Analysing GCN4 translational control in yeast by stochastic chemical kinetics modelling and simulation

BMC Systems Biology

Volumn 5, Issue , 2011, Pages

  You, Tao ^a,c   Stansfield, Ian ^b   Romano, M Carmen ^a,b   Brown, Alistair J P ^b   Coghill, George M ^a  

^a UNIVERSITY OF ABERDEEN   (United Kingdom)

^b UNIVERSITY OF ABERDEEN   (United Kingdom)

^c ASTRAZENECA   (United Kingdom)

Author keywords

GCN4; Gillespie algorithm; mRNA translation; Stochastic model

Indexed keywords

SACCHAROMYCES CEREVISIAE;

AMINO ACID; BASIC LEUCINE ZIPPER TRANSCRIPTION FACTOR; GCN4 PROTEIN, S CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; KINETICS; METABOLISM; PHYSIOLOGY; PROTEIN SYNTHESIS; SACCHAROMYCES CEREVISIAE; STATISTICS;

AMINO ACIDS; BASIC-LEUCINE ZIPPER TRANSCRIPTION FACTORS; COMPUTER SIMULATION; GENE EXPRESSION REGULATION, FUNGAL; KINETICS; MODELS, BIOLOGICAL; PROTEIN BIOSYNTHESIS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; STOCHASTIC PROCESSES;

EID: 80051783478     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-131     Document Type: Article

References (31)

1. Natarajan K, Meyer MR, Jackson BM, Slade D, Roberts C, et al. Transcriptional profiling shows that Gcn4p is a master regulator of gene expression during amino acid starvation in yeast. Mol Cell Biol 2001, 21(13):4347-4368. 10.1128/MCB.21.13.4347-4368.2001, 87095, 11390663.
2. Hinnebusch AG. Translational regulation of GCN4 and the general amino acid control of yeast. Annu Rev Microbiol 2005, 59:407-450. 10.1146/annurev.micro.59.031805.133833, 16153175.
3. Szamecz B, Rutkai E, Cuchalová L, Munzarová V, Herrmannová A, et al. eIF3a cooperates with sequences 5' of uORF1 to promote resumption of scanning by post-termination ribosomes for reinitiation on GCN4 mRNA. Genes Dev 2008, 22:2414-2425. 10.1101/gad.480508, 2532924, 18765792.
4. Grant CM, Miller PF, Hinnebusch AG. Requirements for intercistronic distance and level of eukaryotic initiation factor 2 activity in reinitiation on GCN4 mRNA vary with the downstream cistron. Mol Cell Biol 1994, 14(4):2616-2628. 358629, 8139562.
5. You T, Coghill GM, Brown AJP. A quantitative model for the translational control of GCN4 in yeast. 2nd Foundations of Systems Biology in Engineering Conference Proceedings (Stuttgart) 2007, 121-126.
6. Berthelot K, Muldoon M, Rajkowitsch L, Hughes J, McCarthy JE. Dynamics and processivity of 40s ribosome scanning on mrna in yeast. Mol Microbiol 2005, 51(4):987-1002.
7. Kozak M. Regulation of translation via mRNA structure in prokaryotes and eukaryotes. Gene 2005, 361:13-37.
8. Kozak M. Pushing the limits of the scanning mechanism for initiation of translation. Gene 2002, 299:1-34. 10.1016/S0378-1119(02)01056-9, 12459250.
9. Passmore LA, Schmeing TM, Maag D, Applefield DJ, Acker MG, et al. The eukaryotic translation initiation factors eIF1 and eIF1A induce an open conformation of the 40S ribosome. Mol Cell 2007, 26(1):41-50. 10.1016/j.molcel.2007.03.018, 17434125.
10. Gillespie DT. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J Comp Phys 1976, 22(4):403-434.
11. Runarsson TP, Yao X. Search biases in constrained evolutionary optimization. IEEE T Syst Man Cy C 2005, 35(2):233-243.
12. Arava Y, Boas FE, Brown PO, Herschlag D. Dissecting eukaryotic translation and its control by ribosome density mapping. Nucleic Acids Res 2005, 33(8):2421-2432. 10.1093/nar/gki331, 1087779, 15860778.
13. Bergmann JE, Lodish HF. A kinetic model of protein synthesis. Application to hemoglobin synthesis and translational control. J Biol Chem 1979, 254(23):11927-11937.
14. Wang Y, Liu CL, Storey JD, Tibshirani RJ, Herschlag D, et al. Precision and functional specificity in mRNA decay. Proc Natl Acad Sci USA 2002, 99(9):5860-5865. 10.1073/pnas.092538799, 122867, 11972065.
15. Gilchrist MA, Wagner A. A model of protein translation including codon bias, nonsense errors, and ribosome recycling. J Theor Biol 2006, 239(4):417-434. 10.1016/j.jtbi.2005.08.007, 16171830.
16. Algire MA, Maag D, Savio P, Acker MG, Tarun SZ, et al. Development and characterization of a reconstituted yeast translation initiation system. RNA 2002, 8(3):382-397. 10.1017/S1355838202029527, 1370259, 12008673.
17. Zaman S, Lippman SI, Zhao X, Broach JR. How Saccharomyces Responds to Nutrients. Annu Rev Genet 2008, (42):2.1-2.55.
18. Derrida B, Domany E, Mukamel D. An exact solution of a one-dimensional asymmetric exclusion model with open boundaries. J Stat Phys 1992, 69(3/4):667-687.
19. Romano MC, Thiel M, Stansfield I, Grebogi C. Queueing phase transition: theory of translation. Phys Rev Lett 2009, 102(19):198104.
20. Hoyle NP, Castelli LM, Campbell SG, Holmes LE, Ashe MP. Stressdependent relocalization of translationally primed mRNPs to cytoplasmic granules that are kinetically and spatially distinct from P-bodies. J Cell Biol 2007, 179(1):65-74. 10.1083/jcb.200707010, 2064737, 17908917.
21. Dever TE, Yang W, Aström S, Byström AS, Hinnebusch AG. Modulation of tRNA(iMet), eIF-2, and eIF-2B expression shows that GCN4 translation is inversely coupled to the level of eIF-2.GTP.Met-tRNA(iMet) ternary complexes. Mol Cell Biol 1995, 15(11):6351-6363. 230887, 7565788.
22. Olsen DS, Savner EM, Mathew A, Zhang F, Krishnamoorthy T, et al. Domains of eIF1A that mediate binding to eIF2, eIF3 and eIF5B and promote ternary complex recruitment in vivo. EMBO J 2003, 22:193-204. 10.1093/emboj/cdg030, 140105, 12514125.
23. Asano K, Clayton J, Shalev A, Hinnebusch AG. A multifactor complex of eukaryotic initiation factors, eIF1, eIF2, eIF3, eIF5, and initiator tRNA(Met) is an important translation initiation intermediate in vivo. Genes Dev 2000, 14(19):2534-2546. 10.1101/gad.831800, 316978, 11018020.
24. Singh CR, Udagawa T, Lee B, Wassink S, He H, et al. Change in nutritional status modulates the abundance of critical pre-initiation intermediate complexes during translation initiation in vivo. J Mol Biol 2007, 370(2):315-330. 10.1016/j.jmb.2007.04.034, 2041914, 17512538.
25. You T, Coghill GM, Brown AJP. A quantitative model for mRNA translation in Saccharomyces cerevisiae. Yeast 2010, 27:785-800. 10.1002/yea.1770, 20306461.
26. Watanabe R, Murai MJ, Singh CR, Fox S, Ii M, et al. The eukaryotic initiation factor (eIF) 4G HEAT domain promotes translation re-initiation in yeast both dependent on and independent of eIF4A mRNA helicase. J Biol Chem 2010, 285(29):21922-21933. 10.1074/jbc.M110.132027, 2903371, 20463023.
27. Udagawa T, Nemoto N, Wilkinson CR, Narashimhan J, Jiang L, Watt S, Zook A, Jones N, Wek RC, Bähler J, Asano K. Int6/eIF3e promotes general translation and Atf1 abundance to modulate Sty1 MAPK-dependent stress response in fission yeast. J Biol Chem 2008, 283(32):22063-22075. 10.1074/jbc.M710017200, 2494926, 18502752.
28. Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 2009, 324(5924):218-223. 10.1126/science.1168978, 2746483, 19213877.
29. Vilela C, Linz B, Rodrigues-Pousada C, McCarthy JEG. The yeast transcription factor genes YAP1 and YAP2 are subject to differential control at the levels of both translation and mRNA stability. Nucleic Acids Research 1998, 26(5):1150-1159. 10.1093/nar/26.5.1150, 147385, 9469820.
30. Gaba A, Wang Z, Krishnamoorthy T, Hinnebusch AG, Sachs MS. Physical evidence for distinct mechanisms of translational control by upstream open reading frames. EMBO Journal 2001, 20(22):6453-6463. 10.1093/emboj/20.22.6453, 125715, 11707416.
31. Palam LR, Baird TD, Wek RC. Phosphorylation of eIF2 facilitates ribosomal bypass of an inhibitory upstream ORF to enhance CHOP translation. J Biol Chem 2011, 286(13):10939-10949. 10.1074/jbc.M110.216093, 21285359.