The Cyanobacterial Circadian System: From Biophysics to Bioevolution

Johnson, Carl Hirschie; Stewart, Phoebe L.; Egli, Martin

doi:10.1146/annurev-biophys-042910-155317

Cited by 116 publications

(134 citation statements)

References 113 publications

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“…KaiC oscillator contains two ATP-binding domains, CI and CII. The CII domain has autokinase/phosphatase activity crucial for the circadian timing process 36,37 , and the slow ATPase of CI may act as an inputindependent timer 38 . Regulation of FRQ by the two ATPases, CK1a and FRH, could be functionally similar to the regulation of KaiC by its CI and CII domains.…”

Section: Discussionmentioning

confidence: 99%

The RNA helicase FRH is an ATP-dependent regulator of CK1a in the circadian clock of Neurospora crassa

et al. 2014

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The Neurospora clock protein FRQ forms a complex with casein kinase 1a (CK1a) and FRH, a DEAD box-containing RNA helicase with a clock-independent essential function in RNA metabolism. In the course of a circadian period, FRQ is progressively hyperphosphorylated and eventually degraded. Timed hyperphosphorylation of FRQ is crucial for timekeeping of the clock. Here we show that the ATPase activity of FRH attenuates the kinetics of CK1a-mediated hyperphosphorylation of FRQ. Hyperphosphorylation of FRQ is strictly dependent on site-specific recruitment of a CK1a molecule that is activated upon binding. The FRH ATPase cycle regulates the access of CK1a to phosphorylation sites in FRQ in cis, suggesting that FRH is an ATP-dependent remodelling factor acting on the protein complex. We show that the affinity of CK1a for FRQ decreases with increasing FRQ phosphorylation, suggesting functional inactivation of FRQ in the negative feedback loop of the circadian clock before and independent of its degradation.

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Section: Discussionmentioning

confidence: 99%

The RNA helicase FRH is an ATP-dependent regulator of CK1a in the circadian clock of Neurospora crassa

et al. 2014

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“…Surprisingly, however, codon optimization of the cyanobacterial circadian clock genes kaiC and kaiB resulted in more robust clock function, albeit with impaired growth under certain conditions (Xu et al 2013). To reconcile the different results of these two studies, we compared the predicted FRQ and Kai protein structures and found that, while most of the FRQ is predicted to be unstructured, Kai proteins are highly structured with known high-resolution crystal structures (Johnson et al 2011). Such differences raise the possibility that codon usage has distinct effects on different types of protein structures.…”

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confidence: 99%

Codon usage affects the structure and function of the Drosophila circadian clock protein PERIOD

Murphy

Zhou

et al. 2016

Genes Dev.

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Codon usage bias is a universal feature of all genomes, but its in vivo biological functions in animal systems are not clear. To investigate the in vivo role of codon usage in animals, we took advantage of the sensitivity and robustness of the Drosophila circadian system. By codon-optimizing parts of Drosophila period (dper), a core clock gene that encodes a critical component of the circadian oscillator, we showed that dper codon usage is important for circadian clock function. Codon optimization of dper resulted in conformational changes of the dPER protein, altered dPER phosphorylation profile and stability, and impaired dPER function in the circadian negative feedback loop, which manifests into changes in molecular rhythmicity and abnormal circadian behavioral output. This study provides an in vivo example that demonstrates the role of codon usage in determining protein structure and function in an animal system. These results suggest a universal mechanism in eukaryotes that uses a codon usage "code" within genetic codons to regulate cotranslational protein folding.

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“…Circadian clocks or rhythms are widely observed in many species and throughout different kingdoms, from plants and animals to fungi and bacteria. Circadian rhythms are defined as self-sustained and adjustable cycles, typically entrained by light/dark and/or temperature cycles, occurring within 24-h periods (1).…”

mentioning

confidence: 99%

Daily Rhythms in the Cyanobacterium Synechococcus elongatus Probed by High-resolution Mass Spectrometry–based Proteomics Reveals a Small Defined Set of Cyclic Proteins

Guerreiro

Benevento

Lehmann

et al. 2014

Molecular & Cellular Proteomics

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Circadian rhythms are self-sustained and adjustable cycles, typically entrained with light/dark and/or temperature cycles. These rhythms are present in animals, plants, fungi, and several bacteria. The central mechanism behind these "pacemakers" and the connection to the circadian regulated pathways are still poorly understood. The circadian rhythm of the cyanobacterium Synechococcus elongatus PCC 7942 (S. elongatus) is highly robust and controlled by only three proteins, KaiA, KaiB, and KaiC. This central clock system has been extensively studied functionally and structurally and can be reconstituted in vitro. These characteristics, together with a relatively small genome (2.7 Mbp), make S. elongatus an ideal model system for the study of circadian rhythms.Different approaches have been used to reveal the influence of the central S. elongatus clock on rhythmic gene expression, rhythmic mRNA abundance, rhythmic DNA topology changes, and cell division. However, a global analysis of its proteome dynamics has not been reported yet.To uncover the variation in protein abundances during 48 h under light and dark cycles (12:12 h), we used quantitative proteomics, with TMT 6-plex isobaric labeling. We queried the S. elongatus proteome at 10 different time points spanning a single 24-h period, leading to 20 time points over the full 48-h period.Employing multidimensional separation and high-resolution mass spectrometry, we were able to find evidence for a total of 82% of the S. elongatus proteome. Of the 1537 proteins quantified over the time course of the experiment, only 77 underwent significant cyclic variations. Interestingly, our data provide evidence for in-and outof-phase correlation between mRNA and protein levels for a set of specific genes and proteins. As a range of cyclic proteins are functionally not well annotated, this work provides a resource for further studies to explore the role of these proteins in the cyanobacterial circadian rhythm. Molecular & Cellular

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The Cyanobacterial Circadian System: From Biophysics to Bioevolution

Cited by 116 publications

References 113 publications

The RNA helicase FRH is an ATP-dependent regulator of CK1a in the circadian clock of Neurospora crassa

The RNA helicase FRH is an ATP-dependent regulator of CK1a in the circadian clock of Neurospora crassa

Codon usage affects the structure and function of the Drosophila circadian clock protein PERIOD

Daily Rhythms in the Cyanobacterium Synechococcus elongatus Probed by High-resolution Mass Spectrometry–based Proteomics Reveals a Small Defined Set of Cyclic Proteins

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