Interaction between the tRNA-Binding and C-Terminal Domains of Yeast Gcn2 Regulates Kinase Activity In Vivo

English version České info

The survival of all living organisms depends on their capacity to adapt their gene expression program to variations in the environment. When subjected to various stresses, eukaryotic cells modulate general and gene-specific protein synthesis by phosphorylating the α-subunit of eukaryotic translation initiation factor 2 (eIF2α). The yeast Saccharomyces cerevisiae has a single eIF2α kinase, Gcn2, activated by uncharged tRNAs that accumulate in amino acid starved cells, which bind to a regulatory domain homologous to histidyl-tRNA synthetase (HisRS). Gcn2 also contains a C-terminal domain implicated in autoinhibition of Gcn2. Our findings identify a direct interaction between the CTD and a novel regulatory surface in the HisRS domain that is required for inhibition of Gcn2 function in non-starved cells, which is down-regulated by uncharged tRNA. The results further suggest that tRNA binding to the pseudo-active site in the HisRS domain remodels its proximal CTD-binding surface to weaken HisRS/CTD interaction and thereby release the autoinhibitory function of the CTD to activate kinase function. This study provides new molecular insights into how tRNA binding can modulate regulatory interactions among the HisRS, CTD, and kinase domains of Gcn2 to elicit kinase activation.

Vyšlo v časopise: Interaction between the tRNA-Binding and C-Terminal Domains of Yeast Gcn2 Regulates Kinase Activity In Vivo. PLoS Genet 11(2): e32767. doi:10.1371/journal.pgen.1004991
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004991

Souhrn

Zdroje

1. Hinnebusch AG (2005) Translational regulation of GCN4 and the general amino acid control of yeast. Annu Rev Microbiol 59: 407–450. 16153175

2. Lu PD, Harding HP, Ron D (2004) Translation reinitiation at alternative open reading frames regulates gene expression in an integrated stress response. J Cell Biol 167: 27–33. 15479734

3. Vattem KM, Wek RC (2004) Reinitiation involving upstream ORFs regulates ATF4 mRNA translation in mammalian cells. Proc Natl Acad Sci U S A 101: 11269–11274. 15277680

4. Ron D, Harding HP (2007) eIF2α Phosphorylation in Cellular Stress Responses and Disease. In: Mathews M, Sonenberg N, Hershey JWB, editors. Translational Control in Biology and Medicine. Cold Spring Harbor: Cold Spring Harbor Laboratory Press. pp. 345–368.

5. Hao S, Sharp JW, Ross-Inta CM, McDaniel BJ, Anthony TG, et al. (2005) Uncharged tRNA and sensing of amino acid deficiency in mammalian piriform cortex. Science 307: 1776–1778. 15774759

6. Anthony TG, McDaniel BJ, Byerley RL, McGrath BC, Cavener DR, et al. (2004) Preservation of liver protein synthesis during dietary leucine deprivation occurs at the expense of skeletal muscle mass in mice deleted for eIF2 kinase GCN2. J Biol Chem 279: 36553–36561. 15213227

7. Guo F, Cavener DR (2007) The GCN2 eIF2alpha kinase regulates fatty-acid homeostasis in the liver during deprivation of an essential amino acid. Cell Metab 5: 103–114. 17276353

8. Costa-Mattioli M, Gobert D, Harding H, Herdy B, Azzi M, et al. (2005) Translational control of hippocampal synaptic plasticity and memory by the eIF2alpha kinase GCN2. Nature 436: 1166–1173. 16121183

9. Murguia JR, Serrano R (2012) New functions of protein kinase Gcn2 in yeast and mammals. IUBMB Life 64: 971–974. doi: 10.1002/iub.1090 23129244

10. Eyries M, Montani D, Girerd B, Perret C, Leroy A, et al. (2014) EIF2AK4 mutations cause pulmonary veno-occlusive disease, a recessive form of pulmonary hypertension. Nat Genet 46: 65–69. doi: 10.1038/ng.2844 24292273

11. Qiu H, Hu C, Dong J, Hinnebusch AG (2002) Mutations that bypass tRNA binding activate the intrinsically defective kinase domain in GCN2. Genes Dev 16: 1271–1280. 12023305

12. Padyana AK, Qiu H, Roll-Mecak A, Hinnebusch AG, Burley SK (2005) Structural basis for autoinhibition and mutational activation of eukaryotic initiation factor 2alpha protein kinase GCN2. J Biol Chem 280: 29289–29299. 15964839

13. Garriz A, Qiu H, Dey M, Seo EJ, Dever TE, et al. (2008) A network of hydrophobic residues impeding helix {alpha}C rotation maintains latency of eIF2{alpha} kinase Gcn2. Mol Cell Biol. doi: 10.1128/MCB.00782-08 19114562

14. Wek RC, Jackson BM, Hinnebusch AG (1989) Juxtaposition of domains homologous to protein kinases and histidyl-tRNA synthetases in GCN2 protein suggests a mechanism for coupling GCN4 expression to amino acid availability. Proc Natl Acad Sci USA 86: 4579–4583. 2660141

15. Wek SA, Zhu S, Wek RC (1995) The histidyl-tRNA synthetase-related sequence in the eIF-2α protein kinase GCN2 interacts with tRNA and is required for activation in response to starvation for different amino acids. Mol Cell Biol 15: 4497–4506. 7623840

16. Zhu S, Sobolev AY, Wek RC (1996) Histidyl-tRNA synthetase-related sequences in GCN2 protein kinase regulate in vitro phosphorylation of eIF-2. J Biol Chem 271: 24989–24994. 8798780

17. Dong J, Qiu H, Garcia-Barrio M, Anderson J, Hinnebusch AG (2000) Uncharged tRNA activates GCN2 by displacing the protein kinase moiety from a bipartite tRNA-binding domain. Mol Cell 6: 269–279. 10983975

18. Qiu H, Dong J, Hu C, Francklyn CS, Hinnebusch AG (2001) The tRNA-binding moiety in GCN2 contains a dimerization domain that interacts with the kinase domain and is required for tRNA binding and kinase activation. EMBO J 20: 1425–1438. 11250908

19. Murphy JM, Zhang Q, Young SN, Reese ML, Bailey FP, et al. (2014) A robust methodology to subclassify pseudokinases based on their nucleotide-binding properties. Biochem J 457: 323–334. doi: 10.1042/BJ20131174 24107129

20. Wek RC, Ramirez M, Jackson BM, Hinnebusch AG (1990) Identification of positive-acting domains in GCN2 protein kinase required for translational activation of GCN4 expression. Mol Cell Biol 10: 2820–2831. 2188100

21. Lageix S, Rothenburg S, Dever TE, Hinnebusch AG (2014) Enhanced interaction between pseudokinase and kinase domains in Gcn2 stimulates eIF2alpha phosphorylation in starved cells. PLoS Genet 10: e1004326. doi: 10.1371/journal.pgen.1004326 24811037

22. Dey M, Cao C, Sicheri F, Dever TE (2007) Conserved intermolecular salt-bridge required for activation of protein kinases PKR, GCN2 and PERK. J Biol Chem 282: 6650–6660.

23. Dar AC, Dever TE, Sicheri F (2005) Higher-order substrate recognition of eIF2alpha by the RNA-dependent protein kinase PKR. Cell 122: 887–900. 16179258

24. Qiu H, Garcia-Barrio MT, Hinnebusch AG (1998) Dimerization by translation initiation factor 2 kinase GCN2 is mediated by interactions in the C-terminal ribosome-binding region and the protein kinase domain. Mol Cell Biol 18: 2697–2711. 9566889

25. Narasimhan J, Staschke KA, Wek RC (2004) Dimerization is required for activation of eIF2 kinase Gcn2 in response to diverse environmental stress conditions. J Biol Chem 279: 22820–22832. 15010461

26. He H, Singh I, Wek SA, Dey S, Baird TD, et al. (2014) Crystal structures of GCN2 protein kinase C-terminal domains suggest regulatory differences in yeast and mammals. J Biol Chem 289: 15023–15034. doi: 10.1074/jbc.M114.560789 24719324

27. Ramirez M, Wek RC, Hinnebusch AG (1991) Ribosome-association of GCN2 protein kinase, a translational activator of the GCN4 gene of Saccharomyces cerevisae. Mol Cell Biol 11: 3027–3036. 2038314

28. Zhu S, Wek RC (1998) Ribosome-binding domain of eukaryotic initiation factor-2 kinase GCN2 facilitates translation control. J Biol Chem 273: 1808–1814. 9430731

29. Marton MJ, Vasquez de Aldana CR, Qiu H, Charkraburtty K, Hinnebusch AG (1997) Evidence that GCN1 and GCN20, translational regulators of GCN4, function on enlongating ribosomes in activation of the eIF2α kinase GCN2. Mol Cell Biol 17: 4474–4489. 9234705

30. Vazquez de Aldana CR, Marton MJ, Hinnebusch AG (1995) GCN20, a novel ATP binding cassette protein, and GCN1 reside in a complex that mediates activation of the eIF-2α kinase GCN2 in amino acid-starved cells. EMBO J 14: 3184–3199. 7621831

31. Garcia-Barrio M, Dong J, Ufano S, Hinnebusch AG (2000) Association of GCN1/GCN20 regulatory complex with the conserved N-terminal domain of eIF2α kinase GCN2 is required for GCN2 activation in vivo. EMBO J 19: 1887–1899. 10775272

32. Sattlegger E, Hinnebusch AG (2005) Polyribosome binding by GCN1 is required for full activation of eukaryotic translation initiation factor 2{alpha} kinase GCN2 during amino acid starvation. J Biol Chem 280: 16514–16521. 15722345

33. Sattlegger E, Hinnebusch AG (2000) Separate domains in GCN1 for binding protein kinase GCN2 and ribosomes are required for GCN2 activation in amino acid-starved cells. EMBO J 19: 6622–6633. 11101534

34. Visweswaraiah J, Lageix S, Castilho BA, Izotova L, Kinzy TG, et al. (2011) Evidence that eukaryotic translation elongation factor 1A (eEF1A) binds the Gcn2 protein C terminus and inhibits Gcn2 activity. J Biol Chem 286: 36568–36579. doi: 10.1074/jbc.M111.248898 21849502

35. Jimenez-Diaz A, Remacha M, Ballesta JP, Berlanga JJ (2013) Phosphorylation of initiation factor eIF2 in response to stress conditions is mediated by acidic ribosomal P1/P2 proteins in Saccharomyces cerevisiae. PLoS One 8: e84219. doi: 10.1371/journal.pone.0084219 24391917

36. Visweswaraiah J, Lee SJ, Hinnebusch AG, Sattlegger E (2012) Overexpression of eukaryotic translation elongation factor 3 impairs Gcn2 protein activation. J Biol Chem 287: 37757–37768. doi: 10.1074/jbc.M112.368266 22888004

37. Ramirez M, Wek RC, Vazquez de Aldana CR, Jackson BM, Freeman B, et al. (1992) Mutations activating the yeast eIF-2α kinase GCN2: Isolation of alleles altering the domain related to histidyl-tRNA synthetases. Mol Cell Biol 12: 5801–5815. 1448107

38. Jia MH, Larossa RA, Lee JM, Rafalski A, Derose E, et al. (2000) Global expression profiling of yeast treated with an inhibitor of amino acid biosynthesis, sulfometuron methyl. Physiol Genomics 3: 83–92. 11015603

39. Acker MG, Kolitz SE, Mitchell SF, Nanda JS, Lorsch JR (2007) Reconstitution of yeast translation initiation. Methods Enzymol 430: 111–145. 17913637

40. Francklyn C, Arnez J (2005) Histidyl-tRNA Synthetases. In: Ibba M, Francklyn C, Cusack S, editors. Aminoacyl-tRNA Synthetases. Austin, TX: Landes Publishing. pp. 135–148.

41. Merritt EA, Arakaki TL, Gillespie JR, Larson ET, Kelley A, et al. (2010) Crystal structures of trypanosomal histidyl-tRNA synthetase illuminate differences between eukaryotic and prokaryotic homologs. J Mol Biol 397: 481–494. doi: 10.1016/j.jmb.2010.01.051 20132829

42. Bovee ML, Yan W, Sproat BS, Francklyn CS (1999) tRNA discrimination at the binding step by a class II aminoacyl-tRNA synthetase. Biochemistry 38: 13725–13735. 10521280

43. Champagne KS, Sissler M, Larrabee Y, Doublie S, Francklyn CS (2005) Activation of the hetero-octameric ATP phosphoribosyl transferase through subunit interface rearrangement by a tRNA synthetase paralog. J Biol Chem 280: 34096–34104. 16051603

44. Landau M, Mayrose I, Rosenberg Y, Glaser F, Martz E, et al. (2005) ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res 33: W299–302. 15980475

45. DeLano WL (2002) The PyMOL Molecular Graphics System. Palo Alto, CA.

46. Moehle CM, Hinnebusch AG (1991) Association of RAP1 binding sites with stringent control of ribosomal protein gene transcription in Saccharomyces cerevisiae. Mol Cell Biol 11: 2723–2735. 2017175

47. Reid GA, Schatz G (1982) Import of proteins into mitochondria. Yeast cells grown in the presence of carbonyl cyanide m-chlorophenylhydrazone accumulate massive amounts of some mitochondrial precursor polypeptides. J Biol Chem 257: 13056–13061. 6290491

48. Cigan AM, Pabich EK, Feng L, Donahue TF (1989) Yeast translation initiation suppressor sui2 encodes the α subunit of eukaryotic initiation factor 2 and shares identity with the human α subunit. Proc Natl Acad Sci USA 86: 2784–2788. 2649894

49. Romano PR, Garcia-Barrio MT, Zhang X, Wang Q, Taylor DR, et al. (1998) Autophosphorylation in the activation loop is required for full kinase activity in vivo of human and yeast eukaryotic initiation factor 2α kinases PKR and GCN2. Mol Cell Biol 18: 2282–2297. 9528799

50. Bardwell L, Cooper AJ, Friedberg EC (1992) Stable and specific association between the yeast recombination and DNA repair proteins RAD1 and RAD10 in vitro. Mol Cell Biol 12: 3041–3049. 1620114

51. Arnez JG, Augustine JG, Moras D, Francklyn CS (1997) The first step of aminoacylation at the atomic level in histidyl-tRNA synthetase. Proc Natl Acad Sci U S A 94: 7144–7149. 9207058

52. Golemis EA, Gyuris J, Brent R (1996) Interaction trap/two-hybrid system to identify interacting proteins. In: Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG et al., editors. Current Protocols in Molecular Biology. New York: John Wiley. pp. 20.21.21–20.21.28.