Metabolic oscillations on the circadian time scale in Drosophila cells lacking clock genes

Abstract

Circadian rhythms are cell‐autonomous biological oscillations with a period of about 24 h. Current models propose that transcriptional feedback loops are the primary mechanism for the generation of circadian oscillations. Within this framework, Drosophila S2 cells are regarded as “non‐rhythmic” cells, as they do not express several canonical circadian components. Using an unbiased multi‐omics approach, we made the surprising discovery that Drosophila S2 cells do in fact display widespread daily rhythms. Transcriptomics and proteomics analyses revealed that hundreds of genes and their products, and in particular metabolic enzymes, are rhythmically expressed in a 24‐h cycle. Metabolomics analyses extended these findings and demonstrate that central carbon metabolism and amino acid metabolism are core metabolic pathways driven by protein rhythms. We thus demonstrate that 24‐h metabolic oscillations, coupled to gene and protein cycles, take place in nucleated cells without the contribution of any known circadian regulators. These results therefore suggest a reconsideration of existing models of the clockwork in Drosophila and other eukaryotic systems.

12h-clock control of central dogma information flow by XBP1s

“…Consistent with past findings (Zhu et al, 2017), the vast majority of oscillations identified were circadian rhythms and oscillations that cycle at the second (~12h) and third harmonics (~8h) of the circadian rhythm [due to the 2h sampling frequency of the current study, only up to third harmonics can be identified with high confidence (Antoulas et al, 2018)] ( Figure 1E and Table S2). To determine the false discovery rate (FDR) of the identified rhythmic transcripts, we used a permutation-based method that randomly shuffles the time label of gene expression data and subjects each of the permutation dataset to eigenvalue/pencil method as previously described (Rey et al, 2018). As expected, permutation datasets are devoid of distinct populations of oscillations cycling at different harmonics of the circadian rhythm ( Figures S2A-B).…”

Lost in clocks: non‐canonical circadian oscillation discovered in Drosophila cells

“…Drosophila S2 cells do not express CLK, PER, and TIM; thus, the core feedback mechanism does not operate in this cell line. Surprisingly, Rey et al () found hundreds of transcripts, proteins, and metabolites that show apparent circadian rhythmicity under constant culture conditions, suggesting that this rhythmicity is generated through non‐canonical circadian mechanisms.…”

“…The study by Reddy and colleagues provides evidence indicating that circadian oscillations not driven by the canonical TTFL can be observed for hundreds of transcripts, proteins, and metabolites (Rey et al , ). This was demonstrated using Drosophila S2 cells, which do not express per , tim, and other core components of the canonical circadian TTFL.…”

“…Per was the first identified clock gene in the fruit fly and is a core component of the circadian TTFL. Surprisingly, in their recent study, Rey et al () demonstrate the presence of apparent circadian rhythmicity in a fly cell line that does not express several core clock genes including per (Rey et al , ). Quantitative multi‐omics measurements allowed the identification of unknown oscillating components and revealed hundreds of transcripts, proteins, and metabolites showing 24‐h rhythmicity, suggesting that at least in the fly, the circadian clock may be driven by non‐canonical (i.e., independent of per ‐driven TTFL) molecular mechanisms.…”

“… Cell‐autonomous circadian clocks are mostly driven by a transcription‐translation negative feedback loop. In their recent study, Rey et al , ) identify transcripts, proteins and metabolites showing 24‐h rhythmicity in Drosophila cells that do not express core clock genes.

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