Abstract
Marine bacterium Rhodococcus sp. NJ-530 has developed several ultraviolet (UV) adaptive characteristics for survival and growth in extreme Antarctic environment. Rhodococcus sp. NJ-530 DNA photolyase encoded by a 1146 bp photolyase-homologous region (phr) was identified in genome. Quantitative real-time PCR demonstrated that transcriptional levels of phr were highly up-regulated by ultraviolet-B (UV-B) radiation (90 μW·cm−2) and increased to a maximum of 149.17-fold after exposure for 20 min. According to the results of SDS-PAGE and western blot, PHR was effectively induced by isopropyl-β-d-1-thiogalactopyranoside (IPTG) at the genetically engineered BL21(DE3)-pET-32a( +)-phr construct under the condition of 15 °C for 16 h and 37 °C for 4 h. In terms of in vivo activity, compared with a phr-defective E. coli strain, phr-transformed E. coli exhibited higher survival rate under high UV-B intensity of 90 μW·cm−2. Meanwhile, the purified PHR, with blue light, presented obvious photorepair activity toward UV-induced DNA damage in vitro assays. To sum up, studying the mechanisms of Rhodococcus sp. NJ-530 photolyase is of great interest to understand the adaptation of polar bacteria to high UV radiation, and such data present important therapeutic value for further UV-induced human skin and genetic damage diseases.
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References
Armstrong BK, Kricker A (2001) The epidemiology of UV induced skin cancer. J Photochem Photobiol B 63:8–18
Bais AF, McKenzie RL, Bernhard G, Aucamp PJ, Ilyas M, Madronich S, Tourpali K (2015) Ozone depletion and climate change: impacts on UV radiation. Photochem Photobiol Sci Off J Eur Photochem Assoc Eur Soc Photobiol 14:19–52. https://doi.org/10.1039/c4pp90032d
Bennett CJ, Webb M, Willer DO, Evans DH (2003) Genetic and phylogenetic characterization of the type II cyclobutane pyrimidine dimer photolyases encoded by Leporipoxviruses. Virology 315:10–19
Berardesca E, Bertona M, Altabas K, Altabas V, Emanuele E (2012) Reduced ultraviolet-induced DNA damage and apoptosis in human skin with topical application of a photolyase-containing DNA repair enzyme cream: clues to skin cancer prevention. Mol Med Rep 5:570–574. https://doi.org/10.3892/mmr.2011.673
Carducci M, Pavone PS, De Marco G, Lovati S, Altabas V, Altabas K, Emanuele E (2015) Comparative effects of sunscreens alone vs sunscreens plus DNA repair enzymes in patients with actinic keratosis: clinical and molecular findings from a 6-month. Randomized Clin Study J Drugs Dermatol JDD 14:986–990
Dahms HU, Lee JS (2010) UV radiation in marine ectotherms: molecular effects and responses. Aquat Toxicol (Amsterdam, Netherlands) 97:3–14. https://doi.org/10.1016/j.aquatox.2009.12.002
Dehez F, Gattuso H, Bignon E, Morell C, Dumont E, Monari A (2017) Conformational polymorphism or structural invariance in DNA photoinduced lesions: implications for repair rates. Nucl Acids Res 45:3654–3662. https://doi.org/10.1093/nar/gkx148
Dever TE (2002) Gene-specific regulation by general translation factors. Cell 108:545–556
Gill SS, Anjum NA, Gill R, Jha M, Tuteja N (2015) DNA damage and repair in plants under ultraviolet and ionizing radiations. Sci World J 2015:250158. https://doi.org/10.1155/2015/250158
Hader DP, Sinha RP (2005) Solar ultraviolet radiation-induced DNA damage in aquatic organisms: potential environmental impact. Mutat Res 571:221–233. https://doi.org/10.1016/j.mrfmmm.2004.11.017
He Y et al (2019) Molecular cloning and functional analysis of a Delta(12)-fatty acid desaturase from the Antarctic microalga Chlamydomonas sp. ICE-L 3 Biotech 9:328. https://doi.org/10.1007/s13205-019-1858-6
Hu J, Adar S (2017) The cartography of UV-induced DNA damage formation and DNA repair. Photochem Photobiol 93:199–206. https://doi.org/10.1111/php.12668
Isely N, Lamare M, Marshall C, Barker M (2009) Expression of the DNA repair enzyme, photolyase, in developmental tissues and larvae, and in response to ambient UV-R in the Antarctic sea urchin Sterechinus neumayeri. Photochem photobiol 85:1168–1176. https://doi.org/10.1111/j.1751-1097.2009.00566.x
Jans J et al (2005) Powerful skin cancer protection by a CPD-photolyase transgene. Curr Biol CB 15:105–115. https://doi.org/10.1016/j.cub.2005.01.001
Kageyama H, Waditee-Sirisattha R (2019) Antioxidative, anti-inflammatory, and anti-aging properties of mycosporine-like amino acids: molecular and cellular mechanisms in the protection of skin-aging. Mar Drugs. https://doi.org/10.3390/md17040222
Kihara J, Moriwaki A, Matsuo N, Arase S, Honda Y (2004) Cloning, functional characterization, and near-ultraviolet radiation-enhanced expression of a photolyase gene (PHR1) from the phytopathogenic fungus Bipolaris oryzae. Curr Genet 46:37–46. https://doi.org/10.1007/s00294-004-0507-7
Kim JJ, Sundin GW (2001) Construction and analysis of photolyase mutants of Pseudomonas aeruginosa and Pseudomonas syringae: contribution of photoreactivation, nucleotide excision repair, and mutagenic DNA repair to cell survival and mutability following exposure to UV-B radiation. Appl Environ Microbiol 67:1405–1411. https://doi.org/10.1128/aem.67.4.1405-1411.2001
Kobayashi K, Kanno S, Smit B, van der Horst GT, Takao M, Yasui A (1998) Characterization of photolyase/blue-light receptor homologs in mouse and human cells. Nucl Acids Res 26:5086–5092
Laino L, Elia F, Desiderio F, Scarabello A, Sperduti I, Cota C, DiCarlo A (2015) The efficacy of a photolyase-based device on the cancerization field: a clinical and thermographic study. J Exper Clin Cancer Res CR 34:84. https://doi.org/10.1186/s13046-015-0203-0
Landry LG, Stapleton AE, Lim J, Hoffman P, Hays JB, Walbot V, Last RL (1997) An Arabidopsis photolyase mutant is hypersensitive to ultraviolet-B radiation. Proc Natl Acad Sci USA 94:328–332
Lee SJ, Lee MR, Kim S, Kim JC, Park SE, Shin TY, Kim JS (2018) Conidiogenesis-related DNA photolyase gene in Beauveria bassiana. J Invertebr Pathol 153:85–91. https://doi.org/10.1016/j.jip.2018.02.013
Li C et al (2015) Cyclobutane pyrimidine dimers photolyase from extremophilic microalga: remarkable UVB resistance and efficient DNA damage repair. Mutat Res 773:37–42. https://doi.org/10.1016/j.mrfmmm.2014.07.010
Li C, Liu S, Zhang W, Chen K, Zhang P (2019) Transcriptional profiling and physiological analysis reveal the critical roles of ROS-scavenging system in the Antarctic moss Pohlia nutans under Ultraviolet-B radiation. Plant Physiol Biochem PPB 134:113–122. https://doi.org/10.1016/j.plaphy.2018.10.034
Liu Z, Wang L, Zhong D (2015) Dynamics and mechanisms of DNA repair by photolyase. Phys Chem Chem Phys 17:11933–11949. https://doi.org/10.1039/c4cp05286b
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)). Method Methods 25:402–408. https://doi.org/10.1006/meth.2001.1262
Malhotra K, Kim ST, Sancar A (1994) Characterization of a medium wavelength type DNA photolyase: purification and properties of photolyase from Bacillus firmus. Biochemistry 33:8712–8718
Malloy KD, Holman MA, Mitchell D, Detrich HW 3rd (1997) Solar UVB-induced DNA damage and photoenzymatic DNA repair in Antarctic zooplankton. Proc Natl Acad Sci USA 94:1258–1263. https://doi.org/10.1073/pnas.94.4.1258
Marizcurrena JJ, Morel MA, Brana V, Morales D, Martinez-Lopez W, Castro-Sowinski S (2017) Searching for novel photolyases in UVC-resistant Antarctic bacteria. Extremophiles 21:409–418. https://doi.org/10.1007/s00792-016-0914-y
Marizcurrena JJ, Martinez-Lopez W, Ma H, Lamparter T, Castro-Sowinski S (2019) A highly efficient and cost-effective recombinant production of a bacterial photolyase from the Antarctic isolate Hymenobacter sp. UV11. Extremophiles 23:49–57. https://doi.org/10.1007/s00792-018-1059-y
Megna M, Lembo S, Balato N, Monfrecola G (2017) “Active” photoprotection: sunscreens with DNA repair enzymes Giornale italiano di dermatologia e venereologia : organo ufficiale. Societa italiana di dermatologia e sifilografia 152:302–307. https://doi.org/10.23736/s0392-0488.17.05567-5
Mu W, Zhang D, Xu L, Luo Z, Wang Y (2005) Activity assay of His-tagged E. coli DNA photolyase by RP-HPLC and SE-HPLC. J Biochem Biophys Methods 63:111–124. https://doi.org/10.1016/j.jbbm.2005.03.005
Ozturk N (2017) Phylogenetic and functional classification of the photolyase/cryptochrome family. Photochem Photobiol 93:104–111. https://doi.org/10.1111/php.12676
Park HW, Kim ST, Sancar A, Deisenhofer J (1995) Crystal structure of DNA photolyase from Escherichia coli. Science 268:1866–1872
Pfeifer GP, Besaratinia A (2012) UV wavelength-dependent DNA damage and human non-melanoma and melanoma skin cancer. Photochem Photobiol Sci Off J Eur Photochem Assoc Eur Soc Photobiol 11:90–97. https://doi.org/10.1039/c1pp05144j
Purohit NK, Robu M, Shah RG, Geacintov NE, Shah GM (2016) Characterization of the interactions of PARP-1 with UV-damaged DNA in vivo and in vitro. Sci Rep 6:19020. https://doi.org/10.1038/srep19020
Puviani M, Barcella A, Milani M (2013) Efficacy of a photolyase-based device in the treatment of cancerization field in patients with actinic keratosis and non-melanoma skin cancer Giornale italiano di dermatologia e venereologia : organo ufficiale. Societa italiana di dermatologia e sifilografia 148:693–698
Rastogi RP, Richa KA, Tyagi MB, Sinha RP (2010) Molecular mechanisms of ultraviolet radiation-induced DNA damage and repair. J Nucl Acids 1:592980. https://doi.org/10.4061/2010/592980
Rocco V, Oppezzo O, Pizarro R, Sommaruga R, Ferraro M, Zagarese H (2002) Ultraviolet damage and counteracting mechanisms in the freshwater copepod Boeckella poppei from the Antarctic Peninsula. Limnol Oceanogr 47:829–836. https://doi.org/10.4319/lo.2002.47.3.0829
Roldan-Arjona T, Ariza RR (2009) Repair and tolerance of oxidative DNA damage in plants. Mutat Res 681:169–179. https://doi.org/10.1016/j.mrrev.2008.07.003
Sancar A (2004) Photolyase and cryptochrome blue-light photoreceptors. Adv Protein Chem 69:73–100. https://doi.org/10.1016/s0065-3233(04)69003-6
Sancar GB, Smith FW, Lorence MC, Rupert CS, Sancar A (1984) Sequences of the Escherichia coli photolyase gene and protein. J Biol Chem 259:6033–6038
Sinha RP, Hader DP (2002) UV-induced DNA damage and repair: a review. Photochem Photobiol Sci Off J Eur Photochem Assoc Eur Soc Photobiol 1:225–236
Stege H, Roza L, Vink AA, Grewe M, Ruzicka T, Grether-Beck S, Krutmann J (2000) Enzyme plus light therapy to repair DNA damage in ultraviolet-B-irradiated human skin. Proc Natl Acad Sci USA 97:1790–1795. https://doi.org/10.1073/pnas.030528897
Subedi L, Lee TH, Wahedi HM, Baek SH, Kim SY (2017) Resveratrol-enriched rice attenuates UVB-ROS-induced skin aging via downregulation of inflammatory cascades. Oxid Med Cell Longev. https://doi.org/10.1155/2017/8379539
Tagua VG et al (2015) Fungal cryptochrome with DNA repair activity reveals an early stage in cryptochrome evolution. Proc Natl Acad Sci USA 112:15130–15135. https://doi.org/10.1073/pnas.1514637112
Takahashi S, Nakajima N, Saji H, Kondo N (2002) Diurnal change of cucumber CPD photolyase gene (CsPHR) expression and its physiological role in growth under UV-B irradiation. Plant Cell Physiol 43:342–349. https://doi.org/10.1093/pcp/pcf038
Terashima M, Ohashi K, Takasuka TE, Kojima H, Fukui M (2019) Antarctic heterotrophic bacterium Hymenobacter nivis P3(T) displays light-enhanced growth and expresses putative photoactive proteins. Environ Microbiol Rep 11:227–235. https://doi.org/10.1111/1758-2229.12702
Todo T et al (1996) Similarity among the Drosophila (6–4) photolyase, a human photolyase homolog, and the DNA photolyase-blue-light photoreceptor family. Science 272:109–112
Waterhouse A et al (2018) SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res 46:W296-w303. https://doi.org/10.1093/nar/gky427
Zhang M, Wang L, Zhong D (2017) Photolyase: Dynamics and electron-transfer mechanisms of DNA repair. Arch Biochem Biophys 632:158–174. https://doi.org/10.1016/j.abb.2017.08.007
Funding
This study was funded by the National Key Research and Development Program of China (2018YFD0900705), the China Ocean Mineral Resources R&D Association (DY135-B2-14), the Natural Science Foundation of China (41576187), the Natural Science Foundation of Shandong (ZR2019BD023), Key Research and Development Program of Shandong Province (2018GHY115034, 2018GHY115039), Ningbo Public Service Platform for High-Value Utilization of Marine Biological Resources (NBHY-2017-P2), and Youth Fund Project of Shandong Natural Science Foundation (ZR2017QD008).
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Conceptualization: CQ and JM; methodology: YH, CQ and JM; formal analysis and investigation: YH, LZ; writing—original draft preparation: YH; writing—review and editing: YH; funding acquisition: CQ and JM; supervision: CQ and JM.
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Supplementary file1 Supplementary Fig. 1 Protein functional sites prediction of the amino acids sequence of Rhodococcus sp. NJ-530 PHR (TIF 73 KB)
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Supplementary file2 Supplementary Fig. 2 Phylogenetic tree of CPF. PHR from Rhodococcus sp. NJ-530, shown in red box, belongs to CPD Class I PHRs (TIF 3408 KB)
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Supplementary file3 Supplementary Fig. 3 Gene sequence of phr from Rhodococcus sp. NJ-530, before and after codon optimization for the next PHR expression (TIF 1723 KB)
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Supplementary file4 Supplementary Fig. 4 Protein sequence of PHR from Rhodococcus sp. NJ-530. Peptides matched the results of mass spectrometry (MS) shown in bold red (TIF 356 KB)
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He, Y., Qu, C., Zhang, L. et al. DNA photolyase from Antarctic marine bacterium Rhodococcus sp. NJ-530 can repair DNA damage caused by ultraviolet. 3 Biotech 11, 102 (2021). https://doi.org/10.1007/s13205-021-02660-8
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DOI: https://doi.org/10.1007/s13205-021-02660-8