Beyond xeroderma pigmentosum: DNA damage and repair in an ecological context. A tribute to James E. Cleaver

Genomic and morphological characterization of Knufia obscura isolated from the Mars 2020 spacecraft assembly facility

Members of the family Trichomeriaceae, belonging to the Chaetothyriales order and the Ascomycota phylum, are known for their capability to inhabit hostile environments characterized by extreme temperatures, oligotrophic conditions, drought, or presence of toxic compounds. The genus Knufia encompasses many polyextremophilic species. In this report, the genomic and morphological features of the strain FJI-L2-BK-P2 presented, which was isolated from the Mars 2020 mission spacecraft assembly facility located at the Jet Propulsion Laboratory in Pasadena, California. The identification is based on sequence alignment for marker genes, multi-locus sequence analysis, and whole genome sequence phylogeny. The morphological features were studied using a diverse range of microscopic techniques (bright field, phase contrast, differential interference contrast and scanning electron microscopy). The phylogenetic marker genes of the strain FJI-L2-BK-P2 exhibited highest similarities with type strain of Knufia obscura (CBS 148926T) that was isolated from the gas tank of a car in Italy. To validate the species identity, whole genomes of both strains (FJI-L2-BK-P2 and CBS 148926T) were sequenced, annotated, and strain FJI-L2-BK-P2 was confirmed as K. obscura. The morphological analysis and description of the genomic characteristics of K. obscura FJI-L2-BK-P2 may contribute to refining the taxonomy of Knufia species. Key morphological features are reported in this K. obscura strain, resembling microsclerotia and chlamydospore-like propagules. These features known to be characteristic features in black fungi which could potentially facilitate their adaptation to harsh environments.

Structure and mechanism of pyrimidine-pyrimidone (6-4) photoproduct recognition by the Rad4/XPC nucleotide excision repair complex

Failure in repairing ultraviolet radiation-induced DNA damage can lead to mutations and cancer. Among UV-lesions, the pyrimidine–pyrimidone (6-4) photoproduct (6-4PP) is removed from the genome much faster than the cyclobutane pyrimidine dimer (CPD), owing to the more efficient recognition of 6-4PP by XPC-RAD23B, a key initiator of global-genome nucleotide excision repair (NER). Here, we report a crystal structure of a Rad4–Rad23 (yeast XPC-Rad23B ortholog) bound to 6-4PP-containing DNA and 4-μs molecular dynamics (MD) simulations examining the initial binding of Rad4 to 6-4PP or CPD. This first structure of Rad4/XPC bound to a physiological substrate with matched DNA sequence shows that Rad4 flips out both 6-4PP-containing nucleotide pairs, forming an ‘open’ conformation. The MD trajectories detail how Rad4/XPC initiates ‘opening’ 6-4PP: Rad4 initially engages BHD2 to bend/untwist DNA from the minor groove, leading to unstacking and extrusion of the 6-4PP:AA nucleotide pairs towards the major groove. The 5′ partner adenine first flips out and is captured by a BHD2/3 groove, while the 3′ adenine extrudes episodically, facilitating ensuing insertion of the BHD3 β-hairpin to open DNA as in the crystal structure. However, CPD resists such Rad4-induced structural distortions. Untwisting/bending from the minor groove may be a common way to interrogate DNA in NER.

UV-Protective Compounds in Marine Organisms from the Southern Ocean

Solar radiation represents a key abiotic factor in the evolution of life in the oceans. In general, marine, biota-particularly in euphotic and dysphotic zones-depends directly or indirectly on light, but ultraviolet radiation (UV-R) can damage vital molecular machineries. UV-R induces the formation of reactive oxygen species (ROS) and impairs intracellular structures and enzymatic reactions. It can also affect organismal physiologies and eventually alter trophic chains at the ecosystem level. In Antarctica, physical drivers, such as sunlight, sea-ice, seasonality and low temperature are particularly influencing as compared to other regions. The springtime ozone depletion over the Southern Ocean makes organisms be more vulnerable to UV-R. Nonetheless, Antarctic species seem to possess analogous UV photoprotection and repair mechanisms as those found in organisms from other latitudes. The lack of data on species-specific responses towards increased UV-B still limits the understanding about the ecological impact and the tolerance levels related to ozone depletion in this region. The photobiology of Antarctic biota is largely unknown, in spite of representing a highly promising reservoir in the discovery of novel cosmeceutical products. This review compiles the most relevant information on photoprotection and UV-repair processes described in organisms from the Southern Ocean, in the context of this unique marine polar environment.

Developmental Phase-Specific Mortality After Ultraviolet-B Radiation Exposure in the Two-Spotted Spider Mite

Exposure to ambient ultraviolet-B (UVB) radiation generates DNA lesions, such as cyclobutane pyrimidine dimers and 6-4 pyrimidine-pyrimidine photoproducts in Tetranychus urticae Koch (Acari: Tetranychidae). Larvae appeared normal and healthy after UVB irradiation. Conversely, many mites were trapped in their old epidermis or experienced retarded development and shrunk, thus failing to molt from protochrysalises to protonymphs and died. This suggested that DNA lesions per se were not causing lethality in mites unless damaged genes were expressed. UVB-induced DNA lesions may have interfered with DNA replication and gene expression during the physiological changes of morphogenesis in the chrysalis stage. Comprehensive gene expression analysis by RNA sequencing revealed that gene expression involving epidermal tissue (characteristically cuticular protein genes) and myosin heavy chain muscle-like genes were downregulated in protochrysalises irradiated with UVB at the larval stage. We conclude that the success of protochrysalis molting is determined by whether the DNA lesions of genes, particularly those connected with morphogenesis, are repaired before expression at the protochrysalis stage.

Photo-enzymatic repair of UVB-induced DNA damage in the two-spotted spider mite Tetranychus urticae

Ambient ultraviolet-B (UVB) radiation induces lethal effects in the two-spotted spider mite Tetranychus urticae, whereas photoreactivation by irradiation with ultraviolet-A and visible light (VIS) plays an important role to increase survival of mites irradiated by UVB. The physiological mechanisms and ecological significance of photoreactivation in terrestrial arthropods have not been shown clearly. We verified the biological impact and accumulation of DNA lesions by UVB irradiation and the repair of them by photoreactivation in T. urticae larvae. Survival of UVB-irradiated larvae decreased with increasing UVB dose, but recovered remarkably with VIS exposure after UVB irradiation (photoreactivation). The DNA lesions, cyclobutane pyrimidine dimers (CPDs) and 6-4 pyrimidine-pyrimidine photoproducts (6-4PPs) linearly increased with the UVB dose. The CPDs were repaired after exposure to VIS, whereas the frequency of 6-4PPs was unaffected by VIS; CPD photolyase genes, but not (6-4) photolyase genes, have been found in the T. urticae genome. Therefore, DNA damage and CPD photo enzymatic repair (PER) is significant for survival in this mite under ambient UVB radiation. Unexpectedly, gene expression of CPD photolyase was unaffected by irradiation with UVB and VIS. Instead, expression of xeroderma pigmentosum A (XPA) was increased by irradiation. XPA is a core factor in nucleotide excision repair (NER), which is a repair system unrelated to photo energy. The relationship between gene expression and enzymatic repair remains unclear. To elucidate the PER process in T. urticae, further study will be necessary on the gene expression patterns and molecular functions of CPD photolyase in PER and of XPA in NER.

Molecular and physiological effects of environmental UV radiation on fungal conidia

Conidia are specialized structures produced at the end of the asexual life cycle of most filamentous fungi. They are responsible for fungal dispersal and environmental persistence. In pathogenic species, they are also involved in host recognition and infection. Conidial production, survival, dispersal, germination, pathogenicity and virulence can be strongly influenced by exposure to solar radiation, although its effects are diverse and often species dependent. UV radiation is the most harmful and mutagenic waveband of the solar spectrum. Direct exposure to solar radiation for a few hours can kill conidia of most fungal species. Conidia are killed both by solar UV-A and UV-B radiation. In addition to killing conidia, which limits the size of the fungal population and its dispersion, exposures to sublethal doses of UV radiation can reduce conidial germination speed and virulence. The focus of this review is to provide an overview of the effects of solar radiation on conidia and on the major systems involved in protection from and repair of damage induced by solar UV radiation. The efforts that have been made to obtain strains of fungi of interest such as entomopathogens more tolerant to solar radiation will also be reviewed.