Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits

BMC Systems Biology

Volumn 7, Issue , 2013, Pages

  Marchisio, Mario Andrea ^a   Colaiacovo, Moreno ^b   Whitehead, Ellis ^a   Stelling, Jörg ^a  

^a SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^b ISTITUTO NAZIONALE DELLA NUTRIZIONE   (Italy)

Author keywords

Composable parts; Gene circuit modular design; Pools of signal carriers; Rule based modeling

Indexed keywords

BACTERIA (MICROORGANISMS); EUKARYOTA;

MESSENGER RNA; SMALL INTERFERING RNA;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; CYTOLOGY; EUKARYOTE; GENE REGULATORY NETWORK; GENETIC ENGINEERING; GENETICS; METHODOLOGY; OPEN READING FRAME; TRANSCRIPTION TERMINATION;

ANIMALS; EUKARYOTA; GENE REGULATORY NETWORKS; GENETIC ENGINEERING; MODELS, GENETIC; OPEN READING FRAMES; RNA, MESSENGER; RNA, SMALL INTERFERING; TRANSCRIPTION TERMINATION, GENETIC;

EID: 84878041846     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-7-42     Document Type: Article

References (55)

1. Marchisio MA, Stelling J. Computational design of synthetic gene circuits with composable parts. Bioinformatics 2008, 24(17):1903-1910. [http://dx.doi.org/10.1093/bioinformatics/btn330], 10.1093/bioinformatics/btn330, 18579565.
2. Endy D. Foundations for engineering biology. Nature 2005, 438(7067):449-453. [http://dx.doi.org/10.1038/nature04342], 10.1038/nature04342, 16306983.
3. Canton B, Labno A, Endy D. Refinement and standardization of synthetic biological parts and devices. Nat Biotechnol 2008, 26(7):787-793. [http://dx.doi.org/10.1038/nbt1413], 10.1038/nbt1413, 18612302.
4. Kelly JR, Rubin AJ, Davis JH, Ajo-Franklin CM, Cumbers J, Czar MJ, de Mora K, Glieberman AL, Monie DD, Endy D. Measuring the activity of BioBrick promoters using an in vivo reference standard. J Biol Eng 2009, 3(4). [http://dx.doi.org/10.1186/1754-1611-3-4].
5. Salis HM, Mirsky EA, Voigt CA. Automated design of synthetic ribosome binding sites to control protein expression. Nat Biotechnol 2009, 27(10):946-950. [http://dx.doi.org/10.1038/nbt.1568], 10.1038/nbt.1568, 2782888, 19801975.
6. Marchisio MA, Stelling J. Synthetic gene network computational design. Proc. IEEE International Symposium on Circuits and Systems, ISCAS 2009, Taipei (Taiwan) 2009, 309-312. New York: IEEE.
7. Breaker RR. Riboswitches and the RNA world. Cold Spring Harb Perspect Biol 2012, 4(2). [http://dx.doi.org/10.1101/cshperspect.a003566].
8. Marchisio MA, Stelling J. Automatic design of digital synthetic gene circuits. PLoS Comput Biol 2011, 7(2):e1001083. [http://dx.doi.org/10.1371/journal.pcbi.1001083], 10.1371/journal.pcbi.1001083, 3048778, 21399700.
9. Kærn M, Weiss R. Synthetic gene regulatory systems. System Modeling in Cellular Biology 2006, 269-295. Cambridge: The MIT Press, Szallasi Z, Stelling J, Periwal V.
10. Haynes KA, Silver PA. Eukaryotic systems broaden the scope of synthetic biology. J Cell Biol 2009, 187(5):589-596. [http://dx.doi.org/10.1083/jcb.200908138], 10.1083/jcb.200908138, 2806586, 19948487.
11. Blount BA, Weenink T, Ellis T. Construction of synthetic regulatory networks in yeast. FEBS Lett 2012, 586(15):2112-2121. [http://dx.doi.org/10.1016/j.febslet.2012.01.053], 10.1016/j.febslet.2012.01.053, 22309848.
12. Slusarczyk AL, Lin A, Weiss R. Foundations for the design and implementation of synthetic genetic circuits. Nat Rev Genet 2012, 13(6):406-420. [http://dx.doi.org/10.1038/nrg3227], 10.1038/nrg3227, 22596318.
13. Benenson Y. Biomolecular computing systems: principles, progress and potential. Nat Rev Genet 2012, 13(7):455-468. [http://dx.doi.org/10.1038/nrg3197], 10.1038/nrg3197, 22688678.
14. Albers B, Johnson A, Lewis J, Raff M, Roberts K, Walter P. Molecular Biology of the Cell. 2008, New York, Abingdon: Garland Science, Taylor and Francis Group, LLC.
15. Lohmueller JJ, Armel TZ, Silver PA. A tunable zinc finger-based framework for Boolean logic computation in mammalian cells. Nucleic Acids Res 2012, [http://dx.doi.org/10.1093/nar/gks142].
16. Bogdanove AJ, Voytas DF. TAL effectors: customizable proteins for DNA targeting. Science 2011, 333(6051):1843-1846. [http://dx.doi.org/10.1126/science.1204094], 10.1126/science.1204094, 21960622.
17. Benenson Y. Synthetic biology with RNA: progress report. Curr Opin Chem Biol 2012, 16(3-4):278-284. [http://dx.doi.org/10.1016/j.cbpa.2012.05.192], 10.1016/j.cbpa.2012.05.192, 22676891.
18. Liang JC, Smolke CD. Rational design and tuning of ribozyme-based devices. Methods Mol Biol 2012, 848:439-454. [http://dx.doi.org/10.1007/978-1-61779-545-9_27], 10.1007/978-1-61779-545-9_27, 22315085.
19. Chang AL, Wolf JJ, Smolke CD. Synthetic RNA switches as a tool for temporal and spatial control over gene expression. Curr Opin Biotechnol 2012, 23(5):679-688. [http://dx.doi.org/10.1016/j.copbio.2012.01.005], 10.1016/j.copbio.2012.01.005, 22305712.
20. Blinov ML, Faeder JR, Goldstein B, Hlavacek WS. BioNetGensoftware for rule-based modeling of signal transduction based on the interactions of molecular domains. Bioinformatics 2004, 20(17):3289-3291. [http://dx.doi.org/10.1093/bioinformatics/bth378], 10.1093/bioinformatics/bth378, 15217809.
21. Danos V, Laneve C. Formal molecular biology. Theoretical Comput Sci 2004, 325:69-110.
22. Harris LA, Hogg JS, Faeder JR. Compartmental rule-based modeling of biochemical systems. Proceedings of the 2009 Winter Simulation Conference, Austin, TX, USA 2009, Piscataway: IEEE, of the 2009 Winter Simulation Conference P.
23. Ginkel M, Kremling A, Nutsch T, Rehner R, Gilles ED. Modular modeling of cellular systems with ProMoT/Diva. Bioinformatics 2003, 19(9):1169-1176. 10.1093/bioinformatics/btg128, 12801880.
24. Mirschel S, Steinmetz K, Rempel M, Ginkel M, Gilles ED. PROMOT: modular modeling for systems biology. Bioinformatics 2009, 25(5):687-689. [http://dx.doi.org/10.1093/bioinformatics/btp029], 10.1093/bioinformatics/btp029, 2647835, 19147665.
25. Hucka M. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003, 19(4):524-531. 10.1093/bioinformatics/btg015, 12611808.
26. Goler JA. BioJADE: A design and simulation tool for synthetic biological systems. Tech. rep 2004, Cambridge: MIT.
27. Rodrigo G, Carrera J, Jaramillo A. Asmparts: assembly of biological model parts. Syst Synth Biol 2008, 1(4):167-170. [http://dx.doi.org/10.1007/s11693-008-9013-4].
28. Hill AD, Tomshine JR, Weeding EMB, Sotiropoulos V, Kaznessis YN. SynBioSS: the synthetic biology modeling suite. Bioinformatics 2008, 24(21):2551-2553. [http://dx.doi.org/10.1093/bioinformatics/btn468], 10.1093/bioinformatics/btn468, 18757873.
29. Czar MJ, Cai Y, Peccoud J. Writing DNA with GenoCAD. Nucleic Acids Res 2009, 37(Web Server issue):W40-W47. [http://dx.doi.org/10.1093/nar/gkp361], 2703884, 19429897.
30. Chandran D, Bergmann FT, Sauro HM. TinkerCell: modular CAD tool for synthetic biology. J Biol Eng 2009, 3(19). [http://dx.doi.org/10.1186/1754-1611-3-19].
31. Myers CJ, Barker N, Jones K, Kuwahara H, Madsen C, Nguyen NPD. iBioSima tool for the analysis and design of genetic circuits. Bioinformatics 2009, 25(21):2848-2849. [http://dx.doi.org/10.1093/bioinformatics/btp457], 10.1093/bioinformatics/btp457, 19628507.
32. Cooling MT, Rouilly V, Misirli G, Lawson J, Yu T, Hallinan J, Wipat A. Standard virtual biological parts: a repository of modular modeling components for synthetic biology. Bioinformatics 2010, 26(7):925-931. [http://dx.doi.org/10.1093/bioinformatics/btq063], 10.1093/bioinformatics/btq063, 20160009.
33. Xia B, Bhatia S, Bubenheim B, Dadgar M, Densmore D, Anderson JC. Developer's and user's guide to Clotho v2.0 A software platform for the creation of synthetic biological systems. Methods Enzymol 2011, 498:97-135. [http://dx.doi.org/10.1016/B978-0-12-385120-8.00005-X].
34. Bilitchenko L, Liu A, Cheung S, Weeding E, Xia B, Leguia M, Anderson JC, Densmore D. Eugene-a domain specific language for specifying and constraining synthetic biological parts, devices, and systems. PLoS One 2011, 6(4):e18882. [http://dx.doi.org/10.1371/journal.pone.0018882], 10.1371/journal.pone.0018882, 3084710, 21559524.
35. Smith LP, Bergmann FT, Chandran D, Sauro HM. Antimony: a modular model definition language. Bioinformatics 2009, 25(18):2452-2454. [http://dx.doi.org/10.1093/bioinformatics/btp401], 10.1093/bioinformatics/btp401, 2735663, 19578039.
36. Cai Y, Hartnett B, Gustafsson C, Peccoud J. A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts. Bioinformatics 2007, 23(20):2760-2767. [http://dx.doi.org/10.1093/bioinformatics/btm446], 10.1093/bioinformatics/btm446, 17804435.
37. Pedersen M, Phillips A. Towards programming languages for genetic engineering of living cells. J R Soc Interface 2009, 6(Suppl 4):S437-S450. [http://dx.doi.org/10.1098/rsif.2008.0516.focus], 2843955, 19369220.
38. Rinaudo K, Bleris L, Maddamsetti R, Subramanian S, Weiss R, Benenson Y. A universal RNAi-based logic evaluator that operates in mammalian cells. Nat Biotechnol 2007, 25(7):795-801. [http://dx.doi.org/10.1038/nbt1307], 10.1038/nbt1307, 17515909.
39. Silver PA, Brent R, Ptashne M. DNA binding is not sufficient for nuclear localization of regulatory proteins in Saccharomyces cerevisiae. Mol Cell Biol 1986, 6(12):4763-4766. 367265, 3099172.
40. Blount BA, Weenink T, Vasylechko S, Ellis T. Rational diversification of a promoter providing fine-tuned expression and orthogonal regulation for synthetic biology. PLoS One 2012, 7(3):e33279. [http://dx.doi.org/10.1371/journal.pone.0033279], 10.1371/journal.pone.0033279, 3307721, 22442681.
41. Ptashne M. A Genetic Switch. John Inglis 2004,
42. Lewin B. genes VII 2000, New York: Oxford University Press.
43. Koetter P, Weigand JE, Meyer B, Entian KD, Suess B. A fast and efficient translational control system for conditional expression of yeast genes. Nucleic Acids Res 2009, 37(18):e120. [http://dx.doi.org/10.1093/nar/gkp578], 10.1093/nar/gkp578, 2764425, 19592423.
44. Xie Z, Wroblewska L, Prochazka L, Weiss R, Benenson Y. Multi-input RNAi-based logic circuit for identification of specific cancer cells. Science 2011, 333(6047):1307-1311. [http://dx.doi.org/10.1126/science.1205527], 10.1126/science.1205527, 21885784.
45. Jose AM, Soukup GA, Breaker RR. Cooperative binding of effectors by an allosteric ribozyme. Nucleic Acids Res 2001, 29(7):1631-1637. 10.1093/nar/29.7.1631, 31269, 11266567.
46. Mandal M, Lee M, Barrick JE, Weinberg Z, Emilsson GM, Ruzzo WL, Breaker RR. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 2004, 306:275-279. [http://dx.doi.org/10.1126/science.1100829], 10.1126/science.1100829, 15472076.
47. Drinnenberg IA, Weinberg DE, Xie KT, Mower JP, Wolfe KH, Fink GR, Bartel DP. RNAi in budding yeast. Science 2009, 326(5952):544-550. [http://dx.doi.org/10.1126/science.1176945], 10.1126/science.1176945, 19745116.
48. Yamanishi M, Katahira S, Matsuyama T. TPS1 terminator increases mRNA and protein yield in a Saccharomyces cerevisiae expression system. Biosci Biotechnol Biochem 2011, 75(11):2234-2236. 10.1271/bbb.110246, 22056446.
49. Cuccato G, Polynikis A, Siciliano V, Graziano M, di Bernardo M, di Bernardo D. Modeling RNA interference in mammalian cells. BMC Syst Biol 2011, 5(19). [http://dx.doi.org/10.1186/1752-0509-5-19].
50. Kolczyk K, Samaga R, Conzelmann H, Mirschel S, Conradi C. The Process-Interaction-Model: a common representation of rule-based and logical models allows studying signal transduction on different levels of detail. BMC Bioinformatics 2012, 13(251). [http://dx.doi.org/10.1186/1471-2105-13-251].
51. Peccoud J, Anderson JC, Chandran D, Densmore D, Galdzicki M, Lux MW, Rodriguez CA, Stan GB, Sauro HM. Essential information for synthetic DNA sequences. Nat Biotechnol 2011, 29(22):discussion 22-22 discussion 23. [http://dx.doi.org/10.1038/nbt.1753].
52. Galdzicki M, Rodriguez C, Chandran D, Sauro HM, Gennari JH. Standard biological parts knowledgebase. PLoS One 2011, 6(2):e17005. [http://dx.doi.org/10.1371/journal.pone.0017005], 10.1371/journal.pone.0017005, 3044748, 21390321.
53. Saez-Rodriguez J, Kremling A, Gilles E. Dissecting the puzzle of life modularization of signal transduction networks. Comput Chem Eng 2005, 29:619-629.
54. Marquez-Lago TT, Marchisio MA. Synthetic biology: dynamic modeling and construction of cell systems. Dynamic Process Modeling Volume 7 of Process Systems Engineering 2010, 493-544. WILEY-VCH, Georgiadis M, Banga J, Pistikopoulos E.
55. Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U. COPASI-a COmplex PAthway SImulator. Bioinformatics 2006, 22(24):3067-3074. [http://dx.doi.org/10.1093/bioinformatics/btl485], 10.1093/bioinformatics/btl485, 17032683.