Acetyl-CoA carboxylase regulates global histone acetylation

Journal of Biological Chemistry

Volumn 287, Issue 28, 2012, Pages 23865-23876

  Galdieri, Luciano ^a   Vancura, Ales ^a  

^a ST JOHN'S UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETYL-COA; ACETYL-COA CARBOXYLASE; DE NOVO SYNTHESIS; EPIGENETIC MECHANISMS; HISTONE ACETYLATION; HISTONE ACETYLTRANSFERASES; INTERMEDIARY METABOLISM; MALONYL-COA; RATE-LIMITING REACTION; TRANSCRIPTIONAL REGULATION; YEAST SACCHAROMYCES CEREVISIAE;

ACETYLATION; CARBOXYLATION; GENES; METABOLISM; PHYSIOLOGY; YEAST;

PROTEINS;

ACETYL COENZYME A; ACETYL COENZYME A CARBOXYLASE; DNA; FATTY ACID; HISTONE; HISTONE ACETYLTRANSFERASE; MALONYL COENZYME A;

ARTICLE; CARBOXYLATION; CATALYSIS; CHROMATIN; CHROMATIN STRUCTURE; DNA REPLICATION; ENZYME REGULATION; EPIGENETICS; FATTY ACID SYNTHESIS; GENE EXPRESSION; HISTONE ACETYLATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION INITIATION;

ACETYL-COA CARBOXYLASE; ACETYLATION; BLOTTING, WESTERN; CHROMATIN; DOXYCYCLINE; GENE EXPRESSION REGULATION, ENZYMOLOGIC; GENE EXPRESSION REGULATION, FUNGAL; HISTONE ACETYLTRANSFERASES; HISTONES; MUTATION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

SACCHAROMYCES CEREVISIAE;

EID: 84863613036     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M112.380519     Document Type: Article

References (75)

1. Kouzarides, T. (2007) Chromatin modifications and their function. Cell 128, 693-705
2. Kurdistani, S. K., Tavazoie, S., and Grunstein, M. (2004) Mapping global histone acetylation patterns to gene expression. Cell 117, 721-733 (Pubitemid 38748889)
3. Pokholok, D. K., Harbison, C. T., Levine, S., Cole, M., Hannett, N. M., Lee, T. I., Bell, G. W., Walker, K., Rolfe, P. A., Herbolsheimer, E., Zeitlinger, J., Lewitter, F., Gifford, D. K., and Young, R. A. (2005) Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122, 517-527 (Pubitemid 41191151)
4. Millar, C. B., and Grunstein, M. (2006) Genome-wide patterns of histone modifications in yeast. Nat. Rev. Mol. Cell Biol. 7, 657-666 (Pubitemid 44268211)
5. Shukla, V., Vaissière, T., and Herceg, Z. (2008) Histone acetylation and chromatin signature in stem cell identity and cancer. Mutation Res. 637, 1-15 (Pubitemid 350262807)
6. Lafon, A., Chang, C. S., Scott, E. M., Jacobson, S. J., and Pillus, L. (2007) MYST opportunities for growth control. Yeast genes illuminate human cancer gene functions. Oncogene 26, 5373-5384 (Pubitemid 47260462)
7. Takahashi, H., McCaffery, J. M., Irizarry, R. A., and Boeke, J. D. (2006) Nucleocytosolic acetyl-coenzyme A synthetase is required for histone acetylation and global transcription. Mol. Cell 23, 207-217 (Pubitemid 44081880)
8. Ramaswamy, V., Williams, J. S., Robinson, K. M., Sopko, R. L., and Schultz, M. C. (2003) Global control of histone modification by the anaphasepromoting complex. Mol. Cell. Biol. 23, 9136-9149 (Pubitemid 37499803)
9. Sandmeier, J. J., French, S., Osheim, Y., Cheung, W. L., Gallo, C. M., Beyer, A. L., and Smith, J. S. (2002) RPD3 is required for the inactivation of yeast ribosomal DNA genes in stationary phase. EMBO J. 21, 4959-4968
10. Friis, R. M., Wu, B. P., Reinke, S. N., Hockman, D. J., Sykes, B. D., and Schultz, M. C. (2009) A glycolytic burst drives glucose induction of global histone acetylation by picNuA4 and SAGA. Nucleic Acids Res. 37, 3969-3980
11. Wellen, K. E., Hatzivassiliou, G., Sachdeva, U. M., Bui, T. V., Cross, J. R., and Thompson, C. B. (2009) ATP-citrate lyase links cellular metabolism to histone acetylation. Science 324, 1076-1080
12. Rathmell, J. C., and Newgard, C. B. (2009) Biochemistry. A glucose-togene link. Science 324, 1021-1022
13. Cai, L., Sutter, B. M., Li, B., and Tu, B. P. (2011) Acetyl-CoA induces cell growth and proliferation by promoting the acetylation of histones at growth genes. Mol. Cell 42, 426-437
14. Guarente, L. (2011) The logic linking protein acetylation and metabolism. Cell Metab. 14, 151-153
15. Wellen, K. E., and Thompson, C. B. (2012) A two-way street. Reciprocal regulation of metabolism and signaling. Nat. Rev. Mol. Cell Biol. 13, 270-276
16. Gombert, A. K., Moreira dos Santos, M., Christensen, B., and Nielsen, J. (2001) Network identification and flux quantification in the central metabolism of Saccharomyces cerevisiae under different conditions of glucose repression. J. Bacteriol. 183, 1441-1451 (Pubitemid 32107741)
17. Smedsgaard, J., and Nielsen, J. (2005) Metabolite profiling of fungi and yeast. From phenotype to metabolome by MS and informatics. J. Exp. Bot. 56, 273-286 (Pubitemid 40191444)
18. Heyland, J., Fu, J., and Blank, L. M. (2009) Correlation between TCA cycle flux and glucose uptake rate during respiro-fermentative growth of Saccharomyces cerevisiae. Microbiology 155, 3827-3837
19. Starai, V. J., and Escalante-Semerena, J. C. (2004) Acetyl-coenzyme A synthetase (AMP-forming). Cell. Mol. Life Sci. 61, 2020-2030
20. Tehlivets, O., Scheuringer, K., and Kohlwein, S. D. (2007) Fatty acid synthesis and elongation in yeast. Biochim. Biophys. Acta 1771, 255-270 (Pubitemid 46428612)
21. Sherman, F. (1991) Getting started with yeast. Methods Enzymol. 194, 3-21
22. Demczuk, A., Guha, N., Nguyen, P. H., Desai, P., Chang, J., Guzinska, K., Rollins, J., Ghosh, C. C., Goodwin, L., and Vancura, A. (2008) Saccharomyces cerevisiae phospholipase C regulates transcription of Msn2p-dependent stress-responsive genes. Eukaryot. Cell 7, 967-979 (Pubitemid 351961576)
23. Iyer, V., and Struhl, K. (1996) Absolute mRNA levels and transcriptional initiation rates in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 93, 5208-5212 (Pubitemid 26159427)
24. Shirra, M. K., Patton-Vogt, J., Ulrich, A., Liuta-Tehlivets, O., Kohlwein, S. D., Henry, S. A., and Arndt, K. M. (2001) Inhibition of acetyl-coenzyme A carboxylase activity restores expression of the INO1 gene in a snf1 mutant strain of Saccharomyces cerevisiae. Mol. Cell. Biol. 21, 5710-5722 (Pubitemid 32737790)
25. Matsuhashi, M. (1969) Acetyl-CoA carboxylase from yeast. Methods Enzymol. 14, 3-8
26. Geng, F., Cao, Y., and Laurent, B. C. (2001) Essential roles of Snf5p in Snf-Swi chromatin remodeling in vivo. Mol. Cell. Biol. 21, 4311-4320 (Pubitemid 32565312)
27. Guha, N., Desai, P., and Vancura, A. (2007) Plc1p is required for SAGA recruitment and derepression of Sko1p-regulated genes. Mol. Biol. Cell 18, 2419-2428 (Pubitemid 47025708)
28. Allis, C. D., Glover, C. V., and Gorovsky, M. A. (1979) Micronuclei of Tetrahymena contain two types of histone H3. Proc. Natl. Acad. Sci. U.S.A. 76, 4857-4861 (Pubitemid 10229084)
29. Pilch, D. R., Redon, C., Sedelnikova, O. A., and Bonner, W. M. (2004) Two-dimensional gel analysis of histones and other H2AX-related methods. Methods Enzymol. 375, 76-88 (Pubitemid 38124861)
30. Richon, V. M., Zhou, X., Secrist, J. P., Cordon-Cardo, C., Kelly, W. K., Drobnjak, M., and Marks, P. A. (2004) Histone deacetylase inhibitors: assays to assess effectiveness in vitro and in vivo. Methods Enzymol. 376, 199-205 (Pubitemid 38200180)
31. Kuo, M. H., Zhou, J., Jambeck, P., Churchill, M. E., and Allis, C. D. (1998) Histone acetyltransferase activity of yeast Gcn5p is required for the activation of target genes in vivo. Genes Dev. 12, 627-639 (Pubitemid 28134296)
32. Shechter, D., Dormann, H. L., Allis, C. D., and Hake, S. B. (2007) Extraction, purification, and analysis of histones. Nat. Protoc. 2, 1445-1457
33. Lin, Y. Y., Lu, J. Y., Zhang, J., Walter, W., Dang, W., Wan, J., Tao, S. C., Qian, J., Zhao, Y., Boeke, J. D., Berger, S. L., and Zhu, H. (2009) Protein acetylation microarray reveals that NuA4 controls key metabolic target regulating gluconeogenesis. Cell 136, 1073-1084
34. Mitchell, L., Lau, A., Lambert, J. P., Zhou, H., Fong, Y., Couture, J. F., Figeys, D., and Baetz, K. (2011) Regulation of septin dynamics by the Saccharomyces cerevisiae lysine acetyltransferase NuA4. PLoS One 6, e25336
35. Garí, E., Piedrafita, L., Aldea, M., and Herrero, E. (1997) A set of vectors with a tetracycline-regulatable promoter system for modulated gene expression in Saccharomyces cerevisiae. Yeast 13, 837-848 (Pubitemid 27285747)
36. Wishart, J. A., Hayes, A., Wardleworth, L., Zhang, N., and Oliver, S. G. (2005) Doxycycline, the drug used to control the tet-regulatable promoter system, has no effect on global gene expression in Saccharomyces cerevisiae. Yeast 22, 565-569 (Pubitemid 40932157)
37. Schneiter, R., Hitomi, M., Ivessa, A. S., Fasch, E. V., Kohlwein, S. D., and Tartakoff, A. M. (1996) A yeast acetyl-coenzyme A carboxylase mutant links very long chain fatty acid synthesis to the structure and function of the nuclear membrane-pore complex. Mol. Cell. Biol. 16, 7161-7172 (Pubitemid 26389776)
38. Ivessa, A. S., Schneiter, R., and Kohlwein, S. D. (1997) Yeast acetyl-CoA carboxylase is associated with the cytoplasmic surface of the endoplasmic reticulum. Eur. J. Cell Biol. 74, 399-406 (Pubitemid 27517313)
39. Erkina, T. Y., and Erkine, A. M. (2006) Displacement of histones at promoters of Saccharomyces cerevisiae heat shock genes is differentially associated with histone H3 acetylation. Mol. Cell. Biol. 26, 7587-7600 (Pubitemid 44547708)
40. Govind, C. K., Zhang, F., Qiu, H., Hofmeyer, K., and Hinnebusch, A. G. (2007) Gcn5 promotes acetylation, eviction, and methylation of nucleosomes in transcribed coding regions. Mol. Cell 25, 31-42 (Pubitemid 46049060)
41. Kristjuhan, A., and Svejstrup, J. Q. (2004) Evidence for distinct mechanisms facilitating transcript elongation through chromatin in vivo. EMBO J. 23, 4243-4252 (Pubitemid 39546162)
42. Lee, C. K., Shibata, Y., Rao, B., Strahl, B. D., and Lieb, J. D. (2004) Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat. Genet. 36, 900-905 (Pubitemid 39014111)
43. Sabet, N., Volo, S., Yu, C., Madigan, J. P., and Morse, R. H. (2004) Genome-wide analysis of the relationship between transcriptional regulation by Rpd3p and the histone H3 and H4 amino termini in budding yeast. Mol. Cell. Biol. 24, 8823-8833 (Pubitemid 39313889)
44. Lin, Y. Y., Qi, Y., Lu, J. Y., Pan, X., Yuan, D. S., Zhao, Y., Bader, J. S., and Boeke, J. D. (2008) A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation. Genes Dev. 22, 2062-2074
45. Gansheroff, L. J., Dollard, C., Tan, P., and Winston, F. (1995) The Saccharomyces cerevisiae SPT7 gene encodes a very acidic protein important for transcription in vivo. Genetics 139, 523-536
46. Roberts, S. M., and Winston, F. (1996) SPT20/ADA5 encodes a novel protein functionally related to the TATA-binding protein and important for transcription in Saccharomyces cerevisiae. Mol. Cell. Biol. 16, 3206-3213
47. Hudak, K. A., Lopes, J. M., and Henry, S. A. (1994) A pleiotropic phospholipid biosynthetic regulatory mutation in Saccharomyces cerevisiae is allelic to sin3 (sdi1, ume4, rpd1). Genetics 136, 475-483 (Pubitemid 24045471)
48. Clarke, A. S., Lowell, J. E., Jacobson, S. J., and Pillus, L. (1999) Esa1p is an essential histone acetyltransferase required for cell cycle progression. Mol. Cell. Biol. 19, 2515-2526 (Pubitemid 29144495)
49. Choy, J. S., Tobe, B. T., Huh, J. H., and Kron, S. J. (2001) Yng2p-dependent NuA4 histone H4 acetylation activity is required for mitotic and meiotic progression. J. Biol. Chem. 276, 43653-43662
50. Lu, J. Y., Lin, Y. Y., Sheu, J. C., Wu, J. T., Lee, F. J., Chen, Y., Lin, M. I., Chiang, F. T., Tai, T. Y., Berger, S. L., Zhao, Y., Tsai, K. S., Zhu, H., Chuang, L. M., and Boeke, J. D. (2011) Acetylation of yeast AMPK controls intrinsic aging independently of caloric restriction. Cell 146, 969-979
51. Hardie, D. G., Carling, D., and Carlson, M. (1998) The AMP-activated/SNF1 protein kinase subfamily. Metabolic sensors of the eukaryotic cell? Annu. Rev. Biochem. 67, 821-855 (Pubitemid 28411146)
52. Hedbacker, K., and Carlson, M. (2008) SNF1/AMPK pathways in yeast. Front. Biosci. 13, 2408-2420 (Pubitemid 351599694)
53. Woods, A., Munday, M. R., Scott, J., Yang, X., Carlson, M., and Carling, D. (1994) Yeast SNF1 is functionally related to mammalian AMP-activated protein kinase and regulates acetyl-CoA carboxylase in vivo. J. Biol. Chem. 269, 19509-19515 (Pubitemid 24233479)
54. Katan-Khaykovich, Y., and Struhl, K. (2002) Dynamics of global histone acetylation and deacetylation in vivo. Rapid restoration of normal histone acetylation status upon removal of activators and repressors. Genes Dev. 16, 743-752 (Pubitemid 34274043)
55. Kurdistani, S. K., Robyr, D., Tavazoie, S., and Grunstein, M. (2002) Genome-wide binding map of the histone deacetylase Rpd3 in yeast. Nat. Genet. 31, 248-254
56. Kim, C. W., Moon, Y. A., Park, S. W., Cheng, D., Kwon, H. J., and Horton, J. D. (2010) Induced polymerization of mammalian acetyl-CoA carboxylase by MIG12 provides a tertiary level of regulation of fatty acid synthesis. Proc. Natl. Acad. Sci. U.S.A. 107, 9626-9631
57. Colbert, C. L., Kim, C. W., Moon Y. A., Henry L., Palnitkar M., McKean W. B., Fitzgerald K., Deisenhofer J., Horton J. D., and Kwon H. J. (2010) Crystal structure of Spot 14, a modulator of fatty acid synthesis. Proc. Natl. Acad. Sci. U.S.A. 107, 18820-18825
58. Gregolin, C., Ryder, E., Kleinschmidt, A. K., Warner, R. C., and Lane, M. D. (1966) Molecular characteristics of liver acetyl-CoA carboxylase. Proc. Natl. Acad. Sci. U.S.A. 56, 148-155
59. Hasslacher, M., Ivessa, A. S., Paltauf, F., and Kohlwein, S. D. (1993) Acetyl-CoA carboxylase from yeast is an essential enzyme and is regulated by factors that control phospholipid metabolism. J. Biol. Chem. 268, 10946-10952 (Pubitemid 23162278)
60. Chirala, S. S., Zhong, Q., Huang, W., and al-Feel, W. (1994) Analysis of FAS3/ACC regulatory region of Saccharomyces cerevisiae. Identification of a functional UASINO and sequences responsible for fatty acid-mediated repression. Nucleic Acids Res. 22, 412-418
61. Lee, T. I., Causton, H. C., Holstege, F. C., Shen, W. C., Hannett, N., Jennings, E. G., Winston, F., Green, M. R., and Young, R. A. (2000) Redundant roles for the TFIID and SAGA complexes in global transcription. Nature 405, 701-704 (Pubitemid 30428658)
62. Dion, M. F., Altschuler, S. J., Wu, L. F., and Rando, O. J. (2005) Genomic characterization reveals a simple histone H4 acetylation code. Proc. Natl. Acad. Sci. U.S.A. 102, 5501-5506 (Pubitemid 40530287)
63. Tanner, K. G., Langer, M. R., Kim, Y., and Denu, J. M. (2000) Kinetic mechanism of the histone acetyltransferase GCN5 from yeast. J. Biol. Chem. 275, 22048-22055 (Pubitemid 30621782)
64. Albaugh, B. N., Arnold, K. M., and Denu, J. M. (2011) KAT(ching) metabolism by the tail. Insight into the links between lysine acetyltransferases and metabolism. ChemBioChem. 12, 290-298
65. Wakil, S. J., and Abu-Elheiga L. A. (2009) Fatty acid metabolism. Target for metabolic syndrome. J. Lipid Res. 50, S138-S143
66. Tong, L., and Harwood, H. J. (2006) Acetyl-coenzyme A carboxylases. Versatile targets for drug discovery. J. Cell. Biochem. 99, 1476-1488 (Pubitemid 44845709)
67. Zadra, G., Priolo, C., Patnaik, A., and Loda, M. (2010) New strategies in prostate cancer. Targeting lipogenic pathways and the energy sensor AMPK. Clin. Cancer Res. 16, 3322-3328
68. Choudhary, C., Kumar, C., Gnad, F., Nielsen, M. L., Rehman, M., Walther, T. C., Olsen, J. V., and Mann, M. (2009) Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 325, 834-840
69. Zhao, S., Xu, W., Jiang, W., Yu, W., Lin, Y., Zhang, T., Yao, J., Zhou, L., Zeng, Y., Li, H., Li, Y., Shi, J., An, W., Hancock, S. M., He, F., Qin, L., Chin, J., Yang, P., Chen, X., Lei, Q., Xiong, Y., and Guan, K. L. (2010) Regulation of cellular metabolism by protein lysine acetylation. Science 327, 1000-1004
70. Kim, G. W., and Yang, X. J. (2011) Comprehensive lysine acetylomes emerging from bacteria to humans. Trends Biochem. Sci. 36, 211-220
71. Olsen, J. V., Blagoev, B., Gnad, F., Macek, B., Kumar, C., Mortensen, P., and Mann, M. (2006) Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127, 635-648 (Pubitemid 44647421)
72. Villén, J., Beausoleil, S. A., Gerber, S. A., and Gygi, S. P. (2007) Large scale phosphorylation analysis of mouse liver. Proc. Natl. Acad. Sci. U.S.A. 104, 1488-1493 (Pubitemid 46214617)
73. Schneper, L., Düvel, K., and Broach, J. R. (2004) Sense and sensibility. Nutritional response and signal integration in yeast. Curr. Opin. Microbiol. 7, 624-630 (Pubitemid 39536289)
74. Chang, C. S., and Pillus, L. (2009) Collaboration between the essential Esa1 acetyltransferase and the Rpd3 deacetylase is mediated by H4K12 histone acetylation in Saccharomyces cerevisiae. Genetics 183, 149-160
75. Lindstrom, K. C., Vary, J. C., Jr., Parthun, M. R., Delrow, J., and Tsukiyama, T. (2006) Isw1 functions in parallel with the NuA4 and Swr1 complexes in stress-induced gene repression. Mol. Cell. Biol. 26, 6117-6129 (Pubitemid 44204530)