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Portero LR, Alonso-Reyes DG, Zannier F, Vazquez MP, Farías ME, Gärtner W, Albarracín VH. Photolyases and Cryptochromes in UV-resistant Bacteria from High-altitude Andean Lakes. Photochem Photobiol 2019; 95:315-330. [DOI: 10.1111/php.13061] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 11/18/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Luciano Raúl Portero
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA); Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; Tucumán Argentina
- Centro de Investigaciones y Servicios de Microscopía Electrónica (CISME-CONICET-UNT); CCT, CONICET; Tucumán Argentina
| | - Daniel G. Alonso-Reyes
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA); Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; Tucumán Argentina
- Centro de Investigaciones y Servicios de Microscopía Electrónica (CISME-CONICET-UNT); CCT, CONICET; Tucumán Argentina
| | - Federico Zannier
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA); Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; Tucumán Argentina
- Centro de Investigaciones y Servicios de Microscopía Electrónica (CISME-CONICET-UNT); CCT, CONICET; Tucumán Argentina
| | - Martín P. Vazquez
- Instituto de Agrobiotecnología de Rosario (INDEAR); Predio CCT Rosario; Santa Fe Argentina
| | - María Eugenia Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA); Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; Tucumán Argentina
| | - Wolfgang Gärtner
- Institute for Analytical Chemistry; University of Leipzig; Leipzig Germany
| | - Virginia Helena Albarracín
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA); Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; Tucumán Argentina
- Centro de Investigaciones y Servicios de Microscopía Electrónica (CISME-CONICET-UNT); CCT, CONICET; Tucumán Argentina
- Facultad de Ciencias Naturales; Instituto Miguel Lillo; Universidad Nacional de Tucumán; Tucumán Argentina
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Elías-Arnanz M, Padmanabhan S, Murillo FJ. Light-dependent gene regulation in nonphototrophic bacteria. Curr Opin Microbiol 2011; 14:128-35. [DOI: 10.1016/j.mib.2010.12.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 12/15/2010] [Accepted: 12/15/2010] [Indexed: 11/24/2022]
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Rastogi RP, Richa, Kumar A, Tyagi MB, Sinha RP. Molecular mechanisms of ultraviolet radiation-induced DNA damage and repair. J Nucleic Acids 2010; 2010:592980. [PMID: 21209706 PMCID: PMC3010660 DOI: 10.4061/2010/592980] [Citation(s) in RCA: 587] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 08/15/2010] [Accepted: 09/28/2010] [Indexed: 11/20/2022] Open
Abstract
DNA is one of the prime molecules, and its stability is of utmost importance for proper functioning and existence of all living systems. Genotoxic chemicals and radiations exert adverse effects on genome stability. Ultraviolet radiation (UVR) (mainly UV-B: 280-315 nm) is one of the powerful agents that can alter the normal state of life by inducing a variety of mutagenic and cytotoxic DNA lesions such as cyclobutane-pyrimidine dimers (CPDs), 6-4 photoproducts (6-4PPs), and their Dewar valence isomers as well as DNA strand breaks by interfering the genome integrity. To counteract these lesions, organisms have developed a number of highly conserved repair mechanisms such as photoreactivation, base excision repair (BER), nucleotide excision repair (NER), and mismatch repair (MMR). Additionally, double-strand break repair (by homologous recombination and nonhomologous end joining), SOS response, cell-cycle checkpoints, and programmed cell death (apoptosis) are also operative in various organisms with the expense of specific gene products. This review deals with UV-induced alterations in DNA and its maintenance by various repair mechanisms.
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Affiliation(s)
- Rajesh P Rastogi
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
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Light-induced activation of class II cyclobutane pyrimidine dimer photolyases. DNA Repair (Amst) 2010; 9:495-505. [PMID: 20227927 DOI: 10.1016/j.dnarep.2010.01.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Revised: 01/16/2010] [Accepted: 01/19/2010] [Indexed: 11/23/2022]
Abstract
Light-induced activation of class II cyclobutane pyrimidine dimer (CPD) photolyases of Arabidopsis thaliana and Oryza sativa has been examined by UV/Vis and pulsed Davies-type electron-nuclear double resonance (ENDOR) spectroscopy, and the results compared with structure-known class I enzymes, CPD photolyase and (6-4) photolyase. By ENDOR spectroscopy, the local environment of the flavin adenine dinucleotide (FAD) cofactor is probed by virtue of proton hyperfine couplings that report on the electron-spin density at the positions of magnetic nuclei. Despite the amino-acid sequence dissimilarity as compared to class I enzymes, the results indicate similar binding motifs for FAD in the class II photolyases. Furthermore, the photoreduction kinetics starting from the FAD cofactor in the fully oxidized redox state, FAD(ox), have been probed by UV/Vis spectroscopy. In Escherichia coli (class I) CPD photolyase, light-induced generation of FADH from FAD(ox), and subsequently FADH(-) from FADH, proceeds in a step-wise fashion via a chain of tryptophan residues. These tryptophans are well conserved among the sequences and within all known structures of class I photolyases, but completely lacking from the equivalent positions of class II photolyase sequences. Nevertheless, class II photolyases show photoreduction kinetics similar to those of the class I enzymes. We propose that a different, but also effective, electron-transfer cascade is conserved among the class II photolyases. The existence of such electron transfer pathways is supported by the observation that the catalytically active fully reduced flavin state obtained by photoreduction is maintained even under oxidative conditions in all three classes of enzymes studied in this contribution.
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Yamamoto A, Tanbir N, Hirouchi T, Teranishi M, Hidema J, Morioka H, Yamamoto K. Temperature-sensitive photoreactivation of cyclobutane thymine dimer in soybean. JOURNAL OF RADIATION RESEARCH 2008; 49:189-96. [PMID: 18270478 DOI: 10.1269/jrr.07091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
UV radiation induces the formation of two classes of photoproducts in DNA, the cyclobutane pyrimidine dimer (CPD) and the pyrimidine 6-4 pyrimidone photoproduct. CPDs in plants are repaired by class II CPD photolyase via a UV-A/blue light-dependent mechanism. The genes for the class II CPD photolyase have been cloned from higher plants such as Arabidopsis, Cucumis sativus (cucumber), Oryza sativa (rice) and Spinacia oleracea (spinach). Flavin adenine dinucleotide (FAD) has been identified as a cofactor. Here we report the isolation and characterization of the CPD photolyase cDNA from soybean (Glycin max). The sequence of amino acids predicted from the cDNA sequence was highly homologous to sequences of higher plant class II CPD photolyases. When the cDNA was expressed in a photolyase-deficient Escherichia coli, photoreactivation activity was partially restored by illumination with a fluorescent light. The purified enzyme showed CPD binding and light-dependent photoreactivation activities in vitro. When soybean CPD photolyase was heat-treated in vitro from 25 degrees C to 45 degrees C for 3 min, thymine dimer-binding activity and photoreactivation activity were decreased, and FAD was released from the enzyme. On the other hand, when the enzyme-CPD complex was heat-treated, photoreactivation activity was stable. We argue that FAD in the soybean CPD photolyase is labile for temperature, but once the enzyme-CPD complex has formed, FAD becomes tightly bound to the enzyme or complex.
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Affiliation(s)
- Ayumi Yamamoto
- Graduate School of Life Sciences, Tohoku University, Japan
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Yamamoto A, Hirouchi T, Mori T, Teranishi M, Hidema J, Morioka H, Kumagai T, Yamamoto K. Biochemical and biological properties of DNA photolyases derived from utraviolet-sensitive rice cultivars. Genes Genet Syst 2008; 82:311-9. [PMID: 17895582 DOI: 10.1266/ggs.82.311] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Class I and class II CPD photolyases are enzymes which repair pyrimidine dimers using visible light. A detailed characterization of class I CPD photolyases has been carried out, but little is known about the class II enzymes. Photolyases from rice are suitable for functional analyses because systematic breeding for long periods in Asian countries has led to the selection of naturally occurring mutations in the CPD photolyase gene. We report the biochemical characterization of rice mutant CPD photolyases purified as GST-form from Escherichia coli. We identified three amino acid changes, Gln126Arg, Gly255Ser, and Gln296His, among which Gln but not His at 296 is important for complementing phr-defective E. coli, binding UV-damage in E. coli, and binding thymine dimers in vitro. The photolyase with Gln at 296 has an apoenzyme:FAD ratio of 1 : 0.5 and that with His at 296 has an apoenzyme:FAD ratio of 1 : 0.12-0.25, showing a role for Gln at 296 in the binding of FAD not in the binding of thymine dimer. Concerning Gln or Arg at 126, the biochemical activity of the photolyases purified from E. coli and complementing activity for phr-defective E. coli are similarly proficient. However, the sensitivity to UV of cultivars differs depending on whether Gln or Arg is at 126. The role of Gln and Arg at 126 for photoreactivation in rice is discussed.
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Affiliation(s)
- Ayumi Yamamoto
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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Weber S. Light-driven enzymatic catalysis of DNA repair: a review of recent biophysical studies on photolyase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2005; 1707:1-23. [PMID: 15721603 DOI: 10.1016/j.bbabio.2004.02.010] [Citation(s) in RCA: 254] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2003] [Accepted: 02/02/2004] [Indexed: 11/19/2022]
Abstract
More than 50 years ago, initial experiments on enzymatic photorepair of ultraviolet (UV)-damaged DNA were reported [Proc. Natl. Acad. Sci. U. S. A. 35 (1949) 73]. Soon after this discovery, it was recognized that one enzyme, photolyase, is able to repair UV-induced DNA lesions by effectively reversing their formation using blue light. The enzymatic process named DNA photoreactivation depends on a non-covalently bound cofactor, flavin adenine dinucleotide (FAD). Flavins are ubiquitous redox-active catalysts in one- and two-electron transfer reactions of numerous biological processes. However, in the case of photolyase, not only the ground-state redox properties of the FAD cofactor are exploited but also, and perhaps more importantly, its excited-state properties. In the catalytically active, fully reduced redox form, the FAD absorbs in the blue and near-UV ranges of visible light. Although there is no direct experimental evidence, it appears generally accepted that starting from the excited singlet state, the chromophore initiates a reductive cleavage of the two major DNA photodamages, cyclobutane pyrimidine dimers and (6-4) photoproducts, by short-distance electron transfer to the DNA lesion. Back electron transfer from the repaired DNA segment is believed to eventually restore the initial redox states of the cofactor and the DNA nucleobases, resulting in an overall reaction with net-zero exchanged electrons. Thus, the entire process represents a true catalytic cycle. Many biochemical and biophysical studies have been carried out to unravel the fundamentals of this unique mode of action. The work has culminated in the elucidation of the three-dimensional structure of the enzyme in 1995 that revealed remarkable details, such as the FAD-cofactor arrangement in an unusual U-shaped configuration. With the crystal structure of the enzyme at hand, research on photolyases did not come to an end but, for good reason, intensified: the geometrical structure of the enzyme alone is not sufficient to fully understand the enzyme's action on UV-damaged DNA. Much effort has therefore been invested to learn more about, for example, the geometry of the enzyme-substrate complex, and the mechanism and pathways of intra-enzyme and enzyme <-->DNA electron transfer. Many of the key results from biochemical and molecular biology characterizations of the enzyme or the enzyme-substrate complex have been summarized in a number of reviews. Complementary to these articles, this review focuses on recent biophysical studies of photoreactivation comprising work performed from the early 1990s until the present.
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Affiliation(s)
- Stefan Weber
- Institute of Experimental Physics, Free University Berlin, Arnimallee 14, 14195 Berlin, Germany.
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Slamovits CH, Keeling PJ. Class II photolyase in a microsporidian intracellular parasite. J Mol Biol 2004; 341:713-21. [PMID: 15288781 DOI: 10.1016/j.jmb.2004.06.032] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2004] [Revised: 06/11/2004] [Accepted: 06/14/2004] [Indexed: 11/22/2022]
Abstract
Photoreactivation is the repair of DNA damage induced by ultraviolet light radiation using the energy contained in visible-light photons. The process is carried out by a single enzyme, photolyase, which is part of a large and ancient photolyase/cryptochrome gene family. We have characterised a photolyase gene from the microsporidian parasite, Antonospora locustae (formerly Nosema locustae) and show that it encodes a functional photoreactivating enzyme and is expressed in the infectious spore stage of the parasite's life cycle. Sequence and phylogenetic analyses show that it belongs to the class II subfamily of cyclobutane pyrimidine dimer repair enzymes. No photolyase is present in the complete genome sequence of the distantly related microsporidian, Encephalitozoon cuniculi, and this class of photolyase has never yet been described in fungi, the closest relatives of Microsporidia, raising questions about the evolutionary origin of this enzyme. This is the second environmental stress enzyme to be found in A.locustae but absent in E.cuniculi, and in the other case (catalase), the gene is derived by lateral transfer from a bacterium. It appears that A.locustae spores deal with environmental stress differently from E.cuniculi, these results lead to the prediction that they are more robust to environmental damage.
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Affiliation(s)
- Claudio H Slamovits
- Department of Botany, Canadian Institute for Advanced Research, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC, Canada V6T 1Z4
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Kleiner O, Butenandt J, Carell T, Batschauer A. Class II DNA photolyase from Arabidopsis thaliana contains FAD as a cofactor. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 264:161-7. [PMID: 10447684 DOI: 10.1046/j.1432-1327.1999.00590.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The major UV-B photoproduct in DNA is the cyclobutane pyrimidine dimer (CPD). CPD-photolyases repair this DNA damage by a light-driven electron transfer. The chromophores of the class II CPD-photolyase from Arabidopsis thaliana, which was cloned recently [Taylor, R., Tobin, A. & Bray, C. (1996) Plant Physiol. 112, 862; Ahmad, M., Jarillo, J.A., Klimczak, L.J., Landry, L.G., Peng, T., Last, R.L. & Cashmore, A.R. (1997) Plant Cell 9, 199-207], have not been characterized so far. Here we report on the overexpression of the Arabidopsis CPD photolyase in Escherichia coli as a 6 x His-tag fusion protein, its purification and the analysis of the chromophore composition and enzymatic activity. Like class I photolyase, the Arabidopsis enzyme contains FAD but a second chromophore was not detectable. Despite the lack of a second chromophore the purified enzyme has photoreactivating activity.
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Affiliation(s)
- O Kleiner
- FB Biologie/Botanik, Philipps-Universität Marburg, Germany
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Todo T, Tsuji H, Otoshi E, Hitomi K, Kim ST, Ikenaga M. Characterization of a human homolog of (6-4) photolyase. Mutat Res 1997; 384:195-204. [PMID: 9330615 DOI: 10.1016/s0921-8777(97)00032-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
(6-4)Photolyase catalyzes light-dependent repair of UV-induced pyrimidine (6-4) pyrimidone photoproducts. A human cDNA clone which has high sequence homology to the (6-4)photolyase gene (H64PRH gene) was identified. In this paper we also isolated a genomic clone corresponding to the H64PRH cDNA and mapped it to chromosome 12q24.1 by fluorescence in situ hybridization (FISH). Northern-blot analysis revealed transcription of this gene in all human tissues examined. The H64PRH protein was overproduced in E. coli, partially purified and characterized. Like (6-4)photolyase, the enzyme contains two chromophores, one of which is FAD. However, the enzyme does not show any detectable photolyase activity.
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Affiliation(s)
- T Todo
- Radiation Biology Center, Kyoto University, Japan.
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