Publikationsserver der Universitätsbibliothek Marburg

Titel:Studien zur Konversion photochemischer und funktioneller Eigenschaften verschiedener Blaulichtrezeptoren
Autor:Schroeder, Claudia
Weitere Beteiligte: Essen, Lars Oliver (Prof. Dr.)
Veröffentlicht:2009
URI:https://archiv.ub.uni-marburg.de/diss/z2010/0145
URN: urn:nbn:de:hebis:04-z2010-01457
DOI: https://doi.org/10.17192/z2010.0145
DDC: Chemie
Titel (trans.):Studies regarding the conversion of photochemical and functional characteristics of various blue-light receptors
Publikationsdatum:2010-06-24
Lizenz:https://rightsstatements.org/vocab/InC-NC/1.0/

Dokument

Schlagwörter:
BLUF-domains, Photorezeptor, BLUF-Domänen, (6-4)-photolyases, (6-4)-Photolyasen, photoreceptor

Zusammenfassung:
In BLUF-Domänen enthaltenden Proteinen und DNA-Photolyasen wechselwirkt das nichtkovalent gebundene FAD mit Blaulicht und initiiert eine lichtabhängige Signalkaskade bzw. DNA-Reparatur. In beiden Blaulichtrezeptorklassen wurden verschiedene subtypenspezifische funktionelle Eigenschaften beobachtet. Ein Teil dieser Arbeit war die Konversion der E. coli YcgF-(1-137) BLUF-Domäne, welche den Subtyp II repräsentiert, in den Subtyp I (z.B. SyPixD). Zu diesem Zweck wurden verschiedene Oberflächenmutanten zweier in der E. coli YcgF-(1-137) BLUF-Domäne nicht konservierter Aminosäuren (Met 23 und Ala 90) biophysikalisch charakterisiert. Hierbei konnte eine erfolgreiche Konversion des Subtyp II in den BLUF-Domänen Subtyp I anhand veränderter photochemischer Eigenschaften dokumentiert werden. Diese photochemischen Veränderungen zeigten, dass die nativen Aminosäuren Met 23, sowie Ala 90 für einen Großteil der spezifischen Charakteristika der E. coli YcgF BLUF-Domäne verantwortlich sind. Zu diesen veränderten Charakteristika gehören blauverschobene Absorptionsmaxima des Signalzustandes, eine beschleunigte Licht-Dunkel-Konversion, die Flavintriplettzustände und die lichtinduzierte Konformationsänderung des eingefügten Trp 90. Zusätzlich konnte unter Generierung einer Y7F-Oberflächenmutante gezeigt werden, dass dieser in allen BLUF Photorezeptoren konservierte Tyrosinrest auch im E. coli YcgF essentiell für die Schaltung der BLUF-Domäne ist. Aufgrund der fehlenden lichtinduzierten Rotverschiebung und der langlebigen Existenz einer radikalischen Flavinspezies wurde die Y7F-Mutante als Intermediat des BLUF-Photozyklus präsentiert, welches zwischen dem Grundzustand und der Ausbildung des Radikalpaars gefangen ist. Auf Grundlage dieser und zuvor bestimmter Resultate konnte ein möglicher blaulichtinduzierter E. coli YcgF BLUF-Domänen Photozyklus und Signalübertragungsweg vorgestellt werden. Ein weiteres Ziel dieser Arbeit war die A. thaliana (6-4)-Photolyase in den Subtyp der CPDPhotolyasen umzuwandeln. Hierfür wurden Oberflächenmutanten hergestellt, die anstelle der nativen für die Bindung des (6-4)-Schadens benötigten Aminosäuren in ihrer katalytischen Bindungstasche spezifische für die Bindung und Reparatur von CPD-Schäden benötigte Aminosäurereste enthalten. Für alle aufgereinigten A. thaliana (6-4)-Photolyasemutanten wurde analog zum Wildtyp der katalytisch aktive, vollständig reduzierte FADH--Zustand generiert und im Fall der K246R, H364N_L365R und W408Y Varianten eine leicht erhöhte Bindungsaffinität zum CPD-Schaden festgestellt. Weiter konnte gezeigt werden, dass die durch Mutagenese eingefügten Veränderungen nicht ausreichen, um die für die CPDReparaturaktivität im A. thaliana (6-4)-Enzym benötigten Interaktionen zu gewährleisten d. h. die (6-4)-Photolyase in den CPD-Subtyp zu konvertieren, im Gegensatz zum YcgF BLUF-Blaulichtrezeptor. Als Ursache dieser Beobachtung wurde ein unterschiedliches Bindungsverhalten beider DNA-Photolyasesubtypen dokumentiert. Hierbei wurden distinkte Unterschiede in der Art des Flippmechanismus im Verlauf der DNA-Bindung, den Deformierungsgrad der geschädigten DNA betreffend, sowie in der Orientierung der gebundenen doppelsträngigen DNA aufgezeigt. Im letzten Teilprojekt wurde die (6-4)-Photolyase aus dem halophilen Eukaryoten D. salina untersucht. Diese Photolyase weist in vitro einen sehr stabilen neutralen semichinoiden FADZustand auf, der möglicherweise einen Signalzustand ähnlich dem pflanzlicher und tierischer Cryptochrome darstellt. Im Verlauf der Photoaktivierung wurden strukturelle Veränderungen der C-terminalen a-helikalen Extension der D. salina Enzym beobachtet, die eventuell für die Interaktion zwischen dem halbreduzierten Enzym und einem Signalpartner essentiell sind. Anhand dieser Resultate wurde für die D. salina (6-4)-Photolyase neben ihrer Photolyaseaktivität eine zusätzliche Cryptochromaktivität prognostiziert, ähnlich dem A. nidulans Cryptochrom A, sowie ein möglicher Mechanismus des Blaulichtrezeptors vorgestellt, der beide Funktionalitäten kombiniert. Demnach präsentiert das D. salina (6-4)-Enzym möglicherweise einen weiteren Schnittpunkt zwischen Photolyasen und Cryptochromen.

Bibliographie / References

  1. Laemmli, U.K., Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature, 1970. 227(5259): p. 680-5.
  2. Arnold, K., et al., The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics, 2006. 22(2): p. 195-201.
  3. Jung, A., et al., Crystal structures of the AppA BLUF domain photoreceptor provide insights into blue light-mediated signal transduction. J Mol Biol, 2006. 362(4): p. 717- 32.
  4. Edelhoch, H., Spectroscopic determination of tryptophan and tyrosine in proteins. Biochemistry, 1967. 6(7): p. 1948-54.
  5. Rajagopal, S., et al., Purification and initial characterization of a putative blue light- regulated phosphodiesterase from Escherichia coli. Photochem Photobiol, 2004. 80(3): p. 542-7.
  6. Dragnea, V., et al., Time-resolved spectroscopic studies of the AppA blue-light receptor BLUF domain from Rhodobacter sphaeroides. Biochemistry, 2005. 44(49): p. 15978-85.
  7. Bonetti, C., et al., Hydrogen bond switching among flavin and amino acid side chains in the BLUF photoreceptor observed by ultrafast infrared spectroscopy. Biophys J, 2008. 95(10): p. 4790-802.
  8. Saxena, C., A. Sancar, and D.P. Zhong, Femtosecond dynamics of DNA photolyase: energy transfer of antenna initiation and electron transfer of cofactor reduction. J. Phys. Chem. B, 2004. 108: p. 18026-18033.
  9. Schleicher, E., et al., Electron nuclear double resonance differentiates complementary roles for active site histidines in (6-4) photolyase. J Biol Chem, 2007. 282(7): p. 4738- 47.
  10. Schleicher, E., et al., On the reaction mechanism of adduct formation in LOV domains of the plant blue-light receptor phototropin. J Am Chem Soc, 2004. 126(35): p. 11067-76.
  11. Klar, T., et al., Cryptochrome 3 from Arabidopsis thaliana: structural and functional analysis of its complex with a folate light antenna. J Mol Biol, 2007. 366(3): p. 954- 64.
  12. Cashmore, A.R., et al., Cryptochromes: blue light receptors for plants and animals. Science, 1999. 284(5415): p. 760-5.
  13. Park, H.W., et al., Crystal structure of DNA photolyase from Escherichia coli. Science, 1995. 268(5219): p. 1866-72.
  14. Liedvogel, M., et al., Chemical magnetoreception: bird cryptochrome 1a is excited by blue light and forms long-lived radical-pairs. PLoS ONE, 2007. 2(10): p. e1106.
  15. Gauden, M., et al., On the role of aromatic side chains in the photoactivation of BLUF domains. Biochemistry, 2007. 46(25): p. 7405-15.
  16. Grinstead, J.S., et al., Light-induced flipping of a conserved glutamine sidechain and its orientation in the AppA BLUF domain. J Am Chem Soc, 2006. 128(47): p. 15066- 7.
  17. Klar, T., et al., Natural and non-natural antenna chromophores in the DNA photolyase from Thermus thermophilus. Chembiochem, 2006. 7(11): p. 1798-806.
  18. Schroeder, C., et al., Influence of a joining helix on the BLUF domain of the YcgF photoreceptor from Escherichia coli. Chembiochem, 2008. 9(15): p. 2463-73.
  19. Atherton, N.M., Principles of Electron Spin Resonance. Ellis Horwood LTD., Chichester, 1993.
  20. Bennett, J. and K.J. Scott, Quantitative staining of fraction I protein in polyacrylamide gels using Coomassie brillant blue. Anal Biochem, 1971. 43(1): p. 173-82.
  21. Mullis, K.B. and F.A. Faloona, Specific synthesis of DNA in vitro via a polymerase- catalyzed chain reaction. Methods Enzymol, 1987. 155: p. 335-50.
  22. Lukacs, A., et al., Electron hopping through the 15 A triple tryptophan molecular wire in DNA photolyase occurs within 30 ps. J Am Chem Soc, 2008. 130(44): p. 14394-5.
  23. Kleiner, O., et al., Class II DNA photolyase from Arabidopsis thaliana contains FAD as a cofactor. Eur J Biochem, 1999. 264(1): p. 161-7.
  24. Glas, A.F., et al., The archaeal cofactor F0 is a light-harvesting antenna chromophore in eukaryotes. Proc Natl Acad Sci U S A, 2009. 106(28): p. 11540-5.
  25. Park, H., et al., Crystal structure of a DNA decamer containing a cis-syn thymine dimer. Proc Natl Acad Sci U S A, 2002. 99(25): p. 15965-70.
  26. Kort, R., et al., DNA apophotolyase from Anacystis nidulans: 1.8 A structure, 8-HDF reconstitution and X-ray-induced FAD reduction. Acta Crystallogr D Biol Crystallogr, 2004. 60(Pt 7): p. 1205-13.
  27. Mees, A., et al., Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair. Science, 2004. 306(5702): p. 1789-93.
  28. Song, S.H., et al., Formation and function of flavin anion radical in cryptochrome 1 blue-light photoreceptor of monarch butterfly. J Biol Chem, 2007. 282(24): p. 17608- 12.
  29. Byrdin, M., et al., Intraprotein electron transfer and proton dynamics during photoactivation of DNA photolyase from E. coli: review and new insights from an "inverse" deuterium isotope effect. Biochim Biophys Acta, 2004. 1655(1-3): p. 64-70.
  30. Aubert, C., et al., Intraprotein radical transfer during photoactivation of DNA photolyase. Nature, 2000. 405(6786): p. 586-90.
  31. Toh, K.C., et al., On the signaling mechanism and the absence of photoreversibility in the AppA BLUF domain. Biophys J, 2008. 95(1): p. 312-21.
  32. Polissi, A., et al., Changes in Escherichia coli transcriptome during acclimatization at low temperature. Res Microbiol, 2003. 154(8): p. 573-80.
  33. Barends, T.R., et al., Structure and mechanism of a bacterial light-regulated cyclic nucleotide phosphodiesterase. Nature, 2009. 459(7249): p. 1015-8.
  34. Bouly, J.P., et al., Cryptochrome blue light photoreceptors are activated through interconversion of flavin redox states. J Biol Chem, 2007. 282(13): p. 9383-91.
  35. Gauden, M., et al., Photocycle of the flavin-binding photoreceptor AppA, a bacterial transcriptional antirepressor of photosynthesis genes. Biochemistry, 2005. 44(10): p. 3653-62.
  36. Hitomi, K., et al., Role of two histidines in the (6-4) photolyase reaction. J Biol Chem, 2001. 276(13): p. 10103-9.
  37. Glycerin, pH 7.4 gelöst, die Spektren wurden bei 5 °C aufgenommen und dreimal akkumuliert. Die A. thaliana (6-4)-Photolyase (···) war in 2 mM Tris/HCl, 20 mM NaCl,
  38. Abbildung 4.42: A) Bindung der D. salina (6-4)-DNA-Photolyase in unterschiedlichen Redoxzuständen an ein doppelsträngiges ungeschädigtes 50-mer Oligonukleotid und B) Direkt-lineare Auftragung der DNA-Bindung. Oxidierte (a, Schwarz), neutrale semichinoide (b, türkis) und vollständig reduzierte (c, rot) D. salina (6-4)-Photolyase.
  39. Payne, G. and A. Sancar, Absolute action spectrum of E-FADH2 and E-FADH2- MTHF forms of Escherichia coli DNA photolyase. Biochemistry, 1990. 29(33): p. 7715-27.
  40. Shibata, Y., et al., Acceleration of electron-transfer-induced fluorescence quenching upon conversion to the signaling state in the blue-light receptor, TePixD, from Thermosynechococcus elongatus. J Phys Chem B, 2009. 113(23): p. 8192-8.
  41. Sadeghian, K., M. Bocola, and M. Schutz, A conclusive mechanism of the photoinduced reaction cascade in blue light using flavin photoreceptors. J Am Chem Soc, 2008. 130(37): p. 12501-13.
  42. Selby, C.P. and A. Sancar, A cryptochrome/photolyase class of enzymes with single- stranded DNA-specific photolyase activity. Proc Natl Acad Sci U S A, 2006. 103(47): p. 17696-700.
  43. Sancar, G.B., et al., Action mechanism of Escherichia coli DNA photolyase. III. Photolysis of the enzyme-substrate complex and the absolute action spectrum. J Biol Chem, 1987. 262(1): p. 492-8.
  44. Kleine, T., P. Lockhart, and A. Batschauer, An Arabidopsis protein closely related to Synechocystis cryptochrome is targeted to organelles. Plant J, 2003. 35(1): p. 93-103.
  45. Ozturk, N., et al., Animal type 1 cryptochromes. Analysis of the redox state of the flavin cofactor by site-directed mutagenesis. J Biol Chem, 2008. 283(6): p. 3256-63.
  46. Bradford, M.M., A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem, 1976. 72: p. 248-54.
  47. Hitomi, K., et al., Binding and catalytic properties of Xenopus (6-4) photolyase. J Biol Chem, 1997. 272(51): p. 32591-8.
  48. Masuda, S. and T.A. Ono, Biochemical characterization of the major adenylyl cyclase, Cya1, in the cyanobacterium Synechocystis sp. PCC 6803. FEBS Lett, 2004. 577(1-2): p. 255-8.
  49. Gill, S.C. and P.H. von Hippel, Calculation of protein extinction coefficients from amino acid sequence data. Anal Biochem, 1989. 182(2): p. 319-26.
  50. Li, J., et al., Characteristic structure and environment in FAD cofactor of (6-4) photolyase along function revealed by resonance Raman spectroscopy. J Phys Chem B, 2006. 110(33): p. 16724-32.
  51. Malhotra, K., S.T. Kim, and A. Sancar, Characterization of a medium wavelength type DNA photolyase: purification and properties of photolyase from Bacillus firmus. Biochemistry, 1994. 33(29): p. 8712-8.
  52. Schroeder, C., Charakterisierung der Blaulichtrezeptordomäne YcgF aus Escherichia coli. Diplomarbeit, 2005.
  53. Wada, M., T. Kagawa, and Y. Sato, Chloroplast movement. Annu Rev Plant Biol, 2003. 54: p. 455-68.
  54. Jorns, M.S., et al., Chromophore function and interaction in Escherichia coli DNA photolyase: reconstitution of the apoenzyme with pterin and/or flavin derivatives. Biochemistry, 1990. 29(2): p. 552-61.
  55. Kundu, L.M., et al., Cleavable substrate containing molecular beacons for the quantification of DNA-photolyase activity. Chembiochem, 2002. 3(11): p. 1053-60.
  56. Yi, Y., et al., Cloning and sequence analysis of the gene encoding (6-4)photolyase from Dunaliella salina. Biotechnol Lett, 2006. 28(5): p. 309-14.
  57. Li, Q.H. and H.Q. Yang, Cryptochrome signaling in plants. Photochem Photobiol, 2007. 83(1): p. 94-101.
  58. Jancarik, J., et al., Crystallization and preliminary X-ray diffraction study of the ligand-binding domain of the bacterial chemotaxis-mediating aspartate receptor of Salmonella typhimurium. J Mol Biol, 1991. 221(1): p. 31-4.
  59. Maul, M.J., et al., Crystal structure and mechanism of a DNA (6-4) photolyase. Angew Chem Int Ed Engl, 2008. 47(52): p. 10076-80.
  60. Fujihashi, M., et al., Crystal structure of archaeal photolyase from Sulfolobus tokodaii with two FAD molecules: implication of a novel light-harvesting cofactor. J Mol Biol, 2007. 365(4): p. 903-10.
  61. Komori, H., et al., Crystal structure of thermostable DNA photolyase: pyrimidine- dimer recognition mechanism. Proc Natl Acad Sci U S A, 2001. 98(24): p. 13560-5.
  62. Wang, S.Y. and A.J. Varghese, Cytosine-thymine addition product from DNA irradiated with ultraviolet light. Biochem Biophys Res Commun, 1967. 29(4): p. 543- 9.
  63. Harper, S.M., J.M. Christie, and K.H. Gardner, Disruption of the LOV-Jalpha helix interaction activates phototropin kinase activity. Biochemistry, 2004. 43(51): p. 16184-92. 13. Gomelsky, M. and G. Klug, BLUF: a novel FAD-binding domain involved in sensory transduction in microorganisms. Trends Biochem Sci, 2002. 27(10): p. 497-500.
  64. Abbildung 5.20: DNA-Bindungstaschen A) D. melanogaster (6-4)-Photolyase (PDB ID: 3CVV) und B) A. nidulans CPD-Photolyase (PDB ID: 1TEZ). Dargestellt sind der jeweilige Photoschaden (grau), die für die Erkennung und Reparatur des jeweiligen Schadens selektierenden Aminosäuren (grün) und an der Bindung des DNA-Schadens beteiligte
  65. Taylor, J.S., DNA, sunlight and skin cancer. Pure &Appl. Chem., 1995. 67(1): p. 183- 190.
  66. Hosseini Tafreshi, A. and M. Shariati, Dunaliella biotechnology: methods and applications. Journal of Applied Microbiology, 2009. 107: p. 14-35.
  67. Kim, S.T., P.F. Heelis, and A. Sancar, Energy transfer (deazaflavin-->FADH2) and electron transfer (FADH2-->T <> T) kinetics in Anacystis nidulans photolyase. Biochemistry, 1992. 31(45): p. 11244-8.
  68. Vande Berg, B.J. and G.B. Sancar, Evidence for dinucleotide flipping by DNA photolyase. J Biol Chem, 1998. 273(32): p. 20276-84.
  69. Okajima, K., et al., Fate determination of the flavin photoreceptions in the cyanobacterial blue light receptor TePixD (Tll0078). J Mol Biol, 2006. 363(1): p. 10- 8.
  70. Muller, F. and V. Massey, Flavin-sulfite complexes and their structures. J Biol Chem, 1969. 244(15): p. 4007-16.
  71. Koziol, J., [132] Fluorometric analyses of riboflavin and its coenzymes. Methods Enzymol, 1971. 18: p. 253–285.
  72. Dower, W.J., J.F. Miller, and C.W. Ragsdale, High efficiency transformation of E. coli by high voltage electroporation. Nucleic Acids Res, 1988. 16(13): p. 6127-45.
  73. Ueda, T., et al., Identification and characterization of a second chromophore of DNA photolyase from Thermus thermophilus HB27. J Biol Chem, 2005. 280(43): p. 36237- 43.
  74. Brudler, R., et al., Identification of a new cryptochrome class. Structure, function, and evolution. Mol Cell, 2003. 11(1): p. 59-67.
  75. Daiyasu, H., et al., Identification of cryptochrome DASH from vertebrates. Genes Cells, 2004. 9(5): p. 479-95.
  76. Douki, T. and J. Cadet, Individual determination of the yield of the main UV-induced dimeric pyrimidine photoproducts in DNA suggests a high mutagenicity of CC photolesions. Biochemistry, 2001. 40(8): p. 2495-501.
  77. Lindahl, T., Instability and decay of the primary structure of DNA. Nature, 1993. 362(6422): p. 709-15.
  78. Carrington, A. and A.D. McLachlan, Introduction to Magnetic Resonance. Harper International Edition, New York, 1969.
  79. Literatur 1. Hellingwerf, K.J., Key issues in the photochemistry and signalling-state formation of photosensor proteins. J. Photochem. Photobiol. B., 2000. 54(2-3): p. 94-102.
  80. Essen, L.O. and T. Klar, Light-driven DNA repair by photolyases. Cell Mol Life Sci, 2006. 63(11): p. 1266-77.
  81. Weber, S., Light-driven enzymatic catalysis of DNA repair: a review of recent biophysical studies on photolyase. Biochim Biophys Acta, 2005. 1707(1): p. 1-23.
  82. Schleicher, E., et al., Light-generated radical-pairs in BLUF-Domains. Manuscript in progress.
  83. Hasegawa, K., S. Masuda, and T.A. Ono, Light induced structural changes of a full- length protein and its BLUF domain in YcgF(Blrp), a blue-light sensing protein that uses FAD (BLUF). Biochemistry, 2006. 45(11): p. 3785-93.
  84. White-Ziegler, C.A., et al., Low temperature (23 degrees C) increases expression of biofilm-, cold-shock-and RpoS-dependent genes in Escherichia coli K-12. Microbiology, 2008. 154(Pt 1): p. 148-66.
  85. Ahmad, M., et al., Magnetic intensity affects cryptochrome-dependent responses in Arabidopsis thaliana. Planta, 2007. 225(3): p. 615-24.
  86. Manual of the Phusion High-Fidelity DNA Polymerase. Finnzymes, 2009.
  87. Husain, I., et al., Mechanism of damage recognition by Escherichia coli DNA photolyase. J Biol Chem, 1987. 262(27): p. 13188-97.
  88. Trautinger, F., Mechanisms of photodamage of the skin and its functional consequences for skin ageing. Clin Exp Dermatol, 2001. 26(7): p. 573-7.
  89. Kobayashi, Y., et al., Molecular analysis of zebrafish photolyase/cryptochrome family: two types of cryptochromes present in zebrafish. Genes Cells, 2000. 5(9): p. 725-38.
  90. Schroder, H.C., et al., Molecular and functional analysis of the (6-4) photolyase from the hexactinellid Aphrocallistes vastus. Biochim Biophys Acta, 2003. 1651(1-2): p. 41-9.
  91. Sambrook, F., E.F. Fritsch, and T. Maniatis, Molecular Cloning: A Laboratory Manual. Cold Spring Harbor, NY, Cold Spring Harbor Laboratoy Press, 1989.
  92. Watson, J.D. and F.H. Crick, Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature, 1953. 171(4356): p. 737-8.
  93. Niedrige Temperaturen verzögern hierbei die Rückkonversion des Signalzustands der YcgF BLUF-Domäne. Auf diese Weise wird die Mobilität der Bakterien garantiert. .. 139
  94. Tanaka, K., et al., Oligomeric-state-dependent conformational change of the BLUF protein TePixD (Tll0078). J Mol Biol, 2009. 386(5): p. 1290-300.
  95. Gindt, Y.M., et al., Origin of the transient electron paramagnetic resonance signals in DNA photolyase. Biochemistry, 1999. 38(13): p. 3857-66.
  96. Weber, S., et al., Photoactivation of the flavin cofactor in Xenopus laevis (6 -4) photolyase: observation of a transient tyrosyl radical by time-resolved electron paramagnetic resonance. Proc Natl Acad Sci U S A, 2002. 99(3): p. 1319-22.
  97. Heelis, P.F. and A. Sancar, Photochemical properties of Escherichia coli DNA photolyase: a flash photolysis study. Biochemistry, 1986. 25(25): p. 8163-6.
  98. Rahn, R.O. and J.L. Hosszu, Photochemical studies of thymine in ice. Photochem Photobiol, 1969. 10(2): p. 131-7.
  99. Partch, C.L. and A. Sancar, Photochemistry and photobiology of cryptochrome blue- light photopigments: the search for a photocycle. Photochem Photobiol, 2005. 81(6): p. 1291-304.
  100. Fukushima, Y., et al., Photoreactions of Tyr8-and Gln50-mutated BLUF domains of the PixD protein of Thermosynechococcus elongatus BP-1: photoconversion at low temperature without Tyr8. Biochemistry, 2008. 47(2): p. 660-9.
  101. Yan Lv, X., et al., Photoreactivation of (6-4) photolyase in Dunaliella salina. FEMS Microbiol Lett, 2008. 283(1): p. 42-6.
  102. van der Horst, M.A. and K.J. Hellingwerf, Photoreceptor proteins, "star actors of modern times": a review of the functional dynamics in the structure of representative members of six different photoreceptor families. Acc Chem Res, 2004. 37(1): p. 13-20.
  103. Fukushima, Y., et al., Primary intermediate in the photocycle of a blue-light sensory BLUF FAD-protein, Tll0078, of Thermosynechococcus elongatus BP-1. Biochemistry, 2005. 44(13): p. 5149-58.
  104. Dagert, M. and S.D. Ehrlich, Prolonged incubation in calcium chloride improves the competence of Escherichia coli cells. Gene, 1979. 6(1): p. 23-8.
  105. Ozturk, N., et al., Purification and characterization of a type III photolyase from Caulobacter crescentus. Biochemistry, 2008. 47(39): p. 10255-61.
  106. Ozgur, S. and A. Sancar, Purification and properties of human blue-light photoreceptor cryptochrome 2. Biochemistry, 2003. 42(10): p. 2926-32.
  107. Kiener, A., et al., Purification and properties of Methanobacterium thermoautotrophicum DNA photolyase. J Biol Chem, 1989. 264(23): p. 13880-7.
  108. QuikChange® Site-Directed Mutagenesis Kit. Stratagene, 2007.
  109. Payne, G., et al., Reconstitution of Escherichia coli photolyase with flavins and flavin analogues. Biochemistry, 1990. 29(24): p. 5706-11.
  110. Kelley, K.C., et al., Regulation of sCD4-183 gene expression from phage-T7-based vectors in Escherichia coli. Gene, 1995. 156(1): p. 33-6.
  111. Goosen, N. and G.F. Moolenaar, Repair of UV damage in bacteria. DNA Repair (Amst), 2008. 7(3): p. 353-79.
  112. Spudich, J.L., et al., Retinylidene proteins: structures and functions from archaea to humans. Annu Rev Cell Dev Biol, 2000. 16: p. 365-92. 6. Braatsch, S., et al., Responses of the Rhodobacter sphaeroides transcriptome to blue light under semiaerobic conditions. J Bacteriol, 2004. 186(22): p. 7726-35.
  113. Partch, C.L., et al., Role of structural plasticity in signal transduction by the cryptochrome blue-light photoreceptor. Biochemistry, 2005. 44(10): p. 3795-805.
  114. Abbildung 5.11: Schematische Darstellung der gekoppelten photo-und temperatursensorischen Eigenschaften der E. coli YcgF BLUF-Domäne und ihre Interaktion mit YcgE. Unter Lichteinstrahlung bildet die YcgF BLUF-Domäne ihren Signalzustand aus, der konformationelle Änderungen in der C-terminalen EAL-Domäne induziert. Daraufhin ist diese in der Lage, an die MerR-like Domäne des YcgE zu binden, so dass YcgE von der Operatorbindungsstelle abdissoziert. Dieser Vorgang setzt eine Reihe von Mechanismen in Gang, in Folge derer die E. coli Bakterien aus ihren Biofilm abwandern können.
  115. Li, J., et al., Similarities and differences between cyclobutane pyrimidine dimer photolyase and (6-4) photolyase as revealed by resonance Raman spectroscopy: Electron transfer from the FAD cofactor to ultraviolet-damaged DNA. J Biol Chem, 2006. 281(35): p. 25551-9.
  116. Todo, T., et al., Similarity among the Drosophila (6-4)photolyase, a human photolyase homolog, and the DNA photolyase-blue-light photoreceptor family. Science, 1996. 272(5258): p. 109-12. Literatur 200
  117. Reyna, M.M., Spectroscopic characterization of the E.coli YcgF BLUF domain. Diplomarbeit, 2005.
  118. Grossman, T.H., et al., Spontaneous cAMP-dependent derepression of gene expression in stationary phase plays a role in recombinant expression instability. Gene, 1998. 209(1-2): p. 95-103.
  119. Muller, M. and T. Carell, Structural biology of DNA photolyases and cryptochromes.
  120. Wu, Q., W.H. Ko, and K.H. Gardner, Structural requirements for key residues and auxiliary portions of a BLUF domain. Biochemistry, 2008. 47(39): p. 10271-80.
  121. Sancar, A., Structure and function of DNA photolyase and cryptochrome blue-light photoreceptors. Chem Rev, 2003. 103(6): p. 2203-37.
  122. Wu, Q. and K. Gardner, Structure and insight into blue light-induced changes in the BlrP1 BLUF domain. Biochemistry, 2009.
  123. Jung, A., et al., Structure of a bacterial BLUF photoreceptor: insights into blue light- mediated signal transduction. Proc Natl Acad Sci U S A, 2005. 102(35): p. 12350-5.
  124. Kita, A., et al., Structure of a cyanobacterial BLUF protein, Tll0078, containing a novel FAD-binding blue light sensor domain. J Mol Biol, 2005. 349(1): p. 1-9.
  125. Tschowri, N., S. Busse, and R. Hengge, The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli. Genes Dev, 2009. 23(4): p. 522-34. 17. Braatsch, S., et al., A single flavoprotein, AppA, integrates both redox and light signals in Rhodobacter sphaeroides. Mol Microbiol, 2002. 45(3): p. 827-36.
  126. Massey, V., The chemical and biological versatility of riboflavin. Biochem Soc Trans, 2000. 28(4): p. 283-96.
  127. Lin, C. and T. Todo, The cryptochromes. Genome Biol, 2005. 6(5): p. 220.
  128. Kowalczyk, R.M., et al., The photoinduced triplet of flavins and its protonation states. J Am Chem Soc, 2004. 126(36): p. 11393-9.
  129. Heelis, P.F., et al., The photo repair of pyrimidine dimers by DNA photolyase and model systems. J Photochem Photobiol B, 1993. 17(3): p. 219-28.
  130. Massey, V., et al., The reactivity of flavoproteins with sulfite. Possible relevance to the problem of oxygen reactivity. J Biol Chem, 1969. 244(15): p. 3999-4006.
  131. Banerjee, R., et al., The signaling state of Arabidopsis cryptochrome 2 contains flavin semiquinone. J Biol Chem, 2007. 282(20): p. 14916-22.
  132. Kim, J.K. and B.S. Choi, The solution structure of DNA duplex-decamer containing the (6-4) photoproduct of thymidylyl(3'-->5')thymidine by NMR and relaxation matrix refinement. Eur J Biochem, 1995. 228(3): p. 849-54.
  133. Grinstead, J.S., et al., The solution structure of the AppA BLUF domain: insight into the mechanism of light-induced signaling. Chembiochem, 2006. 7(1): p. 187-93. 51. van der Horst, M.A., J. Key, and K.J. Hellingwerf, Photosensing in chemotrophic, non-phototrophic bacteria: let there be light sensing too. Trends Microbiol, 2007. 15(12): p. 554-62.
  134. Shiga, K. and L.H. Piette, Triplet state studies of flavins by electron paramagnetic resonance II. Photochem Photobiol, 1962. 3: p. 223-230.
  135. Saxena, C., et al., Ultrafast dynamics of resonance energy transfer in cryptochrome. J Am Chem Soc, 2005. 127(22): p. 7984-5.
  136. Stelling, A.L., et al., Ultrafast structural dynamics in BLUF domains: transient infrared spectroscopy of AppA and its mutants. J Am Chem Soc, 2007. 129(50): p. 15556-64.
  137. YcgF-(1-137)_A90W 396, 437, 470, 504 341, 385, 427, 452, 482
  138. YcgF-(1-137)_M23I_A90W 394, 436, 468, 502 339, 378, 426, 449, 480
  139. YcgF-(1-137)_M23L 396, 436, 467, 503 343, 378, 424, 449, 481
  140. YcgF-(1-137)_WT 395, 436, 469, 502 340, 378, 427, 451, 481
  141. Salomon, M., et al., Photochemical and mutational analysis of the FMN-binding domains of the plant blue light receptor, phototropin. Biochemistry, 2000. 39(31): p. 9401-10.
  142. Birnboim, H.C. and J. Doly, A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res, 1979. 7(6): p. 1513-23.
  143. Jun, S.H., T.G. Kim, and C. Ban, DNA mismatch repair system. Classical and fresh roles. FEBS J, 2006. 273(8): p. 1609-19.
  144. Kavakli, I.H. and A. Sancar, Analysis of the role of intraprotein electron transfer in photoreactivation by DNA photolyase in vivo. Biochemistry, 2004. 43(48): p. 15103- 10.
  145. Borucki, B., Proton transfer in the photoreceptors phytochrome and photoactive yellow protein. Photochem Photobiol Sci, 2006. 5(6): p. 553-66.
  146. Hasegawa, K., S. Masuda, and T.A. Ono, Spectroscopic analysis of the dark relaxation process of a photocycle in a sensor of blue light using FAD (BLUF) protein Slr1694 of the cyanobacterium Synechocystis sp. PCC6803. Plant Cell Physiol, 2005. 46(1): p. 136-46.
  147. Anderson, S., et al., Structure of a novel photoreceptor, the BLUF domain of AppA from Rhodobacter sphaeroides. Biochemistry, 2005. 44(22): p. 7998-8005.
  148. Masuda, S., K. Hasegawa, and T.A. Ono, Adenosine diphosphate moiety does not participate in structural changes for the signaling state in the sensor of blue-light using FAD domain of AppA. FEBS Lett, 2005. 579(20): p. 4329-32.
  149. Kraft, B.J., et al., Spectroscopic and mutational analysis of the blue-light photoreceptor AppA: a novel photocycle involving flavin stacking with an aromatic amino acid. Biochemistry, 2003. 42(22): p. 6726-34.
  150. Masuda, S., et al., Light-induced structural changes in a putative blue-light receptor with a novel FAD binding fold sensor of blue-light using FAD (BLUF); Slr1694 of synechocystis sp. PCC6803. Biochemistry, 2004. 43(18): p. 5304-13. Literatur 197
  151. Hasegawa, K., S. Masuda, and T.A. Ono, Structural intermediate in the photocycle of a BLUF (sensor of blue light using FAD) protein Slr1694 in a Cyanobacterium Synechocystis sp. PCC6803. Biochemistry, 2004. 43(47): p. 14979-86.
  152. Yuan, H., et al., Crystal structures of the Synechocystis photoreceptor Slr1694 reveal distinct structural states related to signaling. Biochemistry, 2006. 45(42): p. 12687- 94.
  153. Masuda, S. and C.E. Bauer, AppA is a blue light photoreceptor that antirepresses photosynthesis gene expression in Rhodobacter sphaeroides. Cell, 2002. 110(5): p. 613-23.
  154. Unno, M., et al., Orientation of a key glutamine residue in the BLUF domain from AppA revealed by mutagenesis, spectroscopy, and quantum chemical calculations. J Am Chem Soc, 2006. 128(17): p. 5638-9.
  155. Masuda, S., et al., The critical role of a hydrogen bond between Gln63 and Trp104 in the blue-light sensing BLUF domain that controls AppA activity. J Mol Biol, 2007. 368(5): p. 1223-30.
  156. Masuda, S., et al., Crucial role in light signal transduction for the conserved Met93 of the BLUF protein PixD/Slr1694. Plant Cell Physiol, 2008. 49(10): p. 1600-6.
  157. Langmesser, S., et al., Interaction of circadian clock proteins PER2 and CRY with BMAL1 and CLOCK. BMC Mol Biol, 2008. 9: p. 41.
  158. Kelly, S.M. and N.C. Price, The use of circular dichroism in the investigation of protein structure and function. Curr Protein Pept Sci, 2000. 1(4): p. 349-84.
  159. Eker, A.P., et al., DNA photoreactivating enzyme from the cyanobacterium Anacystis nidulans. J Biol Chem, 1990. 265(14): p. 8009-15.
  160. Pick, U., L. Karni, and M. Avron, Determination of Ion Content and Ion Fluxes in the Halotolerant Alga Dunaliella salina. Plant Physiol, 1986. 81(1): p. 92-96.
  161. Cheung, M.S., et al., Pathways of electron transfer in Escherichia coli DNA photolyase: Trp306 to FADH. Biophys J, 1999. 76(3): p. 1241-9.
  162. Todo, T., et al., Flavin adenine dinucleotide as a chromophore of the Xenopus (6-4) photolyase. Nucleic Acids Res, 1997. 25(4): p. 764-8.
  163. Nakajima, S., et al., Cloning and characterization of a gene (UVR3) required for photorepair of 6-4 photoproducts in Arabidopsis thaliana. Nucleic Acids Res, 1998. 26(2): p. 638-44.
  164. Gauden, M., et al., Hydrogen-bond switching through a radical pair mechanism in a flavin-binding photoreceptor. Proc Natl Acad Sci U S A, 2006. 103(29): p. 10895- 900. Literatur 198
  165. Kato, R., et al., Characterization of a thermostable DNA photolyase from an extremely thermophilic bacterium, Thermus thermophilus HB27. J Bacteriol, 1997. 179(20): p. 6499-503.
  166. Domratcheva, T., et al., Molecular models predict light-induced glutamine tautomerization in BLUF photoreceptors. Biophys J, 2008. 94(10): p. 3872-9.
  167. Rao, F., et al., Catalytic mechanism of cyclic di-GMP-specific phosphodiesterase: a study of the EAL domain-containing RocR from Pseudomonas aeruginosa. J Bacteriol, 2008. 190(10): p. 3622-31.
  168. Bayram, O., et al., More than a repair enzyme: Aspergillus nidulans photolyase-like CryA is a regulator of sexual development. Mol Biol Cell, 2008. 19(8): p. 3254-62.
  169. Singh, A.H., et al., Discovering functional novelty in metagenomes: examples from light-mediated processes. J Bacteriol, 2009. 191(1): p. 32-41.
  170. Kao, Y.T., et al., Ultrafast dynamics and anionic active states of the flavin cofactor in cryptochrome and photolyase. J Am Chem Soc, 2008. 130(24): p. 7695-701.
  171. Yoshii, T., M. Ahmad, and C. Helfrich-Forster, Cryptochrome mediates light- dependent magnetosensitivity of Drosophila's circadian clock. PLoS Biol, 2009. 7(4): p. e1000086.
  172. Hitomi, K., et al., Functional motifs in the (6-4) photolyase crystal structure make a comparative framework for DNA repair photolyases and clock cryptochromes. Proc Natl Acad Sci U S A, 2009. 106(17): p. 6962-7.
  173. Coesel, S., et al., Diatom PtCPF1 is a new cryptochrome/photolyase family member with DNA repair and transcription regulation activity. EMBO Rep, 2009. 10(6): p. 655-61.
  174. Matsumura, Y. and H.N. Ananthaswamy, Molecular mechanisms of photocarcinogenesis. Front Biosci, 2002. 7: p. d765-83.
  175. Li, X. and W.D. Heyer, Homologous recombination in DNA repair and DNA damage tolerance. Cell Res, 2008. 18(1): p. 99-113.
  176. Tudek, B., S. Boiteux, and J. Laval, Biological properties of imidazole ring-opened N7-methylguanine in M13mp18 phage DNA. Nucleic Acids Res, 1992. 20(12): p. 3079-84.
  177. Husain, I. and A. Sancar, Binding of E. coli DNA photolyase to a defined substrate containing a single T mean value of T dimer. Nucleic Acids Res, 1987. 15(3): p. 1109- 20. Literatur 201
  178. Sakai, T., et al., Arabidopsis nph1 and npl1: blue light receptors that mediate both phototropism and chloroplast relocation. Proc Natl Acad Sci U S A, 2001. 98(12): p. 6969-74.
  179. Han, Y., et al., A eukaryotic BLUF domain mediates light-dependent gene expression in the purple bacterium Rhodobacter sphaeroides 2.4.1. Proc. Natl. Acad. Sci. U S A, 2004. 101(33): p. 12306-11.
  180. Pokorny, R., et al., Recognition and repair of UV lesions in loop structures of duplex DNA by DASH-type cryptochrome. Proc Natl Acad Sci U S A, 2008. 105(52): p. 21023-7.
  181. Sanger, F., S. Nicklen, and A.R. Coulson, DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A, 1977. 74(12): p. 5463-7.
  182. Johnson, J.L., et al., Identification of the second chromophore of Escherichia coli and yeast DNA photolyases as 5,10-methenyltetrahydrofolate. Proc Natl Acad Sci U S A, 1988. 85(7): p. 2046-50.
  183. Smith, P.K., et al., Measurement of protein using bicinchoninic acid. Anal Biochem, 1985. 150(1): p. 76-85.
  184. Setlow, R.B. and W.L. Carrier, Pyrimidine dimers in ultraviolet-irradiated DNA's. J Mol Biol, 1966. 17(1): p. 237-54.
  185. Ravanat, J.L., T. Douki, and J. Cadet, Direct and indirect effects of UV radiation on DNA and its components. J Photochem Photobiol B, 2001. 63(1-3): p. 88-102.
  186. Song, S.H., et al., Absorption and fluorescence spectroscopic characterization of cryptochrome 3 from Arabidopsis thaliana. J Photochem Photobiol B, 2006. 85(1): p. 1-16.
  187. Harper, S.M., L.C. Neil, and K.H. Gardner, Structural basis of a phototropin light switch. Science, 2003. 301(5639): p. 1541-4.
  188. Iseki, M., et al., A blue-light-activated adenylyl cyclase mediates photoavoidance in Euglena gracilis. Nature, 2002. 415(6875): p. 1047-51.


* Das Dokument ist im Internet frei zugänglich - Hinweise zu den Nutzungsrechten