Abstract
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.
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Acknowledgements
The authors thank the Uruguayan Antarctic Institute for the logistic support during the stay in the Antarctic Base Artigas. S. Castro-Sowinski and J. J. Marizcurrena are members of the National Research System (SNI, Sistema Nacional de Investigadores). This work was partially supported by PEDECIBA (Programa de Desarrollo de las Ciencias Básicas), CSIC (Project C667), and ANII (Project FMV_3_2016_1_1226654). The work of JJM was supported by ANII and CAP (Comisión Académica de Posgrado, UdelaR).
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JJM and SCS conceived and designed research. JJM conducted experiments and analyzed data. TL conducted phylogenetic analysis. JJM, TL, and SCS wrote the manuscript. All the authors read and approved the manuscript.
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Marizcurrena, J.J., Lamparter, T. & Castro-Sowinski, S. A (6-4)-photolyase from the Antarctic bacterium Sphingomonas sp. UV9: recombinant production and in silico features. Extremophiles 24, 887–896 (2020). https://doi.org/10.1007/s00792-020-01202-z
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DOI: https://doi.org/10.1007/s00792-020-01202-z