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Fang M, LiWang A, Golden SS, Partch CL. The inner workings of an ancient biological clock. Trends Biochem Sci 2024; 49:236-246. [PMID: 38185606 PMCID: PMC10939747 DOI: 10.1016/j.tibs.2023.12.007] [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: 09/09/2023] [Revised: 11/30/2023] [Accepted: 12/15/2023] [Indexed: 01/09/2024]
Abstract
Circadian clocks evolved in diverse organisms as an adaptation to the daily swings in ambient light and temperature that derive from Earth's rotation. These timing systems, based on intracellular molecular oscillations, synchronize organisms' behavior and physiology with the 24-h environmental rhythm. The cyanobacterial clock serves as a special model for understanding circadian rhythms because it can be fully reconstituted in vitro. This review summarizes recent advances that leverage new biochemical, biophysical, and mathematical approaches to shed light on the molecular mechanisms of cyanobacterial Kai proteins that support the clock, and their homologues in other bacteria. Many questions remain in circadian biology, and the tools developed for the Kai system will bring us closer to the answers.
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Affiliation(s)
- Mingxu Fang
- Department of Molecular Biology, University of California - San Diego, La Jolla, CA 92093, USA; Center for Circadian Biology, University of California - San Diego, La Jolla, CA 92093, USA
| | - Andy LiWang
- Center for Circadian Biology, University of California - San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California - Merced, Merced, CA 95343, USA; Center for Cellular and Biomolecular Machines, University of California - Merced, Merced, CA 95343, USA
| | - Susan S Golden
- Department of Molecular Biology, University of California - San Diego, La Jolla, CA 92093, USA; Center for Circadian Biology, University of California - San Diego, La Jolla, CA 92093, USA
| | - Carrie L Partch
- Center for Circadian Biology, University of California - San Diego, La Jolla, CA 92093, USA; Department of Chemistry & Biochemistry, University of California - Santa Cruz, Santa Cruz, CA 95064, USA.
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Furuike Y, Yamashita E, Akiyama S. Structure-function relationship of KaiC around dawn. Biophys Physicobiol 2023; 21:e210001. [PMID: 38803331 PMCID: PMC11128299 DOI: 10.2142/biophysico.bppb-v21.0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 12/14/2023] [Indexed: 05/29/2024] Open
Abstract
KaiC is a multifunctional enzyme functioning as the core of the circadian clock system in cyanobacteria: its N-terminal domain has adenosine triphosphatase (ATPase) activity, and its C-terminal domain has autokinase and autophosphatase activities targeting own S431 and T432. The coordination of these multiple biochemical activities is the molecular basis for robust circadian rhythmicity. Therefore, much effort has been devoted to elucidating the cooperative relationship between the two domains. However, structural and functional relationships between the two domains remain unclear especially with respect to the dawn phase, at which KaiC relieves its nocturnal history through autodephosphorylation. In this study, we attempted to design a double mutation of S431 and T432 that can capture KaiC as a fully dephosphorylated form with minimal impacts on its structure and function, and investigated the cooperative relationship between the two domains in the night to morning phases from many perspectives. The results revealed that both domains cooperate at the dawn phase through salt bridges formed between the domains, thereby non-locally co-activating two events, ATPase de-inhibition and S431 dephosphorylation. Our further analysis using existing crystal structures of KaiC suggests that the states of both domains are not always in one-to-one correspondence at every phase of the circadian cycle, and their coupling is affected by the interactions with KaiA or adjacent subunits within a KaiC hexamer.
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Affiliation(s)
- Yoshihiko Furuike
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi 444-8585, Japan
- Molecular Science Program, Graduate Institute for Advanced Studies, SOKENDAI, Okazaki, Aichi 444-8585, Japan
| | - Eiki Yamashita
- Institute for Protein Research, Osaka University, Suita 565-0871, Japan
| | - Shuji Akiyama
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi 444-8585, Japan
- Molecular Science Program, Graduate Institute for Advanced Studies, SOKENDAI, Okazaki, Aichi 444-8585, Japan
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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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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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The mechanism of the simplest biological 24-hour clock. Nature 2023:10.1038/d41586-023-00718-6. [PMID: 36949125 DOI: 10.1038/d41586-023-00718-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
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