Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 1, 2014, Pages 167-172

  Mauvoisin, Daniel ^a,b   Wang, Jingkui ^c   Jouffe, Céline ^a,b   Martin, Eva ^a,b   Atger, Florian ^a,b   Waridel, Patrice ^c   Quadroni, Manfredo ^a   Gachon, Frédéric ^a,b   Naef, Felix ^c  

^a UNIVERSITY OF LAUSANNE   (Switzerland)

^b NESTLÉ RESEARCH CENTER   (Switzerland)

^c EPFL   (Switzerland)

Author keywords

Circadian rhythm; Liver metabolism; Posttranslational regulation; Protein secretion; Proteomics

Indexed keywords

MESSENGER RNA; PROTEOME; TRANSCRIPTION FACTOR;

ARTICLE; CIRCADIAN RHYTHM; CONTROLLED STUDY; ENDOPLASMIC RETICULUM; FEEDING BEHAVIOR; GENE ONTOLOGY; GLUCOSE METABOLISM; GOLGI COMPLEX; HALF LIFE TIME; LIPID METABOLISM; LIVER; MOUSE; NONHUMAN; PHYSIOLOGY; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN PROCESSING; PROTEIN SECRETION; PROTEIN STABILITY; WESTERN BLOTTING;

CIRCADIAN RHYTHM; LIVER METABOLISM; POSTTRANSLATIONAL REGULATION; PROTEIN SECRETION; PROTEOMICS;

ALBUMINS; ALPHA 1-ANTITRYPSIN; ANIMALS; CIRCADIAN CLOCKS; CIRCADIAN RHYTHM; CRYPTOCHROMES; GENE EXPRESSION REGULATION; LIVER; MALE; MASS SPECTROMETRY; MICE; MICE, INBRED C57BL; MICE, KNOCKOUT; MODELS, THEORETICAL; PLASMA; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOME; RNA, MESSENGER;

EID: 84891940889     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1314066111     Document Type: Article

References (57)

1. Bass J (2012) Circadian topology of metabolism. Nature 491(7424): 348-356.
2. Mohawk JA, Green CB, Takahashi JS (2012) Central and peripheral circadian clocks in mammals. Annu Rev Neurosci 35(1): 445-462.
3. Feng D, Lazar MA (2012) Clocks, metabolism, and the epigenome. Mol Cell 47(2): 158-167.
4. Doherty CJ, Kay SA (2010) Circadian control of global gene expression patterns. Annu Rev Genet 44(1): 419-444.
5. Kojima S, Shingle DL, Green CB (2011) Post-transcriptional control of circadian rhythms. J Cell Sci 124(Pt 3): 311-320.
6. Kim T-D, et al. (2007) Rhythmic control of AANAT translation by hnRNP Q in circadian melatonin production. Genes Dev 21(7): 797-810.
7. Jouffe C, et al. (2013) The circadian clock coordinates ribosome biogenesis. PLoS Biol 11(1):e1001455.
8. Kojima S, Sher-Chen EL, Green CB (2012) Circadian control of mRNA polyadenylation dynamics regulates rhythmic protein expression. Genes Dev 26(24): 2724-2736.
9. Reddy AB, et al. (2006) Circadian orchestration of the hepatic proteome. Curr Biol 16(11): 1107-1115.
10. Deery MJ, et al. (2009) Proteomic analysis reveals the role of synaptic vesicle cycling in sustaining the suprachiasmatic circadian clock. Curr Biol 19(23): 2031-2036.
11. Krüger M, et al. (2008) SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell 134(2): 353-364.
12. Hughes ME, et al. (2009) Harmonics of circadian gene transcription in mammals. PLoS Genet 5(4):e1000442.
13. Gimble JM, Sutton GM, Bunnell BA, Ptitsyn AA, Floyd ZE (2011) Prospective influences of circadian clocks in adipose tissue and metabolism. Nat Rev Endocrinol 7(2): 98-107.
14. Rismanchi N, Soderblom C, Stadler J, Zhu P-P, Blackstone C (2008) Atlastin GTPases are required for Golgi apparatus and ER morphogenesis. Hum Mol Genet 17(11): 1591-1604.
15. Rudic RD, et al. (2004) BMAL1 and CLOCK, two essential components of the circadian clock, are involved in glucose homeostasis. PLoS Biol 2(11):e377.
16. Gachon F, Firsov D (2011) The role of circadian timing system on drug metabolism and detoxification. Expert Opin Drug Metab Toxicol 7(2): 147-158.
17. Reinke H, et al. (2008) Differential display of DNA-binding proteins reveals heat-shock factor 1 as a circadian transcription factor. Genes Dev 22(3): 331-345.
18. Le Martelot G, et al. (2012) Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biol 10(11):e1001442.
19. Schwanhäusser B, et al. (2011) Global quantification of mammalian gene expression control. Nature 473(7347): 337-342.
20. Hirano A, et al. (2013) FBXL21 regulates oscillation of the circadian clock through ubiquitination and stabilization of cryptochromes. Cell 152(5): 1106-1118.
21. Vanselow K, et al. (2006) Differential effects of PER2 phosphorylation: Molecular basis for the human familial advanced sleep phase syndrome (FASPS). Genes Dev 20(19): 2660-2672.
22. Yoo S-H, et al. (2013) Competing E3 ubiquitin ligases govern circadian periodicity by degradation of CRY in nucleus and cytoplasm. Cell 152(5): 1091-1105.
23. Scheving LE, Pauly JE, Tsai TH (1968) Circadian fluctuation in plasma proteins of the rat. Am J Physiol 215(5): 1096-1101.
24. Jubiz W, Canterbury JM, Reiss E, Tyler FH (1972) Circadian rhythm in serum parathyroid hormone concentration in human subjects: Correlation with serum calcium, phosphate, albumin, and growth hormone levels. J Clin Invest 51(8): 2040-2046.
25. Mondola P, Gambardella P, Santangelo F, Santillo M, Greco AM(1995) Circadian rhythms of lipid and apolipoprotein pattern in adult fasted rats. Physiol Behav 58(1): 175-180.
26. Pan X, Zhang Y, Wang L, Hussain MM (2010) Diurnal regulation of MTP and plasma triglyceride by CLOCK is mediated by SHP. Cell Metab 12(2): 174-186.
27. Haus E, Cusulos M, Sackett-Lundeen L, Swoyer J (1990) Circadian variations in blood coagulation parameters, alpha-antitrypsin antigen and platelet aggregation and retention in clinically healthy subjects. Chronobiol Int 7(3): 203-216.
28. Soulban G, Labrecque G (1989) Circadian rhythms of blood clotting time and coagulation factors II, VII, IX and X in rats. Life Sci 45(25): 2485-2489.
29. Bertolucci C, et al. (2005) Circadian rhythms in mouse blood coagulation. J Biol Rhythms 20(3): 219-224.
30. Kapiotis S, et al. (1997) Morning hypercoagulability and hypofibrinolysis. Diurnal variations in circulating activated factor VII, prothrombin fragment F1+2, and plasmin- plasmin inhibitor complex. Circulation 96(1): 19-21.
31. Bruguerolle B, et al. (1986) [Circadian rhythms of the so-called inflammation proteins in healthy subjects]. Rev Rhum Mal Osteoartic 53(5): 313-316.
32. Peters T, Jr., Peters JC (1972) The biosynthesis of rat serum albumin. VI. Intracellular transport of albumin and rates of albumin and liver protein synthesis in vivo under various physiological conditions. J Biol Chem 247(12): 3858-3863.
33. Khoriaty R, Vasievich MP, Ginsburg D (2012) The COPII pathway and hematologic disease. Blood 120(1): 31-38.
34. Zanetti G, Pahuja KB, Studer S, Shim S, Schekman R (2012) COPII and the regulation of protein sorting in mammals. Nat Cell Biol 14(1): 20-28.
35. Lee C, Etchegaray J-P, Cagampang FRA, Loudon ASI, Reppert SM(2001) Posttranslational mechanisms regulate the mammalian circadian clock. Cell 107(7): 855-867.
36. Cui ZJ, Han ZQ, Li ZY (2012) Modulating protein activity and cellular function by methionine residue oxidation. Amino Acids 43(2): 505-517.
37. Koike N, et al. (2012) Transcriptional architecture and chromatin landscape of the core circadian clock in mammals. Science 338(6105): 349-354.
38. Menet JS, Rodriguez J, Abruzzi KC, Rosbash M (2012) Nascent-Seq reveals novel features of mouse circadian transcriptional regulation. Elife 1:e00011.
39. Jones B, et al. (2003) Mutations in a Sar1 GTPase of COPII vesicles are associated with lipid absorption disorders. Nat Genet 34(1): 29-31.
40. Levy E, et al. (2011) Expression of Sar1b enhances chylomicron assembly and key components of the coat protein complex II system driving vesicle budding. Arterioscler Thromb Vasc Biol 31(11): 2692-2699.
41. Nichols WC, et al. (1998) Mutations in the ER-Golgi intermediate compartment protein ERGIC-53 cause combined deficiency of coagulation factors V and VIII. Cell 93(1): 61-70.
42. Nyfeler B, et al. (2008) Identification of ERGIC-53 as an intracellular transport receptor of α1-antitrypsin. J Cell Biol 180(4): 705-712.
43. Zhang B, et al. (2003) Bleeding due to disruption of a cargo-specific ER-to-Golgi transport complex. Nat Genet 34(2): 220-225.
44. Zhang B, et al. (2011) Mice deficient in LMAN1 exhibit FV and FVIII deficiencies and liver accumulation of α1-antitrypsin. Blood 118(12): 3384-3391.
45. Tao J, et al. (2012) SEC23B is required for the maintenance of murine professional secretory tissues. Proc Natl Acad Sci USA 109(29): E2001-E2009.
46. Cretenet G, Le Clech M, Gachon F (2010) Circadian clock-coordinated 12 Hr period rhythmic activation of the IRE1alpha pathway controls lipid metabolism in mouse liver. Cell Metab 11(1): 47-57.
47. Hughes ME, et al. (2012) Brain-specific rescue of Clock reveals system-driven transcriptional rhythms in peripheral tissue. PLoS Genet 8(7):e1002835.
48. Brown WJ, Plutner H, Drecktrah D, Judson BL, Balch WE (2008) The lysophospholipid acyltransferase antagonist CI-976 inhibits a late step in COPII vesicle budding. Traffic 9(5): 786-797.
49. Runz H, Miura K, Weiss M, Pepperkok R (2006) Sterols regulate ER-export dynamics of secretory cargo protein ts-O45-G. EMBO J 25(13): 2953-2965.
50. Brown WJ, Schmidt JA (2005) Use of acyltransferase inhibitors to block vesicular traffic between the ER and Golgi complex. Methods in Enzymology 404: 115-125.
51. Erickson SK, Shrewsbury MA, Brooks C, Meyer DJ (1980) Rat liver acyl-coenzyme A: cholesterol acyltransferase: Its regulation in vivo and some of its properties in vitro. J Lipid Res 21(7): 930-941.
52. Szanto A, Ruys J, Balasubramaniam S (1994) Coordinate diurnal regulation of hepatic acyl-coenzyme A: Cholesterol acyltransferase and cellular levels of esterified cholesterol. Biochim Biophys Acta 1214(1): 39-42.
53. van der Horst GTJ, et al. (1999) Mammalian Cry1 and Cry2 are essential for maintenance of circadian rhythms. Nature 398(6728): 627-630.
54. Bur IM, et al. (2009) The circadian clock components CRY1 and CRY2 are necessary to sustain sex dimorphism in mouse liver metabolism. J Biol Chem 284(14): 9066-9073.
55. Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26(12): 1367-1372.
56. Cox J, et al. (2011) Andromeda: A peptide search engine integrated into the Max- Quant environment. J Proteome Res 10(4): 1794-1805.
57. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Statist Soc B 57(1): 289-300.