The timing of many physiological and developmental processes in most eukaryotes is under the control of a circadian clock. This endogenous, self-sustaining oscillator maintains a rhythm of ca. 24 h in processes as diverse as human sleep/wake cycles, insect pupal eclosion, fungal sporulation and the movement of plant leaves. Many of the key events in plant development, such as flowering time, depend on receiving the appropriate environmental signals at the right time, and the circadian timekeeping mechanism allows them to keep pace with and anticipate cyclic events in their environment.
The central pacemaker driving circadian rhythms in plants consists of one or more autoregulatory feedback loops that are still being molecularly dissected. Work in my lab focuses on post-transcriptional control of the clock and in defining the molecular components that comprise the oscillator.
ZEITLUPE (ZTL) is an F-box protein originally isolated as a long period mutant in Arabidopsis. It, and two related family members, are unique among the nearly 700 plant F-box proteins in possessing a blue-light sensing LOV (Light Oxygen and Voltage) domain at its N-terminus, very similar to the flavin-binding regions found in the phototropins. ZTL targets two members of a closely related family of pseudoresponse regulators (TOC1 and PRR5) that are key in setting the pace of the oscillator. Our work with ZTL has focused on understanding the role of each of three domains that comprise the protein, in the context of the circadian system. We identified ZTL as a novel blue light photoreceptor, the first F-box protein to possess this property (Kim et al., 2007).
Model of the HSP90 chaperone cycle with the co-chaperone GIGANTEA acting on the client ZEITLUPE. Nascent ZTL is likely to first interact with HSP40/HSP70. GI is proposed to help introduce ZTL into the HSP90 chaperone cycle via interaction with the N-terminal LOV domain. Subsequently, an HSP90-GI-ZTL complex forms to facilitate maturation of ZTL. Not shown is the effect of blue light in facilitating the initial GI-ZTL interaction.
Ritter A, Iñigo S, Fernández-Calvo P, Heyndrickx KS, Dhondt S, Shi H, De Milde L, Vanden Bossche R, De Clercq R, Eeckhout D, Ron M, Somers DE, Inzé D, Gevaert K, De Jaeger G, Vandepoele K, Pauwels L, Goossens A. The transcriptional repressor complex FRS7-FRS12 regulates flowering time and growth in Arabidopsis. Nat Commun. 2017 May 11;8:15235. doi: 10.1038/ncomms15235.
Pudasaini A, Shim JS, Song YH, Shi H, Kiba T, Somers DE, Imaizumi T, Zoltowski BD. Kinetics of the LOV domain of ZEITLUPE determine its circadian function in Arabidopsis. Elife. 2017 Feb 28;6. pii: e21646. doi: 10.7554/eLife.21646.
Cha JY, Kim J, Kim TS, Zeng Q, Wang L, Lee SY, Kim WY, Somers DE. GIGANTEA is a co-chaperone which facilitates maturation of ZEITLUPE in the Arabidopsis circadian clock. Nat Commun. 2017 Feb 23;8(1):3. doi: 10.1038/s41467-016-0014-9.
Choudhary MK, Nomura Y, Shi H, Nakagami H, Somers DE. Circadian Profiling of the Arabidopsis Proteome Using 2D-DIGE. Front Plant Sci. 2016 Jul 12;7:1007. doi: 10.3389/fpls.2016.01007.
Foo M, Somers DE, Kim PJ. 2016. Kernel architecture of the genetic circuitry of the Arabidopsis circadian system. PLoS.Comput.Biol. 12:e1004748.
Choudhary MK, Nomura Y, Wang L, Nakagami H, Somers DE. 2015. Quantitative circadian phosphoproteomic analysis of Arabidopsis reveals extensive clock control of key components in physiological, metabolic and signaling pathways. Mol Cell Proteomics Aug;14(8):2243-60. doi: 10.1074/mcp.M114.047183.
Kim J, Geng R, Gallenstein RA, Somers DE. 2013. The F-box protein ZEITLUPE controls stability and nucleocytoplasmic partitioning of GIGANTEA. Development 140(19):4060-9.
Liu H, Wang Q, Liu Y, Zhao X, Imaizumi T, Somers DE, Tobin EM, Lin C. 2013. Arabidopsis CRY2 and ZTL mediate blue-light regulation of the transcription factor CIB1 by distinct mechanisms. Proc Natl Acad Sci U S A. Oct 22;110(43):17582-7
Kim Y, Han S, Yeom M, Kim H, Lim J, Cha JY, Kim WY, Somers DE, Putterill J, Nam HG, Hwang D. 2013. Balanced Nucleocytosolic Partitioning Defines a Spatial Network to Coordinate Circadian Physiology in Plants. Dev Cell. doi:pii: S1534-5807(13)00345-6. 10.1016/j.devcel.2013.06.006.
Kim Y, Lim J, Yeom M, Kim H, Kim J, Wang L, Kim WY, Somers DE, Nam HG. 2013. ELF4 regulates GIGANTEA chromatin access through subnuclear sequestration. Cell Rep. Mar 28;3(3):671-7. doi: 10.1016/j.celrep.2013.02.021.
Wang L, Kim J, Somers DE. 2013. Transcriptional corepressor TOPLESS complexes with pseudoresponse regulator proteins and histone deacetylases to regulate circadian transcription. Proc. Natl. Acad. Sci. U. S. A 110: 761-766.
Kim Y, Yeom M, Kim H, Lim J, Koo HJ, Hwang D, Somers D, Nam HG. 2012. GIGANTEA and EARLY FLOWERING 4 in Arabidopsis exhibit differential phase-specific genetic influences over a diurnal cycle. Mol. Plant 5: 678-687.
Kim TS, Kim WY, Fujiwara S, Kim J, Cha JY, Park JH, Lee SY, Somers DE. 2011. HSP90 functions in the circadian clock through stabilization of the client F-box protein ZEITLUPE. Proc Natl Acad Sci U S A. Oct 4;108:16843-8. Epub 2011 Sep 26.
Johansson M., McWatters H.G., Bakó L., Takata N., Gyula P., Hall A., Somers D.E., Millar A.J., Eriksson M.E. 2011. Partners in time: EARLY BIRD associates with ZEITLUPE and regulates the speed of the Arabidopsis clock. Plant Physiol. 155:2108-22.
Kim, J and Somers D.E. 2010. Rapid assessment of gene function in the circadian clock using artificial microRNA in Arabidopsis mesophyll protoplasts. Plant Physiol. 154:611- 21.
Wang , L. Fujiwara, S and Somers, D.E. 2010. PRR5 regulates phosphorylation, nuclear import and subnuclear localization of TOC1 in the Arabidopsis circadian clock. EMBO J. 29:1903-15.
Kim, W.Y., Salome, P.A., Fujiwara, S., Somers, D. E., and McClung, C.R. 2010. Characterization of pseudo- response regulators in plants. In Melvin, I.S. (ed.), Methods in Enzymology: Two-Component Signaling Systems, Part C, . Academic Press, pp. 357-378.
Fujiwara, S., Wang, L., Han, L., Suh, S. S., Salome, P. A., McClung, C. R., Somers, D. E. 2008. Post-translational regulation of the Arabidopsis circadian clock through selective proteolysis and phosphorylation of pseudo- response regulator proteins. J.Biol.Chem. 283: 23073-23083
Jin JB, Jin YH, Lee J, Miura K, Yoo CY, Kim WY, Van Oosten M, Hyun Y, Somers DE, Lee I, Yun DJ, Bressan RA, Hasegawa PM. 2008. The SUMO E3 ligase, AtSIZ1, regulates flowering by controlling a salicylic acid-mediated floral promotion pathway and through affects on FLC chromatin structure. Plant J. 53(3):530-540
Kim, W.Y, Fujiwara, S., Suh, S.S., Kim, J., Kim, Y., Han, L., David, K., Putterill, J., Nam. H.G., and Somers, D.E. 2007. ZEITLUPE is a circadian photoreceptor stabilized by GIGANTEA in blue light. Nature 449: 356-360.
Allen T., Koustenis A., Theodorou G.,Somers, D.E., Kay S.A., Whitelam G.C., Devlin P.F. 2006 Arabidopsis FHY3 specifically gates phytochrome signaling to the circadian clock. Plant Cell 18: 2506-2516[pdf]
Kevei,E., Gyula,P., Hall,A., Kozma-Bognar,L., Kim,W.Y., Eriksson,M.E., Toth,R., Hanano,S., Feher,B., Southern,M.M., Bastow,R.M., Viczian,A., Hibberd,V., Davis,S.J.,Somers, D.E., Nagy,F., and Millar,A.J. 2006 Forward genetic analysis of the circadian clock separates the multiple functions of ZEITLUPE. Plant Physiol 140:933-945 [pdf]
Kim, W.Y., Hicks, K. A. and Somers, D.E. 2005. Independent roles for EARLY FLOWERING 3 and ZEITLUPE in the control of circadian timing, hypocotyl length, and flowering time. Plant Physiol. 139:1557-69. [pdf]
Han, L., Mason, M., Risseeuw, E.P., Crosby, W.L. and Somers, D.E. 2004. Formation of an SCFZTL complex is required for proper regulation of circadian timing. Plant J. 40: 291-301. [pdf]
Somers, D.E., Kim,W.Y., and Geng, R. 2004. The F-Box protein ZEITLUPE confers dosage-dependent control on the circadian clock, photomorphogenesis, and flowering time. Plant Cell 16: 769-782. [pdf]
Mas P., Kim WY, Somers D.E., and Kay S.A. 2003. Targeted degradation of TOC1 by ZTL modulates circadian function in Arabidopsis thaliana. Nature. 426:567-70. [pdf]
Kim, W.Y., Geng, R., and Somers, D.E. 2003. Circadian phase-specific degradation of the F-box protein ZTL is mediated by the proteasome. Proc Natl Acad Sci U S A 100(8): 4933-4938. [pdf]
Risseeuw, E.P., Daskalchuk, T.E., Banks, T.W., Liu, E., Cotelesage, J., Hellmann, H., Estelle, M., Somers, D.E., and Crosby, W.L. 2003. Protein interaction analysis of SCF ubiquitin E3 ligase subunits from Arabidopsis. Plant J. 34(6):753-767. [pdf]
Kim J, Somers DE. An HSP90 co-chaperone controls circadian proteostasis. Cell Cycle. 2017 Jul 19:1-2. doi: 10.1080/15384101.2017.1345238.
Somers D.E. 2012. The Arabidopsis clock: time for an about-face? Genome Biol. 13: 153.
Meier I, Somers D.E. 2011. Regulation of nucleocytoplasmic trafficking in plants.Curr Opin Plant Biol. 2011 Oct 14:538-46.
Nelson, R.J. (ed.), Denlinger, D.L. (ed.), Somers, D. E. (ed.) 2010. Photoperiodism: The Biological Calendar. Oxford University Press, pp. 600.
Somers, D. E. and Fujiwara, S. (2009) Thinking outside the F-box: novel ligands for novel receptors. Trends Plant Sci. 14(4):206-213.
Somers, D. E., Fujiwara, S., Kim, W. Y., Suh, S. S. 2007. Post-translational photomodulation of circadian amplitude. Cold Spring Harb. Symp. Quant. Biol. 72: 193-200
Somers, D.E. 2005. Entrainment of the Circadian Clock. In: Endogenous Plant Rhythms, eds. Hall, A.J.W and McWatters, H.G., Oxford: Blackwell, pp. 85-105
Somers, D.E. 2005. ZEITLUPE and the Control of Circadian Timing. In: Light Sensing in Plants, eds.Wada, M., Shimazaki, K., and Iino, M., Tokyo: Springer, pp. 347-354..
Somers, D.E. 2003. Photobiology of Circadian Rhythms. In: CRC Handbook of Organic Photochemistry and Photobiology, 2nd Edition, William Horspool and Francesco Lenci, eds.
Somers, D.E. 2001. Clock-associated genes in Arabidopsis: a family affair. Philos Trans R Soc Lond B Biol Sci. 356:1745-53. [pdf]
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