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The molecular basis of metabolic cycles and their relationship to circadian rhythms

Abstract

Metabolic cycles result from the partitioning of oxidative and reductive metabolism into rhythmic phases of gene expression and oscillating post-translational protein modifications. Relatively little is known about how these switches in gene expression are controlled, although recent studies have suggested that transcription itself may play a central role. This review explores the molecular basis of the metabolic and gene-expression oscillations in the yeast Saccharomyces cerevisiae, as well as how they relate to other biological time-keeping mechanisms, such as circadian rhythms.

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Figure 1: Factors that contribute to biological rhythms and cycles.
Figure 2: Metabolic cycles in S. cerevisiae. (a) Cycling metabolites during the YMC.
Figure 3: Coupling of growth rate, metabolic cycling, the CDC and gene expression.
Figure 4: Transcriptional-state-switching at YMC-regulated genes.

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References

  1. Pattanayak, G. & Rust, M.J. The cyanobacterial clock and metabolism. Curr. Opin. Microbiol. 18, 90–95 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Ray, S. & Reddy, A.B. Cross-talk between circadian clocks, sleep-wake cycles, and metabolic networks: dispelling the darkness. BioEssays 38, 394–405 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  3. Edgar, R.S. et al. Peroxiredoxins are conserved markers of circadian rhythms. Nature 485, 459–464 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Tomita, J., Nakajima, M., Kondo, T. & Iwasaki, H. No transcription-translation feedback in circadian rhythm of KaiC phosphorylation. Science 307, 251–254 (2005).

    Article  CAS  PubMed  Google Scholar 

  5. O'Neill, J.S. & Reddy, A.B. Circadian clocks in human red blood cells. Nature 469, 498–503 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Causton, H.C., Feeney, K.A., Ziegler, C.A. & O'Neill, J.S. Metabolic cycles in yeast share features conserved among circadian rhythms. Curr. Biol. 25, 1056–1062 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Novák, B. & Tyson, J.J. Design principles of biochemical oscillators. Nat. Rev. Mol. Cell Biol. 9, 981–991 (2008).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  8. Reddy, A.B. & Rey, G. Metabolic and nontranscriptional circadian clocks: eukaryotes. Annu. Rev. Biochem. 83, 165–189 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Schick, S. et al. Identifying novel transcriptional regulators with circadian expression. Mol. Cell. Biol. 36, 545–558 (2015).

    Article  PubMed  CAS  Google Scholar 

  10. Koike, N. et al. Transcriptional architecture and chromatin landscape of the core circadian clock in mammals. Science 338, 349–354 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Morf, J. et al. Cold-inducible RNA-binding protein modulates circadian gene expression posttranscriptionally. Science 338, 379–383 (2012).

    Article  CAS  PubMed  Google Scholar 

  12. Rodriguez, J. et al. Nascent-Seq analysis of Drosophila cycling gene expression. Proc. Natl. Acad. Sci. USA 110, E275–E284 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Hurley, J.M. et al. Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential. Proc. Natl. Acad. Sci. USA 111, 16995–17002 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Guo, J., Cheng, P., Yuan, H. & Liu, Y. The exosome regulates circadian gene expression in a posttranscriptional negative feedback loop. Cell 138, 1236–1246 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Nguyen, T. et al. Transcription mediated insulation and interference direct gene cluster expression switches. eLife 3, e03635 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  16. Hendriks, G.J., Gaidatzis, D., Aeschimann, F. & Großhans, H. Extensive oscillatory gene expression during C. elegans larval development. Mol. Cell 53, 380–392 (2014).

    Article  CAS  PubMed  Google Scholar 

  17. Robles, M.S., Cox, J. & Mann, M. In-vivo quantitative proteomics reveals a key contribution of post-transcriptional mechanisms to the circadian regulation of liver metabolism. PLoS Genet. 10, e1004047 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  18. Jang, C., Lahens, N.F., Hogenesch, J.B. & Sehgal, A. Ribosome profiling reveals an important role for translational control in circadian gene expression. Genome Res. 25, 1836–1847 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Janich, P., Arpat, A.B., Castelo-Szekely, V., Lopes, M. & Gatfield, D. Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames. Genome Res. 25, 1848–1859 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Lipton, J.O. et al. The circadian protein BMAL1 regulates translation in response to S6K1-mediated phosphorylation. Cell 161, 1138–1151 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Murray, D.B., Beckmann, M. & Kitano, H. Regulation of yeast oscillatory dynamics. Proc. Natl. Acad. Sci. USA 104, 2241–2246 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Tu, B.P. et al. Cyclic changes in metabolic state during the life of a yeast cell. Proc. Natl. Acad. Sci. USA 104, 16886–16891 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Mohler, R.E. et al. Identification and evaluation of cycling yeast metabolites in two-dimensional comprehensive gas chromatography-time-of-flight-mass spectrometry data. J. Chromatogr. A 1186, 401–411 (2008).

    Article  CAS  PubMed  Google Scholar 

  24. Dallmann, R., Viola, A.U., Tarokh, L., Cajochen, C. & Brown, S.A. The human circadian metabolome. Proc. Natl. Acad. Sci. USA 109, 2625–2629 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Eckel-Mahan, K.L. et al. Coordination of the transcriptome and metabolome by the circadian clock. Proc. Natl. Acad. Sci. USA 109, 5541–5546 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Ribas-Latre, A. & Eckel-Mahan, K. Interdependence of nutrient metabolism and the circadian clock system: importance for metabolic health. Mol. Metab. 5, 133–152 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Bass, J. Circadian topology of metabolism. Nature 491, 348–356 (2012).

    Article  CAS  PubMed  Google Scholar 

  28. Kaspar von Meyenburg, H. Energetics of the budding cycle of Saccharomyces cerevisiae during glucose limited aerobic growth. Arch. Mikrobiol. 66, 289–303 (1969).

    Article  CAS  PubMed  Google Scholar 

  29. Murray, D.B., Roller, S., Kuriyama, H. & Lloyd, D. Clock control of ultradian respiratory oscillation found during yeast continuous culture. J. Bacteriol. 183, 7253–7259 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Klevecz, R.R., Bolen, J., Forrest, G. & Murray, D.B. A genomewide oscillation in transcription gates DNA replication and cell cycle. Proc. Natl. Acad. Sci. USA 101, 1200–1205 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Tu, B.P., Kudlicki, A., Rowicka, M. & McKnight, S.L. Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science 310, 1152–1158 (2005).

    Article  CAS  PubMed  Google Scholar 

  32. Slavov, N., Macinskas, J., Caudy, A. & Botstein, D. Metabolic cycling without cell division cycling in respiring yeast. Proc. Natl. Acad. Sci. USA 108, 19090–19095 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Slavov, N. & Botstein, D. Coupling among growth rate response, metabolic cycle, and cell division cycle in yeast. Mol. Biol. Cell 22, 1997–2009 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Müller, D., Exler, S., Aguilera-Vázquez, L., Guerrero-Martín, E. & Reuss, M. Cyclic AMP mediates the cell cycle dynamics of energy metabolism in Saccharomyces cerevisiae. Yeast 20, 351–367 (2003).

    Article  PubMed  CAS  Google Scholar 

  35. Burnetti, A.J., Aydin, M. & Buchler, N.E. Cell cycle Start is coupled to entry into the yeast metabolic cycle across diverse strains and growth rates. Mol. Biol. Cell 27, 64–74 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Zhao, G., Chen, Y., Carey, L. & Futcher, B. Cyclin-dependent kinase co-ordinates carbohydrate metabolism and cell cycle in S. cerevisiae. Mol. Cell 62, 546–557 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Cai, L., Sutter, B.M., Li, B. & Tu, B.P. Acetyl-CoA induces cell growth and proliferation by promoting the acetylation of histones at growth genes. Mol. Cell 42, 426–437 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Sohn, H.Y., Murray, D.B. & Kuriyama, H. Ultradian oscillation of Saccharomyces cerevisiae during aerobic continuous culture: hydrogen sulphide mediates population synchrony. Yeast 16, 1185–1190 (2000).

    Article  CAS  PubMed  Google Scholar 

  39. Murray, D.B., Klevecz, R.R. & Lloyd, D. Generation and maintenance of synchrony in Saccharomyces cerevisiae continuous culture. Exp. Cell Res. 287, 10–15 (2003).

    Article  CAS  PubMed  Google Scholar 

  40. Li, C.M. & Klevecz, R.R. A rapid genome-scale response of the transcriptional oscillator to perturbation reveals a period-doubling path to phenotypic change. Proc. Natl. Acad. Sci. USA 103, 16254–16259 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Kuang, Z. et al. High-temporal-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast. Nat. Struct. Mol. Biol. 21, 854–863 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Machné, R. & Murray, D.B. The yin and yang of yeast transcription: elements of a global feedback system between metabolism and chromatin. PLoS One 7, e37906 (2012).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  43. Wang, G.Z. et al. Cycling transcriptional networks optimize energy utilization on a genome scale. Cell Rep. 13, 1868–1880 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Amariei, C., Tomita, M. & Murray, D.B. Quantifying periodicity in omics data. Front. Cell Dev. Biol. 2, 40 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  45. Putker, M. & O'Neill, J.S. Reciprocal control of the circadian clock and cellular redox state: a critical appraisal. Mol. Cells 39, 6–19 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Hurley, J.M., Loros, J.J. & Dunlap, J.C. The circadian system as an organizer of metabolism. Fungal Genet. Biol. 90, 39–43 (2016).

    Article  CAS  PubMed  Google Scholar 

  47. Panda, S. et al. Coordinated transcription of key pathways in the mouse by the circadian clock. Cell 109, 307–320 (2002).

    Article  CAS  PubMed  Google Scholar 

  48. Claridge-Chang, A. et al. Circadian regulation of gene expression systems in the Drosophila head. Neuron 32, 657–671 (2001).

    Article  CAS  PubMed  Google Scholar 

  49. Lloyd, D. & Murray, D.B. Ultradian metronome: timekeeper for orchestration of cellular coherence. Trends Biochem. Sci. 30, 373–377 (2005).

    Article  CAS  PubMed  Google Scholar 

  50. Li, S. & Zhang, L. Circadian control of global transcription. BioMed Res. Int. 2015, 187809 (2015).

    PubMed  PubMed Central  Google Scholar 

  51. Klevecz, R.R. & Li, C.M. Evolution of the clock from yeast to man by period-doubling folds in the cellular oscillator. Cold Spring Harb. Symp. Quant. Biol. 72, 421–429 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Tu, B.P. & McKnight, S.L. Metabolic cycles as an underlying basis of biological oscillations. Nat. Rev. Mol. Cell Biol. 7, 696–701 (2006).

    Article  CAS  PubMed  Google Scholar 

  53. Zhang, L. et al. Dissociation of circadian and circatidal timekeeping in the marine crustacean Eurydice pulchra. Curr. Biol. 23, 1863–1873 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Eelderink-Chen, Z., Olmedo, M., Bosman, J. & Merrow, M. Using circadian entrainment to find cryptic clocks. Methods Enzymol. 551, 73–93 (2015).

    Article  CAS  PubMed  Google Scholar 

  55. Eelderink-Chen, Z. et al. A circadian clock in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 107, 2043–2047 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Paulose, J.K., Rucker, E.B. III & Cassone, V.M. Toward the beginning of time: circadian rhythms in metabolism precede rhythms in clock gene expression in mouse embryonic stem cells. PLoS One 7, e49555 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Murray, D.B., Engelen, F., Lloyd, D. & Kuriyama, H. Involvement of glutathione in the regulation of respiratory oscillation during a continuous culture of Saccharomyces cerevisiae. Microbiology 145, 2739–2745 (1999).

    Article  CAS  PubMed  Google Scholar 

  58. Keulers, M., Suzuki, T., Satroutdinov, A.D. & Kuriyama, H. Autonomous metabolic oscillation in continuous culture of Saccharomyces cerevisiae grown on ethanol. FEMS Microbiol. Lett. 142, 253–258 (1996).

    Article  CAS  PubMed  Google Scholar 

  59. Laxman, S. et al. Sulfur amino acids regulate translational capacity and metabolic homeostasis through modulation of tRNA thiolation. Cell 154, 416–429 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Chen, Z., Odstrcil, E.A., Tu, B.P. & McKnight, S.L. Restriction of DNA replication to the reductive phase of the metabolic cycle protects genome integrity. Science 316, 1916–1919 (2007).

    Article  CAS  PubMed  Google Scholar 

  61. Futcher, B. Metabolic cycle, cell cycle, and the finishing kick to Start. Genome Biol. 7, 107 (2006).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  62. Brauer, M.J. et al. Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. Mol. Biol. Cell 19, 352–367 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. O'Duibhir, E. et al. Cell cycle population effects in perturbation studies. Mol. Syst. Biol. 10, 732 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  64. Stincone, A. et al. The return of metabolism: biochemistry and physiology of the pentose phosphate pathway. Biol. Rev. Camb. Philos. Soc. 90, 927–963 (2015).

    Article  PubMed  Google Scholar 

  65. Campbell, K., Vowinckel, J., Keller, M.A. & Ralser, M. Methionine metabolism alters oxidative stress resistance via the pentose phosphate pathway. Antioxid. Redox Signal. 24, 543–547 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Shi, L. & Tu, B.P. Acetyl-CoA and the regulation of metabolism: mechanisms and consequences. Curr. Opin. Cell Biol. 33, 125–131 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Friis, R.M. et al. Rewiring AMPK and mitochondrial retrograde signaling for metabolic control of aging and histone acetylation in respiratory-defective cells. Cell Rep. 7, 565–574 (2014).

    Article  CAS  PubMed  Google Scholar 

  68. Shi, L. & Tu, B.P. Acetyl-CoA induces transcription of the key G1 cyclin CLN3 to promote entry into the cell division cycle in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 110, 7318–7323 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Nocetti, N. & Whitehouse, I. Nucleosome repositioning underlies dynamic gene expression. Genes Dev. 30, 660–672 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Weiner, A. et al. Systematic dissection of roles for chromatin regulators in a yeast stress response. PLoS Biol. 10, e1001369 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Weiner, A. et al. High-resolution chromatin dynamics during a yeast stress response. Mol. Cell 58, 371–386 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Parnell, T.J., Schlichter, A., Wilson, B.G. & Cairns, B.R. The chromatin remodelers RSC and ISW1 display functional and chromatin-based promoter antagonism. eLife 4, e06073 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  73. Downey, M. et al. Gcn5 and sirtuins regulate acetylation of the ribosomal protein transcription factor Ifh1. Curr. Biol. 23, 1638–1648 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Kim, J.H., Saraf, A., Florens, L., Washburn, M. & Workman, J.L. Gcn5 regulates the dissociation of SWI/SNF from chromatin by acetylation of Swi2/Snf2. Genes Dev. 24, 2766–2771 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Galdieri, L., Zhang, T., Rogerson, D. & Vancura, A. Reduced histone expression or a defect in chromatin assembly induces respiration. Mol. Cell. Biol. 36, 1064–1077 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Hsieh, T.H. et al. Mapping nucleosome resolution chromosome folding in yeast by micro-C. Cell 162, 108–119 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Ioshikhes, I.P., Albert, I., Zanton, S.J. & Pugh, B.F. Nucleosome positions predicted through comparative genomics. Nat. Genet. 38, 1210–1215 (2006).

    Article  CAS  PubMed  Google Scholar 

  78. Segal, E. et al. A genomic code for nucleosome positioning. Nature 442, 772–778 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Menet, J.S., Pescatore, S. & Rosbash, M. CLOCK:BMAL1 is a pioneer-like transcription factor. Genes Dev. 28, 8–13 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Rodriguez, J., Menet, J.S. & Rosbash, M. Nascent-seq indicates widespread cotranscriptional RNA editing in Drosophila. Mol. Cell 47, 27–37 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Kadener, S., Menet, J.S., Schoer, R. & Rosbash, M. Circadian transcription contributes to core period determination in Drosophila. PLoS Biol. 6, e119 (2008).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  82. Rao, A.R. & Pellegrini, M. Regulation of the yeast metabolic cycle by transcription factors with periodic activities. BMC Syst. Biol. 5, 160 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  83. Keogh, M.-C. et al. Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123, 593–605 (2005).

    Article  CAS  PubMed  Google Scholar 

  84. Carrozza, M.J. et al. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123, 581–592 (2005).

    Article  CAS  PubMed  Google Scholar 

  85. Sun, G. et al. Suppression of WHITE COLLAR-independent frequency transcription by histone H3 lysine 36 methyltransferase SET-2 is necessary for clock function in Neurospora. J. Biol. Chem. 291, 11055–11063 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Xue, Z. et al. Transcriptional interference by antisense RNA is required for circadian clock function. Nature 514, 650–653 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Vollmers, C. et al. Circadian oscillations of protein-coding and regulatory RNAs in a highly dynamic mammalian liver epigenome. Cell Metab. 16, 833–845 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Menet, J.S., Rodriguez, J., Abruzzi, K.C. & Rosbash, M. Nascent-Seq reveals novel features of mouse circadian transcriptional regulation. eLife 1, e00011 (2012).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  89. Sauman, I. & Reppert, S.M. Circadian clock neurons in the silkmoth Antheraea pernyi: novel mechanisms of Period protein regulation. Neuron 17, 889–900 (1996).

    Article  CAS  PubMed  Google Scholar 

  90. Swiezewski, S., Liu, F., Magusin, A. & Dean, C. Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature 462, 799–802 (2009).

    Article  CAS  PubMed  Google Scholar 

  91. Murray, S.C. et al. Sense and antisense transcription are associated with distinct chromatin architectures across genes. Nucleic Acids Res. 43, 7823–7837 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Mellor, J., Woloszczuk, R. & Howe, F.S. The interleaved genome. Trends Genet. 32, 57–71 (2016).

    Article  CAS  PubMed  Google Scholar 

  93. Nagoshi, E. et al. Circadian gene expression in individual fibroblasts: cell-autonomous and self-sustained oscillators pass time to daughter cells. Cell 119, 693–705 (2004).

    Article  CAS  PubMed  Google Scholar 

  94. Chen, Z. & McKnight, S.L. A conserved DNA damage response pathway responsible for coupling the cell division cycle to the circadian and metabolic cycles. Cell Cycle 6, 2906–2912 (2007).

    Article  CAS  PubMed  Google Scholar 

  95. Kippert, F. & Lloyd, D. A temperature-compensated ultradian clock ticks in Schizosaccharomyces pombe. Microbiology 141, 883–890 (1995).

    Article  CAS  PubMed  Google Scholar 

  96. Izumo, M., Johnson, C.H. & Yamazaki, S. Circadian gene expression in mammalian fibroblasts revealed by real-time luminescence reporting: temperature compensation and damping. Proc. Natl. Acad. Sci. USA 100, 16089–16094 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Chin, S.L., Marcus, I.M., Klevecz, R.R. & Li, C.M. Dynamics of oscillatory phenotypes in Saccharomyces cerevisiae reveal a network of genome-wide transcriptional oscillators. FEBS J. 279, 1119–1130 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Lloyd, D., Salgado, L.E., Turner, M.P., Suller, M.T. & Murray, D. Cycles of mitochondrial energization driven by the ultradian clock in a continuous culture of Saccharomyces cerevisiae. Microbiology 148, 3715–3724 (2002).

    Article  CAS  PubMed  Google Scholar 

  99. Kwak, W.J., Kwon, G.S., Jin, I., Kuriyama, H. & Sohn, H.Y. Involvement of oxidative stress in the regulation of H(2)S production during ultradian metabolic oscillation of Saccharomyces cerevisiae. FEMS Microbiol. Lett. 219, 99–104 (2003).

    Article  CAS  PubMed  Google Scholar 

  100. Sohn, H.Y., Kum, E.J., Kwon, G.S., Jin, I. & Kuriyama, H. Regulation of branched-chain, and sulfur-containing amino acid metabolism by glutathione during ultradian metabolic oscillation of Saccharomyces cerevisiae. J. Microbiol. 43, 375–380 (2005).

    CAS  PubMed  Google Scholar 

  101. Ouyang, Y., Xu, Q., Mitsui, K., Motizuki, M. & Xu, Z. PSK2 coordinates glucose metabolism and utilization to maintain ultradian clock-coupled respiratory oscillation in Saccharomyces cerevisiae yeast. Arch. Biochem. Biophys. 509, 52–58 (2011).

    Article  CAS  PubMed  Google Scholar 

  102. Peek, C.B. et al. Circadian clock NAD+ cycle drives mitochondrial oxidative metabolism in mice. Science 342, 1243417 (2013).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  103. Cho, C.S., Yoon, H.J., Kim, J.Y., Woo, H.A. & Rhee, S.G. Circadian rhythm of hyperoxidized peroxiredoxin II is determined by hemoglobin autoxidation and the 20S proteasome in red blood cells. Proc. Natl. Acad. Sci. USA 111, 12043–12048 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Milev, N.B. et al. Analysis of the redox oscillations in the circadian clockwork. Methods Enzymol. 552, 185–210 (2015).

    Article  CAS  PubMed  Google Scholar 

  105. O'Neill, J.S. & Feeney, K.A. Circadian redox and metabolic oscillations in mammalian systems. Antioxid. Redox Signal. 20, 2966–2981 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Naruse, Y. et al. Circadian and light-induced transcription of clock gene Per1 depends on histone acetylation and deacetylation. Mol. Cell. Biol. 24, 6278–6287 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Nakahata, Y. et al. The NAD+-dependent deacetylase SIRT1 modulates CLOCK-mediated chromatin remodeling and circadian control. Cell 134, 329–340 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Fogg, P.C. et al. Class IIa histone deacetylases are conserved regulators of circadian function. J. Biol. Chem. 289, 34341–34348 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Aguilar-Arnal, L. et al. Cycles in spatial and temporal chromosomal organization driven by the circadian clock. Nat. Struct. Mol. Biol. 20, 1206–1213 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Welsh, D.K., Yoo, S.H., Liu, A.C., Takahashi, J.S. & Kay, S.A. Bioluminescence imaging of individual fibroblasts reveals persistent, independently phased circadian rhythms of clock gene expression. Curr. Biol. 14, 2289–2295 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This work was funded by the BBSRC (BB/J0054X/1), the Wellcome Trust (089156) and EC FP7 EpiGeneSys. Many thanks to F. Howe, R. Woloszczuk, A. Angel and all members of J.M.'s laboratory.

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Correspondence to Jane Mellor.

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J.M. acts as an advisor to, and holds stock in, Oxford Biodynamics Ltd., Chronos Therapeutics Ltd. and Sibelius Ltd.

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Mellor, J. The molecular basis of metabolic cycles and their relationship to circadian rhythms. Nat Struct Mol Biol 23, 1035–1044 (2016). https://doi.org/10.1038/nsmb.3311

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