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Frontiers in RNA Structure

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Chemical Biology".

Deadline for manuscript submissions: closed (15 April 2020) | Viewed by 39740

Special Issue Editor


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Guest Editor
Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
Interests: biochemistry; cryo-electron microscopy; molecular biology; ribosome; RNA structure and folding; structure prediction; X-ray crystallography

Special Issue Information

Dear Colleagues,

Ribonucleic acids (RNA) can code for information, act as enzymes or change shape upon binding to an effector. Significantly, the dynamic nature of RNA means that RNA is able to adopt transient structures with diverse functions. In addition, the fraction of noncoding RNA in our genomes is much larger than that of messenger RNA. Hence, RNA has now emerged as one of the key molecules in the regulation of gene expression. However, our understanding of the functions and structures of these myriad RNAs pales in comparison to what we know about proteins.

The focus of this Special Issue is on the frontier of RNA structure discovery and the structure–function relationship. We welcome submissions about any type of RNA or ribonucleoprotein complex, and any structural biology methodology, including but not limited to: X-ray/electron crystallography, NMR, cryo-electron microscopy, small-angle X-ray scattering, FRET, structure mapping, and computational modeling.

Articles reporting original research as well as reviews will be considered for publication.

Authors are strongly encouraged to submit a brief abstract (200 words) to the guest editor by October 15, 2019. Abstracts will be reviewed in consultation with the editors at Molecules. Full manuscripts submitted by February 15, 2020 will be guaranteed full consideration.

Dr. Quentin Vicens
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • coding and noncoding RNA
  • regulatory RNA
  • RNA dynamics
  • RNA–protein complex
  • structured RNA element
  • three-dimensional structure

Published Papers (9 papers)

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Editorial

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2 pages, 163 KiB  
Editorial
Special Issue: Frontiers in RNA Structure
by Quentin Vicens
Molecules 2020, 25(20), 4843; https://doi.org/10.3390/molecules25204843 - 21 Oct 2020
Viewed by 1958
Abstract
The frontiers of our knowledge about RNA structure are rapidly moving [...] Full article
(This article belongs to the Special Issue Frontiers in RNA Structure)

Research

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16 pages, 2327 KiB  
Article
High Affinity Binding of N2-Modified Guanine Derivatives Significantly Disrupts the Ligand Binding Pocket of the Guanine Riboswitch
by Michal M. Matyjasik, Simone D. Hall and Robert T. Batey
Molecules 2020, 25(10), 2295; https://doi.org/10.3390/molecules25102295 - 13 May 2020
Cited by 8 | Viewed by 3944
Abstract
Riboswitches are important model systems for the development of approaches to search for RNA-targeting therapeutics. A principal challenge in finding compounds that target riboswitches is that the effector ligand is typically almost completely encapsulated by the RNA, which severely limits the chemical space [...] Read more.
Riboswitches are important model systems for the development of approaches to search for RNA-targeting therapeutics. A principal challenge in finding compounds that target riboswitches is that the effector ligand is typically almost completely encapsulated by the RNA, which severely limits the chemical space that can be explored. Efforts to find compounds that bind the guanine/adenine class of riboswitches with a high affinity have in part focused on purines modified at the C6 and C2 positions. These studies have revealed compounds that have low to sub-micromolar affinity and, in a few cases, have antimicrobial activity. To further understand how these compounds interact with the guanine riboswitch, we have performed an integrated structural and functional analysis of representative guanine derivatives with modifications at the C8, C6 and C2 positions. Our data indicate that while modifications of guanine at the C6 position are generally unfavorable, modifications at the C8 and C2 positions yield compounds that rival guanine with respect to binding affinity. Surprisingly, C2-modified guanines such as N2-acetylguanine completely disrupt a key Watson–Crick pairing interaction between the ligand and RNA. These compounds, which also modulate transcriptional termination as efficiently as guanine, open up a significant new chemical space of guanine modifications in the search for antimicrobial agents that target purine riboswitches. Full article
(This article belongs to the Special Issue Frontiers in RNA Structure)
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19 pages, 3926 KiB  
Article
Good Vibrations: Structural Remodeling of Maturing Yeast Pre-40S Ribosomal Particles Followed by Cryo-Electron Microscopy
by Ramtin Shayan, Dana Rinaldi, Natacha Larburu, Laura Plassart, Stéphanie Balor, David Bouyssié, Simon Lebaron, Julien Marcoux, Pierre-Emmanuel Gleizes and Célia Plisson-Chastang
Molecules 2020, 25(5), 1125; https://doi.org/10.3390/molecules25051125 - 3 Mar 2020
Cited by 13 | Viewed by 4338
Abstract
Assembly of eukaryotic ribosomal subunits is a very complex and sequential process that starts in the nucleolus and finishes in the cytoplasm with the formation of functional ribosomes. Over the past few years, characterization of the many molecular events underlying eukaryotic ribosome biogenesis [...] Read more.
Assembly of eukaryotic ribosomal subunits is a very complex and sequential process that starts in the nucleolus and finishes in the cytoplasm with the formation of functional ribosomes. Over the past few years, characterization of the many molecular events underlying eukaryotic ribosome biogenesis has been drastically improved by the “resolution revolution” of cryo-electron microscopy (cryo-EM). However, if very early maturation events have been well characterized for both yeast ribosomal subunits, little is known regarding the final maturation steps occurring to the small (40S) ribosomal subunit. To try to bridge this gap, we have used proteomics together with cryo-EM and single particle analysis to characterize yeast pre-40S particles containing the ribosome biogenesis factor Tsr1. Our analyses lead us to refine the timing of the early pre-40S particle maturation steps. Furthermore, we suggest that after an early and structurally stable stage, the beak and platform domains of pre-40S particles enter a “vibrating” or “wriggling” stage, that might be involved in the final maturation of 18S rRNA as well as the fitting of late ribosomal proteins into their mature position. Full article
(This article belongs to the Special Issue Frontiers in RNA Structure)
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12 pages, 11099 KiB  
Article
Structural Bases for the Fitness Cost of the Antibiotic-Resistance and Lethal Mutations at Position 1408 of 16S rRNA
by Jiro Kondo and Mai Koganei
Molecules 2020, 25(1), 159; https://doi.org/10.3390/molecules25010159 - 31 Dec 2019
Cited by 3 | Viewed by 3000
Abstract
To understand a structural basis for the fitness cost of the A1408G antibiotic-resistance mutation in the ribosomal A-site RNA, we have determined crystal structures of its A1408C and A1408U lethal mutants, and made comparison with previously solved structures of the wild type and [...] Read more.
To understand a structural basis for the fitness cost of the A1408G antibiotic-resistance mutation in the ribosomal A-site RNA, we have determined crystal structures of its A1408C and A1408U lethal mutants, and made comparison with previously solved structures of the wild type and the antibiotic-resistant mutant. The A-site RNA containing an asymmetric internal loop functions as a molecular switch to discriminate a single cognate tRNA from several near-cognate tRNAs by its conformational ON/OFF switching. Overall structures of the “off” states of the A1408C/U lethal mutants are very similar to those of the wild type and the A1408G antibiotic-resistant mutant. However, significant differences are found in local base stacking interactions including the functionally important A1492 and A1493 residues. In the wild type and the A1408G antibiotic-resistant mutant “off” states, both adenines are exposed to the solvent region. On the other hand, one of the corresponding adenines of the lethal A1408C/U mutants stay deeply inside their A-site helices by forming a purine-pyrimidine AoC or A-U base pair and is sandwiched between the upper and lower bases. Therefore, the ON/OFF switching might unfavorably occur in the lethal mutants compared to the wild type and the A1408G antibiotic-resistant mutant. It is probable that bacteria manage to acquire antibiotic resistance without losing the function of the A-site molecular switch by mutating the position 1408 only from A to G, but not to pyrimidine base C or U. Full article
(This article belongs to the Special Issue Frontiers in RNA Structure)
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Review

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17 pages, 2686 KiB  
Review
Structural Heterogeneities of the Ribosome: New Frontiers and Opportunities for Cryo-EM
by Frédéric Poitevin, Artem Kushner, Xinpei Li and Khanh Dao Duc
Molecules 2020, 25(18), 4262; https://doi.org/10.3390/molecules25184262 - 17 Sep 2020
Cited by 19 | Viewed by 4731
Abstract
The extent of ribosomal heterogeneity has caught increasing interest over the past few years, as recent studies have highlighted the presence of structural variations of the ribosome. More precisely, the heterogeneity of the ribosome covers multiple scales, including the dynamical aspects of ribosomal [...] Read more.
The extent of ribosomal heterogeneity has caught increasing interest over the past few years, as recent studies have highlighted the presence of structural variations of the ribosome. More precisely, the heterogeneity of the ribosome covers multiple scales, including the dynamical aspects of ribosomal motion at the single particle level, specialization at the cellular and subcellular scale, or evolutionary differences across species. Upon solving the ribosome atomic structure at medium to high resolution, cryogenic electron microscopy (cryo-EM) has enabled investigating all these forms of heterogeneity. In this review, we present some recent advances in quantifying ribosome heterogeneity, with a focus on the conformational and evolutionary variations of the ribosome and their functional implications. These efforts highlight the need for new computational methods and comparative tools, to comprehensively model the continuous conformational transition pathways of the ribosome, as well as its evolution. While developing these methods presents some important challenges, it also provides an opportunity to extend our interpretation and usage of cryo-EM data, which would more generally benefit the study of molecular dynamics and evolution of proteins and other complexes. Full article
(This article belongs to the Special Issue Frontiers in RNA Structure)
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19 pages, 2912 KiB  
Review
RNA Granules: A View from the RNA Perspective
by Siran Tian, Harrison A. Curnutte and Tatjana Trcek
Molecules 2020, 25(14), 3130; https://doi.org/10.3390/molecules25143130 - 8 Jul 2020
Cited by 44 | Viewed by 8757
Abstract
RNA granules are ubiquitous. Composed of RNA-binding proteins and RNAs, they provide functional compartmentalization within cells. They are inextricably linked with RNA biology and as such are often referred to as the hubs for post-transcriptional regulation. Much of the attention has been given [...] Read more.
RNA granules are ubiquitous. Composed of RNA-binding proteins and RNAs, they provide functional compartmentalization within cells. They are inextricably linked with RNA biology and as such are often referred to as the hubs for post-transcriptional regulation. Much of the attention has been given to the proteins that form these condensates and thus many fundamental questions about the biology of RNA granules remain poorly understood: How and which RNAs enrich in RNA granules, how are transcripts regulated in them, and how do granule-enriched mRNAs shape the biology of a cell? In this review, we discuss the imaging, genetic, and biochemical data, which have revealed that some aspects of the RNA biology within granules are carried out by the RNA itself rather than the granule proteins. Interestingly, the RNA structure has emerged as an important feature in the post-transcriptional control of granule transcripts. This review is part of the Special Issue in the Frontiers in RNA structure in the journal Molecules. Full article
(This article belongs to the Special Issue Frontiers in RNA Structure)
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28 pages, 4500 KiB  
Review
Structural Insights into RNA Dimerization: Motifs, Interfaces and Functions
by Charles Bou-Nader and Jinwei Zhang
Molecules 2020, 25(12), 2881; https://doi.org/10.3390/molecules25122881 - 23 Jun 2020
Cited by 23 | Viewed by 4924
Abstract
In comparison with the pervasive use of protein dimers and multimers in all domains of life, functional RNA oligomers have so far rarely been observed in nature. Their diminished occurrence contrasts starkly with the robust intrinsic potential of RNA to multimerize through long-range [...] Read more.
In comparison with the pervasive use of protein dimers and multimers in all domains of life, functional RNA oligomers have so far rarely been observed in nature. Their diminished occurrence contrasts starkly with the robust intrinsic potential of RNA to multimerize through long-range base-pairing (“kissing”) interactions, self-annealing of palindromic or complementary sequences, and stable tertiary contact motifs, such as the GNRA tetraloop-receptors. To explore the general mechanics of RNA dimerization, we performed a meta-analysis of a collection of exemplary RNA homodimer structures consisting of viral genomic elements, ribozymes, riboswitches, etc., encompassing both functional and fortuitous dimers. Globally, we found that domain-swapped dimers and antiparallel, head-to-tail arrangements are predominant architectural themes. Locally, we observed that the same structural motifs, interfaces and forces that enable tertiary RNA folding also drive their higher-order assemblies. These feature prominently long-range kissing loops, pseudoknots, reciprocal base intercalations and A-minor interactions. We postulate that the scarcity of functional RNA multimers and limited diversity in multimerization motifs may reflect evolutionary constraints imposed by host antiviral immune surveillance and stress sensing. A deepening mechanistic understanding of RNA multimerization is expected to facilitate investigations into RNA and RNP assemblies, condensates, and granules and enable their potential therapeutical targeting. Full article
(This article belongs to the Special Issue Frontiers in RNA Structure)
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13 pages, 1984 KiB  
Review
Yeast Telomerase RNA Flexibly Scaffolds Protein Subunits: Results and Repercussions
by David C. Zappulla
Molecules 2020, 25(12), 2750; https://doi.org/10.3390/molecules25122750 - 14 Jun 2020
Cited by 8 | Viewed by 3873
Abstract
It is said that “hindsight is 20-20,” so, given the current year, it is an opportune time to review and learn from experiences studying long noncoding RNAs. Investigation of the Saccharomyces cerevisiae telomerase RNA, TLC1, has unveiled striking flexibility in terms of both [...] Read more.
It is said that “hindsight is 20-20,” so, given the current year, it is an opportune time to review and learn from experiences studying long noncoding RNAs. Investigation of the Saccharomyces cerevisiae telomerase RNA, TLC1, has unveiled striking flexibility in terms of both structural and functional features. Results support the “flexible scaffold” hypothesis for this 1157-nt telomerase RNA. This model describes TLC1 acting as a tether for holoenzyme protein subunits, and it also may apply to a plethora of RNAs beyond telomerase, such as types of lncRNAs. In this short perspective review, I summarize findings from studying the large yeast telomerase ribonucleoprotein (RNP) complex in the hope that this hindsight will sharpen foresight as so many of us seek to mechanistically understand noncoding RNA molecules from vast transcriptomes. Full article
(This article belongs to the Special Issue Frontiers in RNA Structure)
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19 pages, 4150 KiB  
Review
Cooperative Analysis of Structural Dynamics in RNA-Protein Complexes by Single-Molecule Förster Resonance Energy Transfer Spectroscopy
by Nathalie Meiser, Christin Fuks and Martin Hengesbach
Molecules 2020, 25(9), 2057; https://doi.org/10.3390/molecules25092057 - 28 Apr 2020
Cited by 4 | Viewed by 3181
Abstract
RNA-protein complexes (RNPs) are essential components in a variety of cellular processes, and oftentimes exhibit complex structures and show mechanisms that are highly dynamic in conformation and structure. However, biochemical and structural biology approaches are mostly not able to fully elucidate the structurally [...] Read more.
RNA-protein complexes (RNPs) are essential components in a variety of cellular processes, and oftentimes exhibit complex structures and show mechanisms that are highly dynamic in conformation and structure. However, biochemical and structural biology approaches are mostly not able to fully elucidate the structurally and especially conformationally dynamic and heterogeneous nature of these RNPs, to which end single molecule Förster resonance energy transfer (smFRET) spectroscopy can be harnessed to fill this gap. Here we summarize the advantages of strategic smFRET studies to investigate RNP dynamics, complemented by structural and biochemical data. Focusing on recent smFRET studies of three essential biological systems, we demonstrate that investigation of RNPs on a single molecule level can answer important functional questions that remained elusive with structural or biochemical approaches alone: The complex structural rearrangements throughout the splicing cycle, unwinding dynamics of the G-quadruplex (G4) helicase RHAU, and aspects in telomere maintenance regulation and synthesis. Full article
(This article belongs to the Special Issue Frontiers in RNA Structure)
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