Macromolecular Assemblies of the Mammalian Circadian Clock

Abstract

The mammalian circadian clock is built on a feedback loop in which PER and CRY proteins repress their own transcription. We found that in mouse liver nuclei all three PERs, both CRYs, and Casein Kinase-1δ (CK1δ) are present together in an ∼1.9-MDa repressor assembly that quantitatively incorporates its CLOCK-BMAL1 transcription factor target. Prior to incorporation, CLOCK-BMAL1 exists in an ∼750-kDa complex. Single-particle electron microscopy (EM) revealed nuclear PER complexes purified from mouse liver to be quasi-spherical ∼40-nm structures. In the cytoplasm, PERs, CRYs, and CK1δ were distributed into several complexes of ∼0.9-1.1 MDa that appear to constitute an assembly pathway regulated by GAPVD1, a cytoplasmic trafficking factor. Single-particle EM of two purified cytoplasmic PER complexes revealed ∼20-nm and ∼25-nm structures, respectively, characterized by flexibly tethered globular domains. Our results define the macromolecular assemblies comprising the circadian feedback loop and provide an initial structural view of endogenous eukaryotic clock machinery.

Figure 1. Nuclear PER complex: mass, circadian profile, and clock proteins

(A) Mass estimate of nuclear PER complex from mouse liver (CT18). Top, Immunoblot of a BN-APAGE gel probed for PER2. Genotypes labeled at top. Molecular weight markers, left. MDa, megadaltons. Bottom, SDS-PAGE immunoblot loading control, RNA Polymerase II large subunit (RNAPII). (B) Nuclear PER complex: relative migration in BN-APAGE vs. log molecular mass. (C) BN-APAGE immunoblot of nuclear extracts from mouse liver, brain, and kidney (CT18) probed for PER2. (D) Circadian profiles of nuclear complexes containing the core negative feedback proteins. Nuclear extracts from mouse livers collected at the indicated circadian times (CT) were analyzed by BN-APAGE, and immunoblots were probed for the proteins indicated at the right of each panel. KO, control sample (CT18) from a null mutant lacking the particular protein probed on each panel, except for CK1δ, which was from Per2^−/−. Asterisk, CRY1 monomer. See Figure S1. (E) Mouse liver nuclear extracts (CT18) were immunodepleted with control IgG or anti-PER2 antibody, and the depleted (unbound) fraction was analyzed by BN-APAGE. Immunoblots were probed for the proteins indicated at the bottom of each panel. Nuclear protein SAP155 (SDS-PAGE) shows input. (F) As in (E), except extracts were immunodepleted with control IgG or anti-CRY1 antibody.

Figure 2. CLOCK-BMAL1 becomes fully incorporated into the PER complex

(A) BN-APAGE immunoblots showing circadian profiles of liver nuclear protein complexes containing BMAL1 (top) or CLOCK (bottom) at the indicated circadian times. Arrow, position of PER complex. Asterisk, non-specific. Loss of CLOCK signal in Bmal1^−/− (Bmal1 KO) suggests instability of CLOCK monomer. See Figure S2. (B) Quantitative incorporation of CLOCK-BMAL1 at the peak of the repression phase. BN-APAGE immunoblots of nuclear extracts from livers collected at CT19 from three wildtype mice, probed for the proteins indicated at bottom. Arrow, trace ~750-kDa complex containing CLOCK-BMAL1. Three biological replicates shown. (C) High molecular-weight complex containing CLOCK-BMAL1 is the PER complex. Mouse liver nuclear extracts (CT19) were immunodepleted with control IgG or anti-PER2 antibody (top), or IgG and anti-CRY1 antibody (bottom), and the depleted (unbound) fraction was analyzed by BN-APAGE. Immunoblots of the gels were probed for proteins indicated at bottom. (D) Genetic analysis of incorporation of CLOCK-BMAL1 into the PER complex. Top, BN-APAGE immunoblot of liver nuclear extracts (CT18) from wildtype (WT) or mutants null for the circadian clock genes indicated at the top (KO) probed for CLOCK. Middle and bottom, SDS-PAGE immunoblots showing CLOCK expression and SAP155 loading control, respectively.

Figure 3. Purification and single-particle EM analysis of mouse liver nuclear PER complex (CT18)

(A) Silver-stained BN-PAGE gel showing wildtype (WT) control (untagged PER2) sample and purified nuclear PER complex from PER2-FH mice. Arrow, purified complex. See Figure S3. (B) PER2 immunoblot of gel in (A). (C–F) Single-particle EM analysis of purified negatively stained PER complexes. (C) Negative control, representative EM image of negatively stained sample from mock-purification of extract from wildtype mice. Scale bar as indicated. (D) Representative EM image of negatively stained PER complexes from PER2-FH mice. (E) Gallery of negatively stained PER complexes obtained in independent experiments. Boxes, 100 nm. (F) Class averages of negatively stained nuclear PER complexes obtained from classifying 10,866 particles into 100 classes. Boxes, 78.3 nm. Asterisks, class average images enlarged in (G). See Figure S4. (G) Enlarged views of the class averages marked in (F).

Figure 4. Action of CK1δ within the purified nuclear PER complex

(A) Protein kinase activity of nuclear PER complex. BN-PAGE autoradiogram showing control sample (WT) or affinity-purified nuclear PER complex (PER2-FH) after incubation with γ-³²P-ATP (25°C, 1 h). (B) SDS-PAGE autoradiogram of material analyzed in (A). See Figure S5. (C) CK1δ in purified PER complex phosphorylates PERs and CLOCK. SDS-PAGE autoradiogram as in (B). Leftmost lane, no inhibitor. Remaining lanes, decreasing concentrations (625, 125, 25, or 5 nM, represented by wedges) of PF-670462, a CK1δ/ε inhibitor (CK1δ/ε), or PF-4800567, a CK1ε-selective inhibitor (CK1ε). (D) Top and Middle, BN-APAGE immunoblots of mouse liver nuclear extracts (CT18) from wildtype (WT) or single mutants null for the circadian clock genes indicated at the top (KO) probed for proteins indicated at right. Bottom, SDS-PAGE SAP155 immunoblot loading control. (E) Top, SDS-PAGE autoradiogram of liver nuclear extracts (CT18) from genotypes indicated at top after immunoprecipitation with anti-CRY1 antibody and incubation with γ-³²P-ATP (25°C, 10 min; linear range for wildtype). Bottom, SDS-PAGE immunoblot for CLOCK served as loading control for PER complexes. (F) Phosphor-imaging quantification of labeled CLOCK bands from (E) after normalization to CLOCK immunoblot signals from (E). Shown are mean ± SEM; t-test (two-tailed). Dashed line, background.

Figure 5. Identification and characterization of cytoplasmic PER complexes

(A) BN-PAGE immunoblots for PER2 showing circadian cycle of PER complexes (arrows) in mouse liver cytoplasm (left) and nucleus (right). UC, upper cytoplasmic complex; LC, lower cytoplasmic complex. (B) Cytoplasmic PER complexes: relative migration in BN-PAGE vs. log molecular mass. (C) BN-PAGE immunoblot of cytoplasmic extracts from mouse liver, brain, and kidney (CT18) probed for PER2. (D) Mouse liver cytoplasmic extracts (CT18) were immunodepleted with control IgG or anti-PER2 antibody, and the depleted (unbound) fraction was analyzed by BN-PAGE. Immunoblots were probed for proteins indicated at the bottom of each panel. Asterisks, non-specific. (E) Silver-stained BN-PAGE gel showing wildtype (WT) control sample and purified UC and LC without (left) and with (middle and right) glycerol-gradient separation of the two. (F) PER2 immnuoblot of gels in (E). See Figure S6. (G) Proteins of LC and UC and their relative representation in the two complexes determined by quantitative TMT mass spectrometry normalized to PER2 (mean ± SEM; n= 3).

Figure 6. PER3 and GAPVD1 are detected in UC but not LC

(A) SDS-PAGE immunoblots of purified LC and UC, probed for proteins indicated at right. (B) BN-PAGE immunoblot of purified cytoplasmic PER complexes, without prior glycerol gradient sedimentation to separate UC from LC, probed for PER2 or GAPVD1, as indicated. (C) Co-immunoprecipitation (IP) with control IgG or anti-PER2 antibody, as indicated, from liver nuclear (N) or cytoplasmic (C) extracts (CT18), probed for proteins indicated at right. IgG-LC, IgG light chain immunoprecipitation positive control. (D) Immunoblots showing depletion of GAPVD1 from bioluminescent circadian reporter cells by two non-overlapping GAPVD1 siRNAs in comparison with control siRNA (duplicate samples). (E) Examples of circadian oscillations of bioluminescence in synchronized reporter fibroblasts after delivery of control siRNA (black) or GAPVD1 siRNA-2 (red). Four independent cultures shown for each. (F) Circadian period lengths of bioluminescent circadian reporter cells after delivery of control siRNA, GAPVD1 siRNA-1, or GAPVD1-siRNA-2, as indicated (mean ± SEM; n = 4; two-tailed, paired t-test).

Figure 7. Single-particle EM analysis of mouse liver cytoplasmic PER complexes (CT18)

(A) Left, negative control: representative EM image of negatively stained sample from LC purification procedure performed on extract from wildtype mice. Scale bar as indicated. Right, representative image of negatively stained LC from PER2-FH mice. (B) Examples of negatively stained LC particles, showing typical four-domain structure. Boxes, 100 nm. (C) The 39 class averages of negatively stained LC obtained by using the iterative stable alignment and classification (ISAC) procedure and stringent classification parameters (100 images per group, pixel error threshold of 0.7). Boxes, 33.4 nm. Asterisk, class average enlarged in (F). See Figure S7A. (D) Gallery of negatively stained UC particles showing typical multi-lobed appearance. Boxes, 100 nm. (E) Some class averages of negatively stained UC generated during analysis with ISAC. Boxes, 52.2 nm. See Figure S7B. (F) Enlarged view of a single LC class average showing four-domain structure. (G) Enlarged view of a single UC class average showing five-domain structure.