1
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Chow GK, Chavan AG, Heisler J, Chang YG, Zhang N, LiWang A, Britt RD. A Night-Time Edge Site Intermediate in the Cyanobacterial Circadian Clock Identified by EPR Spectroscopy. J Am Chem Soc 2022; 144:184-194. [PMID: 34979080 DOI: 10.1021/jacs.1c08103] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As the only circadian oscillator that can be reconstituted in vitro with its constituent proteins KaiA, KaiB, and KaiC using ATP as an energy source, the cyanobacterial circadian oscillator serves as a model system for detailed mechanistic studies of day-night transitions of circadian clocks in general. The day-to-night transition occurs when KaiB forms a night-time complex with KaiC to sequester KaiA, the latter of which interacts with KaiC during the day to promote KaiC autophosphorylation. However, how KaiB forms the complex with KaiC remains poorly understood, despite the available structures of KaiB bound to hexameric KaiC. It has been postulated that KaiB-KaiC binding is regulated by inter-KaiB cooperativity. Here, using spin labeling continuous-wave electron paramagnetic resonance spectroscopy, we identified and quantified two subpopulations of KaiC-bound KaiB, corresponding to the "bulk" and "edge" KaiBC sites in stoichiometric and substoichiometric KaiBiC6 complexes (i = 1-5). We provide kinetic evidence to support the intermediacy of the "edge" KaiBC sites as bridges and nucleation sites between free KaiB and the "bulk" KaiBC sites. Furthermore, we show that the relative abundance of "edge" and "bulk" sites is dependent on both KaiC phosphostate and KaiA, supporting the notion of phosphorylation-state controlled inter-KaiB cooperativity. Finally, we demonstrate that the interconversion between the two subpopulations of KaiC-bound KaiB is intimately linked to the KaiC phosphorylation cycle. These findings enrich our mechanistic understanding of the cyanobacterial clock and demonstrate the utility of EPR in elucidating circadian clock mechanisms.
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Affiliation(s)
- Gary K Chow
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Archana G Chavan
- School of Natural Sciences, University of California, Merced, California 95343, United States
| | - Joel Heisler
- Chemistry and Chemical Biology, University of California, Merced, California 95343, United States
| | - Yong-Gang Chang
- School of Natural Sciences, University of California, Merced, California 95343, United States
| | - Ning Zhang
- School of Natural Sciences, University of California, Merced, California 95343, United States
| | - Andy LiWang
- School of Natural Sciences, Chemistry and Biochemistry, Health Sciences Research Institute, and Center for Cellular and Biomolecular Machines, University of California, Merced, California 95343, United States
- Center for Circadian Biology, University of California, San Diego, La Jolla, California 92093, United States
| | - R David Britt
- Department of Chemistry, University of California, Davis, California 95616, United States
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2
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Chavan AG, Swan JA, Heisler J, Sancar C, Ernst DC, Fang M, Palacios JG, Spangler RK, Bagshaw CR, Tripathi S, Crosby P, Golden SS, Partch CL, LiWang A. Reconstitution of an intact clock reveals mechanisms of circadian timekeeping. Science 2021; 374:eabd4453. [PMID: 34618577 DOI: 10.1126/science.abd4453] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Archana G Chavan
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Jeffrey A Swan
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Joel Heisler
- Department of Chemistry and Biochemistry, University of California, Merced, CA 95343, USA
| | - Cigdem Sancar
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dustin C Ernst
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mingxu Fang
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joseph G Palacios
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Rebecca K Spangler
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Clive R Bagshaw
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Priya Crosby
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Susan S Golden
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA.,Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA.,Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Andy LiWang
- School of Natural Sciences, University of California, Merced, CA 95343, USA.,Department of Chemistry and Biochemistry, University of California, Merced, CA 95343, USA.,Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA.,Center for Cellular and Biomolecular Machines, University of California, Merced, CA 95343, USA.,Health Sciences Research Institute, University of California, Merced, CA 95343, USA
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3
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Cooperative Binding of KaiB to the KaiC Hexamer Ensures Accurate Circadian Clock Oscillation in Cyanobacteria. Int J Mol Sci 2019; 20:ijms20184550. [PMID: 31540310 PMCID: PMC6769508 DOI: 10.3390/ijms20184550] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/08/2019] [Accepted: 09/11/2019] [Indexed: 12/01/2022] Open
Abstract
The central oscillator generating cyanobacterial circadian rhythms comprises KaiA, KaiB, and KaiC proteins. Their interactions cause KaiC phosphorylation and dephosphorylation cycles over approximately 24 h. KaiB interacts with phosphorylated KaiC in competition with SasA, an output protein harboring a KaiB-homologous domain. Structural data have identified KaiB–KaiC interaction sites; however, KaiB mutations distal from the binding surfaces can impair KaiB–KaiC interaction and the circadian rhythm. Reportedly, KaiB and KaiC exclusively form a complex in a 6:6 stoichiometry, indicating that KaiB–KaiC hexamer binding shows strong positive cooperativity. Here, mutational analysis was used to investigate the functional significance of this cooperative interaction. Results demonstrate that electrostatic complementarity between KaiB protomers promotes their cooperative assembly, which is indispensable for accurate rhythm generation. SasA does not exhibit such electrostatic complementarity and noncooperatively binds to KaiC. Thus, the findings explain KaiB distal mutation effects, providing mechanistic insights into clock protein interplay.
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4
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Insights into histidine kinase activation mechanisms from the monomeric blue light sensor EL346. Proc Natl Acad Sci U S A 2019; 116:4963-4972. [PMID: 30808807 DOI: 10.1073/pnas.1813586116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Translation of environmental cues into cellular behavior is a necessary process in all forms of life. In bacteria, this process frequently involves two-component systems in which a sensor histidine kinase (HK) autophosphorylates in response to a stimulus before subsequently transferring the phosphoryl group to a response regulator that controls downstream effectors. Many details of the molecular mechanisms of HK activation are still unclear due to complications associated with the multiple signaling states of these large, multidomain proteins. To address these challenges, we combined complementary solution biophysical approaches to examine the conformational changes upon activation of a minimal, blue-light-sensing histidine kinase from Erythrobacter litoralis HTCC2594, EL346. Our data show that multiple conformations coexist in the dark state of EL346 in solution, which may explain the enzyme's residual dark-state activity. We also observe that activation involves destabilization of the helices in the dimerization and histidine phosphotransfer-like domain, where the phosphoacceptor histidine resides, and their interactions with the catalytic domain. Similar light-induced changes occur to some extent even in constitutively active or inactive mutants, showing that light sensing can be decoupled from activation of kinase activity. These structural changes mirror those inferred by comparing X-ray crystal structures of inactive and active HK fragments, suggesting that they are at the core of conformational changes leading to HK activation. More broadly, our findings uncover surprising complexity in this simple system and allow us to outline a mechanism of the multiple steps of HK activation.
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5
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Abstract
Life has adapted to Earth's day-night cycle with the evolution of endogenous biological clocks. Whereas these circadian rhythms typically involve extensive transcription-translation feedback in higher organisms, cyanobacteria have a circadian clock, which functions primarily as a protein-based post-translational oscillator. Known as the Kai system, it consists of three proteins KaiA, KaiB, and KaiC. In this chapter, we provide a detailed structural overview of the Kai components and how they interact to produce circadian rhythms of global gene expression in cyanobacterial cells. We discuss how the circadian oscillation is coupled to gene expression, intertwined with transcription-translation feedback mechanisms, and entrained by input from the environment. We discuss the use of mathematical models and summarize insights into the cyanobacterial circadian clock from theoretical studies. The molecular details of the Kai system are well documented for the model cyanobacterium Synechococcus elongatus, but many less understood varieties of the Kai system exist across the highly diverse phylum of Cyanobacteria. Several species contain multiple kai-gene copies, while others like marine Prochlorococcus strains have a reduced kaiBC-only system, lacking kaiA. We highlight recent findings on the genomic distribution of kai genes in Bacteria and Archaea and finally discuss hypotheses on the evolution of the Kai system.
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Affiliation(s)
- Joost Snijder
- Snijder Bioscience, Zevenwouden 143, 3524CN, Utrecht, The Netherlands
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Ilka Maria Axmann
- Synthetic Microbiology, Biology Department, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany.
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6
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Murakami R, Hokonohara H, Che DC, Kawai T, Matsumoto T, Ishiura M. Atomic force microscopy analysis of SasA-KaiC complex formation involved in information transfer from the KaiABC clock machinery to the output pathway in cyanobacteria. Genes Cells 2018. [PMID: 29527779 DOI: 10.1111/gtc.12574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cyanobacterial clock oscillator is composed of three clock proteins: KaiA, KaiB and KaiC. SasA, a KaiC-binding EnvZ-like orthodox histidine kinase involved in the main clock output pathway, exists mainly as a trimer (SasA3mer ) and occasionally as a hexamer (SasA6mer ) in vitro. Previously, the molecular mass of the SasA-KaiCDD complex, where KaiCDD is a mutant KaiC with two Asp substitutions at the two phosphorylation sites, has been estimated by gel-filtration chromatography to be larger than 670 kDa. This value disagrees with the theoretical estimation of 480 kDa for a SasA3mer -KaiC hexamer (KaiC6mer ) complex with a 1:1 molecular ratio. To clarify the structure of the SasA-KaiC complex, we analyzed KaiCDD with 0.1 mmol/L ATP and 5 mmol/L MgCl2 (Mg-ATP), SasA and a mixture containing SasA and KaiCDD6mer with Mg-ATP by atomic force microscopy (AFM). KaiCDD images were classified into two types with height distribution corresponding to KaiCDD monomer (KaiCDD1mer ) and KaiCDD6mer , respectively. SasA images were classified into two types with height corresponding to SasA3mer and SasA6mer , respectively. The AFM images of the SasA-KaiCDD mixture indicated not only KaiCDD1mer , KaiCDD6mer , SasA3mer and SasA6mer , but also wider area "islands," suggesting the presence of a polymerized form of the SasA-KaiCDD complex.
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Affiliation(s)
- Reiko Murakami
- Center for Gene Research, Nagoya University, Nagoya, Japan.,Division of Biological Sciences, Nagoya University, Nagoya, Japan
| | - Hitomi Hokonohara
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan.,Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, Japan
| | - Dock-Chil Che
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Tomoji Kawai
- Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, Japan
| | - Takuya Matsumoto
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Masahiro Ishiura
- Center for Gene Research, Nagoya University, Nagoya, Japan.,Division of Biological Sciences, Nagoya University, Nagoya, Japan
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7
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Swan JA, Golden SS, LiWang A, Partch CL. Structure, function, and mechanism of the core circadian clock in cyanobacteria. J Biol Chem 2018; 293:5026-5034. [PMID: 29440392 DOI: 10.1074/jbc.tm117.001433] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/09/2018] [Indexed: 01/09/2023] Open
Abstract
Circadian rhythms enable cells and organisms to coordinate their physiology with the cyclic environmental changes that come as a result of Earth's light/dark cycles. Cyanobacteria make use of a post-translational oscillator to maintain circadian rhythms, and this elegant system has become an important model for circadian timekeeping mechanisms. Composed of three proteins, the KaiABC system undergoes an oscillatory biochemical cycle that provides timing cues to achieve a 24-h molecular clock. Together with the input/output proteins SasA, CikA, and RpaA, these six gene products account for the timekeeping, entrainment, and output signaling functions in cyanobacterial circadian rhythms. This Minireview summarizes the current structural, functional and mechanistic insights into the cyanobacterial circadian clock.
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Affiliation(s)
- Jeffrey A Swan
- From the Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064
| | - Susan S Golden
- the Department of Molecular Biology and.,Center for Circadian Biology and Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, and
| | - Andy LiWang
- Center for Circadian Biology and Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, and.,the Department of Chemistry and Chemical Biology, University of California Merced, Merced, California 95343
| | - Carrie L Partch
- From the Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, .,Center for Circadian Biology and Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, and
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8
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Murakami R, Mutoh R, Ishii K, Ishiura M. Circadian oscillations of KaiA-KaiC and KaiB-KaiC complex formations in an in vitro
reconstituted KaiABC clock oscillator. Genes Cells 2016; 21:890-900. [DOI: 10.1111/gtc.12392] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 05/31/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Reiko Murakami
- Center for Gene Research; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8602 Japan
| | - Risa Mutoh
- Center for Gene Research; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8602 Japan
| | - Ketaro Ishii
- Center for Gene Research; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8602 Japan
| | - Masahiro Ishiura
- Center for Gene Research; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8602 Japan
- Division of Biological Sciences; Nagoya University; Furo-cho Chikusa Nagoya 464-8602 Japan
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9
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Becker NB, Mugler A, Ten Wolde PR. Optimal Prediction by Cellular Signaling Networks. PHYSICAL REVIEW LETTERS 2015; 115:258103. [PMID: 26722947 DOI: 10.1103/physrevlett.115.258103] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Indexed: 06/05/2023]
Abstract
Living cells can enhance their fitness by anticipating environmental change. We study how accurately linear signaling networks in cells can predict future signals. We find that maximal predictive power results from a combination of input-noise suppression, linear extrapolation, and selective readout of correlated past signal values. Single-layer networks generate exponential response kernels, which suffice to predict Markovian signals optimally. Multilayer networks allow oscillatory kernels that can optimally predict non-Markovian signals. At low noise, these kernels exploit the signal derivative for extrapolation, while at high noise, they capitalize on signal values in the past that are strongly correlated with the future signal. We show how the common motifs of negative feedback and incoherent feed-forward can implement these optimal response functions. Simulations reveal that E. coli can reliably predict concentration changes for chemotaxis, and that the integration time of its response kernel arises from a trade-off between rapid response and noise suppression.
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Affiliation(s)
- Nils B Becker
- Bioquant, Universtität Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Andrew Mugler
- Department of Physics, Purdue University, West Lafayette, Indiana 47907, USA
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10
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Chang YG, Cohen SE, Phong C, Myers WK, Kim YI, Tseng R, Lin J, Zhang L, Boyd JS, Lee Y, Kang S, Lee D, Li S, Britt RD, Rust MJ, Golden SS, LiWang A. Circadian rhythms. A protein fold switch joins the circadian oscillator to clock output in cyanobacteria. Science 2015; 349:324-8. [PMID: 26113641 PMCID: PMC4506712 DOI: 10.1126/science.1260031] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 05/08/2015] [Indexed: 12/26/2022]
Abstract
Organisms are adapted to the relentless cycles of day and night, because they evolved timekeeping systems called circadian clocks, which regulate biological activities with ~24-hour rhythms. The clock of cyanobacteria is driven by a three-protein oscillator composed of KaiA, KaiB, and KaiC, which together generate a circadian rhythm of KaiC phosphorylation. We show that KaiB flips between two distinct three-dimensional folds, and its rare transition to an active state provides a time delay that is required to match the timing of the oscillator to that of Earth's rotation. Once KaiB switches folds, it binds phosphorylated KaiC and captures KaiA, which initiates a phase transition of the circadian cycle, and it regulates components of the clock-output pathway, which provides the link that joins the timekeeping and signaling functions of the oscillator.
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Affiliation(s)
- Yong-Gang Chang
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Susan E Cohen
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Connie Phong
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - William K Myers
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Yong-Ick Kim
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Roger Tseng
- School of Natural Sciences, University of California, Merced, CA 95343, USA. Quantitative and Systems Biology, University of California, Merced, CA 95343, USA
| | - Jenny Lin
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Li Zhang
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Joseph S Boyd
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yvonne Lee
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Shannon Kang
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - David Lee
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sheng Li
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - R David Britt
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Michael J Rust
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Susan S Golden
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA. Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Andy LiWang
- School of Natural Sciences, University of California, Merced, CA 95343, USA. Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA. Quantitative and Systems Biology, University of California, Merced, CA 95343, USA. Chemistry and Chemical Biology, University of California, Merced, CA 95343, USA. Health Sciences Research Institute, University of California, Merced, CA 95343, USA.
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11
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Chen AH, Lubkowicz D, Yeong V, Chang RL, Silver PA. Transplantability of a circadian clock to a noncircadian organism. SCIENCE ADVANCES 2015; 1:e1500358. [PMID: 26229984 PMCID: PMC4517858 DOI: 10.1126/sciadv.1500358] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 04/24/2015] [Indexed: 05/25/2023]
Abstract
Circadian oscillators are posttranslationally regulated and affect gene expression in autotrophic cyanobacteria. Oscillations are controlled by phosphorylation of the KaiC protein, which is modulated by the KaiA and KaiB proteins. However, it remains unclear how time information is transmitted to transcriptional output. We show reconstruction of the KaiABC oscillator in the noncircadian bacterium Escherichia coli. This orthogonal system shows circadian oscillations in KaiC phosphorylation and in a synthetic transcriptional reporter. Coexpression of KaiABC with additional native cyanobacterial components demonstrates a minimally sufficient set of proteins for transcriptional output from a native cyanobacterial promoter in E. coli. Together, these results demonstrate that a circadian oscillator is transplantable to a heterologous organism for reductive study as well as wide-ranging applications.
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Affiliation(s)
- Anna H. Chen
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA 02115, USA
| | - David Lubkowicz
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA 02115, USA
| | - Vivian Yeong
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA 02115, USA
| | - Roger L. Chang
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA 02115, USA
| | - Pamela A. Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA 02115, USA
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12
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Iida T, Mutoh R, Onai K, Morishita M, Furukawa Y, Namba K, Ishiura M. Importance of the monomer-dimer-tetramer interconversion of the clock protein KaiB in the generation of circadian oscillations in cyanobacteria. Genes Cells 2014; 20:173-90. [DOI: 10.1111/gtc.12211] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 10/30/2014] [Indexed: 01/15/2023]
Affiliation(s)
- Takahiro Iida
- Center for Gene Research; Nagoya University; Furo-cho Chikusa-ku Nagoya Aichi 464-8602 Japan
- Division of Biological Science; Graduate School of Science; Nagoya University; Furo-cho Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Risa Mutoh
- Center for Gene Research; Nagoya University; Furo-cho Chikusa-ku Nagoya Aichi 464-8602 Japan
- Division of Biological Science; Graduate School of Science; Nagoya University; Furo-cho Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Kiyoshi Onai
- Center for Gene Research; Nagoya University; Furo-cho Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Megumi Morishita
- Center for Gene Research; Nagoya University; Furo-cho Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Yukio Furukawa
- Graduate School of Frontier Biosciences; Osaka University; 3-2 Yamadaoka Suita Osaka 565-0871 Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences; Osaka University; 3-2 Yamadaoka Suita Osaka 565-0871 Japan
| | - Masahiro Ishiura
- Center for Gene Research; Nagoya University; Furo-cho Chikusa-ku Nagoya Aichi 464-8602 Japan
- Division of Biological Science; Graduate School of Science; Nagoya University; Furo-cho Chikusa-ku Nagoya Aichi 464-8602 Japan
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13
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Mutoh R, Nishimura A, Yasui S, Onai K, Ishiura M. The ATP-mediated regulation of KaiB-KaiC interaction in the cyanobacterial circadian clock. PLoS One 2013; 8:e80200. [PMID: 24244649 PMCID: PMC3823767 DOI: 10.1371/journal.pone.0080200] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 10/01/2013] [Indexed: 11/19/2022] Open
Abstract
The cyanobacterial circadian clock oscillator is composed of three clock proteins—KaiA, KaiB, and KaiC, and interactions among the three Kai proteins generate clock oscillation in vitro. However, the regulation of these interactions remains to be solved. Here, we demonstrated that ATP regulates formation of the KaiB-KaiC complex. In the absence of ATP, KaiC was monomeric (KaiC1mer) and formed a complex with KaiB. The addition of ATP plus Mg2+ (Mg-ATP), but not that of ATP only, to the KaiB-KaiC1mer complex induced the hexamerization of KaiC and the concomitant release of KaiB from the KaiB-KaiC1mer complex, indicating that Mg-ATP and KaiB compete each other for KaiC. In the presence of ATP and Mg2+ (Mg-ATP), KaiC became a homohexameric ATPase (KaiC6mer) with bound Mg-ATP and formed a complex with KaiB, but KaiC hexamerized by unhydrolyzable substrates such as ATP and Mg-ATP analogs, did not. A KaiC N-terminal domain protein, but not its C-terminal one, formed a complex with KaiB, indicating that KaiC associates with KaiB via its N-terminal domain. A mutant KaiC6mer lacking N-terminal ATPase activity did not form a complex with KaiB whereas a mutant lacking C-terminal ATPase activity did. Thus, the N-terminal domain of KaiC is responsible for formation of the KaiB-KaiC complex, and the hydrolysis of the ATP bound to N-terminal ATPase motifs on KaiC6mer is required for formation of the KaiB-KaiC6mer complex. KaiC6mer that had been hexamerized with ADP plus aluminum fluoride, which are considered to mimic ADP-Pi state, formed a complex with KaiB, suggesting that KaiB is able to associate with KaiC6mer with bound ADP-Pi.
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Affiliation(s)
- Risa Mutoh
- Center for Gene Research, Nagoya University, Nagoya, Aichi, Japan
| | - Atsuhito Nishimura
- Center for Gene Research, Nagoya University, Nagoya, Aichi, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - So Yasui
- Center for Gene Research, Nagoya University, Nagoya, Aichi, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Kiyoshi Onai
- Center for Gene Research, Nagoya University, Nagoya, Aichi, Japan
| | - Masahiro Ishiura
- Center for Gene Research, Nagoya University, Nagoya, Aichi, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
- * E-mail:
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14
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Tseng R, Chang YG, Bravo I, Latham R, Chaudhary A, Kuo NW, Liwang A. Cooperative KaiA-KaiB-KaiC interactions affect KaiB/SasA competition in the circadian clock of cyanobacteria. J Mol Biol 2013; 426:389-402. [PMID: 24112939 DOI: 10.1016/j.jmb.2013.09.040] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 08/22/2013] [Accepted: 09/27/2013] [Indexed: 10/26/2022]
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. We also show that the A-loops of KaiC exist in a dynamic equilibrium between KaiA-accessible exposed and KaiA-inaccessible buried positions. Phosphorylation at the S431 residues of KaiC shift the A-loops toward the buried position, thereby weakening the KaiA-KaiC interaction, which is expected to be an additional mechanism promoting formation of the KaiABC complex. We also show that KaiB and the clock-output protein SasA compete for overlapping binding sites, which include the B-loops on the CI ring of KaiC. KaiA strongly shifts the competition in KaiB's favor. Thus, in addition to stimulating KaiC phosphorylation, it is likely that KaiA plays roles in switching KaiC from phosphorylation to dephosphorylation, as well as regulating clock output.
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Affiliation(s)
- Roger Tseng
- School of Natural Sciences, University of California, Merced, CA 95343, USA; Quantitative and Systems Biology Graduate Group, University of California, Merced, CA 95343, USA
| | - Yong-Gang Chang
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Ian Bravo
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Robert Latham
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | | | - Nai-Wei Kuo
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Andy Liwang
- School of Natural Sciences, University of California, Merced, CA 95343, USA; Quantitative and Systems Biology Graduate Group, University of California, Merced, CA 95343, USA; Chemistry and Chemical Biology, University of California, Merced, CA 95343, USA; Center for Chronobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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15
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Abstract
The SasA-RpaA two-component system constitutes a key output pathway of the cyanobacterial Kai circadian oscillator. To date, rhythm of phycobilisome associated (rpaA) is the only gene other than kaiA, kaiB, and kaiC, which encode the oscillator itself, whose mutation causes completely arrhythmic gene expression. Here we report a unique transposon insertion allele in a small ORF located immediately upstream of rpaA in Synechococcus elongatus PCC 7942 termed crm (for circadian rhythmicity modulator), which results in arrhythmic promoter activity but does not affect steady-state levels of RpaA. The crm ORF complements the defect when expressed in trans, but only if it can be translated, suggesting that crm encodes a small protein. The crm1 insertion allele phenotypes are distinct from those of an rpaA null; crm1 mutants are able to grow in a light:dark cycle and have no detectable oscillations of KaiC phosphorylation, whereas low-amplitude KaiC phosphorylation rhythms persist in the absence of RpaA. Levels of phosphorylated RpaA in vivo measured over time are significantly altered compared with WT in the crm1 mutant as well as in the absence of KaiC. Taken together, these results are consistent with the hypothesis that the Crm polypeptide modulates a circadian-specific activity of RpaA.
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16
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Saier MH. Microcompartments and protein machines in prokaryotes. J Mol Microbiol Biotechnol 2013; 23:243-69. [PMID: 23920489 DOI: 10.1159/000351625] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The prokaryotic cell was once thought of as a 'bag of enzymes' with little or no intracellular compartmentalization. In this view, most reactions essential for life occurred as a consequence of random molecular collisions involving substrates, cofactors and cytoplasmic enzymes. Our current conception of a prokaryote is far from this view. We now consider a bacterium or an archaeon as a highly structured, nonrandom collection of functional membrane-embedded and proteinaceous molecular machines, each of which serves a specialized function. In this article we shall present an overview of such microcompartments including (1) the bacterial cytoskeleton and the apparati allowing DNA segregation during cell division; (2) energy transduction apparati involving light-driven proton pumping and ion gradient-driven ATP synthesis; (3) prokaryotic motility and taxis machines that mediate cell movements in response to gradients of chemicals and physical forces; (4) machines of protein folding, secretion and degradation; (5) metabolosomes carrying out specific chemical reactions; (6) 24-hour clocks allowing bacteria to coordinate their metabolic activities with the daily solar cycle, and (7) proteinaceous membrane compartmentalized structures such as sulfur granules and gas vacuoles. Membrane-bound prokaryotic organelles were considered in a recent Journal of Molecular Microbiology and Biotechnology written symposium concerned with membranous compartmentalization in bacteria [J Mol Microbiol Biotechnol 2013;23:1-192]. By contrast, in this symposium, we focus on proteinaceous microcompartments. These two symposia, taken together, provide the interested reader with an objective view of the remarkable complexity of what was once thought of as a simple noncompartmentalized cell.
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Affiliation(s)
- Milton H Saier
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, Calif. 92093-0116, USA.
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17
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Egli M, Johnson CH. A circadian clock nanomachine that runs without transcription or translation. Curr Opin Neurobiol 2013; 23:732-40. [PMID: 23571120 DOI: 10.1016/j.conb.2013.02.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 02/21/2013] [Accepted: 02/23/2013] [Indexed: 11/15/2022]
Abstract
The biochemical basis of circadian timekeeping is best characterized in cyanobacteria. The structures of its key molecular players, KaiA, KaiB, and KaiC are known and these proteins can reconstitute a remarkable circadian oscillation in a test tube. KaiC is rhythmically phosphorylated and its phospho-status is a marker of circadian phase that regulates ATPase activity and the oscillating assembly of a nanomachine. Analyses of the nanomachines have revealed how their timing circuit is ratcheted to be unidirectional and how they stay in synch to ensure a robust oscillator. These insights are likely to elucidate circadian timekeeping in higher organisms, including how transcription and translation could appear to be a core circadian timer when the true pacemaker is an embedded biochemical oscillator.
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Affiliation(s)
- Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA.
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18
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Gutu A, O'Shea EK. Two antagonistic clock-regulated histidine kinases time the activation of circadian gene expression. Mol Cell 2013; 50:288-94. [PMID: 23541768 PMCID: PMC3674810 DOI: 10.1016/j.molcel.2013.02.022] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 02/04/2013] [Accepted: 02/20/2013] [Indexed: 01/13/2023]
Abstract
The cyanobacterial circadian pacemaker consists of a three-protein clock--KaiA, KaiB, and KaiC--that generates oscillations in the phosphorylation state of KaiC. Here we investigate how temporal information encoded in KaiC phosphorylation is transduced to RpaA, a transcription factor required for circadian gene expression. We show that phosphorylation of RpaA is regulated by two antagonistic histidine kinases, SasA and CikA, which are sequentially activated at distinct times by the Kai clock complex. SasA acts as a kinase toward RpaA, whereas CikA, previously implicated in clock input, acts as a phosphatase that dephosphorylates RpaA. CikA and SasA cooperate to generate an oscillation of RpaA activity that is distinct from that generated by either enzyme alone and offset from the rhythm of KaiC phosphorylation. Our observations reveal how circadian clocks can precisely control the timing of output pathways via the concerted action of two oppositely acting enzymes.
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Affiliation(s)
- Andrian Gutu
- Howard Hughes Medical Institute, Harvard University Faculty of Arts and Sciences Center for Systems Biology, Northwest Labs, 52 Oxford Street, Cambridge, MA 02138, USA
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19
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Hertel S, Brettschneider C, Axmann IM. Revealing a two-loop transcriptional feedback mechanism in the cyanobacterial circadian clock. PLoS Comput Biol 2013; 9:e1002966. [PMID: 23516349 PMCID: PMC3597532 DOI: 10.1371/journal.pcbi.1002966] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 01/15/2013] [Indexed: 01/29/2023] Open
Abstract
Molecular genetic studies in the circadian model organism Synechococcus have revealed that the KaiC protein, the central component of the circadian clock in cyanobacteria, is involved in activation and repression of its own gene transcription. During 24 hours, KaiC hexamers run through different phospho-states during daytime. So far, it has remained unclear which phospho-state of KaiC promotes kaiBC expression and which opposes transcriptional activation. We systematically analyzed various combinations of positive and negative transcriptional feedback regulation by introducing a combined TTFL/PTO model consisting of our previous post-translational oscillator that considers all four phospho-states of KaiC and a transcriptional/translational feedback loop. Only a particular two-loop feedback mechanism out of 32 we have extensively tested is able to reproduce existing experimental observations, including the effects of knockout or overexpression of kai genes. Here, threonine and double phosphorylated KaiC hexamers activate and unphosphorylated KaiC hexamers suppress kaiBC transcription. Our model simulations suggest that the peak expression ratio of the positive and the negative component of kaiBC expression is the main factor for how the different two-loop feedback models respond to removal or to overexpression of kai genes. We discuss parallels between our proposed TTFL/PTO model and two-loop feedback structures found in the mammalian clock. Many organisms possess a true circadian clock and coordinate their activities into daily cycles. Among the simplest organisms harboring such a 24 h-clock are cyanobacteria. Interactions among three proteins, KaiA, KaiB, KaiC, and cyclic KaiC phosphorylation govern the daily rhythm from gene expression to metabolism. Thus, the control of the kaiBC gene cluster expression is important for regulating the cyanobacterial clockwork. A picture has emerged in which different KaiC phospho-states activate and inhibit kaiBC expression. However, the mechanism remains to be solved. Here, we investigated the impact of each KaiC phospho-state on kaiBC expression by introducing a model that combines the circadian transcription/translation rhythm with the KaiABC-protein oscillator. We tested 32 combinations of positive and negative transcriptional regulation. It turns out that the kaiBC expression and KaiC phosphorylation dynamics in wild type and kai mutants can only be described by one mechanism: threonine and double phosphorylated KaiC hexamers activate kaiBC expression and the unphosphorylated state suppresses it. Further, we propose that the activator-to-repressor abundance ratio very likely determines the kaiBC expression dynamics in the simulated kai mutants. Our suggested clock model can be extended by further kinetic mechanisms to gain deeper insights into the various underlying processes of circadian gene regulation.
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Affiliation(s)
- Stefanie Hertel
- Institute for Theoretical Biology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- * E-mail:
| | - Christian Brettschneider
- Mathematical Modelling of Cellular Processes, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ilka M. Axmann
- Institute for Theoretical Biology, Charité-Universitätsmedizin Berlin, Berlin, Germany
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20
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Pattanayek R, Yadagiri KK, Ohi MD, Egli M. Nature of KaiB-KaiC binding in the cyanobacterial circadian oscillator. Cell Cycle 2013; 12:810-7. [PMID: 23388462 DOI: 10.4161/cc.23757] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
In the cyanobacteria Synechococcus elongatus and Thermosynechococcus elongatus, the KaiA, KaiB and KaiC proteins in the presence of ATP generate a post-translational oscillator (PTO) that can be reconstituted in vitro. KaiC is the result of a gene duplication and resembles a double doughnut with N-terminal CI and C-terminal CII hexameric rings. Six ATPs are bound between subunits in both the CI and CII ring. CI harbors ATPase activity, and CII catalyzes phosphorylation and dephosphorylation at T432 and S431 with a ca. 24-h period. KaiA stimulates KaiC phosphorylation, and KaiB promotes KaiC subunit exchange and sequesters KaiA on the KaiB-KaiC interface in the final stage of the clock cycle. Studies of the PTO protein-protein interactions are convergent in terms of KaiA binding to CII but have led to two opposing models of the KaiB-KaiC interaction. Electron microscopy (EM) and small angle X-ray scattering (SAXS), together with native PAGE using full-length proteins and separate CI and CII rings, are consistent with binding of KaiB to CII. Conversely, NMR together with gel filtration chromatography and denatured PAGE using monomeric CI and CII domains support KaiB binding to CI. To resolve the existing controversy, we studied complexes between KaiB and gold-labeled, full-length KaiC with negative stain EM. The EM data clearly demonstrate that KaiB contacts the CII ring. Together with the outcomes of previous analyses, our work establishes that only CII participates in interactions with KaiA and KaiB as well as with the His kinase SasA involved in the clock output pathway.
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Affiliation(s)
- Rekha Pattanayek
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
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21
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Rhythmic ring-ring stacking drives the circadian oscillator clockwise. Proc Natl Acad Sci U S A 2012; 109:16847-51. [PMID: 22967510 DOI: 10.1073/pnas.1211508109] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The oscillator of the circadian clock of cyanobacteria is composed of three proteins, KaiA, KaiB, and KaiC, which together generate a self-sustained ∼24-h rhythm of phosphorylation of KaiC. The mechanism propelling this oscillator has remained elusive, however. We show that stacking interactions between the CI and CII rings of KaiC drive the transition from the phosphorylation-specific KaiC-KaiA interaction to the dephosphorylation-specific KaiC-KaiB interaction. We have identified the KaiB-binding site, which is on the CI domain. This site is hidden when CI domains are associated as a hexameric ring. However, stacking of the CI and CII rings exposes the KaiB-binding site. Because the clock output protein SasA also binds to CI and competes with KaiB for binding, ring stacking likely regulates clock output. We demonstrate that ADP can expose the KaiB-binding site in the absence of ring stacking, providing an explanation for how it can reset the clock.
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22
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Murakami R, Mutoh R, Iwase R, Furukawa Y, Imada K, Onai K, Morishita M, Yasui S, Ishii K, Valencia Swain JO, Uzumaki T, Namba K, Ishiura M. The roles of the dimeric and tetrameric structures of the clock protein KaiB in the generation of circadian oscillations in cyanobacteria. J Biol Chem 2012; 287:29506-15. [PMID: 22722936 DOI: 10.1074/jbc.m112.349092] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The molecular machinery of the cyanobacterial circadian clock consists of three proteins, KaiA, KaiB, and KaiC. The three Kai proteins interact with each other and generate circadian oscillations in vitro in the presence of ATP (an in vitro KaiABC clock system). KaiB consists of four subunits organized as a dimer of dimers, and its overall shape is that of an elongated hexagonal plate with a positively charged cleft flanked by two negatively charged ridges. We found that a mutant KaiB with a C-terminal deletion (KaiB(1-94)), which lacks the negatively charged ridges, was a dimer. Despite its dimeric structure, KaiB(1-94) interacted with KaiC and generated normal circadian oscillations in the in vitro KaiABC clock system. KaiB(1-94) also generated circadian oscillations in cyanobacterial cells, but they were weak, indicating that the C-terminal region and tetrameric structure of KaiB are necessary for the generation of normal gene expression rhythms in vivo. KaiB(1-94) showed the highest affinity for KaiC among the KaiC-binding proteins we examined and inhibited KaiC from forming a complex with SasA, which is involved in the main output pathway from the KaiABC clock oscillator in transcription regulation. This defect explains the mechanism underlying the lack of normal gene expression rhythms in cells expressing KaiB(1-94).
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Affiliation(s)
- Reiko Murakami
- Center for Gene Research, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya 464-8602, Japan
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