Abstract
Amidst the discussions regarding how the information about light or darkness is transduced to the cyanobacterial circadian clock, it was found that it turned out to be affected by metabolites that reflect photosynthetic activity. Reconstituting the bacterial timekeeper in a test tube containing only KaiA, KaiB, KaiC, ATP, and magnesium enabled a detailed functional analysis of the circadian clock. Here we added CikA, which competes with KaiA for the common binding site on KaiB. Quinone is a redox-sensing metabolite used as an electron shuttle in both photosynthesis and cellular respiration, and its oxidized form as a proxy for darkness becomes acutely abundant at the onset of sunset. Applying a dark pulse to cyanobacteria forces their gene expression rhythm to be shifted in a phase-dependent manner. In our attempt to mimic this process in vitro, oxidized quinone inactivated KaiA and CikA and generated a phase advance and delay respectively, in agreement with the in vivo data. Additionally, magnesium showed a role in inhibiting the KaiC phosphorylation in vitro. A possible history of clock evolution can be suggested from this finding since magnesium could directly modulate the KaiC-only pacemaker, a supposed timekee** relic of the past that gave rise to today’s intricate KaiABC clock.
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References
Chang YG, Tseng R, Kuo NW, LiWang A (2012) Rhythmic ring-ring stacking drives the circadian oscillator clockwise. Proc Natl Acad Sci U S A 109:16847–16851. https://doi.org/10.1073/pnas.1211508109
Chang YG et al (2015) Circadian rhythms. A protein fold switch joins the circadian oscillator to clock output in cyanobacteria. Science 349:324–328. https://doi.org/10.1126/science.1260031
Diamond S, Rubin BE, Shultzaberger RK, Chen Y, Barber CD, Golden SS (2017) Redox crisis underlies conditional light-dark lethality in cyanobacterial mutants that lack the circadian regulator, RpaA. Proc Natl Acad Sci U S A 114:E580–E589. https://doi.org/10.1073/pnas.1613078114
Dong G et al (2010) Elevated ATPase activity of KaiC applies a circadian checkpoint on cell division in Synechococcus elongatus. Cell 140:529–539. https://doi.org/10.1016/j.cell.2009.12.042
Dvornyk V (2009) The circadian clock gear in cyanobacteria: assembled by evolution. In: Ditty JL, Mackey SR, Johnson CH (eds) Bacterial circadian programs. Springer, Berlin, Heidelberg, pp 241–258. https://doi.org/10.1007/978-3-540-88431-6_14
Dvornyk V, Vinogradova O, Nevo E (2003) Origin and evolution of circadian clock genes in prokaryotes. Proc Natl Acad Sci U S A 100:2495–2500. https://doi.org/10.1073/pnas.0130099100
Egli M, Mori T, Pattanayek R, Xu Y, Qin X, Johnson CH (2012) Dephosphorylation of the core clock protein KaiC in the cyanobacterial KaiABC circadian oscillator proceeds via an ATP synthase mechanism. Biochemistry 51:1547–1558. https://doi.org/10.1021/bi201525n
Escoubas JM, Lomas M, LaRoche J, Falkowski PG (1995) Light intensity regulation of cab gene transcription is signaled by the redox state of the plastoquinone pool. Proc Natl Acad Sci U S A 92:10237–10241. https://doi.org/10.1073/pnas.92.22.10237
Feeney KA et al (2016) Daily magnesium fluxes regulate cellular timekee** and energy balance. Nature 532:375–379. https://doi.org/10.1038/nature17407
Förstner U, Wittmann GTW (1979) Metal transfer between solid and aqueous phases. In: Förstner U, Wittmann GTW (eds) Metal pollution in the aquatic environment. Springer, Berlin, Heidelberg, pp 197–270. https://doi.org/10.1007/978-3-642-96511-1_5
Gao T, Zhang X, Ivleva NB, Golden SS, LiWang A (2007) NMR structure of the pseudo-receiver domain of CikA. Protein Sci 16:465–475. https://doi.org/10.1110/ps.062532007
Gutu A, O'Shea EK (2013) Two antagonistic clock-regulated histidine kinases time the activation of circadian gene expression. Mol Cell 50:288–294. https://doi.org/10.1016/j.molcel.2013.02.022
Horita J, Zimmermann H, Holland HD (2002) Chemical evolution of seawater during the Phanerozoic: Implications from the record of marine evaporites. Geochimica et Cosmochimica Acta 66:3733–3756. https://doi.org/10.1016/S0016-7037(01)00884-5
Ito H et al (2009) Cyanobacterial daily life with Kai-based circadian and diurnal genome-wide transcriptional control in Synechococcus elongatus. Proc Natl Acad Sci U S A 106:14168–14173. https://doi.org/10.1073/pnas.0902587106
Ivleva NB, Bramlett MR, Lindahl PA, Golden SS (2005) LdpA: a component of the circadian clock senses redox state of the cell. EMBO J 24:1202–1210. https://doi.org/10.1038/sj.emboj.7600606
Ivleva NB, Gao T, LiWang AC, Golden SS (2006) Quinone sensing by the circadian input kinase of the cyanobacterial circadian clock. Proc Natl Acad Sci U S A 103:17468–17473. https://doi.org/10.1073/pnas.0606639103
Iwasaki H, Nishiwaki T, Kitayama Y, Nakajima M, Kondo T (2002) KaiA-stimulated KaiC phosphorylation in circadian timing loops in cyanobacteria. Proc Natl Acad Sci U S A 99:15788–15793. https://doi.org/10.1073/pnas.222467299
Jeong YM et al (2019) Magnesium regulates the circadian oscillator in cyanobacteria. J Biol Rhythms 34:380–390. https://doi.org/10.1177/0748730419851655
Johnson CH (1999) Forty years of PRCs--what have we learned? Chronobiol Int 16:711–743. https://doi.org/10.3109/07420529909016940
Johnson CH, Zhao C, Xu Y, Mori T (2017) Timing the day: what makes bacterial clocks tick? Nat Rev Microbiol 15:232–242. https://doi.org/10.1038/nrmicro.2016.196
Kageyama H, Nishiwaki T, Nakajima M, Iwasaki H, Oyama T, Kondo T (2006) Cyanobacterial circadian pacemaker: Kai protein complex dynamics in the KaiC phosphorylation cycle in vitro. Mol Cell 23:161–171. https://doi.org/10.1016/j.molcel.2006.05.039
Kaur M, Ng A, Kim P, Diekman C, Kim YI (2019) CikA modulates the effect of KaiA on the period of the circadian oscillation in KaiC phosphorylation. J Biol Rhythms 34:218–223. https://doi.org/10.1177/0748730419828068
Kim YI, Dong G, Carruthers CW Jr, Golden SS, LiWang A (2008) The day/night switch in KaiC, a central oscillator component of the circadian clock of cyanobacteria. Proc Natl Acad Sci U S A 105:12825–12830. https://doi.org/10.1073/pnas.0800526105
Kim YI, Vinyard DJ, Ananyev GM, Dismukes GC, Golden SS (2012) Oxidized quinones signal onset of darkness directly to the cyanobacterial circadian oscillator. Proc Natl Acad Sci U S A 109:17765–17769. https://doi.org/10.1073/pnas.1216401109
Kim YI, Boyd JS, Espinosa J, Golden SS (2015) Detecting KaiC phosphorylation rhythms of the cyanobacterial circadian oscillator in vitro and in vivo. Methods Enzymol 551:153–173. https://doi.org/10.1016/bs.mie.2014.10.003
Kim P, Kaszuba A, Jang H-I, Kim Y-I (2020a) Purification of GST-fused cyanobacterial central oscillator protein KaiC. Appl Biochem Microbiol 56:395–399
Kim P, Porr B, Mori T, Kim YS, Johnson CH, Diekman CO, Kim YI (2020b) CikA, an input pathway component, senses the oxidized Quinone signal to generate phase delays in the cyanobacterial circadian clock J Biol Rhythms 748730419900868. https://doi.org/10.1177/0748730419900868
Kitayama Y, Iwasaki H, Nishiwaki T, Kondo T (2003) KaiB functions as an attenuator of KaiC phosphorylation in the cyanobacterial circadian clock system. EMBO J 22:2127–2134. https://doi.org/10.1093/emboj/cdg212
Kitayama Y, Nishiwaki T, Terauchi K, Kondo T (2008) Dual KaiC-based oscillations constitute the circadian system of cyanobacteria. Genes Dev 22:1513–1521. https://doi.org/10.1101/gad.1661808
Kiyohara YB, Katayama M, Kondo T (2005) A novel mutation in kaiC affects resetting of the cyanobacterial circadian clock. J Bacteriol 187:2559–2564. https://doi.org/10.1128/JB.187.8.2559-2564.2005
Kondo T, Strayer CA, Kulkarni RD, Taylor W, Ishiura M, Golden SS, Johnson CH (1993) Circadian rhythms in prokaryotes: luciferase as a reporter of circadian gene expression in cyanobacteria. Proc Natl Acad Sci U S A 90:5672–5676
Lyu H, Lazar D (2017) Modeling the light-induced electric potential difference DeltaPsi across the thylakoid membrane based on the transition state rate theory. Biochim Biophys Acta Bioenerg 1858:239–248. https://doi.org/10.1016/j.bbabio.2016.12.009
Mackey SR, Choi J-S, Kitayama Y, Iwasaki H, Dong G, Golden SS (2008) Proteins found in a CikA interaction assay link the circadian clock, metabolism, and cell division in Synechococcus elongatus. J Bacteriol 190:3738. https://doi.org/10.1128/JB.01721-07
Markson JS, Piechura JR, Puszynska AM, O'Shea EK (2013) Circadian control of global gene expression by the cyanobacterial master regulator. RpaA Cell 155:1396–1408. https://doi.org/10.1016/j.cell.2013.11.005
Montgomery BL, Lagarias JC (2002) Phytochrome ancestry: sensors of bilins and light. Trends Plant Sci 7:357–366. https://doi.org/10.1016/s1360-1385(02)02304-x
Mullineaux CW (2014) Co-existence of photosynthetic and respiratory activities in cyanobacterial thylakoid membranes. Biochim Biophys Acta 1837:503–511. https://doi.org/10.1016/j.bbabio.2013.11.017
Mutsuda M, Michel KP, Zhang X, Montgomery BL, Golden SS (2003) Biochemical properties of CikA, an unusual phytochrome-like histidine protein kinase that resets the circadian clock in Synechococcus elongatus PCC 7942. J Biol Chem 278:19102–19110. https://doi.org/10.1074/jbc.M213255200
Nakajima M et al (2005) Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro. Science 308:414–415. https://doi.org/10.1126/science.1108451
Nishiwaki T, Iwasaki H, Ishiura M, Kondo T (2000) Nucleotide binding and autophosphorylation of the clock protein KaiC as a circadian timing process of cyanobacteria. Proc Natl Acad Sci U S A 97:495–499. https://doi.org/10.1073/pnas.97.1.495
Nishiwaki T, Satomi Y, Kitayama Y, Terauchi K, Kiyohara R, Takao T, Kondo T (2007) A sequential program of dual phosphorylation of KaiC as a basis for circadian rhythm in cyanobacteria. EMBO J 26:4029–4037. https://doi.org/10.1038/sj.emboj.7601832
Ouyang Y, Andersson CR, Kondo T, Golden SS, Johnson CH (1998) Resonating circadian clocks enhance fitness in cyanobacteria. Proc Natl Acad Sci U S A 95:8660–8664. https://doi.org/10.1073/pnas.95.15.8660
Pattanayek R, Wang J, Mori T, Xu Y, Johnson CH, Egli M (2004) Visualizing a circadian clock protein: crystal structure of KaiC and functional insights. Mol Cell 15:375–388. https://doi.org/10.1016/j.molcel.2004.07.013
Pattanayek R et al (2006) Analysis of KaiA-KaiC protein interactions in the cyano-bacterial circadian clock using hybrid structural methods. EMBO J 25:2017–2028. https://doi.org/10.1038/sj.emboj.7601086
Pattanayek R, Mori T, Xu Y, Pattanayek S, Johnson CH, Egli M (2009) Structures of KaiC circadian clock mutant proteins: a new phosphorylation site at T426 and mechanisms of kinase, ATPase and phosphatase. PLoS One 4:e7529. https://doi.org/10.1371/journal.pone.0007529
Pattanayek R, Sidiqi SK, Egli M (2012) Crystal structure of the redox-active cofactor dibromothymoquinone bound to circadian clock protein KaiA and structural basis for dibromothymoquinone's ability to prevent stimulation of KaiC phosphorylation by KaiA. Biochemistry 51:8050–8052. https://doi.org/10.1021/bi301222t
Piechura JR, Amarnath K, O'Shea EK (2017) Natural changes in light interact with circadian regulation at promoters to control gene expression in cyanobacteria. Elife 6:e32032. https://doi.org/10.7554/eLife.32032
Pohland AC, Schneider D (2019) Mg2+ homeostasis and transport in cyanobacteria – at the crossroads of bacterial and chloroplast Mg2+ import. Biol Chem 400:1289–1301. https://doi.org/10.1515/hsz-2018-0476
Puszynska AM, O'Shea EK (2017) Switching of metabolic programs in response to light availability is an essential function of the cyanobacterial circadian output pathway. Elife 6:e23210. https://doi.org/10.7554/eLife.23210
Rust MJ, Markson JS, Lane WS, Fisher DS, O'Shea EK (2007) Ordered phosphorylation governs oscillation of a three-protein circadian clock. Science 318:809–812. https://doi.org/10.1126/science.1148596
Rust MJ, Golden SS, O'Shea EK (2011) Light-driven changes in energy metabolism directly entrain the cyanobacterial circadian oscillator. Science 331:220–223. https://doi.org/10.1126/science.1197243
Schmitz O, Katayama M, Williams SB, Kondo T, Golden SS (2000) CikA, a bacteriophytochrome that resets the cyanobacterial circadian clock. Science 289:765–768. https://doi.org/10.1126/science.289.5480.765
Takai N et al (2006) A KaiC-associating SasA-RpaA two-component regulatory system as a major circadian timing mediator in cyanobacteria. Proc Natl Acad Sci U S A 103:12109–12114. https://doi.org/10.1073/pnas.0602955103
Taniguchi Y, Takai N, Katayama M, Kondo T, Oyama T (2010) Three major output pathways from the KaiABC-based oscillator cooperate to generate robust circadian kaiBC expression in cyanobacteria. Proc Natl Acad Sci U S A 107:3263–3268. https://doi.org/10.1073/pnas.0909924107
Teng SW, Mukherji S, Moffitt JR, de Buyl S, O'Shea EK (2013) Robust circadian oscillations in growing cyanobacteria require transcriptional feedback. Science 340:737–740. https://doi.org/10.1126/science.1230996
Tomita J, Nakajima M, Kondo T, Iwasaki H (2005) No transcription-translation feedback in circadian rhythm of KaiC phosphorylation. Science 307:251–254. https://doi.org/10.1126/science.1102540
Tseng R et al (2017) Structural basis of the day-night transition in a bacterial circadian clock. Science 355:1174–1180. https://doi.org/10.1126/science.aag2516
Utkilen HC (1982) Magnesium-limited growth of the cyanobacterium Anacystis nidulans. Microbiology 128:1849–1862. https://doi.org/10.1099/00221287-128-8-1849
Vakonakis I, LiWang AC (2004) Structure of the C-terminal domain of the clock protein KaiA in complex with a KaiC-derived peptide: implications for KaiC regulation. Proc Natl Acad Sci U S A 101:10925–10930. https://doi.org/10.1073/pnas.0403037101
Vakonakis I, Sun J, Wu T, Holzenburg A, Golden SS, LiWang AC (2004) NMR structure of the KaiC-interacting C-terminal domain of KaiA, a circadian clock protein: implications for KaiA-KaiC interaction. Proc Natl Acad Sci U S A 101:1479–1484. https://doi.org/10.1073/pnas.0305516101
Vijayan V, Zuzow R, O'Shea EK (2009) Oscillations in supercoiling drive circadian gene expression in cyanobacteria. Proc Natl Acad Sci U S A 106:22564–22568. https://doi.org/10.1073/pnas.0912673106
Waldron KJ, Rutherford JC, Ford D, Robinson NJ (2009) Metalloproteins and metal sensing. Nature 460:823–830. https://doi.org/10.1038/nature08300
Williams SB, Vakonakis I, Golden SS, AC LW (2002) Structure and function from the circadian clock protein KaiA of Synechococcus elongatus: a potential clock input mechanism. Proc Natl Acad Sci U S A 99:15357–15362. https://doi.org/10.1073/pnas.232517099
Wood TL et al (2010) The KaiA protein of the cyanobacterial circadian oscillator is modulated by a redox-active cofactor. Proc Natl Acad Sci U S A 107:5804–5809. https://doi.org/10.1073/pnas.0910141107
Xu Y, Mori T, Johnson CH (2003) Cyanobacterial circadian clockwork: roles of KaiA, KaiB and the kaiBC promoter in regulating KaiC. EMBO J 22:2117–2126. https://doi.org/10.1093/emboj/cdg168
Zhang X, Dong G, Golden SS (2006) The pseudo-receiver domain of CikA regulates the cyanobacterial circadian input pathway. Mol Microbiol 60:658–668. https://doi.org/10.1111/j.1365-2958.2006.05138.x
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Kim, P., Kim, YI. (2021). An In Vitro Approach to Elucidating Clock-Modulating Metabolites. In: Johnson, C.H., Rust, M.J. (eds) Circadian Rhythms in Bacteria and Microbiomes. Springer, Cham. https://doi.org/10.1007/978-3-030-72158-9_11
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