The first (6-4) photolyase with DNA damage repair activity from the Antarctic microalga Chlamydomonas sp. ICE-L

Dissecting sequence-structure-function-diversity in plant cryptochromes

Ubiquitous to every stratum of life, cryptochromes regulate numerous light dependent functions in terrestrial plants. These include light-dependent transcription, circadian rhythm, inhibition of hypocotyl elongation, programmed cell death, promotion of floral initiation, mediation of gravitropic response, responding to biotic and abiotic stress etc. There have been quite a few seminal reviews including on plant cryptochromes, focusing mostly on the detailed functional aspects. This review primarily focuses on understanding the link connecting sequence-structure hierarchy behind the functional diversity in plant cryptochromes. With available sequence information and 3D structure data, we hereby explore the molecular origin of functional diversity in both the subtypes i.e., CRY1 and CRY2. First, we discuss the structural details and functional distinctiveness of all subtypes of plant cryptochromes. Next we draw a comparison not just between two cryptochromes but also other Cryptochrome/Photolyase Family (CPF) members e.g. CRY-DASH/CRY3 and CPD/6-4 photolyases of plant origin. Further, by constructing a phylogenetic profile from multiple sequence alignment we investigate how a crucial activity like DNA repair is restricted to some members of CPF and not all. It is a well-known fact that the function of a protein is heavily if not solely guided by the structure-sequence relationship. Therefore, the resultant hypothesis as drawn from this comparative and collective study could predict functions of many under-studied plant cryptochromes when compared with their well-studied counterparts like Arabidopsis cryptochromes. An extensive sequence-structure-function analysis complemented with evolutionary studies and bibliographic survey is useful towards understanding the immensely diverse CPF.

The photoreactivation of 6 - 4 photoproducts in chloroplast and nuclear DNA depends on the amount of the Arabidopsis UV repair defective 3 protein

BACKGROUND

6 - 4 photoproducts are the second most common UV-induced DNA lesions after cyclobutane pyrimidine dimers. In plants, they are mainly repaired by photolyases in a process called photoreactivation. While pyrimidine dimers can be deleterious, leading to mutagenesis or even cell death, 6 - 4 photoproducts can activate specific signaling pathways. Therefore, their removal is particularly important, especially for plants exposed to high UV intensities due to their sessile nature. Although photoreactivation in nuclear DNA is well-known, its role in plant organelles remains unclear. In this paper we analyzed the activity and localization of GFP-tagged AtUVR3, the 6 - 4 photoproduct specific photolyase.

RESULTS

Using transgenic Arabidopsis with different expression levels of AtUVR3, we confirmed a positive trend between these levels and the rate of 6 - 4 photoproduct removal under blue light. Measurements of 6 - 4 photoproduct levels in chloroplast and nuclear DNA of wild type, photolyase mutants, and transgenic plants overexpressing AtUVR3 showed that the photoreactivation is the main repair pathway responsible for the removal of these lesions in both organelles. The GFP-tagged AtUVR3 was predominantly located in nuclei with a small fraction present in chloroplasts and mitochondria of transgenic Arabidopsis thaliana and Nicotiana tabacum lines. In chloroplasts, this photolyase co-localized with the nucleoid marked by plastid envelope DNA binding protein.

CONCLUSIONS

Photolyases are mainly localized in plant nuclei, with only a small fraction present in chloroplasts and mitochondria. Despite this unbalanced distribution, photoreactivation is the primary mechanism responsible for the removal of 6 - 4 photoproducts from nuclear and chloroplast DNA in adult leaves. The amount of the AtUVR3 photolyase is the limiting factor influencing the photoreactivation rate of 6 - 4 photoproducts. The efficient photoreactivation of 6 - 4 photoproducts in 35S: AtUVR3-GFP Arabidopsis and Nicotiana tabacum is a promising starting point to evaluate whether transgenic crops overproducing this photolyase are more tolerant to high UV irradiation and how they respond to other abiotic and biotic stresses under field conditions.

Multifaceted photoreceptor compositions in dual phototrophic systems - A genomic analysis

For microbes and their hosts, sensing of external cues is essential for their survival. For example, in the case of plant associated microbes, the light absorbing pigment composition of the plant as well as the ambient light conditions determine the well-being of the microbe. In addition to light sensing, some microbes can utilize xanthorhodopsin based proton pumps and bacterial photosynthetic complexes that work in parallel for energy production. They are called dual phototrophic systems. Light sensing requirements in these type of systems are obviously demanding. In nature, the photosensing machinery follows mainly the same composition in all organisms. However, the specific role of each photosensor in specific light conditions is elusive. In this study, we provide an overall picture of photosensors present in dual phototrophic systems. We compare the genomes of the photosensor proteins from dual phototrophs to those from similar microbes with "single" phototrophicity or microbes without phototrophicity. We find that the dual phototrophic bacteria obtain a larger variety of photosensors than their light inactive counterparts. Their rich domain composition and functional repertoire remains similar across all microbial photosensors. Our study calls further investigations of this particular group of bacteria. This includes protein specific biophysical characterization in vitro, microbiological studies, as well as clarification of the ecological meaning of their host microbial interactions.

Enzymes for dermatological use

Skin is the ultimate barrier between body and environment and prevents water loss and penetration of pathogens and toxins. Internal and external stressors, such as ultraviolet radiation (UVR), can damage skin integrity and lead to disorders. Therefore, skin health and skin ageing are important concerns and increased research from cosmetic and pharmaceutical sectors aims to improve skin conditions and provide new anti-ageing treatments. Biomolecules, compared to low molecular weight drugs and cosmetic ingredients, can offer high levels of specificity. Topically applied enzymes have been investigated to treat the adverse effects of sunlight, pollution and other external agents. Enzymes, with a diverse range of targets, present potential for dermatological use such as antioxidant enzymes, proteases and repairing enzymes. In this review, we discuss enzymes for dermatological applications and the challenges associated in this growing field.

Preparation of CPD Photolyase Nanoliposomes Derived from Antarctic Microalgae and Their Effect on UVB-Induced Skin Damage in Mice

UVB radiation is known to trigger the block of DNA replication and transcription by forming cyclobutane pyrimidine dimer (CPD), which results in severe skin damage. CPD photolyase, a kind of DNA repair enzyme, can efficiently repair CPDs that are absent in humans and mice. Although exogenous CPD photolyases have beneficial effects on skin diseases, the mechanisms of CPD photolyases on the skin remain unknown. Here, this study prepared CPD photolyase nanoliposomes (CPDNL) from Antarctic Chlamydomonas sp. ICE-L, which thrives in harsh, high-UVB conditions, and evaluated their protective mechanisms against UVB-induced damage in mice. CPDNL were optimized using response surface methodology, characterized by a mean particle size of 105.5 nm, with an encapsulation efficiency of 63.3%. Topical application of CPDNL prevented UVB-induced erythema, epidermal thickness, and wrinkles in mice. CPDNL mitigated UVB-induced DNA damage by significantly decreasing the CPD concentration. CPDNL exhibited antioxidant properties as they reduced the production of reactive oxygen species (ROS) and malondialdehyde. Through activation of the NF-κB pathway, CPDNL reduced the expression of pro-inflammatory cytokines including IL-6, TNF-α, and COX-2. Furthermore, CPDNL suppressed the MAPK signaling activation by downregulating the mRNA and protein expression of ERK, JNK, and p38 as well as AP-1. The MMP-1 and MMP-2 expressions were also remarkably decreased, which inhibited the collagen degradation. Therefore, we concluded that CPDNL exerted DNA repair, antioxidant, anti-inflammation, and anti-wrinkle properties as well as collagen protection via regulation of the NF-κB/MAPK/MMP signaling pathways in UVB-induced mice, demonstrating that Antarctic CPD photolyases have the potential for skincare products against UVB and photoaging.

Recombinant Photolyase-Thymine Alleviated UVB-Induced Photodamage in Mice by Repairing CPD Photoproducts and Ameliorating Oxidative Stress

Cyclobutane pyrimidine dimers (CPDs) are the main mutagenic DNA photoproducts caused by ultraviolet B (UVB) radiation and represent the major cause of photoaging and skin carcinogenesis. CPD photolyase can efficiently and rapidly repair CPD products. Therefore, they are candidates for the prevention of photodamage. However, these photolyases are not present in placental mammals. In this study, we produced a recombinant photolyase-thymine (rPHO) from Thermus thermophilus (T. thermophilus). The rPHO displayed CPD photorepair activity. It prevented UVB-induced DNA damage by repairing CPD photoproducts to pyrimidine monomers. Furthermore, it inhibited UVB-induced ROS production, lipid peroxidation, inflammatory responses, and apoptosis. UVB-induced wrinkle formation, epidermal hyperplasia, and collagen degradation in mice skin was significantly inhibited when the photolyase was applied topically to the skin. These results demonstrated that rPHO has promising protective effects against UVB-induced photodamage and may contribute to the development of anti-UVB skin photodamage drugs and cosmetic products.

Photolyase Production and Current Applications: A Review

The photolyase family consists of flavoproteins with enzyme activity able to repair ultraviolet light radiation damage by photoreactivation. DNA damage by the formation of a cyclobutane pyrimidine dimer (CPD) and a pyrimidine-pyrimidone (6-4) photoproduct can lead to multiple affections such as cellular apoptosis and mutagenesis that can evolve into skin cancer. The development of integrated applications to prevent the negative effects of prolonged sunlight exposure, usually during outdoor activities, is imperative. This study presents the functions, characteristics, and types of photolyases, their therapeutic and cosmetic applications, and additionally explores some photolyase-producing microorganisms and drug delivery systems.

A diguanylate cyclase regulates biofilm formation in Rhodococcus sp. NJ-530 from Antarctica

Biofilms represent a protective survival mode in which bacteria adapt themselves to the natural environment for survival purposes. Biofilm formation is regulated by 3,5-cyclic diguanylic acid (c-di-GMP), which is a universal second messenger molecule in bacteria. Diguanylate cyclase (DGC) catalyses c-di-GMP intracellular synthesis, which plays important roles in bacterial adaptation to the natural environment. In this study, the DGC gene was first cloned from Antarctic Rhodococcus sp. NJ-530. DGC contained 948 nucleotides and encoded 315 amino acids with a molecular weight of 34.6 KDa and an isoelectric point of 5.58. qRT-PCR demonstrated that the DGC expression level was significantly affected by lower salinity and temperature. Consistently, more biofilm formation occurred under the same stress. It has been shown that Rhodococcus sp. NJ-530 can adapt to the extreme environment in Antarctica, which is closely related to biofilm formation. These results provide an important reference for studying the adaptive mechanism of Antarctic microorganisms to this extreme environment.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03093-z.

A CPD photolyase gene PnPHR1 from Antarctic moss Pohlia nutans is involved in the resistance to UV-B radiation and salinity stress

In Antarctic continent, the organisms are exposed to high ultraviolet (UV) radiation because of damaged stratospheric ozone. UV causes DNA lesions due to the accumulation of photoproducts. Photolyase can repair UV-damaged DNA in a light-dependent process by electron transfer mechanism. Here, we isolated a CPD photolyase gene PnPHR1 from Antarctic moss Pohlia nutans, which encodes a protein of theoretical molecular weight of 69.1 KDa. The expression level of PnPHR1 was increased by UV-B irradiation. Enzyme activity assay in vitro showed that PnPHR1 exhibited photoreactivation activity, which can repair CPD photoproducts in a light-dependent manner. The complementation assay of repair-deficient E. coli strain SY2 demonstrated that PnPHR1 gene enhanced the survival rate of SY2 strain after UV-B radiation. Additionally, overexpression of PnPHR1 enhanced the Arabidopsis resistance to UV-B radiation and salinity stress, which also conferred plant tolerance to oxidative stress by decreasing ROS production and increasing ROS clearance. Our work shows that PnPHR1 encodes an active CPD photolyase, which may participate in the adaptation of P. nutans to polar environments.

Two class II CPD photolyases, PiPhr1 and PiPhr2, with CPD repair activity from the Antarctic diatom Phaeodactylum tricornutum ICE-H

Two gene of class II photolyases, PiPhr1 (1833 bp) and PiPhr2 (1809 bp), from the Antarctic diatom Phaeodactylum tricornutum ICE-H were cloned, the recombinant proteins expressed and purified. The molecular weight of the recombinant photolyases were determined to be 68 kDa with a pI of 9.04 and 68.82 with a pI of 7.31, respectively. Activity studies showed that both the recombinant enzymes were involved in the repair DNA damaged by UV light, that is they were most likely photolyases involved in photorepair of DNA. Further confirmation of this function was demonstrated by the increased expression of PiPhr1 and PiPhr2 after exposure to UV radiation, blue light and dark conditions by qRT-PCR. In summary, PiPhr1 and PiPhr2 were up regulated by UVB irradiation and blue light at 0.5 h and 3 h. Longtime (3 h) exposure to dark also increased the expression of PiPhr1 and PiPhr2. In vitro photoreactivation assays showed that PiPhr1 and PiPhr2 could repair CPDs utilizing blue light. This is the first time CPD Class II photolyase has been reported from Antarctic diatom. These results will add to the knowledge of the diatom CPF family and assist in understanding the functional role of these genes in Antarctic diatoms.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02927-0.

A Class II CPD Photolyase and a 6-4 Photolyase with Photorepair Activity from the Antarctic Moss Pohlia nutans M211

Antarctic mosses are the dominant vegetation in the Antarctic continent. Because of stratospheric ozone depletion, they can withstand physiological extreme UV. The formation of CPD and 6-4PP is one of the most harmful damages of UV to DNA. DNA damage can interfere with replication and transcription, resulting in mutation and death. Two types of photolyase, CPD photolyase and 6-4 photolyase, are capable of specific binding CPD or 6-4PP and repairing these lesions. However, there is little research on photolyase in Antarctic moss. Here, we isolated a gene encoding class II CPD photolyase (PnCPDPhr) and a gene encoding 6-4 photolyase (Pn6-4Phr) from Antarctic moss P. nutans M211. When exposed to UVB, CPDs accumulated in gametophytes and the gene expressions of PnCPDPhr and Pn6-4Phr were both up-regulated. In addition, the in vitro expression and photoreactivation assays of PnCPDPhr and Pn6-4Phr were performed. Our results demonstrated that PnCPDPhr and Pn6-4Phr have an effective activity of DNA repair. This is the first study to determine the CPD accumulation in Antarctic moss as well as the first report isolating CPD photolyase and 6-4 photolyase from Antarctic moss. These results will enrich the knowledge of photolyase family and benefit the exploitation of functioning gene in Antarctic moss.

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 (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.

Antioxidant cinnamaldehyde attenuates UVB-induced photoaging

BACKGROUND

Ultraviolet (UV) irradiation disrupts skin through several deleterious actions, such as induction of reactive oxygen species (ROS), DNA damage, and collagen degradation. Cinnamaldehyde (CIN) is a major constituent of the cinnamon and it possesses potent antioxidative activity; however, it is unclear whether CIN is capable of inhibiting the adverse effects of UVB.

OBJECTIVE

To investigate protective effects of CIN against UVB-induced photodamage.

METHODS

HaCaT keratinocytes were pretreated with CIN, irradiated with UVB, and assessed for the ROS production by flow cytometry and for the DNA damage by ELISA. As in vivo mouse model, Hos:HR-1 hairless mice were treated with ointments containing DMSO or CIN and irradiated multiple times with UVB. After 10 weeks of irradiation, wrinkle formation, epidermal thickness, infiltrating cell number, malondialdehyde amount, collagen amount, MAP kinase signaling, and related gene expressions (Hmox1, Col1a1, Mmp1a, and Mmp13) were analyzed.

RESULTS

CIN significantly reduced the ROS production and accelerated the repair of DNA damage pyrimidine(6-4)pyrimidone photoproducts in UVB-irradiated human keratinocytes in vitro. In the mouse model, topical application of CIN significantly inhibited wrinkle formation, epidermal hyperplasia, and dermal inflammatory cell infiltration. The antioxidative process was significantly promoted in the CIN-applied site, as evidenced by upregulation of the antioxidative enzyme Hmox1 as well as the reduced accumulation of malondialdehyde. In addition, topical application of CIN normalized the UVB-induced collagen/Col1a1 downregulation and the UVB-induced Mmp13 upregulation, implying the prevention of UVB-induced collagen degradation.

CONCLUSIONS

CIN and CIN-containing herbal agents may exert potent protective effects against UVB exposure on skin.