Qualitative modelling and formal verification of the FLR1 gene mancozeb response in Saccharomyces cerevisiae

IET Systems Biology

Volumn 5, Issue 5, 2011, Pages 308-316

  Monteiro, P T ^a,b   Dias, P J ^c,d   Ropers, D ^b   Oliveira, A L ^a   Sa Correia I ^c,d   Teixeira, M C ^c,d   Freitas, A T ^a  

^a INESC ID   (Portugal)

^b INRIA RHÔNE ALPES   (France)

^c INSTITUTO SUPERIOR TÉCNICO   (Portugal)

^d Instituto de Biotecnologia e Bioengenharia Lisboa   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTABLE MODELS; DYNAMICAL PROPERTIES; EXPERIMENTAL DATA; EXPERIMENTAL VALIDATIONS; FORMAL VERIFICATION METHODS; FORMAL VERIFICATIONS; GENE DELETION; GENE REGULATORY NETWORKS; GENE RESPONSE; MANCOZEB; MODEL PREDICTION; MODEL ROBUSTNESS; MULTIDRUG RESISTANCE; QUALITATIVE MODEL; QUALITATIVE MODELLING; TEST OF HYPOTHESIS; TRANSCRIPTIONAL ACTIVATIONS; TRANSCRIPTIONAL REGULATORY NETWORKS;

ACTIVATION ANALYSIS; FORECASTING; GENES; MODEL CHECKING; TRANSCRIPTION; TRANSCRIPTION FACTORS; YEAST;

COMPUTER SIMULATION;

FLR1 PROTEIN, S CEREVISIAE; FUNGICIDE; MANCOZEB; MANEB; ORGANIC ANION TRANSPORTER; SACCHAROMYCES CEREVISIAE PROTEIN; TRANSCRIPTION FACTOR; YAP1 PROTEIN, S CEREVISIAE; ZINEB;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; METABOLISM; METHODOLOGY; SACCHAROMYCES CEREVISIAE; STATISTICAL MODEL; SYSTEMS BIOLOGY; THEORETICAL MODEL; TRANSCRIPTION INITIATION;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; FUNGICIDES, INDUSTRIAL; GENE EXPRESSION REGULATION, FUNGAL; GENE REGULATORY NETWORKS; MANEB; MODELS, BIOLOGICAL; MODELS, STATISTICAL; MODELS, THEORETICAL; ORGANIC ANION TRANSPORTERS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SYSTEMS BIOLOGY; TRANSCRIPTION FACTORS; TRANSCRIPTIONAL ACTIVATION; ZINEB;

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 80054711652     PISSN: 17518849     EISSN: None     Source Type: Journal    
DOI: 10.1049/iet-syb.2011.0001     Document Type: Article

References (36)

1. Gilbert, D., Heiner, M., and Lehrack, S.: 'A unifying framework for modelling and analysing biochemical pathways using Petri nets', (LNBI, 4695), Proc. Fifth Conf. Computational Methods in Systems Biology (CMSB 2007), p. 200-216
2. Antoniotti, M., Policriti, A., Ugel, N., and Mishra, B.: 'Model building and model checking for biochemical processes', Cell Biochem. Biophys., 2003, 38, (3), p. 271-28610.1385/CBB:38:3:271
3. Batt, G., Ropers, D., and de Jong, H.: et al. 'Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli', Bioinformatics, 2005, 21, (Suppl. 1), p. i19-i2810.1093/bioinformatics/bti1048
4. Batt, G., Yordanov, B., Belta, C., and Weiss, R.: 'Robustness analysis and tuning of synthetic gene networks', Bioinformatics, 2007, 23, (18), p. 2415-242210.1093/bioinformatics/btm362
5. Bernot, G., Comet, J.P., Richard, A., and Guespin, J.: 'Application of formal methods to biological regulatory networks: extending Thomas' asynchronous logical approach with temporal logic', J. Theor. Biol., 2004, 229, (3), p. 339-34810.1016/j.jtbi.2004.04.003
6. Calder, M., Vyshemirsky, V., Gilbert, D., and Orton, R.: 'Analysis of signalling pathways using the PRISM model checker', Proc. Third Conf. Computational Methods in Systems Biology (CMSB 2005), 2005), p. 79-90
7. Chabrier-Rivier, N., Chiaverini, M., Danos, V., Fages, F., and Schächter, V.: 'Modeling and querying biomolecular interaction networks', Theor. Comput. Sci., 2004, 325, p. 25-4410.1016/j.tcs.2004.03.063 0304-3975
8. Fisher, J., Piterman, N., Hajnal, A., and Henzinger, T.: 'Predictive modeling of signaling crosstalk during C. elegans vulval development', PLoS Comput. Biol., 2007, 3, (5), p. p. e9210.1371/journal.pcbi.0030092
9. Shen, X., Collier, J., Dill, D., Shapiro, L., Horowitz, M., and Mcadams, H.: 'Architecture and inherent robustness of a bacterial cell-cycle control system', Proc. Natl. Acad. Sci. USA, 2008, 105, (32), p. 11340-1134510.1073/pnas.0805258105 0027-8424
10. Thomas, R.: 'Logical analysis of systems comprising feedback loops', J. Theor. Biol., 1978, 73, p. 631-65610.1016/0022-5193(78)90127-3
11. Li, F., Long, T., Lu, Y., Ouyang, Q., and Tang, C.: 'The yeast cell-cycle network is robustly designed', Proc. Natl. Acad. Sci. USA, 2004, 101, (14), p. 4781-478610.1073/pnas.0305937101 0027-8424
12. Shmulevich, I., Dougherty, E., Kim, S., and Zhang, W.: 'Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks', Bioinformatics, 2002, 18, (2), p. 261-27410.1093/bioinformatics/18.2.261
13. Koch, I., Junker, B., and Heiner, M.: 'Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber', Bioinformatics, 2005, 21, (7), p. 1219-122610.1093/bioinformatics/bti145
14. Chaouiya, C., Remy, E., and Thieffry, D.: 'Qualitative Petri net modelling of genetic networks', Istrail, S., Pevzner, P., Waterman, M., Transactions on computational systems biology VI (LNCS, 4220), (Springer, Berlin 2006), p. 95-112
15. Teixeira, M., Dias, P., Simoes, T., and Sá-Correia, I.: 'Yeast adaptation to mancozeb involves the up-regulation of FLR1 under the coordinate control of Yap1, Rpn4, Pdr3, and Yrr1', Biochem. Biophys. Res. Commun., 2008, 367, (2), p. 249-25510.1016/j.bbrc.2007.12.056
16. Brôco, N., Tenreiro, S., Viegas, C., and Sá-Correia, I.: 'FLR1 gene (ORF YBR008c) is required for benomyl and methotrexate resistance in Saccharomyces cerevisiae and its benomyl-induced expression is dependent on Pdr3 transcriptional regulator', Yeast, 1999, 15, p. 1595-160810.1002/(SICI)1097-0061(199911)15:15<1595::AID-YEA484>3.0.CO;2-6
17. Nguyen, D., Alarco, A., and Raymond, M.: 'Multiple Yap1p-binding sites mediate induction of the yeast major facilitator FLR1 gene in response to drugs, oxidants, and alkylating agents', J. Biol. Chem., 2001, 276, p. 1138-114510.1074/jbc.M008377200
18. Tenreiro, S., Fernandes, A., and Sá-Correia, I.: 'Transcriptional activation of FLR1 gene during Saccharomyces cerevisiae adaptation to growth with benomyl: role of Yap1p and Pdr3p', Biochem. Biophys. Res. Commun., 2001, 280, p. 216-22210.1006/bbrc.2000.4100
19. Cabrito, T., Teixeira, M., and Sá-Correia, I.: 'Global adaptive response and resistance to agricultural fungicides: lessons from yeast and phytopathogenic fungi', Costa, P.D., Bezerra, P., Fungicides: chemistry, environmental impact and health effects, (Nova Science Publishers, New York, USA 2009), p. 228-253
20. Teixeira, M., Dias, P., and Monteiro, P.: et al. 'Refining current knowledge on the yeast FLR1 regulatory network by combined experimental and computational approaches', Mol. Biosyst., 2010, 6, (12), p. 2471-248110.1039/c004881j
21. Lucau-Danila, A., Lelandais, G., and Kozovska, Z.: et al. 'Early expression of yeast genes affected by chemical stress', Mol. Cell. Biol., 2005, 25, (5), p. 1860-186810.1128/MCB.25.5.1860-1868.2005
22. Le Crom, S., Devaux, F., Marc, P., Zhang, X., Moye-Rowley, W., and Jacq, C.: 'New insights into the pleiotropic drug resistance network from genome-wide characterization of the YRR1 transcription factor regulation system', Mol. Cell. Biol., 2002, 22, (8), p. 2642-264910.1128/MCB.22.8.2642-2649.2002
23. Fisher, J., and Henzinger, T.: 'Executable cell biology', Nat. Biotechnol., 2007, 25, (11), p. 1239-125010.1038/nbt1356
24. Clarke, E., Grumberg, O., and Peled, D.: 'Model checking', (MIT Press 2000)
25. Monteiro, P., Dumas, E., and Besson, B.: et al. 'A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks', BMC Bioinformatics, 2009, 10, p. 45010.1186/1471-2105-10-450
26. de Jong, H., Geiselmann, J., Hernandez, C., and Page, M.: 'Genetic network analyzer: qualitative simulation of genetic regulatory networks', Bioinformatics, 2003, 19, (3), p. 336-34410.1093/bioinformatics/btf851
27. Glass, L., and Kauffman, S.: 'The logical analysis of continuous non-linear biochemical control networks', J. Theor. Biol., 1973, 39, p. 103-12910.1016/0022-5193(73)90208-7
28. Chaves, M., Sontag, E., and Albert, R.: 'Methods of robustness analysis for Boolean models of gene control networks', Syst. Biol. (Stevenage), 2006, 153, (4), p. 154-16710.1049/ip-syb:20050079
29. Ropers, D., Baldazzi, V., and de Jong, H.: 'Model reduction using piecewise-linear approximations preserves dynamic properties of the carbon starvation response in Escherichia coli', IEEE/ACM Trans. Comput. Biol. Bioinform., 2011, 8, p. 166-18110.1109/TCBB.2009.49
30. Cantone, I., Marucci, L., and Iorio, F.: et al. 'A yeast synthetic network for in vivo assessment of reverse-engineering and modeling approaches', Cell, 2009, 137, p. 172-18110.1016/j.cell.2009.01.055
31. Azevedo, D., Tacnet, F., Delaunay, A., Rodrigues-Pousada, C., and Toledano, M.: 'Two redox centers within Yap1 for H2O2 and thiol-reactive chemicals signaling', Free Radic. Biol. Med., 2003, 35, (8), p. 889-90010.1016/S0891-5849(03)00434-9
32. Locke, J., Southern, M., and Kozma-Bognár, L.: et al. 'Extension of a genetic network model by iterative experimentation and mathematical analysis', Mol. Syst. Biol., 2005, 1, p. 2005.001310.1038/msb4100018
33. Rubinstein, A., Gurevich, V., Kasulin-Boneh, Z., Pnueli, L., Kassir, Y., and Pinter, R.Y.: 'Faithful modeling of transient expression and its application to elucidating negative feedback regulation', Proc. Natl. Acad. Sci. USA, 2007, 104, (15), p. 6241-624610.1073/pnas.0611168104 0027-8424
34. Drulhe, S.: 'Identification of genetic regulatory networks from gene expression data: an approach based on piecewise-affine models', 2008, PhD, Université Joseph Fourier - Grenoble I
35. de Jong, H., and Page, M.: 'Search for steady states of piecewise-linear differential equation models of genetic regulatory networks', ACM/IEEE Trans. Comput. Biol. Bioinform., 2008, 5, (2), p. 508-52210.1109/TCBB.2007.70254
36. Monteiro, P., Ropers, D., Mateescu, R., Freitas, A., and de Jong, H.: 'Temporal logic patterns for querying dynamic models of cellular interaction networks', Bioinformatics, 2008, 24, (16), p. i227-i23310.1093/bioinformatics/btn275