Plasmid-borne prokaryotic gene expression: Sources of variability and quantitative system characterization

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 77, Issue 2, 2008, Pages

  Bagh, Sangram ^a   Mazumder, Mostafizur ^a   Velauthapillai, Tharsan ^a   Sardana, Vandit ^a   Dong, Guang Qiang ^a   Movva, Ashok B ^a   Lim, Len H ^a   McMillen, David R ^a  

^a UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMEDICAL ENGINEERING; CELLS; ESCHERICHIA COLI; MICROORGANISMS;

BACTERIAL CELLS; CELL DIVISION; QUANTITATIVE SYSTEM; SYNTHETIC BIOLOGY;

GENE EXPRESSION;

EID: 40849145522     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.77.021919     Document Type: Article

References (66)

1. J. Hasty, D. McMillen, and J. J. Collins, Nature (London) NATUAS 0028-0836 10.1038/nature01257 420, 224 (2002).
2. M. Kaern, W. Blake, and J. J. Collins, Annu. Rev. Biochem. Eng. 5, 179 (2003).
3. E. Andrianantoandro, S. Basu, D. K. Karig, and R. Weiss, Mol. Syst. Biol. 2, 2006.0028 (2006).
4. R. Weiss, S. Basu, S. Hooshangi, A. Kalmbach, D. Karig, R. Mehreja, and I. Netravali, Natural Comput. 2, 47 (2003). 1567-7818
5. M. B. Elowitz and S. Leibler, Nature (London) NATUAS 0028-0836 10.1038/35002125 403, 335 (2000).
6. T. Gardner, C. R. Cantor, and J. J. Collins, Nature (London) NATUAS 0028-0836 10.1038/35002131 403, 339 (2000).
7. A. Becskei and L. Serrano, Nature (London) NATUAS 0028-0836 10.1038/35014651 405, 590 (2000).
8. Y. Dublanche, K. Michalodimitrakis, N. Kummerer, M. Foglierini, and L. Serrano, Mol. Syst. Biol. 2, 133 (2006).
9. C. C. Guet, M. B. Elowitz, W. Hsing, and S. Leibler, Science SCIEAS 0036-8075 10.1126/science.1067407 296, 1466 (2002).
10. J. C. Anderson, C. A. Voigt, and A. P. Arkin, Mol. Syst. Biol. 3, 133 (2007).
11. S. Basu, Y. Gerchman, C. H. Collins, F. H. Arnold, and R. Weiss, Nature (London) NATUAS 0028-0836 10.1038/nature03461 434, 1130 (2005).
12. Y. Yokobayashi, C. H. Collins, J. R. Leadbetter, R. Weiss, and F. H. Arnold, Adv. Complex Syst. 6, 37 (2003). 0219-5259
13. L. You, R. S. Cox, R. Weiss, and F. H. Arnold, Nature (London) NATUAS 0028-0836 10.1038/nature02491 428, 868 (2004).
14. M. Ramachandra, Nat. Biotechnol. 19, 1035 (2001). 1087-0156
15. C. A. Voigt, Curr. Opin. Biotechnol. CUOBE3 0958-1669 10.1016/j.copbio.2006.09.001 17, 548 (2006).
16. C. Grilly, J. Strickler, W. L. Pang, M. R. Bennett, and J. Hasty, Mol. Syst. Biol. 3, 127 (2007). 1741-2471
17. W. Weber, J. Stelling, M. Rimann, B. Keller, M. Daoud-El Baba, C. C. Weber, D. Aube, and M. Fussenegger, Proc. Natl. Acad. Sci. U.S.A. 104, 2643 (2007). 0027-8424
18. A. B. Cubitt, R. Heim, S. R. Adams, A. E. Boyd, L. A. Gross, and R. Y. Tsien, Trends Biochem. Sci. TBSCDB 0167-7640 10.1016/S0968-0004(00)89099-4 20, 448 (1995).
19. S. Ghaemmaghami, W.-K. Huh, K. Bower, R. W. Howson, A. Belle, N. Dephoure, E. K. O'Shea, and J. S. Weissman, Nature (London) NATUAS 0028-0836 10.1038/nature02046 425, 737 (2003).
20. A. Bar-Even, J. Paulsson, N. Maheshri, M. Carmi, E. O'Shea, Y. Pilpel, and N. Barkai, Nat. Genet. NGENEC 1061-4036 10.1038/ng1807 38, 636 (2006).
21. Y. Gerena-Lopez, J. Nolan, L. Wang, A. Gaigalas, A. Schwartz, and E. Fernandez-Repollet, Cytom. Part A 60, 21 (2004).
22. N. Rosenfeld, T. J. Perkins, U. Alon, M. B. Elowitz, and P. S. Swain, Biophys. J. 91, 759 (2006). 0006-3495
23. K. Baetz and M. Kaern, Nat. Genet. 38, 610 (2006). 1061-4036
24. M. B. Elowitz, A. J. Levine, E. D. Siggia, and P. S. Swain, Science SCIEAS 0036-8075 10.1126/science.1070919 297, 1183 (2002).
25. H. B. Fraser, A. E. Hirsh, G. Giaever, J. Kumm, and M. B. Eisen, PLoS Biol. 2, e137 (2004). 1544-9173
26. J. Hasty, D. McMillen, F. Isaacs, and J. J. Collins, Nat. Rev. Genet. NRGAAM 1471-0056 10.1038/35066056 2, 268 (2001).
27. M. Kaern, T. C. Elston, W. J. Blake, and J. J. Collins, Nat. Rev. Genet. NRGAAM 1471-0056 10.1038/nrg1615 6, 451 (2005).
28. J. R. S. Newman, S. Ghaemmaghami, J. Ihmels, D. K. Breslow, M. Noble, J. L. DeRisi, and J. S. Weissman, Nature (London) NATUAS 0028-0836 10.1038/nature04785 441, 840 (2006).
29. E. M. Ozbudak, M. Thattai, I. Kurtser, A. D. Grossman, and A. van Oudenaarden, Nat. Genet. NGENEC 1061-4036 10.1038/ng869 31, 69 (2002).
30. J. Paulsson, Nature (London) NATUAS 0028-0836 10.1038/nature02257 427, 415 (2004).
31. J. Paulsson and M. Ehrenberg, Q. Rev. Biophys. QURBAW 0033-5835 10.1017/S0033583501003663 34, 1 (2001).
32. J. M. Pedraza and A. van Oudenaarden, Science SCIEAS 0036-8075 10.1126/science.1109090 307, 1965 (2005).
33. J. M. Raser and E. K. O'Shea, Science SCIEAS 0036-8075 10.1126/science.1098641 304, 1811 (2004).
34. J. M. Raser and E. K. O'Shea, Science SCIEAS 0036-8075 10.1126/science.1105891 309, 2010 (2005).
35. D. Reanney, Nature (London) 0028-0836 307, 318 (2002).
36. N. Rosenfeld, J. W. Young, U. Alon, P. S. Swain, and M. B. Elowitz, Science SCIEAS 0036-8075 10.1126/science.1106914 307, 1962 (2005).
37. P. S. Swain, M. B. Elowitz, and E. D. Siggia, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.162041399 99, 12795 (2002).
38. P. S. Swain and A. Longtin, Chaos CHAOEH 1054-1500 10.1063/1.2213613 16, 026101 (2006).
39. M. Thattai and A. van Oudenaarden, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.151588598 98, 8614 (2001).
40. D. Volfson, J. Marciniak, W. J. Blake, N. Ostroff, L. S. Tsimring, and J. Hasty, Nature (London) NATUAS 0028-0836 10.1038/nature04281 439, 861 (2006).
41. R. Lutz and H. Bujard, Nucleic Acids Res. NARHAD 0305-1048 10.1093/nar/25.6.1203 25, 1203 (1997).
42. P. Balbas and F. Bolivar, in Recombinant Gene Expression: Reviews and Protocols, 2nd ed., edited by, P. Balbas, and, A. Lorence, Methods in Molecular Biology Vol. 267 (Humana Press, Totowa, NJ, 2004), pp. 77-90.
43. C. L. Lee, D. S. W. Ow, and S. K. W. Oh, J. Microbiol. Methods JMIMDQ 0167-7012 10.1016/j.mimet.2005.07.019 65, 258 (2006).
44. J. R. Lupski, S. J. Projan, L. S. Ozaki, and G. N. Godson, Proc. Natl. Acad. Sci. U.S.A. 83, 7381 (1986). 0027-8424
45. J. Vieira and J. Messing, Gene 19, 259 (1982). 0378-1119
46. W. J. Blake and G. Balazsi, M. A. Kohanski, F. J. Isaacs, K. F. Murphy, Y. Kuang, C. R. Cantor, D. R. Walt, and J. J. Collins, Mol. Cells 24, 853 (2007). 1016-8478
47. W. J. Blake, M. Kaern, C. R. Cantor, and J. J. Collins, Nature (London) NATUAS 0028-0836 10.1038/nature01546 422, 633 (2003).
48. R. Kemkemer, S. Schrank, W. Vogel, H. Gruler, and D. Kaufmann, Proc. Natl. Acad. Sci. U.S.A. 99, 13783 (2002). 0027-8424
49. F. J. Trueba and L. J. H. Koppes, Arch. Microbiol. AMICCW 0302-8933 10.1007/s002030050601 169, 491 (1998).
50. P. Corish and C. Tyler-Smith, Protein Eng. PRENE9 0269-2139 10.1093/protein/12.12.1035 12, 1035 (1999).
51. A. Varshavsky, Genes Cells GECEFL 1356-9597 10.1046/j.1365-2443.1997. 1020301.x 2, 13 (1997).
52. M. A. Henson, Curr. Opin. Biotechnol. 14, 460 (2003). 0958-1669
53. Z. Kutalik, M. Razaz, and J. Baranyi, J. Theor. Biol. 232, 285 (2005). 0022-5193
54. H. M. Shapiro, Practical Flow Cytometry, 3rd ed. (John Wiley & Sons, New York, 1995).
55. O. Julia, J. Comas, and J. Vives-Rego, J. Microbiol. Methods 40, 57 (2000). 0167-7012
56. S. Birnbaum and J. E. Bailey, Biotechnol. Bioeng. 37, 736 (1991). 0006-3592
57. Z. Wang, L. Xiang, J. Shao, A. Wegrzyn, and G. Wegrzyn, Microbial Cell Factories 5, 34 (2006).
58. P. Balbas, X. Soberon, E. Merino, M. Zurita, H. Lomeli, F. Valle, N. Flores, and F. Bolivar, Gene GENED6 0378-1119 10.1016/0378-1119(86)90307-0 50, 3 (1986).
59. F. Bolivar, R. L. Rodriguez, P. J. Green, M. C. Betlach, H. L. Heyneker, H. W. Boyer, J. H. Crosa, and S. Falkow, Gene 2, 75 (1977). 0378-1119
60. S. Lin-Chao, W.-T. Chen, and T.-T. Wong, Mol. Microbiol. 6, 3385 (1992). 0950-382X
61. D. Adalsteinsson, D. McMillen, and T. C. Elston, BMC Bioinf. BBMIC4 1471-2105 10.1186/1471-2105-5-24 5, 24 (2004).
62. D. Gillespie, J. Phys. Chem. JPCHAX 0022-3654 10.1021/j100540a008 81, 2340 (1977).
63. X.-j. Feng, S. Hooshangi, D. Chen, G. Li, R. Weiss, and H. Rabitz, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.104.044131 87, 2195 (2004).
64. T. J. Perkins, J. Jaeger, J. Reinitz, and L. Glass, PLOS Comput. Biol. 1553-734X 2, e51 (2006).
65. J. Sambrook and D. W. Russell, Molecular Cloning: A Laboratory Manual, 3rd ed. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2001).
66. S. Bagh and M. F. Paige, Can. J. Chem. 83, 435 (2005). 0008-4042