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The Science of the Total Environment May 2024Solar ultraviolet-B (UVB) radiation has increased due to stratospheric ozone depletion, climate and ecosystem changes and is a driver of amphibian population declines....
Solar ultraviolet-B (UVB) radiation has increased due to stratospheric ozone depletion, climate and ecosystem changes and is a driver of amphibian population declines. Photoenzymatic repair (PER) is a critical mechanism for limiting UVB lethality in amphibian larvae. However, the link between PER and the UVB-induced effects remains understudied through long-term investigations in vivo. Here, we assessed how larval PER determines the lethal and sublethal effects induced by environmentally relevant acute UVB exposure until the juvenile phase in the Neotropical frog Odontophrynus americanus. We conducted laboratory-based controlled experiments in which tadpoles were or were not exposed to UVB and subsequently were exposed to light (for PER activation) or dark treatments. Results showed that the rates of mortality and apoptosis observed in post-UVB dark treatment are effectively limited in post-UVB light treatment, indicating PER (and not dark repair, i.e. nucleotide excision repair) is critical to limit the immediate genotoxic impact of UVB-induced pyrimidine dimers. Nonetheless, even tadpoles that survived UVB exposure using PER showed sublethal complications that extended to the juvenile phase. Tadpole responses included alterations in morphology, chromosomal instability, increased skin susceptibility to fungal proliferation, as well as increased generation of reactive oxygen species. The short-term effects were carried over to later stages of life because metamorphosis time increased and juveniles were smaller. No body abnormalities were visualized in tadpoles, metamorphs, and juveniles, suggesting that O. americanus is UVB-resistant concerning these responses. This study reveals that even frog species equipped with an effective PER are not immune to carry-over effects from early UVB exposure, which are of great ecological relevance as late metamorphosis and smaller juveniles may impact individual performance and adult recruitment to breeding. Future ecological risk assessments and conservation and management efforts for amphibian species should exercise caution when linking PER effectiveness to UVB resistance.
Topics: Animals; Larva; Ecosystem; DNA Repair; DNA Damage; Anura; Ultraviolet Rays
PubMed: 38479531
DOI: 10.1016/j.scitotenv.2024.171647 -
Structure-specific DNA endonuclease T7 endonuclease I cleaves DNA containing UV-induced DNA lesions.Journal of Biochemistry Mar 2024The T7 gene 3 product, T7 endonuclease I, acts on various substrates with DNA structures, including Holliday junctions, heteroduplex DNAs, and single-mismatch DNAs....
The T7 gene 3 product, T7 endonuclease I, acts on various substrates with DNA structures, including Holliday junctions, heteroduplex DNAs, and single-mismatch DNAs. Genetic analyses have suggested the occurrence of DNA recombination, replication, and repair in E.coli. In this study, T7 endonuclease I digested UV-irradiated covalently closed circular plasmid DNA into linear and nicked plasmid DNA, suggesting that the enzyme generates single- and double-strand breaks (SSB and DSB). To further investigate the biochemical functions of T7 endonuclease I, we have analyzed endonuclease activity in UV-induced DNA substrates containing a single lesion, cyclobutane pyrimidine dimers (CPD), and 6-4 photoproducts (6-4PP). Interestingly, the leading cleavage site for CPD by T7 endonuclease I is at the second and fifth phosphodiester bonds that are 5' to the lesion of CPD on the lesion strand. However, in the case of 6-4PP, the cleavage pattern on the lesion strand resembled that of CPD, and T7 endonuclease I could also cleave the second phosphodiester bond that is 5' to the adenine-adenine residues opposite the lesion, indicating that the enzyme produces DSB in DNA containing 6-4PP. These findings suggest that T7 endonuclease I accomplished successful UV damage repair by SSB in CPD and DSB in 6-4PP.
PubMed: 38426948
DOI: 10.1093/jb/mvae024 -
Biofouling Jan 2024The use of ultraviolet-C (UV-C) irradiation in marine biofouling control is a relatively new and potentially disruptive technology. This study examined effects of UV-C...
The use of ultraviolet-C (UV-C) irradiation in marine biofouling control is a relatively new and potentially disruptive technology. This study examined effects of UV-C exposure on the biofilm-forming diatom, . UV-C-induced mutations were identified Illumina HiSeq. A genome was assembled from control sequences and reads from UV-C-exposed treatments were mapped to this genome, with a quantitative estimate of mutagenesis then derived from the frequency of single nucleotide polymorphisms. UV-C exposure increased cyclobutane pyrimidine dimer (CPD) abundance with a direct correlation between lesion formation and fluency. Cellular repair mechanisms gradually reduced CPDs over time, with the highest UV-C fluence treatments having the fastest repair rates. Mutation abundances were, however, negatively correlated with CPD abundance suggesting that UV-C exposure may influence lesion repair. The threshold fluence for CPD formation exceeding CPD repair was >1.27 J cm. Fluences >2.54 J cm were predicted to inhibit repair mechanisms. While UV-C holds considerable promise for marine antifouling, diatoms are just one, albeit an important, component of marine biofouling communities. Determining fluence thresholds for other representative taxa, highlighting the most resistant, would allow UV-C treatments to be specifically tuned to target biofouling organisms, whilst limiting environmental effects and the power requirement.
Topics: Pyrimidine Dimers; Diatoms; Biofilms; DNA Repair; Mutagenesis; Ultraviolet Rays
PubMed: 38384189
DOI: 10.1080/08927014.2024.2319178 -
Critical Reviews in Food Science and... Feb 2024Foodborne illnesses occur due to the contamination of fresh, frozen, or processed food products by some pathogens. Among several pathogens responsible for the illnesses,... (Review)
Review
Foodborne illnesses occur due to the contamination of fresh, frozen, or processed food products by some pathogens. Among several pathogens responsible for the illnesses, is one of the lethal bacteria that endangers public health. Several preexisting and novel technologies, especially non-thermal technologies are being studied for their antimicrobial effects, particularly toward . Some noteworthy emerging technologies include ultraviolet (UV) or light-emitting diode (LED), pulsed light, cold plasma, and ozonation. These technologies are gaining popularity since no heat is employed and undesirable deterioration of food quality, especially texture, and taste is devoided. This review aims to summarize the most recent advances in non-thermal processing technologies and their effect on inactivating in food products and on sanitizing packaging materials. These technologies use varying mechanisms, such as photoinactivation, photosensitization, disruption of bacterial membrane and cytoplasm, etc. This review can help food processing industries select the appropriate processing techniques for optimal benefits, in which the structural integrity of food can be preserved while simultaneously destroying present in foods. To eliminate spp., different technologies possess varying mechanisms such as rupturing the cell wall, formation of pyrimidine dimers in the DNA through photochemical effect, excitation of endogenous porphyrins by photosensitizers, generating reactive species, causing leakage of cellular contents and oxidizing proteins and lipids. These technologies provide an alternative to heat-based sterilization technologies and further development is still required to minimize the drawbacks associated with some technologies.
PubMed: 38380625
DOI: 10.1080/10408398.2024.2316295 -
Photochemistry and Photobiology Feb 2024In recent years, interest is growing in the biological cutaneous effects of high-energy visible light (400-450 nm). In the present study, we explored the impact of...
In recent years, interest is growing in the biological cutaneous effects of high-energy visible light (400-450 nm). In the present study, we explored the impact of blue light (BL) on the repair of pyrimidine dimers, the major class of premutagenic DNA damage induced by exposure to sunlight. We unambiguously demonstrate that the exposure of in vitro reconstructed human epidermis to environmentally relevant doses of BL strongly decreases the rate of repair of cyclobutane pyrimidine dimers and pyrimidine (6-4) pyrimidone photoproducts induced by a subsequent UVB irradiation. Using the highly sensitive and specific liquid chromatography-tandem mass spectrometry assay, we did not observe induction of pyrimidine dimers by BL alone. Finally, we showed that application, during the BL exposure step, of a formula containing a new filter, named TriAsorB and affording BL photoprotection, prevented the decrease in DNA repair efficiency. These results emphasize the potential deleterious effects of BL on DNA repair and the interest in providing adequate skin protection against this wavelength range of sunlight.
PubMed: 38348536
DOI: 10.1111/php.13921 -
Plant Physiology Apr 2024Photoreactivation enzyme that repairs cyclobutane pyrimidine dimer (CPD) induced by ultraviolet-B radiation, commonly called CPD photolyase (PHR) is essential for plants...
Photoreactivation enzyme that repairs cyclobutane pyrimidine dimer (CPD) induced by ultraviolet-B radiation, commonly called CPD photolyase (PHR) is essential for plants living under sunlight. Rice (Oryza sativa) PHR (OsPHR) is a unique triple-targeting protein. The signal sequences required for its translocation to the nucleus or mitochondria are located in the C-terminal region but have yet to be identified for chloroplasts. Here, we identified sequences located in the N-terminal region, including the serine-phosphorylation site at position 7 of OsPHR, and found that OsPHR is transported/localized to chloroplasts via a vesicle transport system under the control of serine-phosphorylation. However, the sequence identified in this study is only conserved in some Poaceae species, and in many other plants, PHR is not localized to the chloroplasts. Therefore, we reasoned that Poaceae species need the ability to repair CPD in the chloroplast genome to survive under sunlight and have uniquely acquired this mechanism for PHR chloroplast translocation.
Topics: Chloroplasts; Deoxyribodipyrimidine Photo-Lyase; Ultraviolet Rays; Oryza; Plant Proteins; Pyrimidine Dimers; Poaceae; Amino Acid Sequence; Protein Transport
PubMed: 38345835
DOI: 10.1093/plphys/kiae060 -
Chemical Science Feb 2024Charge separation is one of the most common consequences of the absorption of UV light by DNA. Recently, it has been shown that this process can enable efficient...
Charge separation is one of the most common consequences of the absorption of UV light by DNA. Recently, it has been shown that this process can enable efficient self-repair of cyclobutane pyrimidine dimers (CPDs) in specific short DNA oligomers such as the GAT[double bond, length as m-dash]T sequence. The mechanism was characterized as sequential electron transfer through the nucleobase stack which is controlled by the redox potentials of nucleobases and their sequence. Here, we demonstrate that the inverse sequence T[double bond, length as m-dash]TAG promotes self-repair with higher quantum yields (0.58 ± 0.23%) than GAT[double bond, length as m-dash]T (0.44 ± 0.18%) in a comparative study involving UV-irradiation experiments. After extended exposure to UV irradiation, a photostationary equilibrium between self-repair and damage formation is reached at 33 ± 13% for GAT[double bond, length as m-dash]T and at 40 ± 16% for T[double bond, length as m-dash]TAG, which corresponds to the maximum total yield of self-repair. Molecular dynamics and quantum mechanics/molecular mechanics (QM/MM) simulations allowed us to assign this disparity to better stacking overlap between the G and A bases, which lowers the energies of the key A˙G˙ charge transfer state in the dominant conformers of the T[double bond, length as m-dash]TAG tetramer. These conformational differences also hinder alternative photorelaxation pathways of the T[double bond, length as m-dash]TAG tetranucleotide, which otherwise compete with the sequential electron transfer mechanism responsible for CPD self-repair. Overall, we demonstrate that photoinduced electron transfer is strongly dependent on conformation and the availability of alternative photodeactivation mechanisms. This knowledge can be used in the identification and prediction of canonical and modified DNA sequences exhibiting efficient electron transfer. It also further contributes to our understanding of DNA self-repair and its potential role in the photochemical selection of the most photostable sequences on the early Earth.
PubMed: 38332835
DOI: 10.1039/d3sc04971j -
Scientific Reports Feb 2024Ultraviolet (UV) component of solar radiation impairs genome stability by inducing the formation of pyrimidine-pyrimidone (6-4) photoproducts [(6-4)PPs] in plant...
Ultraviolet (UV) component of solar radiation impairs genome stability by inducing the formation of pyrimidine-pyrimidone (6-4) photoproducts [(6-4)PPs] in plant genomes. (6-4)PPs disrupt growth and development by interfering with transcription and DNA replication. To resist UV stress, plants employ both photoreactivation and nucleotide excision repair that excises oligonucleotide containing (6-4)PPs through two subpathways: global and transcription-coupled excision repair (TCR). Here, we analyzed the genome-wide excision repair-mediated repair of (6-4)PPs in Arabidopsis thaliana and found that (6-4)PPs can be repaired by TCR; however, the main subpathway to remove (6-4)PPs from the genome is global repair. Our analysis showed that open chromatin genome regions are more rapidly repaired than heterochromatin regions, and the repair level peaks at the promoter, transcription start site and transcription end site of genes. Our study revealed that the repair of (6-4)PP in plants showed a distinct genome-wide repair profile compared to the repair of other major UV-induced DNA lesion called cyclobutane pyrimidine dimers (CPDs).
Topics: DNA Repair; Arabidopsis; Pyrimidinones; Excision Repair; Pyrimidine Dimers; DNA Damage; Receptors, Antigen, T-Cell; Ultraviolet Rays
PubMed: 38332020
DOI: 10.1038/s41598-024-53472-8 -
The Journal of Physical Chemistry... Feb 2024Despite the widely recognized importance of noncovalent interactions involving aromatic rings in many fields, our understanding of the underlying forces and structural...
Despite the widely recognized importance of noncovalent interactions involving aromatic rings in many fields, our understanding of the underlying forces and structural patterns, especially the impact of heteroaromaticity, is still incomplete. Here, we investigate the relaxation processes that follow inner-valence ionization in a range of molecular dimers involving various combinations of benzene, pyridine, and pyrimidine, which initiate an ultrafast intermolecular Coulombic decay process. Multiparticle coincidence momentum spectroscopy, combined with calculations, enables us to explore the principal orientations of these fundamental dimers and, thus, to elucidate the influence of N heteroatoms on the relative preference of the aromatic π-stacking, H-bonding, and CH-π interactions and their dependence on the number of nitrogen atoms in the rings. Our studies reveal a sensitive tool for the structural imaging of molecular complexes and provide a more complete understanding of the effects of N heteroatoms on the noncovalent aromatic interactions at the molecular level.
PubMed: 38299504
DOI: 10.1021/acs.jpclett.3c02979 -
Journal of Chemical Information and... Feb 2024Endonuclease V (EndoV) is a single-metal-dependent enzyme that repairs deaminated DNA nucleobases in cells by cleaving the phosphodiester bond, and this enzyme has...
Endonuclease V (EndoV) is a single-metal-dependent enzyme that repairs deaminated DNA nucleobases in cells by cleaving the phosphodiester bond, and this enzyme has proven to be a powerful tool in biotechnology and medicine. The catalytic mechanism used by EndoV must be understood to design new disease detection and therapeutic solutions and further exploit the enzyme in interdisciplinary applications. This study has used a mixed molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) approach to compare eight distinct catalytic pathways and provides the first proposed mechanism for bacterial EndoV. The calculations demonstrate that mechanisms involving either direct or indirect metal coordination to the leaving group of the substrate previously proposed for other nucleases are unlikely for EndoV, regardless of the general base (histidine, aspartate, and substrate phosphate moiety). Instead, distinct catalytic pathways are characterized for EndoV that involve K139 stabilizing the leaving group, a metal-coordinated water stabilizing the transition structure, and either H214 or a substrate phosphate group activating the water nucleophile. K139A and H214A mutational results support the newly proposed roles of these residues. Although this is a previously unseen combination of general base, general acid, and metal-binding architecture for a one-metal-dependent endonuclease, our proposed catalytic mechanisms are fully consistent with experimental kinetic, structural, and mutational data. In addition to substantiating a growing body of literature, suggesting that one metal is enough to catalyze P-O bond cleavage in nucleic acids, this new fundamental understanding of the catalytic function will promote the exploration of new and improved applications of EndoV.
Topics: Nucleic Acids; Deoxyribonuclease (Pyrimidine Dimer); Lysine; Metals; Phosphates; Water
PubMed: 38253321
DOI: 10.1021/acs.jcim.3c01775