Parts and Pools: A framework for modular design of synthetic gene circuits

Frontiers in Bioengineering and Biotechnology

Volumn 2, Issue OCT, 2014, Pages

  Marchisio, Mario Andrea ^a  

^a HARBIN INSTITUTE OF TECHNOLOGY   (China)

Author keywords

Boolean gates; Gene circuits; Modeling; Parts; Pools; Synthetic biology

Indexed keywords

BACTERIA; DIGITAL DEVICES; GENES; LAKES; MAMMALS; MODELS; NUCLEIC ACIDS;

BOOLEAN GATE; GENE CIRCUITS; PARTS; POOLS; SYNTHETIC BIOLOGY;

RECONFIGURABLE HARDWARE;

EID: 84994546251     PISSN: None     EISSN: 22964185     Source Type: Journal    
DOI: 10.3389/fbioe.2014.00042     Document Type: Article

References (55)

1. Ajo-Franklin, C. M., Drubin, D. A., Eskin, J. A., Gee, E. P. S., Landgraf, D., Phillips, I., et al. (2007). Rational design of memory in eukaryotic cells. Genes Dev. 21, 2271-2276. doi: 10.1101/gad.1586107
2. Alon, U. (2007). Network motifs: theory and experimental approaches. Nat. Rev. Genet. 8, 450-461. doi:10.1038/nrg2102
3. Andrianantoandro, E., Basu, S., Karig, D. K., and Weiss, R. (2006). Synthetic biology: new engineering rules for an emerging discipline. Mol. Syst. Biol. 2, 2006.0028. doi:10.1038/msb4100073
4. Atkinson, M. R., Savageau, M. A., Myers, J. T., and Ninfa, A. J. (2003). Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 113, 597-607. doi:10.1016/S0092-8674(03)00346-5
5. Beal, J., Weiss, R., Densmore, D., Adler, A., Appleton, E., Babb, J., et al. (2012). An end-to-end workflow for engineering of biological networks from high-level specifications. ACS Synth. Biol. 1, 317-331. doi:10.1021/sb300030d
6. Bintu, L., Buchler, N. E., Garcia, H. G., Gerland, U., Hwa, T., Kondev, J., et al. (2005). Transcriptional regulation by the numbers: applications. Curr. Opin. Genet. Dev. 15, 125-135. doi:10.1016/j.gde.2005.02.007
7. Blinov, M. L., Faeder, J. R., Goldstein, B., and Hlavacek, W. S. (2004). BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. Bioinformatics 20, 3289-3291. doi:10.1093/bioinformatics/bth378
8. Blount, B. A., Weenink, T., Vasylechko, S., and Ellis, T. (2012). Rational diversification of a promoter providing fine-tuned expression and orthogonal regulation for synthetic biology. PLoS ONE 7:e33279. doi:10.1371/journal.pone.0033279
9. Brayton, R. K., Sangiovanni-Vincentelli, A. L., McMullen, C. T., and Hachtel, G. D. (1984). Logic Minimization Algorithms for VLSI Synthesis. Norwell, MA: Kluwer Academic Publishers.
10. Breaker, R. R. (2012). Riboswitches and the RNA world. Cold Spring Harb. Perspect. Biol. 4, a003566. doi:10.1101/cshperspect.a003566
11. Cai, Y., Hartnett, B., Gustafsson, C., and Peccoud, J. (2007). A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts. Bioinformatics 23, 2760-2767. doi:10.1093/bioinformatics/btm446
12. Chandran, D., Bergmann, F. T., and Sauro, H. M. (2009). TinkerCell: modular CAD tool for synthetic biology. J. Biol. Eng. 3, 19. doi:10.1186/1754-1611-3-19
13. Cooling, M. T., Rouilly, V., Misirli, G., Lawson, J., Yu, T., Hallinan, J., et al. (2010). Standard virtual biological parts: a repository of modular modeling components for synthetic biology. Bioinformatics 26, 925-931. doi:10.1093/bioinformatics/btq063
14. Cuellar, A. A., Lloyd, C. M., Nielsen, P. F., Bullivant, D. P., Nickerson, D. P., and Hunter, P. J. (2003). An overview of CellML 1.1, a biological model description language. Simulation 79, 740-747. doi:10.1177/0037549703040939
15. Czar, M. J., Cai, Y., and Peccoud, J. (2009). Writing DNA with GenoCAD. Nucleic Acids Res. 37, W40-W47. doi:10.1093/nar/gkp361
16. Danos, V., and Laneve, C. (2004). Formal molecular biology. Theor. Comput. Sci. 325, 69-110. doi:10.1016/j.tcs.2004.03.065
17. Dasika, M. S., and Maranas, C. D. (2008). OptCircuit: an optimization based method for computational design of genetic circuits. BMC Syst. Biol. 2:24. doi:10.1186/1752-0509-2-24
18. Elowitz, M. B., and Leibler, S. (2000). A synthetic oscillatory network of transcriptional regulators. Nature 403, 335-338. doi:10.1038/35002125
19. Endy, D. (2005). Foundations for engineering biology. Nature 438, 449-453. doi:10.1038/nature04342
20. Faeder, J. R., Blinov, M. L., and Hlavacek, W. S. (2009). Rule-based modeling of biochemical systems with BioNetGen. Methods Mol. Biol. 500, 113-167. doi:10.1007/978-1-59745-525-1_5
21. Francois, P., and Hakim, V. (2004). Design of genetic networks with specified functions by evolution in silico. Proc. Natl. Acad. Sci. U.S.A. 101, 580-585. doi:10.1073/pnas.0304532101
22. Galdzicki, M., Clancy, K. P., Oberortner, E., Pocock, M., Quinn, J. Y., Rodriguez, C. A., et al. (2014). The synthetic biology open language (SBOL) provides a community standard for communicating designs in synthetic biology. Nature 32, 545-550. doi:10.1038/nbt.2891
23. Ginkel, M., Kremling, A., Nutsch, T., Rehner, R., and Gilles, E. D. (2003). Modular modeling of cellular systems with ProMoT/Diva. Bioinformatics 19, 1169-1176. doi:10.1093/bioinformatics/btg128
24. Goler, J. A. (2004). BioJADE: A Design and Simulation Tool for Synthetic Biological Systems. Technical Report. Cambridge, MA: AITR-2004-003.
25. Hill, A. D., Tomshine, J. R., Weeding, E. M. B., Sotiropoulos, V., and Kaznessis, Y. N. (2008). SynBioSS: the synthetic biology modeling suite. Bioinformatics 24, 2551-2553. doi:10.1093/bioinformatics/btn468
26. Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., et al. (2003). The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19, 524-531. doi:10.1093/bioinformatics/btg015
27. Huynh, L., and Tagkopoulos, I. (2014). Optimal part and module selection for synthetic gene circuit design automation. ACS Synth. Biol. 3, 556-564. doi:10.1021/sb400139h
28. Huynh, L., Tsoukalas, A., Köppe, M., and Tagkopoulos, I. (2013). SBROME: a scalable optimization and module matching framework for automated biosystems design. ACS Synth. Biol. 2, 263-273. doi:10.1021/sb300095m
29. Isaacs, F. J., Dwyer, D. J., and Collins, J. J. (2006). RNA synthetic biology. Nat. Biotechnol. 24, 545-554. doi:10.1038/nbt1208
30. Jose, A. M., Soukup, G. A., and Breaker, R. R. (2001). Cooperative binding of effectors by an allosteric ribozyme. Nucleic Acids Res. 29, 1631-1637. doi:10.1093/nar/29.7.1631
31. Karnaugh, M. (1953). The map method for synthesis of combinational logic circuits. Trans. Am. Inst. Electr. Eng. 72, 593-599.
32. MacDonald, J. T., Barnes, C., Kitney, R. I., Freemont, P. S., and Stan, G.-B. V. (2011). Computational design approaches and tools for synthetic biology. Integr. Biol. 3, 97-108. doi:10.1039/c0ib00077a
33. Mandal, M., Lee, M., Barrick, J. E., Weinberg, Z., Emilsson, G. M., Ruzzo, W. L., et al. (2004). A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 306, 275-279. doi:10.1126/science.1100829
34. Marchisio, M. A. (2012). In silico implementation of synthetic gene networks. Methods Mol. Biol. 813, 3-21. doi:10.1007/978-1-61779-412-4_1
35. Marchisio, M. A. (2014). In silico design and in vivo implementation of yeast gene Boolean gates. J. Biol. Eng. 8, 6. doi:10.1186/1754-1611-8-6
36. Marchisio, M. A., Colaiacovo, M., Whitehead, E., and Stelling, J. (2013). Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits. BMC Syst. Biol. 7:42. doi:10.1186/1752-0509-7-42
37. Marchisio, M. A., and Stelling, J. (2008). Computational design of synthetic gene circuits with composable parts. Bioinformatics 24, 1903-1910. doi:10.1093/bioinformatics/btn330
38. Marchisio, M. A., and Stelling, J. (2009). "Synthetic gene network computational design," in IEEE International Symposium on Circuits and Systems, ISCAS (Taipei: IEEE), 309-312.
39. Marchisio, M. A., and Stelling, J. (2011). Automatic design of digital synthetic gene circuits. PLoS Comput. Biol. 7:e1001083. doi:10.1371/journal.pcbi.1001083
40. Marchisio, M. A., and Stelling, J. (2014). "Simplified computational design of digital synthetic gene circuits," in A Systems Theoretic Approach to Systems and Synthetic Biology II: Analysis and Design of Cellular Systems, eds V. V. Kulkarni, G. B. Stan, and K. Raman (Dordrecht: Springer-Verlag), 257-271. doi:10.1007/978-94-017-9047-5_11
41. Mirschel, S., Steinmetz, K., Rempel, M., Ginkel, M., and Gilles, E. D. (2009). PROMOT: modular modeling for systems biology. Bioinformatics 25, 687-689. doi:10.1093/bioinformatics/btp029
42. Myers, C. J. (2013). "Platforms for genetic design automation," in Microbial Synthetic Biology eds C. Harwood and A. Wipat (Oxford: Elsevier), 177-202.
43. Myers, C. J., Barker, N., Jones, K., Kuwahara, H., Madsen, C., and Nguyen, N.-P. D. (2009). iBioSim: a tool for the analysis and design of genetic circuits. Bioinformatics 25, 2848-2849. doi:10.1093/bioinformatics/btp457
44. Nagel, L. W., and Pederson, D. O. (1973). Simulation Program with Integrated Circuit Emphasis (SPICE). Technical Report. Memorandum No. ERLM382, Berkeley, CA: University of California.
45. Pedersen, M., and Phillips, A. (2009). Towards programming languages for genetic engineering of living cells. J. R. Soc. Interface 6(Suppl. 4), S437-S450. doi:10.1098/rsif.2008.0516.focus
46. Regot, S., Macia, J., Conde, N., Furukawa, K., Kjellén, J., Peeters, T., et al. (2011). Distributed biological computation with multicellular engineered networks. Nature 469, 207-211. doi:10.1038/nature09679
47. Rinaudo, K., Bleris, L., Maddamsetti, R., Subramanian, S., Weiss, R., and Benenson, Y. (2007). A universal RNAi-based logic evaluator that operates in mammalian cells. Nat. Biotechnol. 25, 795-801. doi:10.1038/nbt1307
48. Rodrigo, G., Carrera, J., and Jaramillo, A. (2007a). Asmparts: assembly of biological model parts. Syst. Synth. Biol. 1, 167-170. doi:10.1007/s11693-008-9013-4
49. Rodrigo, G., Carrera, J., and Jaramillo, A. (2007b). Genetdes: automatic design of transcriptional networks. Bioinformatics 23, 1857-1858. doi:10.1093/bioinformatics/btm237
50. Rodrigo, G., and Jaramillo, A. (2013). AutoBioCAD: full biodesign automation of genetic circuits. ACS Synth. Biol. 2, 230-236. doi:10.1021/sb300084h
51. Roehner, N., and Myers, C. J. (2014). Directed acyclic graph-based technology mapping of genetic circuit models. ACS Synth. Biol. 3, 543-555. doi:10.1021/sb400135t
52. Stevens, J. T., and Myers, C. J. (2013). Dynamic modeling of cellular populations within iBioSim. ACS Synth. Biol. 2, 223-229. doi:10.1021/sb300082b
53. Xia, B., Bhatia, S., Bubenheim, B., Dadgar, M., Densmore, D., and Anderson, J. C. (2011). Developer's and user's guide to Clotho v2.0 A software platform for the creation of synthetic biological systems. Meth. Enzymol. 498, 97-135. doi:10.1016/B978-0-12-385120-8.00005-X
54. Yaman, F., Bhatia, S., Adler, A., Densmore, D., and Beal, J. (2012). Automated selection of synthetic biology parts for genetic regulatory networks. ACS Synth. Biol. 1, 332-344. doi:10.1021/sb300032y
55. Yamanishi, M., Katahira, S., and Matsuyama, T. (2011). TPS1 terminator increases mRNA and protein yield in a Saccharomyces cerevisiae expression system. Biosci. Biotechnol. Biochem. 75, 2234-2236. doi:10.1271/bbb.110246