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Molecular Mechanisms of Archaea
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Molecular Mechanisms of Archaea

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

Deadline for manuscript submissions: closed (31 January 2023) | Viewed by 5297

Special Issue Editors

Dr. Mariarosaria De Falco

E-Mail Website
Guest Editor
Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, 80131 Naples, Italy
Interests: DNA replication and repair; genome stability; archaea
Special Issues, Collections and Topics in MDPI journals
Dr. Mariarita De Felice

E-Mail Website
Guest Editor
Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, 80131 Naples, Italy
Interests: DNA repair; DNA nuclease; DNA helicase; archaea; HR
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Genomic integrity is a fundamental requirement for the proper functioning of all cellular processes and for the transmission of genetic information to offspring. It is true that random genome mutations are the driving force of biodiversity and guide the evolution of living organisms; however genomic instability proves detrimental in most cases.

DNA damage can be caused by exogenous sources (i.e. chemical cross-linkers or UV-light), but also by endogenous errors during replication, recombination, and chromosome segregation as the incorporation of mismatch errors, torsional stress of the DNA helix, and spontaneous deamination or hydrolysis. To counteract damage all organisms have developed several DNA repair pathways and the choice among them is linked to the type of DNA damage and/or cell cycle phases. Compared to Eukarya and Bacteria, Archaea must have more robust DNA replication and repair complexes to ensure genome fidelity due to the environmental stresses they usually live under. Since archaeal enzyme structures provide critical data about the architecture and mechanisms of key DNA repair proteins, the study of archaeal structural biology is fundamental for both medical and industrial impacts. With this Special Issue of IJMS we aim to enlarge current knowledge on molecular mechanisms of DNA replication and recombinational repair, particularly in Archaea which have been considered the most efficient model of DNA repair pathways for decades now. We hope to contribute to the knowledge in DNA repair mechanisms and consequently to identify new strategies for the most accurate treatments in human diseases.

Dr. Mariarosaria De Falco
Dr. Mariarita De Felice
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

  • DNA replication
  • DNA repair
  • DNA damage response (DDR)
  • genome stability
  • archaea
  • homologous recombination

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Published Papers (2 papers)

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Research

17 pages, 10483 KiB  
Article
Generating a Small Shuttle Vector for Effective Genetic Engineering of Methanosarcina mazei Allowed First Insights in Plasmid Replication Mechanism in the Methanoarchaeon
by Johanna Thomsen and Ruth A. Schmitz
Int. J. Mol. Sci. 2022, 23(19), 11910; https://doi.org/10.3390/ijms231911910 - 7 Oct 2022
Cited by 2 | Viewed by 2828
Abstract
Due to their role in methane production, methanoarchaea are of high ecological relevance and genetic systems have been ever more established in the last two decades. The system for protein expression in Methanosarcina using a comprehensive shuttle vector is established; however, details about [...] Read more.
Due to their role in methane production, methanoarchaea are of high ecological relevance and genetic systems have been ever more established in the last two decades. The system for protein expression in Methanosarcina using a comprehensive shuttle vector is established; however, details about its replication mechanism in methanoarchaea remain unknown. Here, we report on a significant optimisation of the rather large shuttle vector pWM321 (8.9 kbp) generated by Metcalf through a decrease in its size by about 35% by means of the deletion of several non-coding regions and the ssrA gene. The resulting plasmid (pRS1595) still stably replicates in M. mazei and—most likely due to its reduced size—shows a significantly higher transformation efficiency compared to pWM321. In addition, we investigate the essential gene repA, coding for a rep type protein. RepA was heterologously expressed in Escherichia coli, purified and characterised, demonstrating the significant binding and nicking activity of supercoiled plasmid DNA. Based on our findings we propose that the optimised shuttle vector replicates via a rolling circle mechanism with RepA as the initial replication protein in Methanosarcina. On the basis of bioinformatic comparisons, we propose the presence and location of a double-strand and a single-strand origin, which need to be further verified. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Archaea)
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14 pages, 6951 KiB  
Article
Mechanism Underlying the Bypass of Apurinic/Pyrimidinic Site Analogs by Sulfolobus acidocaldarius DNA Polymerase IV
by Qin-Ying Huang, Dong Song, Wei-Wei Wang, Li Peng, Hai-Feng Chen, Xiang Xiao and Xi-Peng Liu
Int. J. Mol. Sci. 2022, 23(5), 2729; https://doi.org/10.3390/ijms23052729 - 1 Mar 2022
Viewed by 1863
Abstract
The spontaneous depurination of genomic DNA occurs frequently and generates apurinic/pyrimidinic (AP) site damage that is mutagenic or lethal to cells. Error-prone DNA polymerases are specifically responsible for the translesion synthesis (TLS) of specific DNA damage, such as AP site damage, generally with [...] Read more.
The spontaneous depurination of genomic DNA occurs frequently and generates apurinic/pyrimidinic (AP) site damage that is mutagenic or lethal to cells. Error-prone DNA polymerases are specifically responsible for the translesion synthesis (TLS) of specific DNA damage, such as AP site damage, generally with relatively low fidelity. The Y-family DNA polymerases are the main error-prone DNA polymerases, and they employ three mechanisms to perform TLS, including template-skipping, dNTP-stabilized misalignment, and misincorporation-misalignment. The bypass mechanism of the dinB homolog (Dbh), an archaeal Y-family DNA polymerase from Sulfolobus acidocaldarius, is unclear and needs to be confirmed. In this study, we show that the Dbh primarily uses template skipping accompanied by dNTP-stabilized misalignment to bypass AP site analogs, and the incorporation of the first nucleotide across the AP site is the most difficult. Furthermore, based on the reported crystal structures, we confirmed that three conserved residues (Y249, R333, and I295) in the little finger (LF) domain and residue K78 in the palm subdomain of the catalytic core domain are very important for TLS. These results deepen our understanding of how archaeal Y-family DNA polymerases deal with intracellular AP site damage and provide a biochemical basis for elucidating the intracellular function of these polymerases. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Archaea)
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