Identification of AMP-activated protein kinase targets by a consensus sequence search of the proteome
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- 作者：Traci L Marin (1) (5)
Brendan Gongol (1) (5)
Marcy Martin (1) (2)
Stephanie J King (1)
Lemar Smith (1)
David A Johnson (1)
Shankar Subramaniam (3)
Shu Chien (3) (4)
John Y-J Shyy (1) (2)
1. Divisions of Biochemistry and Molecular Biology and Biomedical Sciences ; University of California ; Riverside ; CA ; 92521-0121 ; USA
5. Department of Cardiopulmonary Sciences and Anatomy ; Schools of Allied Health and Medicine ; Loma Linda University ; Loma Linda ; CA ; 92350 ; USA
2. Division of Cardiology ; Department of Medicine ; University of California ; San Diego ; La Jolla ; CA ; 92093 ; USA
3. Division of Physiology ; Department of Medicine ; University of California ; San Diego ; La Jolla ; CA ; 92093 ; USA
4. Department of Bioengineering and Institute of Engineering in Medicine ; University of California ; San Diego La Jolla ; CA ; 92093 ; USA - 关键词：AMPK ; AKT2 ; ATF2 ; MMP ; 2 ; FOXO3a ; NADSYN1 ; Phosphorylation consensus sequence ; Bioinformatics ; Proteome ; Network prediction
- 刊名：BMC Systems Biology
- 出版年：2015
- 出版时间：December 2015
- 年：2015
- 卷：9
- 期：1
- 全文大小：1,928 KB
- 参考文献：1. Kahn, BB, Alquier, T, Carling, D, Hardie, DG (2005) AMP-activated protein kinase: ancient energy gauge provides clues to modern understanding of metabolism. Cell Metab 1: pp. 15-25 ternal" href="http://dx.doi.org/10.1016/j.cmet.2004.12.003" target="_blank" title="It opens in new window">CrossRef
2. Hardie, DG, Ross, FA, Hawley, SA (2012) AMPK: a nutrient and energy sensor that maintains energy homeostasis. Nat Rev Mol Cell Biol 13: pp. 251-62 ternal" href="http://dx.doi.org/10.1038/nrm3311" target="_blank" title="It opens in new window">CrossRef
3. Woods, A, Dickerson, K, Heath, R, Hong, SP, Momcilovic, M, Johnstone, SR (2005) Ca2+/calmodulin-dependent protein kinase kinase-beta acts upstream of AMP-activated protein kinase in mammalian cells. Cell Metab 2: pp. 21-33 ternal" href="http://dx.doi.org/10.1016/j.cmet.2005.06.005" target="_blank" title="It opens in new window">CrossRef
4. Sanz, P1, Rubio, T, Garcia-Gimeno, MA (2013) AMPK beta subunits: more than just a scaffold in the formation of AMPK complex. FEBS J 280: pp. 3723-33 ternal" href="http://dx.doi.org/10.1111/febs.12364" target="_blank" title="It opens in new window">CrossRef
5. Towler, MC, Hardie, DG (2007) AMP-Activated Protein Kinase in Metabolic Control and Insulin Signaling. Circ Res 100: pp. 328-41 ternal" href="http://dx.doi.org/10.1161/01.RES.0000256090.42690.05" target="_blank" title="It opens in new window">CrossRef
6. Leff, T (2003) AMP-activated protein kinase regulates gene expression by direct phosphorylation of nuclear proteins. Biochem Soc Trans 31: pp. 224-7 ternal" href="http://dx.doi.org/10.1042/BST0310224" target="_blank" title="It opens in new window">CrossRef
7. Xu, Q, Yang, C, Du, Y, Chen, Y, Liu, H, Deng, M (2014) AMPK regulates histone H2B O-GlcNAcylation. Nucleic Acids Res 42: pp. 5594-604 ternal" href="http://dx.doi.org/10.1093/nar/gku236" target="_blank" title="It opens in new window">CrossRef
8. Shannon, PT, Reiss, DJ, Bonneau, R, Baliga, NS (2006) The Gaggle: an open-source software system for integrating bioinformatics software and data sources. BMC Bioinformatics 7: pp. 176 ternal" href="http://dx.doi.org/10.1186/1471-2105-7-176" target="_blank" title="It opens in new window">CrossRef
9. Cant贸, C, Gerhart-Hines, Z, Feige, JN, Lagouge, M, Noriega, L, Milne, JC (2009) AMPK regulates energy expenditure by modulating NAD+ metabolism and SIRT1 activity. Nature 458: pp. 1056-60 ternal" href="http://dx.doi.org/10.1038/nature07813" target="_blank" title="It opens in new window">CrossRef
10. LaRonde-LeBlanc, N, Resto, M, Gerratana, B (2009) Regulation of active site coupling in glutamine-dependent NAD (+) synthetase. Nat Struct Mol Biol 16: pp. 421-9 ternal" href="http://dx.doi.org/10.1038/nsmb.1567" target="_blank" title="It opens in new window">CrossRef
11. Greer, EL, Oskoui, PR, Banko, MR, Maniar, JM, Gygi, MP, Gygi, SP (2007) The energy sensor AMP-activated protein kinase directly regulates the mammalian FOXO3 transcription factor. J Biol Chem 282: pp. 30107-19 ternal" href="http://dx.doi.org/10.1074/jbc.M705325200" target="_blank" title="It opens in new window">CrossRef
12. Nagata, D, Mogi, M, Walsh, K (2003) AMP-activated protein kinase (AMPK) signaling in endothelial cells is essential for angiogenesis in response to hypoxic stress. J Biol Chem 278: pp. 31000-6 ternal" href="http://dx.doi.org/10.1074/jbc.M300643200" target="_blank" title="It opens in new window">CrossRef
13. Liu, Y, Tang, G, Zhang, Z, Wang, Y, Yang, GY (2014) Metformin promotes focal angiogenesis and neurogenesis in mice following middle cerebral artery occlusion. Neurosci Lett 579C: pp. 46-51 ternal" href="http://dx.doi.org/10.1016/j.neulet.2014.07.006" target="_blank" title="It opens in new window">CrossRef
14. Zhu, F, Zhang, Y, Bode, AM, Dong, Z (2004) Involvement of ERKs and mitogen- and stress-activated protein kinase in UVC-induced phosphorylation of ATF2 in JB6cells. Carcinogenesis 25: pp. 1847-52 ternal" href="http://dx.doi.org/10.1093/carcin/bgh202" target="_blank" title="It opens in new window">CrossRef
15. Fan, Y, Gong, Y, Ghosh, PK, Graham, LM, Fox, PL (2009) Spatial coordination of actin polymerization and ILK-Akt2 activity during endothelial cell migration. Dev Cell 16: pp. 661-74 ternal" href="http://dx.doi.org/10.1016/j.devcel.2009.03.009" target="_blank" title="It opens in new window">CrossRef
16. Song, H, Ki, SH, Kim, SG, Moon, A (2006) Activating transcription factor 2 mediates matrix metalloproteinase-2 transcriptional activation induced by p38 in breast epithelial cells. Cancer Res 66: pp. 10487-96 ternal" href="http://dx.doi.org/10.1158/0008-5472.CAN-06-1461" target="_blank" title="It opens in new window">CrossRef
17. Ben-Yosef, Y, Miller, A, Shapiro, S, Lahat, N (2005) Hypoxia of endothelial cells leads to MMP-2-dependent survival and death. Am J Physiol Cell Physiol 289: pp. C1321-31 ternal" href="http://dx.doi.org/10.1152/ajpcell.00079.2005" target="_blank" title="It opens in new window">CrossRef
18. Shenoy, SK, Drake, MT, Nelson, CD, Houtz, DA, Xiao, K, Madabushi, S (2006) Beta-arrestin-dependent, G protein-independent ERK1/2 activation by the beta2 adrenergic receptor. J Biol Chem 281: pp. 1261-73 ternal" href="http://dx.doi.org/10.1074/jbc.M506576200" target="_blank" title="It opens in new window">CrossRef
19. Witherow, DS, Garrison, TR, Miller, WE, Lefkowitz, RJ (2004) Beta-arrestin inhibits NF-kappaB activity by means of its interaction with the NF-kappaB inhibitor IkappaBalpha. Proc Natl Acad Sci U S A 101: pp. 8603-7 ternal" href="http://dx.doi.org/10.1073/pnas.0402851101" target="_blank" title="It opens in new window">CrossRef
20. Kang, J, Shi, Y, Xiang, B, Qu, B, Su, W, Zhu, M (2005) A nuclear function of beta-arrestin1 in GPCR signaling: regulation of histone acetylation and gene transcription. Cell 123: pp. 833-47 ternal" href="http://dx.doi.org/10.1016/j.cell.2005.09.011" target="_blank" title="It opens in new window">CrossRef
21. DeWire, SM, Ahn, S, Lefkowitz, RJ, Shenoy, SK (2007) Beta-arrestins and cell signaling. Annu Rev Physiol 69: pp. 483-510 ternal" href="http://dx.doi.org/10.1146/annurev.physiol.69.022405.154749" target="_blank" title="It opens in new window">CrossRef
22. Yu, MC, Su, LL, Zou, L, Liu, Y, Wu, N, Kong, L (2008) An essential function for beta-arrestin 2 in the inhibitory signaling of natural killer cells. Nat Immunol 9: pp. 898-907 ternal" href="http://dx.doi.org/10.1038/ni.1635" target="_blank" title="It opens in new window">CrossRef
23. Zirwes, RF, Eilbracht, J, Kneissel, S, Schmidt-Zachmann, MS (2000) A novel helicase-type protein in the nucleolus: protein NOH61. Mol Biol Cell 11: pp. 1153-67 ternal" href="http://dx.doi.org/10.1091/mbc.11.4.1153" target="_blank" title="It opens in new window">CrossRef
24. Avni, D, Biberman, Y, Meyuhas, O (1997) The 5鈥?terminal oligopyrimidine tract confers translational control on TOP mRNAs in a cell type- and sequence context-dependent manner. Nucleic Acids Res 25: pp. 995-1001 ternal" href="http://dx.doi.org/10.1093/nar/25.5.995" target="_blank" title="It opens in new window">CrossRef
25. Reiter, AK, Bolster, DR, Crozier, SJ, Kimball, SR, Jefferson, LS (2008) AMPK represses TOP mRNA translation but not global protein synthesis in liver. Biochem Biophys Res Commun 374: pp. 345-50 ternal" href="http://dx.doi.org/10.1016/j.bbrc.2008.07.025" target="_blank" title="It opens in new window">CrossRef
26. Hebert, DN, Molinari, M (2007) In and out of the ER: protein folding, quality control, degradation, and related human diseases. Physiol Rev 87: pp. 1377-408 ternal" href="http://dx.doi.org/10.1152/physrev.00050.2006" target="_blank" title="It opens in new window">CrossRef
27. Coe, H, Bedard, K, Groenendyk, J, Jung, J, Michalak, M (2008) Endoplasmic reticulum stress in the absence of calnexin. Cell Stress and Chaperones 13: pp. 497-507 ternal" href="http://dx.doi.org/10.1007/s12192-008-0049-x" target="_blank" title="It opens in new window">CrossRef
28. Zhang, K, Kaufman, RJ (2004) Signaling the unfolded protein response from the endoplasmic reticulum. J Biol Chem 279: pp. 25935-8 ternal" href="http://dx.doi.org/10.1074/jbc.R400008200" target="_blank" title="It opens in new window">CrossRef
29. Roderick, HL, Lechleiter, JD, Camacho, P (2000) Cytosolic phosphorylation of calnexin controls intracellular Ca (2+) oscillations via an interaction with SERCA2b. J Cell Biol 149: pp. 1235-48 ternal" href="http://dx.doi.org/10.1083/jcb.149.6.1235" target="_blank" title="It opens in new window">CrossRef
30. Cardozo, AK, Ortis, F, Storling, J, Feng, YM, Rasschaert, J, Tonnesen, M (2005) Cytokines downregulate the sarcoendoplasmic reticulum pump Ca2+ ATPase 2b and deplete endoplasmic reticulum Ca2+, leading to induction of endoplasmic reticulum stress in pancreatic beta-cells. Diabetes 54: pp. 452-61 ternal" href="http://dx.doi.org/10.2337/diabetes.54.2.452" target="_blank" title="It opens in new window">CrossRef
31. Dong, Y, Zhang, M, Liang, B, Xie, Z, Zhao, Z, Asfa, S (2010) Reduction of AMP-activated protein kinase alpha2 increases endoplasmic reticulum stress and atherosclerosis in vivo. Circ Res 121: pp. 792-803 ternal" href="http://dx.doi.org/10.1161/CIRCULATIONAHA.109.900928" target="_blank" title="It opens in new window">CrossRef
32. Foti, D, Iuliano, R, Chiefari, E, Brunettii, A (2003) A nucleoprotein complex containing Sp1, C/EBPb, and HMGI-Y controls human insulin receptor gene transcription. Mol Cell Biol 23: pp. 2720-32 ternal" href="http://dx.doi.org/10.1128/MCB.23.8.2720-2732.2003" target="_blank" title="It opens in new window">CrossRef
33. Ha, TK, Chi, SG (2012) CAV1/caveolin 1 enhances aerobic glycolysis in colon cancer cells via activation of SLC2A3/GLUT3 transcription. Autophagy 8: pp. 1684-5 ternal" href="http://dx.doi.org/10.4161/auto.21487" target="_blank" title="It opens in new window">CrossRef
34. Salani, B, Maffioli, S, Hamoudane, M, Parodi, A, Ravera, S, Passalacqua, M (2012) Caveolin-1 is essential for metformin inhibitory effect on IGF1 action in non-small-cell lung cancer cells. FASEB J 26: pp. 788-98 ternal" href="http://dx.doi.org/10.1096/fj.11-192088" target="_blank" title="It opens in new window">CrossRef
35. Anderson, KP, Kern, CB, Crable, SC, Lingrel, JB (1995) Isolation of a gene encoding a functional zinc finger protein homologous to erythroid Kr眉ppel-like factor: identification of a new multigene family. Mol Cell Biol 15: pp. 5957-65
36. Evans, PM, Zhang, W, Chen, X, Yang, J, Bhakat, KK, Liu, C (2007) Kruppel-like factor 4 is acetylated by p300 and regulates gene transcription via modulation of histoneacetylation. J Biol Chem 282: pp. 33994-4002 ternal" href="http://dx.doi.org/10.1074/jbc.M701847200" target="_blank" title="It opens in new window">CrossRef
37. Li, D, Yea, S, Dolios, G, Martignetti, JA, Narla, G, Wang, R (2005) Regulation of Kruppel-like factor 6 tumor suppressor activity by acetylation. Cancer Res 65: pp. 9216-25 ternal" href="http://dx.doi.org/10.1158/0008-5472.CAN-05-1040" target="_blank" title="It opens in new window">CrossRef
38. Kuo, CT, Veselits, ML, Barton, KP, Lu, MM, Clendenin, C, Leiden, JM (1997) The KLF transcription factor is required for normal tunica media formation and blood vessel stabilization during murine embryogenesis. Genes Dev 11: pp. 2996-3006 ternal" href="http://dx.doi.org/10.1101/gad.11.22.2996" target="_blank" title="It opens in new window">CrossRef
39. Wu, J, Bohanan, CS, Neumann, JC, Lingrel, JB (2008) KLF2 transcription factor modulates blood vessel maturation through smooth muscle cell migration. J Biol Chem 283: pp. 3942-50 ternal" href="http://dx.doi.org/10.1074/jbc.M707882200" target="_blank" title="It opens in new window">CrossRef
40. Sumida, H, Noguchi, K, Kihara, Y, Abe, M, Yanagida, K, Hamano, F (2010) LPA4 regulates blood and lymphatic vessel formation during mouse embryogenesis. Blood 116: pp. 5060-70 ternal" href="http://dx.doi.org/10.1182/blood-2010-03-272443" target="_blank" title="It opens in new window">CrossRef
41. Young, A, Wu, W, Sun, W, Benjamin Larman, H, Wang, N, Li, YS (2009) Flow activation of AMP-activated protein kinase in vascular endothelium leads to Kr眉ppel-like factor 2 expression. Arterioscler Thromb Vasc Biol 29: pp. 1902-8 ternal" href="http://dx.doi.org/10.1161/ATVBAHA.109.193540" target="_blank" title="It opens in new window">CrossRef
42. Valdez, BC, Henning, D, So, RB, Dixon, J, Dixon, MJ (2004) The Treacher Collins syndrome (TCOF1) gene product is involved in ribosomal DNA gene transcription by interacting with upstream binding factor. Proc Natl Acad Sci U S A 101: pp. 10709-14 ternal" href="http://dx.doi.org/10.1073/pnas.0402492101" target="_blank" title="It opens in new window">CrossRef
43. Poortinga, G, Hannan, KM, Snelling, H, Walkley, CR, Jenkins, A, Sharkey, K (2004) MAD1 and cMYC regulate UBF and rDNA transcription during granulocyte differentiation. EBMO J 23: pp. 3325-35
44. Dixon, J, Jones, NC, Sandell, LL, Jayasinghe, SM, Crane, J, Rey, JP (2006) Tcof1/Treacle is required for neural crest cell formation and proliferation deficiencies that cause craniofacial abnormalities. Proc Natl Acad Sci U S A 103: pp. 13403-8 ternal" href="http://dx.doi.org/10.1073/pnas.0603730103" target="_blank" title="It opens in new window">CrossRef
45. Viollet, B, Athea, Y, Mounier, R, Guigas, B, Zarrinpashneh, E, Horman, S (2009) AMPK: Lessons from transgenic and knockout animals. Front Biosci 14: pp. 19-44 ternal" href="http://dx.doi.org/10.2741/3229" target="_blank" title="It opens in new window">CrossRef
46. Howard, TL, Stauffer, DR, Degnin, CR, Hollenberg, SM (2001) CHMP1 functions as a member of a newly defined family of vesicle trafficking proteins. J Cell Sci 114: pp. 2395-404
47. Stauffer, DR, Howard, TL, Nyun, T, Hollenberg, SM (2001) CHMP1 is a novel nuclear matrix protein affecting chromatin structure and cell-cycle progression. J Cell Sci 114: pp. 2383-93
48. Cheung, P, Tanner, KG, Cheung, WL, Sassone-Corsi, P, Denu, JM, Allis, CD (2000) Synergistic coupling of histone H3 phosphorylation and acetylation in response to epidermal growth factor stimulation. Mol Cell 5: pp. 905-15 ternal" href="http://dx.doi.org/10.1016/S1097-2765(00)80256-7" target="_blank" title="It opens in new window">CrossRef
49. Chan, S, Choi, EA, Shi, Y (2011) Pre-mRNA 3鈥?end processing complex assembly and function. Wiley Interdiscip Rev RNA 2: pp. 321-35 ternal" href="http://dx.doi.org/10.1002/wrna.54" target="_blank" title="It opens in new window">CrossRef
50. Drosos, Y, Kouloukoussa, M, 脴stvold, AC, Grundt, K, Goutas, N, Vlachodimitropoulos, D (2009) NUCKS overexpression in breast cancer. Cancer Cell Int 9: pp. 19 ternal" href="http://dx.doi.org/10.1186/1475-2867-9-19" target="_blank" title="It opens in new window">CrossRef
51. Grundt, K, Skjeldal, L, Anthonsen, HW, Skauge, T, Huitfeldt, HS, 脴stvold, AC (2002) A putative DNA-binding domain in the NUCKS protein. Arch Biochem Biophys 407: pp. 168-75 ternal" href="http://dx.doi.org/10.1016/S0003-9861(02)00513-1" target="_blank" title="It opens in new window">CrossRef
52. Price, JL, Blau, J, Rothenfluh, A, Abodeely, M, Kloss, B, Young, MW (1998) Double-time is a novel Drosophila clock gene that regulates PERIOD protein accumulation. Cell 94: pp. 83-95 ternal" href="http://dx.doi.org/10.1016/S0092-8674(00)81224-6" target="_blank" title="It opens in new window">CrossRef
53. Um, JH, Pendergast, JS, Springer, DA, Foretz, M, Viollet, B, Brown, A (2011) AMPK regulates circadian rhythms in a tissue- and isoform-specific manner. PLoS One 6: pp. e18450 ternal" href="http://dx.doi.org/10.1371/journal.pone.0018450" target="_blank" title="It opens in new window">CrossRef
54. Richly, H, Rocha-Viegas, L, Ribeiro, JD, Demajo, S, Gundem, G, Lopez-Bigas, N (2010) Transcriptional activation of polycomb-repressed genes by ZRF1. Nature 468: pp. 1124-8 ternal" href="http://dx.doi.org/10.1038/nature09574" target="_blank" title="It opens in new window">CrossRef
55. Otto, H, Conz, C, Maier, P, W枚lfle, T, Suzuki, CK, Jen枚, P (2005) The chaperones MPP11 and Hsp70L1 form the mammalian ribosome-associated complex. Proc Natl Acad Sci U S A 102: pp. 10064-9 ternal" href="http://dx.doi.org/10.1073/pnas.0504400102" target="_blank" title="It opens in new window">CrossRef
56. Hundley, HA, Walter, W, Bairstow, S, Craig, EA (2005) Human Mpp11 J protein: ribosome- tethered molecular chaperones are ubiquitous. Science 308: pp. 1032-4 ternal" href="http://dx.doi.org/10.1126/science.1109247" target="_blank" title="It opens in new window">CrossRef
57. Johnson, LN (2001) Structural basis for substrate recognition and control in protein kinases. Ernst Schering Res Found Workshop 34: pp. 47-69
58. Xu, J (2005) Preparation, culture, and immortalization of mouse embryonic fibroblasts. Curr Protoc Mol Biol Chapter 28: pp. 1 - 刊物主题：Bioinformatics; Systems Biology; Simulation and Modeling; Computational Biology/Bioinformatics; Physiological, Cellular and Medical Topics; Algorithms;
- 出版者：BioMed Central
- ISSN：1752-0509
文摘
Background AMP-activated protein kinase (AMPK) is a heterotrimeric serine/threonine protein kinase that is activated by cellular perturbations associated with ATP depletion or stress. While AMPK modulates the activity of a variety of targets containing a specific phosphorylation consensus sequence, the number of AMPK targets and their influence over cellular processes is currently thought to be limited. Results We queried the human and the mouse proteomes for proteins containing AMPK phosphorylation consensus sequences. Integration of this database into Gaggle software facilitated the construction of probable AMPK-regulated networks based on known and predicted molecular associations. In vitro kinase assays were conducted for preliminary validation of 12 novel AMPK targets across a variety of cellular functional categories, including transcription, translation, cell migration, protein transport, and energy homeostasis. Following initial validation, pathways that include NAD synthetase 1 (NADSYN1) and protein kinase B (AKT2) were hypothesized and experimentally tested to provide a mechanistic basis for AMPK regulation of cell migration and maintenance of cellular NAD+ concentrations during catabolic processes. Conclusions This study delineates an approach that encompasses both in silico procedures and in vitro experiments to produce testable hypotheses for AMPK regulation of cellular processes.