Photolyases and Cryptochromes in UV-resistant Bacteria from High-altitude Andean Lakes

Redox-State-Dependent Structural Changes within a Prokaryotic 6-4 Photolyase

Photolyases repair UV damage to DNA by using absorbed blue light. Within the photolyase/cryptochrome superfamily (PCSf), a major subgroup consists of prokaryotic (6-4) photolyases. These enzymes rely on flavin adenine dinucleotide (FAD) as a catalytic cofactor, besides an ancillary antenna chromophore, and a [4Fe-4S] cluster with yet unknown function. For the prokaryotic 6-4 photolyase of Caulobacter crescentus, we investigated structural changes associated with its different redox states by damage-free crystallography using X-ray free-electron lasers. EPR and optical spectroscopy confirmed redox-dependent structural transitions, including the formation of an oxidized [4Fe-4S]3+ cluster with the dynamic cleavage of a single iron-sulfur bond. Photoreduction to the catalytic FADH- state alters the flavin binding site at the proximal aromatic pair Y390/F394 that is part of the electron transport pathway. Upon oxidation, the observable structural transitions of the protein matrix around the [4Fe-4S] cluster may affect DNA binding and are consistent with the much-debated role of the iron-sulfur cluster in DNA-binding proteins for quenching electron holes.

The Genetic Determinants of Extreme UV Radiation and Desiccation Tolerance in a Bacterium Recovered from the Stratosphere

Microbes that survive transport to and in the stratosphere endure extremes of low temperature, atmospheric pressure, and relative humidity, as well as high fluxes in ultraviolet radiation (UVR). The high atmosphere thus provides an ideal environment to explore the genetic and physiological determinants conveying high tolerance to desiccation and UVR. In this study, we examined Curtobacterium aetherium L6-1, an actinobacterium obtained from stratospheric aerosol sampling that displays high resistance to desiccation and UVR. We found that its phylogenetic relatives are resistant to desiccation, but only C. aetherium displayed a high tolerance to UVR. Comparative genome analysis and directed evolution experiments implicated genes encoding photolyase, DNA nucleases and helicases, and catalases as responsible for UVR resistance in C. aetherium. Differential gene expression analysis revealed the upregulation of DNA repair and stress response mechanisms when cells were exposed to UVR, while genes encoding sugar transporters, sugar metabolism enzymes, and antioxidants were induced upon desiccation. Based on changes in gene expression as a function of water content, C. aetherium can modulate its metabolism through transcriptional regulation at very low moisture levels (Xw < 0.25 g H2O per gram dry weight). Uncovering the genetic underpinnings of desiccation and UVR resistance in C. aetherium provides new insights into how bacterial DNA repair and antioxidant mechanisms function to exhibit traits at the extreme ends of phenotypic distributions.

From genes to nanotubes: exploring the UV-resistome in the Andean extremophile Exiguobacterium sp. S17

Exiguobacterium sp. S17, a polyextremophile isolated from a High-Altitude Andean Lake, exhibits a multi-resistance profile against toxic arsenic concentrations, high UV radiation, and elevated salinity. Here, we characterize the mechanisms underlying the UV resistance of Exiguobacterium sp. S17 (UV-resistome) through comparative genomics within the Exiguobacterium genus and describe morphological and ultrastructural changes using Scanning (SEM) and Transmission (TEM) Electron Microscopy.UV-resistome in Exiguobacterium species ranges from 112 to 132 genes. While we anticipated Exiguobacterium sp. S17 to lead the non-HAAL UV-resistome, it ranked eleventh with 113 genes. This larger UV-resistome in Exiguobacterium spp. aligns with their known adaptation to extreme environments. With SEM/TEM analyses we observed the formation of nanotubes (NTs), a novel finding in Exiguobacterium spp., which increased with higher UV-B doses. These NTs, confirmed to be membranous structures through sensitivity studies and imaging, suggest a role in cellular communication and environmental sensing. Genomic evidence supports the presence of essential NT biogenesis genes in Exiguobacterium sp. S17, further elucidating its adaptive capabilities.Our study highlights the complex interplay of genetic and phenotypic adaptations enabling Exiguobacterium sp. S17 to thrive in extreme UV environments. The novel discovery of NTs under UV stress presents a new avenue for understanding bacterial survival strategies in harsh conditions.

Composition and distribution of bacterial communities and potential radiation-resistant bacteria at different elevations in the eastern Pamirs

Altitude and ultraviolet (UV) radiation may affect the community composition and distribution of microorganisms in soil ecosystems. In this study, 49 soil samples from 10 locations were collected from different elevations on the eastern Pamir Plateau and analyzed for soil microbial community structure and function using high-throughput sequencing. The results showed that soil samples from different elevations of the eastern Pamir Plateau contained 6834 OTUs in 26 phyla and 399 genera. The dominant phyla common to different elevations were Actinobacteria, Proteobacteria, Bacteroidota, Acidobacteriota, and Gemmatimonadota. The dominant genera were Rubrobacter, Sphingomonas, Nocardioides, and Solirubrobacter. Species richness increased slightly with elevation, and there were significant differences in community composition between the elevations. Elevation and UV exposure are important factors that drive changes in bacterial communities. The results of the KEGG pathway showed that drug resistance, antineoplastic, aging, replication, and repair were enhanced and then slightly decreased with increasing elevation. Bacterial communities at different elevations were rich in radiation-resistant microorganisms, and the main genera were Rubrobacter, Sphingomonas, Nocardioides, Pontibacter, and Streptomyces. The findings have shown the composition and distribution of bacterial communities at different elevations on the Eastern Pamir Plateau. Potentially radiation tolerant microbial species were also examined. The results are of considerable importance for the succession of bacterial microorganisms in the plateau region, the study of radiation tolerant bacterial germplasm resources, and the application of biofunctionality.

Halotolerant Bacteria from Genus Nesterenkonia sandarakina VSA9 as a Potential Polyhydroxyalkanoate Producer

Nesterenkonia sandarakina VSA9 pigmented bacteria isolated from Sargassum is being reported to produce polyhydroxyalkanoates (PHA) deduced through detecting the presence of pha C gene using the molecular method. The PHA synthase gene was of type I which has been concluded from the phylogenetic tree and multiple sequence analysis. The amino acid analysis of pha C gene confirms the involvement of the lipase box having a sequence of G-Y-C-I-G-G with cysteine as the active center of the PHA synthase. Homology modeling predicted the 3D protein structure which is similar to the PHA synthase of Chromobacterium sp. USM2. The solvent extract of N. sandarakina VSA9 showed the presence of Carotenoid compound with maximum wavelength at 475 nm. The study's findings could have far-reaching implications, contributing to advancements in the biotechnology, industrial processes, and sustainable practices. The simultaneous production of carotenoids and PHAs by N. sandarakina VSA9 presents exciting opportunities for the development of innovative and environmentally friendly applications.

Screening and evaluation of skin potential probiotic from high-altitude Tibetans to repair ultraviolet radiation damage

Human skin microbes play critical roles in skin health and diseases. Microbes colonizing on the skin of Tibetans living in the high-altitude area for generations may have a stronger ability to resist the harsh environment, such as high ultraviolet radiation (UV). Isolation of a potential probiotic from Tibetans skin is beneficial for resistance of skin disease for humans in the world. In this study, the signature microbiota for Tibetan skin were characterized compared to low-altitude humans. Next, using culture-omics, 118 species were isolated. The culturability of high-altitude of Tibetan skin microbiome reached approximate 66.8%. Next, we found that one strain, Pantoea eucrina, had the greatest ability to repair UV damage to the skin as the lowest pathological score was observed in this group. Interestingly, another animal trial found this bacterium resisted UV rather than its metabolites. Using whole genome sequencing, this strain P. eucrina KBFS172 was confirmed, and its functions were annotated. It might involve in the metabolic pathway of carotenoid biosynthesis with anti-oxidative stress properties, which plays critical roles in UV-damage repair. In conclusion, we characterized the signature microbes of skin in high-altitude Tibetans, isolated a skin bacterium of Pantoea eucrina KBFS172 which could repair UV damage via involving the metabolic pathway of carotenoid biosynthesis. Our results provide a new potential skin probiotic for skin disease prevention or sunburn.

Community Vertical Composition of the Laguna Negra Hypersaline Microbial Mat, Puna Region (Argentinean Andes)

The Altiplano-Puna region is a high-altitude plateau in South America characterized by extreme conditions, including the highest UV incidence on Earth. The Laguna Negra is a hypersaline lake located in the Catamarca Province, northwestern Argentina, where stromatolites and other microbialites are found, and where life is mostly restricted to microbial mats. In this study, a particular microbial mat that covers the shore of the lake was explored, to unravel its layer-by-layer vertical structure in response to the environmental stressors therein. Microbial community composition was assessed by high-throughput 16S rRNA gene sequencing and pigment content analyses, complemented with microscopy tools to characterize its spatial arrangement within the mat. The top layer of the mat has a remarkable UV-tolerance feature, characterized by the presence of Deinococcus-Thermus and deinoxanthin, which might reflect a shielding strategy to cope with high UV radiation. Chloroflexi and Deltaproteobacteria were abundant in the second and third underlying layers, respectively. The bottom layer harbors copious Halanaerobiaeota. Subspherical aggregates composed of calcite, extracellular polymeric substances, abundant diatoms, and other microorganisms were observed all along the mat as the main structural component. This detailed study provides insights into the strategies of microbial communities to thrive under high UV radiation and hypersalinity in high-altitude lakes in the Altiplano-Puna region.

Proteomic Signatures of Microbial Adaptation to the Highest Ultraviolet-Irradiation on Earth: Lessons From a Soil Actinobacterium

In the Central Andean region in South America, high-altitude ecosystems (3500-6000 masl) are distributed across Argentina, Chile, Bolivia, and Peru, in which poly-extremophilic microbes thrive under extreme environmental conditions. In particular, in the Puna region, total solar irradiation and UV incidence are the highest on Earth, thus, restraining the physiology of individual microorganisms and the composition of microbial communities. UV-resistance of microbial strains thriving in High-Altitude Andean Lakes was demonstrated and their mechanisms were partially characterized by genomic analysis, biochemical and physiological assays. Then, the existence of a network of physiological and molecular mechanisms triggered by ultraviolet light exposure was hypothesized and called "UV-resistome". It includes some or all of the following subsystems: (i) UV sensing and effective response regulators, (ii) UV-avoidance and shielding strategies, (iii) damage tolerance and oxidative stress response, (iv) energy management and metabolic resetting, and (v) DNA damage repair. Genes involved in the described UV-resistome were recently described in the genome of Nesterenkonia sp. Act20, an actinobacterium which showed survival to high UV-B doses as well as efficient photorepairing capability. The aim of this work was to use a proteomic approach together with photoproduct measurements to help dissecting the molecular events involved in the adaptive response of a model High-Altitude Andean Lakes (HAAL) extremophilic actinobacterium, Nesterenkonia sp. Act20, under artificial UV-B radiation. Our results demonstrate that UV-B exposure induced over-abundance of a well-defined set of proteins while recovery treatments restored the proteomic profiles present before the UV-challenge. The proteins involved in this complex molecular network were categorized within the UV-resistome subsystems: damage tolerance and oxidative stress response, energy management and metabolic resetting, and DNA damage repair.

Genomic insights into an andean multiresistant soil actinobacterium of biotechnological interest

Central-Andean Ecosystems (between 2000 and 6000 m above sea level (masl) are typical arid-to-semiarid environments suffering from the highest total solar and ultraviolet-B radiation on the planet but displaying numerous salt flats and shallow lakes. Andean microbial ecosystems isolated from these environments are of exceptional biodiversity enduring multiple severe conditions. Furthermore, the polyextremophilic nature of the microbes in such ecosystems indicates the potential for biotechnological applications. Within this context, the study undertaken used genome mining, physiological and microscopical characterization to reveal the multiresistant profile of Nesterenkonia sp. Act20, an actinobacterium isolated from the soil surrounding Lake Socompa, Salta, Argentina (3570 masl). Ultravioet-B, desiccation, and copper assays revealed the strain's exceptional resistance to all these conditions. Act20's genome presented coding sequences involving resistance to antibiotics, low temperatures, ultraviolet radiation, arsenic, nutrient-limiting conditions, osmotic stress, low atmospheric-oxygen pressure, heavy-metal stress, and toxic fluoride and chlorite. Act20 can also synthesize proteins and natural products such as an insecticide, bacterial cellulose, ectoine, bacterial hemoglobin, and even antibiotics like colicin V and aurachin C. We also found numerous enzymes for animal- and vegetal-biomass degradation and applications in other industrial processes. The resilience of Act20 and its biotechnologic potential were thoroughly demonstrated in this work.

Redox stress response and UV tolerance in the acidophilic iron-oxidizing bacteria Leptospirillum ferriphilum and Acidithiobacillus ferrooxidans

The oxidative stress response represents a sum of antioxidative mechanisms that are essential for determining the adaptation and abundance of microorganisms in the environment. Leptospirillum ferriphilum and Acidithiobacillus ferrooxidans are chemolithotrophic bacteria that obtain their energy from the oxidation of ferrous ion. Both microorganisms are important for bioleaching of sulfidic ores and both are tolerant to high levels of heavy metals and other factors that can induce oxidative stress. In this work, we compared the tolerance and response of L. ferriphilum and At. ferrooxidans to Fe³⁺, H₂O₂, K₂CrO₄, and UV-C radiation. We evaluated growth, generation of reactive oxygen species (ROS), oxidative damage to lipid membranes and DNA, and the activity of antioxidative proteins in cells exposed to these stressors. L. ferriphilum had higher cell density, lower ROS content and less lipid and DNA damage than At. ferrooxidans. Consistent with this, the activity levels of thioredoxin and superoxide dismutase in L. ferriphilum were upregulated and higher than in At. ferrooxidans. This indicated that L. ferriphilum has a higher capacity to respond to oxidative stress and to manage redox homeostasis. This capacity could largely contribute to the high abundance of this species in natural and anthropogenic sites.

Can multidrug-resistant organisms become resistant to ultraviolet (UV) light following serial exposures? Characterization of post-UV genomic changes using whole-genome sequencing

OBJECTIVES

No-touch disinfection systems like xenon- or mercury-based ultraviolet (UV) are now commonly being used for hospital room disinfection. However, serial exposure to UV light can potentially lead to the development of bacterial resistance. We sought to determine whether UV resistance develops due to serial exposure to UV light using 3 epidemiologically important multidrug-resistant microbial strains.

METHODS

Methicillin-resistant Staphylococcus aureus (MRSA), carbapenemase-producing Klebsiella pneumoniae (KPC) and metallo-β-lactamase-producing Klebsiella pneumoniae (MBL) were serially exposed to 25 growth-irradiation cycles of UV produced by a xenon-based UV (Xe-UV) lamp for 5 minutes or a mercury-based UV (Hg-UV) lamp for 10 minutes. After each UV exposure cycle, the surviving colony-forming units (CFUs) were measured and compared with the initial inoculum of each cycle for each strain, respectively.

RESULTS

In each cycle, ˜1-10 million of MRSA, KPC, and MBL were used to test the effect of UV irradiation. Postexposure colony counts remained low (3-100 colonies) throughout the 25 serial exposures to both xenon- and mercury-based UV. The log-kill rate after each exposure showed no changes following UV disinfection by Xe-UV. The MRSA log-kill rate increased after repeated exposure to Hg-UV unlike KPC and MBL K. pneumoniae, which did not change. Whole-genome sequencing (WGS) analyses performed on these 3 strains demonstrated no significant genetic changes after multiple UV irradiation cycles.

CONCLUSIONS

Exposure of multidrug-resistant bacteria to UV produced from 2 different UV sources did not engender UV resistance after 25 serial exposures, as demonstrated by WGS analysis; thus, UV disinfection is unlikely to generate UV-resistant hospital flora.

Immobilization strategies of photolyases: Challenges and perspectives for DNA repairing application

Photolyases are enzymes that repair DNA damage caused by solar radiation. Due to their photorepair potential, photolyases added in topical creams and used in medical treatments has allowed to reverse skin damage and prevent the development of different diseases, including actinic keratosis, premature photoaging and cancer. For this reason, research has been oriented to the study of new photolyases performing in extreme environments, where high doses of UV radiation may be a key factor for these enzymes to have perfected their photorepair potential. Generally, the extracted enzymes are first encapsulated and then added to the topical creams to increase their stability. However, other well consolidated immobilization methods are interesting strategies to be studied that may improve the biocatalyst performance. This review aims to go through the different Antarctic organisms that have exhibited photoreactivation activity, explaining the main mechanisms of photolyase DNA photorepair. The challenges of immobilizing these enzymes on porous and nanostructured supports is also discussed. The comparison of the most reported immobilization methods with respect to the structure of photolyases show that both covalent and ionic immobilization methods produced an increase in their stability. Moreover, the use of nanosized materials as photolyase support would permit the incorporation of the biocatalyst into the target cell, which is a technological requirement that photolyase based biocatalysts must fulfill.

A rather dry subject; investigating the study of arid-associated microbial communities

Almost one third of Earth's land surface is arid, with deserts alone covering more than 46 million square kilometres. Nearly 2.1 billion people inhabit deserts or drylands and these regions are also home to a great diversity of plant and animal species including many that are unique to them. Aridity is a multifaceted environmental stress combining a lack of water with limited food availability and typically extremes of temperature, impacting animal species across the planet from polar cold valleys, to Andean deserts and the Sahara. These harsh environments are also home to diverse microbial communities, demonstrating the ability of bacteria, fungi and archaea to settle and live in some of the toughest locations known. We now understand that these microbial ecosystems i.e. microbiotas, the sum total of microbial life across and within an environment, interact across both the environment, and the macroscopic organisms residing in these arid environments. Although multiple studies have explored these microbial communities in different arid environments, few studies have examined the microbiota of animals which are themselves arid-adapted. Here we aim to review the interactions between arid environments and the microbial communities which inhabit them, covering hot and cold deserts, the challenges these environments pose and some issues arising from limitations in the field. We also consider the work carried out on arid-adapted animal microbiotas, to investigate if any shared patterns or trends exist, whether between organisms or between the animals and the wider arid environment microbial communities. We determine if there are any patterns across studies potentially demonstrating a general impact of aridity on animal-associated microbiomes or benefits from aridity-adapted microbiomes for animals. In the context of increasing desertification and climate change it is important to understand the connections between the three pillars of microbiome, host genome and environment.

A (6-4)-photolyase from the Antarctic bacterium Sphingomonas sp. UV9: recombinant production and in silico features

Photolyases are proteins that enzymatically repair the UV-induced DNA damage by a protein-DNA electron transfer mechanism. They repair either cyclobutane pyrimidine dimers or pyrimidine (6-4) pyrimidone photoproducts or just (6-4)-photoproducts. In this work, we report the production and partial characterization of a recombinant (6-4)-photolyase (SphPhrB97) from a bacterial psychrotolerant Antarctic isolate identified as Sphingomonas sp. strain UV9. The spectrum analysis and the in silico study of SphPhrB97 suggest that this enzyme has similar features as compared to the (6-4)-photolyase from Agrobacterium tumefaciens (4DJA; PhrB), including the presence of three cofactors: FAD, DMRL (6,7-dimethyl-8-(1'-D-ribityl) lumazine), and an Fe-S cluster. The homology model of SphPhrB97 predicts that the DNA-binding pocket (area and volume) is larger as compared to (6-4)-photolyases from mesophilic microbes. Based on sequence comparison and on the homology model, we propose an electron transfer pathway towards the FAD cofactor involving the residues Trp342, Trp390, Tyr40, Tyr391, and Tyr399. The phylogenetic tree performed using curated and well-characterized prokaryotic (6-4)-photolyases suggests that SphPhrB97 may have an ancient evolutionary origin. The results suggest that SphPhrB97 is a cold-adapted enzyme, ready to cope with the UV irradiation stress found in a hostile environment, such as Antarctica.

Effect of stress factors associated with postharvest citrus conditions on the viability and biocontrol activity of Clavispora lusitaniae strain 146

Only quite recently, we have shown that yeast strains Clavispora lusitaniae 146 and Pichia fermentans 27 can act as efficient biocontrol agents for combating postharvest fungal diseases in lemons. During postharvest and storage conditions, microorganisms are subject to different stress factors that could affect both their survival and their protective capacity. Understanding the tolerance of yeasts to environmental stress factors could support the future development and commercial application of biological control formulations based on such organisms. Thus, the impact of different stressors on the viability and protection efficiency of C. lusitaniae strain 146 and P. fermentans strain 27 was evaluated, and the yeasts were subjected to oxidative stress, thermal treatments, exposure to NaOCl, osmotic stress, and ultraviolet irradiation. Candida oleophila strain O served as the reference control. C. lusitaniae 146 was more resistant to H₂O₂ in plate assays; however, in liquid media there was no significant difference to the other strains. Strain 146 was less affected by NaOCl, being able to survive with 300 ppm. P. fermentans 27 was the strain most heavily affected by osmotic pressure, while strains 146 and strain O showed a similar adaptation. UV-B irradiation severely affected C. oleophila and P. fermentans, while C. lusitaniae was the most resistant. Strains 146 and 27 were similarly tolerant to thermal shocks, compared to the reference strain, which was less viable. In in vivo tests, exposure to 10 mM H₂O₂, 45°C or 200 ppm NaOCl prior to fruit inoculation, reduced the antagonistic activity against the pathogen Penicillium digitatum. However, in no case was the biocontrol efficiency reduced to less than 50%. As C. lusitaniae 146 demonstrated a great potential to combat P. digitatum under a wide range of conditions, the organism is a promising candidate as an effective and valuable alternative to toxic fungicides.

Novel Genes Involved in Resistance to Both Ultraviolet Radiation and Perchlorate From the Metagenomes of Hypersaline Environments

Microorganisms that thrive in hypersaline environments on the surface of our planet are exposed to the harmful effects of ultraviolet radiation. Therefore, for their protection, they have sunscreen pigments and highly efficient DNA repair and protection systems. The present study aimed to identify new genes involved in UV radiation resistance from these microorganisms, many of which cannot be cultured in the laboratory. Thus, a functional metagenomic approach was used and for this, small-insert libraries were constructed with DNA isolated from microorganisms of high-altitude Andean hypersaline lakes in Argentina (Diamante and Ojo Seco lakes, 4,589 and 3,200 m, respectively) and from the Es Trenc solar saltern in Spain. The libraries were hosted in a UV radiation-sensitive strain of Escherichia coli (recA mutant) and they were exposed to UVB. The resistant colonies were analyzed and as a result, four clones were identified with environmental DNA fragments containing five genes that conferred resistance to UV radiation in E. coli. One gene encoded a RecA-like protein, complementing the mutation in recA that makes the E. coli host strain more sensitive to UV radiation. Two other genes from the same DNA fragment encoded a TATA-box binding protein and an unknown protein, both responsible for UV resistance. Interestingly, two other genes from different and remote environments, the Ojo Seco Andean lake and the Es Trenc saltern, encoded two hypothetical proteins that can be considered homologous based on their significant amino acid similarity (49%). All of these genes also conferred resistance to 4-nitroquinoline 1-oxide (4-NQO), a compound that mimics the effect of UV radiation on DNA, and also to perchlorate, a powerful oxidant that can induce DNA damage. Furthermore, the hypothetical protein from the Es Trenc salterns was localized as discrete foci possibly associated with damaged sites in the DNA in cells treated with 4-NQO, so it could be involved in the repair of damaged DNA. In summary, novel genes involved in resistance to UV radiation, 4-NQO and perchlorate have been identified in this work and two of them encoding hypothetical proteins that could be involved in DNA damage repair activities not previously described.