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Circadian rhythms. Atomic-scale origins of slowness in the cyanobacterial circadian clock.

Abe J, Hiyama TB, Mukaiyama A, Son S, Mori T, Saito S, Osako M, Wolanin J, Yamashita E, Kondo T, Akiyama S
Science 349 312-6 (2015)
Related entries: 4tl6, 4tl8, 4tl9, 4tla, 4tlb, 4tlc, 4tld, 4tle

Cited: 57 times
EuropePMC logo PMID: 26113637

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.

Articles - 4tl7 mentioned but not cited (3)

  1. Conformational rearrangements of the C1 ring in KaiC measure the timing of assembly with KaiB. Mukaiyama A, Furuike Y, Abe J, Koda SI, Yamashita E, Kondo T, Akiyama S. Sci Rep 8 8803 (2018)
  2. Molecular dynamics simulations of nucleotide release from the circadian clock protein KaiC reveal atomic-resolution functional insights. Hong L, Vani BP, Thiede EH, Rust MJ, Dinner AR. Proc Natl Acad Sci U S A 115 E11475-E11484 (2018)
  3. Common Mechanism of Activated Catalysis in P-loop Fold Nucleoside Triphosphatases-United in Diversity. Kozlova MI, Shalaeva DN, Dibrova DV, Mulkidjanian AY. Biomolecules 12 1346 (2022)


Reviews citing this publication (16)

  1. Circadian Oscillators: Around the Transcription-Translation Feedback Loop and on to Output. Hurley JM, Loros JJ, Dunlap JC. Trends Biochem Sci 41 834-846 (2016)
  2. The mammalian circadian system: a hierarchical multi-oscillator structure for generating circadian rhythm. Honma S. J Physiol Sci 68 207-219 (2018)
  3. Timing the day: what makes bacterial clocks tick? Johnson CH, Zhao C, Xu Y, Mori T. Nat Rev Microbiol 15 232-242 (2017)
  4. Structure, function, and mechanism of the core circadian clock in cyanobacteria. Swan JA, Golden SS, LiWang A, Partch CL. J Biol Chem 293 5026-5034 (2018)
  5. Circadian oscillator proteins across the kingdoms of life: structural aspects. Saini R, Jaskolski M, Davis SJ. BMC Biol 17 13 (2019)
  6. Functional and Regulatory Roles of Fold-Switching Proteins. Kim AK, Porter LL. Structure 29 6-14 (2021)
  7. Orchestration of Circadian Timing by Macromolecular Protein Assemblies. Partch CL. J Mol Biol 432 3426-3448 (2020)
  8. Non-transcriptional processes in circadian rhythm generation. Wong DC, O'Neill JS. Curr Opin Physiol 5 117-132 (2018)
  9. Design Principles of Phosphorylation-Dependent Timekeeping in Eukaryotic Circadian Clocks. Ode KL, Ueda HR. Cold Spring Harb Perspect Biol 10 a028357 (2018)
  10. Spectres of Clock Evolution: Past, Present, and Yet to Come. Jabbur ML, Johnson CH. Front Physiol 12 815847 (2021)
  11. Toward Multiscale Models of Cyanobacterial Growth: A Modular Approach. Westermark S, Steuer R. Front Bioeng Biotechnol 4 95 (2016)
  12. A period without PER: understanding 24-hour rhythms without classic transcription and translation feedback loops. Millius A, Ode KL, Ueda HR. F1000Res 8 F1000 Faculty Rev-499 (2019)
  13. Architecture and mechanism of the central gear in an ancient molecular timer. Egli M. J R Soc Interface 14 20161065 (2017)
  14. Spatial-Temporal Genome Regulation in Stress-Response and Cell-Fate Change. Erenpreisa J, Giuliani A, Yoshikawa K, Falk M, Hildenbrand G, Salmina K, Freivalds T, Vainshelbaum N, Weidner J, Sievers A, Pilarczyk G, Hausmann M. Int J Mol Sci 24 2658 (2023)
  15. Biophysical research in Okazaki, Japan. Akiyama S, Aoki K, Kubo Y. Biophys Rev 12 237-243 (2020)
  16. Studying the Human Microbiota: Advances in Understanding the Fundamentals, Origin, and Evolution of Biological Timekeeping. Siebieszuk A, Sejbuk M, Witkowska AM. Int J Mol Sci 24 16169 (2023)

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