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Advanced Studies in Ribosomal RNA
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Advanced Studies in Ribosomal 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 March 2024) | Viewed by 4743

Special Issue Editors

Dr. Silvia Fischer

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Guest Editor
Department of Biochemistry, Medical School, Justus-Liebig-University, 35392 Giessen, Germany
Interests: homeostasis; extracellular nucleic acids; vascular endothelium; inflammation; DAMPs
Special Issues, Collections and Topics in MDPI journals
Dr. Karsten Grote

E-Mail
Guest Editor
Department of Cardiology, Angiology and Intensive Care, Philipps University Marburg, 35043 Marburg, Germany
Interests: vascular endothelium; vascular inflammation; atherosclerosis; Toll-like receptors; extracellular RNAs; PAMPs/DAMPs

Special Issue Information

Dear Colleagues,

Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA, constituting the main structural component of ribosomes and the predominant form of RNA found in most cells. The eukaryotic ribosome consists of more than 80 proteins and four distinct types of rRNAs. Its role is to ensure the flow of genetic information during translation. Furthermore, non-canonical functions of rRNAs have been described. These include the formation of ribonucleoproteins in addition to complexes between proteins and different kinds of rRNAs but also ncRNAs derived from rRNA, termed rRNA-derived fragments, which have diverse functions in biological processes and cellular activities and are released by nearly all cell types. These extracellular rRNAs have been characterized as major damage-inducing molecules with danger-associated molecular patterns (DAMPs) that are released under pathological conditions from damaged tissue, and have recently been identified as a new alarmin. They are involved in the progression of several diseases such as thrombosis, cardiovascular diseases, central nervous system pathologies, hyperinflammation, and tumor progression.

The present Special Issue aims to demonstrate new advances in the structure and topography of rRNAs, rRNA biogenesis, and its regulation, while highlighting the intra- and extracellular activities of rRNAs, modified rRNAs, or rRNA-derived fragments.

Dr. Silvia Fischer
Dr. Karsten Grote
Guest Editors

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

  • rRNA
  • ribosomes
  • ribonucleoproteins
  • danger-associated molecular pattern
  • signaling pathways

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Published Papers (3 papers)

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Research

16 pages, 2003 KiB  
Article
Loss of Conserved rRNA Modifications in the Peptidyl Transferase Center Leads to Diminished Protein Synthesis and Cell Growth in Budding Yeast
by Margus Leppik, Liisa Pomerants, Anett Põldes, Piret Mihkelson, Jaanus Remme and Tiina Tamm
Int. J. Mol. Sci. 2024, 25(10), 5194; https://doi.org/10.3390/ijms25105194 - 10 May 2024
Viewed by 1291
Abstract
Ribosomal RNAs (rRNAs) are extensively modified during the transcription and subsequent maturation. Three types of modifications, 2′-O-methylation of ribose moiety, pseudouridylation, and base modifications, are introduced either by a snoRNA-driven mechanism or by stand-alone enzymes. Modified nucleotides are clustered at the functionally important [...] Read more.
Ribosomal RNAs (rRNAs) are extensively modified during the transcription and subsequent maturation. Three types of modifications, 2′-O-methylation of ribose moiety, pseudouridylation, and base modifications, are introduced either by a snoRNA-driven mechanism or by stand-alone enzymes. Modified nucleotides are clustered at the functionally important sites, including peptidyl transferase center (PTC). Therefore, it has been hypothesised that the modified nucleotides play an important role in ensuring the functionality of the ribosome. In this study, we demonstrate that seven 25S rRNA modifications, including four evolutionarily conserved modifications, in the proximity of PTC can be simultaneously depleted without loss of cell viability. Yeast mutants lacking three snoRNA genes (snR34, snR52, and snR65) and/or expressing enzymatically inactive variants of spb1(D52A/E679K) and nop2(C424A/C478A) were constructed. The results show that rRNA modifications in PTC contribute collectively to efficient translation in eukaryotic cells. The deficiency of seven modified nucleotides in 25S rRNA resulted in reduced cell growth, cold sensitivity, decreased translation levels, and hyperaccurate translation, as indicated by the reduced missense and nonsense suppression. The modification m5C2870 is crucial in the absence of the other six modified nucleotides. Thus, the pattern of rRNA-modified nucleotides around the PTC is essential for optimal ribosomal translational activity and translational fidelity. Full article
(This article belongs to the Special Issue Advanced Studies in Ribosomal RNA)
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17 pages, 1689 KiB  
Article
DNA and RNA Stability of Marine Microalgae in Cold-Stored Sediments and Its Implications in Metabarcoding Analyses
by Zhaoyang Chai, Yuyang Liu, Siyang Jia, Fengting Li, Zhangxi Hu, Yunyan Deng, Caixia Yue and Ying-Zhong Tang
Int. J. Mol. Sci. 2024, 25(3), 1724; https://doi.org/10.3390/ijms25031724 - 31 Jan 2024
Viewed by 1249
Abstract
The ever-increasing applications of metabarcoding analyses for environmental samples demand a well-designed assessment of the stability of DNA and RNA contained in cells that are deposited or buried in marine sediments. We thus conducted a qPCR quantification of the DNA and RNA in [...] Read more.
The ever-increasing applications of metabarcoding analyses for environmental samples demand a well-designed assessment of the stability of DNA and RNA contained in cells that are deposited or buried in marine sediments. We thus conducted a qPCR quantification of the DNA and RNA in the vegetative cells of three microalgae entrapped in facsimile marine sediments and found that >90% of DNA and up to 99% of RNA for all microalgal species were degraded within 60 days at 4 °C. A further examination of the potential interference of the relic DNA of the vegetative cells with resting cyst detection in sediments was performed via a metabarcoding analysis in artificial marine sediments spiked with the vegetative cells of two Kareniaceae dinoflagellates and the resting cysts of another three dinoflagellates. The results demonstrated a dramatic decrease in the relative abundances of the two Kareniaceae dinoflagellates in 120 days, while those of the three resting cysts increased dramatically. Together, our results suggest that a positive detection of microalgae via metabarcoding analysis in DNA or RNA extracted from marine sediments strongly indicates the presence of intact or viable cysts or spores due to the rapid decay of relic DNA/RNA. This study provides a solid basis for the data interpretation of metabarcoding surveys, particularly in resting cyst detection. Full article
(This article belongs to the Special Issue Advanced Studies in Ribosomal RNA)
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22 pages, 9239 KiB  
Article
Molecular Apomorphies in the Secondary and Tertiary Structures of Length-Variable Regions (LVRs) of 18S rRNA Shed Light on the Systematic Position of the Family Thaumastellidae (Hemiptera: Heteroptera: Pentatomoidea)
by Jerzy A. Lis
Int. J. Mol. Sci. 2023, 24(9), 7758; https://doi.org/10.3390/ijms24097758 - 24 Apr 2023
Cited by 3 | Viewed by 1617
Abstract
The SSU nrDNA, a small subunit of the nuclear ribosomal DNA (coding 18S rRNA), is one of the most frequently sequenced genes in molecular studies in Hexapoda. In insects, including true bugs (Hemiptera: Heteroptera), only its primary structures (i.e., aligned sequences) [...] Read more.
The SSU nrDNA, a small subunit of the nuclear ribosomal DNA (coding 18S rRNA), is one of the most frequently sequenced genes in molecular studies in Hexapoda. In insects, including true bugs (Hemiptera: Heteroptera), only its primary structures (i.e., aligned sequences) are predominantly used in phylogenetic reconstructions. It is known that including RNA secondary structures in the alignment procedure is essential for improving accuracy and robustness in phylogenetic tree reconstruction. Moreover, local plasticity in rRNAs might impact their tertiary structures and corresponding functions. To determine the systematic position of Thaumastellidae within the superfamily Pentatomoidea, the secondary and—for the first time among all Hexapoda—tertiary structures of 18S rRNAs in twelve pentatomoid families were compared and analysed. Results indicate that the shapes of the secondary and tertiary structures of the length-variable regions (LVRs) in the 18S rRNA are phylogenetically highly informative. Based on these results, it is suggested that the Thaumastellidae is maintained as an independent family within the superfamily Pentatomoidea, rather than as a part of the family Cydnidae. Moreover, the analyses indicate a close relationship between Sehirinae and Parastrachiidae, expressed in morpho-molecular synapomorphies in the predicted secondary and tertiary structures of the length-variable region L (LVR L). Full article
(This article belongs to the Special Issue Advanced Studies in Ribosomal RNA)
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