Submit to IJMS Review for IJMS Propose a Special Issue

Journal Menu

Journal Browser

Mechanisms of DNA Replication Fork Progression, Stalling, and Rescue 2.0

Print Special Issue Flyer
Special Issue Editors
Special Issue Information
Keywords
Published Papers

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

Deadline for manuscript submissions: closed (15 September 2023) | Viewed by 10426

Share This Special Issue

Special Issue Editor

Dr. Piero R. Bianco

E-Mail Website
Guest Editor

Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA
Interests: stalled DNA replication fork rescue; single-molecule studies of DNA motor proteins; DNA helicases; single-stranded DNA binding protein
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The DNA replication fork is an essential structure in DNA metabolism. In the absence of impediments, it is moved from the origin to the terminus by dynamic, multi-subunit replisome complexes. When replication fork progress is impeded by obstacles or discontinuities in one or both strands of the DNA duplex, there are dramatic consequences for the cell. These range from checkpoints to cell death or cancer in multicellular organisms when replication fails to restart. Consequently, significant cellular resources are reserved to ensure DNA replication fork progress ranging from unexpected behavior attributed to replisome components, proteins to stabilize fork structures, and multiple types of enzymes to the regression, repair, and restoration of fork structures. Furthermore, the structure of the fork itself plays an important role in facilitating the interactions of both replication and repair proteins with itself. Protein and nucleic acid components work together to ensure that DNA replication is completed with minimal errors in the genome.

Dr. Piero R. Bianco
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

genome instability
DNA helicases
replication restart
recombinational repair
replication fork
DNA repair
recombination
single-strand binding protein
replisomes

Published Papers (6 papers)

Download All Papers

Research

Jump to: Review

21 pages, 4178 KiB

Open AccessArticle

3′dNTP Binding Is Modulated during Primer Synthesis and Translesion by Human PrimPol

by Cristina Velázquez-Ruiz, Luis Blanco and María Isabel Martínez-Jiménez

Int. J. Mol. Sci. 2024, 25(1), 51; https://doi.org/10.3390/ijms25010051 - 19 Dec 2023

Cited by 1 | Viewed by 761

Abstract

PrimPol is a DNA primase/polymerase from the Archaeo-Eukaryotic Primase (AEP) superfamily that enables the progression of stalled replication forks by synthesizing DNA primers ahead of blocking lesions or abnormal structures in the ssDNA template. PrimPol’s active site is formed by three AEP-conserved motifs: A, B and C. Motifs A and C of human PrimPol (HsPrimPol) harbor the catalytic residues (Asp¹¹⁴, Glu¹¹⁶, Asp²⁸⁰) acting as metal ligands, whereas motif B includes highly conserved residues (Lys¹⁶⁵, Ser¹⁶⁷ and His¹⁶⁹), which are postulated to stabilize 3′ incoming deoxynucleotides (dNTPs). Additionally, other putative nucleotide ligands are situated close to motif C: Lys²⁹⁷, almost invariant in the whole AEP superfamily, and Lys³⁰⁰, specifically conserved in eukaryotic PrimPols. Here, we demonstrate that His¹⁶⁹ is absolutely essential for 3′dNTP binding and, hence, for both primase and polymerase activities of HsPrimPol, whereas Ser¹⁶⁷ and Lys²⁹⁷ are crucial for the dimer synthesis initiation step during priming, but dispensable for subsequent dNTP incorporation on growing primers. Conversely, the elimination of Lys¹⁶⁵ does not affect the overall primase function; however, it is required for damage avoidance via primer–template realignments. Finally, Lys³⁰⁰ is identified as an extra anchor residue to stabilize the 3′ incoming dNTP. Collectively, these results demonstrate that individual ligands modulate the stabilization of 3′ incoming dNTPs to optimize DNA primer synthesis efficiency during initiation and primer maturation. Full article

(This article belongs to the Special Issue Mechanisms of DNA Replication Fork Progression, Stalling, and Rescue 2.0)

► Show Figures

Figure 1

12 pages, 2552 KiB

Open AccessArticle

Characterization of Unidirectional Replication Forks in the Mouse Genome

by Avital Zerbib and Itamar Simon

Int. J. Mol. Sci. 2023, 24(11), 9611; https://doi.org/10.3390/ijms24119611 - 1 Jun 2023

Viewed by 1132

Abstract

Origins of replication are genomic regions in which replication initiates in a bidirectional manner. Recently, a new methodology (origin-derived single-stranded DNA sequencing; ori-SSDS) was developed that allows the detection of replication initiation in a strand-specific manner. Reanalysis of the strand-specific data revealed that 18–33% of the peaks are non-symmetrical, suggesting a single direction of replication. Analysis of replication fork direction data revealed that these are origins of replication in which the replication is paused in one of the directions, probably due to the existence of a replication fork barrier. Analysis of the unidirectional origins revealed a preference of G4 quadruplexes for the blocked leading strand. Taken together, our analysis identified hundreds of genomic locations in which the replication initiates only in one direction, and suggests that G4 quadruplexes may serve as replication fork barriers in such places. Full article

(This article belongs to the Special Issue Mechanisms of DNA Replication Fork Progression, Stalling, and Rescue 2.0)

► Show Figures

Figure 1

20 pages, 4648 KiB

Open AccessArticle

The Impact of Single-Stranded DNA-Binding Protein SSB and Putative SSB-Interacting Proteins on Genome Integrity in the Thermophilic Crenarchaeon Sulfolobus acidocaldarius

by Shoji Suzuki and Norio Kurosawa

Int. J. Mol. Sci. 2023, 24(5), 4558; https://doi.org/10.3390/ijms24054558 - 25 Feb 2023

Cited by 1 | Viewed by 1538

Abstract

The study of DNA repair in hyperthermophiles has the potential to elucidate the mechanisms of genome integrity maintenance systems under extreme conditions. Previous biochemical studies have suggested that the single-stranded DNA-binding protein (SSB) from the hyperthermophilic crenarchaeon Sulfolobus is involved in the maintenance of genome integrity, namely, in mutation avoidance, homologous recombination (HR), and the repair of helix-distorting DNA lesions. However, no genetic study has been reported that elucidates whether SSB actually maintains genome integrity in Sulfolobus in vivo. Here, we characterized mutant phenotypes of the ssb-deleted strain Δssb in the thermophilic crenarchaeon S. acidocaldarius. Notably, an increase (29-fold) in mutation rate and a defect in HR frequency was observed in Δssb, indicating that SSB was involved in mutation avoidance and HR in vivo. We characterized the sensitivities of Δssb, in parallel with putative SSB-interacting protein-encoding gene-deleted strains, to DNA-damaging agents. The results showed that not only Δssb but also Δalhr1 and ΔSaci_0790 were markedly sensitive to a wide variety of helix-distorting DNA-damaging agents, indicating that SSB, a novel helicase SacaLhr1, and a hypothetical protein Saci_0790, were involved in the repair of helix-distorting DNA lesions. This study expands our knowledge of the impact of SSB on genome integrity and identifies novel and key proteins for genome integrity in hyperthermophilic archaea in vivo. Full article

(This article belongs to the Special Issue Mechanisms of DNA Replication Fork Progression, Stalling, and Rescue 2.0)

► Show Figures

Figure 1

22 pages, 2216 KiB

Open AccessArticle

Bacillus subtilis RadA/Sms-Mediated Nascent Lagging-Strand Unwinding at Stalled or Reversed Forks Is a Two-Step Process: RadA/Sms Assists RecA Nucleation, and RecA Loads RadA/Sms

by Rubén Torres, Begoña Carrasco and Juan C. Alonso

Int. J. Mol. Sci. 2023, 24(5), 4536; https://doi.org/10.3390/ijms24054536 - 25 Feb 2023

Cited by 2 | Viewed by 957

Abstract

Replication fork rescue requires Bacillus subtilis RecA, its negative (SsbA) and positive (RecO) mediators, and fork-processing (RadA/Sms). To understand how they work to promote fork remodeling, reconstituted branched replication intermediates were used. We show that RadA/Sms (or its variant, RadA/Sms C13A) binds to the 5′-tail of a reversed fork with longer nascent lagging-strand and unwinds it in the 5′→3′ direction, but RecA and its mediators limit unwinding. RadA/Sms cannot unwind a reversed fork with a longer nascent leading-strand, or a gapped stalled fork, but RecA interacts with and activates unwinding. Here, the molecular mechanism by which RadA/Sms, in concert with RecA, in a two-step reaction, unwinds the nascent lagging-strand of reversed or stalled forks is unveiled. First, RadA/Sms, as a mediator, contributes to SsbA displacement from the forks and nucleates RecA onto single-stranded DNA. Then, RecA, as a loader, interacts with and recruits RadA/Sms onto the nascent lagging strand of these DNA substrates to unwind them. Within this process, RecA limits RadA/Sms self-assembly to control fork processing, and RadA/Sms prevents RecA from provoking unnecessary recombination. Full article

(This article belongs to the Special Issue Mechanisms of DNA Replication Fork Progression, Stalling, and Rescue 2.0)

► Show Figures

Graphical abstract

Review

Jump to: Research

21 pages, 1593 KiB

Open AccessReview

Cellular Responses to Widespread DNA Replication Stress

by Jac A. Nickoloff, Aruna S. Jaiswal, Neelam Sharma, Elizabeth A. Williamson, Manh T. Tran, Dominic Arris, Ming Yang and Robert Hromas

Int. J. Mol. Sci. 2023, 24(23), 16903; https://doi.org/10.3390/ijms242316903 - 29 Nov 2023

Cited by 3 | Viewed by 1863

Abstract

Replicative DNA polymerases are blocked by nearly all types of DNA damage. The resulting DNA replication stress threatens genome stability. DNA replication stress is also caused by depletion of nucleotide pools, DNA polymerase inhibitors, and DNA sequences or structures that are difficult to replicate. Replication stress triggers complex cellular responses that include cell cycle arrest, replication fork collapse to one-ended DNA double-strand breaks, induction of DNA repair, and programmed cell death after excessive damage. Replication stress caused by specific structures (e.g., G-rich sequences that form G-quadruplexes) is localized but occurs during the S phase of every cell division. This review focuses on cellular responses to widespread stress such as that caused by random DNA damage, DNA polymerase inhibition/nucleotide pool depletion, and R-loops. Another form of global replication stress is seen in cancer cells and is termed oncogenic stress, reflecting dysregulated replication origin firing and/or replication fork progression. Replication stress responses are often dysregulated in cancer cells, and this too contributes to ongoing genome instability that can drive cancer progression. Nucleases play critical roles in replication stress responses, including MUS81, EEPD1, Metnase, CtIP, MRE11, EXO1, DNA2-BLM, SLX1-SLX4, XPF-ERCC1-SLX4, Artemis, XPG, FEN1, and TATDN2. Several of these nucleases cleave branched DNA structures at stressed replication forks to promote repair and restart of these forks. We recently defined roles for EEPD1 in restarting stressed replication forks after oxidative DNA damage, and for TATDN2 in mitigating replication stress caused by R-loop accumulation in BRCA1-defective cells. We also discuss how insights into biological responses to genome-wide replication stress can inform novel cancer treatment strategies that exploit synthetic lethal relationships among replication stress response factors. Full article

(This article belongs to the Special Issue Mechanisms of DNA Replication Fork Progression, Stalling, and Rescue 2.0)

► Show Figures

Figure 1

21 pages, 1830 KiB

Open AccessReview

Inhibition of Replication Fork Formation and Progression: Targeting the Replication Initiation and Primosomal Proteins

by Holly M. Radford, Casey J. Toft, Alanna E. Sorenson and Patrick M. Schaeffer

Int. J. Mol. Sci. 2023, 24(10), 8802; https://doi.org/10.3390/ijms24108802 - 15 May 2023

Viewed by 3573

Abstract

Over 1.2 million deaths are attributed to multi-drug-resistant (MDR) bacteria each year. Persistence of MDR bacteria is primarily due to the molecular mechanisms that permit fast replication and rapid evolution. As many pathogens continue to build resistance genes, current antibiotic treatments are being rendered useless and the pool of reliable treatments for many MDR-associated diseases is thus shrinking at an alarming rate. In the development of novel antibiotics, DNA replication is still a largely underexplored target. This review summarises critical literature and synthesises our current understanding of DNA replication initiation in bacteria with a particular focus on the utility and applicability of essential initiation proteins as emerging drug targets. A critical evaluation of the specific methods available to examine and screen the most promising replication initiation proteins is provided. Full article

(This article belongs to the Special Issue Mechanisms of DNA Replication Fork Progression, Stalling, and Rescue 2.0)

► Show Figures