing both universal and unique features of different strains. The method highlighted the three-dimensional properties and allowed for proposing long-range interactions in the RNA secondary structure. The combination of 4sU mapping with chemical mapping and bioinformatic analysis could enhance RNA structure determination and target recognition for antisense strategies or viral RNA detection.

JOURNAL OF BIOLOGICAL CHEMISTRY (2021)

Article Medicine, Research & Experimental

Inhibition of Zika virus replication by G-quadruplex-binding ligands

Prativa Majee et al.

Summary: Research identified potential non-canonical G-quadruplex structures in the Zika virus genome, which can be targeted by ligands like Braco-19 and TMPyP4 to inhibit virus replication and protein production.

MOLECULAR THERAPY-NUCLEIC ACIDS (2021)

Article Virology

Generation of A Stable GFP-reporter Zika Virus System for High-throughput Screening of Zika Virus Inhibitors

Jing-Wei Zhang et al.

Summary: The study developed an efficient high-throughput screening assay for ZIKV inhibitors and validated several compounds with therapeutic potential for inhibiting ZIKV infection.

VIROLOGICA SINICA (2021)

Article Pharmacology & Pharmacy

Identification of a novel inhibitor targeting influenza A virus group 2 hemagglutinins

Ruikun Du et al.

Summary: A novel antiviral agent, CBS1194, specific to group 2 IAVs was identified through high-throughput screening, showing potential as a lead compound for further development.

ANTIVIRAL RESEARCH (2021)

Article Multidisciplinary Sciences

RNA secondary structure prediction using deep learning with thermodynamic integration

Kengo Sato et al.

Summary: Combining thermodynamic information with deep learning can improve the robustness of RNA secondary structure prediction compared to existing algorithms.

NATURE COMMUNICATIONS (2021)

Article Microbiology

Motif mutations in pseudoknot stem I upstream of start codon in Senecavirus A genome: Impacts on activity of viral IRES and on rescue of recombinant virus

Fuxiao Liu et al.

Summary: SVA, a virus belonging to the genus Senecavirus in the family Picornaviridae, has a genome of approximately 7300 nucleotides with 5' and 3' UTRs. The study showed that PKS-Ib is essential for viral growth.

VETERINARY MICROBIOLOGY (2021)

Article Immunology

Next-generation sequencing technologies: An overview

Taishan Hu et al.

Summary: This review discusses the development and advantages or disadvantages of short-read and long-read sequencing technologies, pointing out that emerging developments for third-generation technologies hold promise for the next wave of sequencing evolution, with the co-existence of longer read lengths and high accuracy.

HUMAN IMMUNOLOGY (2021)

Article Cell Biology

High-throughput screening identifies established drugs as SARS-CoV-2 PLpro inhibitors

Yao Zhao et al.

Summary: This study identified four compounds that inhibit SARS-CoV-2 PLpro with strong antiviral activities, particularly highlighting YM155's unique binding mode targeted at three hot spots on PLpro, suggesting their potential as clinical leads for COVID-19 treatments.

PROTEIN & CELL (2021)

Article Chemistry, Medicinal

Targeting a Potential G-Quadruplex Forming Sequence Found in the West Nile Virus Genome by Complementary Gamma-Peptide Nucleic Acid Oligomers

Srijani Sarkar et al.

Summary: This study designed gamma-modified peptide nucleic acid (gamma PNA) oligomers to target a newly identified guanine-rich gene sequence in the WNV genome, showing potential for inhibiting WNV replication and transcription. The gamma PNAs demonstrated strong binding to the target with low femtomolar affinity at physiological temperature, indicating a promising antiviral strategy.

ACS INFECTIOUS DISEASES (2021)

Article Biochemistry & Molecular Biology

Identification and Structural Aspects of G-Quadruplex-Forming Sequences from the Influenza A Virus Genome

Maria Tomaszewska et al.

Summary: Influenza A virus (IAV) is a significant research subject due to its ability to cause seasonal epidemics and pandemics. This study focused on the presence of G-rich sequences in the IAV genome and their potential to form RNA G-quadruplex structures. The researchers identified 12 potential quadruplex-forming sequences (PQS), with three confirmed to adopt G4 structures by various biophysical methods, potentially indicating their role in virus biology.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Article Biochemistry & Molecular Biology

High-Throughput Fluorescent Assay for Inhibitor Screening of Proteases from RNA Viruses

Bara Cihlova et al.

Summary: This study developed an inexpensive high-throughput fluorescent energy transfer assay for testing inhibitors of viral proteases, demonstrating versatility and robustness for detecting the inhibitory effects on papain-like protease from SARS-CoV-2 and other viruses, with monitoring of reaction progress through loss of FRET signal.

MOLECULES (2021)

Review Biochemistry & Molecular Biology

RNA structure probing uncovers RNA structure-dependent biological functions

Xi-Wen Wang et al.

Summary: RNA molecules fold into complex structures to perform diverse functions in cells, and recent advancements in RNA structural probing have led to profound discoveries linking RNA regulation and biological processes. Understanding how long noncoding RNAs form unique secondary structures is crucial for studying their interactions with proteins and regulating RNA functions. These dynamic structures play a key role in mediating RNA regulatory functions and future developments aim to improve sensitivity and resolution for more physiologically relevant studies.

NATURE CHEMICAL BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Cryo-EM and antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome

Kaiming Zhang et al.

Summary: A 6.9 angstrom resolution cryo-EM structure of the SARS-CoV-2 frameshift stimulation element (FSE) was successfully demonstrated in this study, guiding the development of antisense oligonucleotides that impair virus replication. The FSE, crucial for balanced expression of viral proteins, is becoming a key target for drug discovery campaigns against COVID-19.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2021)

Article Virology

Discovery of an imidazonaphthyridine and a riminophenazine as potent anti-Zika virus agents through a replicon-based high-throughput screening

Rafaela Sachetto Fernandes et al.

Summary: The 2015/16 Zika virus epidemic caused nearly 1 million confirmed cases in 84 countries and was associated with congenital microcephaly and Guillain-Barre syndrome. A ZIKV replicon cell line was developed and characterized for screening viral replication inhibitors. Two molecules with potent anti-ZIKV activities were identified through this replicon-based cell system, showing potential for antiviral drug discovery.

VIRUS RESEARCH (2021)

Article Multidisciplinary Sciences

Comprehensive mapping of SARS-CoV-2 interactions in vivo reveals functional virus-host interactions

Siwy Ling Yang et al.

Summary: The study identified functional structural elements within the SARS-CoV-2 genome, showed differences in RNA folding between wildtype and mutant viruses, and found hundreds of RNA-RNA interactions within the virus genome and between virus and host RNAs. The virus genome strongly binds to mitochondrial and small nucleolar RNAs and undergoes extensive 2'-O-methylation.

NATURE COMMUNICATIONS (2021)

Article Multidisciplinary Sciences

Structural dynamics of single SARS-CoV-2 pseudoknot molecules reveal topologically distinct conformers

Krishna Neupane et al.

Summary: The RNA pseudoknot of SARS-CoV-2 that induces programmed ribosomal frameshifting is a potential drug target. Through optical tweezer experiments, researchers identified two pseudoknotted conformers with distinct topologies and revealed the folding mechanism of the frameshift signal, shedding light on its conformational heterogeneity and implications for drug discovery based on structure.

NATURE COMMUNICATIONS (2021)

Article Microbiology

Extensive C->U transition biases in the genomes of a wide range of mammalian RNA viruses; potential associations with transcriptional mutations, damage- or host-mediated editing of viral RNA

Peter Simmonds et al.

Summary: The study found a preponderance of C->U transitions in diverse mammalian RNA viruses, suggesting a potential RNA editing process driving this phenomenon. The presence of genome scale RNA secondary structure was significantly associated with C->U/U->C transition asymmetries, indicating a possible RNA structure dependence of sites targeted for C->U mutations. These C->U mutations accounted for a significant portion of standing sequence variability of structured viruses, potentially driving their sequence diversification and longer-term evolution.

PLOS PATHOGENS (2021)

Review Biochemistry & Molecular Biology

Cryo-electron microscopy for the study of virus assembly

Daniel Luque et al.

NATURE CHEMICAL BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Mapping RNA-capsid interactions and RNA secondary structure within virus particles using next-generation sequencing

Yiyang Zhou et al.

NUCLEIC ACIDS RESEARCH (2020)

Editorial Material Microbiology

The Challenges of Vaccine Development against a New Virus during a Pandemic

Michael S. Diamond et al.

CELL HOST & MICROBE (2020)

Article Biochemical Research Methods

Viral RNA structure analysis using DMS-MaPseq

Phillip Tomezsko et al.

METHODS (2020)

Article Multidisciplinary Sciences

Discovery of direct-acting antiviral agents with a graphene-based fluorescent nanosensor

Se-Jin Park et al.

SCIENCE ADVANCES (2020)

Article Multidisciplinary Sciences

Determination of RNA structural diversity and its role in HIV-1 RNA splicing

Phillip J. Tomezsko et al.

NATURE (2020)

Article Infectious Diseases

Genetic diversity and evolution of SARS-CoV-2

Tung Phan

INFECTION GENETICS AND EVOLUTION (2020)

Article Biochemistry & Molecular Biology

High Throughput Virtual Screening to Discover Inhibitors of the Main Protease of the Coronavirus SARS-CoV-2

Olujide O. Olubiyi et al.

MOLECULES (2020)

Article Cell Biology

Mapping of Influenza Virus RNA-RNA Interactions Reveals a Flexible Network

Valerie Le Sage et al.

CELL REPORTS (2020)

Article Biochemistry & Molecular Biology

Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy

Anna Wacker et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Virology

Physical and Functional Analysis of Viral RNA Genomes by SHAPE

Mark A. Boerneke et al.

ANNUAL REVIEW OF VIROLOGY, VOL 6, 2019 (2019)

Article Microbiology

The structure of the influenza A virus genome

Bernadeta Dadonaite et al.

NATURE MICROBIOLOGY (2019)

Article Biochemical Research Methods

In-cell RNA structure probing with SHAPE-MaP

Matthew J. Smola et al.

NATURE PROTOCOLS (2018)

Review Microbiology

Structural and Functional Motifs in Influenza Virus RNAs

Damien Ferhadian et al.

FRONTIERS IN MICROBIOLOGY (2018)

Review Microbiology

Signals Involved in Regulation of Hepatitis C Virus RNA Genome Translation and Replication

Michael Niepmann et al.

FRONTIERS IN MICROBIOLOGY (2018)

Review Plant Sciences

New Era of Studying RNA Secondary Structure and Its Influence on Gene Regulation in Plants

Xiaofei Yang et al.

FRONTIERS IN PLANT SCIENCE (2018)

Review Immunology

RNA Structure-A Neglected Puppet Master for the Evolution of Virus and Host Immunity

Redmond P. Smyth et al.

FRONTIERS IN IMMUNOLOGY (2018)

Article Multidisciplinary Sciences

Cryo-EM structure of the Ebola virus nucleoprotein-RNA complex at 3.6 angstrom resolution

Yukihiko Sugita et al.

NATURE (2018)

Article Multidisciplinary Sciences

Pervasive tertiary structure in the dengue virus RNA genome

Elizabeth A. Dethoff et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Multidisciplinary Sciences

The chaperone-like activity of the hepatitis C virus IRES and CRE elements regulates genome dimerization

Cristina Romero-Lopez et al.

SCIENTIFIC REPORTS (2017)

Article Biochemistry & Molecular Biology

Identification of dengue viral RNA-dependent RNA polymerase inhibitor using computational fragment-based approaches and molecular dynamics study

Shanmugam Anusuya et al.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2016)

Article Biochemistry & Molecular Biology

Modeling Three-Dimensional Structural Motifs of Viral IRES

Gloria Lozano et al.

JOURNAL OF MOLECULAR BIOLOGY (2016)

Article Biochemistry & Molecular Biology

A Potassium Ion-Dependent RNA Structural Switch Regulates Human Pre-miRNA 92b Maturation

Gayan Mirihana Arachchilage et al.

CHEMISTRY & BIOLOGY (2015)

Article Multidisciplinary Sciences

Structure of influenza A polymerase bound to the viral RNA promoter

Alexander Pflug et al.

NATURE (2014)

Article Multidisciplinary Sciences

Single-molecule FRET reveals a corkscrew RNA structure for the polymerase-bound influenza virus promoter

Alexandra I. Tomescu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Review Biochemistry & Molecular Biology

Selective packaging of the influenza A genome and consequences for genetic reassortment

Marie Gerber et al.

TRENDS IN MICROBIOLOGY (2014)

Article Biochemistry & Molecular Biology

RNAstructure: web servers for RNA secondary structure prediction and analysis

Stanislav Bellaousov et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Multidisciplinary Sciences

A functional sequence-specific interaction between influenza A virus genomic RNA segments

Cyrille Gavazzi et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Review Biochemistry & Molecular Biology

The Role of RNA Structure in Posttranscriptional Regulation of Gene Expression

Elina Jacobs et al.

JOURNAL OF GENETICS AND GENOMICS (2012)

Article Biochemical Research Methods

ViennaRNA Package 2.0

Ronny Lorenz et al.

ALGORITHMS FOR MOLECULAR BIOLOGY (2011)

Article Biochemical Research Methods

TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences

Arif O. Harmanci et al.

BMC BIOINFORMATICS (2011)

Review Immunology

Influenza Virus RNA Structure: Unique and Common Features

Alexander P. Gultyaev et al.

INTERNATIONAL REVIEWS OF IMMUNOLOGY (2010)

Article Virology

Functional analysis of structural motifs in dicistroviruses

Nobuhiko Nakashima et al.

VIRUS RESEARCH (2009)

Article Biochemistry & Molecular Biology

The Vienna RNA Websuite

Andreas R. Gruber et al.

NUCLEIC ACIDS RESEARCH (2008)

Review Microbiology

Viral RNA pseudoknots: versatile motifs in gene expression and replication

Ian Brierley et al.

NATURE REVIEWS MICROBIOLOGY (2007)

Article Biochemistry & Molecular Biology

Mfold web server for nucleic acid folding and hybridization prediction

M Zuker

NUCLEIC ACIDS RESEARCH (2003)

Article Biochemistry & Molecular Biology

Structure and function analysis of the poliovirus cis-acting replication element (CRE)

IG Goodfellow et al.