A protein fold switch joins the circadian oscillator to clock output in cyanobacteria

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Science  17 Jul 2015:
Vol. 349, Issue 6245, pp. 324-328
DOI: 10.1126/science.1260031
  • Fig. 1 KaiB switches its fold to bind KaiC.

    (A) Plots of chemical shift–based secondary structures of KaiBte*, KaiBte* + CIte*, and G89A,D91R-KaiBte* determined by TALOS+ (18). Unassigned proline and nonproline residues are indicated by small red and blue dots along the horizontal axis at y = 0. The secondary structures of KaiBte and G89A,D91R-KaiBte* are shown for comparison. KaiBte* residues Q52 to E56 in KaiBte* bound to CIte* were not assignable, probably owing to exchange broadening. Vertical dashed lines are visual guides separating the N-terminal and C-terminal halves of KaiB. (B) Structural comparisons of KaiBte, G89A,D91R-KaiBte*, and N-SasAse. Residues K58, G89, and D91 are highlighted for their roles in fold switching.

  • Fig. 2 KaiB fold switching regulates oscillator function and clock output.

    (A) In vitro KaiC phosphorylation assays using KaiCse, KaiAse, and KaiBse, G88A-KaiBse, D90R-KaiBse, or G88A,D90R-KaiBse. (B) Gel-filtration profiles of G88A-KaiBse, KaiAse, and G88A-KaiBse + KaiAse. Peaks (a) to (c) were analyzed by SDS–polyacrylamide gel electrophoresis (fig. S13). (C) Bioluminescence from strains that carry a PkaiB luc reporter for circadian rhythmicity. Cells harbored kaiBse, G88A-kaiBse, D90R-kaiBse, or G88A,D90R-kaiBse, or cells with kaiBse deletion. Time in LL, time under low-light conditions. (D) Bioluminescence from strains that carry a PkaiB luc reporter expressing kaiBse, G88A-kaiBse, D90R-kaiBse, G88A,D90R-kaiBse, or empty vector, in addition to chromosomal kaiBse. (E) Representative micrographs of cells expressing kaiBse, lacking kaiBse, or harboring G88A,D90R-kaiBse. Cellular autofluorescence in red. Scale bars, 2.5 μm. (F) Histograms showing cell-length distributions of strains expressing kaiBse, ΔkaiBse, G88A-kaiBse, D90R-kaiBse, or G88A,D90R-kaiBse as the only copy of kaiB. (G) SasAse kinase activities in the presence of S431E-KaiCse and KaiBse, G88A-KaiBse, D90R-KaiBse, or G88A,D90R-KaiBse. The mixtures were incubated for 2 hours before SasAse, RpaAse and [γ−32P]ATP (32P-labeled adenosine triphosphate) were added. Relative kinase activities compare the mean steady-state amount of 32P-labeled RpaAse to that of a reaction of S431E-KaiCse alone (n = 4, error bars denote SEM). One-way analysis of variance (ANOVA) gives P < 0.001, and **** denotes Bonferroni-corrected values (P < 0.001) for pairwise comparisons against kinase activity with KaiBse (α = 0.05). (H) CikA phosphatase activity toward phosphorylated RpaA in the presence of KaiCse and KaiBse, G88A-KaiBse, D90R-KaiBse, or G88A,D90R-KaiBse (n = 4–5, error bars denote SEM). KaiCse alone or KaiBse alone did not activate CikA phosphatase activity (fig. S17). (I) In vitro KaiCse phosphorylation assays as a function of concentration of PsR-CikAse. (J) Same as (I) except for using PsR-KaiAse instead of PsR-CikAse. The black curves in (I) and (J) are identical.

  • Fig. 3 KaiB fold-switching regulates slow formation of the KaiB-KaiC complex.

    (A) Fluorescence anisotropies of 6-iodoacetamidofluorescein (6-IAF)–labeled KaiBte, G89A-KaiBte, D91R-KaiBte, and G89A,D91R-KaiBte in the presence of S431E-KaiCte. KaiB samples were incubated for 1 hour (circles) before addition (arrow) of S431E-KaiCte. A54C mutation was introduced to all KaiB for fluorescence labeling. (B) Scheme for modeling. (C) Forward fold-switching rate constants, kB+ (maroon), and burst-phase binding to S431E-KaiCte (tan). Burst-phase binding—defined as the percentage of KaiBte-S431E-KaiCte complexes formed at t = 0.1 hours in the model relative to steady-state binding at t = 24 hours—were derived from fitting data after adding S431E-KaiCte in (A) to the model shown in (B). Burst-phase error bars show the standard deviation from model calculations by bootstrap resampling the raw data (n = 20). kB+ values used in these fits were predetermined from analysis of the kinetics of binding of KaiBte variants to the isolated CIte* domain (fig. S21), a condition where we assumed the rate-limiting step in complex formation is due only to KaiB fold switching. Error bars for kB+ were estimated by bootstrap resampling the original data set 500 times. (D) Mathematical modeling of KaiC phosphorylation period (black) and probability of stable oscillation (purple), as a function of the forward fold-switching rate constant, kB+. Each black point represents the mean period from 100 simulations at fixed kB+, while randomly varying all other parameters (Gaussian with 10% standard deviation). The shaded region represents standard deviations of the periods for those parameter sets that produced stable oscillations. Oscillations became unstable outside of the plotted range. The purple plot is the fraction of simulations that produced stable oscillations at each kB+ value. The dashed line runs parallel to the x axis and intersects the y axis at 24 hours.

  • Fig. 4 KaiB and SasA bind to similar sites on CI.

    (A) An electron paramagnetic resonance)–restrained model of the CIte*–N-SasAte complex. The HADDOCK (32) model of the complex with the best score is superimposed on the crystal structure of KaiCte (PDB ID: 4O0m). (B) Qualitative structural model of the interaction of CIte* and fsKaiB (G89A,D91R-KaiBte*) based on HDX-MS data and mutagenesis. Dark blue and cyan spheres represent CI residues whose mutations strongly or moderately weaken binding, respectively. Dark blue and cyan ribbons represent protection against H/D exchange upon complex formation that are >1.5 and 0.5 to 1.5 standard deviations above the average, respectively, as determined by HDX-MS (figs. S32 to S35).

  • Fig. 5 Model of KaiB fold switching as linchpin for the cyanobacterial clock.

    Excursion of KaiB to the rare fold-switch state causes fsKaiB to displace SasA for binding to KaiC. KaiC-stabilized fsKaiB captures KaiA, initiating the dephosphorylation phase of the cycle. These aspects control oscillator period. CikA and KaiA compete for binding to fsKaiB, which further links oscillator function related to KaiA and output activity via CikA-mediated dephosphorylation of RpaA. The competitive interactions of fsKaiB with SasA, and KaiA with CikA, implicate “output components” CikA and SasA as parts of an extended oscillator.

Supplementary Materials

  • A protein fold switch joins the circadian oscillator to clock output in cyanobacteria

    Yong-Gang Chang, Susan E. Cohen, Connie Phong, William K. Myers, Yong-Ick Kim, Roger Tseng, Jenny Lin, Li Zhang, Joseph S. Boyd, Yvonne Lee, Shannon Kang, David Lee, Sheng Li, R. David Britt, Michael J. Rust, Susan S. Golden, Andy LiWang

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods
    • Figs. S1 to S41
    • Tables S1 to S14
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    Correction (17 July 2015): URL links updated for print.
    Correction (22 July 2015): The current version has been corrected to show the updated references that reflect changes made for the print publication. The number of supplementary tables has also been updated.
    The original version is accessible here.

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