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Using Computational Modeling and Experimental Synthetic Perturbations to Probe Biological Circuits

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Computational Methods in Synthetic Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1244))

Abstract

This chapter describes approaches for using computational modeling of synthetic biology perturbations to analyze endogenous biological circuits, with a particular focus on signaling and metabolic pathways. We describe a bottom-up approach in which ordinary differential equations are constructed to model the core interactions of a pathway of interest. We then discuss methods for modeling synthetic perturbations that can be used to investigate properties of the natural circuit. Keeping in mind the importance of the interplay between modeling and experimentation, we next describe experimental methods for constructing synthetic perturbations to test the computational predictions. Finally, we present a case study of the p53 tumor-suppressor pathway, illustrating the process of modeling the core network, designing informative synthetic perturbations in silico, and testing the predictions in vivo.

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References

  1. Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403(6767):335–338. doi:10.1038/35002125

    Article  CAS  PubMed  Google Scholar 

  2. Benenson Y (2012) Biomolecular computing systems: principles, progress and potential. Nat Rev Genet 13(7):455–468. doi:10.1038/nrg3197

    Article  CAS  PubMed  Google Scholar 

  3. Atkinson MR, Savageau MA, Myers JT, Ninfa AJ (2003) Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 113(5):597–607. doi:10.1016/S0092-8674(03)00346-5

    Article  CAS  PubMed  Google Scholar 

  4. Stricker J, Cookson S, Bennett MR, Mather WH, Tsimring LS, Hasty J (2008) A fast, robust and tunable synthetic gene oscillator. Nature 456(7221):516–519. doi:10.1038/nature07389

    Article  CAS  PubMed  Google Scholar 

  5. Nguyen QT, Merlo ME, Medema MH, Jankevics A, Breitling R, Takano E (2012) Metabolomics methods for the synthetic biology of secondary metabolism. FEBS Lett 586(15):2177–2183. doi:10.1016/j.febslet.2012.02.008

    Article  CAS  PubMed  Google Scholar 

  6. Keasling JD (2012) Synthetic biology and the development of tools for metabolic engineering. Metab Eng 14(3):189–195. doi:10.1016/j.ymben.2012.01.004

    Article  CAS  PubMed  Google Scholar 

  7. Lee WP, Tzou WS (2009) Computational methods for discovering gene networks from expression data. Brief Bioinform 10(4):408–423. doi:10.1093/bib/bbp028

    CAS  PubMed  Google Scholar 

  8. Chen WW, Niepel M, Sorger PK (2010) Classic and contemporary approaches to modeling biochemical reactions. Genes Dev 24(17):1861–1875. doi:10.1101/gad.1945410

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  9. Mallavarapu A, Thomson M, Ullian B, Gunawardena J (2009) Programming with models: modularity and abstraction provide powerful capabilities for systems biology. J R Soc Interface 6(32):257–270. doi:10.1098/rsif.2008.0205

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  10. Hlavacek WS, Faeder JR, Blinov ML, Posner RG, Hucka M, Fontana W (2006) Rules for modeling signal-transduction systems. Sci STKE 2006 (344):re6. doi:10.1126/stke.3442006re6

  11. Danos V, Feret J, Fontana W, Harmer R, Krivine J (2008) Rule-based modeling, symmetries, refinements. In: Formal methods in systems biology, vol 5054, Lecture notes in bioinformatics 2008. Springer, Berlin, pp 103–122

    Chapter  Google Scholar 

  12. Meier-Schellersheim M, Xu X, Angermann B, Kunkel EJ, Jin T, Germain RN (2006) Key role of local regulation in chemosensing revealed by a new molecular interaction-based modeling method. PLoS Comput Biol 2(7):e82. doi:10.1371/journal.pcbi.0020082

    Article  PubMed Central  PubMed  Google Scholar 

  13. Lopez CF, Muhlich JL, Bachman JA, Sorger PK (2013) Programming biological models in Python using PySB. Mol Syst Biol 9:646. doi:10.1038/msb.2013.1

    Article  PubMed Central  PubMed  Google Scholar 

  14. Alon U (2007) Network motifs: theory and experimental approaches. Nat Rev Genet 8(6):450–461. doi:10.1038/nrg2102

    Article  CAS  PubMed  Google Scholar 

  15. Murphy KC (2012) Phage recombinases and their applications. Adv Virus Res 83:367–414. doi:10.1016/B978-0-12-394438-2.00008-6

    Article  CAS  PubMed  Google Scholar 

  16. Turan S, Zehe C, Kuehle J, Qiao J, Bode J (2012) Recombinase-mediated cassette exchange (RMCE)—a rapidly-expanding toolbox for targeted genomic modifications. Gene 515(1):1–27. doi:10.1016/j.gene.2012.11.016

    Article  PubMed  Google Scholar 

  17. Gaj T, Gersbach CA, Barbas CF 3rd (2013) ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 31(7):397–405. doi:10.1016/j.tibtech.2013.04.004

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  18. Terpe K (2006) Overview of bacterial expression systems for heterologous protein production: from molecular and biochemical fundamentals to commercial systems. Appl Microbiol Biotechnol 72(2):211–222. doi:10.1007/s00253-006-0465-8

    Article  CAS  PubMed  Google Scholar 

  19. Maya D, Quintero MJ, de la Cruz Munoz-Centeno M, Chavez S (2008) Systems for applied gene control in Saccharomyces cerevisiae. Biotechnol Lett 30(6):979–987. doi:10.1007/s10529-008-9647-z

    Article  CAS  PubMed  Google Scholar 

  20. Gossen M, Bujard H (1992) Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. Proc Natl Acad Sci U S A 89(12):5547–5551

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  21. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391(6669):806–811. doi:10.1038/35888

    Article  CAS  PubMed  Google Scholar 

  22. Rogers S, Wells R, Rechsteiner M (1986) Amino acid sequences common to rapidly degraded proteins: the PEST hypothesis. Science 234(4774):364–368

    Article  CAS  PubMed  Google Scholar 

  23. Grilly C, Stricker J, Pang WL, Bennett MR, Hasty J (2007) A synthetic gene network for tuning protein degradation in Saccharomyces cerevisiae. Mol Syst Biol 3:127. doi:10.1038/msb4100168

    Article  PubMed Central  PubMed  Google Scholar 

  24. Bashor CJ, Helman NC, Yan S, Lim WA (2008) Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics. Science 319(5869):1539–1543. doi:10.1126/science.1151153

    Article  CAS  PubMed  Google Scholar 

  25. Szobota S, McKenzie C, Janovjak H (2013) Optical control of ligand-gated ion channels. Methods Mol Biol 998:417–435. doi:10.1007/978-1-62703-351-0_32

    Article  CAS  PubMed  Google Scholar 

  26. Wu YI, Frey D, Lungu OI, Jaehrig A, Schlichting I, Kuhlman B, Hahn KM (2009) A genetically encoded photoactivatable Rac controls the motility of living cells. Nature 461(7260):104–108. doi:10.1038/nature08241

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  27. Riley T, Sontag E, Chen P, Levine A (2008) Transcriptional control of human p53-regulated genes. Nat Rev Mol Cell Biol 9(5):402–412

    Article  CAS  PubMed  Google Scholar 

  28. Geva-Zatorsky N, Rosenfeld N, Itzkovitz S, Milo R, Sigal A, Dekel E, Yarnitzky T, Liron Y, Polak P, Lahav G, Alon U (2006) Oscillations and variability in the p53 system. Mol Syst Biol 2(2006):0033

    PubMed  Google Scholar 

  29. Toettcher JE, Mock C, Batchelor E, Loewer A, Lahav G (2010) A synthetic-natural hybrid oscillator in human cells. Proc Natl Acad Sci U S A 107(39):17047–17052. doi:10.1073/pnas.1005615107

    Article  CAS  PubMed Central  PubMed  Google Scholar 

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Acknowledgment

This work was supported by the Intramural Research Program of the Center for Cancer Research, National Cancer Institute, National Institutes of Health.

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Authors and Affiliations

  1. Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 10, Room B1B42, 10 Center Dr., MSC 1500, Bethesda, MD, 20892, USA

    Joshua R. Porter & Eric Batchelor

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  1. Joshua R. Porter
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  2. Eric Batchelor
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Corresponding author

Correspondence to Eric Batchelor .

Editor information

Editors and Affiliations

  1. School of Life Science and Technology, Harbin Institute of Technology, Harbin, China

    Mario Andrea Marchisio

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Porter, J.R., Batchelor, E. (2015). Using Computational Modeling and Experimental Synthetic Perturbations to Probe Biological Circuits. In: Marchisio, M. (eds) Computational Methods in Synthetic Biology. Methods in Molecular Biology, vol 1244. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1878-2_12

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  • DOI: https://doi.org/10.1007/978-1-4939-1878-2_12

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-1877-5

  • Online ISBN: 978-1-4939-1878-2

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