Considerations for using integral feedback control to construct a perfectly adapting synthetic gene network

Journal of Theoretical Biology

Volumn 266, Issue 4, 2010, Pages 723-738

  Ang, Jordan ^a   Bagh, Sangram ^a   Ingalls, Brian P ^b   McMillen, David R ^a  

^a UNIVERSITY OF TORONTO   (Canada)

^b UNIVERSITY OF WATERLOO   (Canada)

Author keywords

Control systems; Gene regulation; Regulatory feedback; Synthetic biology

Indexed keywords

BACTERIUM; CONTROL SYSTEM; FEEDBACK MECHANISM; GENE; NUMERICAL MODEL; PROTEIN;

ARTICLE; ESCHERICHIA COLI; EVOLUTIONARY ADAPTATION; FEEDBACK SYSTEM; GENE REGULATORY NETWORK; GENETIC REGULATION; MATHEMATICAL ANALYSIS; MOLECULAR BIOLOGY; NONHUMAN; PRIORITY JOURNAL; PROCESS CONTROL; PROMOTER REGION; SYNTHETIC BIOLOGY;

ADAPTATION, PHYSIOLOGICAL; COMPUTER SIMULATION; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; FEEDBACK, PHYSIOLOGICAL; GENE EXPRESSION REGULATION, BACTERIAL; GENE REGULATORY NETWORKS; GENES, SYNTHETIC; LAC REPRESSORS; PROMOTER REGIONS, GENETIC; SYNTHETIC BIOLOGY;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 77955690481     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2010.07.034     Document Type: Article

References (34)

1. Alon U., Surette M.G., Barkai N., Leibler S. Robustness in bacterial chemotaxis. Nature 1999, 397:168-171.
2. Andrianantoandro E., Basu S., Karig D.K., Weiss R. Synthetic biology: new engineering rules for an emerging discipline. Mol. Syst. Biol. 2006, 2. 2006.0028.
3. Bagh S., Mazumder M., Velauthapillai T., Sardana V., Dong G.Q., Movva A.B., Lim L.H., McMillen D.R. Plasmid-borne prokaryotic gene expression: Sources of variability and quantitative system characterization. Phys. Rev. E 2008, 77:021919.
4. Barkai N., Leibler S. Robustness in simple biochemical networks. Nature 1997, 387:913-917.
5. Cannon W.B. A Genetic Switch 1932, W.W. Norton, New York.
6. Doyle J., Francis B., Tannenbaum A. Feedback Control Theory 1992, Macmillan, New York.
7. El-Samad H., Goff J.P., Khammash M. Calcium homeostasis and parturient hypocalcemia: an integral feedback perspective. J. Theor. Biol. 2002, 214:17-29.
8. Francis B.A., Wonham W.M. Internal model principle of control-theory. Automatica 1976, 12:457-465.
9. Gottesman S., Roche E., Zhou Y.N., Sauer R.T. The clpxp and clpap proteases degrade proteins with carboxy-terminal peptide tails added by the ssra-tagging system. Genes Dev. 1998, 12:1338-1347.
10. Grilly C., Strickler J., Pang W.L., Bennett M.R., Hasty J. A synthetic gene network for tuning protein degradation in Saccharomyces cerevisiae. Mol. Syst. Biol. 2007, 3:127.
11. Hasty J., Dolnik M., Rottschafer V., Collins J.J. Synthetic gene network for entraining and amplifying cellular oscillations. Phys. Rev. Lett. 2002, 88:4.
12. Hasty J., Isaacs F., Dolnik M., McMillen D., Collins J.J. Designer gene networks: towards fundamental cellular control. Chaos 2001, 11:207-220.
13. Hersch G.L., Baker T.A., Sauer R.T. Sspb delivery of substrates for clpxp proteolysis probed by the design of improved degradation tags. Proc. Natl. Acad. Sci. 2004, 101:12136-12141.
14. Isaacs F.J., Hasty J., Cantor C.R., Collins J.J. Prediction and measurement of an autoregulatory genetic module. Proc. Natl. Acad. Sci. 2003, 100:7714-7719.
15. Isidori A., Byrnes C.I. Output regulation of nonlinear-systems. IEEE Trans. Automat. Control 1990, 35:131-140.
16. Kaern M., Blake W., Collins J.J. The engineering of gene regulatory networks. Annu. Rev. Biomed. Eng. 2003, 5:179-206.
17. Kaern M., Weiss R. Synthetic gene regulatory systems. System Modeling in Cellular Biology 2006, 269-295. MIT Press, Cambridge. Z. Szallasi, J. Stelling, V. Periwal (Eds.).
18. Khalil A.S., Collins J.J. Synthetic biology: applications come of age. Nat. Rev. Genet. 2010, 11:367-379.
19. Lutz R., Bujard H. Independent and tight regulation of transcriptional units in escherichia coli via the lacr/o, the tetr/o and arac/i1-i2 regulatory elements. Nucleic Acids Res. 1997, 25:1203-1210.
20. Mello B.A., Tu Y. Perfect and near-perfect adaptation in a model of bacterial chemotaxis. Biophys. J. 2003, 84:2943-2956.
21. Mieschendahl M., Mullerhill B. F'-coded, temperature-sensitive lambda-ci857 repressor gene for easy construction and regulation of lambda-promoter-dependent expression systems. J. Bacteriol. 1985, 164:1366-1369.
22. Mukherji S., van Oudenaarden A. Synthetic biology: understanding biological design from synthetic circuits. Nat. Rev. Genet. 2009, 10:859-871.
23. Pedersen M., Phillips A. Towards programming languages for genetic engineering of living cells. J. R. Soc. Interface 2009, 6:S437-S450.
24. Ptashne M. A Genetic Switch: Phage Lambda and Higher Organisms 1986, Cell Press and Blackwell Scientific Publications, Cambridge, MA.
25. Ptashne M., Jeffrey A., Johnson A.D., Maurer R., Meyer B.J., Pabo C.O., Roberts T.M., Sauer R.T. How the lambda-repressor and cro work. Cell 1980, 19:1-11.
26. Purnick P.E.M., Weiss R. The second wave of synthetic biology: from modules to systems. Nat. Rev. Mol. Cell Biol. 2009, 10:410-422.
27. Rosati B., McKinnon D. Regulation of ion channel expression. Circ. Res. 2004, 94:874-883.
28. Sontag E.D. Adaptation and regulation with signal detection implies internal model. Syst. Control Lett. 2003, 50:119-126.
29. Trueba F.J., Koppes L.J.H. Exponential growth of escherichia coli b/r during its division cycle is demonstrated by the size distribution in liquid culture. Arch. Microbiol. 1998, 169:491-496.
30. Villaverde A., Benito A., Viaplana E., Cubarsi R. Fine regulation of ci857-controlled gene-expression in continuous-culture of recombinant Escherichia coli by temperature. Appl. Environ. Microbiol. 1993, 59:3485-3487.
31. Weiss R., Basu S., Hooshangi S., Kalmbach A., Karig D., Mehreja R., Netravali I. Genetic circuit building blocks for cellular computation, communications, and signal processing. Nat. Comput. 2003, 2:4784.
32. Wong W.W., Tsai T.Y., Liao J.C. Single-cell zeroth-order protein degradation enhances the robustness of synthetic oscillator. Mol. Syst. Biol. 2007, 3:8.
33. Yagil G., Yagil E. Relation between effector concentration and rate of induced enzyme synthesis. Biophys. J. 1971, 11:11-27.
34. Yi T.M., Huang Y., Simon M.I., Doyle J. Robust perfect adaptation in bacterial chemotaxis through integral feedback control. Proc. Natl. Acad. Sci. USA 2000, 97:4649-4653.