Abstract
Phototropin (phot) is a blue light (BL) receptor kinase involved in the BL responses of several species, ranging from green algae to higher plants. Phot converts BL signals from the environment into biochemical signals that trigger cellular responses. In phot, the LOV1 and LOV2 domains of the N-terminal region utilize BL for cyclic photoreactions and regulate C-terminal serine/threonine kinase (STK) activity. LOV2–STK peptides are the smallest functional unit of phot and are useful for understanding regulation mechanisms. The combined analysis of spectroscopy and STK activity assay in Arabidopsis phots suggests that the decay speed of the photo-intermediate S390 in LOV2 is one of the factors contributing to light sensitive kinase activity. LOV2 and STK are thought to be adjacent to each other in LOV2–STK with small angle scattering (SAXS). BL irradiation induces LOV2–STK elongation, resulting in LOV2 shifting away from STK. The N- and C-terminal lateral regions of LOV2, A′α-helix, Jα-helix, and A′α/Aβ gap are responsible for the propagation of the BL signal to STK via conformational changes. The comparison between LOV2–STK and full-length phot from Chlamydomonas suggests that LOV1 is directly adjacent to LOV2 in LOV2–STK; therefore, LOV1 may indirectly regulate STK. The molecular mechanism of phot is discussed.
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References
Aihara Y, Yamamoto T, Okajima K, Yamamoto K, Suzuki T, Tokutomi S, Tanaka K, Nagatani A (2012) Mutations in N-terminal flanking region of blue light-sensing light-oxygen and voltage 2 (LOV2) domain disrupt its repressive activity on kinase domain in the Chlamydomonas phototropin. J Biol Chem 287:9901–9909
Bogre L, Okresz L, Henriques R, Anthony RG (2003) Growth signalling pathways in Arabidopsis and the AGC protein kinases. Trends Plant Sci 8:424–431
Chen M, Chory J, Fankhauser C (2004) Light signal transduction in higher plants. Annu Rev Genet 38:87–117
Cheng P, He Q, Yang Y, Wang L, Liu Y (2003) Functional conservation of light, oxygen, or voltage domains in light sensing. Proc Natl Acad Sci USA 100:5938–5943
Christie JM (2007) Phototropin blue-light receptors. Annu Rev Plant Biol 58:21–45
Christie JM, Reymond P, Powell GK, Bernasconi P, Raibekas AA, Liscum E, Briggs WR (1998) Arabidopsis NPH1: a flavoprotein with the properties of a photoreceptor for phototropism. Science 282:1698–1701
Christie JM, Salomon M, Nozue K, Wada M, Briggs WR (1999) LOV (light, oxygen, or voltage) domains of the blue-light photoreceptor phototropin (nph1): binding sites for the chromophore flavin mononucleotide. Proc Natl Acad Sci USA 96:8779–8783
Christie JM, Swartz TE, Bogomolni RA, Briggs WR (2002) Phototropin LOV domains exhibit distinct roles in regulating photoreceptor function. Plant J 32:205–219
Christie JM, Yang H, Richter GL, Sullivan S, Thomson CE, Lin J, Titapiwatanakun B, Ennis M, Kaiserli E, Lee OR, Adamec J, Peer WA, Murphy AS (2011) phot1 inhibition of ABCB19 primes lateral auxin fluxes in the shoot apex required for phototropism. PLoS Biol 9:e1001076
Christie JM, Hitomi K, Arvai AS, Hartfield KA, Mettlen M, Pratt AJ, Tainer JA, Getzoff ED (2012) Structural tuning of the fluorescent protein iLOV for improved photostability. J Biol Chem 287:22295–22304
Crosson S, Moffat K (2001) Structure of a flavin-binding plant photoreceptor domain: insights into light-mediated signal transduction. Proc Natl Acad Sci USA 98:2995–3000
Crosson S, Moffat K (2002) Photoexcited structure of a plant photoreceptor domain reveals a light-driven molecular switch. Plant Cell 14:1067–1075
de Carbonnel M, Davis P, Roelfsema MR, Inoue S, Schepens I, Lariguet P, Geisler M, Shimazaki K, Hangarter R, Fankhauser C (2010) The Arabidopsis PHYTOCHROME KINASE SUBSTRATE2 protein is a phototropin signaling element that regulates leaf flattening and leaf positioning. Plant Physiol 152:1391–1405
Demarsy E, Schepens I, Okajima K, Hersch M, Bergmann S, Christie J, Shimazaki K, Tokutomi S, Fankhauser C (2012) Phytochrome kinase Substrate 4 is phosphorylated by the phototropin 1 photoreceptor. EMBO J 31:3457–3467
Eitoku T, Nakasone Y, Matsuoka D, Tokutomi S, Terazima M (2005) Conformational dynamics of phototropin 2 LOV2 domain with the linker upon photoexcitation. J Am Chem Soc 127:13238–13244
Fedorov R, Schlichting I, Hartmann E, Domratcheva T, Fuhrmann M, Hegemann P (2003) Crystal structures and molecular mechanism of a light-induced signaling switch: the Phot–LOV1 domain from Chlamydomonas reinhardtii. Biophys J 84:2474–2482
Franklin KA, Quail PH (2010) Phytochrome functions in Arabidopsis development. J Exp Bot 61:11–24
Freddolino PL, Gardner KH, Schulten K (2013) Signaling mechanisms of LOV domains: new insights from molecular dynamics studies. Photochem Photobiol Sci 12:1158–1170
Guinier A, Fournet G (1955) Small-angle scattering of X-rays. Wiley, New York
Guo H, Kottke T, Hegemann P, Dick B (2005) The phot LOV2 domain and its interaction with LOV1. Biophys J 89:402–412
Halavaty AS, Moffat K (2007) N- and C-terminal flanking regions modulate light-induced signal transduction in the LOV2 domain of the blue light sensor phototropin 1 from Avena sativa. Biochemistry 46:14001–14009
Halavaty AS, Moffat K (2013) Coiled-coil dimerization of the LOV2 domain of the blue-light photoreceptor phototropin 1 from Arabidopsis thaliana. Acta Crystallogr Sect F Struct Biol Cryst Commun 69:1316–1321
Harper SM, Neil LC, Gardner KH (2003) Structural basis of a phototropin light switch. Science 301:1541–1544
Harper SM, Christie JM, Gardner KH (2004a) Disruption of the LOV–Jalpha helix interaction activates phototropin kinase activity. Biochemistry 43:16184–16192
Harper SM, Neil LC, Day IJ, Hore PJ, Gardner KH (2004b) Conformational changes in a photosensory LOV domain monitored by time-resolved NMR spectroscopy. J Am Chem Soc 126:3390–3391
Holzer W, Penzkofer A, Fuhrmann M, Hegemann P (2002) Spectroscopic characterization of flavin mononucleotide bound to the LOV1 domain of Phot1 from Chlamydomonas reinhardtii. Photochem Photobiol 75:479–487
Huang K, Beck CF (2003) Phototropin is the blue-light receptor that controls multiple steps in the sexual life cycle of the green alga Chlamydomonas reinhardtii. Proc Natl Acad Sci USA 100:6269–6274
Huang K, Merkle T, Beck CF (2002) Isolation and characterization of a Chlamydomonas gene that encodes a putative blue-light photoreceptor of the phototropin family. Physiol Plant 115:613–622
Im CS, Eberhard S, Huang K, Beck CF, Grossman AR (2006) Phototropin involvement in the expression of genes encoding chlorophyll and carotenoid biosynthesis enzymes and LHC apoproteins in Chlamydomonas reinhardtii. Plant J 48:1–16
Inoue S, Kinoshita T, Matsumoto M, Nakayama KI, Doi M, Shimazaki K (2008) Blue light-induced autophosphorylation of phototropin is a primary step for signaling. Proc Natl Acad Sci USA 105:5626–5631
Iwata T, Nozaki D, Tokutomi S, Kagawa T, Wada M, Kandori H (2003) Light-induced structural changes in the LOV2 domain of Adiantum phytochrome3 studied by low-temperature FTIR and UV-visible spectroscopy. Biochemistry 42:8183–8191
Jarillo JA, Gabrys H, Capel J, Alonso JM, Ecker JR, Cashmore AR (2001) Phototropin-related NPL1 controls chloroplast relocation induced by blue light. Nature 410:952–954
Kagawa T, Sakai T, Suetsugu N, Oikawa K, Ishiguro S, Kato T, Tabata S, Okada K, Wada M (2001) Arabidopsis NPL1: a phototropin homolog controlling the chloroplast high-light avoidance response. Science 291:2138–2141
Kaiserli E, Sullivan S, Jones MA, Feeney KA, Christie JM (2009) Domain swapping to assess the mechanistic basis of Arabidopsis phototropin 1 receptor kinase activation and endocytosis by blue light. Plant Cell 21:3226–3244
Kasahara M, Swartz TE, Olney MA, Onodera A, Mochizuki N, Fukuzawa H, Asamizu E, Tabata S, Kanegae H, Takano M, Christie JM, Nagatani A, Briggs WR (2002) Photochemical properties of the flavin mononucleotide-binding domains of the phototropins from Arabidopsis, rice, and Chlamydomonas reinhardtii. Plant Physiol 129:762–773
Kashojiya S, Okajima K, Shimada T, Tokutomi S (2015) Essential role of the A’α/Aβ gap in the N-terminal upstream of LOV2 for the blue light signaling from LOV2 to kinase in Arabidopsis photototropin1, a plant blue light receptor. PLoS One 10:e0124284
Kashojiya S, Yoshihara S, Okajima K, Tokutomi S (2016) The linker between LOV2-Jα and STK plays an essential role in the kinase activation by blue light in Arabidopsis phototropin1, a plant blue light receptor. FEBS Lett (in press)
Katsura H, Zikihara K, Okajima K, Yoshihara S, Tokutomi S (2009) Oligomeric structure of LOV domains in Arabidopsis phototropin. FEBS Lett 583:526–530
Kinoshita T, Doi M, Suetsugu N, Kagawa T, Wada M, Shimazaki K (2001) Phot1 and phot2 mediate blue light regulation of stomatal opening. Nature 414:656–660
Kornev AP, Haste NM, Taylor SS, Eyck LF (2006) Surface comparison of active and inactive protein kinases identifies a conserved activation mechanism. Proc Natl Acad Sci USA 103:17783–17788
Koyama T, Iwata T, Yamamoto A, Sato Y, Matsuoka D, Tokutomi S, Kandori H (2009) Different role of the Jalpha helix in the light-induced activation of the LOV2 domains in various phototropins. Biochemistry 48:7621–7628
Kozuka T, Kong SG, Doi M, Shimazaki K, Nagatani A (2011) Tissue-autonomous promotion of palisade cell development by phototropin 2 in Arabidopsis. Plant Cell 23:3684–3695
Li FW, Rothfels CJ, Melkonian M, Villarreal JC, Stevenson DW, Graham SW, Wong GK, Mathews S, Pryer KM (2015) The origin and evolution of phototropins. Front Plant Sci 12:637
Liu H, Liu B, Zhao C, Pepper M, Lin C (2011) The action mechanisms of plant cryptochromes. Trends Plant Sci 16:684–691
Matsuoka D, Tokutomi S (2005) Blue light-regulated molecular switch of Ser/Thr kinase in phototropin. Proc Natl Acad Sci USA 102:13337–13342
Möglich A, Ayers RA, Moffat K (2009) Structure and signaling mechanism of Per-ARNT-Sim domains. Structure 17:1282–1294
Nakasako M, Iwata T, Matsuoka D, Tokutomi S (2004) Light-induced structural changes of LOV domain-containing polypeptides from Arabidopsis phototropin 1 and 2 studied by small-angle X-ray scattering. Biochemistry 43:14881–14890
Nakasako M, Zikihara K, Matsuoka D, Katsura H, Tokutomi S (2008) Structural basis of the LOV1 dimerization of Arabidopsis phototropins 1 and 2. J Mol Biol 381:718–733
Nakasone Y, Eitoku T, Matsuoka D, Tokutomi S, Terazima M (2007) Dynamics of conformational changes of Arabidopsis phototropin 1 LOV2 with the linker domain. J Mol Biol 367:432–442
Nash AI, Ko WH, Harper SM, Gardner KH (2008) A conserved glutamine plays a central role in LOV domain signal transmission and its duration. Biochemistry 47:13842–13849
Nozaki D, Iwata T, Ishikawa T, Todo T, Tokutomi S, Kandori H (2004) Role of Gln 1029 in the photoactivation processes of the LOV2 domain in Adiantum phytochrome3. Biochemistry 43:8373–8379
Okajima K, Matsuoka D, Tokutomi S (2011) LOV2-linker-kinase phosphorylates LOV1-containing N-terminal polypeptide substrate via photoreaction of LOV2 in Arabidopsis phototropin1. FEBS Lett 585:3391–3395
Okajima K, Kashojiya S, Tokutomi S (2012) Photosensitivity of kinase activation by blue light involves the lifetime of a cysteinyl-flavin adduct intermediate, S390, in the photoreaction cycle of the LOV2 domain in phototropin, a plant blue light receptor. J Biol Chem 287:40972–40981
Okajima K, Aihara Y, Takayama Y, Nakajima M, Kashojiya S, Hikima T, Oroguchi T, Kobayashi A, Sekiguchi Y, Yamamoto M, Suzuki T, Nagatani A, Nakasako M, Tokutomi S (2014) Light-induced conformational changes of LOV1 (light oxygen voltage-sensing domain 1) and LOV2 relative to the kinase domain and regulation of kinase activity in Chlamydomonas phototropin. J Biol Chem 289:413–422
Onodera A, Kong SG, Doi M, Shimazaki K, Christie J, Mochizuki N, Nagatani A (2005) Phototropin from Chlamydomonas reinhardtii is functional in Arabidopsis thaliana. Plant Cell Physiol 46:367–374
Peter E, Dick B, Stambolic I, Baeurle SA (2014) Exploring the multiscale signaling behavior of phototropin1 from Chlamydomonas reinhardtii using a full-residue space kinetic Monte Carlo molecular dynamics technique. Proteins 82:2018–2040
Pfeifer A, Mathes T, Lu Y, Hegemann P, Kottke T (2010) Blue light induces global and localized conformational changes in the kinase domain of full-length phototropin. Biochemistry 49:1024–1032
Quail PH (2002) Photosensory perception and signalling in plant cells: new paradigms? Curr Opin Cell Biol 14:180–188
Sakai T, Kagawa T, Kasahara M, Swartz TE, Christie JM, Briggs WR, Wada M, Okada K (2001) Arabidopsis nph1 and npl1: blue light receptors that mediate both phototropism and chloroplast relocation. Proc Natl Acad Sci USA 98:6969–6974
Salomon M, Christie JM, Knieb E, Lempert U, Briggs WR (2000) Photochemical and mutational analysis of the FMN-binding domains of the plant blue light receptor, phototropin. Biochemistry 39:9401–9410
Salomon M, Lempert U, Rüdiger W (2004) Dimerization of the plant photoreceptor phototropin is probably mediated by the LOV1 domain. FEBS Lett 572:8–10
Svergun DI (1992) Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J Appl Crystallogr 25:495–503
Svergun DI, Petoukhov MV, Koch MH (2001) Determination of domain structure of proteins from X-ray solution scattering. Biophys J 80:2946–2953
Swartz TE, Corchnoy SB, Christie JM, Lewis JW, Szundi I, Briggs WR, Bogomolni RA (2001) The photocycle of a flavin-binding domain of the blue light photoreceptor phototropin. J Biol Chem 276:36493–36500
Takayama Y, Nakasako M, Okajima K, Iwata A, Kashojiya S, Matsui Y, Tokutomi S (2011) Light-induced movement of the LOV2 domain in an Asp720Asn mutant LOV2-kinase fragment of Arabidopsis phototropin 2. Biochemistry 50:1174–1183
Takeda K, Nakasone Y, Zikihara K, Tokutomi S, Terazima M (2013) Dynamics of the amino-terminal and carboxyl-terminal helices of Arabidopsis phototropin 1 LOV2 studied by the transient grating. J Phys Chem B 117:15606–15613
Takemiya A, Sugiyama N, Fujimoto H, Tsutsumi T, Yamauchi S, Hiyama A, Tada Y, Christie JM, Shimazaki K (2013) Phosphorylation of BLUS1 kinase by phototropins is a primary step in stomatal opening. Nat Commun 4:2094
Taylor SS, Kornev AP (2011) Protein kinases: evolution of dynamic regulatory proteins. Trends Biochem Sci 36:65–77
Tokutomi S, Matsuoka D, Zikihara K (2008) Molecular structure and regulation of phototropin kinase by blue light. Biochim Biophys Acta 1784:133–142
Trippens J, Greiner A, Schellwat J, Neukam M, Rottmann T, Lu Y, Kateriya S, Hegemann P, Kreimer G (2012) Phototropin influence on eyespot development and regulation of phototactic behavior in Chlamydomonas reinhardtii. Plant Cell 24:4687–4702
van der Steen JB, Nakasone Y, Hendriks J, Hellingwerf KJ (2013) Modeling the functioning of YtvA in the general stress response in Bacillus subtilis. Mol BioSyst 9:2331–2343
Zayner JP, Sosnick TR (2014) Factors that control the chemistry of the LOV domain photocycle. PLoS One 9:e87074
Zayner JP, Antoniou C, Sosnick TR (2012) The amino-terminal helix modulates light-activated conformational changes in AsLOV2. J Mol Biol 419:61–74
Acknowledgments
I would like to thank Prof. M. Nakasako (Keio Univ.) for discussing structural analysis and for help writing the manuscript. I would like to thank Prof. S. Tokutomi (Osaka prefecture Univ.) for execution of the project. I would like to thank Mao Oide for discussing SAXS simulation. I would like to thank Dr. Y. Nakasone (Kyoto Univ.) for discussing kinetics. This work was supported by Grants-in-Aid from the JSPS Japan to S.T. (No. 22120005 and No. 23657105) and Grant-in-Aid for Young Scientists (B) to K.O. (No. 15K18559).
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Okajima, K. Molecular mechanism of phototropin light signaling. J Plant Res 129, 149–157 (2016). https://doi.org/10.1007/s10265-016-0783-6
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DOI: https://doi.org/10.1007/s10265-016-0783-6