Canonical and Non-Canonical Roles of Human DNA Polymerase η.

DNA damage tolerance pathways that allow for the completion of replication following fork arrest are critical in maintaining genome stability during cell division. The main DNA damage tolerance pathways include strand switching, replication fork reversal and translesion synthesis (TLS). The TLS pathway is mediated by specialised DNA polymerases that can accommodate altered DNA structures during DNA synthesis, and are important in allowing replication to proceed after fork arrest, preventing fork collapse that can generate more deleterious double-strand breaks in the genome. TLS may occur directly at the fork, or at gaps remaining behind the fork, in the process of post-replication repair. Inactivating mutations in the human POLH gene encoding the Y-family DNA polymerase Pol η causes the skin cancer-prone genetic disease xeroderma pigmentosum variant (XPV). Pol η also contributes to chemoresistance during cancer treatment by bypassing DNA lesions induced by anti-cancer drugs including cisplatin. We review the current understanding of the canonical role of Pol η in translesion synthesis following replication arrest, as well as a number of emerging non-canonical roles of the protein in other aspects of DNA metabolism.

Molecular mechanisms of avian immunoglobulin gene diversification and prospect for industrial applications.

Poultry immunoglobulin genes undergo diversification through homologous recombination (HR) and somatic hypermutation (SHM). Most animals share a similar system in immunoglobulin diversification, with the rare exception that human and murine immunoglobulin genes diversify through V(D)J recombination. Poultry possesses only one functional variable gene for each immunoglobulin heavy (HC) and light chains (LC), with clusters of non-productive pseudogenes upstream. During the B cell development, the functional variable gene is overwritten by sequences from the pseudo-variable genes via a process known as gene conversion (GC), a kind of HR. Point mutations caused in the functional variable gene also contribute to immunoglobulin diversification. This review discusses the latest findings on the molecular mechanisms of antibody gene diversification in poultry, using chickens as a model. Additionally, it will outline how these basic research findings have recently been applied especially in the medical field.

Tolerating DNA damage by repriming: Gap filling in the spotlight.

Timely and accurate DNA replication is critical for safeguarding genome integrity and ensuring cell viability. Yet, this process is challenged by DNA damage blocking the progression of the replication machinery. To counteract replication fork stalling, evolutionary conserved DNA damage tolerance (DDT) mechanisms promote DNA damage bypass and fork movement. One of these mechanisms involves "skipping" DNA damage through repriming downstream of the lesion, leaving single-stranded DNA (ssDNA) gaps behind the advancing forks (also known as post-replicative gaps). In vertebrates, repriming in damaged leading templates is proposed to be mainly promoted by the primase and polymerase PRIMPOL. In this review, we discuss recent advances towards our understanding of the physiological and pathological conditions leading to repriming activation in human models, revealing a regulatory network of PRIMPOL activity. Upon repriming by PRIMPOL, post-replicative gaps formed can be filled-in by the DDT mechanisms translesion synthesis and template switching. We discuss novel findings on how these mechanisms are regulated and coordinated in time to promote gap filling. Finally, we discuss how defective gap filling and aberrant gap expansion by nucleases underlie the cytotoxicity associated with post-replicative gap accumulation. Our increasing knowledge of this repriming mechanism - from gap formation to gap filling - is revealing that targeting the last step of this pathway is a promising approach to exploit post-replicative gaps in anti-cancer therapeutic strategies.

The multifaceted roles of the Ctf4 replisome hub in the maintenance of genome integrity.

At the core of cellular life lies a carefully orchestrated interplay of DNA replication, recombination, chromatin assembly, sister-chromatid cohesion and transcription. These fundamental processes, while seemingly discrete, are inextricably linked during genome replication. A set of replisome factors integrate various DNA transactions and contribute to the transient formation of sister chromatid junctions involving either the cohesin complex or DNA four-way junctions. The latter structures serve DNA damage bypass and may have additional roles in replication fork stabilization or in marking regions of replication fork blockage. Here, we will discuss these concepts based on the ability of one replisome component, Ctf4, to act as a hub and functionally link these processes during DNA replication to ensure genome maintenance.

Restoration of Strength in Polyamide Woven Glass Fiber Organosheets by Hot Pressing: Case Study of Impact and Compression after Impact.

Thermoplastic composite organosheets (OSs) are increasingly recognized as a viable solution for automotive and aerospace structures, offering a range of benefits including cost-effectiveness through high-rate production, lightweight design, impact resistance, formability, and recyclability. This study examines the impact response, post-impact strength evaluation, and hot-pressing repair effectiveness of woven glass fiber nylon composite OSs across varying impact energy levels. Experimental investigations involved subjecting composite specimens to impact at varying energy levels using a drop-tower test rig, followed by compression-after-impact (CAI) tests. The results underscore the exceptional damage tolerance and improved residual compressive strength of the OSs compared to traditional thermoset composites. This enhancement was primarily attributed to the matrix's ductility, which mitigated transverse crack propagation and significantly increased the amount of absorbed energy. To mitigate impact-induced damage, a localized hot-pressing repair approach was developed. This allowed to restore the post-impact strength of the OSs to pristine levels for impact energies below 40 J and by 83.6% for higher impact energies, when OS perforation was observed. The measured levels of post-repair strength demonstrate a successful restoration of OS strength over a wide range of impact energies, and despite limitations in achieving complete strength recovery above 40 J, hot-pressing repair emerges as a promising strategy for ensuring the longevity of thermoplastic composites through repairability.

Compressive Failure Characteristics of 3D Four-Directional Braided Composites with Prefabricated Holes.

The low delamination tendency and high damage tolerance of three-dimensional (3D) braided composites highlight their significant potential in handling defects. To enhance the engineering potential of three-dimensional four-directional (3D4d) braided composites and assess the failure mode of hole defects, this study introduces a series of 3D4d braided composites with prefabricated holes, studying their compressive properties and failure mechanisms through experimental and finite element methods. Digital image correlation (DIC) was used to monitor the compressive strain on the surface of materials. Scanning acoustic microscope (SAM) and scanning electron microscopy (SEM) were used to characterize the longitudinal compression failure mode inside the material. A macroscopic model is established, and the porous materials are predicted by using the general braided composite material prediction theory. While reducing the forecast cost, the error is also controlled within 21%. The analysis of failure mechanisms elucidates the damage extension mode, and the porous damage tolerance ability aligns closely with the bearing mode of braided material structure. Different braiding angles will lead to different bearing modes of materials. Under longitudinal compression, the average strength loss of 15° specimens is 38.21%, and that of 30° specimens is 8.1%. The larger the braided angle, the stronger the porous damage tolerance. Different types of prefabricated holes will also affect their mechanical properties and damage tolerance.

Effects of PCNA Stability on the Formation of Mutations.

The fidelity of replication, especially in the presence of DNA damage, is essential for the proper function of cells. Mutations that inactivate genes involved in DNA damage repair or bypass are enriched in several types of cancer cells. Thus, it is important to further our understanding of the mechanisms governing replication fidelity. PCNA is a ring-shaped complex that encircles DNA at the front of the replication fork, at the double-stranded/single-stranded DNA junction. It serves as a processivity factor for the different DNA replication polymerases, allowing them to replicate longer stretches of DNA by physically tethering them to the DNA and preventing their detachment. In addition, PCNA also regulates and coordinates different DNA damage bypass pathways meant to allow DNA replication in the presence of DNA damage. Due to its essentiality and the numerous functions it has in the cell, much is still unclear about PCNA. Here, we utilize PCNA mutants that lower the stability of the PCNA complex on the chromatin, and thus tend to disassociate and fall from the DNA. Using these mutants, we show that PCNA's physical presence on the DNA can prevent DNA misalignment at repetitive sequences, leading to increased mutation formation. We also show that PCNA-interacting proteins play an important role in strengthening the ring's stability on the chromatin. Such repetitive sequence-induced mutations are common in several human diseases and it is important to study their formation and the mechanisms guarding against them.

Protein Assemblies in Translesion Synthesis.

Translesion synthesis (TLS) is a mechanism of DNA damage tolerance utilized by eukaryotic cells to replicate DNA across lesions that impede the high-fidelity replication machinery. In TLS, a series of specialized DNA polymerases are employed, which recognize specific DNA lesions, insert nucleotides across the damage, and extend the distorted primer-template. This allows cells to preserve genetic integrity at the cost of mutations. In humans, TLS enzymes include the Y-family, inserter polymerases, Polη, Polι, Polκ, Rev1, and the B-family extender polymerase Polζ, while in S. cerevisiae only Polη, Rev1, and Polζ are present. To bypass DNA lesions, TLS polymerases cooperate, assembling into a complex on the eukaryotic sliding clamp, PCNA, termed the TLS mutasome. The mutasome assembly is contingent on protein-protein interactions (PPIs) between the modular domains and subunits of TLS enzymes, and their interactions with PCNA and DNA. While the structural mechanisms of DNA lesion bypass by the TLS polymerases and PPIs of their individual modules are well understood, the mechanisms by which they cooperate in the context of TLS complexes have remained elusive. This review focuses on structural studies of TLS polymerases and describes the case of TLS holoenzyme assemblies in action emerging from recent high-resolution Cryo-EM studies.

Epoxy/Graphene Nanoplatelet (GNP) Nanocomposites: An Experimental Study on Tensile, Compressive, and Thermal Properties.

This paper presents an experimental investigation of nanocomposites composed of three ratios of epoxy/graphene nanoplatelets (GNPs) by weight. The 0.1, 0.2, and 0.3 wt.% specimens were carefully manufactured, and their mechanical and thermal conductivity properties were examined. The tensile strength and modulus of epoxy/GNPs were enhanced by the large surface area of graphene nanoplatelets, causing crack deflection that created new fracture fronts and friction because of the rough fracture surface. However, the compressive strength was gradually reduced as GNP loading percentages increased. This was probably due to severe plastic yielding on the epoxy, leading to catastrophic axial splitting caused by premature fractures. Furthermore, the highest thermal conductivity was 0.1283 W/m-K, representing a 20.92% improvement over neat epoxy (0.1061 W/m-K) when 0.3 wt.% GNPs were added to the epoxy. This was because of efficient heat propagation in the GNPs due to electron movement through percolative paths. The tensile failure mode in epoxy/GNP nanocomposites showed a few deflected and bifurcated rough cracks and brittle, dimple-like fractures. Contrarily, compressive failure mode in GNP-added epoxy showed plastic flexural buckling and brittle large-axial splitting. The epoxy/GNP nanocomposites were considered a damage-tolerant material.

Perspectives Toward Damage-Tolerant Nanostructure Ceramics.

Advanced ceramic materials and devices call for better reliability and damage tolerance. In addition to their strong bonding nature, there are examples demonstrating superior mechanical properties of nanostructure ceramics, such as damage-tolerant ceramic aerogels that can withstand high deformation without cracking and local plasticity in dense nanocrystalline ceramics. The recent progresses shall be reviewed in this perspective article. Three topics including highly elastic nano-fibrous ceramic aerogels, load-bearing nanoceramics with improved mechanical properties, and implementing machine learning-assisted simulations toolbox in understanding the relationship among structure, deformation mechanisms, and microstructure-properties shall be discussed. It is hoped that the perspectives present here can help the discovery, synthesis, and processing of future structural ceramic materials that are insensitive to processing flaws and local damages in service.

Studying Translesion DNA Synthesis Using Xenopus In Vitro Systems.

Cell-free extracts derived from Xenopus eggs have been widely used to decipher molecular pathways involved in several cellular processes including DNA synthesis, the DNA damage response, and genome integrity maintenance. We set out assays using Xenopus cell-free extracts to study translesion DNA synthesis (TLS), a branch of the DNA damage tolerance pathway that allows replication of damaged DNA. Using this system, we were able to recapitulate TLS activities that occur naturally in vivo during early embryogenesis. This chapter describes protocols to detect chromatin-bound TLS factors by western blotting and immunofluorescence microscopy upon induction of DNA damage by UV irradiation, monitor TLS-dependent mutagenesis, and perform proteomic screening.

Superior Strength, Toughness, and Damage-Tolerance Observed in Microlattices of Aperiodic Unit Cells.

Characterized by periodic cellular unit cells, microlattices offer exceptional potential as lightweight and robust materials. However, their inherent periodicity poses the risk of catastrophic global failure. To address this limitation, a novel approach, that is to introduce microlattices composed of aperiodic unit cells inspired by Einstein's tile, where the orientation of cells never repeats in the same orientation is proposed. Experiments and simulations are conducted to validate the concept by comparing compressive responses of the aperiodic microlattices with those of common periodic microlattices. Indeed, the microlattices exhibit stable and progressive compressive deformation, contrasting with catastrophic fracture of periodic structures. At the same relative density, the microlattices outperform the periodic ones, exhibiting fracture strain, energy absorption, crushing stress efficiency, and smoothness coefficients at least 830%, 300%, 130%, and 160% higher, respectively. These improvements can be attributed to aperiodicity, where diverse failure thresholds exist locally due to varying strut angles and contact modes during compression. This effectively prevents both global fracture and abrupt stress drops. Furthermore, the aperiodic microlattice exhibits good damage tolerance with excellent deformation recoverability, retaining 76% ultimate stress post-recovery at 30% compressive strain. Overall, a novel concept of adopting aperiodic cell arrangements to achieve damage-tolerant microlattice metamaterials is presented.

TREX2 deficiency suppresses spontaneous and genotoxin-associated mutagenesis.

TREX2, a 3'-5' exonuclease, is a part of the DNA damage tolerance (DDT) pathway that stabilizes replication forks (RFs) by ubiquitinating PCNA along with the ubiquitin E3 ligase RAD18 and other DDT factors. Mismatch repair (MMR) corrects DNA polymerase errors, including base mismatches and slippage. Here we demonstrate that TREX2 deletion reduces mutations in cells upon exposure to genotoxins, including those that cause base lesions and DNA polymerase slippage. Importantly, we show that TREX2 generates most of the spontaneous mutations in MMR-mutant cells derived from mice and people. TREX2-induced mutagenesis is dependent on the nuclease and DNA-binding attributes of TREX2. RAD18 deletion also reduces spontaneous mutations in MMR-mutant cells, albeit to a lesser degree. Inactivation of both MMR and TREX2 additively increases RF stalls, while it decreases DNA breaks, consistent with a synthetic phenotype.

A Flexible Escape Skin Bioinspired by the Defensive Behavior of Shedding Scales.

Artificial skins with functions such as sensing, variable stiffness, actuation, self-healing, display, adhesion, and camouflage have been developed and widely used, but artificial skins with escape function are still a research gap. In nature, every species of animal can use its innate skills and functions to escape capture. Inspired by the behavior of fish-scale geckoes escaping predation by shedding scales when grasped or touched, we propose a flexible escape skin by attaching artificial scales to a flexible film. Experiments demonstrate that the escape skin has significant effects in reducing escape force, escaping from harmful force environments, and resisting mechanical damage. Furthermore, we enabled active control of escape force and skin hardness by changing temperature, increasing the adaptability of the escape skin to the surrounding. Our study helps lay the foundation for engineering systems that depend on escape skin to improve robustness.

Processing of stalled replication forks in Bacillus subtilis.

Accurate DNA replication and transcription elongation are crucial for preventing the accumulation of unreplicated DNA and genomic instability. Cells have evolved multiple mechanisms to deal with impaired replication fork progression, challenged by both intrinsic and extrinsic impediments. The bacterium Bacillus subtilis, which adopts multiple forms of differentiation and development, serves as an excellent model system for studying the pathways required to cope with replication stress to preserve genomic stability. This review focuses on the genetics, single molecule choreography, and biochemical properties of the proteins that act to circumvent the replicative arrest allowing the resumption of DNA synthesis. The RecA recombinase, its mediators (RecO, RecR, and RadA/Sms) and modulators (RecF, RecX, RarA, RecU, RecD2, and PcrA), repair licensing (DisA), fork remodelers (RuvAB, RecG, RecD2, RadA/Sms, and PriA), Holliday junction resolvase (RecU), nucleases (RnhC and DinG), and translesion synthesis DNA polymerases (PolY1 and PolY2) are key functions required to overcome a replication stress, provided that the fork does not collapse.

Exploring RAD18-dependent replication of damaged DNA and discontinuities: A collection of advanced tools.

DNA damage tolerance (DDT) pathways mitigate the effects of DNA damage during replication by rescuing the replication fork stalled at a DNA lesion or other barriers and also repair discontinuities left in the newly replicated DNA. From yeast to mammalian cells, RAD18-regulated translesion synthesis (TLS) and template switching (TS) represent the dominant pathways of DDT. Monoubiquitylation of the polymerase sliding clamp PCNA by HRAD6A-B/RAD18, an E2/E3 protein pair, enables the recruitment of specialized TLS polymerases that can insert nucleotides opposite damaged template bases. Alternatively, the subsequent polyubiquitylation of monoubiquitin-PCNA by Ubc13-Mms2 (E2) and HLTF or SHPRH (E3) can lead to the switching of the synthesis from the damaged template to the undamaged newly synthesized sister strand to facilitate synthesis past the lesion. When immediate TLS or TS cannot occur, gaps may remain in the newly synthesized strand, partly due to the repriming activity of the PRIMPOL primase, which can be filled during the later phases of the cell cycle. The first part of this review will summarize the current knowledge about RAD18-dependent DDT pathways, while the second part will offer a molecular toolkit for the identification and characterization of the cellular functions of a DDT protein. In particular, we will focus on advanced techniques that can reveal single-stranded and double-stranded DNA gaps and their repair at the single-cell level as well as monitor the progression of single replication forks, such as the specific versions of the DNA fiber and comet assays. This collection of methods may serve as a powerful molecular toolkit to monitor the metabolism of gaps, detect the contribution of relevant pathways and molecular players, as well as characterize the effectiveness of potential inhibitors.

Response of PRIMPOL-Knockout Human Lung Adenocarcinoma A549 Cells to Genotoxic Stress.

Human DNA primase/polymerase PrimPol synthesizes DNA primers de novo after replication fork stalling at the sites of DNA damage, thus contributing to the DNA damage tolerance. The role of PrimPol in response to the different types of DNA damage is poorly understood. We knocked out the PRIMPOL gene in the lung carcinoma A549 cell line and characterized the response of the obtained cells to the DNA damage caused by hydrogen peroxide, methyl methanesulfonate (MMS), cisplatin, bleomycin, and ionizing radiation. The PRIMPOL knockout reduced the number of proliferating cells and cells in the G2 phase after treatment with MMS and caused a more pronounced delay of the S phase in the cisplatin-treated cells. Ionizing radiation at a dose of 10 Gy significantly increased the content of apoptotic cells among the PRIMPOL-deficient cells, while the proportion of cells undergoing necroptosis increased in both parental and knockout cells at any radiation dose. The viability of PRIMPOL-deficient cells upon the hydrogen peroxide-induced oxidative stress increased compared to the control cells, as determined by the methyl tetrazolium (MTT) assay. The obtained data indicate the involvement of PRIMPOL in the modulation of adaptive cell response to various types of genotoxic stress.

Development of bioinspired damage-tolerant calcium phosphate bulk materials.

Improving the damage tolerance and reliability of ceramic artificial bone materials, such as sintered bodies of hydroxyapatite (HAp), that remain in vivo for long periods of time is of utmost importance. However, the intrinsic brittleness and low damage tolerance of ceramics make this challenging. This paper reports the synthesis of highly damage tolerant calcium phosphate-based materials with a bioinspired design for novel artificial bones. The heat treatment of isophthalate ion-containing octacalcium phosphate compacts in a nitrogen atmosphere at 1000°C for 24 h produced an HAp/ß-tricalcium phosphate/pyrolytic carbon composite with a brick-and-mortar structure (similar to that of the nacreous layer). This composite exhibited excellent damage tolerance, with no brittle fracture upon nailing, likely attributable to the specific mechanical properties derived from its unique microstructure. Its maximum bending stress, maximum bending strain, Young's modulus, and Vickers hardness were 11.7 MPa, 2.8 × 10‒2, 5.3 GPa, and 11.7 kgf/mm2, respectively. The material exhibited a lower Young's modulus and higher fracture strain than that of HAp-sintered bodies and sintered-body samples prepared from pure octacalcium phosphate compacts. Additionally, the apatite-forming ability of the obtained material was confirmed in vitro, using a simulated body fluid. The proposed bioinspired material design could enable the fabrication of highly damage tolerant artificial bones that remain in vivo for long durations of time.

Implications of Translesion DNA Synthesis Polymerases on Genomic Stability and Human Health.

Replication fork arrest-induced DNA double strand breaks (DSBs) caused by lesions are effectively suppressed in cells due to the presence of a specialized mechanism, commonly referred to as DNA damage tolerance (DDT). In eukaryotic cells, DDT is facilitated through translesion DNA synthesis (TLS) carried out by a set of DNA polymerases known as TLS polymerases. Another parallel mechanism, referred to as homology-directed DDT, is error-free and involves either template switching or fork reversal. The significance of the DDT pathway is well established. Several diseases have been attributed to defects in the TLS pathway, caused either by mutations in the TLS polymerase genes or dysregulation. In the event of a replication fork encountering a DNA lesion, cells switch from high-fidelity replicative polymerases to low-fidelity TLS polymerases, which are associated with genomic instability linked with several human diseases including, cancer. The role of TLS polymerases in chemoresistance has been recognized in recent years. In addition to their roles in the DDT pathway, understanding noncanonical functions of TLS polymerases is also a key to unraveling their importance in maintaining genomic stability. Here we summarize the current understanding of TLS pathway in DDT and its implication for human health.

The Adaptive Mechanisms and Checkpoint Responses to a Stressed DNA Replication Fork.

DNA replication is a tightly controlled process that ensures the faithful duplication of the genome. However, DNA damage arising from both endogenous and exogenous assaults gives rise to DNA replication stress associated with replication fork slowing or stalling. Therefore, protecting the stressed fork while prompting its recovery to complete DNA replication is critical for safeguarding genomic integrity and cell survival. Specifically, the plasticity of the replication fork in engaging distinct DNA damage tolerance mechanisms, including fork reversal, repriming, and translesion DNA synthesis, enables cells to overcome a variety of replication obstacles. Furthermore, stretches of single-stranded DNA generated upon fork stalling trigger the activation of the ATR kinase, which coordinates the cellular responses to replication stress by stabilizing the replication fork, promoting DNA repair, and controlling cell cycle and replication origin firing. Deregulation of the ATR checkpoint and aberrant levels of chronic replication stress is a common characteristic of cancer and a point of vulnerability being exploited in cancer therapy. Here, we discuss the various adaptive responses of a replication fork to replication stress and the roles of ATR signaling that bring fork stabilization mechanisms together. We also review how this knowledge is being harnessed for the development of checkpoint inhibitors to trigger the replication catastrophe of cancer cells.