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

BMC Systems Biology

George M Coghill³  Alistair JP Brown¹  M Carmen Romano¹  Ian Stansfield¹  Tao You² 

[1] School of Medical Sciences, University of Aberdeen, Institute of Medical Sciences, Aberdeen, UK;AstraZeneca, Mereside, Alderley Park, Macclesfield, UK;School of Natural and Computing Sciences, University of Aberdeen, Computing Science Department, Aberdeen, UK

关键词: stochastic model;    Gillespie algorithm;    GCN4;    mRNA translation;   

Others  :  1160437
DOI  :  10.1186/1752-0509-5-131

 received in 2011-03-25, accepted in 2011-08-18,  发布年份 2011

【 摘 要 】

Background

The yeast Saccharomyces cerevisiae responds to amino acid starvation by inducing the transcription factor Gcn4. This is mainly mediated via a translational control mechanism dependent upon the translation initiation eIF2·GTP·Met-tRNA_i^Met ternary complex, and the four short upstream open reading frames (uORFs) in its 5' mRNA leader. These uORFs act to attenuate GCN4 mRNA translation under normal conditions. During amino acid starvation, levels of ternary complex are reduced. This overcomes the GCN4 translation attenuation effect via a scanning/reinitiation control mechanism dependent upon uORF spacing.

Results

Using published experimental data, we have developed and validated a probabilistic formulation of GCN4 translation using the Chemical Master Equation (Model 1). Model 1 explains GCN4 translation's nonlinear dependency upon uORF placements, and predicts that an as yet unidentified factor, which was proposed to regulate GCN4 translation under some conditions, only has pronounced effects upon GCN4 translation when intercistronic distances are unnaturally short. A simpler Model 2 that does not include this unidentified factor could well represent the regulation of a natural GCN4 mRNA. Using parameter values optimised for this algebraic Model 2, we performed stochastic simulations by Gillespie algorithm to investigate the distribution of ribosomes in different sections of GCN4 mRNA under distinct conditions. Our simulations demonstrated that ribosomal loading in the 5'-untranslated region is mainly determined by the ratio between the rates of 5'-initiation and ribosome scanning, but was not significantly affected by rate of ternary complex binding. Importantly, the translation rate for codons starved of cognate tRNAs is predicted to be the most significant contributor to the changes in ribosomal loading in the coding region under repressing and derepressing conditions.

Conclusions

Our integrated probabilistic Models 1 and 2 explained GCN4 translation and helped to elucidate the role of a yet unidentified factor. The ensuing stochastic simulations evaluated different factors that may impact on the translation of GCN4 mRNA, and integrated translation status with ribosomal density.

【 授权许可】

   
2011 You et al; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [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.
• [2]Hinnebusch AG: Translational regulation of GCN4 and the general amino acid control of yeast. Annu Rev Microbiol 2005, 59:407-450.
• [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.
• [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.
• [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.
• [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]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.
• [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.
• [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.
• [16]Algire MA, Maag D, Savio P, Acker MG, Tarun SZ Jr, et al.: Development and characterization of a reconstituted yeast translation initiation system. RNA 2002, 8(3):382-397.
• [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.
• [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.
• [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.
• [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.
• [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.
• [25]You T, Coghill GM, Brown AJP: A quantitative model for mRNA translation in Saccharomyces cerevisiae. Yeast 2010, 27:785-800.
• [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.
• [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.
• [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.
• [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.
• [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.
• [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.