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Science (New York, N.Y.) Sep 2021The human small subunit processome mediates early maturation of the small ribosomal subunit by coupling RNA folding to subsequent RNA cleavage and processing steps. We...
The human small subunit processome mediates early maturation of the small ribosomal subunit by coupling RNA folding to subsequent RNA cleavage and processing steps. We report the high-resolution cryo–electron microscopy structures of maturing human small subunit (SSU) processomes at resolutions of 2.7 to 3.9 angstroms. These structures reveal the molecular mechanisms that enable crucial progressions during SSU processome maturation. RNA folding states within these particles are communicated to and coordinated with key enzymes that drive irreversible steps such as targeted exosome-mediated RNA degradation, protein-guided site-specific endonucleolytic RNA cleavage, and tightly controlled RNA unwinding. These conserved mechanisms highlight the SSU processome’s impressive structural plasticity, which endows this 4.5-megadalton nucleolar assembly with the distinctive ability to mature the small ribosomal subunit from within.
Topics: Cell Nucleolus; Cryoelectron Microscopy; DEAD-box RNA Helicases; Humans; RNA Cleavage; RNA Folding; RNA Splicing Factors; RNA Stability; RNA, Small Nucleolar
PubMed: 34516797
DOI: 10.1126/science.abj5338 -
RNA (New York, N.Y.) Apr 2022Multistrand RNA complexes play a critical role in RNA-related biological processes. The understanding of RNA functions and the rational design of RNA nanostructures...
Multistrand RNA complexes play a critical role in RNA-related biological processes. The understanding of RNA functions and the rational design of RNA nanostructures require accurate prediction of the structure and folding stability of the complexes, including those containing pseudoknots. Here, we present VfoldMCPX, a new model for predicting two-dimensional (2D) structures and folding stabilities of multistrand RNA complexes. Based on a partition function-based algorithm combined with physical loop free energy parameters, the VfoldMCPX model predicts not only the native structure but also the folding stability of the complex. An important advantage of the model is the ability to treat pseudoknotted structures. Extensive tests on structure predictions show the VfoldMCPX model provides improved accuracy for multistranded RNA complexes, especially for RNA complexes with three or more strands and/or containing pseudoknots. We have developed a freely accessible VfoldMCPX web server at http://rna.physics.missouri.edu/vfoldMCPX2.
Topics: Algorithms; Nanostructures; Nucleic Acid Conformation; RNA
PubMed: 35058350
DOI: 10.1261/rna.079020.121 -
Transcription Aug 2021To exert their functions, RNAs adopt diverse structures, ranging from simple secondary to complex tertiary and quaternary folds. , RNA folding starts with RNA...
To exert their functions, RNAs adopt diverse structures, ranging from simple secondary to complex tertiary and quaternary folds. , RNA folding starts with RNA transcription, and a wide variety of processes are coupled to co-transcriptional RNA folding events, including the regulation of fundamental transcription dynamics, gene regulation by mechanisms like attenuation, RNA processing or ribonucleoprotein particle formation. While co-transcriptional RNA folding and associated co-transcriptional processes are by now well accepted as pervasive regulatory principles in all organisms, investigations into the role of the transcription machinery in co-transcriptional folding processes have so far largely focused on effects of the order in which RNA regions are produced and of transcription kinetics. Recent structural and structure-guided functional analyses of bacterial transcription complexes increasingly point to an additional role of RNA polymerase and associated transcription factors in supporting co-transcriptional RNA folding by fostering or preventing strategic contacts to the nascent transcripts. In general, the results support the view that transcription complexes can act as RNA chaperones, a function that has been suggested over 30 years ago. Here, we discuss transcription complexes as RNA chaperones based on recent examples from bacterial transcription.
Topics: DNA-Directed RNA Polymerases; Nucleic Acid Conformation; RNA; RNA Folding; RNA Processing, Post-Transcriptional; Transcription, Genetic
PubMed: 34719334
DOI: 10.1080/21541264.2021.1985931 -
The Journal of Physical Chemistry. B Aug 2022Gaussian accelerated molecular dynamics (GaMD) is a computational technique that provides both unconstrained enhanced sampling and free energy calculations of...
Gaussian accelerated molecular dynamics (GaMD) is a computational technique that provides both unconstrained enhanced sampling and free energy calculations of biomolecules. Here, we present the implementation of GaMD in the OpenMM simulation package and validate it on model systems of alanine dipeptide and RNA folding. For alanine dipeptide, 30 ns GaMD production simulations reproduced free energy profiles of 1000 ns conventional molecular dynamics (cMD) simulations. In addition, GaMD simulations captured the folding pathways of three hyperstable RNA tetraloops (UUCG, GCAA, and CUUG) and binding of the rbt203 ligand to the HIV-1 Tar RNA, both of which involved critical electrostatic interactions such as hydrogen bonding and base stacking. Together with previous implementations, GaMD in OpenMM will allow for wider applications in simulations of proteins, RNA, and other biomolecules.
Topics: Alanine; Dipeptides; Molecular Dynamics Simulation; RNA; Thermodynamics
PubMed: 35895977
DOI: 10.1021/acs.jpcb.2c03765 -
PLoS Computational Biology Apr 2022The 3-dimensional fold of an RNA molecule is largely determined by patterns of intramolecular hydrogen bonds between bases. Predicting the base pairing network from the...
The 3-dimensional fold of an RNA molecule is largely determined by patterns of intramolecular hydrogen bonds between bases. Predicting the base pairing network from the sequence, also referred to as RNA secondary structure prediction or RNA folding, is a nondeterministic polynomial-time (NP)-complete computational problem. The structure of the molecule is strongly predictive of its functions and biochemical properties, and therefore the ability to accurately predict the structure is a crucial tool for biochemists. Many methods have been proposed to efficiently sample possible secondary structure patterns. Classic approaches employ dynamic programming, and recent studies have explored approaches inspired by evolutionary and machine learning algorithms. This work demonstrates leveraging quantum computing hardware to predict the secondary structure of RNA. A Hamiltonian written in the form of a Binary Quadratic Model (BQM) is derived to drive the system toward maximizing the number of consecutive base pairs while jointly maximizing the average length of the stems. A Quantum Annealer (QA) is compared to a Replica Exchange Monte Carlo (REMC) algorithm programmed with the same objective function, with the QA being shown to be highly competitive at rapidly identifying low energy solutions. The method proposed in this study was compared to three algorithms from literature and, despite its simplicity, was found to be competitive on a test set containing known structures with pseudoknots.
Topics: Algorithms; Computational Biology; Computers; Computing Methodologies; Nucleic Acid Conformation; Quantum Theory; RNA; RNA Folding
PubMed: 35404931
DOI: 10.1371/journal.pcbi.1010032 -
Viruses Oct 2020Viral RNA genomes change shape as virus particles disassemble, form replication complexes, attach to ribosomes for translation, evade host defense mechanisms, and... (Review)
Review
Viral RNA genomes change shape as virus particles disassemble, form replication complexes, attach to ribosomes for translation, evade host defense mechanisms, and assemble new virus particles. These structurally dynamic RNA shapeshifters present a challenging RNA folding problem, because the RNA sequence adopts multiple structures and may sometimes contain regions of partial disorder. Recent advances in high resolution asymmetric cryoelectron microscopy and chemical probing provide new ways to probe the degree of structure and disorder, and have identified more than one conformation in dynamic equilibrium in viral RNA. Chemical probing and the Detection of RNA Folding Ensembles using Expectation Maximization (DREEM) algorithm has been applied to studies of the dynamic equilibrium conformations in HIV RNA in vitro, in virio, and in vivo. This new type of data provides insight into important questions about virus assembly mechanisms and the fundamental physical forces driving virus particle assembly.
Topics: Base Sequence; Cryoelectron Microscopy; Genome, Viral; Nucleic Acid Conformation; RNA Folding; RNA, Viral; Virion; Virus Assembly
PubMed: 33027988
DOI: 10.3390/v12101126 -
The Journal of Biological Chemistry 2021Since the characterization of mRNA in 1961, our understanding of the roles of RNA molecules has significantly grown. Beyond serving as a link between DNA and proteins,... (Review)
Review
Since the characterization of mRNA in 1961, our understanding of the roles of RNA molecules has significantly grown. Beyond serving as a link between DNA and proteins, RNA molecules play direct effector roles by binding to various ligands, including proteins, DNA, other RNAs, and metabolites. Through these interactions, RNAs mediate cellular processes such as the regulation of gene transcription and the enhancement or inhibition of protein activity. As a result, the misregulation of RNA molecules is often associated with disease phenotypes, and RNA molecules have been increasingly recognized as potential targets for drug development efforts, which in the past had focused primarily on proteins. Although both small molecule-based and oligonucleotide-based therapies have been pursued in efforts to target RNA, small-molecule modalities are often favored owing to several advantages including greater oral bioavailability. In this review, we discuss three general frameworks (sets of premises and hypotheses) that, in our view, have so far dominated the discovery of small-molecule ligands for RNA. We highlight the unique merits of each framework as well as the pitfalls associated with exclusive focus of ligand discovery efforts within only one framework. Finally, we propose that RNA ligand discovery can benefit from using progress made within these three frameworks to move toward a paradigm that formulates RNA-targeting questions at the level of RNA structural subclasses.
Topics: Drug Discovery; Ligands; Nucleic Acid Conformation; RNA; Small Molecule Libraries
PubMed: 33334887
DOI: 10.1074/jbc.REV120.015203 -
Bioinformatics (Oxford, England) Sep 2023Understanding RNA folding at the level of secondary structures can give important insights concerning the function of a molecule. We are interested to learn how...
MOTIVATION
Understanding RNA folding at the level of secondary structures can give important insights concerning the function of a molecule. We are interested to learn how secondary structures change dynamically during transcription, as well as whether particular secondary structures form already during or only after transcription. While different approaches exist to simulate cotranscriptional folding, the current strategies for visualization are lagging behind. New, more suitable approaches are necessary to help with exploring the generated data from cotranscriptional folding simulations.
RESULTS
We present DrForna, an interactive visualization app for viewing the time course of a cotranscriptional RNA folding simulation. Specifically, users can scroll along the time axis and see the population of structures that are present at any particular time point.
AVAILABILITY AND IMPLEMENTATION
DrForna is a JavaScript project available on Github at https://github.com/ViennaRNA/drforna and deployed at https://viennarna.github.io/drforna.
Topics: Computer Simulation; RNA Folding
PubMed: 37682108
DOI: 10.1093/bioinformatics/btad555 -
Nature Communications Jan 2023Guanine (G)-rich nucleic acids can fold into G-quadruplex (G4) structures under permissive conditions. Although many RNAs contain sequences that fold into RNA G4s (rG4s)...
Guanine (G)-rich nucleic acids can fold into G-quadruplex (G4) structures under permissive conditions. Although many RNAs contain sequences that fold into RNA G4s (rG4s) in vitro, their folding and functions in vivo are not well understood. In this report, we showed that the folding of putative rG4s in human cells into rG4 structures is dynamically regulated under stress. By using high-throughput dimethylsulfate (DMS) probing, we identified hundreds of endogenous stress-induced rG4s, and validated them by using an rG4 pull-down approach. Our results demonstrate that stress-induced rG4s are enriched in mRNA 3'-untranslated regions and enhance mRNA stability. Furthermore, stress-induced rG4 folding is readily reversible upon stress removal. In summary, our study revealed the dynamic regulation of rG4 folding in human cells and suggested that widespread rG4 motifs may have a global regulatory impact on mRNA stability and cellular stress response.
Topics: Humans; RNA; RNA, Messenger; G-Quadruplexes; RNA Folding; RNA Stability
PubMed: 36639366
DOI: 10.1038/s41467-023-35811-x -
Molecular Cell May 2023Small ribonucleoproteins (sRNPs) target nascent precursor RNAs to guide folding, modification, and splicing during transcription. Yet, rapid co-transcriptional folding...
Small ribonucleoproteins (sRNPs) target nascent precursor RNAs to guide folding, modification, and splicing during transcription. Yet, rapid co-transcriptional folding of the RNA can mask sRNP sites, impeding target recognition and regulation. To examine how sRNPs target nascent RNAs, we monitored binding of bacterial Hfq⋅DsrA sRNPs to rpoS transcripts using single-molecule co-localization co-transcriptional assembly (smCoCoA). We show that Hfq⋅DsrA recursively samples the mRNA before transcription of the target site to poise it for base pairing with DsrA. We adapted smCoCoA to precisely measure when the target site is synthesized and revealed that Hfq⋅DsrA often binds the mRNA during target site synthesis close to RNA polymerase (RNAP). We suggest that targeting transcripts near RNAP allows an sRNP to capture a site before the transcript folds, providing a kinetic advantage over post-transcriptional targeting. We propose that other sRNPs may also use RNAP-proximal targeting to hasten recognition and regulation.
Topics: Bacterial Proteins; RNA, Small Untranslated; Escherichia coli; RNA, Messenger; Base Pairing; RNA, Bacterial; Host Factor 1 Protein; Escherichia coli Proteins; Gene Expression Regulation, Bacterial
PubMed: 37116495
DOI: 10.1016/j.molcel.2023.04.003