Systematic identification of signal integration by protein kinase A

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

Volumn 112, Issue 14, 2015, Pages 4501-4506

  Filteau, Marie ^a   Diss, Guillaume ^a   Torres Quiroz, Francisco ^a,d   Dubé, Alexandre K ^a   Schraffl, Andrea ^b   Bachmann, Verena A ^b   Gagnon Arsenault, Isabelle ^a   Chrétien, Andrée Ève ^a   Steunou, Anne Lise ^a,c   Dionne, Ugo ^a,c   Côté, Jacques ^a,c   Bisson, Nicolas ^a,c   Stefan, Eduard ^b   Landry, Christian R ^a  

^a UNIVERSITÉ LAVAL   (Canada)

^b UNIVERSITY OF INNSBRUCK   (Austria)

^c LAVAL UNIVERSITY   (Canada)

^d UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

Author keywords

Acetylation; Autophagy; Methionine; Ras cAMP PKA pathway; TOR

Indexed keywords

CARBOHYDRATE; CYCLIC AMP DEPENDENT PROTEIN KINASE; LYSINE; METHIONINE; PROTEIN; CYCLIC AMP; GALACTOSE; GLUCOSE; RENILLA LUCIFERIN 2 MONOOXYGENASE; SACCHAROMYCES CEREVISIAE PROTEIN; TARGET OF RAPAMYCIN KINASE;

ACETYLATION; AGING; ANIMAL CELL; ARTICLE; AUTOPHAGY; BIOSYNTHESIS; CARBON SOURCE; COMPLEX FORMATION; CONTROLLED STUDY; ENZYME ACTIVE SITE; ENZYME SUBUNIT; GENE DELETION; GENE IDENTIFICATION; GENE INTERACTION; HOMEOSTASIS; HUMAN; HUMAN CELL; LUCIFERASE ASSAY; MAMMAL; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTEIN INTERACTION; SIGNAL TRANSDUCTION; YEAST; AMINO ACID SEQUENCE; ANIMAL; CHEMISTRY; GENETICS; HEK293 CELL LINE; METABOLISM; MOLECULAR GENETICS; PROTEIN PROCESSING; RAT; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY;

EUKARYOTA; MAMMALIA;

ACETYLATION; AMINO ACID SEQUENCE; ANIMALS; AUTOPHAGY; CYCLIC AMP; CYCLIC AMP-DEPENDENT PROTEIN KINASES; GALACTOSE; GLUCOSE; HEK293 CELLS; HOMEOSTASIS; HUMANS; LUCIFERASES, RENILLA; METHIONINE; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN PROCESSING, POST-TRANSLATIONAL; RATS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; SIGNAL TRANSDUCTION; TOR SERINE-THREONINE KINASES;

EID: 84928809593     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1409938112     Document Type: Article

References (56)

1. Landry CR, Levy ED, Abd Rabbo D, Tarassov K, Michnick SW (2013) Extracting insight from noisy cellular networks. Cell 155(5):983-989
2. Vidal M, Cusick ME, Barabási AL (2011) Interactome networks and human disease. Cell 144(6):986-998
3. Jacunski A, Tatonetti NP (2013) Connecting the dots: Applications of network medicine in pharmacology and disease. Clin Pharmacol Ther 94(6):659-669
4. Lee MJ, et al. (2012) Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks. Cell 149(4):780-794
5. Ideker T, Krogan NJ (2012) Differential network biology. Mol Syst Biol 8:565
6. Diss G, et al. (2013) Integrative avenues for exploring the dynamics and evolution of protein interaction networks. Curr Opin Biotechnol 24(4):775-783
7. Taylor SS, Ilouz R, Zhang P, Kornev AP (2012) Assembly of allosteric macromolecular switches: Lessons from PKA. Nat Rev Mol Cell Biol 13(10):646-658
8. Vandamme J, Castermans D, Thevelein JM (2012) Molecular mechanisms of feedback inhibition of protein kinase A on intracellular cAMP accumulation. Cell Signal 24(8): 1610-1618
9. Wong W, Scott JD (2004) AKAP signalling complexes: Focal points in space and time. Nat Rev Mol Cell Biol 5(12):959-970
10. Fontana L, Partridge L, Longo VD (2010) Extending healthy life span-from yeast to humans. Science 328(5976):321-326
11. Stephan JS, Yeh YY, Ramachandran V, Deminoff SJ, Herman PK (2009) The Tor and PKA signaling pathways independently target the Atg1/Atg13 protein kinase complex to control autophagy. Proc Natl Acad Sci USA 106(40):17049-17054
12. Yang Z, Klionsky DJ (2009) An overview of the molecular mechanism of autophagy. Curr Top Microbiol Immunol 335:1-32
13. Beuschlein F, et al. (2014) Constitutive activation of PKA catalytic subunit in adrenal Cushing's syndrome. N Engl J Med 370(11):1019-1028
14. Fuller KK, Rhodes JC (2012) Protein kinase A and fungal virulence: A sinister side to a conserved nutrient sensing pathway. Virulence 3(2):109-121
15. Cullen PJ, Sprague GF, Jr (2012) The regulation of filamentous growth in yeast. Genetics 190(1):23-49
16. Soulard A, et al. (2010) The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates. Mol Biol Cell 21(19): 3475-3486
17. Scott JD, Pawson T (2009) Cell signaling in space and time: Where proteins come together and when they're apart. Science 326(5957):1220-1224
18. Feliciello A, Gottesman ME, Avvedimento EV (2005) cAMP-PKA signaling to the mitochondria: Protein scaffolds, mRNA and phosphatases. Cell Signal 17(3):279-287
19. Griffioen G, Anghileri P, Imre E, Baroni MD, Ruis H (2000) Nutritional control of nucleocytoplasmic localization of cAMP-dependent protein kinase catalytic and regulatory subunits in Saccharomyces cerevisiae. J Biol Chem 275(2):1449-1456
20. Griffioen G, et al. (2001) Nucleocytoplasmic distribution of budding yeast protein kinase A regulatory subunit Bcy1 requires Zds1 and is regulated by Yak1-dependent phosphorylation of its targeting domain. Mol Cell Biol 21(2):511-523
21. Freschi L, Torres-Quiroz F, Dubé AK, Landry CR (2013) qPCA: A scalable assay to measure the perturbation of protein-protein interactions in living cells. Mol Biosyst 9(1):36-43
22. Stefan E, et al. (2007) Quantification of dynamic protein complexes using Renilla luciferase fragment complementation applied to protein kinase A activities in vivo. Proc Natl Acad Sci USA 104(43):16916-16921
23. Diss G, Dubé AK, Boutin J, Gagnon-Arsenault I, Landry CR (2013) A systematic approach for the genetic dissection of protein complexes in living cells. Cell Reports 3(6): 2155-2167
24. Wilson WA, Wang Z, Roach PJ (2002) Systematic identification of the genes affecting glycogen storage in the yeast Saccharomyces cerevisiae: Implication of the vacuole as a determinant of glycogen level. Mol Cell Proteomics 1(3):232-242
25. Chatr-Aryamontri A, et al. (2013) The BioGRID interaction database: 2013 update. Nucleic Acids Res 41(Database issue):D816-D823
26. Ptacek J, et al. (2005) Global analysis of protein phosphorylation in yeast. Nature 438(7068):679-684
27. Haesendonckx S, et al. (2012) The activation loop of PKA catalytic isoforms is differentially phosphorylated by Pkh protein kinases in Saccharomyces cerevisiae. Biochem J 448(3):307-320
28. Tudisca V, et al. (2010) Differential localization to cytoplasm, nucleus or P-bodies of yeast PKA subunits under different growth conditions. Eur J Cell Biol 89(4):339-348
29. Loewith R, Hall MN (2011) Target of rapamycin (TOR) in nutrient signaling and growth control. Genetics 189(4):1177-1201
30. Smets B, et al. (2010) Life in the midst of scarcity: Adaptations to nutrient availability in Saccharomyces cerevisiae. Curr Genet 56(1):1-32
31. Shin CS, Huh WK (2011) Bidirectional regulation between TORC1 and autophagy in Saccharomyces cerevisiae. Autophagy 7(8):854-862
32. Ramachandran V, Herman PK (2011) Antagonistic interactions between the cAMPdependent protein kinase and Tor signaling pathways modulate cell growth in Saccharomyces cerevisiae. Genetics 187(2):441-454
33. Sutter BM, Wu X, Laxman S, Tu BP (2013) Methionine inhibits autophagy and promotes growth by inducing the SAM-responsive methylation of PP2A. Cell 154(2): 403-415
34. Henriksen P, et al. (2012) Proteome-wide analysis of lysine acetylation suggests its broad regulatory scope in Saccharomyces cerevisiae. Mol Cell Proteomics 11(11): 1510-1522
35. Weinert BT, et al. (2014) Acetylation dynamics and stoichiometry in Saccharomyces cerevisiae. Mol Syst Biol 10:716
36. Lundby A, et al. (2012) Proteomic analysis of lysine acetylation sites in rat tissues reveals organ specificity and subcellular patterns. Cell Reports 2(2):419-431
37. Kim SC, et al. (2006) Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Mol Cell 23(4):607-618
38. Samokhvalov V, Ignatov V, Kondrashova M (2004) Reserve carbohydrates maintain the viability of Saccharomyces cerevisiae cells during chronological aging. Mech Ageing Dev 125(3):229-235
39. Petti AA, Crutchfield CA, Rabinowitz JD, Botstein D (2011) Survival of starving yeast is correlated with oxidative stress response and nonrespiratory mitochondrial function. Proc Natl Acad Sci USA 108(45):E1089-E1098
40. Li DD, et al. (2013) ECM17-dependent methionine/cysteine biosynthesis contributes to biofilm formation in Candida albicans. Fungal Genet Biol 51:50-59
41. Liu WJ, et al. (2011) Inhibition of hepatic glycogen synthesis by hyperhomocysteinemia mediated by TRB3. Am J Pathol 178(4):1489-1499
42. Zhao S, et al. (2010) Regulation of cellular metabolism by protein lysine acetylation. Science 327(5968):1000-1004
43. Yi C, et al. (2012) Function and molecular mechanism of acetylation in autophagy regulation. Science 336(6080):474-477
44. Tarassov K, et al. (2008) An in vivo map of the yeast protein interactome. Science 320(5882):1465-1470
45. Gagnon-Arsenault I, et al. (2013) Transcriptional divergence plays a role in the rewiring of protein interaction networks after gene duplication. J Proteomics 81:112-125
46. Costanzo M, et al. (2010) The genetic landscape of a cell. Science 327(5964):425-431
47. Giaever G, et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418(6896):387-391
48. Ghaemmaghami S, et al. (2003) Global analysis of protein expression in yeast. Nature 425(6959):737-741
49. Huh WK, et al. (2003) Global analysis of protein localization in budding yeast. Nature 425(6959):686-691
50. Tamura K, et al. (2011) MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731-2739
51. Bachmann VA, et al. (2013) Reciprocal regulation of PKA and Rac signaling. Proc Natl Acad Sci USA 110(21):8531-8536
52. Legube G, et al. (2002) Tip60 is targeted to proteasome-mediated degradation by Mdm2 and accumulates after UV irradiation. EMBO J 21(7):1704-1712
53. Yang XJ, Ogryzko VV, Nishikawa J, Howard BH, Nakatani Y (1996) A p300/CBPassociated factor that competes with the adenoviral oncoprotein E1A. Nature 382(6589):319-324
54. Stefan E, et al. (2011) PKA regulatory subunits mediate synergy among conserved G-protein-coupled receptor cascades. Nat Commun 2:598
55. Searle JS, Wood MD, Kaur M, Tobin DV, Sanchez Y (2011) Proteins in the nutrientsensing and DNA damage checkpoint pathways cooperate to restrain mitotic progression following DNA damage. PLoS Genet 7(7):e1002176
56. Murakami C, Kaeberlein M (2009) Quantifying yeast chronological life span by outgrowth of aged cells. JoVE (27):e1156.