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Small Prokaryotic Proteins Interacting with Nucleic Acids 2.0

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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 (30 December 2023) | Viewed by 3476

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Special Issue Editor

Prof. Dr. Grzegorz Wegrzyn

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Guest Editor

Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
Interests: gene expression regulation; DNA replication; bacteriophages; plasmids; human genetic diseases; neurodegeneration
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

There are many known proteins which specifically or non-specifically interacts with DNA or RNA. However, a special role is played by small proteins, present in prokaryotic cells, which interact with nucleic acids. Their functions were previously underestimated, but currently it appears that they play crucial roles in many processes occurring in prokaryotic cells, including gene expression regulation, DNA replication, genetic recombination and others. This special issue is devoted to publish papers focused on structures and functions of these proteins. Manuscripts on in vivo and in vitro studies are welcome, as are works presenting in silico analyses. Papers on genetic, biophysical and biochemical investigations will be considered. Both original papers and review articles can be submitted, provided they concern aspects of biological or biotechnological significance of small prokaryotic proteins interacting with DNA or RNA. It is expected that articles published in this special issue will significantly extend our understanding of regulation of molecular processes by these proteins.

Prof. Dr. Grzegorz Wegrzyn
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

small proteins
protein-nucleic acids interactions
prokaryotic cells
gene expression regulation
DNA replication
DNA recombination
DNA repair
RNA metabolism

Published Papers (2 papers)

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Research

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23 pages, 5202 KiB

Open AccessArticle

Investigating the Prevalence of RNA-Binding Metabolic Enzymes in E. coli

by Thomas Klein, Franziska Funke, Oliver Rossbach, Gerhard Lehmann, Michael Vockenhuber, Jan Medenbach, Beatrix Suess, Gunter Meister and Patrick Babinger

Int. J. Mol. Sci. 2023, 24(14), 11536; https://doi.org/10.3390/ijms241411536 - 16 Jul 2023

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Abstract

An open research field in cellular regulation is the assumed crosstalk between RNAs, metabolic enzymes, and metabolites, also known as the REM hypothesis. High-throughput assays have produced extensive interactome data with metabolic enzymes frequently found as hits, but only a few examples have been biochemically validated, with deficits especially in prokaryotes. Therefore, we rationally selected nineteen Escherichia coli enzymes from such datasets and examined their ability to bind RNAs using two complementary methods, iCLIP and SELEX. Found interactions were validated by EMSA and other methods. For most of the candidates, we observed no RNA binding (12/19) or a rather unspecific binding (5/19). Two of the candidates, namely glutamate-5-kinase (ProB) and quinone oxidoreductase (QorA), displayed specific and previously unknown binding to distinct RNAs. We concentrated on the interaction of QorA to the mRNA of yffO, a grounded prophage gene, which could be validated by EMSA and MST. Because the physiological function of both partners is not known, the biological relevance of this interaction remains elusive. Furthermore, we found novel RNA targets for the MS2 phage coat protein that served us as control. Our results indicate that RNA binding of metabolic enzymes in procaryotes is less frequent than suggested by the results of high-throughput studies, but does occur. Full article

(This article belongs to the Special Issue Small Prokaryotic Proteins Interacting with Nucleic Acids 2.0)

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Review

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16 pages, 606 KiB

Open AccessReview

IHF and Fis as Escherichia coli Cell Cycle Regulators: Activation of the Replication Origin oriC and the Regulatory Cycle of the DnaA Initiator

by Kazutoshi Kasho, Shogo Ozaki and Tsutomu Katayama

Int. J. Mol. Sci. 2023, 24(14), 11572; https://doi.org/10.3390/ijms241411572 - 18 Jul 2023

Cited by 2 | Viewed by 1610

Abstract

This review summarizes current knowledge about the mechanisms of timely binding and dissociation of two nucleoid proteins, IHF and Fis, which play fundamental roles in the initiation of chromosomal DNA replication in Escherichia coli. Replication is initiated from a unique replication origin called oriC and is tightly regulated so that it occurs only once per cell cycle. The timing of replication initiation at oriC is rigidly controlled by the timely binding of the initiator protein DnaA and IHF to oriC. The first part of this review presents up-to-date knowledge about the timely stabilization of oriC-IHF binding at oriC during replication initiation. Recent advances in our understanding of the genome-wide profile of cell cycle-coordinated IHF binding have revealed the oriC-specific stabilization of IHF binding by ATP-DnaA oligomers at oriC and by an initiation-specific IHF binding consensus sequence at oriC. The second part of this review summarizes the mechanism of the timely regulation of DnaA activity via the chromosomal loci DARS2 (DnaA-reactivating sequence 2) and datA. The timing of replication initiation at oriC is controlled predominantly by the phosphorylated form of the adenosine nucleotide bound to DnaA, i.e., ATP-DnaA, but not ADP-ADP, is competent for initiation. Before initiation, DARS2 increases the level of ATP-DnaA by stimulating the exchange of ADP for ATP on DnaA. This DARS2 function is activated by the site-specific and timely binding of both IHF and Fis within DARS2. After initiation, another chromosomal locus, datA, which inactivates ATP-DnaA by stimulating ATP hydrolysis, is activated by the timely binding of IHF. A recent study has shown that ATP-DnaA oligomers formed at DARS2-Fis binding sites competitively dissociate Fis via negative feedback, whereas IHF regulation at DARS2 and datA still remains to be investigated. This review summarizes the current knowledge about the specific role of IHF and Fis in the regulation of replication initiation and proposes a mechanism for the regulation of timely IHF binding and dissociation at DARS2 and datA. Full article

(This article belongs to the Special Issue Small Prokaryotic Proteins Interacting with Nucleic Acids 2.0)

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