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Bacterial Non-coding RNA
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Bacterial Non-coding RNA

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 13227

Special Issue Editor

Prof. Dr. Jonathan Perreault

E-Mail Website
Guest Editor
Institut National de la Recherche Scientifique, Centre Armand-Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada

Special Issue Information

Dear Colleagues,

Since 2000, the discovery of new types of prokaryotic non-coding (nc)RNAs has continued to surprise us, from the identification of the now well-known CRISPR RNA derived from bacterial anti-bacteriophage systems to that of riboswitches. In addition to ncRNAs, hundreds of novel small (s)RNAs and conserved RNA structures have also been uncovered, many of which still have no defined function. Comparative genomics, in particular, is being crucial for the discovery of ncRNAs, riboswitches, and other structured RNAs, though techniques based on RNA-seq are also considerably contributing. Various roles have been established for many of these RNAs, mostly related to the control of gene expression. RNAs whose function is now known include a subclass of the former “orphan riboswitch” ykkC, which specifically bind guanidine, the ROSE elements thermoregulators, the RsmY sRNA, which sequesters the RsmA protein preventing its binding to mRNAs, and many sRNAs whose targets have been confirmed. In other cases, even if the biological role of ncRNAs was not discovered, some biochemical activities were defined, such as for ribozymes found within bacteria and bacteriophages. This Special Issue will welcome original research articles and reviews that highlight the discovery of novel bacterial ncRNAs and/or their mechanistic or functional characterization. Given the scope of IJMS, the submitted papers are expected to present some molecular insight, with regard to RNA structure, processing, expression, biological roles, or other biochemical activities.

Prof. Dr. Jonathan Perreault
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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 (ncRNA)
  • Structured RNA
  • Small RNA (sRNA)
  • RNA regulator
  • RNA binding protein
  • Regulation
  • Cis-regulation
  • Riboswitch
  • Ribozyme
  • Thermoregulator

Published Papers (5 papers)

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18 pages, 5937 KiB  
Article
Bacterial 2′-Deoxyguanosine Riboswitch Classes as Potential Targets for Antibiotics: A Structure and Dynamics Study
by Deborah Antunes, Lucianna H. S. Santos, Ernesto Raul Caffarena and Ana Carolina Ramos Guimarães
Int. J. Mol. Sci. 2022, 23(4), 1925; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23041925 - 09 Feb 2022
Cited by 4 | Viewed by 1667
Abstract
The spread of antibiotic-resistant bacteria represents a substantial health threat. Current antibiotics act on a few metabolic pathways, facilitating resistance. Consequently, novel regulatory inhibition mechanisms are necessary. Riboswitches represent promising targets for antibacterial drugs. Purine riboswitches are interesting, since they play essential roles [...] Read more.
The spread of antibiotic-resistant bacteria represents a substantial health threat. Current antibiotics act on a few metabolic pathways, facilitating resistance. Consequently, novel regulatory inhibition mechanisms are necessary. Riboswitches represent promising targets for antibacterial drugs. Purine riboswitches are interesting, since they play essential roles in the genetic regulation of bacterial metabolism. Among these, class I (2′-dG-I) and class II (2′-dG-II) are two different 2′-deoxyguanosine (2′-dG) riboswitches involved in the control of deoxyguanosine metabolism. However, high affinity for nucleosides involves local or distal modifications around the ligand-binding pocket, depending on the class. Therefore, it is crucial to understand these riboswitches’ recognition mechanisms as antibiotic targets. In this work, we used a combination of computational biophysics approaches to investigate the structure, dynamics, and energy landscape of both 2′-dG classes bound to the nucleoside ligands, 2′-deoxyguanosine, and riboguanosine. Our results suggest that the stability and increased interactions in the three-way junction of 2′-dG riboswitches were associated with a higher nucleoside ligand affinity. Also, structural changes in the 2′-dG-II aptamers enable enhanced intramolecular communication. Overall, the 2′-dG-II riboswitch might be a promising drug design target due to its ability to recognize both cognate and noncognate ligands. Full article
(This article belongs to the Special Issue Bacterial Non-coding RNA)
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16 pages, 2100 KiB  
Article
The Signaling Pathway That cGAMP Riboswitches Found: Analysis and Application of Riboswitches to Study cGAMP Signaling in Geobacter sulfurreducens
by Zhesen Tan, Chi Ho Chan, Michael Maleska, Bryan Banuelos Jara, Brian K. Lohman, Nathan J. Ricks, Daniel R. Bond and Ming C. Hammond
Int. J. Mol. Sci. 2022, 23(3), 1183; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23031183 - 21 Jan 2022
Cited by 2 | Viewed by 2559
Abstract
The Hypr cGAMP signaling pathway was discovered via the function of the riboswitch. In this study, we show the development of a method for affinity capture followed by sequencing to identify non-coding RNA regions that bind nucleotide signals such as cGAMP. The RNAseq [...] Read more.
The Hypr cGAMP signaling pathway was discovered via the function of the riboswitch. In this study, we show the development of a method for affinity capture followed by sequencing to identify non-coding RNA regions that bind nucleotide signals such as cGAMP. The RNAseq of affinity-captured cGAMP riboswitches from the Geobacter sulfurreducens transcriptome highlights general challenges that remain for this technique. Furthermore, by applying riboswitch reporters in vivo, we identify new growth conditions and transposon mutations that affect cGAMP levels in G. sulfurreducens. This work reveals an extensive regulatory network and supports a second functional cGAMP synthase gene in G. sulfurreducens. The activity of the second synthase was validated using riboswitch-based fluorescent biosensors, and is the first known example of an active enzyme with a variant GGDDF motif. Full article
(This article belongs to the Special Issue Bacterial Non-coding RNA)
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23 pages, 5408 KiB  
Article
Regulation of Heterogenous LexA Expression in Staphylococcus aureus by an Antisense RNA Originating from Transcriptional Read-Through upon Natural Mispairings in the sbrB Intrinsic Terminator
by Laurène Bastet, Pilar Bustos-Sanmamed, Arancha Catalan-Moreno, Carlos J. Caballero, Sergio Cuesta, Leticia Matilla-Cuenca, Maite Villanueva, Jaione Valle, Iñigo Lasa and Alejandro Toledo-Arana
Int. J. Mol. Sci. 2022, 23(1), 576; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23010576 - 05 Jan 2022
Cited by 2 | Viewed by 3852
Abstract
Bacterial genomes are pervasively transcribed, generating a wide variety of antisense RNAs (asRNAs). Many of them originate from transcriptional read-through events (TREs) during the transcription termination process. Previous transcriptome analyses revealed that the lexA gene from Staphylococcus aureus, which encodes the main [...] Read more.
Bacterial genomes are pervasively transcribed, generating a wide variety of antisense RNAs (asRNAs). Many of them originate from transcriptional read-through events (TREs) during the transcription termination process. Previous transcriptome analyses revealed that the lexA gene from Staphylococcus aureus, which encodes the main SOS response regulator, is affected by the presence of an asRNA. Here, we show that the lexA antisense RNA (lexA-asRNA) is generated by a TRE on the intrinsic terminator (TTsbrB) of the sbrB gene, which is located downstream of lexA, in the opposite strand. Transcriptional read-through occurs by a natural mutation that destabilizes the TTsbrB structure and modifies the efficiency of the intrinsic terminator. Restoring the mispairing mutation in the hairpin of TTsbrB prevented lexA-asRNA transcription. The level of lexA-asRNA directly correlated with cellular stress since the expressions of sbrB and lexA-asRNA depend on the stress transcription factor SigB. Comparative analyses revealed strain-specific nucleotide polymorphisms within TTsbrB, suggesting that this TT could be prone to accumulating natural mutations. A genome-wide analysis of TREs suggested that mispairings in TT hairpins might provide wider transcriptional connections with downstream genes and, ultimately, transcriptomic variability among S. aureus strains. Full article
(This article belongs to the Special Issue Bacterial Non-coding RNA)
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11 pages, 22455 KiB  
Communication
Bioinformatic Prediction of an tRNASec Gene Nested inside an Elongation Factor SelB Gene in Alphaproteobacteria
by Takahito Mukai
Int. J. Mol. Sci. 2021, 22(9), 4605; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22094605 - 27 Apr 2021
Cited by 1 | Viewed by 1859
Abstract
In bacteria, selenocysteine (Sec) is incorporated into proteins via the recoding of a particular codon, the UGA stop codon in most cases. Sec-tRNASec is delivered to the ribosome by the Sec-dedicated elongation factor SelB that also recognizes a Sec-insertion sequence element following [...] Read more.
In bacteria, selenocysteine (Sec) is incorporated into proteins via the recoding of a particular codon, the UGA stop codon in most cases. Sec-tRNASec is delivered to the ribosome by the Sec-dedicated elongation factor SelB that also recognizes a Sec-insertion sequence element following the codon on the mRNA. Since the excess of SelB may lead to sequestration of Sec-tRNASec under selenium deficiency or oxidative stress, the expression levels of SelB and tRNASec should be regulated. In this bioinformatic study, I analyzed the Rhizobiales SelB species because they were annotated to have a non-canonical C-terminal extension. I found that the open reading frame (ORF) of diverse Alphaproteobacteria selB genes includes an entire tRNASec sequence (selC) and overlaps with the start codon of the downstream ORF. A remnant tRNASec sequence was found in the Sinorhizobium melilotiselB genes whose products have a shorter C-terminal extension. Similar overlapping traits were found in Gammaproteobacteria and Nitrospirae. I hypothesized that once the tRNASec moiety is folded and processed, the expression of the full-length SelB may be repressed. This is the first report on a nested tRNA gene inside a protein ORF in bacteria. Full article
(This article belongs to the Special Issue Bacterial Non-coding RNA)
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14 pages, 1450 KiB  
Perspective
Small RNAs beyond Model Organisms: Have We Only Scratched the Surface?
by Emilie Boutet, Samia Djerroud and Jonathan Perreault
Int. J. Mol. Sci. 2022, 23(8), 4448; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23084448 - 18 Apr 2022
Cited by 4 | Viewed by 2417
Abstract
Small RNAs (sRNAs) are essential regulators in the adaptation of bacteria to environmental changes and act by binding targeted mRNAs through base complementarity. Approximately 550 distinct families of sRNAs have been identified since their initial characterization in the 1980s, accelerated by the emergence [...] Read more.
Small RNAs (sRNAs) are essential regulators in the adaptation of bacteria to environmental changes and act by binding targeted mRNAs through base complementarity. Approximately 550 distinct families of sRNAs have been identified since their initial characterization in the 1980s, accelerated by the emergence of RNA-sequencing. Small RNAs are found in a wide range of bacterial phyla, but they are more prominent in highly researched model organisms compared to the rest of the sequenced bacteria. Indeed, Escherichia coli and Salmonella enterica contain the highest number of sRNAs, with 98 and 118, respectively, with Enterobacteriaceae encoding 145 distinct sRNAs, while other bacteria families have only seven sRNAs on average. Although the past years brought major advances in research on sRNAs, we have perhaps only scratched the surface, even more so considering RNA annotations trail behind gene annotations. A distinctive trend can be observed for genes, whereby their number increases with genome size, but this is not observable for RNAs, although they would be expected to follow the same trend. In this perspective, we aimed at establishing a more accurate representation of the occurrence of sRNAs in bacteria, emphasizing the potential for novel sRNA discoveries. Full article
(This article belongs to the Special Issue Bacterial Non-coding RNA)
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