Abstract
The Bacillus subtilis protein YtvA is related to plant phototropins in that it senses UVA—blue-light by means of the flavin binding LOV domain, linked to a nucleotide-binding STAS domain. The structural basis for interdomain interactions and functional regulation are not known. Here we report the conformational analysis of three YtvA constructs, by means of size exclusion chromatography, circular dichroism (CD) and molecular docking simulations. The isolated YtvA-LOV domain (YLOV, aa 25–126) has a strong tendency to dimerize, prevented in full-length YtvA, but still observed in YLOV carrying the N-terminal extension (N-YLOV, aa 1–126). The analysis of CD data shows that both the N-terminal cap and the linker region (aa 127–147) between the LOV and the STAS domain are helical and that the central β-scaffold is distorted in the LOV domains dimers. The involvement of the central β-scaffold in dimerization is supported by docking simulation of the YLOV dimer and the importance of this region is highlighted by light-induced conformational changes, emerging from the CD data analysis. In YtvA, the β-strand fraction is notably less distorted and distinct light-driven changes in the loops/turn fraction are detected. The data uncover a common surface for LOV–LOV and intraprotein interaction, involving the central β-scaffold, and offer hints to investigate the molecular basis of light-activation and regulation in LOV proteins.
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M. H. Hefti, K. J. Francoijs, S. C. de Vries, R. Dixon, J. Vervoort, The PAS fold: A redefinition of the PAS domain based upon structural prediction, FEBS J., 2004, 271, 1198–1208.
W. R. Briggs, C. F. Beck, A. R. Cashmore, J. M. Christie, J. Hughes, J. A. Jarillo, T. Kagawa, H. Kanegae, E. Liscum, A. Nagatani, K. Okada, M. Salomon, W. Rüdiger, T. Sakai, M. Takano, M. Wada, J. C. Watson, The phototropin family of photoreceptors, Plant Cell, 2001, 13, 993–997.
W. R. Briggs, J. M. Christie, Phototropins 1 and 2: versatile plant blue-light receptors, Trends Plant Sci., 2002, 7, 204–210.
R. Banerjee, A. Batschauer, Plant blue-light receptors, Planta, 2005, 220, 498–502.
E. Huala, P. W. Oeller, E. Liscum, I. S. Han, E. Larsen, W. R. Briggs, Arabidopsis NPH1: A Protein Kinase with a Putative Redox-Sensing Domain, Science, 1997, 278, 2120–2123.
E. Knieb, M. Salomon, W. Rüdiger, Autophosphorylation, electrophoretic mobility and immunoreaction of oat Phototropin 1 Under UV and Blue Light, Photochem. Photobiol., 2005, 81, 177–182.
M. Salomon, J. M. Christie, E. Knieb, U. Lempert, W. R. Briggs, Photochemical and mutational analysis of the FMN-binding domains of the plant blue light receptor phototropin, Biochemistry, 2000, 39, 9401–9410.
M. Salomon, W. Eisenreich, H. Dürr, E. Scleicher, E. Knieb, V. Massey, W. Rüdiger, F. Müller, A. Bacher, G. Richter, An optomechanical transducer in the blue light receptor phototropin from Avena sativa, Proc. Natl. Acad. Sci. U. S. A., 2001, 98, 12357–12361.
M. Kasahara, T. E. Swartz, M. A. Olney, A. Onodera, N. Mochizuki, H. Fukuzawa, E. Asamizu, S. Tabata, H. Kanegae, M. Takano, J. M. Christie, A. Nagatani, W. R. Briggs, Photochemical properties of the flavin mononucleotide-binding domains of the phototropins from Arabidopsis, rice, and Chlamydomonas reinhardtii, Plant Physiol., 2002, 129, 762–773.
S. Crosson, K. Moffat, Photoexcited structure of a plant photoreceptor domain reveals a light-driven molecular switch, Plant Cell, 2002, 14, 1067–1075.
C. W. M. Kay, E. Schleicher, A. Kuppig, H. Hofner, W. Rüdiger, M. Schleicher, M. Fischer, A. Bacher, S. Weber, G. Richter, Blue light perception in plants. Detection and characterization of a light-induced neutral flavin radical in a C450A mutant of phototropin, J. Biol. Chem., 2003, 278, 10973–10982.
J. T. M. Kennis, S. Crosson, M. Gauden, I. H. M. van Stokkum, K. Moffat, R. van Grondelle, Primary Reactions of the LOV2 Domain of Phototropin, a Plant Blue-Light Photoreceptor, Biochemistry, 2003, 42, 3385–3392.
T. E. Swartz, S. B. Corchnoy, J. M. Christie, J. W. Lewis, I. Szundi, W. R. Briggs, R. A. Bogomolni, The photocycle of a flavin-binding domain of the blue light photoreceptor phototropin, J. Biol. Chem., 2001, 276, 36493–36500.
T. Kottke, J. Heberle Dominic Hehn, P. Hegemann, Phot-LOV1: Photocycle of a Blue-Light Receptor Domain from the Green Alga Chlamydomonas reinhardtii, Biophys. J., 2003, 84, 1192–1201.
D. Matsuoka, S. Tokutomi, Blue light-regulated molecular switch of Ser/Thr kinase in phototropin, Proc. Natl. Acad. Sci. U. S. A., 2005, 102, 13337–13342.
J. M. Christie, T. E. Swartz, R. A. Bogomolni, W. R. Briggs, Phototropin LOV domains exhibit distinct roles in regulating photoreceptor function, Plant J., 2002, 32, 205–219.
S. Crosson, S. Rajagopal, K. Moffat, The LOV domain family: photoresponsive signaling modules coupled to diverse output domains, Biochemistry, 2003, 42, 2–10.
A. Losi, The bacterial counterparts of plants phototropins, Photochem. Photobiol. Sci., 2004, 3, 566–574.
A. Losi, E. Polverini, B. Quest, W. Gärtner, First evidence for phototropin-related blue-light receptors in prokaryotes, Biophys. J., 2002, 82, 2627–2634.
U. Krauss, A. Losi, W. Gärtner, K.-E. Jaeger, T. Eggert, Initial characterization of a blue-light sensing, phototropin-related protein from Pseudomonas putida: a paradigm for an extended LOV construct, Phys. Chem. Chem. Phys., 2005, 7, 2229–2236.
E. Schleicher, R. M. Kowalczyk, C. W. M. Kay, P. Hegemann, A. Bacher, M. Fischer, R. Bittl, G. Richter, S. Weber, On the reaction mechanism of adduct formation in LOV domains of the plant blue-light receptor phototropin, J. Am. Chem. Soc., 2004, 126, 11067–11076.
S. Crosson, K. Moffat, Structure of a flavin-binding plant photoreceptor domain: insights into light-mediated signal transduction, Proc. Natl. Acad. Sci. U. S. A., 2001, 98, 2995–3000.
R. Fedorov, I. Schlichting, E. Hartmann, T. Domratcheva, M. Fuhrmann, P. Hegemann, Crystal structures and molecular mechanism of a light-induced signaling switch: the Phot-LOV1 domain from Chlamydomonas reinhardtii, Biophys. J., 2003, 84, 2492–2501.
S. M. Harper, L. C. Neil, K. H. Gardner, Structural basis of a phototropin light switch, Science, 2003, 301, 1541–1544.
S. M. Harper, J. M. Christie, K. H. Gardner, Disruption of the LOV-Jalpha helix interaction activates phototropin kinase activity, Biochemistry, 2004, 43, 16184–16192.
A. Losi, in Flavin photochemistry and photobiology, ed. D.-P. Häder and G. Jori, Elsevier, Amsterdam, 4th edn, 2006, ch. 10, pp. 223–276.
T. Eitoku, Y. Nakasone, D. Matsuoka, S. Tokutomi, M. Terazima, Conformational dynamics of phototropin 2 LOV2 domain with the linker upon photoexcitation, J. Am. Chem. Soc., 2005, 127, 13238–13244.
B. L. Taylor, I. B. Zhulin, PAS domains: internal sensors of oxygen, redox potential and light, Microbiol. Mol. Biol. Rev., 1999, 63, 479–506.
M. A. Gilles-Gonzalez, G. Gonzalez, Heme-based sensors: defining characteristics, recent developments, and regulatory hypotheses, J. Inorg. Biochem., 2005, 99, 1–22.
M. Salomon, U. Lempert, W. Rüdiger, Dimerization of the plant photoreceptor phototropin is probably mediated by the LOV1 domain, FEBS Lett., 2004, 572, 8–10.
Y. Nakasone, T. Eitoku, D. Matsuoka, S. Tokutomi, M. Terazima, Kinetic Measurement of Transient Dimerization and Dissociation Reactions of Arabidopsis Phototropin 1 LOV2 Domain, Biophys. J., 2006, 91, 645–653.
M. Nakasako, D. Matsuoka, K. Zikihara, S. Tokutomi, Quaternary structure of LOV-domain containing polypeptide of Arabidopsis FKF1 protein, FEBS Lett., 2005, 579, 1067–1071.
M. Nakasako, T. Iwata, D. Matsuoka, S. Tokutomi, Light-Induced Structural Changes of LOV Domain-Containing Polypeptides from Arabidopsis Phototropin 1 and 2 Studied by Small-Angle X-ray Scattering, Biochemistry, 2004, 43, 14881–1489.
P. Ballario, C. Talora, D. Galli, H. Linden, G. Macino, Roles in dimerization and blue light photoresponse of the PAS and LOV domains of Neurospora crassa white collar proteins, Mol. Microbiol., 1998, 29, 719–729.
L. Aravind, E. V. Koonin, The STAS domain a link between anion transporters and antisigma-factor antagonists, Curr. Biol., 2000, 10, R53–R55.
S. Akbar, T. A. Gaidenko, K. Min, M. O’Reilly, K. M. Devine, C. W. Price, New family of regulators in the environmental signaling pathway which activates the general stress transcription factor of Bacillus subtilis, J. Bacteriol., 2001, 183, 1329–1338.
T. A. Gaidenko, T. J. Kim, A. L. Weigel, M. S. Brody, C. W. Price, The blue-light receptor YtvA acts in the environmental stress signaling pathway of Bacillus subtilis, J. Bacteriol., 2006, 188, 6387–6395.
M. Avila-Perez, K. J. Hellingwerf, R. Kort, Blue light activates the sigmaB-dependent stress response of Bacillus subtilis via YtvA, J. Bacteriol., 2006, 188, 6411–6414.
V. Buttani, A. Losi, E. Polverini, W. Gärtner, Blue news: NTP binding properties of the blue-light sensitive YtvA protein from Bacillus subtilis, FEBS Lett., 2006, 580, 3818–3822.
S. M. Najafi, D. A. Harris, M. D. Yudkin, The SpoIIAA protein of Bacillus subtilis has GTP-binding properties, J. Bacteriol., 1996, 178, 6632–6634.
A. Losi, E. Ghiraldelli, S. Jansen, W. Gärtner, Mutational effects on protein structural changes and interdomain interactions in the blue-light sensing LOV protein YtvA, Photochem. Photobiol., 2005, 81, 1145–1152.
A. Losi, B. Quest, W. Gärtner, Listening to the blue: the time-resolved thermodynamics of the bacterial blue-light receptor YtvA and its isolated LOV domain, Photochem. Photobiol. Sci., 2003, 2, 759–766.
A. Perczel, M. Hollosi, G. Tusnady, G. D. Fasman, Convex constraint analysis: a natural deconvolution of circular dichroism curves of proteins, Protein Eng., 1991, 4, 669–679.
A. Perczel, K. Park, G. D. Fasman, Analysis of the circular dichroism spectrum of proteins using the convex constraint algorithm: A practical guide, Anal. Biochem., 1992, 203, 83–93.
I. R. Bates, P. Matharu, N. Ishiyama, D. Rochon, D. D. Wood, E. Polverini, M. A. Moscarello, N. J. Viner, G. Harauz, Characterization of a Recombinant Murine 18.5-kDa Myelin Basic Protein, Protein Expression Purif., 2000, 20, 285–299.
C. Combet, C. Blanchet, C. Geourjon, G. Deleage, NPS@: Network Protein Sequence Analysis, Trends Biochem. Sci., 2000, 25, 147–150.
S. R. Comeau, D. W. Gatchell, S. Vajda, C. J. Camacho, ClusPro: An automated docking and discrimination method for the prediction of protein complexes, Bioinformatics, 2004, 20, 45–50.
J. G. Mandell, V. A. Roberts, M. E. Pique, V. Kotlovyi, J. C. Mitchell, E. Nelson, I. Tsigelny, L. F. Ten Eyck, Protein docking using continuum electrostatics and geometric fit, Protein Eng., 2001, 14, 105–113.
R. Chen, L. Li, Z. Weng, ZDOCK: an initial-stage protein-docking algorithm, Proteins, 2003, 52, 80–87.
L. Willard, A. Ranjan, H. Zhang, H. Monzavi, R. F. Boyko, B. D. Sykes, D. S. Wishart, VADAR: a web server for quantitative evaluation of protein structure quality, Nucleic Acids Res., 2003, 31, 3316–3319.
R. A. Laskowski, M. W. MacArthur, D. S. Moss, J. M. Thornton, PROCHECK-A program to check the stereochemical quality of protein structures, J. Appl. Crystallogr., 1993, 26, 283–291.
R. W. Hooft, G. Vriend, C. Sander, E. E. Abola, Errors in protein structures, Nature, 1996, 381, 272–272.
C. Colovos, T. O. Yeates, Verification of protein structures: patterns of nonbonded atomic interactions, Protein Sci., 1993, 2, 1511–1519.
R. Luthy, J. U. Bowie, D. Eisenberg, Assessment of protein models with three-dimensional profiles, Nature, 1992, 356, 83–85.
J. Pontius, J. Richelle, S. J. Wodak, Deviations from standard atomic volumes as a quality measure for protein crystal structures, J. Mol. Biol., 1996, 264, 121–136.
J. R. Bradford, D. R. Westhead, Improved prediction of protein-protein binding sites using a support vector machines approach, Bioinformatics, 2005, 21, 1487–1494.
T. Kortemme, D. E. Kim, D. Baker, Computational alanine scanning of protein–protein interfaces, Sci. STKE, 2004, 2004219, pl2.
N. Sreerama, S. Y. Venyaminov, R. W. Woody, Estimation of protein secondary structure from circular dichroism spectra: inclusion of denatured proteins with native proteins in the analysis, Anal. Biochem., 2000, 287, 243–251.
N. Sreerama, S. Y. Venyaminov, R. W. Woody, Estimation of the number of alpha-helical and beta-strand segments in proteins using circular dichroism spectroscopy, Protein Sci., 1999, 8, 370–380.
K. Matsuo, R. Yonehara, K. Gekko, Improved Estimation of the Secondary Structures of Proteins by Vacuum-Ultraviolet Circular Dichroism Spectroscopy, J. Biochem., 2005, 138, 79–88.
N. Sreerama, R. W. Woody, Structural composition of betaI- and betaII-proteins, Protein Sci., 2003, 12, 384–388.
N. J. Greenfield, Analysis of circular dichroism data, Methods Enzymol., 2004, 383, 282–317.
R. W. Woody, A. Koslowski, Recent developments in the electronic spectroscopy of amides and alpha-helical polypeptides, Biophys. Chem., 2002, 101–102, 535–551.
N. J. Greenfield, Methods to estimate the conformation of proteins and polypeptides from circular dichroism data, Anal. Biochem., 1996, 235, 1–10.
C. T. Chang, C. S. Wu, J. T. Yang, Circular dichroic analysis of protein conformation: inclusion of the beta-turns, Anal. Biochem., 1978, 91, 13–31.
T. Iwata, D. Nozaki, S. Tokutomi, H. Kandori, Comparative investigation of the LOV1 and LOV2 domains in Adiantum Phytochrome3, Biochemistry, 2005, 44, 7427–7434.
S. B. Corchnoy, T. E. Swartz, J. W. Lewis, I. Szundi, W. R. Briggs, R. A. Bogomolni, Intramolecular proton transfers and structural changes during the photocycle of the LOV2 domain of phototropin 1, J. Biol. Chem., 2003, 278, 724–731.
T. Bednarz, A. Losi, W. Gärtner, P. Hegemann, J. Heberle, Functional variations among LOV domains as revealed by FT-IR difference spectroscopy, Photochem. Photobiol. Sci., 2004, 3, 575–579.
P. B. Card, P. J. A. Erbel, K. H. Gardner, Structural Basis of ARNT PAS-B dimerization: use of a common beta-sheet interface for hetero- and homodimerization, J. Mol. Biol., 2005, 353, 664–677.
H. J. Park, C. Suquet, J. D. Satterlee, C. Kang, Insights into signal transduction involving PAS domain oxygen-sensing heme proteins from the X-ray crystal structure of Escherichia Coli Dos Heme Domain (EcDosH), Biochemistry, 2004, 43, 2738–2746.
H. Miyatake, M. Mukai, S. Y. Park, S. Adachi, K. Tamura, H. Nakamura, K. Nakamura, T. Tsuchiya, T. Iizuka, Y. Shiro, Sensory mechanism of oxygen sensor FixL from Rhizobium meliloti: crystallographic, mutagenesis and resonance Raman spectroscopic studies, J. Mol. Biol., 2000, 301, 415–431.
W. Gong, B. Hao, S. S. Mansy, G. Gonzalez, M. A. Gilles-Gonzalez, M. K. Chan, Structure of a biological oxygen sensor: a new mechanism for heme-driven signal transduction, Proc. Natl. Acad. Sci. U. S. A., 1998, 95, 15177–15182.
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† Electronic supplementary information (ESI) available: Calculation of accessible and buried surface areas using the VADAR tool. See DOI:10.1039/b610375h
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Buttani, V., Losi, A., Eggert, T. et al. Conformational analysis of the blue-light sensing protein YtvA reveals a competitive interface for LOV—LOV dimerization and interdomain interactions. Photochem Photobiol Sci 6, 41–49 (2007). https://doi.org/10.1039/b610375h
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DOI: https://doi.org/10.1039/b610375h