Circadian (daily) rhythms are a crucial component of human health that regulates sleep, alertness, hormones, metabolism, and many other biological processes. The ultimate explanation for the mechanism of circadian oscillators will require characterizing the structures, functions, and interactions of the molecular components of these clocks. The current project is to elucidate the basic principles of circadian clocks at a biophysical/molecular level in the cyanobacterial model system, where genetic/biochemical studies have identified three key clock proteins, KaiA, KaiB, and KaiC, that can reconstitute a circadian oscillator in vitro. This remarkable demonstration has led to a re-evaluation of our understanding of circadian clocks in all organisms, including mammals. Moreover, atomic resolution structures of KaiA, KaiB, and KaiC proteins have been determined that enable truly molecular analyses of clock mechanisms. This research project will focus on answering two fundamental questions in chronobiology: how do circadian enzymes work? and what is the adaptive advantage of circadian mechanisms? Regarding the first question of enzymatic mechanism, we will determine the basis of the central property of temperature compensation of the core clockwork by biochemical/biophysical, genetic, and structural approaches. Temperature-compensation mutations of the Kai proteins will be studied to generate specific hypotheses that will be tested by novel in vitro biochemical analyses (e.g., single-molecule dynamics) and targeted mutations. The biochemical data that result from the analyses of these mutants will be used to generate models that account for the temperature compensated, 24 h time constant of the circadian oscillator. Regarding the second overall question of adaptive advantage, differential expression of circadian rhythms under some conditions but not others is based on novel mechanisms of codon usage, and the mechanism of this adaptive phenomenon will be analyzed, as well as recruited to maximize cost-effective synthesis of bioproducts. Finally, a novel hypothesis with far-reaching implications will be evaluated, namely that accurate circadian timekeeping requires compensation for metabolic perturbations, of which temperature change is only one among many such perturbations. The answers to these questions will lead to wide-ranging general insights into the mechanisms and applications of biological timekeeping.

Public Health Relevance

This MERIT project will clarify circadian mechanisms at molecular levels that were heretofore unreachable. Biological clocks have been found to be crucial for physical and mental health, and knowledge of circadian mechanisms along with the development of therapies to properly phase sleep will allow us to enhance health, performance, and well-being in addition to improving the quality of life for depressed subjects.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Method to Extend Research in Time (MERIT) Award (R37)
Project #
4R37GM067152-18
Application #
9747606
Study Section
Special Emphasis Panel (NSS)
Program Officer
Sesma, Michael A
Project Start
2003-01-01
Project End
2024-12-31
Budget Start
2020-01-01
Budget End
2020-12-31
Support Year
18
Fiscal Year
2020
Total Cost
Indirect Cost
Name
Vanderbilt University Medical Center
Department
Type
DUNS #
965717143
City
Nashville
State
TN
Country
United States
Zip Code
37203
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Johnson, Carl Hirschie; Zhao, Chi; Xu, Yao et al. (2017) Timing the day: what makes bacterial clocks tick? Nat Rev Microbiol 15:232-242
Tackenberg, Michael C; Johnson, Carl H; Page, Terry L et al. (2017) Revealing Oft-cited but Unpublished Papers of Colin Pittendrigh and Coworkers. J Biol Rhythms 32:291-294
Jazmin, Lara J; Xu, Yao; Cheah, Yi Ern et al. (2017) Isotopically nonstationary 13C flux analysis of cyanobacterial isobutyraldehyde production. Metab Eng 42:9-18
Ma, Peijun; Mori, Tetsuya; Zhao, Chi et al. (2016) Evolution of KaiC-Dependent Timekeepers: A Proto-circadian Timing Mechanism Confers Adaptive Fitness in the Purple Bacterium Rhodopseudomonas palustris. PLoS Genet 12:e1005922
Shi, S-q; White, M J; Borsetti, H M et al. (2016) Molecular analyses of circadian gene variants reveal sex-dependent links between depression and clocks. Transl Psychiatry 6:e748
Zhang, Yunfei; Robertson, J Brian; Xie, Qiguang et al. (2016) Monitoring Intracellular pH Change with a Genetically Encoded and Ratiometric Luminescence Sensor in Yeast and Mammalian Cells. Methods Mol Biol 1461:117-30
Egli, Martin; Johnson, Carl H (2015) Biochemistry that times the day. Biochemistry 54:104-9
Mori, Tetsuya; Mchaourab, Hassane; Johnson, Carl Hirschie (2015) Circadian Clocks: Unexpected Biochemical Cogs. Curr Biol 25:R842-4
Qin, Ximing; Mori, Tetsuya; Zhang, Yunfei et al. (2015) PER2 Differentially Regulates Clock Phosphorylation versus Transcription by Reciprocal Switching of CK1? Activity. J Biol Rhythms 30:206-16

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