Proteomics and circadian rhythms: It's all about signaling!

Proteomics

Volumn 15, Issue 2-3, 2015, Pages 310-317

  Mauvoisin, Daniel ^a   Dayon, Loïc ^a   Gachon, Frédéric ^a   Kussmann, Martin ^a,b,c  

^a NESTLÉ RESEARCH CENTER   (Switzerland)

^b EPFL   (Switzerland)

^c AARHUS UNIVERSITY   (Denmark)

Author keywords

Animal proteomics; Circadian rhythms; Metabolism; Phosphorylation; Posttranslational modifications; SILAC

Indexed keywords

CASEIN KINASE IEPSILON; PER2 PROTEIN; PROTEIN; STEROL REGULATORY ELEMENT BINDING PROTEIN; TRANSCRIPTION FACTOR CLOCK;

ACETYLATION; CANCER RISK; CIRCADIAN RHYTHM; DNA BINDING; ENVIRONMENTAL FACTOR; GLUCOSE METABOLISM; HUMAN; MASS SPECTROMETRY; METABOLIC SYNDROME X; METABOLISM; MOLECULAR CLOCK; NONHUMAN; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN EXPRESSION; PROTEIN PHOSPHORYLATION; PROTEIN STABILITY; PROTEOMICS; REVIEW; SIGNAL TRANSDUCTION; SUMOYLATION; SURVIVAL RATE; SYNAPSE VESICLE; UBIQUITINATION; VASCULAR DISEASE; WEIGHT REDUCTION; ANIMAL; PHOSPHORYLATION; PROCEDURES; PROTEIN PROCESSING;

ANIMALIA; MAMMALIA;

ANIMALS; CIRCADIAN CLOCKS; CIRCADIAN RHYTHM; HUMANS; MASS SPECTROMETRY; PHOSPHORYLATION; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEINS; PROTEOMICS; SIGNAL TRANSDUCTION;

EID: 84921297143     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201400187     Document Type: Review

References (64)

1. Abraham, U., Granada, A. E., Westermark, P. O., Heine, M. et al., Coupling governs entrainment range of circadian clocks. Mol. Syst. Biol. 2010, 6, 438.
2. Moore, R. Y., Eichler, V. B., Loss of a circadian adrenal corticosterone rhythm following suprachiasmatic lesions in the rat. Brain Res. 1972, 42, 201-206.
3. Stephan, F. K., Zucker, I., Circadian rhythms in drinking behavior and locomotor activity of rats are eliminated by hypothalamic lesions. Proc. Natl. Acad. Sci. USA 1972, 69, 1583-1586.
4. Ralph, M. R., Foster, R. G., Davis, F. C., Menaker, M., Transplanted suprachiasmatic nucleus determines circadian period. Science 1990, 247, 975-978.
5. Nagoshi, E., Brown, S. A., Dibner, C., Kornmann, B., Schibler, U., Circadian gene expression in cultured cells. Methods Enzymol. 2005, 393, 543-557.
6. Dibner, C., Schibler, U., Albrecht, U., The mammalian circadian timing system: organization and coordination of central and peripheral clocks. Ann. Rev. Physiol. 2010, 72, 517-549.
7. Garaulet, M., Gomez-Abellan, P., Chronobiology and obesity. Nutr. Hosp. 2013, 28(Suppl 5), 114-120.
8. Vyas, M. V., Garg, A. X., Iansavichus, A. V., Costella, J. et al., Shift work and vascular events: systematic review and meta-analysis. BMJ 2012, 345, e4800.
9. Haus, E. L., Smolensky, M. H., Shift work and cancer risk: potential mechanistic roles of circadian disruption, light at night, and sleep deprivation. Sleep Med. Rev. 2013, 17, 273-284.
10. Bandin, C., Martinez-Nicolas, A., Ordovás, J. M., Madrid, J. A., Garaulet, M., Circadian rhythmicity as a predictor of weight-loss effectiveness. Int. J. Obes. 2014, 38, 1083-1088.
11. Innominato, P. F., Giacchetti, S., Bjarnason, G. A., Focan, C. et al., Prediction of overall survival through circadian rest-activity monitoring during chemotherapy for metastatic colorectal cancer. Int. J. Cancer 2012, 131, 2684-2692.
12. Innominato, P. F., Giacchetti, S., Moreau, T., Bjarnason, G. A. et al., Fatigue and weight loss predict survival on circadian chemotherapy for metastatic colorectal cancer. Cancer 2013, 119, 2564-2573.
13. Sephton, S. E., Lush, E., Dedert, E. A., Floyd, A. R. et al., Diurnal cortisol rhythm as a predictor of lung cancer survival. Brain Behav. Immun. 2013, 30, S163-S170.
14. Ramsey, K. M., Yoshino, J., Brace, C. S., Abrassart, D. et al., Circadian clock feedback cycle through NAMPT-mediated NAD+ biosynthesis. Science 2009, 324, 651-654.
15. Rutter, J., Reick, M., Wu, L. C., McKnight, S. L., Regulation of clock and NPAS2 DNA binding by the redox state of NAD cofactors. Science 2001, 293, 510-514.
16. Nakahata, Y., Kaluzova, M., Grimaldi, B., Sahar, S. et al., The NAD+-dependent deacetylase SIRT1 modulates CLOCK-mediated chromatin remodeling and circadian control. Cell 2008, 134, 329-340.
17. Asher, G., Gatfield, D., Stratmann, M., Reinke, H. et al., SIRT1 regulates circadian clock gene expression through PER2 deacetylation. Cell 2008, 134, 317-328.
18. Asher, G., Reinke, H., Altmeyer, M., Gutierrez-Arcelus, M. et al., Poly(ADP-ribose) polymerase 1 participates in the phase entrainment of circadian clocks to feeding. Cell 2010, 142, 943-953.
19. Cardone, L., Hirayama, J., Giordano, F., Tamaru, T. et al., Circadian clock control by SUMOylation of BMAL1. Science 2005, 309, 1390-1394.
20. Lee, J., Lee, Y., Lee, M. J., Park, E. et al., Dual modification of BMAL1 by SUMO2/3 and ubiquitin promotes circadian activation of the CLOCK/BMAL1 complex. Mol. Cell. Biol. 2008, 28, 6056-6065.
21. Reischl, S., Kramer, A., Kinases and phosphatases in the mammalian circadian clock. FEBS Lett. 2011, 585, 1393-1399.
22. Lamia, K. A., Sachdeva, U. M., DiTacchio, L., Williams, E. C. et al., AMPK regulates the circadian clock by cryptochrome phosphorylation and degradation. Science 2009, 326, 437-440.
23. Um, J. H., Yang, S., Yamazaki, S., Kang, H. et al., Activation of 5'-AMP-activated kinase with diabetes drug metformin induces casein kinase Iepsilon (CKIepsilon)-dependent degradation of clock protein mPer2. J. Biol. Chem. 2007, 282, 20794-20798.
24. Asher, G., Schibler, U., Crosstalk between components of circadian and metabolic cycles in mammals. Cell Metab. 2011, 13, 125-137.
25. Johnson, C. H., Mori, T., Xu, Y., A cyanobacterial circadian clockwork. Curr. Biol. 2008, 18, R816-R825.
26. O'Neill, J. S., Reddy, A. B., Circadian clocks in human red blood cells. Nature 2011, 469, 498-503.
27. Panda, S., Antoch, M. P., Miller, B. H., Su, A. I. et al., Coordinated transcription of key pathways in the mouse by the circadian clock. Cell 2002, 109, 307-320.
28. Kornmann, B., Schaad, O., Bujard, H., Takahashi, J. S., Schibler, U., System-driven and oscillator-dependent circadian transcription in mice with a conditionally active liver clock. PLoS Biol. 2007, 5, e34.
29. Lamia, K. A., Storch, K. F., Weitz, C. J., Physiological significance of a peripheral tissue circadian clock. Proc. Natl. Acad. Sci. USA 2008, 105, 15172-15177.
30. Marcheva, B., Ramsey, K. M., Buhr, E. D., Kobayashi, Y. et al., Disruption of the clock components CLOCK and BMAL1 leads to hypoinsulinaemia and diabetes. Nature 2010, 466, 627-631.
31. Sadacca, L. A., Lamia, K. A., deLemos, A. S., Blum, B., Weitz, C. J., An intrinsic circadian clock of the pancreas is required for normal insulin release and glucose homeostasis in mice. Diabetologia 2011, 54, 120-124.
32. Damiola, F., Le Minh, N., Preitner, N., Kornmann, B. et al., Restricted feeding uncouples circadian oscillators in peripheral tissues from the central pacemaker in the suprachiasmatic nucleus. Genes Dev. 2000, 14, 2950-2961.
33. Stokkan, K. A., Yamazaki, S., Tei, H., Sakaki, Y., Menaker, M., Entrainment of the circadian clock in the liver by feeding. Science 2001, 291, 490-493.
34. Mauvoisin, D., Wang, J., Jouffe, C., Martin, E. et al., Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver. Proc. Natl. Acad Sci. USA 2014, 111, 167-172.
35. Lamia, K. A., Papp, S. J., Yu, R. T., Barish, G. D. et al., Cryptochromes mediate rhythmic repression of the glucocorticoid receptor. Nature 2011, 480, 552-556.
36. Zhang, E. E., Liu, Y., Dentin, R., Pongsawakul, P. Y. et al., Cryptochrome mediates circadian regulation of cAMP signaling and hepatic gluconeogenesis. Nat. Med. 2010, 16, 1152-1156.
37. Rudic, R. D., McNamara, P., Curtis, A. M., Boston, R. C. et al., BMAL1 and CLOCK, two essential components of the circadian clock, are involved in glucose homeostasis. PLoS Biol 2004, 2, e377.
38. Shimba, S., Ishii, N., Ohta, Y., Ohno, T., et al., Brain and muscle Arnt-like protein-1 (BMAL1), a component of the molecular clock, regulates adipogenesis. Proc. Natl. Acad. Sci. USA 2005, 102, 12071-12076.
39. Grimaldi, B., Bellet, M. M., Katada, S., Astarita, G. et al., PER2 controls lipid metabolism by direct regulation of PPARgamma. Cell Metab. 2010, 12, 509-520.
40. Yin, L., Wu, N., Curtin, J. C., Qatanani, M. et al., Rev-erbalpha, a heme sensor that coordinates metabolic and circadian pathways. Science 2007, 318, 1786-1789.
41. Chawla, A., Lazar, M. A., Induction of Rev-ErbA alpha, an orphan receptor encoded on the opposite strand of the alpha-thyroid hormone receptor gene, during adipocyte differentiation. J Biol. Chem. 1993, 268, 16265-16269.
42. Pircher, P., Chomez, P., Yu, F., Vennstrom, B., Larsson, L., Aberrant expression of myosin isoforms in skeletal muscles from mice lacking the rev-erbAalpha orphan receptor gene. Am. J. Physiol. Regul. Integr. Comp. Physiol. 2005, 288, R482-R490.
43. Le Martelot, G., Claudel, T., Gatfield, D., Schaad, O. et al., REV-ERBalpha participates in circadian SREBP signaling and bile acid homeostasis. PLoS Biol. 2009, 7, e1000181.
44. Brewer, M., Lange, D., Baler, R., Anzulovich, A., SREBP-1 as a transcriptional integrator of circadian and nutritional cues in the liver. J. Biol. Rhythms 2005, 20, 195-205.
45. Cretenet, G., Le Clech, M., Gachon, F., Circadian clock-coordinated 12 Hr period rhythmic activation of the IRE1alpha pathway controls lipid metabolism in mouse liver. Cell Metab. 2010, 11, 47-57.
46. Gilardi, F., Migliavacca, E., Naldi, A., Baruchet, M. et al., Genome-wide analysis of SREBP1 activity around the clock reveals its combined dependency on nutrient and circadian signals. PLoS Genet. 2014, 10, e1004155.
47. Robles, M. S., Mann, M., Proteomic approaches in circadian biology. Handb. Exp. Pharmacol. 2013, 217, 389-407.
48. Moller, M., Sparre, T., Bache, N., Roepstorff, P., Vorum, H., Proteomic analysis of day-night variations in protein levels in the rat pineal gland. Proteomics 2007, 7, 2009-2018.
49. Reddy, A. B., Karp, N. A., Maywood, E. S., Sage, E. A. et al., Circadian orchestration of the hepatic proteome. Curr. Biol. 2006, 16, 1107-1115.
50. Deery, M. J., Maywood, E. S., Chesham, J. E., Sládek, M. et al., Proteomic analysis reveals the role of synaptic vesicle cycling in sustaining the suprachiasmatic circadian clock. Curr. Biol. 2009, 19, 2031-2036.
51. Martino, T. A., Tata, N., Bjarnason, G. A., Straume, M., Sole, M. J., Diurnal protein expression in blood revealed by high throughput mass spectrometry proteomics and implications for translational medicine and body time of day. Am. J. Physiol. Regul. Integr. Comp. Physiol. 2007, 293, R1430-R1437.
52. Tian, R., Alvarez-Saavedra, M., Cheng, H. Y., Figeys, D., Uncovering the proteome response of the master circadian clock to light using an AutoProteome system. Mol. Cell. Proteomics 2011, 10, M110 007252.
53. Ethier, M., Hou, W., Duewel, H. S., Figeys, D., The proteomic reactor: a microfluidic device for processing minute amounts of protein prior to mass spectrometry analysis. J. Proteome Res. 2006, 5, 2754-2759.
54. Jouffe, C., Cretenet, G., Symul, L., Martin, E. et al., The circadian clock coordinates ribosome biogenesis. PLoS Biol. 2013, 11, e1001455.
55. Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B. et al., Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 2002, 1, 376-386.
56. Krüger, M., Moser, M., Ussar, S., Thievessen, I. et al., SILAC Mouse for quantitative proteomics uncovers Kindlin-3 as an essential factor for red blood cell function. Cell 2008, 134, 353-364.
57. 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. 2014, 10, e1004047.
58. Dayon, L., Hainard, A., Licker, V., Turck, N. et al., Relative quantification of proteins in human cerebrospinal fluids by MS/MS using 6-plex isobaric tags. Anal. Chem. 2008, 80, 2921-2931.
59. Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B. et al., Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 2004, 3, 1154-1169.
60. O'Neill, J. S., van Ooijen, G., Dixon, L. E., Troein, C. et al., Circadian rhythms persist without transcription in a eukaryote. Nature 2011, 469, 554-558.
61. Edgar, R. S., Green, E. W., Zhao, Y., van Ooijen, G. et al., Peroxiredoxins are conserved markers of circadian rhythms. Nature 2012, 485, 459-464.
62. Mehra, A., Baker, C. L., Loros, J. J., Dunlap, J. C., Post-translational modifications in circadian rhythms. Trends Biochem. Sci. 2009, 34, 483-490.
63. Masri, S., Patel, V. R., Eckel-Mahan, K. L., Peleg, S. et al., Circadian acetylome reveals regulation of mitochondrial metabolic pathways. Proc. Natl. Acad. Sci. USA 2013, 110, 3339-3344.
64. Eckel-Mahan, K. L., Patel, V. R., Mohney, R. P., Vignola, K. S. et al., Coordination of the transcriptome and metabolome by the circadian clock. Proc. Natl. Acad. Sci. USA 2012, 109, 5541-5546.