The Proteomic Landscape of the Suprachiasmatic Nucleus Clock Reveals Large-Scale Coordination of Key Biological Processes

The suprachiasmatic nucleus (SCN) acts as the central clock to coordinate circadian oscillations in mammalian behavior, physiology and gene expression. Despite our knowledge of the circadian transcriptome of the SCN, how it impacts genome-wide protein expression is not well understood. Here, we interrogated the murine SCN proteome across the circadian cycle using SILAC-based quantitative mass spectrometry. Of the 2112 proteins that were accurately quantified, 20% (421 proteins) displayed a time-of-day-dependent expression profile. Within this time-of-day proteome, 11% (48 proteins) were further defined as circadian based on a sinusoidal expression pattern with a ∼24 h period. Nine circadianly expressed proteins exhibited 24 h rhythms at the transcript level, with an average time lag that exceeded 8 h. A substantial proportion of the time-of-day proteome exhibited abrupt fluctuations at the anticipated light-to-dark and dark-to-light transitions, and was enriched for proteins involved in several key biological pathways, most notably, mitochondrial oxidative phosphorylation. Additionally, predicted targets of miR-133ab were enriched in specific hierarchical clusters and were inversely correlated with miR133ab expression in the SCN. These insights into the proteomic landscape of the SCN will facilitate a more integrative understanding of cellular control within the SCN clock.Author Summary: The suprachiasmatic nucleus (SCN) serves as the master circadian pacemaker in mammals, coordinating the physiological responses of a myriad of peripheral clocks throughout the body and linking their rhythms to the environmental light-dark cycle. In this study, we interrogated the murine SCN proteome across the circadian cycle using stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative mass spectrometry. Among 3275 identified proteins in the SCN, 421 displayed a time-of-day-dependent expression profile, 48 fit a circadian expression profile with a ∼24 h period, and a surprising number of proteins were ultradianly expressed. Nine circadianly expressed proteins were accompanied by transcripts that were also 24 h rhythmic, but with a significant time lag (>8 h) between the phases of peak mRNA vs. protein expression. A substantial proportion of the time-of-day proteome exhibited abrupt fluctuations at the anticipated dawn and dusk, and was involved in mitochondrial oxidative phosphorylation. Additionally, predicted targets of miR-133ab were enriched in specific hierarchical clusters and were inversely correlated with miR133ab expression in the SCN. Our study underscores the significance of post-transcriptional regulation, the surprising prevalence of ultradian protein expression, and the functional implications on mitochondrial energy metabolism.