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Small Prokaryotic Proteins Interacting with Nucleic Acids

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 15295

Special Issue Editors


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Guest Editor
Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 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
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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.

Dr. Alicja Wegrzyn
Prof. Dr. Grzegorz Wegrzyn
Guest Editors

Manuscript Submission Information

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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.

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Keywords

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

Published Papers (6 papers)

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Editorial

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3 pages, 178 KiB  
Editorial
Small Prokaryotic Proteins Interacting with Nucleic Acids
by Alicja Węgrzyn and Grzegorz Węgrzyn
Int. J. Mol. Sci. 2022, 23(17), 9876; https://doi.org/10.3390/ijms23179876 - 30 Aug 2022
Viewed by 1132
Abstract
Among proteins that interact with DNA or RNA, more or less specifically, there is a special group of relatively small polypeptides which are present in prokaryotic cells and interact with nucleic acids [...] Full article
(This article belongs to the Special Issue Small Prokaryotic Proteins Interacting with Nucleic Acids)

Research

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17 pages, 26648 KiB  
Article
A Novel Family of Winged-Helix Single-Stranded DNA-Binding Proteins from Archaea
by Can Huang, Xuehui Liu, Yuanyuan Chen, Junshi Zhou, Wenqian Li, Niannian Ding, Li Huang, Jingyu Chen and Zhenfeng Zhang
Int. J. Mol. Sci. 2022, 23(7), 3455; https://doi.org/10.3390/ijms23073455 - 22 Mar 2022
Cited by 3 | Viewed by 1938
Abstract
The winged helix superfamily comprises a large number of structurally related nucleic acid-binding proteins. While these proteins are often shown to bind dsDNA, few are known to bind ssDNA. Here, we report the identification and characterization of Sul7s, a novel winged-helix single-stranded DNA [...] Read more.
The winged helix superfamily comprises a large number of structurally related nucleic acid-binding proteins. While these proteins are often shown to bind dsDNA, few are known to bind ssDNA. Here, we report the identification and characterization of Sul7s, a novel winged-helix single-stranded DNA binding protein family highly conserved in Sulfolobaceae. Sul7s from Sulfolobus islandicus binds ssDNA with an affinity approximately 15-fold higher than that for dsDNA in vitro. It prefers binding oligo(dT)30 over oligo(dC)30 or a dG-rich 30-nt oligonucleotide, and barely binds oligo(dA)30. Further, binding by Sul7s inhibits DNA strand annealing, but shows little effect on the melting temperature of DNA duplexes. The solution structure of Sul7s determined by NMR shows a winged helix-turn-helix fold, consisting of three α-helices, three β-strands, and two short wings. It interacts with ssDNA via a large positively charged binding surface, presumably resulting in ssDNA deformation. Our results shed significant light on not only non-OB fold single-stranded DNA binding proteins in Archaea, but also the divergence of the winged-helix proteins in both function and structure during evolution. Full article
(This article belongs to the Special Issue Small Prokaryotic Proteins Interacting with Nucleic Acids)
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20 pages, 3741 KiB  
Article
Regulation of Ribosomal Protein Synthesis in Mycobacteria: The Autogenous Control of rpsO
by Leonid V. Aseev, Ludmila S. Koledinskaya, Oksana S. Bychenko and Irina V. Boni
Int. J. Mol. Sci. 2021, 22(18), 9679; https://doi.org/10.3390/ijms22189679 - 07 Sep 2021
Cited by 3 | Viewed by 2149
Abstract
The autogenous regulation of ribosomal protein (r-protein) synthesis plays a key role in maintaining the stoichiometry of ribosomal components in bacteria. In this work, taking the rpsO gene as a classic example, we addressed for the first time the in vivo regulation of [...] Read more.
The autogenous regulation of ribosomal protein (r-protein) synthesis plays a key role in maintaining the stoichiometry of ribosomal components in bacteria. In this work, taking the rpsO gene as a classic example, we addressed for the first time the in vivo regulation of r-protein synthesis in the mycobacteria M. smegmatis (Msm) and M. tuberculosis (Mtb). We used a strategy based on chromosomally integrated reporters under the control of the rpsO regulatory regions and the ectopic expression of Msm S15 to measure its impact on the reporter expression. Because the use of E. coli as a host appeared inefficient, a fluorescent reporter system was developed by inserting Msm or Mtb rpsO-egfp fusions into the Msm chromosome and expressing Msm S15 or E. coli S15 in trans from a novel replicative shuttle vector, pAMYC. The results of the eGFP expression measurements in Msm cells provided evidence that the rpsO gene in Msm and Mtb was feedback-regulated at the translation level. The mutagenic analysis showed that the folding of Msm rpsO 5′UTR in a pseudoknot appeared crucial for repression by both Msm S15 and E. coli S15, thus indicating a striking resemblance of the rpsO feedback control in mycobacteria and in E. coli. Full article
(This article belongs to the Special Issue Small Prokaryotic Proteins Interacting with Nucleic Acids)
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22 pages, 2716 KiB  
Article
Differential Chromosome- and Plasmid-Borne Resistance of Escherichia coli hfq Mutants to High Concentrations of Various Antibiotics
by Lidia Gaffke, Krzysztof Kubiak, Zuzanna Cyske and Grzegorz Węgrzyn
Int. J. Mol. Sci. 2021, 22(16), 8886; https://doi.org/10.3390/ijms22168886 - 18 Aug 2021
Cited by 8 | Viewed by 2441
Abstract
The Hfq protein is a bacterial RNA chaperone, involved in many molecular interactions, including control of actions of various small RNA regulatory molecules. We found that the presence of Hfq was required for survival of plasmid-containing Escherichia coli cells against high concentrations of [...] Read more.
The Hfq protein is a bacterial RNA chaperone, involved in many molecular interactions, including control of actions of various small RNA regulatory molecules. We found that the presence of Hfq was required for survival of plasmid-containing Escherichia coli cells against high concentrations of chloramphenicol (plasmid p27cmr), tetracycline (pSC101, pBR322) and ampicillin (pBR322), as hfq+ strains were more resistant to these antibiotics than the hfq-null mutant. In striking contrast, production of Hfq resulted in low resistance to high concentrations of kanamycin when the antibiotic-resistance marker was chromosome-borne, with deletion of hfq resulting in increasing bacterial survival. These results were observed both in solid and liquid medium, suggesting that antibiotic resistance is an intrinsic feature of these strains rather than a consequence of adaptation. Despite its major role as RNA chaperone, which also affects mRNA stability, Hfq was not found to significantly affect kan and tet mRNAs turnover. Nevertheless, kan mRNA steady-state levels were higher in the hfq-null mutant compared to the hfq+ strain, suggesting that Hfq can act as a repressor of kan expression.This observation does correlate with the enhanced resistance to high levels of kanamycin observed in the hfq-null mutant. Furthermore, dependency on Hfq for resistance to high doses of tetracycline was found to depend on plasmid copy number, which was only observed when the resistance marker was expressed from a low copy plasmid (pSC101) but not from a medium copy plasmid (pBR322). This suggests that Hfq may influence survival against high doses of antibiotics through mechanisms that remain to be determined. Studies with pBR322Δrom may also suggest an interplay between Hfq and Rom in the regulation of ColE1-like plasmid replication. Results of experiments with a mutant devoid of the part of the hfq gene coding for the C-terminal region of Hfq suggested that this region, as well as the N-terminal region, may be involved in the regulation of expression of antibiotic resistance in E. coli independently. Full article
(This article belongs to the Special Issue Small Prokaryotic Proteins Interacting with Nucleic Acids)
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17 pages, 12369 KiB  
Article
Mutational Analysis of Redβ Single Strand Annealing Protein: Roles of the 14 Lysine Residues in DNA Binding and Recombination In Vivo
by Katerina Zakharova, Brian J. Caldwell, Shalya Ta, Carter T. Wheat and Charles E. Bell
Int. J. Mol. Sci. 2021, 22(14), 7758; https://doi.org/10.3390/ijms22147758 - 20 Jul 2021
Cited by 3 | Viewed by 2533
Abstract
Redβ is a 261 amino acid protein from bacteriophage λ that promotes a single-strand annealing (SSA) reaction for repair of double-stranded DNA (dsDNA) breaks. While there is currently no high-resolution structure available for Redβ, models of its DNA binding domain (residues 1–188) have [...] Read more.
Redβ is a 261 amino acid protein from bacteriophage λ that promotes a single-strand annealing (SSA) reaction for repair of double-stranded DNA (dsDNA) breaks. While there is currently no high-resolution structure available for Redβ, models of its DNA binding domain (residues 1–188) have been proposed based on homology with human Rad52, and a crystal structure of its C-terminal domain (CTD, residues 193-261), which binds to λ exonuclease and E. coli single-stranded DNA binding protein (SSB), has been determined. To evaluate these models, the 14 lysine residues of Redβ were mutated to alanine, and the variants tested for recombination in vivo and DNA binding and annealing in vitro. Most of the lysines within the DNA binding domain, including K36, K61, K111, K132, K148, K154, and K172, were found to be critical for DNA binding in vitro and recombination in vivo. By contrast, none of the lysines within the CTD, including K214, K245, K251, K253, and K258 were required for DNA binding in vitro, but two, K214 and K253, were critical for recombination in vivo, likely due to their involvement in binding to SSB. K61 was identified as a residue that is critical for DNA annealing, but not for initial ssDNA binding, suggesting a role in binding to the second strand of DNA incorporated into the complex. The K148A variant, which has previously been shown to be defective in oligomer formation, had the lowest affinity for ssDNA, and was the only variant that was completely non-cooperative, suggesting that ssDNA binding is coupled to oligomerization. Full article
(This article belongs to the Special Issue Small Prokaryotic Proteins Interacting with Nucleic Acids)
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Review

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15 pages, 866 KiB  
Review
Small Prokaryotic DNA-Binding Proteins Protect Genome Integrity throughout the Life Cycle
by Katja Molan and Darja Žgur Bertok
Int. J. Mol. Sci. 2022, 23(7), 4008; https://doi.org/10.3390/ijms23074008 - 04 Apr 2022
Cited by 14 | Viewed by 3639
Abstract
Genomes of all organisms are persistently threatened by endogenous and exogenous assaults. Bacterial mechanisms of genome maintenance must provide protection throughout the physiologically distinct phases of the life cycle. Spore-forming bacteria must also maintain genome integrity within the dormant endospore. The nucleoid-associated proteins [...] Read more.
Genomes of all organisms are persistently threatened by endogenous and exogenous assaults. Bacterial mechanisms of genome maintenance must provide protection throughout the physiologically distinct phases of the life cycle. Spore-forming bacteria must also maintain genome integrity within the dormant endospore. The nucleoid-associated proteins (NAPs) influence nucleoid organization and may alter DNA topology to protect DNA or to alter gene expression patterns. NAPs are characteristically multifunctional; nevertheless, Dps, HU and CbpA are most strongly associated with DNA protection. Archaea display great variety in genome organization and many inhabit extreme environments. As of yet, only MC1, an archaeal NAP, has been shown to protect DNA against thermal denaturation and radiolysis. ssDNA are intermediates in vital cellular processes, such as DNA replication and recombination. Single-stranded binding proteins (SSBs) prevent the formation of secondary structures but also protect the hypersensitive ssDNA against chemical and nuclease degradation. Ionizing radiation upregulates SSBs in the extremophile Deinococcus radiodurans. Full article
(This article belongs to the Special Issue Small Prokaryotic Proteins Interacting with Nucleic Acids)
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