Focusing on the nuclear and subnuclear dynamics of light and circadian signalling.
circadian
growth
light quality
nucleus
proteome
Journal
Plant, cell & environment
ISSN: 1365-3040
Titre abrégé: Plant Cell Environ
Pays: United States
ID NLM: 9309004
Informations de publication
Date de publication:
10 2019
10 2019
Historique:
received:
19
06
2019
revised:
27
07
2019
accepted:
30
07
2019
pubmed:
2
8
2019
medline:
1
7
2020
entrez:
2
8
2019
Statut:
ppublish
Résumé
Circadian clocks provide organisms the ability to synchronize their internal physiological responses with the external environment. This process, termed entrainment, occurs through the perception of internal and external stimuli. As with other organisms, in plants, the perception of light is a critical for the entrainment and sustainment of circadian rhythms. Red, blue, far-red, and UV-B light are perceived by the oscillator through the activity of photoreceptors. Four classes of photoreceptors signal to the oscillator: phytochromes, cryptochromes, UVR8, and LOV-KELCH domain proteins. In most cases, these photoreceptors localize to the nucleus in response to light and can associate to subnuclear structures to initiate downstream signalling. In this review, we will highlight the recent advances made in understanding the mechanisms facilitating the nuclear and subnuclear localization of photoreceptors and the role these subnuclear bodies have in photoreceptor signalling, including to the oscillator. We will also highlight recent progress that has been made in understanding the regulation of the nuclear and subnuclear localization of components of the plant circadian clock.
Substances chimiques
Arabidopsis Proteins
0
Chromosomal Proteins, Non-Histone
0
Cryptochromes
0
Uvr8 protein, Arabidopsis
0
Phytochrome
11121-56-5
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
2871-2884Subventions
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/M000435/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/N018540/1
Pays : United Kingdom
Informations de copyright
© 2019 John Wiley & Sons Ltd.
Références
Adam, E., Kircher, S., Liu, P., Merai, Z., Gonzalez-Schain, N., Horner, M., … Nagy, F. (2013). Comparative functional analysis of full-length and N-terminal fragments of phytochrome C, D and E in red light-induced signaling. The New Phytologist, 200, 86-96. https://doi.org/10.1111/nph.12364
Al-Sady, B., Ni, W., Kircher, S., Schafer, E., & Quail, P. H. (2006). Photoactivated phytochrome induces rapid PIF3 phosphorylation prior to proteasome-mediated degradation. Molecular Cell, 23, 439-446. https://doi.org/10.1016/j.molcel.2006.06.011
Ang, L.-H., Chattopadhyay, S., Wei, N., Oyama, T., Okada, K., Batschauer, A., & Deng, X.-W. (1998). Molecular interaction between COP1 and HY5 defines a regulatory switch for light control of Arabidopsis development. Molecular Cell, 1, 213-222. https://doi.org/10.1016/S1097-2765(00)80022-2
Anwer, M. U., Boikoglou, E., Herrero, E., Hallstein, M., Davis, A. M., Velikkakam, J. G., … Davis, S. J. (2014). Natural variation reveals that intracellular distribution of ELF3 protein is associated with function in the circadian clock. eLife, 3, e02206. https://doi.org/10.7554/eLife.02206
Ballesteros, M. L., Bolle, C., Lois, L. M., Moore, J. M., Vielle-Calzada, J. P., Grossniklaus, U., & Chua, N. H. (2001). LAF1, a MYB transcription activator for phytochrome A signaling. Genes & Development, 15, 2613-2625. https://doi.org/10.1101/gad.915001
Baudry, A., Ito, S., Song, Y. H., Strait, A. A., Kiba, T., Lu, S., … Imaizumi, T. (2010). F-box proteins FKF1 and LKP2 act in concert with ZEITLUPE to control Arabidopsis clock progression. Plant Cell, 22, 606-622. https://doi.org/10.1105/tpc.109.072843
Bauer, D., Viczián, A., Kircher, S., Nobis, T., Nitschke, R., Kunkel, T., … Nagy, F. (2004). Constitutive photomorphogenesis 1 and multiple photoreceptors control degradation of phytochrome interacting factor 3, a transcription factor required for light signaling in Arabidopsis. The Plant Cell, 16, 1433-1445. https://doi.org/10.1105/tpc.021568
Berr, A., Pecinka, A., Meister, A., Kreth, G., Fuchs, J., Blattner, F. R., … Schubert, I. (2006). Chromosome arrangement and nuclear architecture but not centromeric sequences are conserved between Arabidopsis thaliana and Arabidopsis lyrata. The Plant Journal, 48, 771-783. https://doi.org/10.1111/j.1365-313X.2006.02912.x
Berr, A., & Schubert, I. (2007). Interphase chromosome arrangement in Arabidopsis thaliana is similar in differentiated and meristematic tissues and shows a transient mirror symmetry after nuclear division. Genetics, 176, 853-863. https://doi.org/10.1534/genetics.107.073270
Binkert, M., Crocco, C. D., Ekundayo, B., Lau, K., Raffelberg, S., Tilbrook, K., … Ulm, R. (2016). Revisiting chromatin binding of the Arabidopsis UV-B photoreceptor UVR8. BMC Plant Biology, 16, 42-42. https://doi.org/10.1186/s12870-016-0732-5
Binkert, M., Kozma-Bognár, L., Terecskei, K., De Veylder, L., Nagy, F., & Ulm, R. (2014). UV-B-responsive association of the Arabidopsis bZIP transcription factor ELONGATED HYPOCOTYL5 with target genes, including its own promoter. The Plant Cell, 26, 4200-4213. https://doi.org/10.1105/tpc.114.130716
Brown, B. A., Cloix, C., Jiang, G. H., Kaiserli, E., Herzyk, P., Kliebenstein, D. J., & Jenkins, G. I. (2005). A UV-B-specific signaling component orchestrates plant UV protection. Proceedings of the National Academy of Sciences of the United States of America, 102, 18225-18230. https://doi.org/10.1073/pnas.0507187102
Carré, I. A., & Kim, J. Y. (2002). MYB transcription factors in the Arabidopsis circadian clock. Journal of Experimental Botany, 53, 1551-1557. https://doi.org/10.1093/jxb/erf027
Casal, J. J., Davis, S. J., Kirchenbauer, D., Viczian, A., Yanovsky, M. J., Clough, R. C., … Vierstra, R. D. (2002). The serine-rich N-terminal domain of oat phytochrome a helps regulate light responses and subnuclear localization of the photoreceptor. Plant Physiology, 129, 1127-1137. https://doi.org/10.1104/pp.010977
Cha, J. Y., Kim, J., Kim, T. S., Zeng, Q., Wang, L., Lee, S. Y., … Somers, D. E. (2017). GIGANTEA is a co-chaperone which facilitates maturation of ZEITLUPE in the Arabidopsis circadian clock. Nature Communications, 8, 3. https://doi.org/10.1038/s41467-016-0014-9
Chen, M., Galvão, R. M., Li, M., Burger, B., Bugea, J., Bolado, J., & Chory, J. (2010). Arabidopsis HEMERA/pTAC12 initiates photomorphogenesis by phytochromes. Cell, 141, 1230-1240. https://doi.org/10.1016/j.cell.2010.05.007
Chen, M., Schwab, R., & Chory, J. (2003). Characterization of the requirements for localization of phytochrome B to nuclear bodies. Proceedings of the National Academy of Sciences of the United States of America, 100, 14493-14498. https://doi.org/10.1073/pnas.1935989100
Chen, M., Tao, Y., Lim, J., Shaw, A., & Chory, J. (2005). Regulation of phytochrome B nuclear localization through light-dependent unmasking of nuclear-localization signals. Current Biology, 15, 637-642. https://doi.org/10.1016/j.cub.2005.02.028
Christie, J. M., Arvai, A. S., Baxter, K. J., Heilmann, M., Pratt, A. J., O'Hara, A., … Getzoff, E. D. (2012). Plant UVR8 photoreceptor senses UV-B by tryptophan-mediated disruption of cross-dimer salt bridges. Science, 335, 1492-1496. https://doi.org/10.1126/science.1218091
Clack, T., Mathews, S., & Sharrock, R. A. (1994). The phytochrome apoprotein family in Arabidopsis is encoded by five genes: The sequences and expression of PHYD and PHYE. Plant Molecular Biology, 25, 413-427. https://doi.org/10.1007/BF00043870
Cohen, S. E., & Golden, S. S. (2015). Circadian rhythms in cyanobacteria. Microbiology and Molecular Biology Reviews, 79, 373-385. https://doi.org/10.1128/MMBR.00036-15
Debrieux, D., & Fankhauser, C. (2010). Light-induced degradation of phyA is promoted by transfer of the photoreceptor into the nucleus. Plant Molecular Biology, 73, 687-695. https://doi.org/10.1007/s11103-010-9649-9
Devlin, P. F., & Kay, S. A. (2000). Cryptochromes are required for phytochrome signaling to the circadian clock but not for rhythmicity. The Plant Cell, 12, 2499-2509. https://doi.org/10.1105/tpc.12.12.2499
Dong, J., Ni, W., Yu, R., Deng, X. W., Chen, H., & Wei, N. (2017). Light-dependent degradation of PIF3 by SCF (EBF1/2) promotes a photomorphogenic response in Arabidopsis. Current Biology: CB, 27, 2420-2430.e2426. https://doi.org/10.1016/j.cub.2017.06.062
Enderle, B., Sheerin, D. J., Paik, I., Kathare, P. K., Schwenk, P., Klose, C., … Hiltbrunner, A. (2017). PCH1 and PCHL promote photomorphogenesis in plants by controlling phytochrome B dark reversion. Nature Communications, 8, 2221. https://doi.org/10.1038/s41467-017-02311-8
Favory, J.-J., Stec, A., Gruber, H., Rizzini, L., Oravecz, A., Funk, M., … Ulm, R. (2009). Interaction of COP1 and UVR8 regulates UV-B-induced photomorphogenesis and stress acclimation in Arabidopsis. The EMBO Journal, 28, 591-601. https://doi.org/10.1038/emboj.2009.4
Feher, B., Kozma-Bognar, L., Kevei, E., Hajdu, A., Binkert, M., Davis, S. J., … Nagy, F. (2011). Functional interaction of the circadian clock and UV RESISTANCE LOCUS 8-controlled UV-B signaling pathways in Arabidopsis thaliana. The Plant Journal, 67, 37-48. https://doi.org/10.1111/j.1365-313X.2011.04573.x
Fukamatsu, Y., Mitsui, S., Yasuhara, M., Tokioka, Y., Ihara, N., Fujita, S., & Kiyosue, T. (2005). Identification of LOV KELCH PROTEIN2 (LKP2)-interacting factors that can recruit LKP2 to nuclear bodies. Plant & Cell Physiology, 46, 1340-1349. https://doi.org/10.1093/pcp/pci144
Gangappa, S. N., & Botto, J. F. (2016). The multifaceted roles of HY5 in plant growth and development. Molecular Plant, 9, 1353-1365. https://doi.org/10.1016/j.molp.2016.07.002
Gendron, J. M., Pruneda-Paz, J. L., Doherty, C. J., Gross, A. M., Kang, S. E., & Kay, S. A. (2012). Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor. Proceedings of the National Academy of Sciences, 109, 3167-3172. https://doi.org/10.1073/pnas.1200355109
Genoud, T., Schweizer, F., Tscheuschler, A., Debrieux, D., Casal, J. J., Schäfer, E., … Fankhauser, C. (2008). FHY1 mediates nuclear import of the light-activated phytochrome A photoreceptor. PLoS Genetics, 4, e1000143. https://doi.org/10.1371/journal.pgen.1000143
Gil, P., Kircher, S., Adam, E., Bury, E., Kozma-Bognar, L., Schafer, E., & Nagy, F. (2000). Photocontrol of subcellular partitioning of phytochrome-B: GFP fusion protein in tobacco seedlings. The Plant Journal, 22, 135-145. https://doi.org/10.1046/j.1365-313x.2000.00730.x
Gu, N.-N., Zhang, Y.-C., & Yang, H.-Q. (2012). Substitution of a conserved glycine in the PHR domain of Arabidopsis CRYPTOCHROME 1 confers a constitutive light response. Molecular Plant, 5, 85-97. https://doi.org/10.1093/mp/ssr052
Guo, H., Duong, H., Ma, N., & Lin, C. (1999). The Arabidopsis blue light receptor cryptochrome 2 is a nuclear protein regulated by a blue light-dependent post-transcriptional mechanism. The Plant Journal, 19, 279-287. https://doi.org/10.1046/j.1365-313X.1999.00525.x
Hajdu, A., Dobos, O., Domijan, M., Balint, B., Nagy, I., Nagy, F., & Kozma-Bognar, L. (2018). ELONGATED HYPOCOTYL 5 mediates blue light signalling to the Arabidopsis circadian clock. The Plant Journal, 96, 1242-1254. https://doi.org/10.1111/tpj.14106
Han, L., Mason, M., Risseeuw, E. P., Crosby, W. L., & Somers, D. E. (2004). Formation of an SCF (ZTL) complex is required for proper regulation of circadian timing. The Plant Journal, 40, 291-301. https://doi.org/10.1111/j.1365-313X.2004.02207.x
Heijde, M., & Ulm, R. (2013). Reversion of the Arabidopsis UV-B photoreceptor UVR8 to the homodimeric ground state. Proceedings of the National Academy of Sciences of the United States of America, 110, 1113-1118. https://doi.org/10.1073/pnas.1214237110
Heilmann, M., & Jenkins, G. I. (2013). Rapid reversion from monomer to dimer regenerates the ultraviolet-B photoreceptor UV RESISTANCE LOCUS8 in intact Arabidopsis plants. Plant Physiology, 161, 547-555. https://doi.org/10.1104/pp.112.206805
Herrero, E., & Davis, S. J. (2012). Time for a nuclear meeting: Protein trafficking and chromatin dynamics intersect in the plant circadian system. Molecular Plant, 5, 554-565. https://doi.org/10.1093/mp/sss010
Herrero, E., Kolmos, E., Bujdoso, N., Yuan, Y., Wang, M., Berns, M. C., … Davis, S. J. (2012). EARLY FLOWERING4 recruitment of EARLY FLOWERING3 in the nucleus sustains the Arabidopsis circadian clock. The Plant Cell, 24, 428-443. https://doi.org/10.1105/tpc.111.093807
Hiltbrunner, A., Tscheuschler, A., Viczian, A., Kunkel, T., Kircher, S., & Schafer, E. (2006). FHY1 and FHL act together to mediate nuclear accumulation of the phytochrome A photoreceptor. Plant & Cell Physiology, 47, 1023-1034. https://doi.org/10.1093/pcp/pcj087
Hoecker, U. (2017). The activities of the E3 ubiquitin ligase COP1/SPA, a key repressor in light signaling. Current Opinion in Plant Biology, 37, 63-69. https://doi.org/10.1016/j.pbi.2017.03.015
Huang, H., McLoughlin, K. E., Sorkin, M. L., Burgie, E. S., Bindbeutel, R. K., Vierstra, R. D., & Nusinow, D. A. (2019). PCH1 regulates light, temperature, and circadian signaling as a structural component of phytochrome B-photobodies in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 116, 8603-8608. https://doi.org/10.1073/pnas.1818217116
Huang, H., Yoo, C. Y., Bindbeutel, R., Goldsworthy, J., Tielking, A., Alvarez, S., … Nusinow, D. A. (2016). PCH1 integrates circadian and light-signaling pathways to control photoperiod-responsive growth in Arabidopsis. eLife, 5, e13292. https://doi.org/10.7554/eLife.13292
Huang, X., Ouyang, X., Yang, P., Lau, O. S., Chen, L., Wei, N., & Deng, X. W. (2013). Conversion from CUL4-based COP1-SPA E3 apparatus to UVR8-COP1-SPA complexes underlies a distinct biochemical function of COP1 under UV-B. Proceedings of the National Academy of Sciences, 110, 16669-16674. https://doi.org/10.1073/pnas.1316622110
Huq, E., Al-Sady, B., & Quail, P. H. (2003). Nuclear translocation of the photoreceptor phytochrome B is necessary for its biological function in seedling photomorphogenesis. The Plant Journal, 35, 660-664. https://doi.org/10.1046/j.1365-313X.2003.01836.x
Ito, S., Matsushika, A., Yamada, H., Sato, S., Kato, T., Tabata, S., … Mizuno, T. (2003). Characterization of the APRR9 pseudo-response regulator belonging to the APRR1/TOC1 quintet in Arabidopsis thaliana. Plant & Cell Physiology, 44, 1237-1245. https://doi.org/10.1093/pcp/pcg136
Ito, S., Song, Y. H., & Imaizumi, T. (2012). LOV domain-containing F-box proteins: Light-dependent protein degradation modules in Arabidopsis. Molecular Plant, 5, 573-582. https://doi.org/10.1093/mp/sss013
Jones, M. A., Hu, W., Litthauer, S., Lagarias, J. C., & Harmer, S. L. (2015). A constitutively active allele of phytochrome B maintains circadian robustness in the absence of light. Plant Physiology, 169, 814-825. https://doi.org/10.1104/pp.15.00782
Kaiserli, E., & Jenkins, G. I. (2007). UV-B promotes rapid nuclear translocation of the Arabidopsis UV-B-specific signaling component UVR8 and activates its function in the nucleus. The Plant Cell, 19, 2662-2673. https://doi.org/10.1105/tpc.107.053330
Kaiserli, E., Paldi, K., O'Donnell, L., Batalov, O., Pedmale, U. V., Nusinow, D. A., … Chory, J. (2015). Integration of light and photoperiodic signaling in transcriptional nuclear foci. Developmental Cell, 35, 311-321. https://doi.org/10.1016/j.devcel.2015.10.008
Kaiserli, E., Perrella, G., & Davidson, M. L. (2018). Light and temperature shape nuclear architecture and gene expression. Current Opinion in Plant Biology, 45, 103-111. https://doi.org/10.1016/j.pbi.2018.05.018
Kim, J., Geng, R., Gallenstein, R. A., & Somers, D. E. (2013). The F-box protein ZEITLUPE controls stability and nucleocytoplasmic partitioning of GIGANTEA. Development (Cambridge, England), 140, 4060-4069. https://doi.org/10.1242/dev.096651
Kim, L., Kircher, S., Toth, R., Adam, E., Schäfer, E., & Nagy, F. (2000). Light-induced nuclear import of phytochrome-A: GFP fusion proteins is differentially regulated in transgenic tobacco and Arabidopsis. The Plant Journal, 22, 125-133. https://doi.org/10.1046/j.1365-313x.2000.00729.x
Kim, T. S., Kim, W. Y., Fujiwara, S., Kim, J., Cha, J. Y., Park, J. H., … Somers, D. E. (2011). HSP90 functions in the circadian clock through stabilization of the client F-box protein ZEITLUPE. Proceedings of the National Academy of Sciences of the United States of America, 108, 16843-16848. https://doi.org/10.1073/pnas.1110406108
Kim, W. Y., Fujiwara, S., Suh, S. S., Kim, J., Kim, Y., Han, L., … Somers, D. E. (2007). ZEITLUPE is a circadian photoreceptor stabilized by GIGANTEA in blue light. Nature, 449, 356-360. https://doi.org/10.1038/nature06132
Kim, Y., Lim, J., Yeom, M., Kim, H., Kim, J., Wang, L., … Nam, H. G. (2013). ELF4 regulates GIGANTEA chromatin access through subnuclear sequestration. Cell Reports, 3, 671-677. https://doi.org/10.1016/j.celrep.2013.02.021
Kircher, S., Gil, P., Kozma-Bognár, L., Fejes, E., Speth, V., Husselstein-Muller, T., … Nagy, F. (2002). Nucleocytoplasmic partitioning of the plant photoreceptors phytochrome A, B, C, D, and E is regulated differentially by light and exhibits a diurnal rhythm. The Plant Cell, 14, 1541-1555. https://doi.org/10.1105/tpc.001156
Kleiner, O., Kircher, S., Harter, K., & Batschauer, A. (1999). Nuclear localization of the Arabidopsis blue light receptor cryptochrome 2. The Plant Journal, 19, 289-296. https://doi.org/10.1046/j.1365-313X.1999.00535.x
Klose, C., Viczian, A., Kircher, S., Schafer, E., & Nagy, F. (2015). Molecular mechanisms for mediating light-dependent nucleo/cytoplasmic partitioning of phytochrome photoreceptors. The New Phytologist, 206, 965-971. https://doi.org/10.1111/nph.13207
Kolmos, E., Herrero, E., Bujdoso, N., Millar, A. J., Toth, R., Gyula, P., … Davis, S. J. (2011). A reduced-function allele reveals that EARLY FLOWERING3 repressive action on the circadian clock is modulated by phytochrome signals in Arabidopsis. Plant Cell, 23, 3230-3246. https://doi.org/10.1105/tpc.111.088195
Kolmos, E., Nowak, M., Werner, M., Fischer, K., Schwarz, G., Mathews, S., … Davis, S. J. (2009). Integrating ELF4 into the circadian system through combined structural and functional studies. HFSP journal, 3, 350-366. https://doi.org/10.2976/1.3218766
Lamond, A. I., & Sleeman, J. E. (2003). Nuclear substructure and dynamics. Current Biology, 13, R825-R828. https://doi.org/10.1016/j.cub.2003.10.012
Lee, C.-M., Feke, A., Li, M.-W., Adamchek, C., Webb, K., Pruneda-Paz, J., … Gendron, J. M. (2018). Decoys untangle complicated redundancy and reveal targets of circadian clock F-box proteins. eLife, 177, 1170-1186.
Legris, M., Klose, C., Burgie, E. S., Rojas, C. C., Neme, M., Hiltbrunner, A., … Casal, J. J. (2016). Phytochrome B integrates light and temperature signals in Arabidopsis. Science, 354, 897-900. https://doi.org/10.1126/science.aaf5656
Li, G., Siddiqui, H., Teng, Y., Lin, R., Wan, X. Y., Li, J., … Wang, H. (2011). Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis. Nature Cell Biology, 13, 616-622. https://doi.org/10.1038/ncb2219
Lian, H.-L., He, S.-B., Zhang, Y.-C., Zhu, D.-M., Zhang, J.-Y., Jia, K.-P., … Yang, H.-Q. (2011). Blue-light-dependent interaction of cryptochrome 1 with SPA1 defines a dynamic signaling mechanism. Genes & Development, 25, 1023-1028. https://doi.org/10.1101/gad.2025111
Litthauer, S., Battle, M. W., & Jones, M. A. (2015). Phototropins do not alter accumulation of evening-phased circadian transcripts under blue light. Plant Signaling & Behavior, 11, e1126029-e1126029. https://doi.org/10.1080/15592324.2015.1126029
Litthauer, S., Battle, M. W., Lawson, T., & Jones, M. A. (2015). Phototropins maintain robust circadian oscillation of PSII operating efficiency under blue light. The Plant Journal, 83, 1034-1045. https://doi.org/10.1111/tpj.12947
Liu, H., Yu, X., Li, K., Klejnot, J., Yang, H., Lisiero, D., & Lin, C. (2008). Photoexcited CRY2 interacts with CIB1 to regulate transcription and floral initiation in Arabidopsis. Science, 322, 1535-1539. https://doi.org/10.1126/science.1163927
Liu, Q., Wang, Q., Deng, W., Wang, X., Piao, M., Cai, D., … Lin, C. (2017). Molecular basis for blue light-dependent phosphorylation of Arabidopsis cryptochrome 2. Nature Communications, 8, 15234. https://doi.org/10.1038/ncomms15234
Liu, X. L., Covington, M. F., Fankhauser, C., Chory, J., & Wagner, D. R. (2001). ELF3 encodes a circadian clock-regulated nuclear protein that functions in an Arabidopsis PHYB signal transduction pathway. Plant Cell, 13, 1293-1304.
Lorrain, S., Allen, T., Duek, P. D., Whitelam, G. C., & Fankhauser, C. (2008). Phytochrome-mediated inhibition of shade avoidance involves degradation of growth-promoting bHLH transcription factors. The Plant Journal, 53, 312-323. https://doi.org/10.1111/j.1365-313X.2007.03341.x
Lu, X.-D., Zhou, C.-M., Xu, P.-B., Luo, Q., Lian, H.-L., & Yang, H.-Q. (2015). Red-light-dependent interaction of phyB with SPA1 promotes COP1-SPA1 dissociation and photomorphogenic development in Arabidopsis. Molecular Plant, 8, 467-478. https://doi.org/10.1016/j.molp.2014.11.025
Ma, D., Li, X., Guo, Y., Chu, J., Fang, S., Yan, C., … Liu, H. (2016). Cryptochrome 1 interacts with PIF4 to regulate high temperature-mediated hypocotyl elongation in response to blue light. Proceedings of the National Academy of Sciences of the United States of America, 113, 224-229. https://doi.org/10.1073/pnas.1511437113
Más, P., Alabadí, D., Yanovsky, M. J., Oyama, T., & Kay, S. A. (2003). Dual role of TOC1 in the control of circadian and photomorphogenic responses in Arabidopsis. The Plant Cell, 15, 223-236. https://doi.org/10.1105/tpc.006734
Más, P., Devlin, P. F., Panda, S., & Kay, S. A. (2000). Functional interaction of phytochrome B and cryptochrome 2. Nature, 408, 207-211. https://doi.org/10.1038/35041583
Matera, A. G., Izaguire-Sierra, M., Praveen, K., & Rajendra, T. K. (2009). Nuclear bodies: Random aggregates of sticky proteins or crucibles of macromolecular assembly? Developmental Cell, 17, 639-647. https://doi.org/10.1016/j.devcel.2009.10.017
Matsumoto, N., Hirano, T., Iwasaki, T., & Yamamoto, N. (2003). Functional analysis and intracellular localization of rice cryptochromes. Plant Physiology, 133, 1494-1503. https://doi.org/10.1104/pp.103.025759
Matsushita, T., Mochizuki, N., & Nagatani, A. (2003). Dimers of the N-terminal domain of phytochrome B are functional in the nucleus. Nature, 424, 571-574. https://doi.org/10.1038/nature01837
McClung, C. R. (2019). The Plant Circadian Oscillator. Biology, 8, 14. https://doi.org/10.3390/biology8010014
Millar, A. J. (2004). Input signals to the plant circadian clock. Journal of Experimental Botany, 55, 277-283.
Mizoguchi, T., Wheatley, K., Hanzawa, Y., Wright, L., Mizoguchi, M., Song, H. R., … Coupland, G. (2002). LHY and CCA1 are partially redundant genes required to maintain circadian rhythms in Arabidopsis. Developmental Cell, 2, 629-641. https://doi.org/10.1016/S1534-5807(02)00170-3
Nagatani, A. (2004). Light-regulated nuclear localization of phytochromes. Current Opinion in Plant Biology, 7, 708-711. https://doi.org/10.1016/j.pbi.2004.09.010
Nagel, D. H., Doherty, C. J., Pruneda-Paz, J. L., Schmitz, R. J., Ecker, J. R., & Kay, S. A. (2015). Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 112, E4802-E4810. https://doi.org/10.1073/pnas.1513609112
Nakamichi, N., Kiba, T., Henriques, R., Mizuno, T., Chua, N.-H., & Sakakibara, H. (2010). PSEUDO-RESPONSE REGULATORS 9, 7, and 5 are transcriptional repressors in the Arabidopsis circadian clock. The Plant Cell, 22, 594-605. https://doi.org/10.1105/tpc.109.072892
Nakamichi, N., Kita, M., Ito, S., Yamashino, T., & Mizuno, T. (2005). PSEUDO-RESPONSE REGULATORS, PRR9, PRR7 and PRR5, together play essential roles close to the circadian clock of Arabidopsis thaliana. Plant and Cell Physiology, 46, 686-698. https://doi.org/10.1093/pcp/pci086
Ni, W., Xu, S. L., Chalkley, R. J., Pham, T. N., Guan, S., Maltby, D. A., … Quail, P. H. (2013). Multisite light-induced phosphorylation of the transcription factor PIF3 is necessary for both its rapid degradation and concomitant negative feedback modulation of photoreceptor phyB levels in Arabidopsis. Plant Cell, 25, 2679-2698. https://doi.org/10.1105/tpc.113.112342
Ni, W., Xu, S.-L., González-Grandío, E., Chalkley, R. J., Huhmer, A. F. R., Burlingame, A. L., … Quail, P. H. (2017). PPKs mediate direct signal transfer from phytochrome photoreceptors to transcription factor PIF3. Nature Communications, 8, 15236. https://doi.org/10.1038/ncomms15236
Nieto, C., Lopez-Salmeron, V., Daviere, J. M., & Prat, S. (2015). ELF3-PIF4 interaction regulates plant growth independently of the evening complex. Current Biology, 25, 187-193. https://doi.org/10.1016/j.cub.2014.10.070
Nusinow, D. A., Helfer, A., Hamilton, E. E., King, J. J., Imaizumi, T., Schultz, T. F., … Kay, S. A. (2011). The ELF4-ELF3-LUX complex links the circadian clock to diurnal control of hypocotyl growth. Nature, 475, 398-402. https://doi.org/10.1038/nature10182
Oakenfull, R. J., & Davis, S. J. (2017). Shining a light on the Arabidopsis circadian clock. Plant, Cell & Environment, 40, 2571-2585. https://doi.org/10.1111/pce.13033
Oravecz, A., Baumann, A., Máté, Z., Brzezinska, A., Molinier, J., Oakeley, E. J., … Ulm, R. (2006). CONSTITUTIVELY PHOTOMORPHOGENIC1 is required for the UV-B response in Arabidopsis. The Plant Cell, 18, 1975-1990. https://doi.org/10.1105/tpc.105.040097
Palágyi, A., Terecskei, K., Adám, E., Kevei, E., Kircher, S., Mérai, Z., … Kozma-Bognár, L. (2010). Functional analysis of amino-terminal domains of the photoreceptor phytochrome B. Plant Physiology, 153, 1834-1845. https://doi.org/10.1104/pp.110.153031
Pecinka, A., Schubert, V., Meister, A., Kreth, G., Klatte, M., Lysak, M. A., … Schubert, I. (2004). Chromosome territory arrangement and homologous pairing in nuclei of Arabidopsis thaliana are predominantly random except for NOR-bearing chromosomes. Chromosoma, 113, 258-269. https://doi.org/10.1007/s00412-004-0316-2
Pedmale, U. V., Huang, S. C., Zander, M., Cole Benjamin, J., Hetzel, J., Ljung, K., … Chory, J. (2016). Cryptochromes interact directly with PIFs to control plant growth in limiting blue light. Cell, 164, 233-245. https://doi.org/10.1016/j.cell.2015.12.018
Pfeiffer, A., Nagel, M.-K., Popp, C., Wüst, F., Bindics, J., Viczián, A., … Schäfer, E. (2012). Interaction with plant transcription factors can mediate nuclear import of phytochrome B. Proceedings of the National Academy of Sciences of the United States of America, 109, 5892-5897. https://doi.org/10.1073/pnas.1120764109
Pruneda-Paz, J. L., Breton, G., Para, A., & Kay, S. A. (2009). A functional genomics approach reveals CHE as a component of the Arabidopsis circadian clock. Science, 323, 1481-1485. https://doi.org/10.1126/science.1167206
Qiu, Y., Li, M., Kim, R. J.-A., Moore, C. M., & Chen, M. (2019). Daytime temperature is sensed by phytochrome B in Arabidopsis through a transcriptional activator HEMERA. Nature Communications, 10, 140. https://doi.org/10.1038/s41467-018-08059-z
Rausenberger, J., Tscheuschler, A., Nordmeier, W., Wüst, F., Timmer, J., Schäfer, E., … Hiltbrunner, A. (2011). Photoconversion and nuclear trafficking cycles determine phytochrome A's response profile to far-red light. Cell, 146, 813-825. https://doi.org/10.1016/j.cell.2011.07.023
Rizzini, L., Favory, J. J., Cloix, C., Faggionato, D., O'Hara, A., Kaiserli, E., … Ulm, R. (2011). Perception of UV-B by the Arabidopsis UVR8 protein. Science, 332, 103-106. https://doi.org/10.1126/science.1200660
Rockwell, N. C., Su, Y.-S., & Lagarias, J. C. (2006). Phytochrome structure and signaling mechanisms. Annual Review of Plant Biology, 57, 837-858. https://doi.org/10.1146/annurev.arplant.56.032604.144208
Ronald, J., & Davis, S. (2017). Making the clock tick: The transcriptional landscape of the plant circadian clock [version 1; referees: 2 approved]. F1000 Research, 6. https://doi.org/10.12688/f1000research.11319.1
Rosenfeldt, G., Viana, R. M., Mootz, H. D., von Arnim, A. G., & Batschauer, A. (2008). Chemically induced and light-independent cryptochrome photoreceptor activation. Molecular Plant, 1, 4-14. https://doi.org/10.1093/mp/ssm002
Sanchez, S. E., & Kay, S. A. (2016). The plant circadian clock: From a simple timekeeper to a complex developmental manager. Cold Spring Harbor Perspectives in Biology, 8. https://doi.org/10.1101/cshperspect.a027748
Sheerin, D. J., Menon, C., zur Oven-Krockhaus, S., Enderle, B., Zhu, L., Johnen, P., … Hiltbrunner, A. (2015). Light-activated phytochrome A and B interact with members of the SPA family to promote photomorphogenesis in Arabidopsis by reorganizing the COP1/SPA complex. The Plant Cell, 27, 189-201. https://doi.org/10.1105/tpc.114.134775
Siddiqui, H., Khan, S., Rhodes, B. M., & Devlin, P. F. (2016). FHY3 and FAR1 act downstream of light stable phytochromes. Frontiers in Plant Science, 7. https://doi.org/10.3389/fpls.2016.00175
Stacey, M. G., Hicks, S. N., & von Arnim, A. G. (1999). Discrete domains mediate the light-responsive nuclear and cytoplasmic localization of Arabidopsis COP1. The Plant Cell, 11, 349-363. https://doi.org/10.1105/tpc.11.3.349
Takahashi, J. S. (2017). Transcriptional architecture of the mammalian circadian clock. Nature Reviews. Genetics, 18, 164-179. https://doi.org/10.1038/nrg.2016.150
Trupkin, S. A., Legris, M., Buchovsky, A. S., Tolava Rivero, M. B., & Casal, J. J. (2014). Phytochrome B nuclear bodies respond to the low red to far-red ratio and to the reduced irradiance of canopy shade in Arabidopsis. Plant Physiology, 165, 1698-1708. https://doi.org/10.1104/pp.114.242438
Ulm, R., Baumann, A., Oravecz, A., Mate, Z., Adam, E., Oakeley, E. J., … Nagy, F. (2004). Genome-wide analysis of gene expression reveals function of the bZIP transcription factor HY5 in the UV-B response of Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 101, 1397-1402. https://doi.org/10.1073/pnas.0308044100
Van Buskirk, E. K., Reddy, A. K., Nagatani, A., & Chen, M. (2014). Photobody localization of phytochrome B is tightly correlated with prolonged and light-dependent inhibition of hypocotyl elongation in the dark. Plant Physiology, 165, 595-607. https://doi.org/10.1104/pp.114.236661
Wang, H., Ma, L.-G., Li, J.-M., Zhao, H.-Y., & Deng, X. W. (2001). Direct interaction of Arabidopsis cryptochromes with COP1 in light control development. Science, 294, 154-158. https://doi.org/10.1126/science.1063630
Wang, L., Fujiwara, S., & Somers, D. E. (2010). PRR5 regulates phosphorylation, nuclear import and subnuclear localization of TOC1 in the Arabidopsis circadian clock. The EMBO Journal, 29, 1903-1915. https://doi.org/10.1038/emboj.2010.76
Wang, Q., Zuo, Z., Wang, X., Gu, L., Yoshizumi, T., Yang, Z., … Lin, C. (2016). Photoactivation and inactivation of Arabidopsis cryptochrome 2. Science (New York, N.Y.), 354, 343-347. https://doi.org/10.1126/science.aaf9030
Wang, S., Li, L., Xu, P., Lian, H., Wang, W., Xu, F., … Yang, H. (2018). CRY1 interacts directly with HBI1 to regulate its transcriptional activity and photomorphogenesis in Arabidopsis. Journal of Experimental Botany, 69, 3867-3881. https://doi.org/10.1093/jxb/ery209
Wang, X., Wang, Q., Han, Y.-J., Liu, Q., Gu, L., Yang, Z., … Lin, C. (2017). A CRY-BIC negative-feedback circuitry regulating blue light sensitivity of Arabidopsis. The Plant Journal, 92, 426-436. https://doi.org/10.1111/tpj.13664
Wang, Z.-Y., & Tobin, E. M. (1998). Constitutive expression of the CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) gene disrupts circadian rhythms and suppresses its own expression. Cell, 93, 1207-1217. https://doi.org/10.1016/S0092-8674(00)81464-6
Webb, A. A. R., Seki, M., Satake, A., & Caldana, C. (2019). Continuous dynamic adjustment of the plant circadian oscillator. Nature Communications, 10, 550. https://doi.org/10.1038/s41467-019-08398-5
Weidler, G., zur Oven-Krockhaus, S., Heunemann, M., Orth, C., Schleifenbaum, F., Harter, K., … Batschauer, A. (2012). Degradation of Arabidopsis CRY2 is regulated by SPA proteins and phytochrome A. The Plant Cell, 24, 2610-2623. https://doi.org/10.1105/tpc.112.098210
Wu, G., & Spalding, E. P. (2007). Separate functions for nuclear and cytoplasmic cryptochrome 1 during photomorphogenesis of Arabidopsis seedlings. Proceedings of the National Academy of Sciences of the United States of America, 104, 18813-18818. https://doi.org/10.1073/pnas.0705082104
Xu, P., Xiang, Y., Zhu, H., Xu, H., Zhang, Z., Zhang, C., … Ma, Z. (2009). Wheat cryptochromes: Subcellular localization and involvement in photomorphogenesis and osmotic stress responses. Plant Physiology, 149, 760-774. https://doi.org/10.1104/pp.108.132217
Yakir, E., Hilman, D., Kron, I., Hassidim, M., Melamed-Book, N., & Green, R. M. (2009). Posttranslational regulation of CIRCADIAN CLOCK ASSOCIATED1 in the circadian oscillator of Arabidopsis. Plant Physiology, 150, 844-857. https://doi.org/10.1104/pp.109.137414
Yang, H.-Q., Wu, Y.-J., Tang, R.-H., Liu, D., Liu, Y., & Cashmore, A. R. (2000). The C termini of Arabidopsis cryptochromes mediate a constitutive light response. Cell, 103, 815-827. https://doi.org/10.1016/S0092-8674(00)00184-7
Yang, Y., Liang, T., Zhang, L., Shao, K., Gu, X., Shang, R., … Liu, H. (2018). UVR8 interacts with WRKY36 to regulate HY5 transcription and hypocotyl elongation in Arabidopsis. Nature Plants, 4, 98-107. https://doi.org/10.1038/s41477-017-0099-0
Yeom, M., Kim, H., Lim, J., Shin, A. Y., Hong, S., Kim, J. I., & Nam, H. G. (2014). How do phytochromes transmit the light quality information to the circadian clock in Arabidopsis? Molecular Plant, 7, 1701-1704. https://doi.org/10.1093/mp/ssu086
Yin, R., Skvortsova, M. Y., Loubéry, S., & Ulm, R. (2016). COP1 is required for UV-B-induced nuclear accumulation of the UVR8 photoreceptor. Proceedings of the National Academy of Sciences of the United States of America, 113, E4415-E4422. https://doi.org/10.1073/pnas.1607074113
Yu, J. W., Rubio, V., Lee, N. Y., Bai, S., Lee, S. Y., Kim, S. S., … Deng, X. W. (2008). COP1 and ELF3 control circadian function and photoperiodic flowering by regulating GI stability. Molecular Cell, 32, 617-630. https://doi.org/10.1016/j.molcel.2008.09.026
Yu, X., Liu, H., Klejnot, J., & Lin, C. (2010). The cryptochrome blue light receptors. The arabidopsis book, 8, e0135-e0135. https://doi.org/10.1199/tab.0135
Yu, X., Sayegh, R., Maymon, M., Warpeha, K., Klejnot, J., Yang, H., … Lin, C. (2009). Formation of nuclear bodies of Arabidopsis CRY2 in response to blue light is associated with its blue light-dependent degradation. The Plant Cell, 21, 118-130. https://doi.org/10.1105/tpc.108.061663
Zoltowski, B. D., & Imaizumi, T. (2014). Structure and function of the ZTL/FKF1/LKP2 group proteins in Arabidopsis. The Enzymes, 35, 213-239. https://doi.org/10.1016/B978-0-12-801922-1.00009-9
Zuo, Z., Liu, H., Liu, B., Liu, X., & Lin, C. (2011). Blue light-dependent interaction of CRY2 with SPA1 regulates COP1 activity and floral initiation in Arabidopsis. Current Biology, 21, 841-847. https://doi.org/10.1016/j.cub.2011.03.048
Zuo, Z.-C., Meng, Y.-Y., Yu, X.-H., Zhang, Z.-L., Feng, D.-S., Sun, S.-F., … Lin, C.-T. (2012). A study of the blue-light-dependent phosphorylation, degradation, and photobody formation of Arabidopsis CRY2. Molecular Plant, 5, 726-733. https://doi.org/10.1093/mp/sss007