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ncRNA
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Structural Studies of Ribozymes and Regulatory ncRNA Machineries
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Structural Studies of Ribozymes and Regulatory ncRNA Machineries

A special issue of Non-Coding RNA (ISSN 2311-553X).

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 9953

Special Issue Editor

Dr. Benoit Masquida

E-Mail Website
Guest Editor
GMGM - CNRS - UNISTRA, Institute of Biological Physics and Chemistry, University of Strasbourg, 67084 Strasbourg, France
Interests: study of mitochondrial import of RNAs using synchrotron-based methods and synthetic biology; structural studies of ribozymes and ncRNA regulatory machineries like PKR-related processes; hCOV transcriptional and translational regulation; maturation of mitochondrial ribosomes; recent edition of a book on ribozymes

Special Issue Information

Dear Colleagues,

Ribozymes and ncRNAs are spread over the whole tree of life and their roles in the regulation of biological processes from gene regulation to the response to pathogens are treated with increasing attention. Although the role of ncRNAs like riboswitches are more and more understood due to their associations with metabolites, the functions of ribozymes or other ncRNAs often remain quite mysterious since identifying the controlled processes or the molecular partners is difficult. The journal ncRNA offers the opportunity to publish your most recent research on this topic rapidly and visibly. This special issue will encover experimental studies or reviews dealing with RNA structure analysis by experimental, theoretical, or integrated approaches. This set of papers will constitute an interesting snapshot of current RNA structural studies and of the employed investigation methods.

Dr. Benoit Masquida
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. Non-Coding RNA 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 1800 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

  • non coding RNA
  • ribozyme function
  • RNA structure
  • structure mapping and probing
  • structure-activity relationships

Published Papers (3 papers)

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Research

27 pages, 10438 KiB  
Article
Structural and Functional Insight into the Mechanism of Bacillus subtilis 6S-1 RNA Release from RNA Polymerase
by Sweetha Ganapathy, Philipp G. Hoch, Marcus Lechner, Malte Bussiek and Roland K. Hartmann
Non-Coding RNA 2022, 8(1), 20; https://doi.org/10.3390/ncrna8010020 - 16 Feb 2022
Cited by 1 | Viewed by 2662
Abstract
Here we investigated the refolding of Bacillus subtilis 6S-1 RNA and its release from σA-RNA polymerase (σA-RNAP) in vitro using truncated and mutated 6S-1 RNA variants. Truncated 6S-1 RNAs, only consisting of the central bubble (CB) flanked by two [...] Read more.
Here we investigated the refolding of Bacillus subtilis 6S-1 RNA and its release from σA-RNA polymerase (σA-RNAP) in vitro using truncated and mutated 6S-1 RNA variants. Truncated 6S-1 RNAs, only consisting of the central bubble (CB) flanked by two short helical arms, can still traverse the mechanistic 6S RNA cycle in vitro despite ~10-fold reduced σA-RNAP affinity. This indicates that the RNA’s extended helical arms including the ‘−35′-like region are not required for basic 6S-1 RNA functionality. The role of the ‘central bubble collapse helix’ (CBCH) in pRNA-induced refolding and release of 6S-1 RNA from σA-RNAP was studied by stabilizing mutations. This also revealed base identities in the 5’-part of the CB (5’-CB), upstream of the pRNA transcription start site (nt 40), that impact ground state binding of 6S-1 RNA to σA-RNAP. Stabilization of the CBCH by the C44/45 double mutation shifted the pRNA length pattern to shorter pRNAs and, combined with a weakened P2 helix, resulted in more effective release from RNAP. We conclude that formation of the CBCH supports pRNA-induced 6S-1 RNA refolding and release. Our mutational analysis also unveiled that formation of a second short hairpin in the 3′-CB is detrimental to 6S-1 RNA release. Furthermore, an LNA mimic of a pRNA as short as 6 nt, when annealed to 6S-1 RNA, retarded the RNA’s gel mobility and interfered with σA-RNAP binding. This effect incrementally increased with pLNA 7- and 8-mers, suggesting that restricted conformational flexibility introduced into the 5’-CB by base pairing with pRNAs prevents 6S-1 RNA from adopting an elongated shape. Accordingly, atomic force microscopy of free 6S-1 RNA versus 6S-1:pLNA 8- and 14-mer complexes revealed that 6S-1:pRNA hybrid structures, on average, adopt a more compact structure than 6S-1 RNA alone. Overall, our findings also illustrate that the wild-type 6S-1 RNA sequence and structure ensures an optimal balance of the different functional aspects involved in the mechanistic cycle of 6S-1 RNA. Full article
(This article belongs to the Special Issue Structural Studies of Ribozymes and Regulatory ncRNA Machineries)
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21 pages, 22666 KiB  
Article
Progress toward SHAPE Constrained Computational Prediction of Tertiary Interactions in RNA Structure
by Grégoire De Bisschop, Delphine Allouche, Elisa Frezza, Benoît Masquida, Yann Ponty, Sebastian Will and Bruno Sargueil
Non-Coding RNA 2021, 7(4), 71; https://doi.org/10.3390/ncrna7040071 - 05 Nov 2021
Cited by 4 | Viewed by 3171
Abstract
As more sequencing data accumulate and novel puzzling genetic regulations are discovered, the need for accurate automated modeling of RNA structure increases. RNA structure modeling from chemical probing experiments has made tremendous progress, however accurately predicting large RNA structures is still challenging for [...] Read more.
As more sequencing data accumulate and novel puzzling genetic regulations are discovered, the need for accurate automated modeling of RNA structure increases. RNA structure modeling from chemical probing experiments has made tremendous progress, however accurately predicting large RNA structures is still challenging for several reasons: RNA are inherently flexible and often adopt many energetically similar structures, which are not reliably distinguished by the available, incomplete thermodynamic model. Moreover, computationally, the problem is aggravated by the relevance of pseudoknots and non-canonical base pairs, which are hardly predicted efficiently. To identify nucleotides involved in pseudoknots and non-canonical interactions, we scrutinized the SHAPE reactivity of each nucleotide of the 188 nt long lariat-capping ribozyme under multiple conditions. Reactivities analyzed in the light of the X-ray structure were shown to report accurately the nucleotide status. Those that seemed paradoxical were rationalized by the nucleotide behavior along molecular dynamic simulations. We show that valuable information on intricate interactions can be deduced from probing with different reagents, and in the presence or absence of Mg2+. Furthermore, probing at increasing temperature was remarkably efficient at pointing to non-canonical interactions and pseudoknot pairings. The possibilities of following such strategies to inform structure modeling software are discussed. Full article
(This article belongs to the Special Issue Structural Studies of Ribozymes and Regulatory ncRNA Machineries)
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13 pages, 12588 KiB  
Article
A Phylogenetic Approach to Structural Variation in Organization of Nuclear Group I Introns and Their Ribozymes
by Betty M. N. Furulund, Bård O. Karlsen, Igor Babiak and Steinar D. Johansen
Non-Coding RNA 2021, 7(3), 43; https://doi.org/10.3390/ncrna7030043 - 22 Jul 2021
Cited by 3 | Viewed by 3401
Abstract
Nuclear group I introns are restricted to the ribosomal DNA locus where they interrupt genes for small subunit and large subunit ribosomal RNAs at conserved sites in some eukaryotic microorganisms. Here, the myxomycete protists are a frequent source of nuclear group I introns [...] Read more.
Nuclear group I introns are restricted to the ribosomal DNA locus where they interrupt genes for small subunit and large subunit ribosomal RNAs at conserved sites in some eukaryotic microorganisms. Here, the myxomycete protists are a frequent source of nuclear group I introns due to their unique life strategy and a billion years of separate evolution. The ribosomal DNA of the myxomycete Mucilago crustacea was investigated and found to contain seven group I introns, including a direct repeat-containing intron at insertion site S1389 in the small subunit ribosomal RNA gene. We collected, analyzed, and compared 72 S1389 group IC1 introns representing diverse myxomycete taxa. The consensus secondary structure revealed a conserved ribozyme core, but with surprising sequence variations in the guanosine binding site in segment P7. Some S1389 introns harbored large extension sequences in the peripheral region of segment P9 containing direct repeat arrays. These repeats contained up to 52 copies of a putative internal guide sequence motif. Other S1389 introns harbored homing endonuclease genes in segment P1 encoding His-Cys proteins. Homing endonuclease genes were further interrupted by small spliceosomal introns that have to be removed in order to generate the open reading frames. Phylogenetic analyses of S1389 intron and host gene indicated both vertical and horizontal intron transfer during evolution, and revealed sporadic appearances of direct repeats, homing endonuclease genes, and guanosine binding site variants among the myxomycete taxa. Full article
(This article belongs to the Special Issue Structural Studies of Ribozymes and Regulatory ncRNA Machineries)
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