1
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Géron A, Werner J, Wattiez R, Matallana-Surget S. Towards the discovery of novel molecular clocks in Prokaryotes. Crit Rev Microbiol 2024; 50:491-503. [PMID: 37330701 DOI: 10.1080/1040841x.2023.2220789] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 01/17/2023] [Accepted: 02/15/2023] [Indexed: 06/19/2023]
Abstract
Diel cycle is of enormous biological importance as it imposes daily oscillation in environmental conditions, which temporally structures most ecosystems. Organisms developed biological time-keeping mechanisms - circadian clocks - that provide a significant fitness advantage over competitors by optimising the synchronisation of their biological activities. While circadian clocks are ubiquitous in Eukaryotes, they are so far only characterised in Cyanobacteria within Prokaryotes. However, growing evidence suggests that circadian clocks are widespread in the bacterial and archaeal domains. As Prokaryotes are at the heart of crucial environmental processes and are essential to human health, unravelling their time-keeping systems provides numerous applications in medical research, environmental sciences, and biotechnology. In this review, we elaborate on how novel circadian clocks in Prokaryotes offer research and development perspectives. We compare and contrast the different circadian systems in Cyanobacteria and discuss about their evolution and taxonomic distribution. We necessarily provide an updated phylogenetic analysis of bacterial and archaeal species that harbour homologs of the main cyanobacterial clock components. Finally, we elaborate on new potential clock-controlled microorganisms that represent opportunities of ecological and industrial relevance in prokaryotic groups such as anoxygenic photosynthetic bacteria, methanogenic archaea, methanotrophs or sulphate-reducing bacteria.
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Affiliation(s)
- Augustin Géron
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, UK
- Proteomic and Microbiology Department, University of Mons, Mons, Belgium
| | - Johannes Werner
- High Performance and Cloud Computing Group, Zentrum für Datenverarbeitung (ZDV), University of Tübingen, Tübingen, Germany
| | - Ruddy Wattiez
- Proteomic and Microbiology Department, University of Mons, Mons, Belgium
| | - Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, UK
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2
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Zheng C, Tang E. A topological mechanism for robust and efficient global oscillations in biological networks. Nat Commun 2024; 15:6453. [PMID: 39085205 PMCID: PMC11291491 DOI: 10.1038/s41467-024-50510-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 07/11/2024] [Indexed: 08/02/2024] Open
Abstract
Long and stable timescales are often observed in complex biochemical networks, such as in emergent oscillations. How these robust dynamics persist remains unclear, given the many stochastic reactions and shorter time scales demonstrated by underlying components. We propose a topological model that produces long oscillations around the network boundary, reducing the system dynamics to a lower-dimensional current in a robust manner. Using this to model KaiC, which regulates the circadian rhythm in cyanobacteria, we compare the coherence of oscillations to that in other KaiC models. Our topological model localizes currents on the system edge, with an efficient regime of simultaneously increased precision and decreased cost. Further, we introduce a new predictor of coherence from the analysis of spectral gaps, and show that our model saturates a global thermodynamic bound. Our work presents a new mechanism and parsimonious description for robust emergent oscillations in complex biological networks.
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Affiliation(s)
- Chongbin Zheng
- Center for Theoretical Biological Physics, Rice University, Houston, TX, 77005, USA
- Department of Physics and Astronomy, Rice University, Houston, TX, 77005, USA
| | - Evelyn Tang
- Center for Theoretical Biological Physics, Rice University, Houston, TX, 77005, USA.
- Department of Physics and Astronomy, Rice University, Houston, TX, 77005, USA.
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3
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Han X, Zhang D, Hong L, Yu D, Wu Z, Yang T, Rust M, Tu Y, Ouyang Q. Determining subunit-subunit interaction from statistics of cryo-EM images: observation of nearest-neighbor coupling in a circadian clock protein complex. Nat Commun 2023; 14:5907. [PMID: 37737245 PMCID: PMC10516925 DOI: 10.1038/s41467-023-41575-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 09/08/2023] [Indexed: 09/23/2023] Open
Abstract
Biological processes are typically actuated by dynamic multi-subunit molecular complexes. However, interactions between subunits, which govern the functions of these complexes, are hard to measure directly. Here, we develop a general approach combining cryo-EM imaging technology and statistical modeling and apply it to study the hexameric clock protein KaiC in Cyanobacteria. By clustering millions of KaiC monomer images, we identify two major conformational states of KaiC monomers. We then classify the conformational states of (>160,000) KaiC hexamers by the thirteen distinct spatial arrangements of these two subunit states in the hexamer ring. We find that distributions of the thirteen hexamer conformational patterns for two KaiC phosphorylation mutants can be fitted quantitatively by an Ising model, which reveals a significant cooperativity between neighboring subunits with phosphorylation shifting the probability of subunit conformation. Our results show that a KaiC hexamer can respond in a switch-like manner to changes in its phosphorylation level.
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Affiliation(s)
- Xu Han
- State Key Laboratory of Artificial Microstructure and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China
| | - Dongliang Zhang
- State Key Laboratory of Artificial Microstructure and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China
| | - Lu Hong
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Daqi Yu
- State Key Laboratory of Artificial Microstructure and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China
| | - Zhaolong Wu
- State Key Laboratory of Artificial Microstructure and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China
| | - Tian Yang
- State Key Laboratory of Artificial Microstructure and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China
| | - Michael Rust
- Departments of Molecular Genetics and Cell Biology and of Physics, University of Chicago, Chicago, IL, 60637, USA.
| | - Yuhai Tu
- IBM T. J. Watson Research Center, Yorktown Heights, NY, 10598, USA.
| | - Qi Ouyang
- State Key Laboratory of Artificial Microstructure and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China.
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, AAIC, Peking University, Beijing, 100871, China.
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4
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Pitsawong W, Pádua RAP, Grant T, Hoemberger M, Otten R, Bradshaw N, Grigorieff N, Kern D. From primordial clocks to circadian oscillators. Nature 2023; 616:183-189. [PMID: 36949197 PMCID: PMC10076222 DOI: 10.1038/s41586-023-05836-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 02/13/2023] [Indexed: 03/24/2023]
Abstract
Circadian rhythms play an essential part in many biological processes, and only three prokaryotic proteins are required to constitute a true post-translational circadian oscillator1. The evolutionary history of the three Kai proteins indicates that KaiC is the oldest member and a central component of the clock2. Subsequent additions of KaiB and KaiA regulate the phosphorylation state of KaiC for time synchronization. The canonical KaiABC system in cyanobacteria is well understood3-6, but little is known about more ancient systems that only possess KaiBC. However, there are reports that they might exhibit a basic, hourglass-like timekeeping mechanism7-9. Here we investigate the primordial circadian clock in Rhodobacter sphaeroides, which contains only KaiBC, to elucidate its inner workings despite missing KaiA. Using a combination of X-ray crystallography and cryogenic electron microscopy, we find a new dodecameric fold for KaiC, in which two hexamers are held together by a coiled-coil bundle of 12 helices. This interaction is formed by the carboxy-terminal extension of KaiC and serves as an ancient regulatory moiety that is later superseded by KaiA. A coiled-coil register shift between daytime and night-time conformations is connected to phosphorylation sites through a long-range allosteric network that spans over 140 Å. Our kinetic data identify the difference in the ATP-to-ADP ratio between day and night as the environmental cue that drives the clock. They also unravel mechanistic details that shed light on the evolution of self-sustained oscillators.
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Affiliation(s)
- Warintra Pitsawong
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA, USA
- Biomolecular Discovery, Relay Therapeutics, Cambridge, MA, USA
| | - Ricardo A P Pádua
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA, USA
| | - Timothy Grant
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Madison, WI, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Marc Hoemberger
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA, USA
- Treeline Biosciences, Watertown, MA, USA
| | - Renee Otten
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA, USA
- Treeline Biosciences, Watertown, MA, USA
| | - Niels Bradshaw
- Department of Biochemistry, Brandeis University, Waltham, MA, USA
| | - Nikolaus Grigorieff
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Howard Hughes Medical Institute, RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Dorothee Kern
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA, USA.
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5
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Swan JA, Sandate CR, Chavan AG, Freeberg AM, Etwaru D, Ernst DC, Palacios JG, Golden SS, LiWang A, Lander GC, Partch CL. Coupling of distant ATPase domains in the circadian clock protein KaiC. Nat Struct Mol Biol 2022; 29:759-766. [PMID: 35864165 DOI: 10.1038/s41594-022-00803-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 06/06/2022] [Indexed: 11/09/2022]
Abstract
The AAA+ family member KaiC is the central pacemaker for circadian rhythms in the cyanobacterium Synechococcus elongatus. Composed of two hexameric rings of adenosine triphosphatase (ATPase) domains with tightly coupled activities, KaiC undergoes a cycle of autophosphorylation and autodephosphorylation on its C-terminal (CII) domain that restricts binding of clock proteins on its N-terminal (CI) domain to the evening. Here, we use cryogenic-electron microscopy to investigate how daytime and nighttime states of CII regulate KaiB binding on CI. We find that the CII hexamer is destabilized during the day but takes on a rigidified C2-symmetric state at night, concomitant with ring-ring compression. Residues at the CI-CII interface are required for phospho-dependent KaiB association, coupling ATPase activity on CI to cooperative KaiB recruitment. Together, these studies clarify a key step in the regulation of cyanobacterial circadian rhythms by KaiC phosphorylation.
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Affiliation(s)
- Jeffrey A Swan
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Colby R Sandate
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Archana G Chavan
- Department of Chemistry and Biochemistry, University of California, Merced, CA, USA
| | - Alfred M Freeberg
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Diana Etwaru
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Dustin C Ernst
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA, USA
| | - Joseph G Palacios
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Susan S Golden
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA, USA.,Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Andy LiWang
- Department of Chemistry and Biochemistry, University of California, Merced, CA, USA.,Center for Circadian Biology, University of California, San Diego, La Jolla, CA, USA.,Center for Cellular and Biomolecular Machines, University of California, Merced, CA, USA
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA. .,Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
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6
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Abstract
KaiC, a core clock protein in the cyanobacterial circadian clock system, hydrolyzes adenosine triphosphate (ATP) at two distinct sites in a slow but ordered manner to measure the circadian timescale. We used biochemical and structural biology techniques to characterize the properties and interplay of dual-adenosine triphosphatase (ATPase) active sites. Our results show that the N-terminal and C-terminal ATPases communicate with each other through an interface between the N-terminal and C-terminal domains in KaiC. The dual-ATPase sites are regulated rhythmically in a concerted or opposing manner dependent on the phase of the circadian clock system, controlling the affinities of KaiC for other clock proteins, KaiA and KaiB. KaiC is a dual adenosine triphosphatase (ATPase), with one active site in its N-terminal domain and another in its C-terminal domain, that drives the circadian clock system of cyanobacteria through sophisticated coordination of the two sites. To elucidate the coordination mechanism, we studied the contribution of the dual-ATPase activities in the ring-shaped KaiC hexamer and these structural bases for activation and inactivation. At the N-terminal active site, a lytic water molecule is sequestered between the N-terminal domains, and its reactivity to adenosine triphosphate (ATP) is controlled by the quaternary structure of the N-terminal ring. The C-terminal ATPase activity is regulated mostly by water-incorporating voids between the C-terminal domains, and the size of these voids is sensitive to phosphoryl modification of S431. The up-regulatory effect on the N-terminal ATPase activity inversely correlates with the affinity of KaiC for KaiB, a clock protein constitutes the circadian oscillator together with KaiC and KaiA, and the complete dissociation of KaiB from KaiC requires KaiA-assisted activation of the dual ATPase. Delicate interactions between the N-terminal and C-terminal rings make it possible for the components of the dual ATPase to work together, thereby driving the assembly and disassembly cycle of KaiA and KaiB.
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7
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Dimer dissociation is a key energetic event in the fold-switch pathway of KaiB. Biophys J 2022; 121:943-955. [PMID: 35151633 PMCID: PMC8943816 DOI: 10.1016/j.bpj.2022.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 12/14/2021] [Accepted: 02/09/2022] [Indexed: 11/21/2022] Open
Abstract
Cyanobacteria possesses the simplest circadian clock, composed of three proteins that act as a phosphorylation oscillator: KaiA, KaiB, and KaiC. The timing of this oscillator is determined by the fold-switch of KaiB, a structural rearrangement of its C-terminal half that is accompanied by a change in the oligomerization state. During the day, KaiB forms a stable tetramer (gsKaiB), whereas it adopts a monomeric thioredoxin-like fold during the night (fsKaiB). Although the structures and functions of both native states are well studied, little is known about the sequence and structure determinants that control their structural interconversion. Here, we used confinement molecular dynamics (CCR-MD) and folding simulations using structure-based models to show that the dissociation of the gsKaiB dimer is a key energetic event for the fold-switch. Hydrogen-deuterium exchange mass spectrometry (HDXMS) recapitulates the local stability of protein regions reported by CCR-MD, with both approaches consistently indicating that the energy and backbone flexibility changes are solely associated with the region that fold-switches between gsKaiB and fsKaiB and that the localized regions that differentially stabilize gsKaiB also involve regions outside the dimer interface. Moreover, two mutants (R23C and R75C) previously reported to be relevant for altering the rhythmicity of the Kai clock were also studied by HDXMS. Particularly, R75C populates dimeric and monomeric states with a deuterium incorporation profile comparable to the one observed for fsKaiB, emphasizing the importance of the oligomerization state of KaiB for the fold-switch. These findings suggest that the information necessary to control the rhythmicity of the cyanobacterial biological clock is, to a great extent, encoded within the KaiB sequence.
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8
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Koda SI, Saito S. Multimeric structure enables the acceleration of KaiB-KaiC complex formation induced by ADP/ATP exchange inhibition. PLoS Comput Biol 2022; 18:e1009243. [PMID: 35255087 PMCID: PMC8929707 DOI: 10.1371/journal.pcbi.1009243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 03/17/2022] [Accepted: 02/25/2022] [Indexed: 11/19/2022] Open
Abstract
Circadian clocks tick a rhythm with a nearly 24-hour period in a variety of organisms. In the clock proteins of cyanobacteria, KaiA, KaiB, and KaiC, known as a minimum circadian clock, the slow KaiB-KaiC complex formation is essential in determining the clock period. This complex formation, occurring when the C1 domain of KaiC hexamer binds ADP molecules produced by the ATPase activity of C1, is considered to be promoted by accumulating ADP molecules in C1 through inhibiting the ADP/ATP exchange (ADP release) rather than activating the ATP hydrolysis (ADP production). Significantly, this ADP/ATP exchange inhibition accelerates the complex formation together with its promotion, implying a potential role in the period robustness under environmental perturbations. However, the molecular mechanism of this simultaneous promotion and acceleration remains elusive because inhibition of a backward process generally slows down the whole process. In this article, to investigate the mechanism, we build several reaction models of the complex formation with the pre-binding process concerning the ATPase activity. In these models, six KaiB monomers cooperatively and rapidly bind to C1 when C1 binds ADP molecules more than a given threshold while stabilizing the binding-competent conformation of C1. Through comparison among the models proposed here, we then extract three requirements for the simultaneous promotion and acceleration: the stabilization of the binding-competent C1 by KaiB binding, slow ADP/ATP exchange in the binding-competent C1, and relatively fast ADP/ATP exchange occurring in the binding-incompetent C1 in the presence of KaiB. The last two requirements oblige KaiC to form a multimer. Moreover, as a natural consequence, the present models can also explain why the binding of KaiB to C1 reduces the ATPase activity of C1.
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Affiliation(s)
- Shin-ichi Koda
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi, Japan
- School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, Japan
| | - Shinji Saito
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi, Japan
- School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, Japan
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9
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Behera AK, Junco CD, Vaikuntanathan S. Mechanism for the Generation of Robust Circadian Oscillations through Ultransensitivity and Differential Binding Affinity. J Phys Chem B 2021; 125:11179-11187. [PMID: 34609867 PMCID: PMC8515790 DOI: 10.1021/acs.jpcb.1c05915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
Biochemical circadian rhythm oscillations
play an important role
in many signaling mechanisms. In this work, we explore some of the
biophysical mechanisms responsible for sustaining robust oscillations
by constructing a minimal but analytically tractable model of the
circadian oscillations in the KaiABC protein system found in the cyanobacteria S. elongatus. In particular, our minimal model explicitly
accounts for two experimentally characterized biophysical features
of the KaiABC protein system, namely, a differential binding affinity
and an ultrasensitive response. Our analytical work shows how these
mechanisms might be crucial for promoting robust oscillations even
in suboptimal nutrient conditions. Our analytical and numerical work
also identifies mechanisms by which biological clocks can stably maintain
a constant time period under a variety of nutrient conditions. Finally,
our work also explores the thermodynamic costs associated with the
generation of robust sustained oscillations and shows that the net
rate of entropy production alone might not be a good figure of merit
to asses the quality of oscillations.
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Affiliation(s)
- Agnish Kumar Behera
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Clara Del Junco
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Suriyanarayanan Vaikuntanathan
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States.,The James Franck Institute, University of Chicago, Chicago, Illinois 60637, United States
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10
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Kim P, Thati N, Peshori S, Jang HI, Kim YI. Shift in Conformational Equilibrium Underlies the Oscillatory Phosphoryl Transfer Reaction in the Circadian Clock. Life (Basel) 2021; 11:life11101058. [PMID: 34685430 PMCID: PMC8538168 DOI: 10.3390/life11101058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 11/26/2022] Open
Abstract
Oscillatory phosphorylation/dephosphorylation can be commonly found in a biological system as a means of signal transduction though its pivotal presence in the workings of circadian clocks has drawn significant interest: for example in a significant portion of the physiology of Synechococcus elongatus PCC 7942. The biological oscillatory reaction in the cyanobacterial circadian clock can be visualized through its reconstitution in a test tube by mixing three proteins—KaiA, KaiB and KaiC—with adenosine triphosphate and magnesium ions. Surprisingly, the oscillatory phosphorylation/dephosphorylation of the hexameric KaiC takes place spontaneously and almost indefinitely in a test tube as long as ATP is present. This autonomous post-translational modification is tightly regulated by the conformational change of the C-terminal peptide of KaiC called the “A-loop” between the exposed and the buried states, a process induced by the time-course binding events of KaiA and KaiB to KaiC. There are three putative hydrogen-bond forming residues of the A-loop that are important for stabilizing its buried conformation. Substituting the residues with alanine enabled us to observe KaiB’s role in dephosphorylating hyperphosphorylated KaiC, independent of KaiA’s effect. We found a novel role of KaiB that its binding to KaiC induces the A-loop toward its buried conformation, which in turn activates the autodephosphorylation of KaiC. In addition to its traditional role of sequestering KaiA, KaiB’s binding contributes to the robustness of cyclic KaiC phosphorylation by inhibiting it during the dephosphorylation phase, effectively shifting the equilibrium toward the correct phase of the clock.
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Affiliation(s)
- Pyonghwa Kim
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ 07102, USA;
| | - Neha Thati
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ 07102, USA; (N.T.); (S.P.)
| | - Shreya Peshori
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ 07102, USA; (N.T.); (S.P.)
| | - Hye-In Jang
- School of Cosmetic Science and Beauty Biotechnology, Semyung University, Jecheon 27136, Korea
- Correspondence: (H.-I.J.); (Y.-I.K.)
| | - Yong-Ick Kim
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ 07102, USA;
- Institute for Brain and Neuroscience Research, New Jersey Institute of Technology, Newark, NJ 07102, USA
- Correspondence: (H.-I.J.); (Y.-I.K.)
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11
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Mutoh R, Iwata K, Iida T, Ishiura M, Onai K. Rhythmic adenosine triphosphate release from the cyanobacterial circadian clock protein KaiC revealed by real-time monitoring of bioluminescence using firefly luciferase. Genes Cells 2021; 26:83-93. [PMID: 33341998 DOI: 10.1111/gtc.12825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/16/2020] [Accepted: 12/16/2020] [Indexed: 11/27/2022]
Abstract
The cyanobacterial circadian clock is composed of three clock proteins, KaiA, KaiB and KaiC. This KaiABC clock system can be reconstituted in vitro in the presence of adenosine triphosphate (ATP) and Mg2+ , and shows circadian rhythms in the phosphorylation level and ATPase activity of KaiC. Previously, we found that ATP regulates a complex formation between KaiB and KaiC, and KaiC releases ATP from KaiC itself (PLoS One, 8, 2013, e80200). In this study, we examined whether the ATP release from KaiC shows any rhythms in vitro. We monitored the release of ATP from wild-type and ATPase motif mutants of KaiC as a bioluminescence in real time using a firefly luciferase assay in vitro and obtained the following results: (a) ATP release from KaiC oscillated even without KaiA and KaiB although period of the oscillation was not 24 hr; (b) ATP was mainly released from the N-terminal domain of KaiC; and (c) the ATP release was enhanced and suppressed by KaiB and KaiA, respectively. These results suggest that KaiC can generate basal oscillation as a core clock without KaiA and KaiB, whereas these two proteins contribute to adjusting and stabilizing the oscillation.
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Affiliation(s)
- Risa Mutoh
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Keita Iwata
- Center for Gene Research, Nagoya University, Nagoya, Japan.,Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Takahiro Iida
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Masahiro Ishiura
- Center for Gene Research, Nagoya University, Nagoya, Japan.,Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Kiyoshi Onai
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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12
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Chow GK, Chavan AG, Heisler JC, Chang YG, LiWang A, Britt RD. Monitoring Protein-Protein Interactions in the Cyanobacterial Circadian Clock in Real Time via Electron Paramagnetic Resonance Spectroscopy. Biochemistry 2020; 59:2387-2400. [PMID: 32453554 PMCID: PMC7346098 DOI: 10.1021/acs.biochem.0c00279] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
The cyanobacterial circadian clock
in Synechococcus elongatus consists of three proteins,
KaiA, KaiB, and KaiC. KaiA and KaiB
rhythmically interact with KaiC to generate stable oscillations of
KaiC phosphorylation with a period of 24 h. The observation of stable
circadian oscillations when the three clock proteins are reconstituted
and combined in vitro makes it an ideal system for understanding its
underlying molecular mechanisms and circadian clocks in general. These
oscillations were historically monitored in vitro by gel electrophoresis
of reaction mixtures based on the differing electrophoretic mobilities
between various phosphostates of KaiC. As the KaiC phospho-distribution
represents only one facet of the oscillations, orthogonal tools are
necessary to explore other interactions to generate a full description
of the system. However, previous biochemical assays are discontinuous
or qualitative. To circumvent these limitations, we developed a spin-labeled
KaiB mutant that can differentiate KaiC-bound KaiB from free KaiB
using continuous-wave electron paramagnetic resonance spectroscopy
that is minimally sensitive to KaiA. Similar to wild-type (WT-KaiB),
this labeled mutant, in combination with KaiA, sustains robust circadian
rhythms of KaiC phosphorylation. This labeled mutant is hence a functional
surrogate of WT-KaiB and thus participates in and reports on autonomous
macroscopic circadian rhythms generated by mixtures that include KaiA,
KaiC, and ATP. Quantitative kinetics could be extracted with improved
precision and time resolution. We describe design principles, data
analysis, and limitations of this quantitative binding assay and discuss
future research necessary to overcome these challenges.
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Affiliation(s)
- Gary K Chow
- Department of Chemistry, University of California, Davis, California 95616, United States
| | | | | | | | - Andy LiWang
- 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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13
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Nagata K, Oyama K, Ota A, Azai C, Terauchi K. Mutation of alanine-422 in KaiC leads to a low amplitude of rhythm in the reconstituted cyanobacterial circadian clock. J GEN APPL MICROBIOL 2020; 66:140-146. [PMID: 32224606 DOI: 10.2323/jgam.2020.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The cyanobacterial circadian oscillator can be reconstituted by mixing the purified clock proteins KaiA, KaiB, and KaiC with ATP in vitro, leading to a 24-h oscillation of KaiC phosphorylation. The cyanobacterial mutant pr1 carrying valine instead of alanine at position 422 of KaiC (KaiC-A422V) lost the ability to shift the phase of the circadian rhythm. In this study, we analyzed KaiC-A422V to investigate the effect of this single-residue substitution on the in vitro reconstitution of KaiC oscillation. KaiC-A422V exhibited low amplitude oscillations of phosphorylation with a smaller amount of Kai complex than wild-type KaiC (KaiC-WT). Although KaiA can stimulate KaiC phosphorylation, the phosphorylation level of KaiC-A422V is much lower than that of KaiC-WT even at higher KaiA concentrations. It has been suggested that monomer shuffling of KaiC is involved in entraining the in vitro rhythm. To examine whether KaiC-A422V has the capacity for monomer shuffling, we used the difference in the amplitude of the phosphorylation rhythms between KaiC-WT and KaiC-A422V as the indicator of monomer shuffling. When KaiC-A422V and KaiC-WT were mixed, the amplitude of the phosphorylation rhythm changed according to the mixing ratio. This suggests that KaiC-A422V has a reduced ability to shuffle monomers in hexameric KaiC. In addition, the A422V mutation resulted in a change of the stability of the KaiC protein.
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Affiliation(s)
- Kazuki Nagata
- Graduate School of Life Sciences, Ritsumeikan University
| | - Katsuaki Oyama
- Graduate School of Life Sciences, Ritsumeikan University
| | - Atsushi Ota
- Graduate School of Life Sciences, Ritsumeikan University
| | - Chihiro Azai
- Graduate School of Life Sciences, Ritsumeikan University.,College of Life Sciences, Ritsumeikan University
| | - Kazuki Terauchi
- Graduate School of Life Sciences, Ritsumeikan University.,College of Life Sciences, Ritsumeikan University
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14
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Hong L, Lavrentovich DO, Chavan A, Leypunskiy E, Li E, Matthews C, LiWang A, Rust MJ, Dinner AR. Bayesian modeling reveals metabolite-dependent ultrasensitivity in the cyanobacterial circadian clock. Mol Syst Biol 2020; 16:e9355. [PMID: 32496641 PMCID: PMC7271899 DOI: 10.15252/msb.20199355] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 12/22/2022] Open
Abstract
Mathematical models can enable a predictive understanding of mechanism in cell biology by quantitatively describing complex networks of interactions, but such models are often poorly constrained by available data. Owing to its relative biochemical simplicity, the core circadian oscillator in Synechococcus elongatus has become a prototypical system for studying how collective dynamics emerge from molecular interactions. The oscillator consists of only three proteins, KaiA, KaiB, and KaiC, and near-24-h cycles of KaiC phosphorylation can be reconstituted in vitro. Here, we formulate a molecularly detailed but mechanistically naive model of the KaiA-KaiC subsystem and fit it directly to experimental data within a Bayesian parameter estimation framework. Analysis of the fits consistently reveals an ultrasensitive response for KaiC phosphorylation as a function of KaiA concentration, which we confirm experimentally. This ultrasensitivity primarily results from the differential affinity of KaiA for competing nucleotide-bound states of KaiC. We argue that the ultrasensitive stimulus-response relation likely plays an important role in metabolic compensation by suppressing premature phosphorylation at nighttime.
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Affiliation(s)
- Lu Hong
- Graduate Program in Biophysical SciencesUniversity of ChicagoChicagoILUSA
| | - Danylo O Lavrentovich
- Department of ChemistryUniversity of ChicagoChicagoILUSA
- Present address:
Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMAUSA
| | - Archana Chavan
- School of Natural SciencesUniversity of CaliforniaMercedCAUSA
| | - Eugene Leypunskiy
- Graduate Program in Biophysical SciencesUniversity of ChicagoChicagoILUSA
| | - Eileen Li
- Department of StatisticsUniversity of ChicagoChicagoILUSA
| | - Charles Matthews
- Department of StatisticsUniversity of ChicagoChicagoILUSA
- Present address:
School of MathematicsUniversity of EdinburghEdinburghUK
| | - Andy LiWang
- School of Natural SciencesUniversity of CaliforniaMercedCAUSA
- Quantitative and Systems BiologyUniversity of CaliforniaMercedCAUSA
- Center for Circadian BiologyUniversity of CaliforniaSan Diego, La JollaCAUSA
- Chemistry and Chemical BiologyUniversity of CaliforniaMercedCAUSA
- Health Sciences Research InstituteUniversity of CaliforniaMercedCAUSA
- Center for Cellular and Biomolecular MachinesUniversity of CaliforniaMercedCAUSA
| | - Michael J Rust
- Department of Molecular Genetics and Cell BiologyUniversity of ChicagoChicagoILUSA
- Institute for Biophysical DynamicsUniversity of ChicagoChicagoILUSA
- Institute for Genomics and Systems BiologyUniversity of ChicagoChicagoILUSA
| | - Aaron R Dinner
- Department of ChemistryUniversity of ChicagoChicagoILUSA
- Institute for Biophysical DynamicsUniversity of ChicagoChicagoILUSA
- James Franck InstituteUniversity of ChicagoChicagoILUSA
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15
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Partch CL. Orchestration of Circadian Timing by Macromolecular Protein Assemblies. J Mol Biol 2020; 432:3426-3448. [DOI: 10.1016/j.jmb.2019.12.046] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/13/2019] [Accepted: 12/18/2019] [Indexed: 12/13/2022]
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16
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Synechocystis KaiC3 Displays Temperature- and KaiB-Dependent ATPase Activity and Is Important for Growth in Darkness. J Bacteriol 2020; 202:JB.00478-19. [PMID: 31767776 PMCID: PMC6989803 DOI: 10.1128/jb.00478-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/17/2019] [Indexed: 02/05/2023] Open
Abstract
Cyanobacteria form a heterogeneous bacterial group with diverse lifestyles, acclimation strategies, and differences in the presence of circadian clock proteins. In Synechococcus elongatus PCC 7942, a unique posttranslational KaiABC oscillator drives circadian rhythms. ATPase activity of KaiC correlates with the period of the clock and mediates temperature compensation. Synechocystis sp. strain PCC 6803 expresses additional Kai proteins, of which KaiB3 and KaiC3 proteins were suggested to fine-tune the standard KaiAB1C1 oscillator. In the present study, we therefore characterized the enzymatic activity of KaiC3 as a representative of nonstandard KaiC homologs in vitro KaiC3 displayed ATPase activity lower than that of the Synechococcus elongatus PCC 7942 KaiC protein. ATP hydrolysis was temperature dependent. Hence, KaiC3 is missing a defining feature of the model cyanobacterial circadian oscillator. Yeast two-hybrid analysis showed that KaiC3 interacts with KaiB3, KaiC1, and KaiB1. Further, KaiB3 and KaiB1 reduced in vitro ATP hydrolysis by KaiC3. Spot assays showed that chemoheterotrophic growth in constant darkness is completely abolished after deletion of ΔkaiAB1C1 and reduced in the absence of kaiC3 We therefore suggest a role for adaptation to darkness for KaiC3 as well as a cross talk between the KaiC1- and KaiC3-based systems.IMPORTANCE The circadian clock influences the cyanobacterial metabolism, and deeper understanding of its regulation will be important for metabolic optimizations in the context of industrial applications. Due to the heterogeneity of cyanobacteria, characterization of clock systems in organisms apart from the circadian model Synechococcus elongatus PCC 7942 is required. Synechocystis sp. strain PCC 6803 represents a major cyanobacterial model organism and harbors phylogenetically diverged homologs of the clock proteins, which are present in various other noncyanobacterial prokaryotes. By our in vitro studies we unravel the interplay of the multiple Synechocystis Kai proteins and characterize enzymatic activities of the nonstandard clock homolog KaiC3. We show that the deletion of kaiC3 affects growth in constant darkness, suggesting its involvement in the regulation of nonphotosynthetic metabolic pathways.
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17
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Yunoki Y, Ishii K, Yagi-Utsumi M, Murakami R, Uchiyama S, Yagi H, Kato K. ATP hydrolysis by KaiC promotes its KaiA binding in the cyanobacterial circadian clock system. Life Sci Alliance 2019; 2:2/3/e201900368. [PMID: 31160381 PMCID: PMC6549140 DOI: 10.26508/lsa.201900368] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 12/01/2022] Open
Abstract
ATP hydrolysis in the KaiC hexamer triggers the exposure of its C-terminal segments into the solvent so as to capture KaiA, providing mechanistic insights into the circadian periodicity regulation. The cyanobacterial clock is controlled via the interplay among KaiA, KaiB, and KaiC, which generate a periodic oscillation of KaiC phosphorylation in the presence of ATP. KaiC forms a homohexamer harboring 12 ATP-binding sites and exerts ATPase activities associated with its autophosphorylation and dephosphorylation. The KaiC nucleotide state is a determining factor of the KaiB–KaiC interaction; however, its relationship with the KaiA–KaiC interaction has not yet been elucidated. With the attempt to address this, our native mass spectrometric analyses indicated that ATP hydrolysis in the KaiC hexamer promotes its interaction with KaiA. Furthermore, our nuclear magnetic resonance spectral data revealed that ATP hydrolysis is coupled with conformational changes in the flexible C-terminal segments of KaiC, which carry KaiA-binding sites. From these data, we conclude that ATP hydrolysis in KaiC is coupled with the exposure of its C-terminal KaiA-binding sites, resulting in its high affinity for KaiA. These findings provide mechanistic insights into the ATP-mediated circadian periodicity.
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Affiliation(s)
- Yasuhiro Yunoki
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Japan
| | - Kentaro Ishii
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan.,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Japan
| | - Maho Yagi-Utsumi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan.,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Japan
| | - Reiko Murakami
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Susumu Uchiyama
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan.,Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan .,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Japan
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18
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Sasai M. Effects of Stochastic Single-Molecule Reactions on Coherent Ensemble Oscillations in the KaiABC Circadian Clock. J Phys Chem B 2019; 123:702-713. [PMID: 30629448 DOI: 10.1021/acs.jpcb.8b10584] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
How do many constituent molecules in a biochemical system synchronize, giving rise to coherent system-level oscillations? One system that is particularly suitable for use in studying this problem is a mixture solution of three cyanobacterial proteins, KaiA, KaiB, and KaiC: the phosphorylation level of KaiC shows stable oscillations with a period of approximately 24 h when these three Kai proteins are incubated with ATP in vitro. Here, we analyze the mechanism behind synchronization in the KaiABC system theoretically by enhancing a model previously developed by the present author. Our simulation results suggest that positive feedback between stochastic ATP hydrolysis and the allosteric structural transitions in KaiC molecules drives oscillations of individual molecules and promotes synchronization of oscillations of many KaiC molecules. Our simulations also show that the ATPase activity of KaiC is correlated with the oscillation frequency of an ensemble of KaiC molecules. These results suggest that stochastic ATP hydrolysis in each KaiC molecule plays an important role in regulating the coherent system-level oscillations. This property is robust against changes in the binding and unbinding rate constants for KaiA to/from KaiC or KaiB, but the oscillations are sensitive to the rate constants of the KaiC phosphorylation and dephosphorylation reactions.
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Affiliation(s)
- Masaki Sasai
- Department of Applied Physics , Nagoya University , Nagoya 464-8603 , Japan
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19
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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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20
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Hong L, Vani BP, Thiede EH, Rust MJ, Dinner AR. Molecular dynamics simulations of nucleotide release from the circadian clock protein KaiC reveal atomic-resolution functional insights. Proc Natl Acad Sci U S A 2018; 115:E11475-E11484. [PMID: 30442665 PMCID: PMC6298084 DOI: 10.1073/pnas.1812555115] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The cyanobacterial clock proteins KaiA, KaiB, and KaiC form a powerful system to study the biophysical basis of circadian rhythms, because an in vitro mixture of the three proteins is sufficient to generate a robust ∼24-h rhythm in the phosphorylation of KaiC. The nucleotide-bound states of KaiC critically affect both KaiB binding to the N-terminal domain (CI) and the phosphotransfer reactions that (de)phosphorylate the KaiC C-terminal domain (CII). However, the nucleotide exchange pathways associated with transitions among these states are poorly understood. In this study, we integrate recent advances in molecular dynamics methods to elucidate the structure and energetics of the pathway for Mg·ADP release from the CII domain. We find that nucleotide release is coupled to large-scale conformational changes in the KaiC hexamer. Solvating the nucleotide requires widening the subunit interface leading to the active site, which is linked to extension of the A-loop, a structure implicated in KaiA binding. These results provide a molecular hypothesis for how KaiA acts as a nucleotide exchange factor. In turn, structural parallels between the CI and CII domains suggest a mechanism for allosteric coupling between the domains. We relate our results to structures observed for other hexameric ATPases, which perform diverse functions.
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Affiliation(s)
- Lu Hong
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL 60637
| | - Bodhi P Vani
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| | - Erik H Thiede
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| | - Michael J Rust
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637;
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL 60637
| | - Aaron R Dinner
- Department of Chemistry, The University of Chicago, Chicago, IL 60637;
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
- James Franck Institute, The University of Chicago, Chicago, IL 60637
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21
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Mori T, Sugiyama S, Byrne M, Johnson CH, Uchihashi T, Ando T. Revealing circadian mechanisms of integration and resilience by visualizing clock proteins working in real time. Nat Commun 2018; 9:3245. [PMID: 30108211 PMCID: PMC6092398 DOI: 10.1038/s41467-018-05438-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 07/09/2018] [Indexed: 11/09/2022] Open
Abstract
The circadian clock proteins KaiA, KaiB, and KaiC reconstitute a remarkable circa-24 h oscillation of KaiC phosphorylation that persists for many days in vitro. Here we use high-speed atomic force microscopy (HS-AFM) to visualize in real time and quantify the dynamic interactions of KaiA with KaiC on sub-second timescales. KaiA transiently interacts with KaiC, thereby stimulating KaiC autokinase activity. As KaiC becomes progressively more phosphorylated, KaiA's affinity for KaiC weakens, revealing a feedback of KaiC phosphostatus back onto the KaiA-binding events. These non-equilibrium interactions integrate high-frequency binding and unbinding events, thereby refining the period of the longer term oscillations. Moreover, this differential affinity phenomenon broadens the range of Kai protein stoichiometries that allow rhythmicity, explaining how the oscillation is resilient in an in vivo milieu that includes noise. Therefore, robustness of rhythmicity on a 24-h scale is explainable by molecular events occurring on a scale of sub-seconds.
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Affiliation(s)
- Tetsuya Mori
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - Shogo Sugiyama
- Department of Physics, College of Science and Engineering, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Mark Byrne
- Department of Chemistry, Physics, and Engineering, Spring Hill College, 4000 Dauphin St., Mobile, AL, 36608, USA
| | - Carl Hirschie Johnson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA. .,Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.
| | - Takayuki Uchihashi
- Department of Physics and Structural Biology Research Center, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan.
| | - Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, 920-1192, Japan.
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22
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Hernansaiz-Ballesteros RD, Cardelli L, Csikász-Nagy A. Single molecules can operate as primitive biological sensors, switches and oscillators. BMC SYSTEMS BIOLOGY 2018; 12:70. [PMID: 29914480 PMCID: PMC6007071 DOI: 10.1186/s12918-018-0596-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 06/05/2018] [Indexed: 01/07/2023]
Abstract
Background Switch-like and oscillatory dynamical systems are widely observed in biology. We investigate the simplest biological switch that is composed of a single molecule that can be autocatalytically converted between two opposing activity forms. We test how this simple network can keep its switching behaviour under perturbations in the system. Results We show that this molecule can work as a robust bistable system, even for alterations in the reactions that drive the switching between various conformations. We propose that this single molecule system could work as a primitive biological sensor and show by steady state analysis of a mathematical model of the system that it could switch between possible states for changes in environmental signals. Particularly, we show that a single molecule phosphorylation-dephosphorylation switch could work as a nucleotide or energy sensor. We also notice that a given set of reductions in the reaction network can lead to the emergence of oscillatory behaviour. Conclusions We propose that evolution could have converted this switch into a single molecule oscillator, which could have been used as a primitive timekeeper. We discuss how the structure of the simplest known circadian clock regulatory system, found in cyanobacteria, resembles the proposed single molecule oscillator. Besides, we speculate if such minimal systems could have existed in an RNA world. Electronic supplementary material The online version of this article (10.1186/s12918-018-0596-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rosa D Hernansaiz-Ballesteros
- Randall Centre for Cell and Molecular Biophysics and Institute for Mathematical and Molecular Biomedicine, King's College London, London, SE1 1UL, UK
| | - Luca Cardelli
- Microsoft Research, 21 Station Road, Cambridge, CB1 2FB, UK.,Department of Computer Science, University of Oxford, Wolfson Building, Parks Road, Oxford, OX1 3QD, UK
| | - Attila Csikász-Nagy
- Randall Centre for Cell and Molecular Biophysics and Institute for Mathematical and Molecular Biomedicine, King's College London, London, SE1 1UL, UK. .,Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, H-1083, Hungary.
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23
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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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24
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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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25
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Oyama K, Azai C, Matsuyama J, Terauchi K. Phosphorylation at Thr432 induces structural destabilization of the CII ring in the circadian oscillator KaiC. FEBS Lett 2017; 592:36-45. [PMID: 29265368 DOI: 10.1002/1873-3468.12945] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 11/28/2017] [Accepted: 12/09/2017] [Indexed: 01/08/2023]
Abstract
KaiC is the central oscillator protein in the cyanobacterial circadian clock. KaiC oscillates autonomously between phosphorylated and dephosphorylated states on a 24-h cycle in vitro by mixing with KaiA and KaiB in the presence of ATP. KaiC forms a C6 -symmetrical hexamer, which is a double ring structure of homologous N-terminal and C-terminal domains termed CI and CII, respectively. Here, through the characterization of an isolated CII domain protein, CIIKaiC , we show that phosphorylation of KaiC Thr432 destabilizes the hexameric state of the CII ring to a monomeric state. The results suggest that the stable hexameric CI ring acts as a molecular bundle to hold the CII ring, which undergoes dynamic structural changes upon phosphorylation.
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Affiliation(s)
- Katsuaki Oyama
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Chihiro Azai
- College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Jun Matsuyama
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Kazuki Terauchi
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Japan.,College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
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26
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Egli M. Architecture and mechanism of the central gear in an ancient molecular timer. J R Soc Interface 2017; 14:rsif.2016.1065. [PMID: 28330987 DOI: 10.1098/rsif.2016.1065] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 02/27/2017] [Indexed: 12/16/2022] Open
Abstract
Molecular clocks are the product of natural selection in organisms from bacteria to human and their appearance early in evolution such as in the prokaryotic cyanobacterium Synechococcus elongatus suggests that these timers served a crucial role in genetic fitness. Thus, a clock allows cyanobacteria relying on photosynthesis and nitrogen fixation to temporally space the two processes and avoid exposure of nitrogenase carrying out fixation to high levels of oxygen produced during photosynthesis. Fascinating properties of molecular clocks are the long time constant, their precision and temperature compensation. Although these are hallmarks of all circadian oscillators, the actual cogs and gears that control clocks vary widely between organisms, indicating that circadian timers evolved convergently multiple times, owing to the selective pressure of an environment with a daily light/dark cycle. In S. elongatus, the three proteins KaiA, KaiB and KaiC in the presence of ATP constitute a so-called post-translational oscillator (PTO). The KaiABC PTO can be reconstituted in an Eppendorf tube and keeps time in a temperature-compensated manner. The ease by which the KaiABC clock can be studied in vitro has made it the best-investigated molecular clock system. Over the last decade, structures of all three Kai proteins and some of their complexes have emerged and mechanistic aspects have been analysed in considerable detail. This review focuses on the central gear of the S. elongatus clock and only enzyme among the three proteins: KaiC. Our determination of the three-dimensional structure of KaiC early in the quest for a better understanding of the inner workings of the cyanobacterial timer revealed its unusual architecture and conformational differences and unique features of the two RecA-like domains constituting KaiC. The structure also pinpointed phosphorylation sites and differential interactions with ATP molecules at subunit interfaces, and helped guide experiments to ferret out mechanistic aspects of the ATPase, auto-phosphorylation and auto-dephosphorylation reactions catalysed by the homo-hexamer. Comparisons between the structure of KaiC and those of nanomachines such as F1-ATPase and CaMKII also exposed shared architectural features (KaiC/ATPase), mechanistic principles (KaiC/CaMKII) and phenomena, such as subunit exchange between hexameric particles critical for function (clock synchronization, KaiABC; memory-storage, CaMKII).
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Affiliation(s)
- Martin Egli
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
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27
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Schmelling NM, Lehmann R, Chaudhury P, Beck C, Albers SV, Axmann IM, Wiegard A. Minimal tool set for a prokaryotic circadian clock. BMC Evol Biol 2017; 17:169. [PMID: 28732467 PMCID: PMC5520375 DOI: 10.1186/s12862-017-0999-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/15/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Circadian clocks are found in organisms of almost all domains including photosynthetic Cyanobacteria, whereby large diversity exists within the protein components involved. In the model cyanobacterium Synechococcus elongatus PCC 7942 circadian rhythms are driven by a unique KaiABC protein clock, which is embedded in a network of input and output factors. Homologous proteins to the KaiABC clock have been observed in Bacteria and Archaea, where evidence for circadian behavior in these domains is accumulating. However, interaction and function of non-cyanobacterial Kai-proteins as well as homologous input and output components remain mainly unclear. RESULTS Using a universal BLAST analyses, we identified putative KaiC-based timing systems in organisms outside as well as variations within Cyanobacteria. A systematic analyses of publicly available microarray data elucidated interesting variations in circadian gene expression between different cyanobacterial strains, which might be correlated to the diversity of genome encoded clock components. Based on statistical analyses of co-occurrences of the clock components homologous to Synechococcus elongatus PCC 7942, we propose putative networks of reduced and fully functional clock systems. Further, we studied KaiC sequence conservation to determine functionally important regions of diverged KaiC homologs. Biochemical characterization of exemplary cyanobacterial KaiC proteins as well as homologs from two thermophilic Archaea demonstrated that kinase activity is always present. However, a KaiA-mediated phosphorylation is only detectable in KaiC1 orthologs. CONCLUSION Our analysis of 11,264 genomes clearly demonstrates that components of the Synechococcus elongatus PCC 7942 circadian clock are present in Bacteria and Archaea. However, all components are less abundant in other organisms than Cyanobacteria and KaiA, Pex, LdpA, and CdpA are only present in the latter. Thus, only reduced KaiBC-based or even simpler, solely KaiC-based timing systems might exist outside of the cyanobacterial phylum, which might be capable of driving diurnal oscillations.
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Affiliation(s)
- Nicolas M. Schmelling
- Institute for Synthetic Microbiology, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, Duesseldorf, 40225 Germany
| | - Robert Lehmann
- Institute for Theoretical Biology, Humboldt University Berlin, Invalidenstrasse 43, Berlin, 10115 Germany
| | - Paushali Chaudhury
- Molecular Biology of Archaea, Albert-Ludwigs-University Freiburg, Institute of Biology II, Schaenzlestrasse 1, Freiburg, 79104 Germany
| | - Christian Beck
- Institute for Theoretical Biology, Humboldt University Berlin, Invalidenstrasse 43, Berlin, 10115 Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Albert-Ludwigs-University Freiburg, Institute of Biology II, Schaenzlestrasse 1, Freiburg, 79104 Germany
| | - Ilka M. Axmann
- Institute for Synthetic Microbiology, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, Duesseldorf, 40225 Germany
| | - Anika Wiegard
- Institute for Synthetic Microbiology, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, Duesseldorf, 40225 Germany
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Paijmans J, Lubensky DK, Ten Wolde PR. Period Robustness and Entrainability of the Kai System to Changing Nucleotide Concentrations. Biophys J 2017; 113:157-173. [PMID: 28700914 PMCID: PMC5510911 DOI: 10.1016/j.bpj.2017.05.048] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 05/01/2017] [Accepted: 05/30/2017] [Indexed: 10/19/2022] Open
Abstract
Circadian clocks must be able to entrain to time-varying signals to keep their oscillations in phase with the day-night rhythm. On the other hand, they must also exhibit input compensation: their period must remain approximately one day in different constant environments. The posttranslational oscillator of the Kai system can be entrained by transient or oscillatory changes in the ATP fraction, yet is insensitive to constant changes in this fraction. We study in three different models of this system how these two seemingly conflicting criteria are met. We find that one of these (our recently published Paijmans model) exhibits the best tradeoff between input compensation and entrainability: on the footing of equal phase-response curves, it exhibits the strongest input compensation. Performing stochastic simulations at the level of individual hexamers allows us to identify a new, to our knowledge, mechanism, which is employed by the Paijmans model to achieve input compensation: at lower ATP fraction, the individual hexamers make a shorter cycle in the phosphorylation state space, which compensates for the slower pace at which they traverse the cycle.
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Affiliation(s)
- Joris Paijmans
- AMOLF, Amsterdam, the Netherlands, University of Michigan, Ann Arbor, Michigan
| | - David K Lubensky
- Department of Physics, University of Michigan, Ann Arbor, Michigan
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29
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Tseng R, Goularte NF, Chavan A, Luu J, Cohen SE, Chang YG, Heisler J, Li S, Michael AK, Tripathi S, Golden SS, LiWang A, Partch CL. Structural basis of the day-night transition in a bacterial circadian clock. Science 2017; 355:1174-1180. [PMID: 28302851 PMCID: PMC5441561 DOI: 10.1126/science.aag2516] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 02/13/2017] [Indexed: 12/14/2022]
Abstract
Circadian clocks are ubiquitous timing systems that induce rhythms of biological activities in synchrony with night and day. In cyanobacteria, timing is generated by a posttranslational clock consisting of KaiA, KaiB, and KaiC proteins and a set of output signaling proteins, SasA and CikA, which transduce this rhythm to control gene expression. Here, we describe crystal and nuclear magnetic resonance structures of KaiB-KaiC,KaiA-KaiB-KaiC, and CikA-KaiB complexes. They reveal how the metamorphic properties of KaiB, a protein that adopts two distinct folds, and the post-adenosine triphosphate hydrolysis state of KaiC create a hub around which nighttime signaling events revolve, including inactivation of KaiA and reciprocal regulation of the mutually antagonistic signaling proteins, SasA and CikA.
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Affiliation(s)
- Roger Tseng
- Quantitative and Systems Biology, University of California, Merced, CA 95343, USA
| | - Nicolette F Goularte
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Archana Chavan
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Jansen Luu
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Susan E Cohen
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yong-Gang Chang
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Joel Heisler
- Chemistry and Chemical Biology, University of California, Merced, CA 95343, USA
| | - Sheng Li
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alicia K Michael
- 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
| | - 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
- Quantitative and Systems Biology, University of California, Merced, CA 95343, USA.
- 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
- Chemistry and Chemical Biology, University of California, Merced, CA 95343, USA
- Health Sciences Research Institute, University of California, Merced, CA 95343, 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
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Paijmans J, Lubensky DK, ten Wolde PR. A thermodynamically consistent model of the post-translational Kai circadian clock. PLoS Comput Biol 2017; 13:e1005415. [PMID: 28296888 PMCID: PMC5371392 DOI: 10.1371/journal.pcbi.1005415] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 03/29/2017] [Accepted: 02/15/2017] [Indexed: 11/18/2022] Open
Abstract
The principal pacemaker of the circadian clock of the cyanobacterium S. elongatus is a protein phosphorylation cycle consisting of three proteins, KaiA, KaiB and KaiC. KaiC forms a homohexamer, with each monomer consisting of two domains, CI and CII. Both domains can bind and hydrolyze ATP, but only the CII domain can be phosphorylated, at two residues, in a well-defined sequence. While this system has been studied extensively, how the clock is driven thermodynamically has remained elusive. Inspired by recent experimental observations and building on ideas from previous mathematical models, we present a new, thermodynamically consistent, statistical-mechanical model of the clock. At its heart are two main ideas: i) ATP hydrolysis in the CI domain provides the thermodynamic driving force for the clock, switching KaiC between an active conformational state in which its phosphorylation level tends to rise and an inactive one in which it tends to fall; ii) phosphorylation of the CII domain provides the timer for the hydrolysis in the CI domain. The model also naturally explains how KaiA, by acting as a nucleotide exchange factor, can stimulate phosphorylation of KaiC, and how the differential affinity of KaiA for the different KaiC phosphoforms generates the characteristic temporal order of KaiC phosphorylation. As the phosphorylation level in the CII domain rises, the release of ADP from CI slows down, making the inactive conformational state of KaiC more stable. In the inactive state, KaiC binds KaiB, which not only stabilizes this state further, but also leads to the sequestration of KaiA, and hence to KaiC dephosphorylation. Using a dedicated kinetic Monte Carlo algorithm, which makes it possible to efficiently simulate this system consisting of more than a billion reactions, we show that the model can describe a wealth of experimental data. Circadian clocks are biological timekeeping devices with a rhythm of 24 hours in living cells pertaining to all kingdoms of life. They help organisms to coordinate their behavior with the day-night cycle. The circadian clock of the cyanobacterium Synechococcus elongatus is one of the simplest and best characterized clocks in biology. The central clock component is the protein KaiC, which is phosphorylated and dephosphorylated in a cyclical manner with a 24 hr period. While we know from elementary thermodynamics that oscillations require a net turnover of fuel molecules, in this case ATP, how ATP hydrolysis drives the clock has remained elusive. Based on recent experimental observations and building on ideas from existing models, we construct the most detailed mathematical model of this system to date. KaiC consists of two domains, CI and CII, which each can bind ATP, yet only CII can be phosphorylated. Moreover, KaiC can exist in two conformational states, an active one in which the phosphorylation level tends to rise, and an inactive one in which it tends to fall. Our model predicts that ATP hydrolysis in the CI domain is the principal energetic driver of the clock, driving the switching between the two conformational states, while phosphorylation in the CII domain provides the timer for the conformational switch. The coupling between ATP hydrolysis in the CI domain and phosphorylation in the CII domain leads to novel testable predictions.
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Affiliation(s)
| | - David K. Lubensky
- Department of Physics, University of Michigan, Ann Arbor, Michigan, United States of America
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31
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Chen Q, Yu L, Tan X, Liu S. Expression and Purification of Cyanobacterial Circadian Clock Protein KaiC and Determination of Its Auto-phosphatase Activity. Bio Protoc 2017; 7:e2140. [PMID: 34458460 DOI: 10.21769/bioprotoc.2140] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 11/22/2016] [Accepted: 01/21/2017] [Indexed: 11/02/2022] Open
Abstract
Circadian rhythms are biological processes displaying an endogenous oscillation with a period of ~24 h. They allow organisms to anticipate and get prepared for the environmental changes caused mainly by the rotation of Earth. Circadian rhythms are driven by circadian clocks that consist of proteins, DNA, and/or RNA. Circadian clocks of cyanobacteria are the simplest and one of the best studied models. They contain the three clock proteins KaiA, KaiB, and KaiC which can be used for in vitro reconstitution experiments and determination of the auto-phosphatase activity of KaiC as described in this protocol.
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Affiliation(s)
- Qiang Chen
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China.,College of Medical Science, China Three Gorges University, Yichang, China
| | - Lingling Yu
- College of Medical Science, China Three Gorges University, Yichang, China
| | - Xiao Tan
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China.,College of Medical Science, China Three Gorges University, Yichang, China
| | - Sen Liu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China.,College of Medical Science, China Three Gorges University, Yichang, China
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32
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Abstract
Chronobiological studies of prokaryotic organisms have generally lagged far behind the study of endogenous circadian clocks in eukaryotes, in which such systems are essentially ubiquitous. However, despite only being studied during the past 25 years, cyanobacteria have become important model organisms for the study of circadian rhythms and, presently, their timekeeping mechanism is the best understood of any system in terms of biochemistry, structural biology, biophysics and adaptive importance. Nevertheless, intrinsic daily rhythmicity among bacteria other than cyanobacteria is essentially unknown; some tantalizing information suggests widespread daily timekeeping among Eubacteria and Archaea through mechanisms that share common elements with the cyanobacterial clock but are distinct. Moreover, the recent surge of information about microbiome-host interactions has largely neglected the temporal dimension and yet daily cycles control important aspects of their relationship.
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33
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Westermark S, Steuer R. Toward Multiscale Models of Cyanobacterial Growth: A Modular Approach. Front Bioeng Biotechnol 2016; 4:95. [PMID: 28083530 PMCID: PMC5183639 DOI: 10.3389/fbioe.2016.00095] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 12/09/2016] [Indexed: 11/29/2022] Open
Abstract
Oxygenic photosynthesis dominates global primary productivity ever since its evolution more than three billion years ago. While many aspects of phototrophic growth are well understood, it remains a considerable challenge to elucidate the manifold dependencies and interconnections between the diverse cellular processes that together facilitate the synthesis of new cells. Phototrophic growth involves the coordinated action of several layers of cellular functioning, ranging from the photosynthetic light reactions and the electron transport chain, to carbon-concentrating mechanisms and the assimilation of inorganic carbon. It requires the synthesis of new building blocks by cellular metabolism, protection against excessive light, as well as diurnal regulation by a circadian clock and the orchestration of gene expression and cell division. Computational modeling allows us to quantitatively describe these cellular functions and processes relevant for phototrophic growth. As yet, however, computational models are mostly confined to the inner workings of individual cellular processes, rather than describing the manifold interactions between them in the context of a living cell. Using cyanobacteria as model organisms, this contribution seeks to summarize existing computational models that are relevant to describe phototrophic growth and seeks to outline their interactions and dependencies. Our ultimate aim is to understand cellular functioning and growth as the outcome of a coordinated operation of diverse yet interconnected cellular processes.
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Affiliation(s)
- Stefanie Westermark
- Fachinstitut für Theoretische Biologie (ITB), Institut für Biologie, Humboldt-Universität zu Berlin , Berlin , Germany
| | - Ralf Steuer
- Fachinstitut für Theoretische Biologie (ITB), Institut für Biologie, Humboldt-Universität zu Berlin , Berlin , Germany
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34
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Schmelling NM, Lehmann R, Chaudhury P, Beck C, Albers SV, Axmann IM, Wiegard A. Minimal Tool Set for a Prokaryotic Circadian Clock.. [DOI: 10.1101/075291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
Abstract
AbstractBackgroundCircadian clocks are found in organisms of almost all domains including photosynthetic Cyanobacteria, whereby large diversity exists within the protein components involved. In the model cyanobacteriumSynechococcus elongatusPCC 7942 circadian rhythms are driven by a unique KaiABC protein clock, which is embedded in a network of input and output factors. Homologous proteins to the KaiABC clock have been observed in Bacteria and Archaea, where evidence for circadian behavior in these domains is accumulating. However, interaction and function of non-cyanobacterial Kai-proteins as well as homologous input and output components remain mainly unclear.ResultsUsing a universal BLAST analyses, we identified putative KaiC-based timing systems in organisms outside as well as variations within Cyanobacteria. A systematic analyses of publicly available microarray data elucidated interesting variations in circadian gene expression between different cyanobacterial strains, which might be correlated to the diversity of genome encoded clock components. Based on statistical analyses of co-occurrences of the clock components homologous toSynechococcus elongatusPCC 7942, we propose putative networks of reduced and fully functional clock systems. Further, we studied KaiC sequence conservation to determine functionally important regions of diverged KaiC homologs. Biochemical characterization of exemplary cyanobacterial KaiC proteins as well as homologs from two thermophilic Archaea demonstrated that kinase activity is always present. However, a KaiA-mediated phosphorylation is only detectable in KaiC1 orthologs.ConclusionOur analysis of 11,264 genomes clearly demonstrates that components of theSynechococcus elongatusPCC 7942 circadian clock are present in Bacteria and Archaea. However, all components are less abundant in other organisms than Cyanobacteria and KaiA, Pex, LdpA, and CdpA are only present in the latter. Thus, only reduced KaiBC-based or even simpler, solely KaiC-based timing systems might exist outside of the cyanobacterial phylum, which might be capable of driving diurnal oscillations.
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35
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Conversion between two conformational states of KaiC is induced by ATP hydrolysis as a trigger for cyanobacterial circadian oscillation. Sci Rep 2016; 6:32443. [PMID: 27580682 PMCID: PMC5007536 DOI: 10.1038/srep32443] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 08/03/2016] [Indexed: 11/12/2022] Open
Abstract
The cyanobacterial circadian oscillator can be reconstituted in vitro by mixing three clock proteins, KaiA, KaiB and KaiC, with ATP. KaiC is the only protein with circadian rhythmic activities. In the present study, we tracked the complex formation of the three Kai proteins over time using blue native (BN) polyacrylamide gel electrophoresis (PAGE), in which proteins are charged with the anionic dye Coomassie brilliant blue (CBB). KaiC was separated as three bands: the KaiABC complex, KaiC hexamer and KaiC monomer. However, no KaiC monomer was observed using gel filtration chromatography and CBB-free native PAGE. These data indicate two conformational states of KaiC hexamer and show that the ground-state KaiC (gs-KaiC) is stable and competent-state KaiC (cs-KaiC) is labile and degraded into monomers by the binding of CBB. Repeated conversions from gs-KaiC to cs-KaiC were observed over 24 h using an in vitro reconstitution system. Phosphorylation of KaiC promoted the conversion from gs-KaiC to cs-KaiC. KaiA sustained the gs-KaiC state, and KaiB bound only cs-KaiC. An E77Q/E78Q-KaiC variant that lacked N-terminal ATPase activity remained in the gs-KaiC state. Taken together, ATP hydrolysis induces the formation of cs-KaiC and promotes the binding of KaiB, which is a trigger for circadian oscillations.
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36
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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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Abstract
Life on earth is subject to daily and predictable fluctuations in light intensity, temperature, and humidity created by rotation of the earth. Circadian rhythms, generated by a circadian clock, control temporal programs of cellular physiology to facilitate adaptation to daily environmental changes. Circadian rhythms are nearly ubiquitous and are found in both prokaryotic and eukaryotic organisms. Here we introduce the molecular mechanism of the circadian clock in the model cyanobacterium Synechococcus elongatus PCC 7942. We review the current understanding of the cyanobacterial clock, emphasizing recent work that has generated a more comprehensive understanding of how the circadian oscillator becomes synchronized with the external environment and how information from the oscillator is transmitted to generate rhythms of biological activity. These results have changed how we think about the clock, shifting away from a linear model to one in which the clock is viewed as an interactive network of multifunctional components that are integrated into the context of the cell in order to pace and reset the oscillator. We conclude with a discussion of how this basic timekeeping mechanism differs in other cyanobacterial species and how information gleaned from work in cyanobacteria can be translated to understanding rhythmic phenomena in other prokaryotic systems.
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Pattanayak GK, Lambert G, Bernat K, Rust MJ. Controlling the Cyanobacterial Clock by Synthetically Rewiring Metabolism. Cell Rep 2015; 13:2362-2367. [PMID: 26686627 PMCID: PMC4691564 DOI: 10.1016/j.celrep.2015.11.031] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/26/2015] [Accepted: 11/07/2015] [Indexed: 10/22/2022] Open
Abstract
Circadian clocks are oscillatory systems that allow organisms to anticipate rhythmic changes in the environment. Several studies have shown that circadian clocks are connected to metabolism, but it is not generally clear whether metabolic signaling is one voice among many that influence the clock or whether metabolic cycling is the major clock synchronizer. To address this question in cyanobacteria, we used a synthetic biology approach to make normally autotrophic cells capable of growth on exogenous sugar. This allowed us to manipulate metabolism independently from light and dark. We found that feeding sugar to cultures blocked the clock-resetting effect of a dark pulse. Furthermore, in the absence of light, the clock efficiently synchronizes to metabolic cycles driven by rhythmic feeding. We conclude that metabolic activity, independent of its source, is the primary clock driver in cyanobacteria.
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Affiliation(s)
- Gopal K Pattanayak
- Department of Molecular Genetics and Cell Biology, Institute for Genomics and Systems Biology, 900 E. 57th Street, KCBD 10124, Chicago, IL 60637, USA
| | - Guillaume Lambert
- Department of Molecular Genetics and Cell Biology, Institute for Genomics and Systems Biology, 900 E. 57th Street, KCBD 10124, Chicago, IL 60637, USA
| | - Kevin Bernat
- Department of Molecular Genetics and Cell Biology, Institute for Genomics and Systems Biology, 900 E. 57th Street, KCBD 10124, Chicago, IL 60637, USA
| | - Michael J Rust
- Department of Molecular Genetics and Cell Biology, Institute for Genomics and Systems Biology, 900 E. 57th Street, KCBD 10124, Chicago, IL 60637, USA.
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39
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Pattanayek R, Egli M. Protein-Protein Interactions in the Cyanobacterial Circadian Clock: Structure of KaiA Dimer in Complex with C-Terminal KaiC Peptides at 2.8 Å Resolution. Biochemistry 2015. [PMID: 26200123 DOI: 10.1021/acs.biochem.5b00694] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the cyanobacterial circadian clock, the KaiA, -B, and -C proteins with ATP constitute a post-translational oscillator. KaiA stimulates the KaiC autokinase, and KaiB antagonizes KaiA action. KaiA contacts the intrinsically disordered C-terminal regions of KaiC hexamer to promote phosphorylation across subunit interfaces. The crystal structure of KaiA dimer from Synechococcus elongatus with two KaiC C-terminal 20mer peptides bound reveals that the latter adopt an α-helical conformation and contact KaiA α-helical bundles via mostly hydrophobic interactions. This complex and the crystal structure of KaiC hexamer with truncated C-terminal tails can be fit into the electron microscopy (EM) density of the KaiA:KaiC complex. The hybrid model helps rationalize clock phenotypes of KaiA and KaiC mutants.
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Affiliation(s)
- Rekha Pattanayek
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, United States
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, United States
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Abe J, Hiyama TB, Mukaiyama A, Son S, Mori T, Saito S, Osako M, Wolanin J, Yamashita E, Kondo T, Akiyama S. Circadian rhythms. Atomic-scale origins of slowness in the cyanobacterial circadian clock. Science 2015; 349:312-6. [PMID: 26113637 DOI: 10.1126/science.1261040] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 06/10/2015] [Indexed: 11/02/2022]
Abstract
Circadian clocks generate slow and ordered cellular dynamics but consist of fast-moving bio-macromolecules; consequently, the origins of the overall slowness remain unclear. We identified the adenosine triphosphate (ATP) catalytic region [adenosine triphosphatase (ATPase)] in the amino-terminal half of the clock protein KaiC as the minimal pacemaker that controls the in vivo frequency of the cyanobacterial clock. Crystal structures of the ATPase revealed that the slowness of this ATPase arises from sequestration of a lytic water molecule in an unfavorable position and coupling of ATP hydrolysis to a peptide isomerization with high activation energy. The slow ATPase is coupled with another ATPase catalyzing autodephosphorylation in the carboxyl-terminal half of KaiC, yielding the circadian response frequency of intermolecular interactions with other clock-related proteins that influences the transcription and translation cycle.
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Affiliation(s)
- Jun Abe
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Takuya B Hiyama
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Atsushi Mukaiyama
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan. Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Seyoung Son
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Toshifumi Mori
- Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan. Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Shinji Saito
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan. Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan. Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Masato Osako
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Julie Wolanin
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan. PSL Research University, Chimie ParisTech, 75005 Paris, France
| | - Eiki Yamashita
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita 565-0871, Japan
| | - Takao Kondo
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Shuji Akiyama
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan. Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan.
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Mukaiyama A, Osako M, Hikima T, Kondo T, Akiyama S. A protocol for preparing nucleotide-free KaiC monomer. Biophysics (Nagoya-shi) 2015; 11:79-84. [PMID: 27493519 PMCID: PMC4736791 DOI: 10.2142/biophysics.11.79] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 03/12/2015] [Indexed: 12/01/2022] Open
Abstract
The hexameric form of the KaiC protein is a core of the cyanobacterial biological clock, and its enzymatic activities exhibit circadian periodicity. The instability of the monomeric form of nucleotide-free KaiC has precluded its storage and detailed analyses of the activities of the reassembled hexamer. Here, we provide a protocol for preparing nucleotide-free KaiC monomer that is stable in solution and for triggering its reassembly into intact KaiC hexamer by the addition of ATP. A phosphate buffer containing glutamic acid and arginine enhanced the stability of KaiC monomer considerably. In addition, we found that reassembled KaiC hexamer was functionally active as the intact hexamer. This protocol provides a methodological basis for further analyses of first-turnover events of the ATPase/autokinase/autophosphatase activities of the KaiC hexamer.
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Affiliation(s)
- Atsushi Mukaiyama
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan; Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan; RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Masato Osako
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Takaaki Hikima
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Takao Kondo
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Shuji Akiyama
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan; Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan; RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
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Abstract
For a biological oscillator to function as a circadian pacemaker that confers a fitness advantage, its timing functions must be stable in response to environmental and metabolic fluctuations. One such stability enhancer, temperature compensation, has long been a defining characteristic of these timekeepers. However, an accurate biological timekeeper must also resist changes in metabolism, and this review suggests that temperature compensation is actually a subset of a larger phenomenon, namely metabolic compensation, which maintains the frequency of circadian oscillators in response to a host of factors that impinge on metabolism and would otherwise destabilize these clocks. The circadian system of prokaryotic cyanobacteria is an illustrative model because it is composed of transcriptional and nontranscriptional oscillators that are coupled to promote resilience. Moreover, the cyanobacterial circadian program regulates gene activity and metabolic pathways, and it can be manipulated to improve the expression of bioproducts that have practical value.
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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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Abstract
Structural approaches have provided insight into the mechanisms of circadian clock oscillators. This review focuses upon the myriad structural methods that have been applied to the molecular architecture of cyanobacterial circadian proteins, their interactions with each other, and the mechanism of the KaiABC posttranslational oscillator. X-ray crystallography and solution NMR were deployed to gain an understanding of the three-dimensional structures of the three proteins KaiA, KaiB, and KaiC that make up the inner timer in cyanobacteria. A hybrid structural biology approach including crystallography, electron microscopy, and solution scattering has shed light on the shapes of binary and ternary Kai protein complexes. Structural studies of the cyanobacterial oscillator demonstrate both the strengths and the limitations of the divide-and-conquer strategy. Thus, investigations of complexes involving domains and/or peptides have afforded valuable information into Kai protein interactions. However, high-resolution structural data are still needed at the level of complexes between the 360-kDa KaiC hexamer that forms the heart of the clock and its KaiA and KaiB partners.
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45
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Mixtures of opposing phosphorylations within hexamers precisely time feedback in the cyanobacterial circadian clock. Proc Natl Acad Sci U S A 2014; 111:E3937-45. [PMID: 25197081 DOI: 10.1073/pnas.1408692111] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Circadian oscillations are generated by the purified cyanobacterial clock proteins, KaiA, KaiB, and KaiC, through rhythmic interactions that depend on multisite phosphorylation of KaiC. However, the mechanisms that allow these phosphorylation reactions to robustly control the timing of oscillations over a range of protein stoichiometries are not clear. We show that when KaiC hexamers consist of a mixture of differentially phosphorylated subunits, the two phosphorylation sites have opposing effects on the ability of each hexamer to bind to the negative regulator KaiB. We likewise show that the ability of the positive regulator KaiA to act on KaiC depends on the phosphorylation state of the hexamer and that KaiA and KaiB recognize alternative allosteric states of the KaiC ring. Using mathematical models with kinetic parameters taken from experimental data, we find that antagonism of the two KaiC phosphorylation sites generates an ultrasensitive switch in negative feedback strength necessary for stable circadian oscillations over a range of component concentrations. Similar strategies based on opposing modifications may be used to support robustness in other timing systems and in cellular signaling more generally.
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46
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Goda K, Kondo T, Oyama T. Effects of adenylates on the circadian interaction of KaiB with the KaiC complex in the reconstituted cyanobacterial Kai protein oscillator. Biosci Biotechnol Biochem 2014; 78:1833-8. [PMID: 25105527 DOI: 10.1080/09168451.2014.940833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Cyanobacteria are photosynthetic prokaryotes that possess circadian oscillators. Clock proteins, KaiA, KaiB, KaiC compose the central circadian oscillator, which can be reconstituted in vitro in the presence of ATP. KaiC has ATPase, autokinase, and autophosphatase enzymatic activities. These activities are modulated by protein-protein interactions among the Kai proteins. The interaction of KaiB with the KaiC complex shows a circadian rhythm in the reconstituted system. We previously developed a quantitative, real-time monitoring system for the dynamic behavior of the complex using fluorescence correlation spectroscopy. Here, we examined the effects of ATP and ADP on the rhythmic interaction of KaiB. We show that increased concentration of ATP or ADP shortened period length. Adding ADP to the Kai protein oscillation shifted its phase in a phase-dependent manner. These results provide insight into how circadian oscillation entrainment mechanism is linked to cellular metabolism.
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Affiliation(s)
- Kazuhito Goda
- a Medical Technology Research and Development Division, Advanced Analysis Technology Research and Development Department , Olympus Corporation , Hachioji , Japan
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47
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Kitayama Y, Nishiwaki-Ohkawa T, Sugisawa Y, Kondo T. KaiC intersubunit communication facilitates robustness of circadian rhythms in cyanobacteria. Nat Commun 2014; 4:2897. [PMID: 24305644 PMCID: PMC3863973 DOI: 10.1038/ncomms3897] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 11/08/2013] [Indexed: 02/08/2023] Open
Abstract
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 measure their autophosphatase and autokinase activities. We identify two types of regulatory mechanisms with distinct functions. First, local interactions between adjacent phosphorylation 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. The cyanobacterial circadian oscillator comprises an autoregulatory loop that is driven by phosphorylation and dephosphorylation of the hexameric kinase KaiC. Kitayama et al. reveal how interactions between KaiC subunits regulate its catalytic activities and ensure robust circadian behaviour.
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Affiliation(s)
- Yohko Kitayama
- 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
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Egli M. Intricate protein-protein interactions in the cyanobacterial circadian clock. J Biol Chem 2014; 289:21267-75. [PMID: 24936066 DOI: 10.1074/jbc.r114.579607] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The cyanobacterial circadian clock consists of a post-translational oscillator (PTO) and a PTO-dependent transcription-translation feedback loop (TTFL). The PTO can be reconstituted in vitro with the KaiA, KaiB, and KaiC proteins, enabling detailed biochemical and biophysical investigations. Both the CI and the CII halves of the KaiC hexamer harbor ATPases, but only the C-terminal CII ring exhibits kinase and phospho-transferase activities. KaiA stimulates the kinase and KaiB associates with KaiC during the dephosphorylation phase and sequesters KaiA. Recent research has led to conflicting models of the KaiB-KaiC interaction, precluding a clear understanding of KaiB function and KaiABC clock mechanism.
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Affiliation(s)
- Martin Egli
- From the Department of Biochemistry and Center for Structural Biology, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232-0146
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49
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Pattanayek R, Xu Y, Lamichhane A, Johnson CH, Egli M. An arginine tetrad as mediator of input-dependent and input-independent ATPases in the clock protein KaiC. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:1375-90. [PMID: 24816106 PMCID: PMC4722857 DOI: 10.1107/s1399004714003228] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 02/12/2014] [Indexed: 11/10/2022]
Abstract
A post-translational oscillator (PTO) composed of the proteins KaiA, KaiB and KaiC is at the heart of the cyanobacterial circadian clock. KaiC interacts with KaiA and KaiB over the daily cycle, and CII domains undergo rhythmic phosphorylation/dephosphorylation with a 24 h period. Both the N-terminal (CI) and C-terminal (CII) rings of KaiC exhibit ATPase activity. The CI ATPase proceeds in an input-independent fashion, but the CII ATPase is subject to metabolic input signals. The crystal structure of KaiC from Thermosynechococcus elongatus allows insight into the different anatomies of the CI and CII ATPases. Four consecutive arginines in CI (Arg linker) that connect the P-loop, CI subunits and CI and CII at the ring interface are primary candidates for the coordination of the CI and CII activities. The mutation of linker residues alters the period or triggers arhythmic behavior. Comparison between the CI and CII structures also reveals differences in loop regions that are key to KaiA and KaiB binding and activation of CII ATPase and kinase. Common packing features in KaiC crystals shed light on the KaiB-KaiC interaction.
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Affiliation(s)
- Rekha Pattanayek
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Yao Xu
- Department of Biological Sciences, College of Arts and Science, Vanderbilt University, Nashville, TN 35235, USA
| | - Aashish Lamichhane
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Carl H. Johnson
- Department of Biological Sciences, College of Arts and Science, Vanderbilt University, Nashville, TN 35235, USA
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
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50
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Pattanayak G, Rust MJ. The cyanobacterial clock and metabolism. Curr Opin Microbiol 2014; 18:90-5. [PMID: 24667330 DOI: 10.1016/j.mib.2014.02.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 02/26/2014] [Accepted: 02/28/2014] [Indexed: 11/26/2022]
Abstract
Cyanobacteria possess the simplest known circadian clock, which presents a unique opportunity to study how rhythms are generated and how input signals from the environment reset the clock time. The kaiABC locus forms the core of the oscillator, and the remarkable ability to reconstitute oscillations using purified KaiABC proteins has allowed researchers to study mechanism using the tools of quantitative biochemistry. Autotrophic cyanobacteria experience major shifts in metabolism following a light-dark transition, and recent work suggests that input mechanisms that couple the day-night cycle to the clock involve energy and redox metabolites acting directly on clock proteins. We offer a summary of the current state of knowledge in this system and present a perspective for future lines of investigation.
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Affiliation(s)
- Gopal Pattanayak
- Department of Molecular Genetics and Cell Biology, Institute for Genomics and Systems Biology, University of Chicago, 900 E 57th Street, Chicago, IL 60637, United States
| | - Michael J Rust
- Department of Molecular Genetics and Cell Biology, Institute for Genomics and Systems Biology, University of Chicago, 900 E 57th Street, Chicago, IL 60637, United States.
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