DOCSLIB.ORG

NMR Structure of the Kaic-Interacting C-Terminal Domain of Kaia, a Circadian Clock Protein: Implications for Kaia–Kaic Interaction

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
NMR Structure of the Kaic-Interacting C-Terminal Domain of Kaia, a Circadian Clock Protein: Implications for Kaia–Kaic Interaction View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Texas A&M Repository NMR structure of the KaiC-interacting C-terminal domain of KaiA, a circadian clock protein: Implications for KaiA–KaiC interaction Ioannis Vakonakis*, Jingchuan Sun†‡, Tianfu Wu†, Andreas Holzenburg*†‡, Susan S. Golden†§, and Andy C. LiWang*¶ Departments of *Biochemistry and Biophysics and †Biology and ‡Microscopy and Imaging Center, Texas A&M University, College Station, TX 77843 Edited by Adriaan Bax, National Institutes of Health, Bethesda, MD, and approved December 5, 2003 (received for review August 27, 2003) KaiA is a two-domain circadian clock protein in cyanobacteria, necessary for phosphorylation. Similar to other pseudo-receiver acting as the positive element in a feedback loop that sustains the domains (16), KaiA activation most likely involves direct pro- oscillation. The structure of the N-terminal domain of KaiA is that tein–protein interactions of the N-terminal domain (with an of a pseudo-receiver, similar to those of bacterial response regu- as-yet-unidentified protein) that result in functional modulation lators, which likely interacts with components of the clock-reset- of the C-terminal effector domain. We postulated that KaiA is ting pathway. The C-terminal domain of KaiA is highly conserved a two-domain response regulator that acts as a timing input among cyanobacteria and enhances the autokinase activity of device to control the phase of the circadian period by modulating KaiC. Here we present the NMR structure of the C-terminal domain the KaiC phosphorylation state (9). of KaiA from the thermophilic cyanobacterium Thermosynecho- Here we report the solution structure of the Ϸ12-kDa KaiC- coccus elongatus BP-1. This domain adopts a novel all ␣-helical interacting C-terminal KaiA domain (residues 180–283, hence- homodimeric structure. Several mutations known to affect the forth named ThKaiA180C) from the thermophilic cyanobacte- period of the circadian oscillator are shown to be located at an rium Thermosynechococcus elongatus BP-1 (17), which grows exposed groove near the dimer interface. This NMR structure and Ͼ a 21-Å-resolution electron microscopy structure of the hexameric naturally at temperatures 50°C. The superior thermal stability KaiC particle allow us to postulate a mode of KaiA–KaiC interac- of this domain compared with the equivalent domain of KaiA tion, in which KaiA binds a linker region connecting two globular from S. elongatus (Fig. 5, which is published as supporting KaiC domains. information on the PNAS web site) enabled us to solve the structure at the physiological temperature of 50°C. We also determined the structure of S. elongatus KaiC by electron ircadian timekeeping oscillators and their accompanying Cmachinery comprise widespread regulatory mechanisms microscopy (EM) and single-particle reconstruction to a reso- that control the Ϸ24-h temporal pattern of diverse physiological lution of 21 Å. The structures raise interesting proposals for the processes, ranging from leaf movement to transcription regula- mode of KaiA–KaiC interaction. tion (1, 2). Circadian oscillators have been identified in virtually Materials and Methods all eucaryotic groups, including insects, fungi, plants, and mam- mals (3), and in cyanobacteria (4) and share mechanistic simi- Protein Preparation. Samples of S. elongatus KaiC and full-length larities, such as positive and negative transcription–translation KaiA were prepared as described (9). Expression and purifica- feedback loops (3). The cyanobacterial clock is the simplest and tion of ThKaiA180C are described elsewhere (18). NMR sam- potentially oldest (5) identified thus far, composed of three ples consisted of Ϸ1.3 mM protein in a buffer containing 20 mM interacting clock proteins, KaiA, KaiB, and KaiC, (4, 6) that form NaCl and 20 mM Na2HPO4, pH 7.07, at 23°C. Heterodimeric heteromultimeric complexes in vivo of sizes that oscillate in a (13C͞12C) samples of ThKaiA180C were prepared by mixing circadian manner (7). Transcription from practically all pro- equimolar amounts of oxidized 13C͞15N-enriched and -unen- moter regions in Synechococcus elongatus PCC 7942 is under riched protein in 6 M GdHCl͞50 mM NaCl͞20 mM Tris⅐HCl, pH circadian control, and transcription levels oscillate in phase or in 7.0, with the addition of 100 mM ␤-mercaptoethanol. Complete antiphase with transcription from the kai locus (4, 8). Indeed, reduction of the intermolecular disulfide bond was monitored by even promoters from other organisms, such as Escherichia coli, SDS͞PAGE. The protein was reconstituted by slow dilution with become rhythmically expressed in S. elongatus (8). a 20-fold excess volume of 50 mM NaCl͞20 mM Tris⅐HCl, pH 7.0, We previously reported that KaiA enhances the autokinase buffer and exchanged to the final NMR buffer and reoxidized. activity of KaiC in vitro (9). The KaiC phosphorylation state The final protein concentration of the heterodimeric samples BIOCHEMISTRY changes in vivo with a circadian pattern (10, 11), and ATP- was a 1.0 mM ThKaiA180C dimer (0.5 mM heterodimer plus binding by KaiC promotes formation of a hexameric KaiC 0.25 mM fully enriched homodimer plus 0.25 mM unenriched particle (12, 13), which is presumed to be the functional form of homodimer). Protein concentration was determined by absor- the protein. Evidence suggests that KaiC binds forked DNA bance at 280 nm by using a corrected extinction coefficient as when in the hexameric form (13). KaiC preparations have been suggested by Pace et al. (19). subjected to electron microscopic studies by two independent groups resulting in two structures (12, 13). KaiB is known to attenuate the KaiA-enhanced KaiC autokinase activity (9, 10, This paper was submitted directly (Track II) to the PNAS office. 14); however, no other information regarding its biochemical Abbreviations: NOE, nuclear Overhauser effect; EM, electron microscopy. function is presently available. Data Deposition: The solution structure has been deposited in the Protein Data Bank, KaiA is a two-domain protein. We previously showed that the www.rcsb.org (PBD ID codes 1Q6A and 1Q6B for the average minimized structure and the C-terminal KaiA domain alone is sufficient in vitro to enhance 25-structure ensemble, respectively). the autokinase activity of KaiC (9), whereas the N-terminal §To whom correspondence regarding circadian aspects should be addressed. E-mail: domain has no effect in that assay. The N-terminal domain of [email protected]. KaiA adopts the fold of a canonical response regulator receiver ¶To whom correspondence regarding structural aspects should be addressed. E-mail: domain (9, 15), although the primary sequence is dissimilar to [email protected]. that of receivers, and it lacks the conserved aspartyl residue © 2004 by The National Academy of Sciences of the USA www.pnas.org͞cgi͞doi͞10.1073͞pnas.0305516101 PNAS ͉ February 10, 2004 ͉ vol. 101 ͉ no. 6 ͉ 1479–1484 NMR Experiments. Sequential backbone and sidechain assign- primarily in the N-terminal pseudo-receiver domain; the C- ments of ThKaiA180C have been reported (18). All experiments terminal domain is highly conserved among all KaiA proteins were performed at 50°C with Varian Inova 600- and 500-MHz known to date (Fig. 7, which is published as supporting infor- spectrometers equipped with triple axis gradient probes. The mation on the PNAS web site). For instance, the S. elongatus and isomerization state of all proline residues was determined as T. elongatus N- and C-terminal domains share 30% and 62% trans (20). Stereospecific assignments of methylene and methyl identical residues, respectively. Furthermore, there are KaiA ␹ ␹ protons and 1 and leucine 2 angle determinations were pre- proteins that lack the N-terminal domain altogether (Anabaena formed as described (9). Interproton nuclear Overhauser effect sp. PCC 7120) or have only a truncated version (Nostoc punc- (NOE) distance restraints were obtained by 13C͞13C-edited 4D tiforme). The highly conserved C-terminal domain does not show NOESY (100-ms mixing time), 15N-edited 3D NOESY (100-ms significant sequence similarity to any other protein or derived mixing time), and 13C-edited͞12C-filtered 3D NOESY (21) domain from any organism studied. This simultaneous high (120-ms mixing time) spectra. Hydrogen bond restraints were degree of conservation in cyanobacteria and absence in other applied based on hydrogen exchange protection data collected organisms suggests that the C-terminal domain of KaiA serves by NMR and the existence of expected regular secondary a function specific to this system. structure NOEs (20). Backbone dynamics measurements (15N The C-terminal domain of the S. elongatus KaiA was unfa- 15 15 Ϫ1 T1, N T2, and N{ H} NOE) were performed and analyzed vorable for NMR structure determination because of limited as described (22). Spectrometer temperature was calibrated with aliphatic proton chemical shift dispersion and fast exchange of a methanol sample. amide protons. In addition, thermal denaturation experiments showed little cooperativity of unfolding (Fig. 5). In contrast, the NMR Structure Calculations. ␸ and ␺ dihedral angle values were C-terminal domain of KaiA from T. elongatus has greater derived from TALOS (23). Only residues for which all 10 predic- chemical shift dispersion and displays excellent cooperativity tions lie in the same region of the Ramachandran plot were used. (Fig. 5). Thus, we proceeded to solve the structure of the T. The XPLOR-NIH software package (24) was used for all stages of elongatus KaiA C-terminal domain, which by sequence identity NMR structure calculations. A distance-geometry simulating should be virtually equivalent to that of S. elongatus. annealing protocol in Cartesian space was used to generate an We previously showed that the N-terminal domain of S. initial set of structures from NOE and dihedral angle data. After elongatus KaiA is monomeric in solution even at high concen- inspection, the structures were refined by a simulated slow- trations (9). Full-length S. elongatus KaiA, however, elutes off a cooling process and a final minimization.
Load more

Recommended publications
  • Computational Modeling of Protein Interactions and Phosphoform Kinetics in the Kaiabc Cyanobacterial Circadian Clock
    Computational modeling of protein interactions and phosphoform kinetics in the KaiABC cyanobacterial circadian clock Mark Byrne1 1 Physics Department, Spring Hill College, 4000 Dauphin St., Mobile AL 36608 Corresponding author: Dr. Mark Byrne Physics Dept. 4000 Dauphin St Spring Hill College Mobile, AL 36608 USA TEL: 251-380-3080 Email: [email protected] Abstract The KaiABC circadian clock from cyanobacteria is the only known three-protein oscillatory system which can be reconstituted outside the cell and which displays sustained periodic dynamics in various molecular state variables. Despite many recent experimental and theoretical studies there are several open questions regarding the central mechanism(s) responsible for creating this ~24 hour clock in terms of molecular assembly/disassembly of the proteins and site- dependent phosphorylation and dephosphorylation of KaiC monomers. Simulations of protein- protein interactions and phosphorylation reactions constrained by analytical fits to partial reaction experimental data support the central mechanism of oscillation as KaiB-induced KaiA sequestration in KaiABC complexes associated with the extent of Ser431 phosphorylation in KaiC hexamers A simple two-state deterministic model in terms of the degree of phosphorylation of Ser431 and Thr432 sites alone can reproduce the previously observed circadian oscillation in the four population monomer phosphoforms in terms of waveform, amplitude and phase. This suggests that a cyclic phosphorylation scheme (involving cooperativity between adjacent Ser431 and Thr432 sites) is not necessary for creating oscillations. Direct simulations of the clock predict the minimum number of serine-only monomer subunits associated with KaiA sequestration and release, highlight the role of monomer exchange in rapid synchronization, and predict the average number of KaiA dimers sequestered per KaiC hexamer.
    [Show full text]
  • The Kaia Protein of the Cyanobacterial Circadian Oscillator Is Modulated by a Redox-Active Cofactor
    The KaiA protein of the cyanobacterial circadian oscillator is modulated by a redox-active cofactor Thammajun L. Wooda,1, Jennifer Bridwell-Rabbb,1, Yong-Ick Kimc,1, Tiyu Gaoa, Yong-Gang Changd, Andy LiWangd, David P. Barondeaub, and Susan S. Goldena,c,2,3 aThe Center for Biological Clocks Research, Department of Biology, and bDepartment of Chemistry, Texas A&M University, College Station, TX 77843; cCenter for Chronobiology and Division of Biological Sciences, University of California-San Diego, La Jolla, CA 92093-0116; and dSchool of Natural Sciences, University of California, Merced, CA 95340 Edited by Steven L. McKnight, The University of Texas Southwestern, Dallas, TX, and approved February 12, 2010 (received for review September 9, 2009) The circadian rhythms exhibited in the cyanobacterium Synechococ- varies inversely with light intensity, with the highest levels in cus elongatus are generated by an oscillator comprised of the the dark; in an ldpA mutant, CikA abundance is locked at its proteins KaiA, KaiB, and KaiC. An external signal that commonly lowest level independent of light intensity, and KaiA, whose affects the circadian clock is light. Previously, we reported that levels are not light dependent, is elevated (17, 20). the bacteriophytochrome-like protein CikA passes environmental We previously used the photosynthetic electron transport signals to the oscillator by directly binding a quinone and using inhibitor 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone cellular redox state as a measure of light in this photosynthetic (DBMIB), a water-soluble halogenated analog of native plasto- organism. Here, we report that KaiA also binds the quinone analog quinone (PQ) (21), in experiments designed to manipulate the 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB), and redox state of the PQ pool in cyanobacterial cells (21).
    [Show full text]
  • Cooperative Kaia–Kaib–Kaic Interactions Affect Kaib/Sasa Competition in the Circadian Clock of Cyanobacteria
    UC Merced UC Merced Previously Published Works Title Cooperative KaiA-KaiB-KaiC interactions affect KaiB/SasA competition in the circadian clock of cyanobacteria. Permalink https://escholarship.org/uc/item/71t4r3th Journal Journal of molecular biology, 426(2) ISSN 0022-2836 Authors Tseng, Roger Chang, Yong-Gang Bravo, Ian et al. Publication Date 2014 DOI 10.1016/j.jmb.2013.09.040 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Article Cooperative KaiA–KaiB–KaiC Interactions Affect KaiB/SasA Competition in the Circadian Clock of Cyanobacteria Roger Tseng 1,2, Yong-Gang Chang 1, Ian Bravo 1, Robert Latham 1, Abdullah Chaudhary 3, Nai-Wei Kuo 1 and Andy LiWang 1,2,4,5 1 - School of Natural Sciences, University of California, Merced, CA 95343, USA 2 - Quantitative and Systems Biology Graduate Group, University of California, Merced, CA 95343, USA 3 - School of Engineering, University of California, Merced, CA 95343, USA 4 - Chemistry and Chemical Biology, University of California, Merced, CA 95343, USA 5 - Center for Chronobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA Correspondence to Andy LiWang: 5200 North Lake Road, Merced, CA 95340, USA. Telephone: (209) 777-6341. [email protected] http://dx.doi.org/10.1016/j.jmb.2013.09.040 Edited by A. G. Palmer III Abstract The circadian oscillator of cyanobacteria is composed of only three proteins, KaiA, KaiB, and KaiC. Together, they generate an autonomous ~24-h biochemical rhythm of phosphorylation of KaiC. KaiA stimulates KaiC phosphorylation by binding to the so-called A-loops of KaiC, whereas KaiB sequesters KaiA in a KaiABC complex far away from the A-loops, thereby inducing KaiC dephosphorylation.
    [Show full text]
  • Kaib–Kaic Interactions Affect Kaib/Sasa Competition in the Circadian Clock of Cyanobacteria
    Article Cooperative KaiA–KaiB–KaiC Interactions Affect KaiB/SasA Competition in the Circadian Clock of Cyanobacteria Roger Tseng 1,2, Yong-Gang Chang 1, Ian Bravo 1, Robert Latham 1, Abdullah Chaudhary 3, Nai-Wei Kuo 1 and Andy LiWang 1,2,4,5 1 - School of Natural Sciences, University of California, Merced, CA 95343, USA 2 - Quantitative and Systems Biology Graduate Group, University of California, Merced, CA 95343, USA 3 - School of Engineering, University of California, Merced, CA 95343, USA 4 - Chemistry and Chemical Biology, University of California, Merced, CA 95343, USA 5 - Center for Chronobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA Correspondence to Andy LiWang: 5200 North Lake Road, Merced, CA 95340, USA. Telephone: (209) 777-6341. [email protected] http://dx.doi.org/10.1016/j.jmb.2013.09.040 Edited by A. G. Palmer III Abstract The circadian oscillator of cyanobacteria is composed of only three proteins, KaiA, KaiB, and KaiC. Together, they generate an autonomous ~24-h biochemical rhythm of phosphorylation of KaiC. KaiA stimulates KaiC phosphorylation by binding to the so-called A-loops of KaiC, whereas KaiB sequesters KaiA in a KaiABC complex far away from the A-loops, thereby inducing KaiC dephosphorylation. The switch from KaiC phosphorylation to dephosphorylation is initiated by the formation of the KaiB–KaiC complex, which occurs upon phosphorylation of the S431 residues of KaiC. We show here that formation of the KaiB–KaiC complex is promoted by KaiA, suggesting cooperativity in the initiation of the dephosphorylation complex. In the KaiA–KaiB interaction, one monomeric subunit of KaiB likely binds to one face of a KaiA dimer, leaving the other face unoccupied.
    [Show full text]
  • Visualizing a Circadian Clock Protein: Crystal Structure of Kaic and Functional Insights
    Molecular Cell, Vol. 15, 375–388, August 13, 2004, Copyright 2004 by Cell Press Visualizing a Circadian Clock Protein: Crystal Structure of KaiC and Functional Insights Rekha Pattanayek,1,4 Jimin Wang,2,4 Tetsuya Mori,3 dian control (Liu et al., 1995; Johnson, 2004). Even heter- Yao Xu,3 Carl Hirschie Johnson,3,* and Martin Egli1,* ologous promoters are expressed rhythmically when 1Department of Biochemistry introduced into cyanobacteria (Katayama et al., 1999; Vanderbilt University Nakahira et al., 2004). A mutational analysis discovered Nashville, Tennessee 37232 that this system is regulated by at least three essential 2 Department of Molecular Biophysics and Biochemistry clock genes, kaiA, kaiB, and kaiC, that form a cluster Bass Center for Structural Biology on the chromosome (Ishiura et al., 1998). The proteins New Haven, Connecticut 06520 encoded by these genes interact with each other (Iwa- 3 Department of Biological Sciences saki et al., 1999; Taniguchi et al., 2001) to form large Vanderbilt University complexes in vivo in which KaiC is the core (Kageyama Nashville, Tennessee 37235 et al., 2003). Not only do these three clock proteins interact, they influence each other’s activity. KaiC appears to be the Summary central protein; it can exist in both phosphorylated and non-phosphorylated forms in vivo (Nishiwaki et al., 2000; Circadian (daily) biological clocks express character- Iwasaki et al., 2002; Xu et al., 2003), and its phosphoryla- istics that are difficult to explain by known biochemical tion status is correlated with clock speed in vivo (Xu mechanisms, and will ultimately require characterizing et al., 2003). KaiC can auto-phosphorylate and auto- the structures, functions, and interactions of their mo- dephosphorylate in vitro (Nishiwaki et al., 2000; Xu et lecular components.
    [Show full text]
  • Structure, Function, and Mechanism of the Core Circadian Clock in Cyanobacteria
    Structure, function, and mechanism of the core circadian clock in cyanobacteria Jeffrey A. Swan1, Susan S. Golden2,3, Andy LiWang3,4, Carrie L. Partch1,3* 1Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064 2Department of Molecular Biology, University of California San Diego, La Jolla, CA 92093 3Center for Circadian Biology and Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093 4Chemistry and Chemical Biology, University of California Merced, Merced, CA 95343 *Correspondence to: [email protected] Running title: Structural review of the cyanobacterial clock Keywords: structural biology, circadian rhythm, circadian clock, cyanobacteria, protein dynamic, protein-protein interaction, post-translational modification, post-translational-oscillator, KaiABC Abbreviations: TTFL, transcription-translation feedback loop; PTO, post-translational oscillator; ATP, adenosine triphosphate; ADP, adenosine diphosphate; PsR, pseudo-receiver; HK, histidine kinase; RR, response regulator ______________________________________________________________________________ Abstract intertwined functions: timekeeping, entrainment Circadian rhythms enable cells and and output signaling. organisms to coordinate their physiology with the Timekeeping is achieved through a cycle of cyclic environmental changes that come as a result slow biochemical processes that together set the of Earth’s light/dark cycles. Cyanobacteria make period of oscillation close to 24 hours. For this use of a post-translational
    [Show full text]
  • A Dynamic Interaction Process Between Kaia and Kaic Is Critical To
    www.nature.com/scientificreports OPEN A dynamic interaction process between KaiA and KaiC is critical to the cyanobacterial circadian Received: 12 November 2015 Accepted: 12 April 2016 oscillator Published: 26 April 2016 Pei Dong1,2, Ying Fan2, Jianqiang Sun3, Mengting Lv2, Ming Yi4, Xiao Tan1,2 & Sen Liu1,2 The core circadian oscillator of cyanobacteria consists of three proteins, KaiA, KaiB, and KaiC. This circadian oscillator could be functionally reconstituted in vitro with these three proteins, and therefore has been a very important model in circadian rhythm research. KaiA can bind to KaiC and then stimulate its phosphorylation, but their interaction mechanism remains elusive. In this study, we followed the “second-site suppressor” strategy to investigate the interaction mechanism of KaiA and KaiC. Using protein sequence analyses, we showed that there exist co-varying residues in the binding interface of KaiA and KaiC. The followed mutagenesis study verified that these residues are important to the functions of KaiA and KaiC, but their roles could not be fully explained by the reported complex structures of KaiA and KaiC derived peptides. Combining our data with previous reports, we suggested a dynamic interaction mechanism in KaiA-KaiC interaction, in which both KaiA and the intrinsically disordered tail of KaiC undergo significant structural changes through conformational selection and induced fit during the binding process. At last, we presented a mathematic model to support this hypothesis and explained the importance of this interaction mechanism for the KaiABC circadian oscillator. Circadian rhythms are natural rhythms generated by biological clocks with a period of approximately 24 h.
    [Show full text]
  • Kaic Intersubunit Communication Facilitates Robustness of Circadian Rhythms in Cyanobacteria
    ARTICLE Received 24 Jun 2013 | Accepted 8 Nov 2013 | Published 5 Dec 2013 DOI: 10.1038/ncomms3897 OPEN KaiC intersubunit communication facilitates robustness of circadian rhythms in cyanobacteria Yohko Kitayama1, Taeko Nishiwaki-Ohkawa1,w, Yukiko Sugisawa1 & Takao Kondo1 The cyanobacterial circadian clock is the only model clock to have been reconstituted in vitro. KaiC, the central clock component, is a homohexameric ATPase with autokinase and autophosphatase activities. Changes in phosphorylation state have been proposed to switch KaiC’s activity between autokinase and autophosphatase. Here we analyse the molecular mechanism underlying the regulation of KaiC’s activity, in the context of its hexameric structure. We reconstitute KaiC hexamers containing different variant protomers, and mea- sure their autophosphatase and autokinase activities. We identify two types of regulatory mechanisms with distinct functions. First, local interactions between adjacent phosphoryla- tion sites regulate KaiC’s activities, coupling the ATPase and nucleotide-binding states at subunit interfaces of the CII domain. Second, the phosphorylation states of the protomers affect the overall activity of KaiC hexamers via intersubunit communication. Our findings indicate that intra-hexameric interactions play an important role in sustaining robust circadian rhythmicity. 1 Division of Biological Science, Graduate School of Science, Nagoya University and CREST, Japan Science and Technology Agency (JST), Furo-cho, Chikusa-ku, Nagoya 464 8602, Japan. w Present address: Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan. Correspondence and requests for materials should be addressed to Y.K. (email: [email protected]). NATURE COMMUNICATIONS | 4:2897 | DOI: 10.1038/ncomms3897 | www.nature.com/naturecommunications 1 & 2013 Macmillan Publishers Limited.
    [Show full text]
  • Cika, an Input Pathway Component, Senses the Oxidized Quinone Signal to Generate Phase Delays in the Cyanobacterial Circadian Clock
    JBRXXX10.1177/0748730419900868Journal Of Biological RhythmsKim et al. / C<sc>IK</sc>A GENERATES PHASE DELAYS IN THE CYANOBACTERIAL CIRCADIAN CLOCK 900868research-article2020 CikA, an Input Pathway Component, Senses the Oxidized Quinone Signal to Generate Phase Delays in the Cyanobacterial Circadian Clock Pyonghwa Kim,* Brianna Porr,* Tetsuya Mori,† Yong-Sung Kim,‡ Carl H. Johnson,† Casey O. Diekman,§,|| and Yong-Ick Kim*,||,1 *Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey, †Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, ‡Department of Physics, Applied Physics, and Astronomy, Rensselaer Polytechnic Institute, Troy, New York, §Department of Mathematical Sciences, New Jersey Institute of Technology, Newark, New Jersey, ||Institute for Brain and Neuroscience Research, New Jersey Institute of Technology, Newark, New Jersey Abstract The circadian clock is a timekeeping system in most organisms that keeps track of the time of day. The rhythm generated by the circadian oscillator must be constantly synchronized with the environmental day/night cycle to make the timekeeping system truly advantageous. In the cyanobacterial circa- dian clock, quinone is a biological signaling molecule used for entraining and fine-tuning the oscillator, a process in which the external signals are transduced into biological metabolites that adjust the phase of the circadian oscillation. Among the clock proteins, the pseudo-receiver domain of KaiA and CikA can sense external cues by detecting the oxidation state of quinone, a metabolite that reflects the light/dark cycle, although the molecular mechanism is not fully understood. Here, we show the antagonistic phase shifts produced by the quinone sensing of KaiA and CikA.
    [Show full text]
  • Japan Academy Prize To: Takao KONDO Designated Professor
    7 Japan Academy Prize to: Takao KONDO Designated Professor, Graduate School of Science and Emeritus Professor, Nagoya University for “Studies of Biological Time Measurement in Cyanobacteria by Reconstitution of the Circadian Clock” Outline of the work: To precisely fit their metabolic activities to day–night alternation of the environment, living organisms on the Earth have a biological clock (circadian clock) with a 24-hour period that originated by the rotation of the Earth. The question of the biological mechanism that generates a stable rhythm with a 24-hour period has fascinated researchers in several areas of the natural sciences. Dr. Takao Kondo devoted his graduate study to the circadian clock and, in the early 1990s, developed a new experimental system for studying the circadian clock in cyanobacteria. With this system, he isolated many clock mutants that enabled identification of the cyanobacterial clock genes kaiA, kaiB, and kaiC. By studying the expression of kai genes, the circadian clock model controlled by negative feedback of kai gene expression was proposed as the cyanobacterial circadian clock, which is similar to that for many eukaryotes. However, Dr. Kondo recognized that it was difficult to explain how the 24-hour periodicity is defined and how it compensates against ambient temperature. Therefore, he focused on biochemical analyses of KaiC activity that could alter the period length. In 2005, his group found that the phosphorylation rhythm of KaiC persisted even under conditions when no transcriptional and translational activity was permitted. This finding generated a major impact to the conventional hypothesis. Further, they found that the 24-hour rhythm of KaiC phosphorylation occur autonomously just by mixing three Kai proteins and ATP in a test tube.
    [Show full text]
  • Intermolecular Associations Determine the Dynamics of the Circadian Kaiabc Oscillator
    Intermolecular associations determine the dynamics of the circadian KaiABC oscillator Ximing Qina, Mark Byrneb, Tetsuya Moria, Ping Zouc, Dewight R. Williamsc, Hassane Mchaourabc, and Carl Hirschie Johnsona,c,1 Departments of aBiological Sciences and cMolecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232; and bPhysics Department, Spring Hill College, Mobile, AL 36608 Edited* by Robert Haselkorn, University of Chicago, Chicago, IL, and approved July 13, 2010 (received for review February 19, 2010) Three proteins from cyanobacteria (KaiA, KaiB, and KaiC) can re- hyperphosphorylated, KaiB binds to the KaiC, and KaiC de- constitute circadian oscillations in vitro. At least three molecular phosphorylates within a KaiA•KaiB•KaiC complex (7). When properties oscillate during this reaction, namely rhythmic phos- KaiC is completely hypophosphorylated, KaiB dissociates from phorylation of KaiC, ATP hydrolytic activity of KaiC, and assembly/ KaiC and the cycle begins anew. disassembly of intermolecular complexes among KaiA, KaiB, and The 3D structures for KaiA, KaiB, and KaiC are known (10). KaiC. We found that the intermolecular associations determine key The crystal structure of the KaiC hexamer elucidated KaiC in- dynamic properties of this in vitro oscillator. For example, mutations tersubunit organization and how KaiC might function as a scaf- within KaiB that alter the rates of binding of KaiB to KaiC also fold for the formation of KaiA•KaiB•KaiC complexes (17). predictably modulate the period of the oscillator. Moreover, we The KaiC structure also illuminated the mechanism of rhythmic show that KaiA can bind stably to complexes of KaiB and hyper- phosphorylation of KaiC by identifying three essential phos- phosphorylated KaiC.
    [Show full text]
  • Light-Driven Changes in Energy Metabolism Directly Entrain the Cyanobacterial Circadian Oscillator Michael J
    Light-Driven Changes in Energy Metabolism Directly Entrain the Cyanobacterial Circadian Oscillator Michael J. Rust, et al. Science 331, 220 (2011); DOI: 10.1126/science.1197243 This copy is for your personal, non-commercial use only. If you wish to distribute this article to others, you can order high-quality copies for your colleagues, clients, or customers by clicking here. Permission to republish or repurpose articles or portions of articles can be obtained by following the guidelines here. The following resources related to this article are available online at www.sciencemag.org (this infomation is current as of January 13, 2011 ): Updated information and services, including high-resolution figures, can be found in the online version of this article at: http://www.sciencemag.org/content/331/6014/220.full.html Supporting Online Material can be found at: http://www.sciencemag.org/content/suppl/2011/01/12/331.6014.220.DC1.html This article cites 27 articles, 17 of which can be accessed free: on January 13, 2011 http://www.sciencemag.org/content/331/6014/220.full.html#ref-list-1 This article appears in the following subject collections: Physiology http://www.sciencemag.org/cgi/collection/physiology www.sciencemag.org Downloaded from Science (print ISSN 0036-8075; online ISSN 1095-9203) is published weekly, except the last week in December, by the American Association for the Advancement of Science, 1200 New York Avenue NW, Washington, DC 20005. Copyright 2011 by the American Association for the Advancement of Science; all rights reserved. The title Science is a registered trademark of AAAS. REPORTS ation of KaiC (4, 5).
    [Show full text]