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Non-coding Small RNAs (sRNAs) in Prokaryotic Systems

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

Deadline for manuscript submissions: closed (28 February 2022) | Viewed by 9772

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Special Issue Editors

Prof. Dr. Alicja Wegrzyn

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Guest Editor

Phage Therapy Center, University Center for Applied and Interdisciplinary Research, University of Gdansk, Gdansk, Poland
Interests: biology of bacteriophages; biodiversity of bacteriophages; regulation of bacteriophage development; regulation of phage gene expression; control of phage DNA replication; phage therapy; phages bearing genes of toxins; bacteriophage genomics
Special Issues, Collections and Topics in MDPI journals

Dr. Sylwia Bloch

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Assistant Guest Editor

Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Gdańsk, Poland
Interests: bacteriophages; phage therapy; EHEC; Shiga toxins; small non-coding RNAs; gene expression
Special Issues, Collections and Topics in MDPI journals

Dr. Monika Maciag-Dorszynska

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Assistant Guest Editor

Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Gdańsk, Poland

Special Issue Information

Dear Colleagues,

Small non-coding RNAs (sRNAs) occur in all kingdoms of life and have become increasingly recognized as a novel class of gene expression regulators. Interestingly, in recent years many sRNA sequences were discovered not only in multicellular organisms, but also in the genomes of wide range of bacteria (also pathogenic species) and bacteriophages (shortly phages). In the case of bacteria, these mysterious molecules affect many important processes such as carbon metabolism, virulence, colonization ability, motility, quorum sensing, biofilm formation, bacterial adaptation to changing conditions, response to stress and cell growth or death. In turn, sRNAs of phage origin play essential roles during the early stage of infection, maintaining the state of lysogeny and silencing the expression of late structural genes, thereby regulating the transition between phage life cycles. However, in comparison to the very large number of reports concerning eukaryotic sRNA molecules, current knowledge about such regulatory particles in prokaryotic systems is only “a drop in the ocean” and there is an urgent need to continue research in this field. In this light, the aim of this Special Issue is to collect and publish results of studies, as well as critical review articles on recent achievements in bacteria- and phages-derived sRNAs unexplored research area. Manuscripts on processes studied on the genome, transcriptome, proteome and metabolome levels will be desirable.

Dr. Alicja Wegrzyn
Dr. Sylwia Bloch
Dr. Monika Maciag-Dorszynska
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

Prokaryotes
Non-coding small RNAs
Gene expression regulators
Pathogenic species of bacteria
Bacteriophages
The genome, transcriptome, proteome and metabolome levels

Published Papers (3 papers)

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Research

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16 pages, 4941 KiB

Open AccessArticle

Involvement of E. coli 6S RNA in Oxidative Stress Response

by Olga Y. Burenina, Daria A. Elkina, Anna Ovcharenko, Valeria A. Bannikova, M. Amri C. Schlüter, Tatiana S. Oretskaya, Roland K. Hartmann and Elena A. Kubareva

Int. J. Mol. Sci. 2022, 23(7), 3653; https://doi.org/10.3390/ijms23073653 - 26 Mar 2022

Cited by 5 | Viewed by 2617

Abstract

6S RNA, a small non-coding RNA present in almost all bacteria, inhibits transcription via direct binding to RNA polymerase holoenzymes. The mechanism of 6S RNA action was investigated to a large extent in E. coli, however, lack of 6S RNA (ΔssrS) was demonstrated to be unfavorable but not essential for cell survival under various growth conditions. In the present study, we revealed, for the first time, a lethal phenotype of the ΔssrS strain in the presence of high concentrations of H₂O₂. This phenotype was rescued by complementation of the ssrS gene on a plasmid. We performed comparative qRT-PCR analyses on an enlarged set of mRNAs of genes associated with the oxidative stress response, allowing us to identify four genes known to be involved in this pathway (soxS, ahpC, sodA and tpx) that had decreased mRNA levels in the ΔssrS strain. Finally, we performed comparative proteomic analyses of the wild-type and ΔssrS strains, confirming that ΔssrS bacteria have reduced levels of the proteins AhpC and Tpx involved in H₂O₂ reduction. Our findings substantiate the crucial role of the riboregulator 6S RNA for bacterial coping with extreme stresses. Full article

(This article belongs to the Special Issue Non-coding Small RNAs (sRNAs) in Prokaryotic Systems)

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13 pages, 2342 KiB

Open AccessArticle

Small RNA F6 Provides Mycobacterium smegmatis Entry into Dormancy

by Artem Grigorov, Oksana Bychenko, Elena G. Salina, Yulia Skvortsova, Arina Mazurova, Timofey Skvortsov, Arseny Kaprelyants and Tatyana Azhikina

Int. J. Mol. Sci. 2021, 22(21), 11536; https://doi.org/10.3390/ijms222111536 - 26 Oct 2021

Cited by 4 | Viewed by 2404

Abstract

Regulatory small non-coding RNAs play a significant role in bacterial adaptation to changing environmental conditions. Various stresses such as hypoxia and nutrient starvation cause a reduction in the metabolic activity of Mycobacterium smegmatis, leading to entry into dormancy. We investigated the functional role of F6, a small RNA of M. smegmatis, and constructed an F6 deletion strain of M. smegmatis. Using the RNA-seq approach, we demonstrated that gene expression changes that accompany F6 deletion contributed to bacterial resistance against oxidative stress. We also found that F6 directly interacted with 5′-UTR of MSMEG_4640 mRNA encoding RpfE2, a resuscitation-promoting factor, which led to the downregulation of RpfE2 expression. The F6 deletion strain was characterized by the reduced ability to enter into dormancy (non-culturability) in the potassium deficiency model compared to the wild-type strain, indicating that F6 significantly contributes to bacterial adaptation to non-optimal growth conditions. Full article

(This article belongs to the Special Issue Non-coding Small RNAs (sRNAs) in Prokaryotic Systems)

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Review

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27 pages, 4427 KiB

Open AccessReview

Specific and Global RNA Regulators in Pseudomonas aeruginosa

by Petra Pusic, Elisabeth Sonnleitner and Udo Bläsi

Int. J. Mol. Sci. 2021, 22(16), 8632; https://doi.org/10.3390/ijms22168632 - 11 Aug 2021

Cited by 17 | Viewed by 3700

Abstract

Pseudomonas aeruginosa (Pae) is an opportunistic pathogen showing a high intrinsic resistance to a wide variety of antibiotics. It causes nosocomial infections that are particularly detrimental to immunocompromised individuals and to patients suffering from cystic fibrosis. We provide a snapshot on regulatory RNAs of Pae that impact on metabolism, pathogenicity and antibiotic susceptibility. Different experimental approaches such as in silico predictions, co-purification with the RNA chaperone Hfq as well as high-throughput RNA sequencing identified several hundreds of regulatory RNA candidates in Pae. Notwithstanding, using in vitro and in vivo assays, the function of only a few has been revealed. Here, we focus on well-characterized small base-pairing RNAs, regulating specific target genes as well as on larger protein-binding RNAs that sequester and thereby modulate the activity of translational repressors. As the latter impact large gene networks governing metabolism, acute or chronic infections, these protein-binding RNAs in conjunction with their cognate proteins are regarded as global post-transcriptional regulators. Full article

(This article belongs to the Special Issue Non-coding Small RNAs (sRNAs) in Prokaryotic Systems)

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