Search Results (205)

Base excision repair (BER) and nucleotide excision repair (NER) are traditionally regarded as independent pathways; however, accumulating evidence indicates that ultraviolet (UV)-damaged DNA-binding protein (UV-DDB), a core NER factor, stimulates BER DNA glycosylases, including alkyladenine DNA glycosylase (AAG). Despite this functional link, the molecular basis of the UV-DDB/AAG interaction and its regulation by DNA remain unclear. This study investigated the direct interaction between AAG and UV-DDB using electrophoretic mobility shift assays (EMSA), surface plasmon resonance (SPR), biolayer interferometry (BLI) and AlphaFold3-based structural modeling under DNA-free and DNA-bound conditions. SPR analysis revealed that AAG and UV-DDB form a high-affinity complex in the absence of DNA ($K_D$ ≈ 17.5 nM), which is maintained but reduced approximately 2.6-fold upon binding to apurinic/apyrimidinic site (AP site)-containing dsDNA ($K_D$ ≈ 46.2 nM). BLI analysis independently confirmed this interaction under both DNA-free and DNA-bound conditions, with inter-platform differences consistent with previously reported BLI/SPR variability. EMSA showed UV-DDB-mediated ternary complex formation accompanied by redistribution of binary AAG/DNA species. AlphaFold3 modeling predicted that AAG associates with DDB1 in the DNA-free state, whereas under DNA-bound conditions, DDB2 recognizes the AP site while AAG repositions toward the lesion with multiple active site residues placed in close proximity. These findings support a model in which DNA binding acts as a molecular switch that reconfigures the UV-DDB/AAG interaction, potentially enabling UV-DDB to function as a recruitment platform that facilitates directional progression of AAG through the BER cycle, and providing a structural basis for coordinated integration of BER and NER. Full article

DNA oxidation damage and its repair are essential for maintaining genomic integrity in the human limbal epithelium, which harbors corneal epithelial stem cells. This study investigated the distribution of the DNA base oxidation 8-oxoguanine (8-oxoG) and the base excision repair (BER) enzymes 8-oxoguanine DNA glycosylase (OGG1) and apurinic/apyrimidinic endonuclease 1 (APE1) in non-cultured and eye-bank organ-cultured human limbal epithelia. Immunohistochemistry was used to assess the localization and staining intensity of 8-oxoG, OGG1, and APE1, evaluated semi-quantitatively and by image analysis. In situ hybridization was performed to detect the distribution of OGG1 and APE1 gene expression in organ-cultured tissue. In non-cultured limbal epithelia, nuclear 8-oxoG staining was more frequently observed in superficial epithelial layers, whereas nuclear OGG1 and APE1 staining predominated in basal layers. In organ-cultured epithelia, a higher proportion of superficial nuclei exhibited 8-oxoG staining, while the basal predominance of OGG1 was reduced and that of APE1 was preserved. Transcripts of OGG1 and APE1 were detected in basal- as well as in suprabasal layers of organ-cultured epithelia. These findings demonstrate the presence of DNA base oxidation and BER-related enzymes in basal and suprabasal human limbal epithelial cells during storage of corneal tissue under commonly used eye-bank organ-cultured conditions prior to transplantation. Full article

Background/Objectives: Bisulfite-based cell-free DNA (cfDNA) methylation assays enable the detection of clinically valuable epigenetic biomarkers but often cause DNA degradation and inconsistent conversion efficiency, limiting performance in low-input liquid biopsy samples. We aimed to develop and evaluate a fully enzymatic cfDNA methylation workflow that preserves DNA integrity and supports quantitative clinical detection. Methods: The assay integrates TET2-mediated oxidation and APOBEC3A deamination with RNase H2-guided primer design, uracil-DNA glycosylase error suppression, and dual-probe detection compatible with quantitative PCR (qPCR) and digital PCR (dPCR). Performance was assessed using serial dilutions of methylated HT29 DNA, unmethylated controls, and plasma cfDNA from colorectal cancer (CRC) patients and healthy donors. Analytical sensitivity, linearity, and concordance between platforms were evaluated. Results: The 40-marker panel demonstrated higher cumulative methylation scores and more frequent methylation-positive signals in CRC cfDNA compared to controls. dPCR confirmed single-molecule resolution and clear discrimination between methylated and unmethylated templates, with occasional double-positive partitions consistent with mixed allelic methylation. Signal intensity across the dilution series followed a four-parameter logistic model, achieving detection sensitivity below 0.2% methylated DNA. qPCR and dPCR results showed strong correlation across the HT29 dilution series (R² = 0.80) and high concordance in classifying CRC and healthy samples. Conclusions: This TET2–APOBEC-based enzymatic cfDNA assay enables sensitive, quantitative, sequencing-free methylation detection under gentle conditions, supporting its application in early colorectal cancer screening and routine clinical liquid biopsy workflows. Full article

Lettuce (Lactuca sativa L.) is an important leafy vegetable crop, yet the efficiency and reliability of genome editing platforms in lettuce remain limited, particularly for precision base editing applications. In this study, we established an optimized PEG-mediated protoplast transformation system for lettuce through systematic evaluation of key parameters, including protoplast density, incubation time, plasmid size, and transformation method. Under optimized conditions, a maximum transient transformation efficiency of up to 81% was achieved. Using this optimized protoplast platform, we comparatively evaluated the performance of three single-base editing systems—adenosine base editor (ABE), glycosylase-based guanine base editor (gGBE), and rice alkylpurine DNA glycosylase-mediated A-to-K base editor (rAKBE)—targeting the LsALS gene, encoding acetolactate synthetase as a herbicide target with great value in weed control. Among the tested editors, ABE exhibited the highest A-to-G editing efficiency, reaching 9.3%. In contrast, gGBE and rAKBE showed lower editing efficiencies. Together, this study established a robust and reproducible protoplast-based platform for transient genome editing in lettuce and provides a practical framework for the rapid evaluation of base editing tools and target sites, firstly for gGBE and rAKBE evaluation in lettuce. The optimized system facilitates functional genomics studies and supports the development of precision breeding strategies in lettuce. Full article

Plant viruses can cause substantial yield losses, yet disease severity often varies between seasons because plants frequently experience heat or cold episodes before infection. In this study, we tested whether such temperature conditions affect the plant’s redox balance and alter its response to Tomato bushy stunt virus (TBSV) infection in Nicotiana benthamiana. Plants were exposed to short-term heat and cold stress, after which they recovered before virus inoculation. Following this, we assessed the reactive oxygen species (ROS) content, lipid peroxidation (LPO), oxidative DNA damage, stress-related proteins, redox-associated enzymes, and antioxidant metabolites. TBSV led to non-parallel ROS responses during infection, with consistently elevated hydrogen peroxide in infected plants but reduced superoxide relative to corresponding mock controls. Heat pre-exposure caused pronounced LPO that decreased further after infection, whereas cold pre-exposure stabilized malondialdehyde near levels observed at 25 °C. Both thermal stress and infection increased 8-oxo-dG and were associated with distinct changes in 8-oxoguanine glycosylase abundance. Infection strongly induced heat shock protein 90 (and moderately heat shock protein 70), while prior heat limited further chaperone induction by TBSV. These results indicate that viral infection develops within and is limited by the host’s oxidative state, where redox homeostasis may restrict infection-related processes, and infection leads to changes in this redox environment that are favorable for its development. Full article

Tuberculosis (TB) remains a global health issue exacerbated by spreading drug resistance and lengthy treatment regimens. Targeting bacterial DNA-repair pathways, particularly those counteracting host-generated genotoxic stress, represents a promising strategy to sensitize Mycobacterium tuberculosis to existing antibiotics. Through structure-based virtual screening of a compound library, we identified novel small-molecule inhibitors of M. tuberculosis uracil–DNA glycosylase (MtbUng), an enzyme essential for the repair of DNA damage inflicted by macrophage-produced reactive nitrogen species. Experimental validation revealed that four derivatives of usnic acid, a lichen-derived metabolite, significantly inhibited MtbUng activity, with the most potent compound, OL10-88-1, exhibiting IC₅₀ 26 ± 7 µM. Molecular docking suggests that OL10-88-1 inhibits MtbUng by occupying both the active site and the DNA-binding groove, thereby disrupting multiple steps of uracil recognition. The compounds also showed variable inhibitory activity against uracil–DNA glycosylases from Escherichia coli, humans, and vaccinia virus. Our findings establish that the compound could potentially be used in combination therapies to enhance the efficacy of current anti-TB drugs by exploiting the vulnerability of DNA-repair-deficient mycobacteria. Full article

OGG1 and MUTYH are base excision repair (BER) DNA glycosylases (DGs) from the Helix–hairpin–Helix superfamily responsible for initiating and coordinating the repair of 8-oxo-7,8-dihydroguanine (OG), and its replication-derived mispair with adenine (OG:A), respectively. The DNA repair activities of these DGs are pivotal to safeguarding nuclear and mitochondrial genomes. Indeed, DG functional impairment is associated with numerous pathologies, including neurodegenerative diseases, metabolic syndromes, and cancer. The timely and precise localization and processing of oxidized nucleobases carried out by these DGs are modulated by a complex regulatory network at both transcriptional and posttranslational levels, as well as intricate protein–protein interaction networks. In the absence of regulation, inappropriate and imbalanced DG activity may trigger telomeric instability, changes in transcriptional profiles and cell death. This review focuses on summarizing key features of OGG1 and MUTYH function, with a special emphasis on structure, regulation, and novel emerging roles. Full article

Adult growth hormone deficiency (GHD) is linked to increased cardiovascular and metabolic risk due to oxidative stress (OS), endothelial dysfunction, and unhealthy body composition. Long-term systemic effects of recombinant human growth hormone (rhGH) therapy remain insufficiently defined. This study assessed the impact of 24-month rhGH replacement on OS, vascular markers, body composition, and bone mineral density (BMD) in adults with severe GHD. Fifteen adults with confirmed GHD received rhGH for 24 months. Serum insulin-like growth factor 1 (IGF-1), oxidized LDL (Ox-LDL), thioredoxin (Trx), 8-oxoguanine DNA glycosylase 1 (OGG1), E-selectin, intercellular adhesion molecule 1 (ICAM-1), and vascular cell adhesion molecule 1 (VCAM-1) were measured at baseline and 12 and 24 months. Body composition and BMD were evaluated by DXA. IGF-1 increased significantly at 12 and 24 months (p < 0.001). Ox-LDL markedly decreased (p < 0.00001), while Trx and OGG1 increased (p < 0.05). Levels of E-selectin, ICAM-1, and VCAM-1 declined, indicating improved endothelial function. Lean body mass and BMD increased, while body fat parameters showed heterogeneous changes. Lipid profiles were unchanged. Significant correlations were observed between vascular markers and adiposity, and between BMD, triglycerides, and IGF-1. A 24-month course of rhGH therapy improves redox balance, vascular function, and body composition in adults with severe GHD, supporting the use of redox and vascular biomarkers to monitor treatment efficacy. Full article

Acrolein, a ubiquitous environmental pollutant, is also formed endogenously as a metabolite under oxidative stress conditions. Its adduct to cytosine, 3,N⁴-α-hydroxypropanocytosine (HPC), has recently been shown to be an in vitro substrate for the AlkB dioxygenase. Using a set of indicator plasmids modified with acrolein, we provide evidence that HPC is a mutagenic non-instructional lesion that predominantly induces C→A transversion, and to a lesser extent C→T and C→G base substitutions. HPC is efficiently repaired in vivo by AlkB, even without induction of the adaptive response. However, the mutation frequency did not differ between the wild-type and AlkA-deficient strains, and AlkA glycosylase fails to excise in vitro the acrolein-modified cytosine from the T₂₂(HPC)₃ oligodeoxynucleotide, both indicating that HPC is not a substrate for AlkA. Based on molecular modeling, we further examined the potential differences in the hydrolytic suspensibility of a known AlkA substrate, the acrolein adduct to adenine (HPA), and the cytosine adduct (HPC) at the glycosylase active site. Analysis of both structural and electrochemical properties indicates that, despite an identical type of modification within an equivalent chemical context, including comparable geometry and topology, the glycosidic bond in HPC is considerably less susceptible to hydrolysis than that in HPA. Full article

For decades, 8-oxoguanine (8-oxoG) has been recognized as a pervasive and pro-mutagenic oxidative DNA lesion. In human cells, 8-oxoG is removed from DNA via the base excision repair pathway initiated by 8-oxoguanine–DNA glycosylase (OGG1). However, emerging evidence over the past twenty years suggests a more complex, regulatory role for this DNA modification. Here, we discuss findings that 8-oxoG, particularly when present in gene promoters, can act as a signal to modulate transcription, establishing an 8-oxoG/OGG1 axis in the inflammatory response. Proposed mechanisms include the generation of 8-oxoG during chromatin remodeling processes involving histone demethylases, the recruitment of transcription factors (NF-κB, HIF1α, Myc, SMAD, etc.) by OGG1, and the lesion’s enrichment in guanine-rich sequences prone to forming G-quadruplex structures. The pro-mutagenic nature of 8-oxoG and the lack of dedicated, functionally separate writer and reader proteins challenge its classification as a true epigenetic DNA mark, distinguishing it from canonical epigenetic nucleobases like 5-methylcytosine and 5-hydroxymethylcytosine. On the other hand, 8-oxoG is well suited for the role of a regulatory signal localized to DNA and involved in the cellular response to oxidative stress and the associated physiological stimuli. Full article

Base editing represents a major breakthrough in the field of genome editing in recent years. By fusing deaminases with the CRISPR/Cas system, it enables precise single-base modifications of DNA. This review systematically summarizes the development of base editing technologies, including cytosine base editors (CBEs), adenine base editors (ABEs), and glycosylase base editors (GBEs), with a particular focus on their applications in crop improvement as well as future trends and prospects. We highlight advances in the creation of novel germplasm with enhanced stress resistance and desirable agronomic traits through base editing in rice, wheat, maize, potato, and other crops, particularly for improving herbicide resistance, disease resistance, and grain quality. Furthermore, we analyze factors that influence base editing efficiency, noting that challenges remain, such as PAM sequence constraints, limited base conversion types, off-target effects, narrow editing windows, and efficiency variation. Future efforts should aim to optimize deaminase activity, expand PAM compatibility, and develop versatile tools to facilitate the broad application of base editing in molecular breeding. This review provides a timely reference for researchers and breeders, offering theoretical guidance and practical insights into harnessing base editing for crop genetic improvement. Full article

This study investigated the influence of long-chain n-3 polyunsaturated fatty acids (PUFAs) on the activity of antioxidant defence systems and DNA repair enzymes in the liver of newborn piglets born to gilts that were supplemented with fish oil or algal oil during pregnancy. The oils were offered in their natural form or as nanoparticles. Daily doses of both natural and nano-encapsulated oils were calculated to provide each gilt with 3100 mg of docosahexaenoic acid (DHA; 600 mg for the gilt and 250 mg for each foetus). Liver samples were collected from six piglets per gilt within 24 h after birth. Activities of superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx) were measured spectrophotometrically, while DNA repair enzyme activities—formamidopyrimidine-DNA glycosylase (FPG), thymine-DNA glycosylase (TDG), and N-methylpurine DNA glycosylase (MPG)—were assessed by Fpg protein digestion. SOD activity was lowest in piglets from gilts supplemented with algal oil, fish oil, and nano-encapsulated fish oil. Piglets born to the gilts that received algal oil nanoparticles showed higher activity (1.57 U/mg), while the highest activity was recorded in control piglets. CAT activity followed a similar trend; it was lowest in algal oil-supplemented mothers and highest in controls. GPx activity was lowest in piglets born to gilts that received algal oil (both forms) and highest in controls. The FPG activity in piglets birthed by PUFA-supplemented gilts was approximately half that of MPG and TDG, indicating reduced oxidative DNA damage. Both fish oil and algal oil, regardless of the form administered, effectively reduce oxidative stress in pregnant gilts and the associated DNA damage in the livers of their offspring. These findings suggest that maternal supplementation with long-chain n-3 PUFAs can protect newborn piglets from oxidative damage. Furthermore, regional disparities in access to functional foods underline the importance of targeted strategies that integrate local food systems and health planning to promote nutritional equity. Full article

DNA repair is a multifaceted biological process that involves multiple pathways to counter the types of damage the genome encounters throughout life. In the past decade zebrafish became a popular model organism to study various aspects of vertebrate DNA repair, and the characterization of several mutant lines deficient in key players of the repair pathways has significantly contributed to our understanding of the roles the corresponding proteins play in the maintenance of genomic integrity. Interestingly, the base-excision repair (BER) pathway remained one of the less characterized DNA repair processes in fish. Here we provide a detailed characterization of zebrafish deficient in one of the key components of BER, the uracil-DNA glycosylase Unga. We show that while these fish are viable, they display an altered response to genotoxic stress and unga mutant males show an interesting form of subfertility. Full article

Uracil−DNA glycosylases (UNGs) are DNA repair enzymes responsible for the removal of uracil, a canonical RNA nucleobase, from DNA, where it appears through cytosine deamination or incorporation from the cellular dUTP pool. While human and Escherichia coli UNGs have been extensively investigated, much less is known about their plant counterparts, of which UNGs from Arabidopsis thaliana are the only studied examples. Here, we show that in sugar beet (Beta vulgaris L.), an important crop species, cold and salt stress induce the expression of the UNG gene (BvUNG) and modulate the level of the uracil-excising activity in the roots. Purified recombinant BvUNG efficiently removes uracil from DNA both in vitro and in an E. coli reporter strain but does not excise 5-hydroxyuracil, 5,6-dihydrouracil, or 5-hydroxymethyluracil. The activity is abolished by Ugi, a protein UNG inhibitor from PBS1 bacteriophage, and by a mutation of a conserved active site His residue. Structural modeling shows the presence of a disordered N-tail prone to undergo phase separation, followed by a long α helix oriented differently from its counterpart in human UNG. Overall, BvUNG is a functional uracil–DNA glycosylase that might participate in the response to abiotic stress. Full article

Ultraviolet radiation (UVR) is a major contributor to skin aging and carcinogenesis, primarily through the induction of DNA damage. While conventional sunscreens provide passive protection by blocking UVR, active photoprotection using DNA repair enzymes offers a strategy to reverse UV-induced DNA lesions at the molecular level. Enzymes such as photolyase, T4 endonuclease V, and 8-oxoguanine glycosylase address distinct types of DNA damage through light-dependent and -independent mechanisms, complementing the skin’s endogenous repair systems. Advances in nanocarrier technologies and encapsulation methods have improved the stability and delivery of these enzymes in topical formulations. Emerging evidence from clinical studies indicates their potential in reducing actinic keratoses, pigmentation disorders, and photoaging signs, although challenges in regulatory approval, long-term efficacy validation, and formulation optimization remain. This review provides a comprehensive synthesis of the mechanistic, clinical, and formulation aspects of enzyme-based photoprotection, outlines regulatory and ethical considerations, and highlights future directions, including CRISPR-based repair and personalized photoprotection strategies, establishing enzyme-assisted sunscreens as a next-generation approach to comprehensive skin care. Full article