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Dynamics and efficiency of photoswitching in biliverdin-binding phytochromes†

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Abstract

The light-driven conversions between the dark-adapted and the photoproduct state were recorded for bacteriophytochromes (BphP) carrying biliverdin IXα (BV) as chromophore by time-resolved absorption spectroscopy. BphPs can be photoswitched between a red absorbing (Pr, maximum at ca. 700 nm) and a far-red/near-infrared (Pfr, maximum at ca. 750 nm) absorbing state, thereby showing a considerable red-shift with respect to plant phytochromes. Representatives for BphPs studied here are: PstBphP1 from Pseudomonas syringae pv. tomato, for which Pfr is the photoproduct; the bathy-phytochrome PaBphP from Pseudomonas aeruginosa for which instead Pfr is the thermally stable parental state. The third BphP-like protein was FphA from the fungus Aspergillus nidulans, a eukaryotic protein also carrying BV as a chromophore, for which Pr is considered to be the dark-adapted state. All three BphPs show a canonical modular arrangement with a three-domain photosensory module (PAS-GAF-PHY) and a histidine-kinase (HK) signalling domain. The quantum yields for Pr-to-Pfr photoconversion are in the range 0.02–0.12, and 0.04–0.08 for the Pfr-to-Pr route. Photoproducts of both bacterial phytochromes thermally recovered in the dark, whereas for the fungal protein (FphA) both Pr and Pfr forms are thermally stable for days and could be interconverted only by selective irradiation. The photoinduced reactions of all three BV-phytochromes are in general kinetically less complex than those of plant phytochromes, with the notable exception of the Pr-to-Pfr route for PstBphP1. By contrast in the Pfr-to-Pr conversion of FphAN753 the final product is already formed during the very early steps of the process, without formation of any further intermediates: to our knowledge it is the first phytochrome showing this behavior. All three proteins investigated are weakly fluorescent in the Pr form, with a maximum fluorescence quantum yield of 0.02 (PaBphP), and have undetectable fluorescence in the Pfr state.

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Notes and references

  1. K. Anders and L.-O. Essen, The family of phytochrome-like photoreceptors: diverse, complex and multi-colored, but very useful, Curr. Opin. Struct. Biol., 2015, 35, 7–16.

    Article  CAS  PubMed  Google Scholar 

  2. S. Nagano, From photon to signal in phytochromes: similarities and differences between prokaryotic and plant phytochromes, J. Plant Res., 2016, 129, 123–135.

    Article  CAS  PubMed  Google Scholar 

  3. C. Mandalari, A. Losi and W. Gärtner, Distance-tree analysis, distribution and co-presence of bilin- and flavinbinding prokaryotic photoreceptors for visible light, Photochem. Photobiol. Sci., 2013, 12, 1144–1157.

    Article  CAS  PubMed  Google Scholar 

  4. A. L. Mitchell, T. K. Attwood, P. C. Babbitt, M. Blum, P. Bork, A. Bridge, S. D. Brown, H.-Y. Chang, S. El-Gebali, M. I. Fraser, J. Gough, D. R. Haft, H. Huang, I. Letunic, R. Lopez, A. Luciani, F. Madeira, A. Marchler-Bauer, H. Mi, D. A. Natale, M. Necci, G. Nuka, C. Orengo, A. P. Pandurangan, T. Paysan-Lafosse, S. Pesseat, S. C. Potter, M. A. Qureshi, N. D. Rawlings, N. Redaschi, L. J. Richardson, C. Rivoire, G. A. Salazar, A. Sangrador- Vegas, C. J. A. Sigrist, I. Sillitoe, G. G. Sutton, N. Thanki, P. D. Thomas, S. C. E. Tosatto, S.-Y. Yong and R. D. Finn, InterPro in 2019: improving coverage, classification and access to protein sequence annotations, Nucleic Acids Res., 2019, 47, D351–D360.

    Article  CAS  PubMed  Google Scholar 

  5. K. Fushimi and R. Narikawa, Cyanobacteriochromes: photoreceptors covering the entire UV-to-visible spectrum, Curr. Opin. Struct. Biol., 2019, 57, 39–46.

    Article  CAS  PubMed  Google Scholar 

  6. G. Gourinchas, S. Etzl and A. Winkler, Bacteriophytochromes –from informative model systems of phytochrome function to powerful tools in cell biology, Curr. Opin. Struct. Biol., 2019, 57, 72–83.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. M. G. Müller, I. Lindner, I. Martin, W. Gärtner and A. R. Holzwarth, Femtosecond Kinetics of Photoconversion of the Higher Plant Photoreceptor Phytochrome Carrying Native and Modified Chromophores, Biophys. J., 2008, 94, 4370–4382.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  8. J. A. Ihalainen, H. Takala and H. Lehtivuori, Fast Photochemistry of Prototypical Phytochromes-A Species vs. Subunit Specific Comparison, Front. Mol. Biosci., 2015, 2, 75.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  9. A. Björling, O. Berntsson, H. Lehtivuori, H. Takala, A. J. Hughes, M. Panman, M. Hoernke, S. Niebling, L. Henry, R. Henning, I. Kosheleva, V. Chukharev, N. V. Tkachenko, A. Menzel, G. Newby, D. Khakhulin, M. Wulff, J. A. Ihalainen and S. Westenhoff, Structural photoactivation of a full-length bacterial phytochrome, Sci. Adv., 2016, 2, e1600920.

  10. D. J. Heyes, S. J. O. Hardman, M. N. Pedersen, J. Woodhouse, E. De La Mora, M. Wulff, M. Weik, M. Cammarata, N. S. Scrutton and G. Schirò, Light-induced structural changes in a full-length cyanobacterial phytochrome probed by time-resolved X-ray scattering, Commun. Biol., 2019, 2, 1.

    Article  PubMed  PubMed Central  Google Scholar 

  11. I. Chizhov, B. Zorn, D. J. Manstein and W. Gärtner, Kinetic and Thermodynamic Analysis of the Light-induced Processes in Plant and Cyanobacterial Phytochromes, Biophys. J., 2013, 105, 2210–2220.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. A. Remberg, I. Lindner, T. Lamparter, J. Hughes, C. Kneip, P. Hildebrandt, S. E. Braslavsky, W. Gärtner and K. Schaffner, Raman Spectroscopic and Light-Induced Kinetic Characterization of a Recombinant Phytochrome of the Cyanobacterium Synechocystis, Biochemistry, 1997, 36, 13389–13395.

    Article  CAS  PubMed  Google Scholar 

  13. S. E. Braslavsky, W. Gärtner and K. Schaffner, Phytochrome photoconversion, Plant, Cell Environ., 1997, 20, 700–706.

    Article  CAS  Google Scholar 

  14. J. J. van Thor, B. Borucki, W. Crielaard, H. Otto, T. Lamparter, J. Hughes, K. J. Hellingwerf and M. P. Heyn, Light-induced proton release and proton uptake reactions in the cyanobacterial phytochrome Cph1., Biochemistry, 2001, 40, 11460–11471.

    Article  PubMed  CAS  Google Scholar 

  15. B. Borucki, D. von Stetten, S. Seibeck, T. Lamparter, N. Michael, M. A. Mroginski, H. Otto, D. H. Murgida, M. P. Heyn and P. Hildebrandt, Light-induced Proton Release of Phytochrome Is Coupled to the Transient Deprotonation of the Tetrapyrrole Chromophore, J. Biol. Chem., 2005, 280, 34358–34364.

    Article  CAS  PubMed  Google Scholar 

  16. B. Borucki, S. Seibeck, M. P. Heyn and T. Lamparter, Characterization of the Covalent and Noncovalent Adducts of Agp1 Phytochrome Assembled with Biliverdin and Phycocyanobilin by Circular Dichroism and Flash Photolysis, Biochemistry, 2009, 48, 6305–6317.

    Article  CAS  PubMed  Google Scholar 

  17. B. Zienicke, I. Molina, R. Glenz, P. Singer, D. Ehmer, F. V. Escobar, P. Hildebrandt, R. Diller and T. Lamparter, Unusual spectral properties of bacteriophytochrome Agp2 result from a deprotonation of the chromophore in the redabsorbing form Pr., J. Biol. Chem., 2013, 288, 31738–31751.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. F. Velazquez Escobar, D. von Stetten, M. Günther-Lütkens, A. Keidel, N. Michael, T. Lamparter, L.-O. Essen, J. Hughes, W. Gärtner, Y. Yang, K. Heyne, M. A. Mroginski and P. Hildebrandt, Conformational heterogeneity of the Pfr chromophore in plant and cyanobacterial phytochromes, Front. Mol. Biosci., 2015, 2, 37.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  19. F. Velazquez Escobar, P. Piwowarski, J. Salewski, N. Michael, M. Fernandez Lopez, A. Rupp, B. M. Qureshi, P. Scheerer, F. Bartl, N. Frankenberg-Dinkel, F. Siebert, M. Andrea Mroginski and P. Hildebrandt, A protonationcoupled feedback mechanism controls the signalling process in bathy phytochromes, Nat. Chem., 2015, 7, 423–430.

    Article  CAS  PubMed  Google Scholar 

  20. S.-H. Bhoo, S. J. Davis, J. Walker, B. Karniol and R. D. Vierstra, Bacteriophytochromes are photochromic histidine kinases using a biliverdin chromophore, Nature, 2001, 414, 776–779.

    Article  CAS  PubMed  Google Scholar 

  21. S. I. Beale, Biosynthesis of phycobilins, Chem. Rev., 1993, 93, 785–802.

    Article  CAS  Google Scholar 

  22. M. E. Auldridge and K. T. Forest, Bacterial phytochromes: More than meets the light, Crit. Rev. Biochem. Mol. Biol., 2011, 46, 67–88.

    Article  CAS  PubMed  Google Scholar 

  23. J. R. Wagner, J. S. Brunzelle, K. T. Forest and R. D. Vierstra, A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome, Nature, 2005, 438, 325–331.

    Article  CAS  PubMed  Google Scholar 

  24. T. Lamparter, N. Krauß and P. Scheerer, Phytochromes from Agrobacterium fabrum, Photochem. Photobiol., 2017, 93, 642–655.

    Article  CAS  PubMed  Google Scholar 

  25. D. Buhrke, U. Kuhlmann, N. Michael and P. Hildebrandt, The Photoconversion of Phytochrome Includes an Unproductive Shunt Reaction Pathway, ChemPhysChem, 2018, 19, 566–570.

    Article  CAS  PubMed  Google Scholar 

  26. G. A. Beattie, B. M. Hatfield, H. Dong and R. S. McGrane, Seeing the Light: The Roles of Red- and Blue-Light Sensing in Plant Microbes, Annu. Rev. Phytopathol., 2018, 56, 41–66.

    Article  CAS  PubMed  Google Scholar 

  27. K. G. Chernov, T. A. Redchuk, E. S. Omelina and V. V. Verkhusha, Near-Infrared Fluorescent Proteins, Biosensors, and Optogenetic Tools Engineered from Phytochromes, Chem. Rev., 2017, 117, 6423–6446.

    Article  CAS  PubMed  Google Scholar 

  28. R. Tasler, T. Moises and N. Frankenberg-Dinkel, Biochemical and spectroscopic characterization of the bacterial phytochrome of Pseudomonas aeruginosa, FEBS J., 2005, 272, 1927–1936.

    Article  CAS  PubMed  Google Scholar 

  29. R. Shah, J. Schwach, N. Frankenberg-Dinkel and W. Gärtner, Complex formation between heme oxygenase and phytochrome during biosynthesis in Pseudomonas syringae pv. tomato, Photochem. Photobiol. Sci., 2012, 11, 1026.

    Article  CAS  PubMed  Google Scholar 

  30. S. Brandt, D. von Stetten, M. Günther, P. Hildebrandt and N. Frankenberg-Dinkel, The fungal phytochrome FphA from Aspergillus nidulans., J. Biol. Chem., 2008, 283, 34605–34614.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. J. Mailliet, G. Psakis, K. Feilke, V. Sineshchekov, L.-O. Essen and J. Hughes, Spectroscopy and a High-Resolution Crystal Structure of Tyr263 Mutants of Cyanobacterial Phytochrome Cph1, J. Mol. Biol., 2011, 413, 115–127.

    Article  CAS  PubMed  Google Scholar 

  32. F. Pennacchietti, A. Losi, X.-L. Xu, K.-H. Zhao, W. Gärtner, C. Viappiani, F. Cella, A. Diaspro and S. Abbruzzetti, Photochromic conversion in a red/green cyanobacteriochrome from Synechocystis PCC6803: Quantum yields in solution and photoswitching dynamics in living E. coli cells, Photochem. Photobiol. Sci., 2015, 14, 229–237.

    Article  CAS  PubMed  Google Scholar 

  33. A. Losi, H. R. Bonomi, N. Michael, K. Tang and K.-H. Zhao, Time-Resolved Energetics of Photoprocesses in Prokaryotic Phytochrome-Related Photoreceptors, Photochem. Photobiol., 2017, 93, 733–740.

    Article  CAS  PubMed  Google Scholar 

  34. J. M. Beechem, Global analysis of biochemical and biophysical data, Methods Enzymol., 1992, 210, 37–54.

    Article  CAS  PubMed  Google Scholar 

  35. I. Chizhov, D. S. Chernavskii, M. Engelhard, K. H. Mueller, B. V. Zubov and B. Hess, Spectrally silent transitions in the bacteriorhodopsin photocycle, Biophys. J., 1996, 71, 2329–2345.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. T. Lamparter, F. Mittmann, W. Gärtner, T. Börner, E. Hartmann and J. Hughes, Characterization of recombinant phytochrome from the cyanobacterium Synechocystis, Proc. Natl. Acad. Sci. U. S. A., 1997, 94, 11792–11797.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. L. H. Pratt, Photochemistry of high molecular weight phytochrome in vitro, Photochem. Photobiol., 1975, 22, 33–36.

    Article  CAS  PubMed  Google Scholar 

  38. L. H. Otero, S. Klinke, J. Rinaldi, F. Velázquez-Escobar, M. A. Mroginski, M. Fernández López, F. Malamud, A. A. Vojnov, P. Hildebrandt, F. A. Goldbaum and H. R. Bonomi, Structure of the Full-Length Bacteriophytochrome from the Plant Pathogen Xanthomonas campestris Provides Clues to its Long-Range Signaling Mechanism, J. Mol. Biol., 2016, 428, 3702–3720.

    Article  CAS  PubMed  Google Scholar 

  39. C. Schumann, R. Groß, N. Michael, T. Lamparter and R. Diller, Sub-Picosecond Mid-Infrared Spectroscopy of Phytochrome Agp1 fromAgrobacterium tumefaciens, ChemPhysChem, 2007, 8, 1657–1663.

    Article  CAS  PubMed  Google Scholar 

  40. C. Schumann, R. Gross, M. M. N. Wolf, R. Diller, N. Michael and T. Lamparter, Subpicosecond midinfrared spectroscopy of the Pfr reaction of phytochrome Agp1 from Agrobacterium tumefaciens., Biophys. J., 2008, 94, 3189–3197.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. H. Lehtivuori, I. Rissanen, H. Takala, J. Bamford, N. V. Tkachenko and J. A. Ihalainen, Fluorescence Properties of the Chromophore-Binding Domain of Bacteriophytochrome from Deinococcus radiodurans, J. Phys. Chem. B, 2013, 117, 11049–11057.

    Article  CAS  PubMed  Google Scholar 

  42. P. Eilfeld and W. Rüdiger, Absorption Spectra of Phytochrome Intermediates, Z. Naturforsch., C: J. Biosci., 1985, 40, 109–114.

    Article  Google Scholar 

  43. J. R. Wagner, J. Zhang, D. von Stetten, M. Günther, D. H. Murgida, M. A. Mroginski, J. M. Walker, K. T. Forest, P. Hildebrandt and R. D. Vierstra, Mutational Analysis of Deinococcus radiodurans Bacteriophytochrome Reveals Key Amino Acids Necessary for the Photochromicity and Proton Exchange Cycle of Phytochromes, J. Biol. Chem., 2008, 283, 12212–12226.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. J. J. van Thor, B. Borucki, W. Crielaard, H. Otto, T. Lamparter, J. Hughes, K. J. Hellingwerf and M. P. Heyn, Light-induced proton release and proton uptake reactions in the cyanobacterial phytochrome Cph1., Biochemistry, 2001, 40, 11460–11471.

    Article  PubMed  CAS  Google Scholar 

  45. M. Biasini, S. Bienert, A. Waterhouse, K. Arnold, G. Studer, T. Schmidt, F. Kiefer, T. Gallo Cassarino, M. Bertoni, L. Bordoli and T. Schwede, SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information., Nucleic Acids Res., 2014, 42, W252–W258.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. S. Altschul, T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller and D. J. Lipman, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 1997, 25, 3389–3402.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. L.-O. Essen, J. Mailliet and J. Hughes, The structure of a complete phytochrome sensory module in the Pr ground state., Proc. Natl. Acad. Sci. U. S. A., 2008, 105, 14709–14714.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. H. Takala, A. Björling, O. Berntsson, H. Lehtivuori, S. Niebling, M. Hoernke, I. Kosheleva, R. Henning, A. Menzel, J. A. Ihalainen and S. Westenhoff, Signal amplification and transduction in phytochrome photosensors., Nature, 2014, 509, 245–248.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. H. Takala, H. K. Lehtivuori, O. Berntsson, A. Hughes, R. Nanekar, S. Niebling, M. Panman, L. Henry, A. Menzel, S. Westenhoff and J. A. Ihalainen, On the (un)coupling of the chromophore, tongue interactions, and overall conformation in a bacterial phytochrome, J. Biol. Chem., 2018, 293, 8161–8172.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. A. T. Ulijasz and R. D. Vierstra, Phytochrome structure and photochemistry: recent advances toward a complete molecular picture, Curr. Opin. Plant Biol., 2011, 14, 498–506.

    Article  CAS  PubMed  Google Scholar 

  51. X. Yang, J. Kuk and K. Moffat, Conformational differences between the Pfr and Pr states in Pseudomonas aeruginosa bacteriophytochrome., Proc. Natl. Acad. Sci. U. S. A., 2009, 106, 15639–15644.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Authors and Affiliations

  1. Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7/A, 43124, Parma, Italy

    Eleonora Consiglieri, Cristiano Viappiani, Stefania Abbruzzetti & Aba Losi

  2. Max-Planck-Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany

    Alexander Gutt

  3. Institute for Analytical Chemistry, University of Leipzig, Linnéstrasse 3, 04103, Leipzig, Germany

    Wolfgang Gärtner

  4. Institute for Physical Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany

    Luiz Schubert

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  1. Eleonora Consiglieri
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Correspondence to Eleonora Consiglieri.

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Electronic supplementary information (ESI) available. See DOI: 10.1039/ c9pp00264b

Present affiliation of L. S.: Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany.

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Consiglieri, E., Gutt, A., Gärtner, W. et al. Dynamics and efficiency of photoswitching in biliverdin-binding phytochromes†. Photochem Photobiol Sci 18, 2484–2496 (2019). https://doi.org/10.1039/c9pp00264b

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