Analysis and design of a genetic circuit for dynamic metabolic engineering

ACS Synthetic Biology

Volumn 2, Issue 8, 2013, Pages 442-452

  Anesiadis, Nikolaos ^a   Kobayashi, Hideki ^b   Cluett, William R ^a   Mahadevan, Radhakrishnan ^a,c  

^a UNIVERSITY OF TORONTO   (Canada)

^b JAPAN AGENCY FOR MARINE EARTH SCIENCE AND TECHNOLOGY   (Japan)

^c UNIVERSITY OF TORONTO   (Canada)

Author keywords

global sensitivity analysis; metabolic engineering; quorum sensing; toggle switch

Indexed keywords

SERINE;

ARTICLE; BACTERIAL STRAIN; BACTERIUM MUTANT; COMPUTER MODEL; COMPUTER SIMULATION; ESCHERICHIA COLI; GENE CLUSTER; GENE SWITCHING; GENETIC CIRCUIT; GENETIC ENGINEERING; GLOBAL SENSITIVITY ANALYSIS; INTEGRATED CIRCUIT; MATHEMATICAL MODEL; METABOLIC ENGINEERING; NONHUMAN; PRIORITY JOURNAL; PRODUCTIVITY; QUORUM SENSING; SENSITIVITY ANALYSIS; THEORETICAL SAMPLE; TIME; TOGGLE SWITCH;

COMPUTER SIMULATION; ESCHERICHIA COLI; GENE REGULATORY NETWORKS; GENETIC ENHANCEMENT; METABOLIC ENGINEERING; MODELS, GENETIC; RECOMBINANT PROTEINS; SERINE;

EID: 84882603873     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/sb300129j     Document Type: Article

References (67)

1. Keasling, J. (2010) Manufacturing molecules through metabolic engineering Science 330, 1355-1358
2. Yadav, V. G., DeMey, M., Lim, C. G., Ajikumar, P. K., and Stephanopoulos, G. (2012) The future of metabolic engineering and synthetic biology: Towards a systematic practice Metab. Eng. 14, 233-241
3. Oberhardt, M., Palsson, B. O., and Papin, J. A. (2009) Applications of genome-scale metabolic reconstructions Mol. Syst. Biol. 5, 320
4. Copeland, W. B., Bartley, B. A., Chandran, D., Galdzicki, M., Kim, K. H., Sleight, S. C., Maranas, C. D., and Sauro, H. M. (2012) Computational tools for metabolic engineering Metab. Eng. 14, 270-280
5. Burgard, A. P., Pharkya, P., and Maranas, C. D. (2003) OptKnock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization Biotechnol. Bioeng. 84, 647-657 (Pubitemid 37420336)
6. Pharkya, P. and Maranas, C. D. (2006) An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems Metab. Eng. 8, 1-13 (Pubitemid 43017837)
7. Lun, D. S., Rockwell, G., Guido, N. J., Baym, M., Kelner, J. A., Berger, B., Galagan, J. E., and Church, G. M. (2009) Large-scale identification of genetic design strategies using local search Mol. Syst. Biol. 5, 296
8. Ranganathan, S., Suthers, P. F., and Maranas, C. D. (2010) OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions PLoS Comput. Biol. 6 (4) e1000744
9. Yang, L., Cluett, W. R., and Mahadevan, R. (2011) EMILiO: a fast algorithm for genome-scale strain design Metab. Eng. 13, 272-281
10. Banga, J. R., Balsa-Canto, E., Moles, C. G., and Alonso, A. A. (2003) Dynamic optimization of bioreactors: a review Proc. Indian Natl. Sci. Acad. 69A, 257-265
11. Varma, A. and Palsson, B. O. (1994) Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110 Appl. Environ. Microbiol. 60, 3724-3731 (Pubitemid 24298868)
12. Mahadevan, R., Edwards, J. S., and Doyle, F. J., III (2002) Dynamic flux balance analysis of diauxic growth in Escherichia coli Biophys. J. 83, 1331-1340 (Pubitemid 34977706)
13. Hjersted, J. L. and Henson, M. A. (2006) Optimization of fed-batch Saccharomyces cerevisiae fermentation using dynamic flux balance models Biotechnol. Prog. 22, 1239-1248 (Pubitemid 44568797)
14. Gadkar, K. G., Doyle, F. J., III, Edwards, J. S., and Mahadevan, R. (2005) Estimating optimal profiles of genetic alterations using constraint-based models Biotechnol. Bioeng. 89, 243-251
15. Gadkar, K. G., Mahadevan, R., and Doyle, F. J., III (2006) Optimal genetic manipulations in batch bioreactor control Automatica 42, 1723-1733 (Pubitemid 44277963)
16. San, K. Y. and Stephanopoulos, G. (1984) A note on the optimality criteria for maximum biomass production in a fed-batch fermentor Biotechnol. Bioeng. 26 (10) 1261-1264 (Pubitemid 14645984)
17. Purnick, P. E. M. and Weiss, R. (2009) The second wave of synthetic biology: from modules to systems Nat. Rev. Mol. Cell Biol. 10, 410-422
18. Khalil, A. S. and Collins, J. J. (2010) Synthetic biology: applications come of age Nat. Rev. Genet. 11, 367-379
19. Nandagopal, N. and Elowitz, M. B. (2011) Synthetic biology: integrated gene circuits Science 333, 1244-1248
20. Voigt, C. A. (2006) Genetic parts to program bacteria Curr. Opin. Biotechnol. 17, 548-557 (Pubitemid 44442933)
21. Alper, H., Fischer, C., Nevoigt, E., and Stephanopoulos, G. (2005) Tuning genetic control through promoter engineering Proc. Natl. Acad. Sci. U.S.A. 102, 12678-12683 (Pubitemid 41279425)
22. Alper, H. and Stephanopoulos, G. (2007) Global transcription machinery engineering: a new approach for improving cellular phenotype Metab. Eng. 9, 258-267 (Pubitemid 46809525)
23. Ellis, T., Wang, X., and Collins, J. J. (2009) Diversity-based, model-guided construction of synthetic gene networks with predicted functions Nat. Biotechnol. 27, 465-471
24. Salis, H. M., Mirsky, E. A., and Voigt, C. A. (2009) Automated design of synthetic ribosome binding sites to control protein expression Nat. Biotechnol. 27, 946-950
25. Culler, S. J., Hoff, K. G., and Smolke, C. D. (2010) Reprogramming cellular behaviour with RNA controllers responsive to endogenous proteins Science 330, 1251-1255
26. Carothers, J. M., Goler, J. A., Juminaga, D., and Keasling, J. D. (2011) Model-driven engineering of RNA devices to quantitatively program gene expression Science 334, 1716-1719
27. Boyle, P. M. and Silver, P. A. (2012) Part plus pipes: synthetic biology approaches to metabolic engineering Metab. Eng. 14, 223-232
28. Callura, J. M., Cantor, C. R., and Collins, J. J. (2012) Genetic switchboard for synthetic biology applications Proc. Natl. Acad. Sci. U.S.A. 109, 5850-5855
29. Keasling, J. (2012) Synthetic biology and the development of tools for metabolic engineering Metab. Eng. 14, 189-195
30. Kobayashi, H., Kaern, M., Araki, M., Chung, K., Gardner, T. S., Cantor, C. R., and Collins, J. J. (2004) Programmable cells: interfacing natural and engineered gene networks Proc. Natl. Acad. Sci. U.S.A. 101, 8414-8419 (Pubitemid 38736589)
31. You, L., Cox, R. S., III, Weiss, R., and Arnold, F. H. (2004) Programmed population control by cell-cell communication and regulated killing Nature 428, 868-871 (Pubitemid 38529503)
32. Basu, S., Gerchman, Y., Collins, C. H., Arnold, F. H., and Weiss, R. (2005) A synthetic multicellular system for programmed pattern formation Nature 434, 1130-1134 (Pubitemid 40663491)
33. Tsao, C., Hooshangi, S., Wu, H. C., Valdes, J. J., and Bentley, W. E. (2010) Autonomous induction of recombinant proteins by minimally rewiring native quorum sensing regulon of E. coli Metab. Eng. 12, 291-297
34. Collins, C. H., Arnold, F. H., and Leadbetter, J. R. (2005) Directed evolution of Vibrio fischeri LuxR for increased sensitivity to a broad spectrum of acyl-homoserine lactones Mol. Microbiol. 55, 712-723 (Pubitemid 40203688)
35. Collins, C. H., Leadbetter, J. R., and Arnold, F. H. (2006) Dual selection enhances the signaling specificity of a variant of the quorum-sensing transcriptional activator LuxR Nat. Biotechnol. 24, 708-712 (Pubitemid 43882123)
36. Anesiadis, N., Cluett, W. R., and Mahadevan, R. (2008) Dynamic metabolic engineering for increasing bioprocess productivity Metab. Eng. 10, 255-266
37. Gardner, T. S., Cantor, C. R., and Collins, J. J. (2000) Construction of a genetic toggle switch in Escherichia coli Nature 403, 339-342 (Pubitemid 30062394)
38. Van Riel, N. A. W. (2006) Dynamic modeling and analysis of biochemical networks: mechanism-based models and model-based experiments Briefings Bioinf. 7, 364-374
39. Haseltine, E. L. and Arnold, F. H. (2007) Synthetic gene circuits: design with directed evolution Annu. Rev. Biophys. Biomol. Struct. 36, 1-19 (Pubitemid 46998107)
40. Chandran, D., Copeland, W. B., Sleight, S. C., and Sauro, H. M. (2008) Mathematical modeling and synthetic biology Drug Discovery Today: Dis. Models 5, 299-309
41. Zheng, Y. and Sriram, G. (2010) Mathematical modelling: bridging the gap between concept and realization in synthetic biology J. Biomed. Biotechnol. 10.1155/2010/541609
42. Biliouris, K., Daoutidis, P., and Kaznessis, Y. N. (2011) Stochastic simulations of the tetracycline operon BMC Syst. Biol. 5, 9
43. Saltelli, A., Ratto, M., Andres, T., Campolongo, F., Cariboni, J., Gatelli, D., Saisana, M., and Tarantola, S. (2008) Global Sensitivity Analysis: The Primer, Wiley, New York.
44. Kiparissides, A., Kucherenko, S. S., Mantalaris, A., and Pistikopoulos, E. N. (2009) Global sensitivity analysis challenges in biological systems modelling Ind. Eng. Chem. Res. 48, 7168-7180
45. Kiparissides, A., Koutinas, M., Kontoravdi, C., Mantalaris, A., and Pistikopoulos, E. N. (2011) 'Closing the loop' in biological systems modeling-From the in silico to the in vitro Automatica 47, 1147-1155
46. Miskovic, L. and Hatzimanikatis, V. (2011) Modeling of uncertainties in biochemical reactions Biotechnol. Bioeng. 108, 413-423
47. Saltelli, A. (2002) Making best use of model evaluations to compute sensitivity indices Comput. Phys. Commun. 145, 280-297 (Pubitemid 34524628)
48. Feng, X., Hooshangi, S., Chen, D., Li, G., Weiss, R., and Rabitz, H. (2004) Optimizing genetic circuits by global sensitivity analysis Biophys. J. 87, 2195-2202 (Pubitemid 41071322)
49. Miller, G. M., Ogunnaike, B. A., Schwaber, J. S., and Vadigepalli, R. (2010) Robust dynamic balance of AP-1 transcription factors in a neuronal gene regulatory network BMC Syst. Biol. 4, 171
50. Zheng, Y. and Rundell, A. (2006) Comparative study of parameter sensitivity analyses of the TCR-activated Erk-MAPK signalling pathway IEE Proc. Syst. Biol. 153, 201-211 (Pubitemid 44151480)
51. Chu, Y., Jayaraman, A., and Hahn, J. (2007) Parameter sensitivity analysis of IL-6 signalling pathways IET Syst. Biol. 1, 342-352 (Pubitemid 351278455)
52. Zhao, J., Fang, Y., Scheibe, T. D., Lovley, D. R., and Mahadevan, R. (2010) Modeling and sensitivity analysis of electron capacitance for Geobacter in sedimentary environments J. Contam. Hydrol. 112, 30-44
53. Zhao, J., Scheibe, T. D., and Mahadevan, R. (2011) Model-based analysis of the role of biological, hydrological and geochemical factors affecting uranium bioremediation Biotechnol. Bioeng. 108, 1537-1548
54. Kiparissides, A., Koutinas, M., Moss, T., Newman, J., Pistikopoulos, E. N., and Mantalaris, A. (2011) Modelling the Delta1/Notch1 pathway: in search of the mediator(s) of neural stem cell differentiation PLoS One 6 (2) e14668
55. Kontoravdi, C., Asprey, S. P., Pistikopoulos, E. N., and Mantalaris, A. (2005) Application of global sensitivity analysis to determine goals for design of experiments: an example study on antibody-producing cell cultures Biotechnol. Prog. 21, 1128-1135 (Pubitemid 41102248)
56. Ho, Y., Kiparissides, A., Pistikopoulos, E. N., and Mantalaris, A. (2012) Computational approach for understanding and improving GS-NSO antibody production under hyperosmotic conditions J. Biosci. Bioeng. 113, 88-98
57. Anesiadis, N., Cluett, W. R., and Mahadevan, R. (2011) Model-driven design based on sensitivity analysis for a synthetic biology application. In Proceedings of the 21st European Symposium on Computer-Aided Process Engineering-ESCAPE 21 (Pistikopoulos, E. N., Georgiadis, M. C., and Kokossis, A. C., Eds.), Vol. 29, pp 1446-1450, Elsevier, Amsterdam.
58. Manefield, M., Rasmussen, T. B., Henzter, M., Andersen, J. B., Steinberg, P., Kjelleberg, S., and Givskov, M. (2002) Halogenated furanones inhibit quorum sensing through accelerated LuxR turnover Microbiology 148, 1119-1127 (Pubitemid 34436786)
59. Huang, D., Holtz, W. J., and Maharbiz, M. M. (2012) A genetic bistable switch utilizing nonlinear protein degradation J. Biol. Eng. 6, 9
60. Fung, E., Wong, W. W., Suen, J. K., Bulter, T., Lee, S., and Liao, J. C. (2005) A synthetic gene-metabolic oscillator Nature 435, 118-122 (Pubitemid 40655919)
61. McCabe, K. M., Lacherndo, E. J., Albino-Flores, I., Sheehan, E., and Hernandez, M. (2011) LacI(Ts)-regulated expression as an in situ intracellular biomolecular thermometer Appl. Environ. Microbiol. 77 (9) 2863-2868
62. Elowitz, M. B., Levine, A. J., Siggia, E. D., and Swain, P. S. (2002) Stochastic gene expression in a single cell Science 297, 1183-1186 (Pubitemid 36193353)
63. Isaacs, F. J., Hasty, J., Cantor, C. R., and Collins, J. J. (2003) Prediction and measurement of an autoregulatory genetic module Proc. Natl. Acad. Sci. U.S.A. 100, 7714-7719 (Pubitemid 36760035)
64. Kaplan, H. B. and Greenberg, E. P. (1985) Diffusion of autoinducer is involved in regulation of the Vibrio fischeri luminescence system J. Bacteriol. 163, 1210-1214 (Pubitemid 15229495)
65. Weingart, C. L., White, C. E., Liu, S., Chai, Y., Cho, H., Tsai, C.-S., Wei, Y., Delay, N. R., Gronquist, M. R., Eberhard, A., and Winans, S. C. (2005) Direct binding of the quorum sensing regulator CepR of Burkholderia cenocepacia to two target promoters in vitro Mol. Microbiol. 57, 452-467 (Pubitemid 40979345)
66. Orth, J. D., Conrad, T. M., Na, J., Lerman, J. A., Nam, H., Feist, A. M., and Palsson, B. O. (2011) A comprehensive genome-scale reconstruction of Escherichia coli metabolism Mol. Syst. Biol. 7, 535
67. Sobol, I. M. (2001) Global sensitivity indices for nonlinear mathematical models and their Monte Carlo estimates. Math. Comput. Simul. 55, 271-280 (Pubitemid 32672729)